# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:24:41 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  23  14  .  2021-08-04  2021-08-04  
;
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  -0.283   4.3110   0.3183  -0.4309
 4BX  C2    C  CR16   0  -0.272   4.1488  -0.9996   0.0206
 4BX  C3    C  CR16   0  -0.341   2.9073  -1.4884   0.3901
 4BX  C4    C  CR16   0  -0.309   3.2357   1.1866  -0.5266
 4BX  N5    N  NR15   0  -0.700   0.7415   1.2378  -0.1106
 4BX  C6    C  CR56   0   0.325   1.9942   0.6873  -0.1536
 4BX  C7    C  CR56   0   0.132   1.8114  -0.6302   0.3023
 4BX  N8    N  N      0  -0.479   0.4878  -0.8438   0.6046
 4BX  C9    C  CR5    0   0.464  -0.1158   0.2877   0.3475
 4BX  C10   C  CH2    0  -0.536  -1.5739   0.5459   0.5081
 4BX  C11   C  CH2    0  -0.587  -2.4196  -0.3402  -0.4019
 4BX  C12   C  C      0   0.419  -3.9403  -0.1522  -0.2473
 4BX  O13   O  O      0  -0.605  -4.3392   0.6861   0.5840
 4BX  O14   O  OC    -1  -0.626  -4.6512  -0.8688  -0.9811
 4BX  H1    H  HCR6   0   0.252   5.2976   0.6651  -0.7087
 4BX  H2    H  HCR6   0   0.249   5.0152  -1.6452   0.0826
 4BX  H3    H  HCR6   0   0.250   2.7875  -2.5065   0.7386
 4BX  H4    H  HCR6   0   0.263   3.3624   2.2037  -0.8744
 4BX  H10   H  HCH2   0   0.253  -1.8448   0.3694   1.5511
 4BX  H10A  H  HCH2   0   0.245  -1.7800   1.5980   0.3073
 4BX  H11   H  HCH2   0   0.236  -2.1504  -0.1584  -1.4476
 4BX  H11A  H  HCH2   0   0.235  -2.1770  -1.3910  -0.2179
 4BX  HN5   H  HNR5   0   0.415   0.4898   2.1785  -0.3694

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  1.402  0.020  1.402
 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  1.395  0.020  1.395
 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  1.359  0.020  1.359
 4BX  N5   C6    aromatic  1.369  0.020  1.369
 4BX  C6   C7    aromatic  1.406  0.020  1.406
 4BX  N8   C7    aromatic  1.374  0.020  1.374
 4BX  C9   N8    aromatic  1.308  0.020  1.308
 4BX  C10  C9    single    1.490  0.020  1.490
 4BX  C11  C10   single    1.526  0.020  1.526
 4BX  C10  H10   single    0.970  0.020  1.090
 4BX  C10  H10A  single    0.970  0.020  1.090
 4BX  C12  C11   single    1.540  0.020  1.540
 4BX  C11  H11   single    0.970  0.020  1.090
 4BX  C11  H11A  single    0.970  0.020  1.090
 4BX  O13  C12   deloc     1.246  0.020  1.246
 4BX  C12  O14   deloc     1.248  0.020  1.248
 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   119.28  3.000
 4BX  H1    C1   C2   119.30  3.000
 4BX  C4    C1   C2   121.43  3.000
 4BX  H2    C2   C3   119.47  3.000
 4BX  H2    C2   C1   119.11  3.000
 4BX  C3    C2   C1   121.43  3.000
 4BX  H3    C3   C7   120.79  3.000
 4BX  H3    C3   C2   121.14  3.000
 4BX  C7    C3   C2   118.07  3.000
 4BX  H4    C4   C6   121.92  3.000
 4BX  H4    C4   C1   121.35  3.000
 4BX  C6    C4   C1   116.73  3.000
 4BX  HN5   N5   C9   125.57  3.000
 4BX  HN5   N5   C6   126.58  3.000
 4BX  C9    N5   C6   107.86  3.000
 4BX  C7    C6   N5   104.34  3.000
 4BX  C7    C6   C4   122.69  3.000
 4BX  N5    C6   C4   132.97  3.000
 4BX  N8    C7   C6   110.01  3.000
 4BX  N8    C7   C3   130.33  3.000
 4BX  C6    C7   C3   119.66  3.000
 4BX  C9    N8   C7   105.47  3.000
 4BX  C10   C9   N8   125.49  3.000
 4BX  C10   C9   N5   122.18  3.000
 4BX  N8    C9   N5   112.33  3.000
 4BX  H10A  C10  H10  106.55  3.000
 4BX  H10A  C10  C11  110.22  3.000
 4BX  H10   C10  C11  109.77  3.000
 4BX  H10A  C10  C9   109.41  3.000
 4BX  H10   C10  C9   108.53  3.000
 4BX  C11   C10  C9   112.18  3.000
 4BX  H11A  C11  H11  105.40  3.000
 4BX  H11A  C11  C12  108.62  3.000
 4BX  H11   C11  C12  108.56  3.000
 4BX  H11A  C11  C10  109.55  3.000
 4BX  H11   C11  C10  109.69  3.000
 4BX  C12   C11  C10  114.62  3.000
 4BX  O14   C12  O13  126.59  3.000
 4BX  O14   C12  C11  115.69  3.000
 4BX  O13   C12  C11  117.72  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  Var_01    C11  C10  C9   N5   116.80  30.0  2
 4BX  Var_02    C12  C11  C10  C9   178.07  30.0  1
 4BX  Var_03    O13  C12  C11  C10    0.09  30.0  2

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

