# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:08:28 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](CC(=O)NC1C2CC3CC(C2)CC1C3)n4c(N)nc5cc(Cl)ccc45
#
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
 EV6  EV6  (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide  ligand  57  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EV6
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
 EV6  C1    C   CR56  0   0.360   1.9554   0.2855   0.0338
 EV6  C2    C   CR16  0  -0.311   2.6849  -0.4833   0.9225
 EV6  C3    C   CR16  0  -0.248   3.1445  -1.7164   0.4778
 EV6  C4    C   CR6   0  -0.056   2.8681  -2.1403  -0.8211
 EV6  C5    C   CR16  0  -0.309   2.1394  -1.3782  -1.7188
 EV6  C6    C   CR56  0   0.173   1.6779  -0.1443  -1.2743
 EV6  N7    N   N     0  -0.521   0.9447   0.8028  -1.9391
 EV6  C8    C   CR5   0   0.617   0.7723   1.7673  -1.0701
 EV6  N9    N   NR5   0  -0.566   1.3600   1.5268   0.1424
 EV6  N10   N   NH2   0  -0.857   0.0053   2.8647  -1.3052
 EV6  CL11  CL  CL    0  -0.146   3.4643  -3.6939  -1.3318
 EV6  C12   C   CH1   0  -0.137   1.3017   2.3252   1.3630
 EV6  C13   C   CH2   0  -0.429   2.0731   3.6376   1.2489
 EV6  C14   C   CH3   0  -0.666   3.5148   3.4486   0.8036
 EV6  C15   C   CH2   0  -0.570  -0.1445   2.5264   1.8302
 EV6  C16   C   C     0   0.538  -0.8522   1.1880   1.8877
 EV6  N17   N   NH1   0  -0.637  -1.7034   0.9510   0.8804
 EV6  O18   O   O     0  -0.502  -0.6008   0.3763   2.7697
 EV6  C19   C   CR16  0  -0.033  -2.3545  -0.3246   0.6585
 EV6  C20   C   C     0  -0.246  -3.7135  -0.4227   1.3661
 EV6  C21   C   C     0  -0.427  -4.2518  -1.8441   1.1861
 EV6  C22   C   CR16  0  -0.243  -4.4337  -2.1412  -0.3036
 EV6  C23   C   C     0  -0.423  -5.4243  -1.1406  -0.9043
 EV6  C24   C   C     0  -0.239  -4.8886   0.2833  -0.7302
 EV6  C25   C   C     0  -0.431  -4.6962   0.5806   0.7592
 EV6  C26   C   CR16  0  -0.278  -2.5417  -0.5864  -0.8418
 EV6  C27   C   C     0  -0.446  -3.5427   0.4024  -1.4506
 EV6  C28   C   CH2   0  -0.424  -3.0851  -2.0083  -1.0155
 EV6  H2    H   HCR6  0   0.274   2.9031  -0.1606   1.9318
 EV6  H3    H   HCR6  0   0.273   3.7180  -2.3461   1.1434
 EV6  H5    H   HCR6  0   0.271   1.9346  -1.7241  -2.7232
 EV6  HN10  H   HNH2  0   0.401  -0.2464   2.9810  -2.2746
 EV6  HN1A  H   HNH2  0   0.402   0.2802   3.7348  -0.8784
 EV6  H12   H   HCH1  0   0.285   1.8027   1.7210   2.1211
 EV6  H13   H   HCH2  0   0.225   1.5634   4.3363   0.5789
 EV6  H13A  H   HCH2  0   0.253   2.0478   4.1089   2.2339
 EV6  H14   H   HCH3  0   0.226   4.0491   2.7668   1.4673
 EV6  H14A  H   HCH3  0   0.229   3.5773   3.0484  -0.2087
 EV6  H14B  H   HCH3  0   0.243   4.0452   4.4004   0.8114
 EV6  H15   H   HCH2  0   0.285  -0.1164   2.9582   2.8315
 EV6  H15A  H   HCH2  0   0.258  -0.6657   3.2383   1.1898
 EV6  HN17  H   HNH1  0   0.397  -1.8272   1.6755   0.1900
 EV6  H19   H   HCR6  0   0.245  -1.6919  -1.0945   1.0646
 EV6  H20   H   H     0   0.232  -3.5737  -0.2121   2.4306
 EV6  H21   H   H     0   0.226  -3.5633  -2.5671   1.6362
 EV6  H21A  H   H     0   0.226  -5.2041  -1.9502   1.7146
 EV6  H22   H   HCR6  0   0.225  -4.8136  -3.1589  -0.4328
 EV6  H23   H   H     0   0.222  -5.5741  -1.3557  -1.9676
 EV6  H23A  H   H     0   0.222  -6.4020  -1.2415  -0.4222
 EV6  H24   H   H     0   0.225  -5.5978   0.9970  -1.1595
 EV6  H25   H   H     0   0.228  -5.6539   0.5205   1.2858
 EV6  H25A  H   H     0   0.225  -4.3348   1.6040   0.9023
 EV6  H26   H   HCR6  0   0.246  -1.5735  -0.4949  -1.3438
 EV6  H27   H   H     0   0.234  -3.6649   0.1776  -2.5151
 EV6  H27A  H   H     0   0.223  -3.1744   1.4336  -1.4079
 EV6  H28   H   HCH2  0   0.227  -2.3702  -2.7358  -0.6181
 EV6  H28A  H   HCH2  0   0.228  -3.2002  -2.2255  -2.0820

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
 EV6  N9   C1    aromatic  1.381  0.020  1.381
 EV6  C6   C1    aromatic  1.405  0.020  1.405
 EV6  C1   C2    aromatic  1.383  0.020  1.383
 EV6  C2   C3    aromatic  1.389  0.020  1.389
 EV6  C2   H2    single    0.930  0.020  1.080
 EV6  C4   C3    aromatic  1.394  0.020  1.394
 EV6  C3   H3    single    0.930  0.020  1.080
 EV6  C5   C4    aromatic  1.385  0.020  1.385
 EV6  C4   CL11  single    1.741  0.020  1.741
 EV6  C6   C5    aromatic  1.390  0.020  1.390
 EV6  C5   H5    single    0.930  0.020  1.080
 EV6  N7   C6    aromatic  1.370  0.020  1.370
 EV6  C8   N7    aromatic  1.310  0.020  1.310
 EV6  N10  C8    single    1.359  0.020  1.359
 EV6  C8   N9    aromatic  1.369  0.020  1.369
 EV6  N9   C12   single    1.460  0.020  1.460
 EV6  N10  HN10  single    0.890  0.020  1.040
 EV6  N10  HN1A  single    0.890  0.020  1.040
 EV6  C15  C12   single    1.533  0.020  1.533
 EV6  C13  C12   single    1.527  0.020  1.527
 EV6  C12  H12   single    0.970  0.020  1.090
 EV6  C13  C14   single    1.521  0.020  1.521
 EV6  C13  H13   single    0.970  0.020  1.090
 EV6  C13  H13A  single    0.970  0.020  1.090
 EV6  C14  H14   single    0.970  0.020  1.090
 EV6  C14  H14A  single    0.970  0.020  1.090
 EV6  C14  H14B  single    0.970  0.020  1.090
 EV6  C15  C16   single    1.515  0.020  1.515
 EV6  C15  H15   single    0.970  0.020  1.090
 EV6  C15  H15A  single    0.970  0.020  1.090
 EV6  N17  C16   single    1.340  0.020  1.340
 EV6  C16  O18   double    1.225  0.020  1.225
 EV6  N17  C19   single    1.449  0.020  1.449
 EV6  N17  HN17  single    0.860  0.020  1.020
 EV6  C20  C19   single    1.535  0.020  1.535
 EV6  C19  C26   single    1.534  0.020  1.534
 EV6  C19  H19   single    0.970  0.020  1.090
 EV6  C25  C20   single    1.530  0.020  1.530
 EV6  C20  C21   single    1.531  0.020  1.531
 EV6  C20  H20   single    0.970  0.020  1.090
 EV6  C21  C22   single    1.530  0.020  1.530
 EV6  C21  H21   single    0.970  0.020  1.090
 EV6  C21  H21A  single    0.970  0.020  1.090
 EV6  C23  C22   single    1.531  0.020  1.531
 EV6  C22  C28   single    1.531  0.020  1.531
 EV6  C22  H22   single    0.970  0.020  1.090
 EV6  C24  C23   single    1.531  0.020  1.531
 EV6  C23  H23   single    0.970  0.020  1.090
 EV6  C23  H23A  single    0.970  0.020  1.090
 EV6  C25  C24   single    1.531  0.020  1.531
 EV6  C24  C27   single    1.531  0.020  1.531
 EV6  C24  H24   single    0.970  0.020  1.090
 EV6  C25  H25   single    0.970  0.020  1.090
 EV6  C25  H25A  single    0.970  0.020  1.090
 EV6  C27  C26   single    1.533  0.020  1.533
 EV6  C26  C28   single    1.532  0.020  1.532
 EV6  C26  H26   single    0.970  0.020  1.090
 EV6  C27  H27   single    0.970  0.020  1.090
 EV6  C27  H27A  single    0.970  0.020  1.090
 EV6  C28  H28   single    0.970  0.020  1.090
 EV6  C28  H28A  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
 EV6  N9    C1   C6    105.25  3.000
 EV6  C6    C1   C2    122.18  3.000
 EV6  N9    C1   C2    132.57  3.000
 EV6  H2    C2   C3    119.78  3.000
 EV6  H2    C2   C1    122.69  3.000
 EV6  C3    C2   C1    117.53  3.000
 EV6  H3    C3   C4    120.12  3.000
 EV6  H3    C3   C2    119.71  3.000
 EV6  C4    C3   C2    120.17  3.000
 EV6  CL11  C4   C5    118.76  3.000
 EV6  CL11  C4   C3    118.48  3.000
 EV6  C5    C4   C3    122.75  3.000
 EV6  H5    C5   C6    121.18  3.000
 EV6  H5    C5   C4    121.70  3.000
 EV6  C6    C5   C4    117.12  3.000
 EV6  N7    C6   C5    129.50  3.000
 EV6  N7    C6   C1    110.25  3.000
 EV6  C5    C6   C1    120.25  3.000
 EV6  C8    N7   C6    104.93  3.000
 EV6  N10   C8   N9    122.50  3.000
 EV6  N9    C8   N7    113.70  3.000
 EV6  N10   C8   N7    123.64  3.000
 EV6  C12   N9   C8    128.87  3.000
 EV6  C12   N9   C1    125.07  3.000
 EV6  C8    N9   C1    105.87  3.000
 EV6  HN1A  N10  HN10  112.08  3.000
 EV6  HN1A  N10  C8    118.04  3.000
 EV6  HN10  N10  C8    113.60  3.000
 EV6  H12   C12  C15   107.10  3.000
 EV6  H12   C12  C13   107.21  3.000
 EV6  C15   C12  C13   112.74  3.000
 EV6  H12   C12  N9    105.06  3.000
 EV6  C13   C12  N9    112.80  3.000
 EV6  C15   C12  N9    111.37  3.000
 EV6  H13A  C13  H13   105.43  3.000
 EV6  H13A  C13  C14   109.86  3.000
 EV6  H13   C13  C14   109.99  3.000
 EV6  H13A  C13  C12   106.97  3.000
 EV6  H13   C13  C12   111.06  3.000
 EV6  C14   C13  C12   113.20  3.000
 EV6  H14B  C14  H14A  107.42  3.000
 EV6  H14B  C14  H14   107.64  3.000
 EV6  H14A  C14  H14   107.90  3.000
 EV6  H14B  C14  C13   110.53  3.000
 EV6  H14A  C14  C13   111.83  3.000
 EV6  H14   C14  C13   111.33  3.000
 EV6  H15A  C15  H15   107.05  3.000
 EV6  H15A  C15  C16   112.07  3.000
 EV6  H15   C15  C16   109.08  3.000
 EV6  H15A  C15  C12   110.96  3.000
 EV6  H15   C15  C12   107.90  3.000
 EV6  C16   C15  C12   109.65  3.000
 EV6  O18   C16  N17   123.68  3.000
 EV6  O18   C16  C15   121.13  3.000
 EV6  N17   C16  C15   115.11  3.000
 EV6  HN17  N17  C19   118.19  3.000
 EV6  HN17  N17  C16   117.75  3.000
 EV6  C19   N17  C16   123.79  3.000
 EV6  H19   C19  C26   108.47  3.000
 EV6  H19   C19  C20   108.67  3.000
 EV6  C26   C19  C20   109.37  3.000
 EV6  H19   C19  N17   106.89  3.000
 EV6  C26   C19  N17   110.78  3.000
 EV6  C20   C19  N17   112.54  3.000
 EV6  H20   C20  C25   109.99  3.000
 EV6  H20   C20  C21   109.76  3.000
 EV6  C25   C20  C21   109.66  3.000
 EV6  H20   C20  C19   108.85  3.000
 EV6  C21   C20  C19   108.45  3.000
 EV6  C25   C20  C19   110.11  3.000
 EV6  H21A  C21  H21   106.53  3.000
 EV6  H21A  C21  C22   110.36  3.000
 EV6  H21   C21  C22   110.29  3.000
 EV6  H21A  C21  C20   109.83  3.000
 EV6  H21   C21  C20   110.11  3.000
 EV6  C22   C21  C20   109.68  3.000
 EV6  H22   C22  C28   109.37  3.000
 EV6  H22   C22  C23   109.70  3.000
 EV6  C28   C22  C23   109.32  3.000
 EV6  H22   C22  C21   109.69  3.000
 EV6  C28   C22  C21   109.34  3.000
 EV6  C23   C22  C21   109.40  3.000
 EV6  H23A  C23  H23   106.70  3.000
 EV6  H23A  C23  C24   110.38  3.000
 EV6  H23   C23  C24   109.93  3.000
 EV6  H23A  C23  C22   110.17  3.000
 EV6  H23   C23  C22   109.95  3.000
 EV6  C24   C23  C22   109.68  3.000
 EV6  H24   C24  C27   109.54  3.000
 EV6  H24   C24  C25   109.67  3.000
 EV6  C27   C24  C25   109.40  3.000
 EV6  H24   C24  C23   109.59  3.000
 EV6  C27   C24  C23   109.05  3.000
 EV6  C25   C24  C23   109.58  3.000
 EV6  H25A  C25  H25   106.10  3.000
 EV6  H25A  C25  C24   110.50  3.000
 EV6  H25   C25  C24   110.33  3.000
 EV6  H25A  C25  C20   110.44  3.000
 EV6  H25   C25  C20   109.58  3.000
 EV6  C24   C25  C20   109.83  3.000
 EV6  H26   C26  C28   109.84  3.000
 EV6  H26   C26  C27   109.97  3.000
 EV6  C28   C26  C27   108.79  3.000
 EV6  H26   C26  C19   109.04  3.000
 EV6  C28   C26  C19   108.21  3.000
 EV6  C27   C26  C19   110.97  3.000
 EV6  H27A  C27  H27   105.58  3.000
 EV6  H27A  C27  C26   111.84  3.000
 EV6  H27   C27  C26   109.06  3.000
 EV6  H27A  C27  C24   110.51  3.000
 EV6  H27   C27  C24   110.08  3.000
 EV6  C26   C27  C24   109.69  3.000
 EV6  H28A  C28  H28   106.89  3.000
 EV6  H28A  C28  C26   109.38  3.000
 EV6  H28   C28  C26   110.13  3.000
 EV6  H28A  C28  C22   110.08  3.000
 EV6  H28   C28  C22   110.42  3.000
 EV6  C26   C28  C22   109.89  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
 EV6  CONST_01  N7    C8   N9   C1      0.00   0.0  0
 EV6  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 EV6  CONST_03  C8    N7   C6   C1      0.00   0.0  0
 EV6  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 EV6  CONST_05  C8    N9   C1   C2    180.00   0.0  0
 EV6  CONST_06  C5    C6   C1   C2      0.00   0.0  0
 EV6  CONST_07  N7    C6   C1   C2    180.00   0.0  0
 EV6  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 EV6  CONST_09  N9    C1   C2   C3    180.00   0.0  0
 EV6  CONST_10  C6    C1   C2   C3      0.00   0.0  0
 EV6  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 EV6  CONST_12  N7    C6   C5   C4    180.00   0.0  0
 EV6  CONST_13  N9    C1   C6   C5    180.00   0.0  0
 EV6  CONST_14  C8    N7   C6   C5    180.00   0.0  0
 EV6  CONST_15  C8    N9   C1   C6      0.00   0.0  0
 EV6  CONST_16  N9    C8   N7   C6      0.00   0.0  0
 EV6  CONST_17  N9    C1   C6   N7      0.00   0.0  0
 EV6  CONST_18  N10   C8   N9   C1    180.00   0.0  0
 EV6  CONST_19  C12   N9   C1   C2      0.00   0.0  0
 EV6  CONST_20  CL11  C4   C3   C2    180.00   0.0  0
 EV6  CONST_21  C12   N9   C1   C6    180.00   0.0  0
 EV6  CONST_22  CL11  C4   C5   C6    180.00   0.0  0
 EV6  CONST_23  N10   C8   N7   C6    180.00   0.0  0
 EV6  CONST_24  C12   N9   C8   N7    180.00   0.0  0
 EV6  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 EV6  CONST_26  H3    C3   C2   C1    180.00   0.0  0
 EV6  CONST_27  H2    C2   C3   C4    180.00   0.0  0
 EV6  CONST_28  HN10  N10  C8   N7      0.00   0.0  0
 EV6  CONST_30  C19   N17  C16  C15   180.00   0.0  0
 EV6  CONST_31  C19   N17  C16  O18     0.00   0.0  0
 EV6  CONST_32  HN17  N17  C16  C15     0.00   0.0  0
 EV6  Var_01    N17   C16  C15  C12  -103.86  30.0  3
 EV6  Var_02    H14   C14  C13  C12   -56.02  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
 EV6  chir_01  C12  N9   C15  C13  positiv
 EV6  chir_02  C19  N17  C20  C26  negativ
 EV6  chir_03  C20  C19  C25  C21  negativ
 EV6  chir_04  C22  C21  C23  C28  negativ
 EV6  chir_05  C24  C23  C25  C27  negativ
 EV6  chir_06  C26  C19  C27  C28  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
 EV6  plan-1  C1    0.020
 EV6  plan-1  C2    0.020
 EV6  plan-1  C3    0.020
 EV6  plan-1  C4    0.020
 EV6  plan-1  C5    0.020
 EV6  plan-1  C6    0.020
 EV6  plan-1  N7    0.020
 EV6  plan-1  C8    0.020
 EV6  plan-1  N9    0.020
 EV6  plan-1  N10   0.020
 EV6  plan-1  CL11  0.020
 EV6  plan-1  C12   0.020
 EV6  plan-1  H2    0.020
 EV6  plan-1  H3    0.020
 EV6  plan-1  H5    0.020
 EV6  plan-2  C15   0.020
 EV6  plan-2  C16   0.020
 EV6  plan-2  N17   0.020
 EV6  plan-2  O18   0.020
 EV6  plan-2  C19   0.020
 EV6  plan-2  HN17  0.020
 EV6  plan-3  C8    0.020
 EV6  plan-3  N10   0.020
 EV6  plan-3  HN10  0.020
 EV6  plan-3  HN1A  0.020

