# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:05:02 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-(5,6-dichloro-1H-benzimidazol-1-yl)butan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCn1cnc2cc(Cl)c(Cl)cc12
#
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
 JMA  JMA  4-(5,6-dichloro-1H-benzimidazol-1-yl)butan-1-ol  ligand  28  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JMA
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
 JMA  C10   C   CR16  0  -0.285   2.2863   1.4810   0.4565
 JMA  C13   C   CR6   0  -0.022   1.7920  -0.8141  -0.1732
 JMA  C15   C   CR16  0  -0.265   0.4824  -0.5071  -0.4920
 JMA  O01   O   OH1   0  -0.674  -6.3363  -1.6307   0.4051
 JMA  C02   C   CH2   0  -0.135  -5.1112  -1.1125   0.8761
 JMA  C03   C   CH2   0  -0.463  -4.3906  -0.4293  -0.2699
 JMA  C04   C   CH2   0  -0.446  -3.0577   0.1543   0.1786
 JMA  N06   N   NR5   0  -0.511  -1.0910   1.4593  -0.5503
 JMA  C07   C   CR15  0   0.115  -0.8847   2.7572  -0.2129
 JMA  N08   N   N     0  -0.465   0.3245   3.0158   0.1978
 JMA  C09   C   CR56  0   0.134   0.9713   1.8078   0.1392
 JMA  C11   C   CR6   0  -0.020   2.6822   0.1678   0.2981
 JMA  CL12  CL  CL    0  -0.105   4.3065  -0.2666   0.6939
 JMA  CL14  CL  CL    0  -0.100   2.3301  -2.4425  -0.3620
 JMA  C16   C   CR56  0   0.357   0.0944   0.8144  -0.3263
 JMA  H101  H   HCR6  0   0.287   2.9787   2.2301   0.8164
 JMA  H151  H   HCR6  0   0.298  -0.1912  -1.2732  -0.8521
 JMA  H011  H   HOH1  0   0.453  -6.8041  -2.0169   1.1509
 JMA  H021  H   HCH2  0   0.192  -5.2668  -0.3877   1.6864
 JMA  H022  H   HCH2  0   0.190  -4.4702  -1.9064   1.2828
 JMA  H031  H   HCH2  0   0.230  -4.2263  -1.1494  -1.0772
 JMA  H032  H   HCH2  0   0.229  -5.0232   0.3664  -0.6755
 JMA  H041  H   HCH2  0   0.239  -3.2155   0.8679   0.9918
 JMA  H042  H   HCH2  0   0.239  -2.4206  -0.6410   0.5768
 JMA  H051  H   HCH2  0   0.267  -2.1462   0.1756  -1.7885
 JMA  H052  H   HCH2  0   0.276  -2.9692   1.6637  -1.3650
 JMA  H071  H   HCR5  0   0.296  -1.6807   3.4832  -0.2974
 JMA  C05   C   CH2   0  -0.310  -2.3456   0.8637  -0.9651

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
 JMA  O01  C02   single    1.411  0.020  1.411
 JMA  C03  C02   single    1.516  0.020  1.516
 JMA  C03  C04   single    1.523  0.020  1.523
 JMA  C04  C05   single    1.523  0.020  1.523
 JMA  C05  N06   single    1.449  0.020  1.449
 JMA  C07  N06   aromatic  1.357  0.020  1.357
 JMA  C07  N08   aromatic  1.303  0.020  1.303
 JMA  N06  C16   aromatic  1.368  0.020  1.368
 JMA  N08  C09   aromatic  1.372  0.020  1.372
 JMA  C16  C09   aromatic  1.404  0.020  1.404
 JMA  C16  C15   aromatic  1.387  0.020  1.387
 JMA  C09  C10   aromatic  1.392  0.020  1.392
 JMA  C15  C13   aromatic  1.382  0.020  1.382
 JMA  C10  C11   aromatic  1.381  0.020  1.381
 JMA  C13  C11   aromatic  1.407  0.020  1.407
 JMA  C13  CL14  single    1.725  0.020  1.725
 JMA  C11  CL12  single    1.727  0.020  1.727
 JMA  C10  H101  single    0.930  0.020  1.080
 JMA  C15  H151  single    0.930  0.020  1.080
 JMA  O01  H011  single    0.850  0.020  0.980
 JMA  C02  H021  single    0.970  0.020  1.090
 JMA  C02  H022  single    0.970  0.020  1.090
 JMA  C03  H031  single    0.970  0.020  1.090
 JMA  C03  H032  single    0.970  0.020  1.090
 JMA  C04  H041  single    0.970  0.020  1.090
 JMA  C04  H042  single    0.970  0.020  1.090
 JMA  C05  H051  single    0.970  0.020  1.090
 JMA  C05  H052  single    0.970  0.020  1.090
 JMA  C07  H071  single    0.930  0.020  1.080

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
 JMA  H101  C10  C11   120.88  3.000
 JMA  H101  C10  C09   121.21  3.000
 JMA  C11   C10  C09   117.91  3.000
 JMA  CL14  C13  C11   119.87  3.000
 JMA  CL14  C13  C15   118.67  3.000
 JMA  C11   C13  C15   121.45  3.000
 JMA  H151  C15  C16   122.70  3.000
 JMA  H151  C15  C13   120.62  3.000
 JMA  C16   C15  C13   116.68  3.000
 JMA  H011  O01  C02   108.12  3.000
 JMA  H022  C02  H021  106.65  3.000
 JMA  H022  C02  C03   109.15  3.000
 JMA  H021  C02  C03   109.12  3.000
 JMA  H022  C02  O01   111.39  3.000
 JMA  H021  C02  O01   111.45  3.000
 JMA  C03   C02  O01   109.01  3.000
 JMA  H032  C03  H031  106.96  3.000
 JMA  H032  C03  C04   109.67  3.000
 JMA  H031  C03  C04   109.76  3.000
 JMA  H032  C03  C02   109.45  3.000
 JMA  H031  C03  C02   109.42  3.000
 JMA  C04   C03  C02   111.48  3.000
 JMA  H042  C04  H041  106.72  3.000
 JMA  H042  C04  C05   109.86  3.000
 JMA  H041  C04  C05   108.78  3.000
 JMA  H042  C04  C03   109.78  3.000
 JMA  H041  C04  C03   110.05  3.000
 JMA  C05   C04  C03   111.51  3.000
 JMA  C16   N06  C07   106.17  3.000
 JMA  C16   N06  C05   127.10  3.000
 JMA  C07   N06  C05   126.57  3.000
 JMA  H071  C07  N08   125.09  3.000
 JMA  H071  C07  N06   120.74  3.000
 JMA  N08   C07  N06   114.16  3.000
 JMA  C09   N08  C07   104.44  3.000
 JMA  C16   C09  N08   110.04  3.000
 JMA  C16   C09  C10   119.96  3.000
 JMA  N08   C09  C10   129.99  3.000
 JMA  CL12  C11  C13   119.75  3.000
 JMA  CL12  C11  C10   118.86  3.000
 JMA  C13   C11  C10   121.39  3.000
 JMA  C09   C16  N06   105.18  3.000
 JMA  C09   C16  C15   122.60  3.000
 JMA  N06   C16  C15   132.21  3.000
 JMA  H052  C05  H051  106.89  3.000
 JMA  H052  C05  N06   107.37  3.000
 JMA  H051  C05  N06   108.47  3.000
 JMA  H052  C05  C04   110.48  3.000
 JMA  H051  C05  C04   111.00  3.000
 JMA  N06   C05  C04   112.41  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
 JMA  CONST_01  C07   N08  C09  C10    180.00   0.0  0
 JMA  CONST_02  N06   C16  C09  C10    180.00   0.0  0
 JMA  CONST_03  C15   C16  C09  C10      0.00   0.0  0
 JMA  CONST_04  C15   C13  C11  C10      0.00   0.0  0
 JMA  CONST_05  N06   C16  C15  C13    180.00   0.0  0
 JMA  CONST_06  C09   C16  C15  C13      0.00   0.0  0
 JMA  CONST_07  C09   C10  C11  C13      0.00   0.0  0
 JMA  CONST_08  C07   N06  C16  C15    180.00   0.0  0
 JMA  CONST_09  N08   C09  C16  C15    180.00   0.0  0
 JMA  CONST_10  C09   N08  C07  N06      0.00   0.0  0
 JMA  CONST_11  N08   C09  C16  N06      0.00   0.0  0
 JMA  CONST_12  C09   C16  N06  C07      0.00   0.0  0
 JMA  CONST_13  C16   C09  N08  C07      0.00   0.0  0
 JMA  CONST_14  C16   N06  C07  N08      0.00   0.0  0
 JMA  CONST_15  C11   C10  C09  N08    180.00   0.0  0
 JMA  CONST_16  C16   C09  C10  C11      0.00   0.0  0
 JMA  CONST_17  C16   C15  C13  C11      0.00   0.0  0
 JMA  CONST_18  CL14  C13  C11  C10    180.00   0.0  0
 JMA  CONST_19  C05   N06  C16  C15      0.00   0.0  0
 JMA  CONST_20  CL12  C11  C13  C15    180.00   0.0  0
 JMA  CONST_21  N08   C07  N06  C05    180.00   0.0  0
 JMA  CONST_22  C09   C16  N06  C05    180.00   0.0  0
 JMA  CONST_23  CL12  C11  C10  C09    180.00   0.0  0
 JMA  CONST_24  C16   C15  C13  CL14   180.00   0.0  0
 JMA  CONST_25  H101  C10  C11  C13    180.00   0.0  0
 JMA  CONST_26  H151  C15  C16  N06      0.00   0.0  0
 JMA  CONST_27  H071  C07  N08  C09    180.00   0.0  0
 JMA  Var_01    C07   N06  C05  C04    -97.97  30.0  2
 JMA  Var_02    N06   C05  C04  C03    178.39  30.0  3
 JMA  Var_03    C04   C03  C02  O01    179.91  30.0  1
 JMA  Var_04    C05   C04  C03  C02   -178.91  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
 JMA  plan-1  C10   0.020
 JMA  plan-1  C13   0.020
 JMA  plan-1  C15   0.020
 JMA  plan-1  N06   0.020
 JMA  plan-1  C07   0.020
 JMA  plan-1  N08   0.020
 JMA  plan-1  C09   0.020
 JMA  plan-1  C11   0.020
 JMA  plan-1  CL12  0.020
 JMA  plan-1  CL14  0.020
 JMA  plan-1  C16   0.020
 JMA  plan-1  H101  0.020
 JMA  plan-1  H151  0.020
 JMA  plan-1  H071  0.020
 JMA  plan-1  C05   0.020

