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par_amber2charmm.inp
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par_amber2charmm.inp
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* AMBER Cornell et al. (parm94) force field conversion
* See: JACS (1995) 117, 5179-5197.
* nucleic acid part converted by tec3, march 1997
* protein part converted by tec3, feb 1999
*
!
! This is a hand-conversion of the Cornell et. al. force field
! parm94.dat file (except for the torsion which were converted via
! a perl script). All the atom type names are the same except where
! otherwise noted.
!
! Any problems? Let me know...
!
! note: types N* remaned to NS
! C* renamed to CS
!
! note: the HO and HW nonbonded parameters, although zero in
! Cornell et al. should not have a 0.0 vdw radius in CHARMM
! to avoid difficulties with the 0.0/0.0 in the FAST OFF
! van der Waal code...
!
! note: the default nonbonded options chosen here are to match AMBER.
! It is not recommended that users actually run with GROUP based
! truncation and a switch unless really trying to match AMBER.
! Better would be ATOM based FSHIFT VSHIFT, however note that this
! does modify the energies (and effectively the parameters).
!
BONDS
OW HW 553.0 0.9572 ! TIP3P water
HW HW 553.0 1.5136 ! TIP3P water
C CA 469.0 1.409 ! JCC,7,(1986),230; TYR
C CB 447.0 1.419 ! JCC,7,(1986),230; GUA
C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA
C CT 317.0 1.522 ! JCC,7,(1986),230; AA
C NS 424.0 1.383 ! JCC,7,(1986),230; CYT,URA
C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA
C NC 457.0 1.358 ! JCC,7,(1986),230; CYT
C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA
C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP
C OH 450.0 1.364 ! JCC,7,(1986),230; TYR
CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP
CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT
CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR
CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned
CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA
CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA
CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA
CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA
CB NS 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA
CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA
CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA
CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA
CK NS 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA
CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA
CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA
CM CT 317.0 1.510 ! JCC,7,(1986),230; THY
CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA
CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA
CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned
CM NS 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA
CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE
CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE
CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS
CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS
CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE
CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS
CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned
CT HP 340.0 1.090 ! changed from 331; AA lysine, methyl ammonium cation
CT NS 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG
CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS
CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS
H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG
H NS 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG
H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS
HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR
HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS
O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES
OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES
OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES
CS HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA
C N 490.0 1.335 ! JCC,7,(1986),230; AA
CS CB 388.0 1.459 ! JCC,7,(1986),230; TRP
CS CT 317.0 1.495 ! JCC,7,(1986),230; TRP
CS CW 546.0 1.352 ! JCC,7,(1986),230; TRP
CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP
CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP
CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS
CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta)
CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon)
CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS
CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS
CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP
CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS
CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS
CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS
CT N 337.0 1.449 ! JCC,7,(1986),230; AA
CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS
CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes
CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes
CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS
CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS
CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP
H N 434.0 1.010 ! JCC,7,(1986),230; AA
H N3 434.0 1.010 ! JCC,7,(1986),230; LYS
HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS
S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA)
CT F 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
!new bond parameters for ligand K51
cd nc 494.6 1.335
cc ha 347.2 1.085
cc na 438.8 1.371
n1 cg 994.7 1.143
cd ha 347.2 1.085
ca ca 478.4 1.387
ca ha 344.3 1.087
c3 h1 335.9 1.093
cd h4 350.1 1.083
cd cd 418.3 1.429
cd nh 449.0 1.364
nd cc 494.6 1.335
ca cc 411.7 1.434
cc cd 504.0 1.371
nh hn 401.2 1.014
cd nd 431.6 1.376
c3 oh 314.1 1.426
c3 hc 337.3 1.092
cc cc 418.3 1.429
nc na 535.7 1.35
oh ho 369.6 0.974
c3 c3 303.1 1.535
cg ca 406.6 1.438
nh c3 332.7 1.458
!
cc nh 449.0 1.364
cc h4 350.1 1.083
os c3 301.5 1.439
cd nd 431.6 1.376
cd na 438.8 1.371
na nd 535.7 1.35
ANGLES
HW OW HW 100. 104.52 ! TIP3P water
HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds)
CB C NA 70.0 111.30 ! NA
CB C O 80.0 128.80 !
CM C NA 70.0 114.10 !
CM C O 80.0 125.30 !
CT C O 80.0 120.40 !
CT C O2 70.0 117.00 !
CT C OH 70.0 117.00 !
NS C NA 70.0 115.40 !
NS C NC 70.0 118.60 !
NS C O 80.0 120.90 !
NA C O 80.0 120.60 !
NC C O 80.0 122.50 !
CT C N 70.0 116.60 ! AA general
N C O 80.0 122.90 ! AA general
O C O 80.0 126.00 ! AA COO terminal residues
O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379)
O C OH 80.0 126.00 !
CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA tyr
CA C OH 70.0 120.00 ! AA tyr
C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes
CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes
CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes
CA CA CT 70.0 120.00 !
CA CA HA 35.0 120.00 !
CA CA H4 35.0 120.00 !
CB CA HA 35.0 120.00 !
CB CA H4 35.0 120.00 !
CB CA N2 70.0 123.50 !
CB CA NC 70.0 117.30 !
CM CA N2 70.0 120.10 !
CM CA NC 70.0 121.50 !
N2 CA NA 70.0 116.00 !
N2 CA NC 70.0 119.30 !
NA CA NC 70.0 123.30 !
C CA HA 35.0 120.00 ! AA tyr
N2 CA N2 70.0 120.00 ! AA arg
CN CA HA 35.0 120.00 ! AA trp
CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua
C CB NB 70.0 130.00 !
CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade
CA CB NB 70.0 132.40 !
CB CB NS 70.0 106.20 !
CB CB NB 70.0 110.40 !
CB CB NC 70.0 127.70 !
NS CB NC 70.0 126.20 !
CS CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
CS CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
H5 CK NS 35.0 123.05 !
H5 CK NB 35.0 123.05 !
NS CK NB 70.0 113.90 !
C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy
C CM CT 70.0 119.70 !
C CM HA 35.0 119.70 !
C CM H4 35.0 119.70 !
CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt
CA CM HA 35.0 123.30 !
CA CM H4 35.0 123.30 !
CM CM CT 70.0 119.70 !
CM CM HA 35.0 119.70 !
CM CM H4 35.0 119.70 !
CM CM NS 70.0 121.20 !
H4 CM NS 35.0 119.10 !
H5 CQ NC 35.0 115.45 !
NC CQ NC 70.0 129.10 !
CM CT HC 50.0 109.50 ! changed based on NMA nmodes
CT CT CT 40.0 109.50 !
CT CT HC 50.0 109.50 ! changed based on NMA nmodes
CT CT H1 50.0 109.50 ! changed based on NMA nmodes
CT CT H2 50.0 109.50 ! changed based on NMA nmodes
CT CT HP 50.0 109.50 ! changed based on NMA nmodes
CT CT NS 50.0 109.50 !
CT CT OH 50.0 109.50 !
CT CT OS 50.0 109.50 !
HC CT HC 35.0 109.50 !
H1 CT H1 35.0 109.50 !
HP CT HP 35.0 109.50 ! AA lys, ch3nh4+
H2 CT NS 50.0 109.50 ! changed based on NMA nmodes
H1 CT NS 50.0 109.50 ! changed based on NMA nmodes
H1 CT OH 50.0 109.50 ! changed based on NMA nmodes
H1 CT OS 50.0 109.50 ! changed based on NMA nmodes
H2 CT OS 50.0 109.50 ! changed based on NMA nmodes
NS CT OS 50.0 109.50 !
H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes
C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes
C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes
H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes
H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes
CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428)
CT CT SH 50.0 108.60 ! AA cys
H2 CT H2 35.0 109.50 ! AA lys
H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes
HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes
CA CT CT 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379)
C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes
C CT N 63.0 110.10 ! AA general
CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439)
CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657)
C CT CT 63.0 111.10 ! AA general
CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes
CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439)
CC CT CT 63.0 113.10 ! AA his
CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes
C CT N3 80.0 111.20 ! AA amino terminal residues
CS CT CT 63.0 115.60 ! AA trp
CS CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes
CT CC NA 70.0 120.00 ! AA his
CT CC CV 70.0 120.00 ! AA his
CT CC NB 70.0 120.00 ! AA his
CV CC NA 70.0 120.00 ! AA his
CW CC NA 70.0 120.00 ! AA his
CW CC NB 70.0 120.00 ! AA his
CT CC CW 70.0 120.00 ! AA his
H5 CR NA 35.0 120.00 ! AA his
H5 CR NB 35.0 120.00 ! AA his
NA CR NA 70.0 120.00 ! AA his
NA CR NB 70.0 120.00 ! AA his
CC CV H4 35.0 120.00 ! AA his
CC CV NB 70.0 120.00 ! AA his
H4 CV NB 35.0 120.00 ! AA his
CC CW H4 35.0 120.00 ! AA his
CC CW NA 70.0 120.00 ! AA his
H4 CW NA 35.0 120.00 ! AA his
CS CW H4 35.0 120.00 ! AA trp
CS CW NA 70.0 108.70 ! AA trp
CT CS CW 70.0 125.00 ! AA trp
CB CS CT 70.0 128.60 ! AA trp
CB CS CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
CA CN NA 70.0 132.80 ! AA trp
CB CN NA 70.0 104.40 ! AA trp
CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp
C N CT 50.0 121.90 ! AA general
C N H 30.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes
CT N H 30.0 118.04 ! AA general, changed based on NMA nmodes
CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232)
H N H 35.0 120.00 ! ade,cyt,gua,gln,asn **
C NS CM 70.0 121.60 !
C NS CT 70.0 117.60 !
C NS H 30.0 119.20 ! changed based on NMA nmodes
CB NS CK 70.0 105.40 !
CB NS CT 70.0 125.80 !
CB NS H 30.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes
CK NS CT 70.0 128.80 !
CK NS H 30.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes
CM NS CT 70.0 121.20 !
CM NS H 30.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes
CA N2 H 35.0 120.00 !
H N2 H 35.0 120.00 !
CT N2 H 35.0 118.40 ! AA arg
CA N2 CT 50.0 123.20 ! AA arg
CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes
CT N3 CT 50.0 109.50 ! AA pro/nt
H N3 H 35.0 109.50 ! AA lys, AA(end)
C NA C 70.0 126.40 !
C NA CA 70.0 125.20 !
C NA H 30.0 116.80 ! changed based on NMA nmodes
CA NA H 30.0 118.00 ! changed based on NMA nmodes
CC NA CR 70.0 120.00 ! AA his
CC NA H 30.0 120.00 ! AA his, changed based on NMA nmodes
CR NA CW 70.0 120.00 ! AA his
CR NA H 30.0 120.00 ! AA his, changed based on NMA nmodes
CW NA H 30.0 120.00 ! AA his, changed based on NMA nmodes
CN NA CW 70.0 111.60 ! AA trp
CN NA H 30.0 123.10 ! AA trp, changed based on NMA nmodes
CB NB CK 70.0 103.80 !
CC NB CR 70.0 117.00 ! AA his
CR NB CV 70.0 117.00 ! AA his
C NC CA 70.0 120.50 !
CA NC CB 70.0 112.20 !
CA NC CQ 70.0 118.60 !
CB NC CQ 70.0 111.00 !
C OH HO 35.0 113.00 !
CT OH HO 55.0 108.50 !
HO OH P 45.0 108.50 !
CT OS CT 60.0 109.50 !
CT OS P 100.0 120.50 !
P OS P 100.0 120.50 !
O2 P OH 45.0 108.23 !
O2 P O2 140.0 119.90 !
O2 P OS 100.0 108.23 !
OH P OS 45.0 102.60 !
OS P OS 45.0 102.60 !
CT S CT 62.0 98.90 ! AA met
CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428)
CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes
HS SH HS 35.0 92.07 ! AA cys
F CT F 77.0 109.10 ! JCC,13,(1992),963;
F CT H1 35.0 109.50 ! JCC,13,(1992),963;
!new angle parameters for K51
nd cc na 74.8 112.076866433
cg ca ca 65.9 120.110942866
ca ca ca 67.2 120.030901911
cc cd nd 71.0 115.038368599
c3 nh hn 46.5 115.008353885
h1 c3 h1 39.2 109.605612611
nh c3 c3 66.6 109.835728854
cd cd nc 71.1 112.617140446
cc cc na 72.2 106.854216306
cd nh c3 63.7 121.241515987
cc cc ha 46.6 123.802815669
cd nd cc 70.5 107.524556369
oh c3 h1 51.0 109.935779618
c3 c3 c3 63.2 110.686160637
c3 c3 oh 67.7 109.485551465
hc c3 hc 39.4 108.405003439
nh c3 h1 49.7 110.015820573
cd nh hn 48.9 117.219475605
ca cc cd 68.2 113.56762242
cc na nc 70.2 113.077374076
cd cc na 72.9 109.475546561
cd cc ha 48.4 122.952384459
cc cc cd 68.2 114.247967962
cc cd ha 48.4 122.952384459
cd nc na 74.2 103.782657898
nc cd nh 72.4 120.170972866
cc cd cd 68.2 114.247967962
cc cd h4 47.2 129.175541656
c3 oh ho 47.1 108.214906815
ca ca ha 48.5 120.070922102
cc na cc 68.9 109.95579
c3 c3 h1 46.4 110.125876242
ca ca cc 66.0 120.160967962
n1 cg ca 58.8 180.091375796
nd cd h4 50.0 120.090932484
ca cc na 67.263 113.662671019
cd cd ha 46.6 123.802815669
cd cd nh 68.6 119.040399172
nd cc cc 71.1 112.617140446
c3 c3 hc 46.4 110.105866433
!
cg ca ca 120.110942866 65.9 0.0 0.0 0.0 0.0
nd cd na 125.383618089 69.7 0.0 0.0 0.0 0.0
cc cc nd 112.617140446 71.1 0.0 0.0 0.0 0.0
ca ca cc 120.160967962 66.0 0.0 0.0 0.0 0.0
ca ca ca 120.030901911 67.2 0.0 0.0 0.0 0.0
cc cd nd 115.038368599 71.0 0.0 0.0 0.0 0.0
cc cd h4 129.175541656 47.2 0.0 0.0 0.0 0.0
cc cd na 109.475546561 72.9 0.0 0.0 0.0 0.0
nd cc cc 112.617140446 71.1 0.0 0.0 0.0 0.0
nh cc cc 119.040399172 68.6 0.0 0.0 0.0 0.0
c3 os c3 113.467571656 62.1 0.0 0.0 0.0 0.0
c3 c3 os 108.475038917 67.8 0.0 0.0 0.0 0.0
nh c3 c3 109.835728854 66.6 0.0 0.0 0.0 0.0
cc nh hn 117.219475605 48.9 0.0 0.0 0.0 0.0
cc cc h4 129.535724522 45.6 0.0 0.0 0.0 0.0
c3 c3 h1 110.125876242 46.4 0.0 0.0 0.0 0.0
os c3 c3 108.475038917 67.8 0.0 0.0 0.0 0.0
cc cc ha 123.802815669 46.6 0.0 0.0 0.0 0.0
na nd cc 103.782657898 74.2 0.0 0.0 0.0 0.0
c3 c3 hc 110.105866433 46.4 0.0 0.0 0.0 0.0
c3 nh hn 115.008353885 46.5 0.0 0.0 0.0 0.0
cd na cd 109.95579 68.9 0.0 0.0 0.0 0.0
cd na nd 113.077374076 70.2 0.0 0.0 0.0 0.0
ca cc cc 111.096368599 67.7 0.0 0.0 0.0 0.0
cd nd cc 107.524556369 70.5 0.0 0.0 0.0 0.0
n1 cg ca 180.091375796 58.8 0.0 0.0 0.0 0.0
nh c3 h1 110.015820573 49.7 0.0 0.0 0.0 0.0
hc c3 hc 108.405003439 39.4 0.0 0.0 0.0 0.0
cc nh c3 121.241515987 63.7 0.0 0.0 0.0 0.0
ca ca ha 120.070922102 48.5 0.0 0.0 0.0 0.0
h1 c3 h1 109.605612611 39.2 0.0 0.0 0.0 0.0
os c3 h1 108.875241975 50.8 0.0 0.0 0.0 0.0
nd cc nh 120.170972866 72.4 0.0 0.0 0.0 0.0
cd cc ha 122.952384459 48.4 0.0 0.0 0.0 0.0
ca cc cd 113.56762242 68.2 0.0 0.0 0.0 0.0
cc cc cd 114.247967962 68.2 0.0 0.0 0.0 0.0
na cd h4 119.720744713 50.2 0.0 0.0 0.0 0.0
nd cc h4 119.170465223 51.4 0.0 0.0 0.0 0.0
c3 c3 c3 110.686160637 63.2 0.0 0.0 0.0 0.0
cd cc cc 114.247967962 68.2 0.0 0.0 0.0 0.0
DIHEDRALS
X C CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6
X C CB X 3.00000000 2 180.0 ! intrpol.bsd.on C6H6
X C CM X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6
X C NS X 1.45000000 2 180.0 ! JCC,7,(1986),230
X C NA X 1.35000000 2 180.0 ! JCC,7,(1986),230
X C NC X 4.00000000 2 180.0 ! JCC,7,(1986),230
X C OH X 0.90000000 2 180.0 ! JCC,7,(1986),230
X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CA CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6
X CA CB X 3.50000000 2 180.0 ! intrpol.bsd.on C6H6
X CA CM X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6
X CA CT X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CA N2 X 2.40000000 2 180.0 ! reinterpolated 93'
X CA NA X 1.50000000 2 180.0 ! JCC,7,(1986),230
X CA NC X 4.80000000 2 180.0 ! JCC,7,(1986),230
X CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6
X CB NS X 1.65000000 2 180.0 ! JCC,7,(1986),230
X CB NB X 2.55000000 2 180.0 ! JCC,7,(1986),230
X CB NC X 4.15000000 2 180.0 ! JCC,7,(1986),230
X CK NS X 1.70000000 2 180.0 ! JCC,7,(1986),230
X CK NB X 10.00000000 2 180.0 ! JCC,7,(1986),230
X CM CM X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6
X CM CT X 0.00000000 3 0.0 ! JCC,7,(1986),230
X CM NS X 1.85000000 2 180.0 ! JCC,7,(1986),230
X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230
X CT CT X 0.15555556 3 0.0 ! JCC,7,(1986),230
X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CT NS X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CT N2 X 0.00000000 3 0.0 ! JCC,7,(1986),230
X CT OH X 0.16666667 3 0.0 ! JCC,7,(1986),230
X CT OS X 0.38333333 3 0.0 ! JCC,7,(1986),230
X OH P X 0.25000000 3 0.0 ! JCC,7,(1986),230
X OS P X 0.25000000 3 0.0 ! JCC,7,(1986),230
X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA
X CT N3 X 0.15555556 3 0.0 ! JCC,7,(1986),230
X CT S X 0.33333333 3 0.0 ! JCC,7,(1986),230
X CT SH X 0.25000000 3 0.0 ! JCC,7,(1986),230
X CS CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa
X CS CT X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CS CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6
X CA CN X 3.62500000 2 180.0 ! reinterpolated 93'
X CB CN X 3.00000000 2 180.0 ! reinterpolated 93'
X CC CT X 0.00000000 2 0.0 ! JCC,7,(1986),230
X CC CV X 5.15000000 2 180.0 ! intrpol.bsd.on C6H6
X CC CW X 5.37500000 2 180.0 ! intrpol.bsd.on C6H6
X CC NA X 1.40000000 2 180.0 ! JCC,7,(1986),230
X CC NB X 2.40000000 2 180.0 ! JCC,7,(1986),230
X CN NA X 1.52500000 2 180.0 ! reinterpolated 93'
X CR NA X 2.32500000 2 180.0 ! JCC,7,(1986),230
X CR NB X 5.00000000 2 180.0 ! JCC,7,(1986),230
X CV NB X 2.40000000 2 180.0 ! JCC,7,(1986),230
X CW NA X 1.50000000 2 180.0 ! JCC,7,(1986),230
CT CT OS CT 0.38300000 3 0.0 !
CT CT OS CT 0.10000000 2 180.0 !
C N CT C 0.20000000 2 180.0 !
N CT C N 0.40000000 4 180.0 !
N CT C N 1.35000000 2 180.0 !
N CT C N 0.75000000 1 180.0 !
CT CT N C 0.50000000 4 180.0 !
CT CT N C 0.15000000 3 180.0 !
CT CT N C 0.53000000 1 0.0 !
CT CT C N 0.10000000 4 0.0 !
CT CT C N 0.07000000 2 0.0 !
H N C O 2.50000000 2 180.0 ! JCC,7,(1986),230
H N C O 2.00000000 1 0.0 ! J.C.cistrans-NMA DE
CT S S CT 3.50000000 2 0.0 ! JCC,7,(1986),230
CT S S CT 0.60000000 3 0.0 ! JCC,7,(1986),230
OS CT CT OS 0.14400000 3 0.0 ! JCC,7,(1986),230
OS CT CT OS 1.00000000 2 0.0 ! pucker anal (93')
OS CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230
OS CT CT OH 1.00000000 2 0.0 ! pucker anal (93')
OH CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230
OH CT CT OH 1.00000000 2 0.0 ! check glicolWC? puc
OH P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230
OH P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2
OS P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230
OS P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2
OS CT NS CK 0.50000000 2 180.0 ! sugar frag calc (PC)
OS CT NS CK 2.50000000 1 0.0 ! sugar frag calc (PC)
OS CT NS CM 0.50000000 2 180.0 ! sugar frag calc (PC)
OS CT NS CM 2.50000000 1 0.0 ! sugar frag calc (PC)
!dihedral parameters for ligands
cc na cc nd 1.1 2 180.091375796
ca ca ca cg 1.1 2 180.091375796
ca cd cc na 1.1 2 180.091375796
cc cc na nc 1.1 2 180.091375796
ca ca ca cc 1.1 2 180.091375796
cc cd cc ha 1.1 2 180.091375796
ca ca ca ha 1.1 2 180.091375796
c3 cd nh hn 1.1 2 180.091375796
cc cd cd ha 1.1 2 180.091375796
cc h4 cd nd 1.1 2 180.091375796
cd nc cd nh 1.1 2 180.091375796
n1 cg ca ca 0.0 2 180.000 ! same as X -c1-ca-X
ca ca cc cd 2.5 2 180.000 ! same as X -c2-ca-X
ca ca cc cc 2.5 2 180.000 ! same as X -c2-ca-X
ca ca cc cd 2.5 2 180.000 ! same as X -c2-ca-X
ca ca cc cc 2.5 2 180.000 ! same as X -c2-ca-X
IMPROPERS
X X C O 10.50000000 2 180.0 ! JCC,7,(1986),230
X O2 C O2 10.50000000 2 180.0 ! JCC,7,(1986),230
X X N H 1.00000000 2 180.0 ! JCC,7,(1986),230
X X N2 H 1.00000000 2 180.0 ! JCC,7,(1986),230
X X NA H 1.00000000 2 180.0 ! JCC,7,(1986),230
X N2 CA N2 10.50000000 2 180.0 ! JCC,7,(1986),230
X CT N CT 1.00000000 2 180.0 ! JCC,7,(1986),230
X X CA HA 1.10000000 2 180.0 ! bsd.on C6H6 nmodes
X X CW H4 1.10000000 2 180.0 !
X X CR H5 1.10000000 2 180.0 !
X X CV H4 1.10000000 2 180.0 !
X X CQ H5 1.10000000 2 180.0 !
X X CK H5 1.10000000 2 180.0 !
X X CM H4 1.10000000 2 180.0 !
X X CM HA 1.10000000 2 180.0 !
X X CA H4 1.10000000 2 180.0 ! bsd.on C6H6 nmodes
X X CA H5 1.10000000 2 180.0 ! bsd.on C6H6 nmodes
CK CB NS CT 1.00000000 2 180.0 !
CM C NS CT 1.00000000 2 180.0 ! dac guess, 9/94
CM C CM CT 1.10000000 2 180.0 !
CT O C OH 10.50000000 2 180.0 !
NA CV CC CT 1.10000000 2 180.0 !
NB CW CC CT 1.10000000 2 180.0 !
NA CW CC CT 1.10000000 2 180.0 !
CW CB CS CT 1.10000000 2 180.0 !
CA CA CA CT 1.10000000 2 180.0 !
C CM CM CT 1.10000000 2 180.0 ! dac guess, 9/94
NC CM CA N2 1.10000000 2 180.0 ! dac guess, 9/94
CB NC CA N2 1.10000000 2 180.0 ! dac, 10/94
NA NC CA N2 1.10000000 2 180.0 ! dac, 10/94
CA CA C OH 1.10000000 2 180.0 !
!improper coeff for ligand K51
cc na nc cd 4.8 2 180.091375796
c3 c3 c3 oh 0.155555556 3 0.0
n1 cg ca ca 0.0 2 180.091375796
nc cd nh hn 1.05 2 180.091375796
nd cc na nc 1.7 2 180.091375796
nh c3 c3 oh 0.155555556 3 0.0
cd nd cc cc 4.75 2 180.091375796
ca cc na cc 1.7 2 180.091375796
cg ca ca ca 3.625 2 180.091375796
c3 c3 c3 h1 0.155555556 3 0.0
cd cc na cc 1.7 2 180.091375796
c3 c3 c3 c3 0.18 3 0.0
nh cd nc na 4.75 2 180.091375796
c3 c3 c3 c3 0.2 1 180.091375796
cc nd cd h4 4.75 2 180.091375796
cc cd nd cc 4.75 2 180.091375796
c3 c3 oh ho 0.25 1 0.0
ca ca cc na 2.55 2 180.091375796
cc na cc cc 1.7 2 180.091375796
cc cc na nc 1.7 2 180.091375796
c3 c3 nh hn 0.0 2 0.0
na cc cd h4 4.0 2 180.091375796
cg ca ca ha 3.625 2 180.091375796
ha cc cd ha 4.0 2 180.091375796
cc na cc nd 1.7 2 180.091375796
cd cc cc na 4.0 2 180.091375796
nd cc cc ha 4.0 2 180.091375796
cc cd cd nh 4.0 2 180.091375796
ca ca ca ha 3.625 2 180.091375796
ca ca cc cd 2.55 2 180.091375796
ca cc cd nd 4.0 2 180.091375796
nh c3 c3 h1 0.155555556 3 0.0
nh cd cd ha 4.0 2 180.091375796
nh c3 c3 c3 0.155555556 3 0.0
cd cd nc na 4.75 2 180.091375796
ca ca ca ca 3.625 2 180.091375796
ca cc na nc 1.7 2 180.091375796
c3 c3 c3 c3 0.25 2 180.091375796
cd cd nh c3 1.05 2 180.091375796
ca ca ca cc 3.625 2 180.091375796
nd cc cc cd 4.0 2 180.091375796
cc cc cd ha 4.0 2 180.091375796
ca cc cd h4 4.0 2 180.091375796
cc ca ca ca 3.625 2 180.091375796
cd nh c3 h1 0.0 2 0.0
h1 c3 c3 hc 0.155555556 3 0.0
cd cc na nc 1.7 2 180.091375796
cc cc cd cd 4.0 2 180.091375796
cc cd cd nc 4.0 2 180.091375796
nc cd cd ha 4.0 2 180.091375796
cd nh c3 c3 0.0 2 0.0
cc ca ca ha 3.625 2 180.091375796
h1 c3 oh ho 0.166666667 3 0.0
cd nd cc na 4.75 2 180.091375796
hn nh c3 h1 0.0 2 0.0
nc cd nh c3 1.05 2 180.091375796
nd cd cc na 4.0 2 180.091375796
c3 c3 c3 hc 0.16 3 0.0
cd cd nh hn 1.05 2 180.091375796
ha ca ca ha 3.625 2 180.091375796
oh c3 c3 h1 0.25 1 0.0
nh c3 c3 hc 0.155555556 3 0.0
h1 c3 c3 h1 0.155555556 3 0.0
na cc cc ha 4.0 2 180.091375796
c3 c3 oh ho 0.16 3 0.0
hc c3 c3 hc 0.15 3 0.0
cd cd cc ha 4.0 2 180.091375796
!
! Note: the HO and HW parameters, although zero in Cornell et al.
! should not have a 0.0 vdw radius in CHARMM to avoid difficulties
! with the 0.0/0.0 in the FAST OFF van der Waal code...
!
! NOTE: the defaults chosen here are to match AMBER. It is not
! recommended that users actually run with GROUP based truncation
! and a switch. Better would be ATOM based FSHIFT VSHIFT
NONBONDED NBXMOD 5 GROUP SWITCH CDIEL -
! CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 0.83333333 WMIN 1.4
! Emin Rmin/2 Emin/2 Rmin (for 1-4's)
! (kcal/mol) (A)
H 0.0 -0.0157 0.6000 0.0 -0.00785 0.6000 ! Ferguson base pair geom.
HO 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! OPLS, JACS,110,(1988),1657
HS 0.0 -0.0157 0.6000 0.0 -0.00785 0.6000 ! W. Cornell CH3SH --> CH3OH FEP
HC 0.0 -0.0157 1.4870 0.0 -0.00785 1.4870 ! OPLS
H1 0.0 -0.0157 1.3870 0.0 -0.00785 1.3870 ! Veenstra JCC,8,(1992),963
H2 0.0 -0.0157 1.2870 0.0 -0.00785 1.2870 ! Veenstra JCC,8,(1992),963
H3 0.0 -0.0157 1.1870 0.0 -0.00785 1.1870 ! Veenstra JCC,8,(1992),963
HP 0.0 -0.0157 1.1000 0.0 -0.00785 1.1000 ! Veenstra JCC,8,(1992),963
HA 0.0 -0.0150 1.4590 0.0 -0.0075 1.4590 ! Spellmeyer
H4 0.0 -0.0150 1.4090 0.0 -0.0075 1.4090 ! Spellmeyer, 1 e- withdr. nghbr
H5 0.0 -0.0150 1.3590 0.0 -0.0075 1.3590 ! Spellmeyer, 2 e- withdr. nghbr
HW 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model
O 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS
O2 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS
OW 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model
OH 0.0 -0.2104 1.7210 0.0 -0.1052 1.7210 ! OPLS
OS 0.0 -0.1700 1.6837 0.0 -0.0850 1.6837 ! OPLS ether
CT 0.0 -0.1094 1.9080 0.0 -0.0547 1.9080 ! Spellmeyer
CA 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer
C 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CM 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer
CS 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CB 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CC 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CN 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CK 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CQ 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CW 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CV 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CR 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CX 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CY 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
CD 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS
N* 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
N 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NA 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NB 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
N1 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
N2 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
N3 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NE1 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NE2 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NE 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NH1 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NH2 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
ND1 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
ND2 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
NZ 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS
S 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's
SH 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's
P 0.0 -0.2000 2.1000 0.0 -0.1000 2.1000 ! JCC,7,(1986),230;
IM 0.0 -0.1 2.47 0.0 -0.05 2.47 ! Cl- Smith, JCP 1994,100:5,3757
Li 0.0 -0.0183 1.1370 0.0 -0.00915 1.1370 ! Li+ Aqvist JPC 1990,94,8021. (adapted)
IP 0.0 -0.00277 1.8680 0.0 -0.001385 1.8680 ! Na+ Aqvist JPC 1990,94,8021. (adapted)
K 0.0 -0.000328 2.6580 0.0 -0.000164 2.6580 ! K+ Aqvist JPC 1990,94,8021. (adapted)
Rb 0.0 -0.00017 2.9560 0.0 -0.000085 2.9560 ! Rb+ Aqvist JPC 1990,94,8021. (adapted)
I 0.0 -0.40 2.35 0.0 -0.20 2.35 ! JCC,7,(1986),230;
F 0.0 -0.061 1.75 0.0 -0.0305 1.75 ! Gough JCC 13,(1992),963.
IB 0.0 -0.1 5.0 0.0 -0.05 5.0 ! solvated ion, vacuum apprx
! nb coeff for ligand K51
nc 0.0 -0.0860000001284 1.90844089227 0.0 -0.0860000001284 1.90844089227
ha 0.0 -0.109399999916 1.90844089255 0.0 -0.109399999916 1.90844089255
c3 0.0 -0.169999999918 1.82442148232 0.0 -0.169999999918 1.82442148232
cc 0.0 -0.169999999918 1.82442148232 0.0 -0.169999999918 1.82442148232
hn 0.0 -0.0150000000642 1.45933713908 0.0 -0.0150000000642 1.45933713908
na 0.0 -0.169999999918 1.82442148232 0.0 -0.169999999918 1.82442148232
cg 0.0 -0.169999999918 1.82442148232 0.0 -0.169999999918 1.82442148232
cd 0.0 -0.0860000001284 1.90844089227 0.0 -0.0860000001284 1.90844089227
ho 0.0 -0.0157000000262 1.48734360937 0.0 -0.0157000000262 1.48734360937
h4 0.0 -0.0150000000642 1.45933713908 0.0 -0.0150000000642 1.45933713908
oh 0.0 -0.109399999916 1.90844089255 0.0 -0.109399999916 1.90844089255
h1 0.0 -0.0157000000985 1.38732050124 0.0 -0.0157000000985 1.38732050124
hc 0.0 -0.0157000000262 1.48734360937 0.0 -0.0157000000262 1.48734360937
h1 0.0 -0.0157000000042 0.600138645426 0.0 -0.0157000000042 0.600138645426
nd 0.0 -0.0860000001284 1.90844089227 0.0 -0.0860000001284 1.90844089227
ca 0.0 -0.0860000001284 1.90844089227 0.0 -0.0860000001284 1.90844089227
n1 0.0 -0.0157000000262 1.48734360937 0.0 -0.0157000000262 1.48734360937
nh 0.0 -0.169999999918 1.82442148232 0.0 -0.169999999918 1.82442148232
!
h4 0.0 0.0150000000642 2.59964245874
hc 0.0 0.0157000000985 2.47135304264
h4 0.0 0.0149999999915 2.51055258758
h1 0.0 0.0157000000262 2.64953278726
n1 0.0 0.0149999999915 2.51055258758
ha 0.0 0.0860000001284 3.39966950794
cc 0.0 0.169999999918 3.24999852403
h1 0.0 0.0157000000042 1.06907846172
ha 0.0 0.0157000000262 2.64953278726
nd 0.0 0.169999999918 3.24999852403
c3 0.0 0.170000000105 3.00001234322
h1 0.0 0.0157000000985 2.47135304264
na 0.0 0.0860000001284 3.39966950794
hc 0.0 0.0157000000262 2.64953278726
cg 0.0 0.169999999918 3.24999852403
cc 0.0 0.0860000001284 3.39966950794
ha 0.0 0.0150000000642 2.59964245874
cd 0.0 0.0860000001284 3.39966950794
cc 0.0 0.109399999916 3.39966950845
hn 0.0 0.0150000000642 2.59964245874
c3 0.0 0.169999999918 3.24999852403
nd 0.0 0.0860000001284 3.39966950794
ca 0.0 0.0860000001284 3.39966950794
nh 0.0 0.0860000001284 3.39966950794
os 0.0 0.109399999916 3.39966950845
c3 0.0 0.109399999916 3.39966950845
END