# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:04:46 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1[nH]c2cc(ccc2n1)C(=O)c3sccc3
#
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
 NZO  NZO  'methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate'  ligand  32  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NZO
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
 NZO  O2    O  O     0  -0.489   3.8774  -1.7494  -0.5822
 NZO  C13   C  C     0   0.763   4.5261  -0.8071  -0.1898
 NZO  O3    O  O2    0  -0.463   5.8360  -0.7905  -0.0326
 NZO  C14   C  CH3   0  -0.421   6.5467  -1.9884  -0.3538
 NZO  N3    N  NH1   0  -0.755   3.9976   0.4052   0.1580
 NZO  C12   C  CR5   0   0.687   2.6692   0.7329   0.1330
 NZO  N1    N  NR15  0  -0.718   1.6868  -0.1069  -0.2648
 NZO  C8    C  CR56  0   0.374   0.5068   0.5855  -0.1361
 NZO  C7    C  CR16  0  -0.338  -0.8063   0.2363  -0.3854
 NZO  N2    N  N     0  -0.509   2.2424   1.9122   0.5033
 NZO  C9    C  CR56  0   0.166   0.8842   1.8519   0.3428
 NZO  C10   C  CR16  0  -0.326  -0.0917   2.8218   0.5677
 NZO  C11   C  CR16  0  -0.285  -1.4062   2.4937   0.3032
 NZO  C6    C  CR6   0  -0.074  -1.7739   1.2135  -0.1512
 NZO  C5    C  C     0   0.368  -3.2073   0.9579  -0.4307
 NZO  O1    O  O     0  -0.399  -3.9228   1.8320  -0.8860
 NZO  C4    C  CR5   0  -0.316  -3.7782  -0.3609  -0.1205
 NZO  C3    C  CR15  0  -0.185  -4.9750  -0.8407  -0.5904
 NZO  C2    C  CR15  0  -0.177  -5.3098  -2.1036  -0.0572
 NZO  C1    C  CR15  0  -0.445  -4.3729  -2.5579   0.8282
 NZO  S     S  S2    0   0.256  -3.0764  -1.4684   1.0032
 NZO  H14   H  HCH3  0   0.259   7.5897  -1.7753  -0.1420
 NZO  H14A  H  HCH3  0   0.246   6.2148  -2.8234   0.2616
 NZO  H14B  H  HCH3  0   0.246   6.4350  -2.2441  -1.4066
 NZO  HN3   H  HNH1  0   0.433   4.6163   1.1378   0.4775
 NZO  H7    H  HCR6  0   0.285  -1.0607  -0.7362  -0.7851
 NZO  H10   H  HCR6  0   0.262   0.1757   3.8034   0.9357
 NZO  H11   H  HCR6  0   0.261  -2.1790   3.2327   0.4682
 NZO  H3    H  HCR5  0   0.278  -5.5864  -0.3033  -1.3010
 NZO  H2    H  HCR5  0   0.276  -6.2046  -2.6522  -0.3123
 NZO  H1    H  HCR5  0   0.309  -4.3829  -3.4827   1.3848
 NZO  HN1   H  HNR5  0   0.430   1.8149  -1.0557  -0.5813

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
 NZO  O2   C13   double    1.209  0.020  1.209
 NZO  N3   C13   single    1.367  0.020  1.367
 NZO  C13  O3    single    1.319  0.020  1.319
 NZO  C14  O3    single    1.429  0.020  1.429
 NZO  C14  H14   single    0.970  0.020  1.090
 NZO  C14  H14A  single    0.970  0.020  1.090
 NZO  C14  H14B  single    0.970  0.020  1.090
 NZO  N3   C12   single    1.368  0.020  1.368
 NZO  N3   HN3   single    0.860  0.020  1.020
 NZO  N2   C12   aromatic  1.308  0.020  1.308
 NZO  C12  N1    aromatic  1.352  0.020  1.352
 NZO  N1   C8    aromatic  1.374  0.020  1.374
 NZO  C9   C8    aromatic  1.406  0.020  1.406
 NZO  C8   C7    aromatic  1.381  0.020  1.381
 NZO  C7   C6    aromatic  1.395  0.020  1.395
 NZO  C7   H7    single    0.930  0.020  1.080
 NZO  N2   C9    aromatic  1.369  0.020  1.369
 NZO  C9   C10   aromatic  1.394  0.020  1.394
 NZO  C10  C11   aromatic  1.380  0.020  1.380
 NZO  C10  H10   single    0.930  0.020  1.080
 NZO  C11  C6    aromatic  1.407  0.020  1.407
 NZO  C11  H11   single    0.930  0.020  1.080
 NZO  C6   C5    single    1.483  0.020  1.483
 NZO  C5   C4    single    1.470  0.020  1.470
 NZO  C5   O1    double    1.218  0.020  1.218
 NZO  C3   C4    aromatic  1.372  0.020  1.372
 NZO  C4   S     aromatic  1.727  0.020  1.727
 NZO  C3   C2    aromatic  1.411  0.020  1.411
 NZO  C3   H3    single    0.930  0.020  1.080
 NZO  C2   C1    aromatic  1.367  0.020  1.367
 NZO  C2   H2    single    0.930  0.020  1.080
 NZO  C1   S     aromatic  1.703  0.020  1.703
 NZO  C1   H1    single    0.930  0.020  1.080
 NZO  N1   HN1   single    0.860  0.020  1.020

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
 NZO  N3    C13  O3    110.01  3.000
 NZO  O3    C13  O2    125.52  3.000
 NZO  N3    C13  O2    124.47  3.000
 NZO  C14   O3   C13   117.15  3.000
 NZO  H14B  C14  H14A  109.57  3.000
 NZO  H14B  C14  H14   109.47  3.000
 NZO  H14A  C14  H14   109.46  3.000
 NZO  H14B  C14  O3    111.27  3.000
 NZO  H14A  C14  O3    111.35  3.000
 NZO  H14   C14  O3    105.63  3.000
 NZO  HN3   N3   C12   115.23  3.000
 NZO  HN3   N3   C13   119.11  3.000
 NZO  C12   N3   C13   125.65  3.000
 NZO  N2    C12  N1    113.97  3.000
 NZO  N1    C12  N3    124.18  3.000
 NZO  N2    C12  N3    121.85  3.000
 NZO  HN1   N1   C8    127.77  3.000
 NZO  HN1   N1   C12   125.76  3.000
 NZO  C8    N1   C12   106.46  3.000
 NZO  C9    C8   C7    122.99  3.000
 NZO  C7    C8   N1    132.22  3.000
 NZO  C9    C8   N1    104.79  3.000
 NZO  H7    C7   C6    121.92  3.000
 NZO  H7    C7   C8    121.16  3.000
 NZO  C6    C7   C8    116.87  3.000
 NZO  C9    N2   C12   104.53  3.000
 NZO  C10   C9   N2    130.16  3.000
 NZO  C10   C9   C8    119.59  3.000
 NZO  N2    C9   C8    110.24  3.000
 NZO  H10   C10  C11   121.08  3.000
 NZO  H10   C10  C9    120.87  3.000
 NZO  C11   C10  C9    118.06  3.000
 NZO  H11   C11  C6    118.95  3.000
 NZO  H11   C11  C10   119.25  3.000
 NZO  C6    C11  C10   121.79  3.000
 NZO  C5    C6   C11   118.05  3.000
 NZO  C5    C6   C7    121.21  3.000
 NZO  C11   C6   C7    120.68  3.000
 NZO  C4    C5   O1    119.64  3.000
 NZO  O1    C5   C6    120.97  3.000
 NZO  C4    C5   C6    119.36  3.000
 NZO  S     C4   C3    110.67  3.000
 NZO  S     C4   C5    123.70  3.000
 NZO  C3    C4   C5    125.45  3.000
 NZO  H3    C3   C2    124.01  3.000
 NZO  H3    C3   C4    123.01  3.000
 NZO  C2    C3   C4    112.98  3.000
 NZO  H2    C2   C1    123.51  3.000
 NZO  H2    C2   C3    124.18  3.000
 NZO  C1    C2   C3    112.31  3.000
 NZO  H1    C1   S     120.15  3.000
 NZO  H1    C1   C2    127.77  3.000
 NZO  S     C1   C2    112.08  3.000
 NZO  C1    S    C4     91.95  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
 NZO  CONST_01  C8   C9   N2   C12     0.00   0.0  0
 NZO  CONST_02  C10  C9   N2   C12   180.00   0.0  0
 NZO  CONST_03  C9   C8   N1   C12     0.00   0.0  0
 NZO  CONST_04  C7   C8   N1   C12   180.00   0.0  0
 NZO  CONST_05  C9   N2   C12  N1      0.00   0.0  0
 NZO  CONST_06  N2   C9   C8   N1      0.00   0.0  0
 NZO  CONST_07  C10  C9   C8   N1    180.00   0.0  0
 NZO  CONST_08  C6   C7   C8   N1    180.00   0.0  0
 NZO  CONST_09  N2   C12  N1   C8      0.00   0.0  0
 NZO  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 NZO  CONST_11  C11  C6   C7   C8      0.00   0.0  0
 NZO  CONST_12  N2   C9   C8   C7    180.00   0.0  0
 NZO  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 NZO  CONST_14  C10  C11  C6   C7      0.00   0.0  0
 NZO  CONST_15  C11  C10  C9   N2    180.00   0.0  0
 NZO  CONST_16  C6   C7   C8   C9      0.00   0.0  0
 NZO  CONST_17  C6   C11  C10  C9      0.00   0.0  0
 NZO  CONST_18  C1   C2   C3   C4      0.00   0.0  0
 NZO  CONST_19  C2   C1   S    C4      0.00   0.0  0
 NZO  CONST_20  C1   S    C4   C3      0.00   0.0  0
 NZO  CONST_21  S    C1   C2   C3      0.00   0.0  0
 NZO  CONST_22  S    C4   C3   C2      0.00   0.0  0
 NZO  CONST_23  C9   N2   C12  N3    180.00   0.0  0
 NZO  CONST_24  C8   N1   C12  N3    180.00   0.0  0
 NZO  CONST_25  C5   C6   C7   C8    180.00   0.0  0
 NZO  CONST_26  C5   C6   C11  C10   180.00   0.0  0
 NZO  CONST_27  C2   C3   C4   C5    180.00   0.0  0
 NZO  CONST_28  C1   S    C4   C5    180.00   0.0  0
 NZO  CONST_29  H7   C7   C8   N1      0.00   0.0  0
 NZO  CONST_30  H10  C10  C9   C8    180.00   0.0  0
 NZO  CONST_31  HN1  N1   C8   C7      0.00   0.0  0
 NZO  CONST_32  H11  C11  C6   C7    180.00   0.0  0
 NZO  CONST_33  H2   C2   C3   C4    180.00   0.0  0
 NZO  CONST_34  H1   C1   S    C4    180.00   0.0  0
 NZO  CONST_35  H3   C3   C2   C1    180.00   0.0  0
 NZO  CONST_36  N2   C12  N3   C13   180.00   0.0  0
 NZO  CONST_37  N1   C12  N3   C13     0.00   0.0  0
 NZO  CONST_38  HN3  N3   C12  N1    180.00   0.0  0
 NZO  CONST_39  C12  N3   C13  O2      0.00   0.0  0
 NZO  CONST_40  C12  N3   C13  O3    180.00   0.0  0
 NZO  Var_01    C4   C5   C6   C7     39.19  30.0  2
 NZO  Var_02    C3   C4   C5   C6   -164.33  30.0  2
 NZO  Var_03    N3   C13  O3   C14   179.97  30.0  1
 NZO  Var_04    H14  C14  O3   C13  -179.00  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
 NZO  plan-1  C5   0.020
 NZO  plan-1  C4   0.020
 NZO  plan-1  C3   0.020
 NZO  plan-1  C2   0.020
 NZO  plan-1  C1   0.020
 NZO  plan-1  S    0.020
 NZO  plan-1  H3   0.020
 NZO  plan-1  H2   0.020
 NZO  plan-1  H1   0.020
 NZO  plan-2  N3   0.020
 NZO  plan-2  C12  0.020
 NZO  plan-2  N1   0.020
 NZO  plan-2  C8   0.020
 NZO  plan-2  C7   0.020
 NZO  plan-2  N2   0.020
 NZO  plan-2  C9   0.020
 NZO  plan-2  C10  0.020
 NZO  plan-2  C11  0.020
 NZO  plan-2  C6   0.020
 NZO  plan-2  C5   0.020
 NZO  plan-2  H7   0.020
 NZO  plan-2  H10  0.020
 NZO  plan-2  H11  0.020
 NZO  plan-2  HN1  0.020
 NZO  plan-3  C13  0.020
 NZO  plan-3  N3   0.020
 NZO  plan-3  C12  0.020
 NZO  plan-3  HN3  0.020
 NZO  plan-4  C6   0.020
 NZO  plan-4  C5   0.020
 NZO  plan-4  O1   0.020
 NZO  plan-4  C4   0.020
 NZO  plan-5  O2   0.020
 NZO  plan-5  C13  0.020
 NZO  plan-5  O3   0.020
 NZO  plan-5  N3   0.020

