# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:04:04 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-(3-methyl-5-oxidanylidene-4-phenyl-4~{H}-pyrazol-1-yl)-3~{H}-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NN(C(=O)[C@@H]1c2ccccc2)c3[nH]c4cc(ccc4n3)C(O)=O
#
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
 MY7  MY7  '2-(3-methyl-5-oxidanylidene-4-phenyl-4~{H}-pyrazol-1-yl)-3~{H}-benzimidazole-5-carboxylic acid'  ligand  38  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY7
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
 MY7  C1   C  CR16   0  -0.297  -4.0048   0.4684   1.3255
 MY7  C11  C  CR5    0   0.370  -2.5688  -1.7143  -0.2524
 MY7  C12  C  CH3    0  -0.728  -3.3385  -2.9218   0.1175
 MY7  C14  C  CR5    0   0.718   0.4388  -0.0744  -0.4852
 MY7  C16  C  CR5    0   0.370   2.5513  -0.3739  -0.0145
 MY7  C17  C  CR5    0   0.150   2.3223   0.8716  -0.6204
 MY7  C19  C  C1     0  -0.329   3.3973   1.7280  -0.8467
 MY7  C2   C  CR16   0  -0.239  -4.9913   1.0605   2.0989
 MY7  C20  C  C1     0  -0.301   4.6566   1.3059  -0.4585
 MY7  C21  C  C      0  -0.130   4.8782   0.0583   0.1497
 MY7  C22  C  C1     0  -0.356   3.8088  -0.8005   0.3780
 MY7  C23  C  C      0   0.400   6.2844  -0.3591   0.5588
 MY7  C3   C  CR16   0  -0.261  -6.2290   1.3577   1.5412
 MY7  C4   C  CR16   0  -0.240  -6.4742   1.0596   0.2084
 MY7  C5   C  CR16   0  -0.314  -5.4865   0.4636  -0.5657
 MY7  C6   C  CR6    0   0.194  -4.2476   0.1652  -0.0126
 MY7  C7   C  CR15   0  -0.686  -3.1696  -0.4762  -0.8456
 MY7  C8   C  CR5    0   0.611  -1.9408   0.4030  -1.0077
 MY7  N10  N  N      0  -0.254  -1.3055  -1.6276  -0.1116
 MY7  N15  N  NR15   0  -0.732   1.3085  -0.9593   0.0570
 MY7  N18  N  N      0  -0.493   0.9839   1.0297  -0.9038
 MY7  N9   N  NR5    0  -0.496  -0.9010  -0.3830  -0.5559
 MY7  O13  O  O      0  -0.398  -1.8726   1.5291  -1.4236
 MY7  O24  O  OC    -1  -0.596   7.2035   0.4468   0.3146
 MY7  O25  O  O      0  -0.596   6.4005  -1.4746   1.1035
 MY7  H1   H  HCR6   0   0.259  -3.0437   0.2389   1.7726
 MY7  H2   H  HCH3   0   0.268  -3.8309  -3.3398  -0.7615
 MY7  H3   H  HCH3   0   0.269  -2.6931  -3.6796   0.5556
 MY7  H4   H  HCH3   0   0.263  -4.1223  -2.6723   0.8342
 MY7  H5   H  H      0   0.247   3.2488   2.6927  -1.3154
 MY7  H6   H  HCR6   0   0.263  -4.7934   1.2901   3.1375
 MY7  H7   H  H      0   0.240   5.5060   1.9541  -0.6259
 MY7  H8   H  H      0   0.254   3.9638  -1.7639   0.8454
 MY7  H9   H  HCR6   0   0.262  -6.9994   1.8200   2.1444
 MY7  H10  H  HCR6   0   0.262  -7.4362   1.2883  -0.2312
 MY7  H11  H  HCR6   0   0.262  -5.6821   0.2289  -1.6047
 MY7  H12  H  HCR5   0   0.357  -3.5600  -0.7051  -1.8445
 MY7  H13  H  HNR5   0   0.425   1.0761  -1.8662   0.4306

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
 MY7  O25  C23  deloc     1.247  0.020  1.247
 MY7  C23  O24  deloc     1.246  0.020  1.246
 MY7  C23  C21  single    1.523  0.020  1.523
 MY7  C20  C21  aromatic  1.406  0.020  1.406
 MY7  C20  C19  aromatic  1.384  0.020  1.384
 MY7  C21  C22  aromatic  1.390  0.020  1.390
 MY7  C19  C17  aromatic  1.393  0.020  1.393
 MY7  C22  C16  aromatic  1.385  0.020  1.385
 MY7  C17  C16  aromatic  1.404  0.020  1.404
 MY7  C17  N18  aromatic  1.377  0.020  1.377
 MY7  C16  N15  aromatic  1.376  0.020  1.376
 MY7  N18  C14  aromatic  1.301  0.020  1.301
 MY7  N15  C14  aromatic  1.354  0.020  1.354
 MY7  C14  N9   single    1.377  0.020  1.377
 MY7  N9   N10  single    1.382  0.020  1.382
 MY7  N9   C8   single    1.380  0.020  1.380
 MY7  N10  C11  double    1.274  0.020  1.274
 MY7  O13  C8   double    1.202  0.020  1.202
 MY7  C8   C7   single    1.520  0.020  1.520
 MY7  C11  C7   single    1.499  0.020  1.499
 MY7  C11  C12  single    1.479  0.020  1.479
 MY7  C7   C6   single    1.506  0.020  1.506
 MY7  C6   C5   aromatic  1.389  0.020  1.389
 MY7  C6   C1   aromatic  1.393  0.020  1.393
 MY7  C5   C4   aromatic  1.389  0.020  1.389
 MY7  C1   C2   aromatic  1.386  0.020  1.386
 MY7  C4   C3   aromatic  1.388  0.020  1.388
 MY7  C2   C3   aromatic  1.390  0.020  1.390
 MY7  C1   H1   single    0.930  0.020  1.080
 MY7  C12  H2   single    0.970  0.020  1.090
 MY7  C12  H3   single    0.970  0.020  1.090
 MY7  C12  H4   single    0.970  0.020  1.090
 MY7  C19  H5   single    0.930  0.020  1.080
 MY7  C2   H6   single    0.930  0.020  1.080
 MY7  C20  H7   single    0.930  0.020  1.080
 MY7  C22  H8   single    0.930  0.020  1.080
 MY7  C3   H9   single    0.930  0.020  1.080
 MY7  C4   H10  single    0.930  0.020  1.080
 MY7  C5   H11  single    0.930  0.020  1.080
 MY7  C7   H12  single    0.970  0.020  1.090
 MY7  N15  H13  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
 MY7  H1   C1   C6   120.29  3.000
 MY7  H1   C1   C2   119.40  3.000
 MY7  C6   C1   C2   120.31  3.000
 MY7  N10  C11  C7   112.65  3.000
 MY7  C7   C11  C12  124.39  3.000
 MY7  N10  C11  C12  122.95  3.000
 MY7  H4   C12  H3   108.73  3.000
 MY7  H4   C12  H2   107.02  3.000
 MY7  H3   C12  H2   108.99  3.000
 MY7  H4   C12  C11  110.58  3.000
 MY7  H3   C12  C11  111.15  3.000
 MY7  H2   C12  C11  110.26  3.000
 MY7  N9   C14  N18  125.57  3.000
 MY7  N9   C14  N15  119.94  3.000
 MY7  N18  C14  N15  114.49  3.000
 MY7  N15  C16  C22  132.43  3.000
 MY7  N15  C16  C17  104.63  3.000
 MY7  C22  C16  C17  122.94  3.000
 MY7  N18  C17  C19  130.24  3.000
 MY7  N18  C17  C16  110.44  3.000
 MY7  C19  C17  C16  119.32  3.000
 MY7  H5   C19  C20  121.20  3.000
 MY7  H5   C19  C17  120.81  3.000
 MY7  C20  C19  C17  117.99  3.000
 MY7  H6   C2   C3   120.18  3.000
 MY7  H6   C2   C1   119.74  3.000
 MY7  C3   C2   C1   120.08  3.000
 MY7  H7   C20  C21  118.37  3.000
 MY7  H7   C20  C19  119.24  3.000
 MY7  C21  C20  C19  122.38  3.000
 MY7  C23  C21  C22  119.79  3.000
 MY7  C22  C21  C20  119.88  3.000
 MY7  C23  C21  C20  120.34  3.000
 MY7  H8   C22  C21  120.72  3.000
 MY7  H8   C22  C16  121.79  3.000
 MY7  C21  C22  C16  117.49  3.000
 MY7  O25  C23  O24  126.53  3.000
 MY7  O24  C23  C21  116.82  3.000
 MY7  O25  C23  C21  116.65  3.000
 MY7  H9   C3   C4   120.09  3.000
 MY7  H9   C3   C2   120.11  3.000
 MY7  C4   C3   C2   119.79  3.000
 MY7  H10  C4   C5   119.76  3.000
 MY7  H10  C4   C3   120.12  3.000
 MY7  C5   C4   C3   120.12  3.000
 MY7  H11  C5   C6   119.77  3.000
 MY7  H11  C5   C4   119.94  3.000
 MY7  C6   C5   C4   120.29  3.000
 MY7  C7   C6   C5   120.64  3.000
 MY7  C5   C6   C1   119.41  3.000
 MY7  C7   C6   C1   119.95  3.000
 MY7  H12  C7   C8   108.15  3.000
 MY7  H12  C7   C6   109.76  3.000
 MY7  C8   C7   C6   113.05  3.000
 MY7  H12  C7   C11  109.32  3.000
 MY7  C6   C7   C11  114.83  3.000
 MY7  C8   C7   C11  101.30  3.000
 MY7  O13  C8   N9   127.17  3.000
 MY7  O13  C8   C7   128.66  3.000
 MY7  N9   C8   C7   104.17  3.000
 MY7  N9   N10  C11  108.42  3.000
 MY7  H13  N15  C16  127.62  3.000
 MY7  H13  N15  C14  126.04  3.000
 MY7  C16  N15  C14  106.34  3.000
 MY7  C17  N18  C14  104.10  3.000
 MY7  N10  N9   C8   113.44  3.000
 MY7  C8   N9   C14  128.50  3.000
 MY7  N10  N9   C14  118.05  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
 MY7  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 MY7  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 MY7  CONST_03  C19  C17  N18  C14  180.00   0.0  0
 MY7  CONST_04  C16  C17  N18  C14    0.00   0.0  0
 MY7  CONST_05  C22  C16  N15  C14  180.00   0.0  0
 MY7  CONST_06  C17  C16  N15  C14    0.00   0.0  0
 MY7  CONST_07  C20  C21  C22  C16    0.00   0.0  0
 MY7  CONST_08  C20  C19  C17  C16    0.00   0.0  0
 MY7  CONST_09  N18  C14  N15  C16    0.00   0.0  0
 MY7  CONST_10  C21  C20  C19  C17    0.00   0.0  0
 MY7  CONST_11  C21  C22  C16  C17    0.00   0.0  0
 MY7  CONST_12  N15  C14  N18  C17    0.00   0.0  0
 MY7  CONST_13  C22  C21  C20  C19    0.00   0.0  0
 MY7  CONST_14  C22  C16  C17  C19    0.00   0.0  0
 MY7  CONST_15  N15  C16  C17  C19  180.00   0.0  0
 MY7  CONST_16  C5   C6   C1   C2     0.00   0.0  0
 MY7  CONST_17  C5   C4   C3   C2     0.00   0.0  0
 MY7  CONST_18  N18  C17  C19  C20  180.00   0.0  0
 MY7  CONST_19  N15  C16  C22  C21  180.00   0.0  0
 MY7  CONST_20  N18  C17  C16  C22  180.00   0.0  0
 MY7  CONST_21  C6   C5   C4   C3     0.00   0.0  0
 MY7  CONST_22  C6   C1   C2   C3     0.00   0.0  0
 MY7  CONST_23  N18  C17  C16  N15    0.00   0.0  0
 MY7  CONST_24  N9   C14  N15  C16  180.00   0.0  0
 MY7  CONST_25  N9   C14  N18  C17  180.00   0.0  0
 MY7  CONST_26  C7   C6   C1   C2   180.00   0.0  0
 MY7  CONST_27  C7   C6   C5   C4   180.00   0.0  0
 MY7  CONST_28  C7   C8   N9   C14  180.00   0.0  0
 MY7  CONST_29  N10  N9   C8   C7     0.00   0.0  0
 MY7  CONST_30  C23  C21  C22  C16  180.00   0.0  0
 MY7  CONST_31  C23  C21  C20  C19  180.00   0.0  0
 MY7  CONST_32  O13  C8   N9   C14    0.00   0.0  0
 MY7  CONST_33  O13  C8   N9   N10  180.00   0.0  0
 MY7  CONST_34  H11  C5   C6   C1   180.00   0.0  0
 MY7  CONST_35  H9   C3   C2   C1   180.00   0.0  0
 MY7  CONST_36  H5   C19  C17  C16  180.00   0.0  0
 MY7  CONST_37  H7   C20  C19  C17  180.00   0.0  0
 MY7  CONST_38  H8   C22  C16  C17  180.00   0.0  0
 MY7  CONST_39  H13  N15  C16  C17  180.00   0.0  0
 MY7  CONST_40  H10  C4   C3   C2   180.00   0.0  0
 MY7  CONST_41  H1   C1   C2   C3   180.00   0.0  0
 MY7  CONST_42  H6   C2   C3   C4   180.00   0.0  0
 MY7  Var_01    C14  N9   N10  C11  179.63  30.0  1
 MY7  Var_02    N18  C14  N9   C8    -3.43  30.0  1
 MY7  Var_03    O25  C23  C21  C20  179.37  30.0  2
 MY7  Var_04    H2   C12  C11  C7    60.69  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 MY7  chir_01  C7  C8  C11  C6  negativ

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
 MY7  plan-1  C1   0.020
 MY7  plan-1  C2   0.020
 MY7  plan-1  C3   0.020
 MY7  plan-1  C4   0.020
 MY7  plan-1  C5   0.020
 MY7  plan-1  C6   0.020
 MY7  plan-1  C7   0.020
 MY7  plan-1  H1   0.020
 MY7  plan-1  H6   0.020
 MY7  plan-1  H9   0.020
 MY7  plan-1  H10  0.020
 MY7  plan-1  H11  0.020
 MY7  plan-2  C14  0.020
 MY7  plan-2  C16  0.020
 MY7  plan-2  C17  0.020
 MY7  plan-2  C19  0.020
 MY7  plan-2  C20  0.020
 MY7  plan-2  C21  0.020
 MY7  plan-2  C22  0.020
 MY7  plan-2  C23  0.020
 MY7  plan-2  N15  0.020
 MY7  plan-2  N18  0.020
 MY7  plan-2  N9   0.020
 MY7  plan-2  H5   0.020
 MY7  plan-2  H7   0.020
 MY7  plan-2  H8   0.020
 MY7  plan-2  H13  0.020
 MY7  plan-3  C21  0.020
 MY7  plan-3  C23  0.020
 MY7  plan-3  O24  0.020
 MY7  plan-3  O25  0.020
 MY7  plan-4  C14  0.020
 MY7  plan-4  C7   0.020
 MY7  plan-4  C8   0.020
 MY7  plan-4  N10  0.020
 MY7  plan-4  N9   0.020
 MY7  plan-4  O13  0.020

