# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:59:07 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-(cyclohexylmethyl)pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](CC(=O)NCC1CCCCC1)n2c(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
 EV5  EV5  (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-(cyclohexylmethyl)pentanamide  ligand  52  25  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EV5
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
 EV5  C1    C   CR56  0   0.359   1.2574   0.2075  -0.0351
 EV5  C2    C   CR16  0  -0.304   1.9945  -0.5718   0.8372
 EV5  C3    C   CR16  0  -0.252   2.3112  -1.8631   0.4345
 EV5  C4    C   CR6   0  -0.057   1.8862  -2.3328  -0.8074
 EV5  C5    C   CR16  0  -0.310   1.1467  -1.5610  -1.6879
 EV5  C6    C   CR56  0   0.172   0.8326  -0.2667  -1.2874
 EV5  N7    N   N     0  -0.521   0.1303   0.7040  -1.9490
 EV5  C8    C   CR5   0   0.625   0.1137   1.7267  -1.1302
 EV5  N9    N   NR5   0  -0.568   0.7790   1.5009   0.0448
 EV5  N10   N   NH2   0  -0.857  -0.5630   2.8762  -1.3797
 EV5  CL11  CL  CL    0  -0.149   2.3037  -3.9600  -1.2662
 EV5  C12   C   CH1   0  -0.137   0.9312   2.3828   1.1976
 EV5  C13   C   CH2   0  -0.432   1.7508   3.6357   0.8921
 EV5  C14   C   CH3   0  -0.665   3.1016   3.3293   0.2636
 EV5  C15   C   CH2   0  -0.567  -0.4225   2.6922   1.8370
 EV5  C16   C   C     0   0.559  -1.1237   1.4014   2.2122
 EV5  N17   N   NH1   0  -0.634  -2.3570   1.2489   1.7138
 EV5  O18   O   O     0  -0.498  -0.5664   0.5616   2.9073
 EV5  C19   C   CH2   0  -0.235  -3.1509   0.0486   1.8630
 EV5  C20   C   CH1   0  -0.280  -3.9744  -0.2449   0.6137
 EV5  C21   C   CH2   0  -0.415  -4.8041  -1.5104   0.8299
 EV5  C22   C   CH2   0  -0.431  -5.6350  -1.8615  -0.4003
 EV5  C23   C   CH2   0  -0.429  -4.7572  -1.9970  -1.6403
 EV5  C24   C   CH2   0  -0.428  -3.9318  -0.7352  -1.8653
 EV5  C25   C   CH2   0  -0.413  -3.1042  -0.3787  -0.6350
 EV5  H2    H   HCR6  0   0.271   2.3196  -0.2139   1.8046
 EV5  H3    H   HCR6  0   0.271   2.8864  -2.5031   1.0888
 EV5  H5    H   HCR6  0   0.269   0.8232  -1.9444  -2.6463
 EV5  HN10  H   HNH2  0   0.399  -0.8665   2.9714  -2.3360
 EV5  HN1A  H   HNH2  0   0.400  -0.2007   3.7357  -1.0027
 EV5  H12   H   HCH1  0   0.282   1.5036   1.8020   1.9216
 EV5  H13   H   HCH2  0   0.225   1.1957   4.3384   0.2639
 EV5  H13A  H   HCH2  0   0.253   1.8958   4.1530   1.8431
 EV5  H14   H   HCH3  0   0.226   3.6753   2.6355   0.8803
 EV5  H14A  H   HCH3  0   0.228   3.0011   2.8887  -0.7287
 EV5  H14B  H   HCH3  0   0.242   3.6888   4.2408   0.1562
 EV5  H15   H   HCH2  0   0.285  -0.2450   3.2690   2.7475
 EV5  H15A  H   HCH2  0   0.255  -1.0350   3.3137   1.1820
 EV5  HN17  H   HNH1  0   0.396  -2.7557   2.0064   1.1828
 EV5  H19   H   HCH2  0   0.234  -2.4728  -0.7839   2.0576
 EV5  H19A  H   HCH2  0   0.238  -3.8146   0.1334   2.7300
 EV5  H20   H   HCH1  0   0.219  -4.6739   0.5887   0.4560
 EV5  H21   H   HCH2  0   0.208  -4.1296  -2.3444   1.0583
 EV5  H21A  H   HCH2  0   0.227  -5.4539  -1.3876   1.7012
 EV5  H22   H   HCH2  0   0.226  -6.1897  -2.7863  -0.2241
 EV5  H22A  H   HCH2  0   0.209  -6.3816  -1.0777  -0.5681
 EV5  H23   H   HCH2  0   0.207  -4.0834  -2.8514  -1.5131
 EV5  H23A  H   HCH2  0   0.224  -5.3718  -2.2111  -2.5184
 EV5  H24   H   HCH2  0   0.225  -3.2728  -0.8569  -2.7284
 EV5  H24A  H   HCH2  0   0.206  -4.6029   0.0981  -2.1021
 EV5  H25   H   HCH2  0   0.237  -2.5565   0.5466  -0.8207
 EV5  H25A  H   HCH2  0   0.204  -2.3462  -1.1537  -0.4663

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
 EV5  C1   C2    aromatic  1.383  0.020  1.383
 EV5  C1   C6    aromatic  1.405  0.020  1.405
 EV5  C1   N9    aromatic  1.381  0.020  1.381
 EV5  C2   C3    aromatic  1.389  0.020  1.389
 EV5  C3   C4    aromatic  1.394  0.020  1.394
 EV5  C4   C5    aromatic  1.385  0.020  1.385
 EV5  C4   CL11  single    1.741  0.020  1.741
 EV5  C5   C6    aromatic  1.391  0.020  1.391
 EV5  C6   N7    aromatic  1.369  0.020  1.369
 EV5  N7   C8    aromatic  1.310  0.020  1.310
 EV5  C8   N9    aromatic  1.369  0.020  1.369
 EV5  C8   N10   single    1.357  0.020  1.357
 EV5  N9   C12   single    1.459  0.020  1.459
 EV5  C12  C13   single    1.528  0.020  1.528
 EV5  C12  C15   single    1.529  0.020  1.529
 EV5  C13  C14   single    1.521  0.020  1.521
 EV5  C15  C16   single    1.516  0.020  1.516
 EV5  C16  N17   single    1.339  0.020  1.339
 EV5  C16  O18   double    1.224  0.020  1.224
 EV5  N17  C19   single    1.447  0.020  1.447
 EV5  C19  C20   single    1.525  0.020  1.525
 EV5  C20  C21   single    1.529  0.020  1.529
 EV5  C20  C25   single    1.528  0.020  1.528
 EV5  C21  C22   single    1.525  0.020  1.525
 EV5  C22  C23   single    1.525  0.020  1.525
 EV5  C23  C24   single    1.525  0.020  1.525
 EV5  C24  C25   single    1.525  0.020  1.525
 EV5  C2   H2    single    0.930  0.020  1.080
 EV5  C3   H3    single    0.930  0.020  1.080
 EV5  C5   H5    single    0.930  0.020  1.080
 EV5  N10  HN10  single    0.890  0.020  1.040
 EV5  N10  HN1A  single    0.890  0.020  1.040
 EV5  C12  H12   single    0.970  0.020  1.090
 EV5  C13  H13   single    0.970  0.020  1.090
 EV5  C13  H13A  single    0.970  0.020  1.090
 EV5  C14  H14   single    0.970  0.020  1.090
 EV5  C14  H14A  single    0.970  0.020  1.090
 EV5  C14  H14B  single    0.970  0.020  1.090
 EV5  C15  H15   single    0.970  0.020  1.090
 EV5  C15  H15A  single    0.970  0.020  1.090
 EV5  N17  HN17  single    0.860  0.020  1.020
 EV5  C19  H19   single    0.970  0.020  1.090
 EV5  C19  H19A  single    0.970  0.020  1.090
 EV5  C20  H20   single    0.970  0.020  1.090
 EV5  C21  H21   single    0.970  0.020  1.090
 EV5  C21  H21A  single    0.970  0.020  1.090
 EV5  C22  H22   single    0.970  0.020  1.090
 EV5  C22  H22A  single    0.970  0.020  1.090
 EV5  C23  H23   single    0.970  0.020  1.090
 EV5  C23  H23A  single    0.970  0.020  1.090
 EV5  C24  H24   single    0.970  0.020  1.090
 EV5  C24  H24A  single    0.970  0.020  1.090
 EV5  C25  H25   single    0.970  0.020  1.090
 EV5  C25  H25A  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
 EV5  N9    C1   C6    105.24  3.000
 EV5  N9    C1   C2    132.52  3.000
 EV5  C6    C1   C2    122.24  3.000
 EV5  H2    C2   C3    119.89  3.000
 EV5  H2    C2   C1    122.55  3.000
 EV5  C3    C2   C1    117.55  3.000
 EV5  H3    C3   C4    120.12  3.000
 EV5  H3    C3   C2    119.75  3.000
 EV5  C4    C3   C2    120.13  3.000
 EV5  CL11  C4   C5    118.77  3.000
 EV5  CL11  C4   C3    118.45  3.000
 EV5  C5    C4   C3    122.78  3.000
 EV5  H5    C5   C6    121.16  3.000
 EV5  H5    C5   C4    121.70  3.000
 EV5  C6    C5   C4    117.14  3.000
 EV5  N7    C6   C5    129.55  3.000
 EV5  N7    C6   C1    110.29  3.000
 EV5  C5    C6   C1    120.17  3.000
 EV5  C8    N7   C6    104.95  3.000
 EV5  N10   C8   N9    122.67  3.000
 EV5  N10   C8   N7    123.55  3.000
 EV5  N9    C8   N7    113.67  3.000
 EV5  C12   N9   C8    128.97  3.000
 EV5  C12   N9   C1    125.13  3.000
 EV5  C8    N9   C1    105.85  3.000
 EV5  HN1A  N10  HN10  112.53  3.000
 EV5  HN1A  N10  C8    118.37  3.000
 EV5  HN10  N10  C8    113.87  3.000
 EV5  H12   C12  C15   107.15  3.000
 EV5  H12   C12  C13   106.74  3.000
 EV5  C15   C12  C13   113.12  3.000
 EV5  H12   C12  N9    104.91  3.000
 EV5  C15   C12  N9    111.12  3.000
 EV5  C13   C12  N9    113.17  3.000
 EV5  H13A  C13  H13   105.26  3.000
 EV5  H13A  C13  C14   109.71  3.000
 EV5  H13   C13  C14   110.04  3.000
 EV5  H13A  C13  C12   106.59  3.000
 EV5  H13   C13  C12   111.68  3.000
 EV5  C14   C13  C12   113.19  3.000
 EV5  H14B  C14  H14A  107.34  3.000
 EV5  H14B  C14  H14   107.71  3.000
 EV5  H14A  C14  H14   107.81  3.000
 EV5  H14B  C14  C13   110.54  3.000
 EV5  H14A  C14  C13   112.06  3.000
 EV5  H14   C14  C13   111.19  3.000
 EV5  H15A  C15  H15   106.91  3.000
 EV5  H15A  C15  C16   111.96  3.000
 EV5  H15   C15  C16   108.57  3.000
 EV5  H15A  C15  C12   111.18  3.000
 EV5  H15   C15  C12   108.15  3.000
 EV5  C16   C15  C12   109.92  3.000
 EV5  O18   C16  N17   123.53  3.000
 EV5  O18   C16  C15   120.93  3.000
 EV5  N17   C16  C15   115.52  3.000
 EV5  HN17  N17  C19   117.46  3.000
 EV5  HN17  N17  C16   118.37  3.000
 EV5  C19   N17  C16   124.16  3.000
 EV5  H19A  C19  H19   107.13  3.000
 EV5  H19A  C19  C20   109.64  3.000
 EV5  H19   C19  C20   109.57  3.000
 EV5  H19A  C19  N17   110.48  3.000
 EV5  H19   C19  N17   108.08  3.000
 EV5  C20   C19  N17   111.81  3.000
 EV5  H20   C20  C25   108.15  3.000
 EV5  H20   C20  C21   107.62  3.000
 EV5  C25   C20  C21   110.62  3.000
 EV5  H20   C20  C19   108.37  3.000
 EV5  C25   C20  C19   112.26  3.000
 EV5  C21   C20  C19   109.67  3.000
 EV5  H21A  C21  H21   106.55  3.000
 EV5  H21A  C21  C22   110.16  3.000
 EV5  H21   C21  C22   109.14  3.000
 EV5  H21A  C21  C20   110.01  3.000
 EV5  H21   C21  C20   108.98  3.000
 EV5  C22   C21  C20   111.85  3.000
 EV5  H22A  C22  H22   106.52  3.000
 EV5  H22A  C22  C23   109.35  3.000
 EV5  H22   C22  C23   110.37  3.000
 EV5  H22A  C22  C21   109.27  3.000
 EV5  H22   C22  C21   109.95  3.000
 EV5  C23   C22  C21   111.26  3.000
 EV5  H23A  C23  H23   106.64  3.000
 EV5  H23A  C23  C24   110.37  3.000
 EV5  H23   C23  C24   109.25  3.000
 EV5  H23A  C23  C22   110.30  3.000
 EV5  H23   C23  C22   109.20  3.000
 EV5  C24   C23  C22   110.98  3.000
 EV5  H24A  C24  H24   106.46  3.000
 EV5  H24A  C24  C25   109.21  3.000
 EV5  H24   C24  C25   109.64  3.000
 EV5  H24A  C24  C23   109.25  3.000
 EV5  H24   C24  C23   110.54  3.000
 EV5  C25   C24  C23   111.61  3.000
 EV5  H25A  C25  H25   106.17  3.000
 EV5  H25A  C25  C24   109.50  3.000
 EV5  H25   C25  C24   109.47  3.000
 EV5  H25A  C25  C20   109.25  3.000
 EV5  H25   C25  C20   110.53  3.000
 EV5  C24   C25  C20   111.76  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
 EV5  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 EV5  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 EV5  CONST_03  C8    N7   C6   C1      0.00   0.0  0
 EV5  CONST_04  N7    C8   N9   C1      0.00   0.0  0
 EV5  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 EV5  CONST_06  N7    C6   C1   C2    180.00   0.0  0
 EV5  CONST_07  C8    N9   C1   C2    180.00   0.0  0
 EV5  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 EV5  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 EV5  CONST_10  N9    C1   C2   C3    180.00   0.0  0
 EV5  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 EV5  CONST_12  N7    C6   C5   C4    180.00   0.0  0
 EV5  CONST_13  N9    C1   C6   C5    180.00   0.0  0
 EV5  CONST_14  C8    N7   C6   C5    180.00   0.0  0
 EV5  CONST_15  C8    N9   C1   C6      0.00   0.0  0
 EV5  CONST_16  N9    C8   N7   C6      0.00   0.0  0
 EV5  CONST_17  N9    C1   C6   N7      0.00   0.0  0
 EV5  CONST_18  N10   C8   N9   C1    180.00   0.0  0
 EV5  CONST_19  C12   N9   C1   C2      0.00   0.0  0
 EV5  CONST_20  CL11  C4   C3   C2    180.00   0.0  0
 EV5  CONST_21  C12   N9   C1   C6    180.00   0.0  0
 EV5  CONST_22  CL11  C4   C5   C6    180.00   0.0  0
 EV5  CONST_23  N10   C8   N7   C6    180.00   0.0  0
 EV5  CONST_24  C12   N9   C8   N7    180.00   0.0  0
 EV5  CONST_25  H3    C3   C2   C1    180.00   0.0  0
 EV5  CONST_26  H5    C5   C6   C1    180.00   0.0  0
 EV5  CONST_27  H2    C2   C3   C4    180.00   0.0  0
 EV5  CONST_28  HN10  N10  C8   N7      0.00   0.0  0
 EV5  CONST_30  C19   N17  C16  C15   180.00   0.0  0
 EV5  CONST_31  C19   N17  C16  O18     0.00   0.0  0
 EV5  CONST_32  HN17  N17  C16  C15     0.00   0.0  0
 EV5  Var_01    C23   C22  C21  C20    55.60  30.0  1
 EV5  Var_02    C23   C24  C25  C20   -55.19  30.0  1
 EV5  Var_03    C24   C23  C22  C21   -55.23  30.0  1
 EV5  Var_04    C25   C24  C23  C22    55.14  30.0  1
 EV5  Var_05    C20   C19  N17  C16  -143.28  30.0  3
 EV5  Var_06    N17   C16  C15  C12  -125.29  30.0  3
 EV5  Var_07    H14   C14  C13  C12   -54.75  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
 EV5  chir_01  C12  N9   C13  C15  negativ
 EV5  chir_02  C20  C19  C21  C25  positiv

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
 EV5  plan-1  C1    0.020
 EV5  plan-1  C2    0.020
 EV5  plan-1  C3    0.020
 EV5  plan-1  C4    0.020
 EV5  plan-1  C5    0.020
 EV5  plan-1  C6    0.020
 EV5  plan-1  N7    0.020
 EV5  plan-1  C8    0.020
 EV5  plan-1  N9    0.020
 EV5  plan-1  N10   0.020
 EV5  plan-1  CL11  0.020
 EV5  plan-1  C12   0.020
 EV5  plan-1  H2    0.020
 EV5  plan-1  H3    0.020
 EV5  plan-1  H5    0.020
 EV5  plan-2  C8    0.020
 EV5  plan-2  N10   0.020
 EV5  plan-2  HN10  0.020
 EV5  plan-2  HN1A  0.020
 EV5  plan-3  C15   0.020
 EV5  plan-3  C16   0.020
 EV5  plan-3  N17   0.020
 EV5  plan-3  O18   0.020
 EV5  plan-3  C19   0.020
 EV5  plan-3  HN17  0.020

