# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:27:51 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VIB  VIB  3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-3-ium  ligand  35  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VIB
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VIB  CM2   C  CH3   0  -0.731   4.8256   1.7520   1.3535
 VIB  O1    O  OH1   0  -0.664  -5.4833   1.4885   0.7224
 VIB  C7    C  CH2   0  -0.123  -4.5221   0.7427   0.0201
 VIB  C6    C  CH2   0  -0.553  -3.3170   0.5571   0.9368
 VIB  C2    C  CR15  0  -0.147  -0.8822  -2.0239  -0.6362
 VIB  S1    S  S2    0   0.399  -2.2449  -1.9552   0.3266
 VIB  C5    C  CR5   0  -0.323  -2.2463  -0.2353   0.2668
 VIB  C4    C  CR5   0   0.530  -1.2145   0.2152  -0.4930
 VIB  N3    N  NR5   1  -0.386  -0.4499  -0.8314  -0.9810
 VIB  C7A   C  CH2   0  -0.471   0.7706  -0.6504  -1.7937
 VIB  C4A   C  CR6   0   0.477   2.5358  -0.7608   0.0509
 VIB  N3A   N  N     0  -0.459   3.4687  -0.1578   0.7887
 VIB  C2A   C  CR6   0   0.366   3.8095   1.0843   0.4844
 VIB  N1A   N  N     0  -0.437   3.3150   1.7945  -0.5268
 VIB  C6A   C  CR16  0  -0.064   2.3589   1.2066  -1.2350
 VIB  C5A   C  CR6   0  -0.041   1.8872  -0.0657  -0.9919
 VIB  HM21  H  HCH3  0   0.262   4.3257   2.4205   2.0581
 VIB  HM22  H  HCH3  0   0.251   5.3953   1.0255   1.9275
 VIB  HM23  H  HCH3  0   0.254   5.5058   2.3593   0.7590
 VIB  H4A1  H  HNH2  0   0.403   1.8582  -2.6508  -0.3288
 VIB  H4A2  H  HNH2  0   0.404   2.8244  -2.4838   1.0470
 VIB  HM41  H  HCH3  0   0.288  -0.0840   2.0104  -0.2040
 VIB  HM42  H  HCH3  0   0.279  -0.6487   1.7642  -1.8606
 VIB  HM43  H  HCH3  0   0.289  -1.7774   2.2541  -0.6133
 VIB  HO1   H  HOH1  0   0.460  -6.2342   1.6357   0.1402
 VIB  HC71  H  HCH2  0   0.208  -4.1988   1.2498  -0.8977
 VIB  HC72  H  HCH2  0   0.205  -4.9038  -0.2420  -0.2788
 VIB  HC61  H  HCH2  0   0.286  -3.6257   0.0596   1.8583
 VIB  HC62  H  HCH2  0   0.282  -2.9121   1.5291   1.2239
 VIB  HC2   H  HCR5  0   0.379  -0.4142  -2.9416  -0.9570
 VIB  H7A1  H  HCH2  0   0.337   0.5152  -0.0057  -2.6337
 VIB  H7A2  H  HCH2  0   0.330   1.0126  -1.6274  -2.2126
 VIB  H6AC  H  HCR6  0   0.278   1.9356   1.7869  -2.0501
 VIB  N4A   N  NH2   0  -0.824   2.2256  -2.0317   0.3739
 VIB  CM4   C  CH3   0  -0.747  -0.9071   1.6330  -0.8104

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VIB  CM2  C2A   single    1.495  0.020  1.495
 VIB  CM2  HM21  single    0.970  0.020  1.090
 VIB  CM2  HM22  single    0.970  0.020  1.090
 VIB  CM2  HM23  single    0.970  0.020  1.090
 VIB  N4A  C4A   single    1.347  0.020  1.347
 VIB  N4A  H4A1  single    0.890  0.020  1.040
 VIB  N4A  H4A2  single    0.890  0.020  1.040
 VIB  CM4  C4    single    1.485  0.020  1.485
 VIB  CM4  HM41  single    0.970  0.020  1.090
 VIB  CM4  HM42  single    0.970  0.020  1.090
 VIB  CM4  HM43  single    0.970  0.020  1.090
 VIB  O1   C7    single    1.405  0.020  1.405
 VIB  O1   HO1   single    0.850  0.020  0.980
 VIB  C7   C6    single    1.525  0.020  1.525
 VIB  C7   HC71  single    0.970  0.020  1.090
 VIB  C7   HC72  single    0.970  0.020  1.090
 VIB  C6   C5    single    1.491  0.020  1.491
 VIB  C6   HC61  single    0.970  0.020  1.090
 VIB  C6   HC62  single    0.970  0.020  1.090
 VIB  C2   S1    aromatic  1.670  0.020  1.670
 VIB  C2   N3    aromatic  1.315  0.020  1.315
 VIB  C2   HC2   single    0.930  0.020  1.080
 VIB  S1   C5    aromatic  1.721  0.020  1.721
 VIB  C5   C4    aromatic  1.358  0.020  1.358
 VIB  C4   N3    aromatic  1.385  0.020  1.385
 VIB  N3   C7A   single    1.477  0.020  1.477
 VIB  C7A  C5A   single    1.494  0.020  1.494
 VIB  C7A  H7A1  single    0.970  0.020  1.090
 VIB  C7A  H7A2  single    0.970  0.020  1.090
 VIB  C4A  N3A   aromatic  1.334  0.020  1.334
 VIB  C4A  C5A   aromatic  1.411  0.020  1.411
 VIB  N3A  C2A   aromatic  1.323  0.020  1.323
 VIB  C2A  N1A   aromatic  1.331  0.020  1.331
 VIB  N1A  C6A   aromatic  1.327  0.020  1.327
 VIB  C6A  C5A   aromatic  1.379  0.020  1.379
 VIB  C6A  H6AC  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VIB  HM23  CM2  HM22  109.49  3.000
 VIB  HM23  CM2  HM21  107.26  3.000
 VIB  HM22  CM2  HM21  107.96  3.000
 VIB  HM23  CM2  C2A   110.88  3.000
 VIB  HM22  CM2  C2A   111.40  3.000
 VIB  HM21  CM2  C2A   109.72  3.000
 VIB  HO1   O1   C7    108.24  3.000
 VIB  HC72  C7   HC71  106.81  3.000
 VIB  HC72  C7   C6    109.22  3.000
 VIB  HC71  C7   C6    109.04  3.000
 VIB  HC72  C7   O1    111.99  3.000
 VIB  HC71  C7   O1    111.99  3.000
 VIB  C6    C7   O1    107.74  3.000
 VIB  HC62  C6   HC61  106.78  3.000
 VIB  HC62  C6   C5    108.97  3.000
 VIB  HC61  C6   C5    109.88  3.000
 VIB  HC62  C6   C7    110.05  3.000
 VIB  HC61  C6   C7    109.84  3.000
 VIB  C5    C6   C7    111.22  3.000
 VIB  HC2   C2   N3    123.44  3.000
 VIB  HC2   C2   S1    124.08  3.000
 VIB  N3    C2   S1    112.47  3.000
 VIB  C5    S1   C2     91.25  3.000
 VIB  C4    C5   S1    110.50  3.000
 VIB  C4    C5   C6    128.36  3.000
 VIB  S1    C5   C6    121.07  3.000
 VIB  N3    C4   C5    111.46  3.000
 VIB  N3    C4   CM4   122.13  3.000
 VIB  C5    C4   CM4   126.40  3.000
 VIB  C7A   N3   C4    123.87  3.000
 VIB  C7A   N3   C2    121.81  3.000
 VIB  C4    N3   C2    114.30  3.000
 VIB  H7A2  C7A  H7A1  106.63  3.000
 VIB  H7A2  C7A  C5A   113.02  3.000
 VIB  H7A1  C7A  C5A   110.95  3.000
 VIB  H7A2  C7A  N3    106.56  3.000
 VIB  H7A1  C7A  N3    107.63  3.000
 VIB  C5A   C7A  N3    111.73  3.000
 VIB  C5A   C4A  N3A   120.51  3.000
 VIB  C5A   C4A  N4A   122.41  3.000
 VIB  N3A   C4A  N4A   117.06  3.000
 VIB  C2A   N3A  C4A   118.51  3.000
 VIB  N1A   C2A  N3A   125.43  3.000
 VIB  N1A   C2A  CM2   117.14  3.000
 VIB  N3A   C2A  CM2   117.43  3.000
 VIB  C6A   N1A  C2A   115.90  3.000
 VIB  H6AC  C6A  C5A   119.47  3.000
 VIB  H6AC  C6A  N1A   116.39  3.000
 VIB  C5A   C6A  N1A   124.14  3.000
 VIB  C6A   C5A  C4A   115.32  3.000
 VIB  C6A   C5A  C7A   121.49  3.000
 VIB  C4A   C5A  C7A   123.19  3.000
 VIB  H4A2  N4A  H4A1  114.04  3.000
 VIB  H4A2  N4A  C4A   116.51  3.000
 VIB  H4A1  N4A  C4A   119.81  3.000
 VIB  HM43  CM4  HM42  107.21  3.000
 VIB  HM43  CM4  HM41  107.81  3.000
 VIB  HM42  CM4  HM41  108.40  3.000
 VIB  HM43  CM4  C4    109.93  3.000
 VIB  HM42  CM4  C4    111.72  3.000
 VIB  HM41  CM4  C4    111.59  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VIB  CONST_01  C4    C5   S1   C2      0.00   0.0  0
 VIB  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 VIB  CONST_03  C4    N3   C2   S1      0.00   0.0  0
 VIB  CONST_04  N3    C4   C5   S1      0.00   0.0  0
 VIB  CONST_05  N3    C2   S1   C5      0.00   0.0  0
 VIB  CONST_06  N1A   C2A  N3A  C4A     0.00   0.0  0
 VIB  CONST_07  N1A   C6A  C5A  C4A     0.00   0.0  0
 VIB  CONST_08  C6A   C5A  C4A  N3A     0.00   0.0  0
 VIB  CONST_09  C6A   N1A  C2A  N3A     0.00   0.0  0
 VIB  CONST_10  C5A   C4A  N3A  C2A     0.00   0.0  0
 VIB  CONST_11  C5A   C6A  N1A  C2A     0.00   0.0  0
 VIB  CONST_12  C4A   N3A  C2A  CM2   180.00   0.0  0
 VIB  CONST_13  C6A   N1A  C2A  CM2   180.00   0.0  0
 VIB  CONST_14  C2A   N3A  C4A  N4A   180.00   0.0  0
 VIB  CONST_15  C6A   C5A  C4A  N4A   180.00   0.0  0
 VIB  CONST_16  S1    C5   C4   CM4   180.00   0.0  0
 VIB  CONST_17  C2    N3   C4   CM4   180.00   0.0  0
 VIB  CONST_18  C2    S1   C5   C6    180.00   0.0  0
 VIB  CONST_19  N3    C4   C5   C6    180.00   0.0  0
 VIB  CONST_20  C7A   N3   C2   S1    180.00   0.0  0
 VIB  CONST_21  C7A   N3   C4   C5    180.00   0.0  0
 VIB  CONST_22  N3A   C4A  C5A  C7A   180.00   0.0  0
 VIB  CONST_23  N1A   C6A  C5A  C7A   180.00   0.0  0
 VIB  CONST_24  HC2   C2   S1   C5    180.00   0.0  0
 VIB  CONST_25  H6AC  C6A  C5A  C4A   180.00   0.0  0
 VIB  CONST_27  H4A2  N4A  C4A  N3A     0.00   0.0  0
 VIB  Var_01    C5A   C7A  N3   C2   -109.61  30.0  2
 VIB  Var_02    C4A   C5A  C7A  N3     68.12  30.0  2
 VIB  Var_03    S1    C5   C6   C7    -86.86  30.0  2
 VIB  Var_04    HM41  CM4  C4   C5    102.25  30.0  2
 VIB  Var_05    HM21  CM2  C2A  N3A  -100.54  30.0  2
 VIB  Var_06    C5    C6   C7   O1    179.70  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VIB  plan-1  C6    0.020
 VIB  plan-1  C2    0.020
 VIB  plan-1  S1    0.020
 VIB  plan-1  C5    0.020
 VIB  plan-1  C4    0.020
 VIB  plan-1  N3    0.020
 VIB  plan-1  C7A   0.020
 VIB  plan-1  HC2   0.020
 VIB  plan-1  CM4   0.020
 VIB  plan-2  CM2   0.020
 VIB  plan-2  C7A   0.020
 VIB  plan-2  C4A   0.020
 VIB  plan-2  N3A   0.020
 VIB  plan-2  C2A   0.020
 VIB  plan-2  N1A   0.020
 VIB  plan-2  C6A   0.020
 VIB  plan-2  C5A   0.020
 VIB  plan-2  H6AC  0.020
 VIB  plan-2  N4A   0.020
 VIB  plan-3  C4A   0.020
 VIB  plan-3  H4A1  0.020
 VIB  plan-3  H4A2  0.020
 VIB  plan-3  N4A   0.020

