# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:21:57 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2cc(Cl)ccc2n1CCCO
#
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
 EV3  EV3  3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol  ligand  27  15  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EV3
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
 EV3  C1    C   CR6   0  -0.054  -2.8233  -0.4203  -0.0453
 EV3  C2    C   CR16  0  -0.250  -2.0003  -1.4414   0.4260
 EV3  C3    C   CR16  0  -0.307  -2.3579   0.8561  -0.3201
 EV3  C4    C   CR16  0  -0.317  -0.6475  -1.2023   0.6408
 EV3  C5    C   CR56  0   0.156  -1.0054   1.0987  -0.1080
 EV3  C6    C   CR56  0   0.358  -0.1764   0.0688   0.3712
 EV3  N7    N   N     0  -0.526  -0.2787   2.2445  -0.3030
 EV3  C8    C   CR5   0   0.627   0.9453   1.9274   0.0469
 EV3  N9    N   NR5   0  -0.557   1.0729   0.6383   0.4798
 EV3  N10   N   NH2   0  -0.855   1.9908   2.7874   0.0565
 EV3  C11   C   CH2   0  -0.352   2.2893  -0.0315   0.8803
 EV3  C12   C   CH2   0  -0.469   2.9991  -0.7023  -0.2899
 EV3  C13   C   CH2   0  -0.140   4.3051  -1.3324   0.1530
 EV3  O14   O   OH1   0  -0.671   4.9136  -1.9389  -0.9645
 EV3  CL15  CL  CL    0  -0.147  -4.5103  -0.7652  -0.3030
 EV3  H2    H   HCR6  0   0.272  -2.4105  -2.4219   0.6242
 EV3  H3    H   HCR6  0   0.270  -3.0164   1.6326  -0.6861
 EV3  H4    H   HCR6  0   0.273  -0.0064  -1.9952   1.0041
 EV3  HN10  H   HNH2  0   0.403   1.8389   3.6427  -0.4533
 EV3  HN1A  H   HNH2  0   0.405   2.9199   2.4172  -0.0637
 EV3  H11   H   HCH2  0   0.272   2.9409   0.6963   1.3677
 EV3  H11A  H   HCH2  0   0.278   2.0351  -0.7637   1.6483
 EV3  H12   H   HCH2  0   0.245   2.3471  -1.4658  -0.7229
 EV3  H12A  H   HCH2  0   0.239   3.1937   0.0379  -1.0710
 EV3  H13   H   HCH2  0   0.196   4.9488  -0.5582   0.5918
 EV3  H13A  H   HCH2  0   0.197   4.1052  -2.0629   0.9481
 EV3  HO14  H   HOH1  0   0.455   5.7497  -2.3189  -0.6809

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
 EV3  C1   C2    aromatic  1.394  0.020  1.394
 EV3  C1   C3    aromatic  1.386  0.020  1.386
 EV3  C1   CL15  single    1.741  0.020  1.741
 EV3  C2   C4    aromatic  1.391  0.020  1.391
 EV3  C3   C5    aromatic  1.390  0.020  1.390
 EV3  C4   C6    aromatic  1.382  0.020  1.382
 EV3  C5   C6    aromatic  1.406  0.020  1.406
 EV3  C5   N7    aromatic  1.371  0.020  1.371
 EV3  C6   N9    aromatic  1.377  0.020  1.377
 EV3  N7   C8    aromatic  1.312  0.020  1.312
 EV3  C8   N9    aromatic  1.366  0.020  1.366
 EV3  C8   N10   single    1.354  0.020  1.354
 EV3  N9   C11   single    1.445  0.020  1.445
 EV3  C11  C12   single    1.524  0.020  1.524
 EV3  C12  C13   single    1.516  0.020  1.516
 EV3  C13  O14   single    1.410  0.020  1.410
 EV3  C2   H2    single    0.930  0.020  1.080
 EV3  C3   H3    single    0.930  0.020  1.080
 EV3  C4   H4    single    0.930  0.020  1.080
 EV3  N10  HN10  single    0.890  0.020  1.040
 EV3  N10  HN1A  single    0.890  0.020  1.040
 EV3  C11  H11   single    0.970  0.020  1.090
 EV3  C11  H11A  single    0.970  0.020  1.090
 EV3  C12  H12   single    0.970  0.020  1.090
 EV3  C12  H12A  single    0.970  0.020  1.090
 EV3  C13  H13   single    0.970  0.020  1.090
 EV3  C13  H13A  single    0.970  0.020  1.090
 EV3  O14  HO14  single    0.850  0.020  0.980

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
 EV3  CL15  C1   C3    118.58  3.000
 EV3  CL15  C1   C2    118.50  3.000
 EV3  C3    C1   C2    122.92  3.000
 EV3  H2    C2   C4    119.78  3.000
 EV3  H2    C2   C1    120.16  3.000
 EV3  C4    C2   C1    120.05  3.000
 EV3  H3    C3   C5    121.22  3.000
 EV3  H3    C3   C1    121.58  3.000
 EV3  C5    C3   C1    117.20  3.000
 EV3  H4    C4   C6    122.50  3.000
 EV3  H4    C4   C2    120.14  3.000
 EV3  C6    C4   C2    117.36  3.000
 EV3  N7    C5   C6    110.37  3.000
 EV3  N7    C5   C3    129.79  3.000
 EV3  C6    C5   C3    119.84  3.000
 EV3  N9    C6   C5    104.99  3.000
 EV3  N9    C6   C4    132.39  3.000
 EV3  C5    C6   C4    122.62  3.000
 EV3  C8    N7   C5    104.76  3.000
 EV3  N10   C8   N9    121.68  3.000
 EV3  N10   C8   N7    124.67  3.000
 EV3  N9    C8   N7    113.56  3.000
 EV3  C11   N9   C8    127.15  3.000
 EV3  C11   N9   C6    126.41  3.000
 EV3  C8    N9   C6    106.30  3.000
 EV3  HN1A  N10  HN10  113.00  3.000
 EV3  HN1A  N10  C8    118.56  3.000
 EV3  HN10  N10  C8    114.80  3.000
 EV3  H11A  C11  H11   105.80  3.000
 EV3  H11A  C11  C12   110.71  3.000
 EV3  H11   C11  C12   110.99  3.000
 EV3  H11A  C11  N9    108.06  3.000
 EV3  H11   C11  N9    108.48  3.000
 EV3  C12   C11  N9    112.53  3.000
 EV3  H12A  C12  H12   107.21  3.000
 EV3  H12A  C12  C13   109.67  3.000
 EV3  H12   C12  C13   109.83  3.000
 EV3  H12A  C12  C11   109.48  3.000
 EV3  H12   C12  C11   109.49  3.000
 EV3  C13   C12  C11   111.08  3.000
 EV3  H13A  C13  H13   106.65  3.000
 EV3  H13A  C13  O14   111.49  3.000
 EV3  H13   C13  O14   111.53  3.000
 EV3  H13A  C13  C12   109.34  3.000
 EV3  H13   C13  C12   109.19  3.000
 EV3  O14   C13  C12   108.60  3.000
 EV3  HO14  O14  C13   108.16  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
 EV3  CONST_01  C6    C4   C2   C1     0.00   0.0  0
 EV3  CONST_02  C6    C5   C3   C1     0.00   0.0  0
 EV3  CONST_03  N7    C5   C3   C1   180.00   0.0  0
 EV3  CONST_04  C5    C3   C1   C2     0.00   0.0  0
 EV3  CONST_05  C5    C6   C4   C2     0.00   0.0  0
 EV3  CONST_06  N9    C6   C4   C2   180.00   0.0  0
 EV3  CONST_07  C4    C2   C1   C3     0.00   0.0  0
 EV3  CONST_08  C4    C6   C5   C3     0.00   0.0  0
 EV3  CONST_09  N9    C6   C5   C3   180.00   0.0  0
 EV3  CONST_10  C8    N7   C5   C3   180.00   0.0  0
 EV3  CONST_11  N7    C5   C6   C4   180.00   0.0  0
 EV3  CONST_12  C8    N9   C6   C4   180.00   0.0  0
 EV3  CONST_13  C8    N9   C6   C5     0.00   0.0  0
 EV3  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 EV3  CONST_15  C8    N7   C5   C6     0.00   0.0  0
 EV3  CONST_16  N7    C8   N9   C6     0.00   0.0  0
 EV3  CONST_17  N9    C6   C5   N7     0.00   0.0  0
 EV3  CONST_18  CL15  C1   C2   C4   180.00   0.0  0
 EV3  CONST_19  C11   N9   C6   C4     0.00   0.0  0
 EV3  CONST_20  CL15  C1   C3   C5   180.00   0.0  0
 EV3  CONST_21  C11   N9   C6   C5   180.00   0.0  0
 EV3  CONST_22  N10   C8   N7   C5   180.00   0.0  0
 EV3  CONST_23  N10   C8   N9   C6   180.00   0.0  0
 EV3  CONST_24  C11   N9   C8   N7   180.00   0.0  0
 EV3  CONST_25  H4    C4   C2   C1   180.00   0.0  0
 EV3  CONST_26  H3    C3   C1   C2   180.00   0.0  0
 EV3  CONST_27  H2    C2   C1   C3   180.00   0.0  0
 EV3  Var_01    C12   C11  N9   C6    86.33  30.0  2
 EV3  Var_02    C13   C12  C11  N9   177.05  30.0  3
 EV3  Var_03    O14   C13  C12  C11  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
 EV3  plan-1  C1    0.020
 EV3  plan-1  C2    0.020
 EV3  plan-1  C3    0.020
 EV3  plan-1  C4    0.020
 EV3  plan-1  C5    0.020
 EV3  plan-1  C6    0.020
 EV3  plan-1  N7    0.020
 EV3  plan-1  C8    0.020
 EV3  plan-1  N9    0.020
 EV3  plan-1  N10   0.020
 EV3  plan-1  C11   0.020
 EV3  plan-1  CL15  0.020
 EV3  plan-1  H2    0.020
 EV3  plan-1  H3    0.020
 EV3  plan-1  H4    0.020
 EV3  plan-2  C8    0.020
 EV3  plan-2  N10   0.020
 EV3  plan-2  HN10  0.020
 EV3  plan-2  HN1A  0.020

