# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:21:20 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1[nH]c2ccccc2n1
#
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
 4BX  4BX  '3-(1H-benzimidazol-2-yl)propanoic acid'  ligand  24  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4BX
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
 4BX  C1    C  CR16  0  -0.281   4.3520   0.2871  -0.1161
 4BX  C2    C  CR16  0  -0.272   4.0646  -1.0857  -0.1176
 4BX  C3    C  CR16  0  -0.338   2.7612  -1.5493  -0.0751
 4BX  C4    C  CR16  0  -0.307   3.3452   1.2374  -0.0711
 4BX  N5    N  NR15  0  -0.706   0.8211   1.3849   0.0172
 4BX  C6    C  CR56  0   0.326   2.0402   0.7622  -0.0281
 4BX  C7    C  CR56  0   0.137   1.7338  -0.6087  -0.0300
 4BX  N8    N  N     0  -0.483   0.3698  -0.7849   0.0120
 4BX  C9    C  CR5   0   0.482  -0.1348   0.4178   0.0393
 4BX  C10   C  CH2   0  -0.544  -1.5840   0.7560   0.1013
 4BX  C11   C  CH2   0  -0.582  -2.4583  -0.4658  -0.1144
 4BX  C12   C  C     0   0.558  -3.9252  -0.1466  -0.0579
 4BX  O13   O  O     0  -0.443  -4.3951   0.9391   0.1742
 4BX  O14   O  OH1   0  -0.597  -4.6670  -1.2234  -0.2971
 4BX  H1    H  HCR6  0   0.253   5.3841   0.6106  -0.1514
 4BX  H2    H  HCR6  0   0.251   4.8812  -1.7945  -0.1531
 4BX  H3    H  HCR6  0   0.252   2.5428  -2.6096  -0.0772
 4BX  H4    H  HCR6  0   0.264   3.5678   2.2962  -0.0706
 4BX  H10   H  HCH2  0   0.279  -1.8003   1.2114   1.0716
 4BX  H10A  H  HCH2  0   0.274  -1.8026   1.5210  -0.6477
 4BX  H11   H  HCH2  0   0.288  -2.2406  -0.9317  -1.0783
 4BX  H11A  H  HCH2  0   0.290  -2.2453  -1.2313   0.6359
 4BX  HO14  H  HOH1  0   0.480  -5.6068  -0.9946  -0.2509
 4BX  HN5   H  HNR5  0   0.418   0.6557   2.3786   0.0246

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
 4BX  C4   C1    aromatic  1.385  0.020  1.385
 4BX  C1   C2    aromatic  1.403  0.020  1.403
 4BX  C1   H1    single    0.930  0.020  1.080
 4BX  C2   C3    aromatic  1.384  0.020  1.384
 4BX  C2   H2    single    0.930  0.020  1.080
 4BX  C7   C3    aromatic  1.394  0.020  1.394
 4BX  C3   H3    single    0.930  0.020  1.080
 4BX  C4   C6    aromatic  1.389  0.020  1.389
 4BX  C4   H4    single    0.930  0.020  1.080
 4BX  N5   C9    aromatic  1.360  0.020  1.360
 4BX  N5   C6    aromatic  1.370  0.020  1.370
 4BX  C6   C7    aromatic  1.405  0.020  1.405
 4BX  N8   C7    aromatic  1.376  0.020  1.376
 4BX  C9   N8    aromatic  1.305  0.020  1.305
 4BX  C10  C9    single    1.489  0.020  1.489
 4BX  C11  C10   single    1.518  0.020  1.518
 4BX  C10  H10   single    0.970  0.020  1.090
 4BX  C10  H10A  single    0.970  0.020  1.090
 4BX  C12  C11   single    1.502  0.020  1.502
 4BX  C11  H11   single    0.970  0.020  1.090
 4BX  C11  H11A  single    0.970  0.020  1.090
 4BX  O13  C12   double    1.206  0.020  1.206
 4BX  C12  O14   single    1.329  0.020  1.329
 4BX  O14  HO14  single    0.850  0.020  0.980
 4BX  N5   HN5   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
 4BX  H1    C1   C4   119.29  3.000
 4BX  H1    C1   C2   119.20  3.000
 4BX  C4    C1   C2   121.51  3.000
 4BX  H2    C2   C3   119.49  3.000
 4BX  H2    C2   C1   119.12  3.000
 4BX  C3    C2   C1   121.38  3.000
 4BX  H3    C3   C7   120.82  3.000
 4BX  H3    C3   C2   121.20  3.000
 4BX  C7    C3   C2   117.98  3.000
 4BX  H4    C4   C6   121.86  3.000
 4BX  H4    C4   C1   121.46  3.000
 4BX  C6    C4   C1   116.69  3.000
 4BX  HN5   N5   C9   125.86  3.000
 4BX  HN5   N5   C6   126.50  3.000
 4BX  C9    N5   C6   107.63  3.000
 4BX  C7    C6   N5   104.45  3.000
 4BX  C7    C6   C4   122.58  3.000
 4BX  N5    C6   C4   132.96  3.000
 4BX  N8    C7   C6   109.95  3.000
 4BX  N8    C7   C3   130.19  3.000
 4BX  C6    C7   C3   119.86  3.000
 4BX  C9    N8   C7   105.42  3.000
 4BX  C10   C9   N8   125.91  3.000
 4BX  C10   C9   N5   121.54  3.000
 4BX  N8    C9   N5   112.55  3.000
 4BX  H10A  C10  H10  106.09  3.000
 4BX  H10A  C10  C11  110.55  3.000
 4BX  H10   C10  C11  110.33  3.000
 4BX  H10A  C10  C9   108.97  3.000
 4BX  H10   C10  C9   108.90  3.000
 4BX  C11   C10  C9   111.83  3.000
 4BX  H11A  C11  H11  105.56  3.000
 4BX  H11A  C11  C12  108.26  3.000
 4BX  H11   C11  C12  108.56  3.000
 4BX  H11A  C11  C10  110.74  3.000
 4BX  H11   C11  C10  110.72  3.000
 4BX  C12   C11  C10  112.71  3.000
 4BX  O14   C12  O13  123.14  3.000
 4BX  O14   C12  C11  111.47  3.000
 4BX  O13   C12  C11  125.39  3.000
 4BX  HO14  O14  C12  109.97  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
 4BX  CONST_01  N5    C6   C4   C1    180.00   0.0  0
 4BX  CONST_02  C7    C6   C4   C1      0.00   0.0  0
 4BX  CONST_03  C7    C3   C2   C1      0.00   0.0  0
 4BX  CONST_04  C6    C4   C1   C2      0.00   0.0  0
 4BX  CONST_05  C6    C7   C3   C2      0.00   0.0  0
 4BX  CONST_06  N8    C7   C3   C2    180.00   0.0  0
 4BX  CONST_07  C4    C1   C2   C3      0.00   0.0  0
 4BX  CONST_08  C4    C6   C7   C3      0.00   0.0  0
 4BX  CONST_09  N5    C6   C7   C3    180.00   0.0  0
 4BX  CONST_10  C9    N8   C7   C3    180.00   0.0  0
 4BX  CONST_11  C9    N5   C6   C4    180.00   0.0  0
 4BX  CONST_12  N8    C7   C6   C4    180.00   0.0  0
 4BX  CONST_13  C7    N8   C9   N5      0.00   0.0  0
 4BX  CONST_14  N8    C7   C6   N5      0.00   0.0  0
 4BX  CONST_15  N8    C9   N5   C6      0.00   0.0  0
 4BX  CONST_16  C9    N8   C7   C6      0.00   0.0  0
 4BX  CONST_17  C9    N5   C6   C7      0.00   0.0  0
 4BX  CONST_18  C10   C9   N5   C6    180.00   0.0  0
 4BX  CONST_19  C10   C9   N8   C7    180.00   0.0  0
 4BX  CONST_20  H3    C3   C2   C1    180.00   0.0  0
 4BX  CONST_21  H4    C4   C1   C2    180.00   0.0  0
 4BX  CONST_22  H1    C1   C2   C3    180.00   0.0  0
 4BX  CONST_23  H2    C2   C1   C4    180.00   0.0  0
 4BX  CONST_24  HN5   N5   C6   C4      0.00   0.0  0
 4BX  CONST_25  HO14  O14  C12  C11   180.00   0.0  0
 4BX  Var_01    C11   C10  C9   N5    170.60  30.0  2
 4BX  Var_02    C12   C11  C10  C9   -179.91  30.0  2
 4BX  Var_03    O13   C12  C11  C10    -2.32  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
 4BX  plan-1  C1    0.020
 4BX  plan-1  C2    0.020
 4BX  plan-1  C3    0.020
 4BX  plan-1  C4    0.020
 4BX  plan-1  N5    0.020
 4BX  plan-1  C6    0.020
 4BX  plan-1  C7    0.020
 4BX  plan-1  N8    0.020
 4BX  plan-1  C9    0.020
 4BX  plan-1  C10   0.020
 4BX  plan-1  H1    0.020
 4BX  plan-1  H2    0.020
 4BX  plan-1  H3    0.020
 4BX  plan-1  H4    0.020
 4BX  plan-1  HN5   0.020
 4BX  plan-2  C11   0.020
 4BX  plan-2  C12   0.020
 4BX  plan-2  O13   0.020
 4BX  plan-2  O14   0.020
 4BX  plan-2  HO14  0.020

