# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 00:30:40 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(1H-benzimidazol-1-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCn1cnc2ccccc12
#
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
 EXB  EXB  '3-(1H-benzimidazol-1-yl)propanoic acid'  ligand  23  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EXB
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
 EXB  C2    C  CR16   0  -0.306  -1.2258  -1.4662   0.3666
 EXB  C5    C  CR16   0  -0.325  -3.5033   0.0601  -0.4063
 EXB  C4    C  CR16   0  -0.275  -3.5703  -1.3138  -0.2636
 EXB  C3    C  CR16   0  -0.278  -2.4478  -2.0657   0.1189
 EXB  C6    C  CR56   0   0.123  -2.2796   0.6849  -0.1621
 EXB  C11   C  CH2    0  -0.599   1.9837  -0.0762  -0.4866
 EXB  N9    N  NR5    0  -0.499  -0.1466   0.8179   0.3818
 EXB  C1    C  CR56   0   0.337  -1.1653  -0.0839   0.2169
 EXB  C8    C  CR15   0   0.102  -0.6682   2.0355   0.0983
 EXB  N7    N  N      0  -0.475  -1.9312   2.0131  -0.2260
 EXB  C12   C  C      0   0.423   3.4577  -0.4125  -0.1924
 EXB  O     O  O      0  -0.605   3.9044  -0.0874   0.9249
 EXB  H2    H  HCR6   0   0.266  -0.3638  -2.0516   0.6605
 EXB  H5    H  HCR6   0   0.253  -4.3721   0.6358  -0.6992
 EXB  H4    H  HCR6   0   0.251  -4.5059  -1.8243  -0.4513
 EXB  H3    H  HCR6   0   0.254  -2.5413  -3.1390   0.2203
 EXB  H11   H  HCH2   0   0.238   1.4782  -0.9815  -0.8364
 EXB  H10   H  HCH2   0   0.253   1.2524  -0.1620   1.5519
 EXB  H10A  H  HCH2   0   0.261   1.7070   1.4447   1.0238
 EXB  H8    H  HCR5   0   0.285  -0.0577   2.9263   0.1532
 EXB  OXT   O  OC    -1  -0.622   4.0804  -0.9788  -1.1115
 EXB  H9    H  HCH2   0   0.242   1.9462   0.6260  -1.3260
 EXB  C10   C  CH2    0  -0.303   1.2389   0.5171   0.6987

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
 EXB  C2   C3    aromatic  1.384  0.020  1.384
 EXB  C2   C1    aromatic  1.392  0.020  1.392
 EXB  C2   H2    single    0.930  0.020  1.080
 EXB  C5   C4    aromatic  1.383  0.020  1.383
 EXB  C5   C6    aromatic  1.395  0.020  1.395
 EXB  C5   H5    single    0.930  0.020  1.080
 EXB  C4   C3    aromatic  1.404  0.020  1.404
 EXB  C4   H4    single    0.930  0.020  1.080
 EXB  C3   H3    single    0.930  0.020  1.080
 EXB  C6   C1    aromatic  1.406  0.020  1.406
 EXB  C6   N7    aromatic  1.375  0.020  1.375
 EXB  C11  C10   single    1.520  0.020  1.520
 EXB  C11  C12   single    1.540  0.020  1.540
 EXB  C11  H11   single    0.970  0.020  1.090
 EXB  C10  N9    single    1.453  0.020  1.453
 EXB  C10  H10   single    0.970  0.020  1.090
 EXB  C10  H10A  single    0.970  0.020  1.090
 EXB  N9   C1    aromatic  1.370  0.020  1.370
 EXB  N9   C8    aromatic  1.355  0.020  1.355
 EXB  C8   N7    aromatic  1.304  0.020  1.304
 EXB  C8   H8    single    0.930  0.020  1.080
 EXB  C12  O     deloc     1.246  0.020  1.246
 EXB  C12  OXT   deloc     1.246  0.020  1.246
 EXB  C11  H9    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
 EXB  H2    C2   C1   122.12  3.000
 EXB  H2    C2   C3   121.16  3.000
 EXB  C1    C2   C3   116.72  3.000
 EXB  H5    C5   C6   120.86  3.000
 EXB  H5    C5   C4   121.15  3.000
 EXB  C6    C5   C4   117.98  3.000
 EXB  H4    C4   C3   119.06  3.000
 EXB  H4    C4   C5   119.51  3.000
 EXB  C3    C4   C5   121.43  3.000
 EXB  H3    C3   C4   119.18  3.000
 EXB  H3    C3   C2   119.30  3.000
 EXB  C4    C3   C2   121.52  3.000
 EXB  N7    C6   C1   109.88  3.000
 EXB  N7    C6   C5   130.29  3.000
 EXB  C1    C6   C5   119.83  3.000
 EXB  H9    C11  H11  105.64  3.000
 EXB  H9    C11  C12  108.61  3.000
 EXB  H11   C11  C12  108.82  3.000
 EXB  H9    C11  C10  109.30  3.000
 EXB  H11   C11  C10  110.23  3.000
 EXB  C12   C11  C10  113.90  3.000
 EXB  C8    N9   C1   106.26  3.000
 EXB  C8    N9   C10  126.80  3.000
 EXB  C1    N9   C10  126.80  3.000
 EXB  N9    C1   C6   105.18  3.000
 EXB  N9    C1   C2   132.29  3.000
 EXB  C6    C1   C2   122.53  3.000
 EXB  H8    C8   N7   125.00  3.000
 EXB  H8    C8   N9   120.83  3.000
 EXB  N7    C8   N9   114.18  3.000
 EXB  C8    N7   C6   104.51  3.000
 EXB  OXT   C12  O    126.90  3.000
 EXB  OXT   C12  C11  115.88  3.000
 EXB  O     C12  C11  117.21  3.000
 EXB  H10A  C10  H10  106.95  3.000
 EXB  H10A  C10  N9   107.39  3.000
 EXB  H10   C10  N9   108.14  3.000
 EXB  H10A  C10  C11  110.77  3.000
 EXB  H10   C10  C11  111.15  3.000
 EXB  N9    C10  C11  112.21  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
 EXB  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 EXB  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 EXB  CONST_03  N7   C6   C1   C2    180.00   0.0  0
 EXB  CONST_04  C8   N9   C1   C2    180.00   0.0  0
 EXB  CONST_05  N9   C1   C6   C5    180.00   0.0  0
 EXB  CONST_06  C8   N7   C6   C5    180.00   0.0  0
 EXB  CONST_07  C1   C6   C5   C4      0.00   0.0  0
 EXB  CONST_08  N7   C6   C5   C4    180.00   0.0  0
 EXB  CONST_09  C1   C2   C3   C4      0.00   0.0  0
 EXB  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 EXB  CONST_11  N9   C1   C2   C3    180.00   0.0  0
 EXB  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 EXB  CONST_13  C8   N9   C1   C6      0.00   0.0  0
 EXB  CONST_14  N9   C8   N7   C6      0.00   0.0  0
 EXB  CONST_15  N7   C6   C1   N9      0.00   0.0  0
 EXB  CONST_16  C8   N7   C6   C1      0.00   0.0  0
 EXB  CONST_17  N7   C8   N9   C1      0.00   0.0  0
 EXB  CONST_18  C10  N9   C1   C2      0.00   0.0  0
 EXB  CONST_19  C10  N9   C1   C6    180.00   0.0  0
 EXB  CONST_20  N7   C8   N9   C10   180.00   0.0  0
 EXB  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 EXB  CONST_22  H3   C3   C4   C5    180.00   0.0  0
 EXB  CONST_23  H2   C2   C3   C4    180.00   0.0  0
 EXB  CONST_24  H5   C5   C4   C3    180.00   0.0  0
 EXB  CONST_25  H8   C8   N7   C6    180.00   0.0  0
 EXB  Var_01    C1   N9   C10  C11    73.32  30.0  2
 EXB  Var_02    C12  C11  C10  N9   -179.90  30.0  2
 EXB  Var_03    O    C12  C11  C10    -4.78  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
 EXB  plan-1  C2   0.020
 EXB  plan-1  C5   0.020
 EXB  plan-1  C4   0.020
 EXB  plan-1  C3   0.020
 EXB  plan-1  C6   0.020
 EXB  plan-1  N9   0.020
 EXB  plan-1  C1   0.020
 EXB  plan-1  C8   0.020
 EXB  plan-1  N7   0.020
 EXB  plan-1  H2   0.020
 EXB  plan-1  H5   0.020
 EXB  plan-1  H4   0.020
 EXB  plan-1  H3   0.020
 EXB  plan-1  H8   0.020
 EXB  plan-1  C10  0.020
 EXB  plan-2  C11  0.020
 EXB  plan-2  C12  0.020
 EXB  plan-2  O    0.020
 EXB  plan-2  OXT  0.020

