# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 22:42:52 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-(3-methoxyphenyl)-1H-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2[nH]c3cccc(C(N)=O)c3n2
#
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
 BZC  BZC  2-(3-methoxyphenyl)-1H-benzimidazole-4-carboxamide  ligand  33  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BZC
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
 BZC  C1    C  CR56  0   0.159  -0.2145   0.1629  -1.8538
 BZC  N2    N  N     0  -0.460   0.2553   0.0829  -0.5724
 BZC  C3    C  CR5   0   0.484  -0.8066  -0.0206   0.1858
 BZC  N4    N  NR15  0  -0.729  -1.9599  -0.0169  -0.5340
 BZC  C5    C  CR56  0   0.344  -1.6197   0.0963  -1.8522
 BZC  C7    C  CR16  0  -0.306  -2.3817   0.1400  -3.0121
 BZC  C4    C  CR6   0  -0.143   0.4722   0.2505  -3.0732
 BZC  C19   C  CR6   0   0.036  -0.7740  -0.1301   1.6434
 BZC  C2    C  CR16  0  -0.297  -0.2886   0.2840  -4.2338
 BZC  C6    C  CR16  0  -0.272  -1.6882   0.2366  -4.2044
 BZC  C8    C  C     0   0.464   1.9597   0.3682  -3.1066
 BZC  N1    N  NH2   0  -0.802   2.5627  -0.2880  -4.1110
 BZC  O1    O  O     0  -0.474   2.5685   1.0328  -2.2815
 BZC  C11   C  CR16  0  -0.402   0.4196   0.1367   2.3028
 BZC  C12   C  CR16  0  -0.328  -1.9044  -0.5007   2.3754
 BZC  C13   C  CR6   0   0.418   0.4974   0.0437   3.6907
 BZC  O2    O  O2    0  -0.471   1.6943   0.3261   4.2345
 BZC  C15   C  CR16  0  -0.383  -0.6319  -0.3217   4.4220
 BZC  C17   C  CR16  0  -0.224  -1.8194  -0.5908   3.7528
 BZC  C18   C  CH3   0  -0.438   1.8341   0.2536   5.6402
 BZC  HN4   H  HNR5  0   0.426  -2.8997  -0.0551  -0.1725
 BZC  H7    H  HCR6  0   0.274  -3.4626   0.1010  -2.9879
 BZC  H2    H  HCR6  0   0.263   0.2024   0.3771  -5.1944
 BZC  H6    H  HCR6  0   0.263  -2.2356   0.2817  -5.1362
 BZC  HN11  H  HNH2  0   0.403   3.5634  -0.2419  -4.2147
 BZC  HN12  H  HNH2  0   0.411   2.0652  -0.9219  -4.7120
 BZC  H11   H  HCR6  0   0.264   1.2966   0.4244   1.7369
 BZC  H12   H  HCR6  0   0.246  -2.8419  -0.7358   1.8893
 BZC  H15   H  HCR6  0   0.285  -0.6068  -0.4030   5.4998
 BZC  H17   H  HCR6  0   0.268  -2.6913  -0.8806   4.3240
 BZC  H181  H  HCH3  0   0.261   2.8644   0.5197   5.8612
 BZC  H182  H  HCH3  0   0.230   1.1713   0.9552   6.1531
 BZC  H183  H  HCH3  0   0.230   1.6425  -0.7538   6.0183

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
 BZC  C1   N2    aromatic  1.367  0.020  1.367
 BZC  C1   C5    aromatic  1.407  0.020  1.407
 BZC  C1   C4    aromatic  1.402  0.020  1.402
 BZC  N2   C3    aromatic  1.309  0.020  1.309
 BZC  C3   N4    aromatic  1.359  0.020  1.359
 BZC  C3   C19   single    1.462  0.020  1.462
 BZC  N4   C5    aromatic  1.366  0.020  1.366
 BZC  N4   HN4   single    0.860  0.020  1.020
 BZC  C5   C7    aromatic  1.388  0.020  1.388
 BZC  C7   C6    aromatic  1.383  0.020  1.383
 BZC  C7   H7    single    0.930  0.020  1.080
 BZC  C4   C2    aromatic  1.388  0.020  1.388
 BZC  C4   C8    single    1.493  0.020  1.493
 BZC  C19  C11   aromatic  1.390  0.020  1.390
 BZC  C19  C12   aromatic  1.397  0.020  1.397
 BZC  C2   C6    aromatic  1.401  0.020  1.401
 BZC  C2   H2    single    0.930  0.020  1.080
 BZC  C6   H6    single    0.930  0.020  1.080
 BZC  C8   N1    single    1.343  0.020  1.343
 BZC  C8   O1    double    1.222  0.020  1.222
 BZC  N1   HN11  single    0.860  0.020  1.020
 BZC  N1   HN12  single    0.860  0.020  1.020
 BZC  C11  C13   aromatic  1.393  0.020  1.393
 BZC  C11  H11   single    0.930  0.020  1.080
 BZC  C12  C17   aromatic  1.383  0.020  1.383
 BZC  C12  H12   single    0.930  0.020  1.080
 BZC  C13  O2    single    1.345  0.020  1.345
 BZC  C13  C15   aromatic  1.394  0.020  1.394
 BZC  O2   C18   single    1.414  0.020  1.414
 BZC  C15  C17   aromatic  1.389  0.020  1.389
 BZC  C15  H15   single    0.930  0.020  1.080
 BZC  C17  H17   single    0.930  0.020  1.080
 BZC  C18  H181  single    0.970  0.020  1.090
 BZC  C18  H182  single    0.970  0.020  1.090
 BZC  C18  H183  single    0.970  0.020  1.090

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
 BZC  C4    C1   C5    119.55  3.000
 BZC  C4    C1   N2    130.58  3.000
 BZC  C5    C1   N2    109.84  3.000
 BZC  C3    N2   C1    105.59  3.000
 BZC  C19   C3   N4    123.16  3.000
 BZC  C19   C3   N2    124.43  3.000
 BZC  N4    C3   N2    112.41  3.000
 BZC  HN4   N4   C5    125.56  3.000
 BZC  HN4   N4   C3    126.95  3.000
 BZC  C5    N4   C3    107.45  3.000
 BZC  C7    C5   N4    132.22  3.000
 BZC  C7    C5   C1    123.08  3.000
 BZC  N4    C5   C1    104.70  3.000
 BZC  H7    C7   C6    121.53  3.000
 BZC  H7    C7   C5    121.91  3.000
 BZC  C6    C7   C5    116.57  3.000
 BZC  C8    C4   C2    121.71  3.000
 BZC  C8    C4   C1    120.83  3.000
 BZC  C2    C4   C1    117.40  3.000
 BZC  C12   C19  C11   119.83  3.000
 BZC  C12   C19  C3    121.62  3.000
 BZC  C11   C19  C3    118.54  3.000
 BZC  H2    C2   C6    118.33  3.000
 BZC  H2    C2   C4    119.69  3.000
 BZC  C6    C2   C4    121.96  3.000
 BZC  H6    C6   C2    119.09  3.000
 BZC  H6    C6   C7    119.46  3.000
 BZC  C2    C6   C7    121.44  3.000
 BZC  O1    C8   N1    123.17  3.000
 BZC  O1    C8   C4    121.62  3.000
 BZC  N1    C8   C4    115.20  3.000
 BZC  HN12  N1   HN11  117.33  3.000
 BZC  HN12  N1   C8    122.22  3.000
 BZC  HN11  N1   C8    120.05  3.000
 BZC  H11   C11  C13   119.56  3.000
 BZC  H11   C11  C19   119.92  3.000
 BZC  C13   C11  C19   120.52  3.000
 BZC  H12   C12  C17   119.12  3.000
 BZC  H12   C12  C19   121.57  3.000
 BZC  C17   C12  C19   119.31  3.000
 BZC  C15   C13  O2    124.33  3.000
 BZC  C15   C13  C11   119.66  3.000
 BZC  O2    C13  C11   116.01  3.000
 BZC  C18   O2   C13   118.62  3.000
 BZC  H15   C15  C17   119.04  3.000
 BZC  H15   C15  C13   121.59  3.000
 BZC  C17   C15  C13   119.37  3.000
 BZC  H17   C17  C15   119.10  3.000
 BZC  H17   C17  C12   119.59  3.000
 BZC  C15   C17  C12   121.31  3.000
 BZC  H183  C18  H182  108.84  3.000
 BZC  H183  C18  H181  108.75  3.000
 BZC  H182  C18  H181  108.80  3.000
 BZC  H183  C18  O2    111.95  3.000
 BZC  H182  C18  O2    111.94  3.000
 BZC  H181  C18  O2    106.45  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
 BZC  CONST_01  N4    C3   N2   C1      0.00   0.0  0
 BZC  CONST_02  C19   C3   N2   C1    180.00   0.0  0
 BZC  CONST_03  C3    N4   C5   C1      0.00   0.0  0
 BZC  CONST_04  C6    C7   C5   C1      0.00   0.0  0
 BZC  CONST_05  C6    C2   C4   C1      0.00   0.0  0
 BZC  CONST_06  N4    C5   C1   N2      0.00   0.0  0
 BZC  CONST_07  C7    C5   C1   N2    180.00   0.0  0
 BZC  CONST_08  C2    C4   C1   N2    180.00   0.0  0
 BZC  CONST_09  C5    N4   C3   N2      0.00   0.0  0
 BZC  CONST_10  C11   C19  C3   N2      0.00   0.0  0
 BZC  CONST_11  C12   C19  C3   N2    180.00   0.0  0
 BZC  CONST_12  C5    C1   N2   C3      0.00   0.0  0
 BZC  CONST_13  C4    C1   N2   C3    180.00   0.0  0
 BZC  CONST_14  C7    C5   N4   C3    180.00   0.0  0
 BZC  CONST_15  C13   C11  C19  C3    180.00   0.0  0
 BZC  CONST_16  C17   C12  C19  C3    180.00   0.0  0
 BZC  CONST_17  C11   C19  C3   N4    180.00   0.0  0
 BZC  CONST_18  C12   C19  C3   N4      0.00   0.0  0
 BZC  CONST_19  C4    C1   C5   N4    180.00   0.0  0
 BZC  CONST_20  C6    C7   C5   N4    180.00   0.0  0
 BZC  CONST_21  C2    C4   C1   C5      0.00   0.0  0
 BZC  CONST_22  C19   C3   N4   C5    180.00   0.0  0
 BZC  CONST_23  C2    C6   C7   C5      0.00   0.0  0
 BZC  CONST_24  C4    C1   C5   C7      0.00   0.0  0
 BZC  CONST_25  C4    C2   C6   C7      0.00   0.0  0
 BZC  CONST_26  C15   C13  C11  C19     0.00   0.0  0
 BZC  CONST_27  C15   C17  C12  C19     0.00   0.0  0
 BZC  CONST_28  C17   C12  C19  C11     0.00   0.0  0
 BZC  CONST_29  C17   C15  C13  C11     0.00   0.0  0
 BZC  CONST_30  C13   C11  C19  C12     0.00   0.0  0
 BZC  CONST_31  C13   C15  C17  C12     0.00   0.0  0
 BZC  CONST_32  C8    C4   C1   N2      0.00   0.0  0
 BZC  CONST_33  C8    C4   C1   C5    180.00   0.0  0
 BZC  CONST_34  O2    C13  C11  C19   180.00   0.0  0
 BZC  CONST_35  C8    C4   C2   C6    180.00   0.0  0
 BZC  CONST_36  C17   C15  C13  O2    180.00   0.0  0
 BZC  CONST_37  HN4   N4   C5   C1    180.00   0.0  0
 BZC  CONST_38  H7    C7   C5   C1    180.00   0.0  0
 BZC  CONST_39  H2    C2   C4   C1    180.00   0.0  0
 BZC  CONST_40  H11   C11  C19  C3      0.00   0.0  0
 BZC  CONST_41  H12   C12  C19  C3      0.00   0.0  0
 BZC  CONST_42  H6    C6   C7   C5    180.00   0.0  0
 BZC  CONST_43  H17   C17  C12  C19   180.00   0.0  0
 BZC  CONST_44  H15   C15  C13  C11   180.00   0.0  0
 BZC  CONST_45  HN11  N1   C8   C4    180.00   0.0  0
 BZC  CONST_46  HN12  N1   C8   C4      0.00   0.0  0
 BZC  Var_01    N1    C8   C4   C1    143.15  30.0  2
 BZC  Var_02    H181  C18  O2   C13  -179.82  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
 BZC  plan-1  C3    0.020
 BZC  plan-1  C19   0.020
 BZC  plan-1  C11   0.020
 BZC  plan-1  C12   0.020
 BZC  plan-1  C13   0.020
 BZC  plan-1  O2    0.020
 BZC  plan-1  C15   0.020
 BZC  plan-1  C17   0.020
 BZC  plan-1  H11   0.020
 BZC  plan-1  H12   0.020
 BZC  plan-1  H15   0.020
 BZC  plan-1  H17   0.020
 BZC  plan-2  C1    0.020
 BZC  plan-2  N2    0.020
 BZC  plan-2  C3    0.020
 BZC  plan-2  N4    0.020
 BZC  plan-2  C5    0.020
 BZC  plan-2  C7    0.020
 BZC  plan-2  C4    0.020
 BZC  plan-2  C19   0.020
 BZC  plan-2  C2    0.020
 BZC  plan-2  C6    0.020
 BZC  plan-2  C8    0.020
 BZC  plan-2  HN4   0.020
 BZC  plan-2  H7    0.020
 BZC  plan-2  H2    0.020
 BZC  plan-2  H6    0.020
 BZC  plan-3  C4    0.020
 BZC  plan-3  C8    0.020
 BZC  plan-3  N1    0.020
 BZC  plan-3  O1    0.020
 BZC  plan-3  HN11  0.020
 BZC  plan-3  HN12  0.020

