# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:24:43 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-cyclohexyl-N-methylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1CCCCC1)C(=O)CCCn2c(N)nc3cc(Cl)ccc23
#
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
 EV4  EV4  4-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-cyclohexyl-N-methylbutanamide  ligand  49  24  .  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_EV4
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
 EV4  C1    C   CR16  0  -0.293   3.1973   0.9263   1.0394
 EV4  C2    C   CR56  0   0.347   3.2050  -0.3169   0.4334
 EV4  C3    C   CR56  0   0.141   4.2895  -0.7745  -0.3370
 EV4  C4    C   CR16  0  -0.306   5.4058   0.0355  -0.5099
 EV4  C5    C   CR6   0  -0.038   5.3946   1.2789   0.1020
 EV4  C6    C   CR16  0  -0.223   4.3180   1.7275   0.8666
 EV4  CL7   CL  CL    0  -0.119   6.7682   2.3186  -0.0902
 EV4  N8    N   NR5   0  -0.560   2.2925  -1.3498   0.4058
 EV4  C9    C   CR5   0   0.624   2.8473  -2.3238  -0.3767
 EV4  N10   N   N     0  -0.469   4.0324  -2.0250  -0.8326
 EV4  N11   N   NH2   0  -0.838   2.2146  -3.5136  -0.5765
 EV4  C12   C   CH2   0  -0.317   0.9994  -1.3791   1.0457
 EV4  C13   C   CH2   0  -0.421  -0.1257  -0.9229   0.1235
 EV4  C14   C   CH2   0  -0.598  -1.4638  -0.9324   0.8432
 EV4  C15   C   C     0   0.582  -2.6032  -0.4769  -0.0596
 EV4  O16   O   O     0  -0.440  -2.4163  -0.3111  -1.2500
 EV4  N17   N   NT    0  -0.470  -3.8059  -0.2758   0.5390
 EV4  C18   C   CH3   0  -0.529  -4.0047  -0.4609   1.9601
 EV4  C19   C   CH1   0  -0.094  -4.9149   0.2727  -0.2388
 EV4  C20   C   CH2   0  -0.417  -6.0720  -0.7177  -0.3690
 EV4  C21   C   CH2   0  -0.429  -7.2035  -0.1279  -1.2068
 EV4  C22   C   CH2   0  -0.423  -7.6766   1.2087  -0.6467
 EV4  C23   C   CH2   0  -0.427  -6.5175   2.1916  -0.5290
 EV4  C24   C   CH2   0  -0.421  -5.3870   1.6157   0.3193
 EV4  H1    H   HCR6  0   0.240   2.3655   1.2823   1.6330
 EV4  H4    H   HCR6  0   0.258   6.2473  -0.2926  -1.1051
 EV4  H6    H   HCR6  0   0.252   4.3558   2.7040   1.3277
 EV4  HN11  H   HNH2  0   0.368   1.2184  -3.4920  -0.7186
 EV4  HN1A  H   HNH2  0   0.379   2.6889  -4.1046  -1.2390
 EV4  H12   H   HCH2  0   0.248   0.8196  -2.3916   1.4165
 EV4  H12A  H   HCH2  0   0.250   1.0525  -0.7411   1.9302
 EV4  H13   H   HCH2  0   0.255   0.0962   0.0787  -0.2492
 EV4  H13A  H   HCH2  0   0.233  -0.1736  -1.5663  -0.7581
 EV4  H14   H   HCH2  0   0.245  -1.6821  -1.9401   1.2148
 EV4  H14A  H   HCH2  0   0.245  -1.4168  -0.2970   1.7330
 EV4  H18   H   HCH3  0   0.229  -3.6712   0.3945   2.5542
 EV4  H18A  H   HCH3  0   0.248  -5.0628  -0.6082   2.1638
 EV4  H18B  H   HCH3  0   0.238  -3.4956  -1.3497   2.3280
 EV4  H19   H   HCH1  0   0.267  -4.5186   0.4507  -1.2395
 EV4  H20   H   HCH2  0   0.236  -5.7085  -1.6437  -0.8203
 EV4  H20A  H   HCH2  0   0.196  -6.4644  -0.9819   0.6193
 EV4  H21   H   HCH2  0   0.214  -6.8544   0.0129  -2.2351
 EV4  H21A  H   HCH2  0   0.228  -8.0332  -0.8360  -1.2589
 EV4  H22   H   HCH2  0   0.229  -8.4645   1.6257  -1.2777
 EV4  H22A  H   HCH2  0   0.203  -8.1224   1.0528   0.3421
 EV4  H23   H   HCH2  0   0.214  -6.1380   2.4278  -1.5285
 EV4  H23A  H   HCH2  0   0.228  -6.8566   3.1362  -0.0986
 EV4  H24   H   HCH2  0   0.202  -5.7441   1.4997   1.3488
 EV4  H24A  H   HCH2  0   0.233  -4.5458   2.3126   0.3533

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
 EV4  C1   C2    aromatic  1.383  0.020  1.383
 EV4  C1   C6    aromatic  1.388  0.020  1.388
 EV4  C2   C3    aromatic  1.407  0.020  1.407
 EV4  C2   N8    aromatic  1.379  0.020  1.379
 EV4  C3   C4    aromatic  1.390  0.020  1.390
 EV4  C3   N10   aromatic  1.370  0.020  1.370
 EV4  C4   C5    aromatic  1.386  0.020  1.386
 EV4  C5   C6    aromatic  1.395  0.020  1.395
 EV4  C5   CL7   single    1.733  0.020  1.733
 EV4  N8   C9    aromatic  1.367  0.020  1.367
 EV4  N8   C12   single    1.443  0.020  1.443
 EV4  C9   N10   aromatic  1.304  0.020  1.304
 EV4  C9   N11   single    1.362  0.020  1.362
 EV4  C12  C13   single    1.525  0.020  1.525
 EV4  C13  C14   single    1.519  0.020  1.519
 EV4  C14  C15   single    1.523  0.020  1.523
 EV4  C15  O16   double    1.216  0.020  1.216
 EV4  C15  N17   single    1.358  0.020  1.358
 EV4  N17  C18   single    1.447  0.020  1.447
 EV4  N17  C19   single    1.461  0.020  1.461
 EV4  C19  C20   single    1.529  0.020  1.529
 EV4  C19  C24   single    1.529  0.020  1.529
 EV4  C20  C21   single    1.526  0.020  1.526
 EV4  C21  C22   single    1.525  0.020  1.525
 EV4  C22  C23   single    1.524  0.020  1.524
 EV4  C23  C24   single    1.526  0.020  1.526
 EV4  C1   H1    single    0.930  0.020  1.080
 EV4  C4   H4    single    0.930  0.020  1.080
 EV4  C6   H6    single    0.930  0.020  1.080
 EV4  N11  HN11  single    0.890  0.020  1.040
 EV4  N11  HN1A  single    0.890  0.020  1.040
 EV4  C12  H12   single    0.970  0.020  1.090
 EV4  C12  H12A  single    0.970  0.020  1.090
 EV4  C13  H13   single    0.970  0.020  1.090
 EV4  C13  H13A  single    0.970  0.020  1.090
 EV4  C14  H14   single    0.970  0.020  1.090
 EV4  C14  H14A  single    0.970  0.020  1.090
 EV4  C18  H18   single    0.970  0.020  1.090
 EV4  C18  H18A  single    0.970  0.020  1.090
 EV4  C18  H18B  single    0.970  0.020  1.090
 EV4  C19  H19   single    0.970  0.020  1.090
 EV4  C20  H20   single    0.970  0.020  1.090
 EV4  C20  H20A  single    0.970  0.020  1.090
 EV4  C21  H21   single    0.970  0.020  1.090
 EV4  C21  H21A  single    0.970  0.020  1.090
 EV4  C22  H22   single    0.970  0.020  1.090
 EV4  C22  H22A  single    0.970  0.020  1.090
 EV4  C23  H23   single    0.970  0.020  1.090
 EV4  C23  H23A  single    0.970  0.020  1.090
 EV4  C24  H24   single    0.970  0.020  1.090
 EV4  C24  H24A  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
 EV4  H1    C1   C6    119.92  3.000
 EV4  H1    C1   C2    122.71  3.000
 EV4  C6    C1   C2    117.36  3.000
 EV4  N8    C2   C3    104.81  3.000
 EV4  N8    C2   C1    132.73  3.000
 EV4  C3    C2   C1    122.46  3.000
 EV4  N10   C3   C4    129.63  3.000
 EV4  N10   C3   C2    110.52  3.000
 EV4  C4    C3   C2    119.84  3.000
 EV4  H4    C4   C5    121.43  3.000
 EV4  H4    C4   C3    121.09  3.000
 EV4  C5    C4   C3    117.48  3.000
 EV4  CL7   C5   C6    118.66  3.000
 EV4  CL7   C5   C4    118.87  3.000
 EV4  C6    C5   C4    122.47  3.000
 EV4  H6    C6   C5    119.84  3.000
 EV4  H6    C6   C1    119.78  3.000
 EV4  C5    C6   C1    120.38  3.000
 EV4  C12   N8   C9    127.09  3.000
 EV4  C12   N8   C2    126.83  3.000
 EV4  C9    N8   C2    106.06  3.000
 EV4  N11   C9   N10   124.80  3.000
 EV4  N11   C9   N8    121.18  3.000
 EV4  N10   C9   N8    113.93  3.000
 EV4  C9    N10  C3    104.67  3.000
 EV4  HN1A  N11  HN11  112.71  3.000
 EV4  HN1A  N11  C9    112.99  3.000
 EV4  HN11  N11  C9    117.49  3.000
 EV4  H12A  C12  H12   105.93  3.000
 EV4  H12A  C12  C13   110.56  3.000
 EV4  H12   C12  C13   111.16  3.000
 EV4  H12A  C12  N8    107.68  3.000
 EV4  H12   C12  N8    108.45  3.000
 EV4  C13   C12  N8    112.77  3.000
 EV4  H13A  C13  H13   105.89  3.000
 EV4  H13A  C13  C14   109.87  3.000
 EV4  H13   C13  C14   110.27  3.000
 EV4  H13A  C13  C12   110.14  3.000
 EV4  H13   C13  C12   109.33  3.000
 EV4  C14   C13  C12   111.19  3.000
 EV4  H14A  C14  H14   105.47  3.000
 EV4  H14A  C14  C15   109.90  3.000
 EV4  H14   C14  C15   109.08  3.000
 EV4  H14A  C14  C13   110.10  3.000
 EV4  H14   C14  C13   109.98  3.000
 EV4  C15   C14  C13   112.09  3.000
 EV4  N17   C15  O16   123.16  3.000
 EV4  N17   C15  C14   116.45  3.000
 EV4  O16   C15  C14   120.39  3.000
 EV4  C19   N17  C18   117.81  3.000
 EV4  C19   N17  C15   119.54  3.000
 EV4  C18   N17  C15   122.38  3.000
 EV4  H18B  C18  H18A  106.33  3.000
 EV4  H18B  C18  H18   108.20  3.000
 EV4  H18A  C18  H18   107.51  3.000
 EV4  H18B  C18  N17   111.86  3.000
 EV4  H18A  C18  N17   109.58  3.000
 EV4  H18   C18  N17   113.06  3.000
 EV4  H19   C19  C24   107.68  3.000
 EV4  H19   C19  C20   107.61  3.000
 EV4  C24   C19  C20   111.50  3.000
 EV4  H19   C19  N17   105.89  3.000
 EV4  C24   C19  N17   111.70  3.000
 EV4  C20   C19  N17   112.12  3.000
 EV4  H20A  C20  H20   106.70  3.000
 EV4  H20A  C20  C21   108.83  3.000
 EV4  H20   C20  C21   110.33  3.000
 EV4  H20A  C20  C19   110.52  3.000
 EV4  H20   C20  C19   109.42  3.000
 EV4  C21   C20  C19   110.95  3.000
 EV4  H21A  C21  H21   106.31  3.000
 EV4  H21A  C21  C22   110.50  3.000
 EV4  H21   C21  C22   109.34  3.000
 EV4  H21A  C21  C20   109.81  3.000
 EV4  H21   C21  C20   109.19  3.000
 EV4  C22   C21  C20   111.54  3.000
 EV4  H22A  C22  H22   106.40  3.000
 EV4  H22A  C22  C23   109.35  3.000
 EV4  H22   C22  C23   110.31  3.000
 EV4  H22A  C22  C21   109.45  3.000
 EV4  H22   C22  C21   110.26  3.000
 EV4  C23   C22  C21   110.96  3.000
 EV4  H23A  C23  H23   106.31  3.000
 EV4  H23A  C23  C24   109.72  3.000
 EV4  H23   C23  C24   109.39  3.000
 EV4  H23A  C23  C22   110.61  3.000
 EV4  H23   C23  C22   109.40  3.000
 EV4  C24   C23  C22   111.28  3.000
 EV4  H24A  C24  H24   106.80  3.000
 EV4  H24A  C24  C23   110.29  3.000
 EV4  H24   C24  C23   108.71  3.000
 EV4  H24A  C24  C19   109.50  3.000
 EV4  H24   C24  C19   110.52  3.000
 EV4  C23   C24  C19   110.93  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
 EV4  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 EV4  CONST_02  N10   C3   C2   C1    180.00   0.0  0
 EV4  CONST_03  C9    N8   C2   C1    180.00   0.0  0
 EV4  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 EV4  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 EV4  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 EV4  CONST_07  C9    N10  C3   C2      0.00   0.0  0
 EV4  CONST_08  N10   C9   N8   C2      0.00   0.0  0
 EV4  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 EV4  CONST_10  C9    N8   C2   C3      0.00   0.0  0
 EV4  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 EV4  CONST_12  N8    C9   N10  C3      0.00   0.0  0
 EV4  CONST_13  N8    C2   C3   C4    180.00   0.0  0
 EV4  CONST_14  C9    N10  C3   C4    180.00   0.0  0
 EV4  CONST_15  N10   C3   C4   C5    180.00   0.0  0
 EV4  CONST_16  N8    C2   C1   C6    180.00   0.0  0
 EV4  CONST_17  N10   C3   C2   N8      0.00   0.0  0
 EV4  CONST_18  C12   N8   C2   C1      0.00   0.0  0
 EV4  CONST_19  CL7   C5   C6   C1    180.00   0.0  0
 EV4  CONST_20  N11   C9   N8   C2    180.00   0.0  0
 EV4  CONST_21  C12   N8   C2   C3    180.00   0.0  0
 EV4  CONST_22  CL7   C5   C4   C3    180.00   0.0  0
 EV4  CONST_23  N11   C9   N10  C3    180.00   0.0  0
 EV4  CONST_24  C12   N8   C9   N10   180.00   0.0  0
 EV4  CONST_25  H6    C6   C1   C2    180.00   0.0  0
 EV4  CONST_26  H4    C4   C3   C2    180.00   0.0  0
 EV4  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 EV4  CONST_29  HN1A  N11  C9   N8    180.00   0.0  0
 EV4  CONST_30  C19   N17  C15  C14   180.00   0.0  0
 EV4  CONST_31  C19   N17  C15  O16     0.00   0.0  0
 EV4  CONST_32  C18   N17  C15  C14     0.00   0.0  0
 EV4  CONST_33  C18   N17  C15  O16   180.00   0.0  0
 EV4  Var_01    C22   C21  C20  C19   -55.20  30.0  1
 EV4  Var_02    C22   C23  C24  C19    55.78  30.0  1
 EV4  Var_03    C23   C22  C21  C20    55.79  30.0  1
 EV4  Var_04    C24   C23  C22  C21   -56.02  30.0  1
 EV4  Var_05    C13   C12  N8   C2     93.45  30.0  2
 EV4  Var_06    C14   C13  C12  N8   -178.49  30.0  3
 EV4  Var_07    H18   C18  N17  C19   -93.12  30.0  3
 EV4  Var_08    C15   C14  C13  C12   179.88  30.0  3
 EV4  Var_09    O16   C15  C14  C13     8.76  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EV4  chir_01  C19  N17  C20  C24  negativ

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
 EV4  plan-1  C1    0.020
 EV4  plan-1  C2    0.020
 EV4  plan-1  C3    0.020
 EV4  plan-1  C4    0.020
 EV4  plan-1  C5    0.020
 EV4  plan-1  C6    0.020
 EV4  plan-1  CL7   0.020
 EV4  plan-1  N8    0.020
 EV4  plan-1  C9    0.020
 EV4  plan-1  N10   0.020
 EV4  plan-1  N11   0.020
 EV4  plan-1  C12   0.020
 EV4  plan-1  H1    0.020
 EV4  plan-1  H4    0.020
 EV4  plan-1  H6    0.020
 EV4  plan-2  C9    0.020
 EV4  plan-2  N11   0.020
 EV4  plan-2  HN11  0.020
 EV4  plan-2  HN1A  0.020
 EV4  plan-3  C14   0.020
 EV4  plan-3  C15   0.020
 EV4  plan-3  O16   0.020
 EV4  plan-3  N17   0.020
 EV4  plan-3  C18   0.020
 EV4  plan-3  C19   0.020

