# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:23:55 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-[3-(aminomethyl)phenyl]-~{N}-[(1~{S})-1,2,3,4-tetrahydronaphthalen-1-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)c2cccc(c2)C(=O)N[C@H]3CCCc4ccccc34
#
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
 E82  E82  3-[3-(aminomethyl)phenyl]-~{N}-[(1~{S})-1,2,3,4-tetrahydronaphthalen-1-yl]benzamide  ligand  51  27  .  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_E82
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
 E82  C3   C  CH1   0  -0.125   3.5355  -0.6000   0.6357
 E82  C42  C  CR16  0  -0.227  -4.9659   2.1250   0.6885
 E82  C44  C  CR16  0  -0.327  -3.7786   1.4995   0.3316
 E82  C46  C  CH2   0  -0.351  -7.4772  -0.6918   0.2810
 E82  C11  C  CH2   0  -0.498   6.4804  -0.7358   0.1746
 E82  C14  C  CR6   0   0.069   5.6950   0.5220  -0.0998
 E82  C15  C  CR6   0   0.071   4.3108   0.5856   0.0858
 E82  C16  C  CR16  0  -0.290   3.6394   1.7750  -0.1999
 E82  C18  C  CR16  0  -0.259   4.3159   2.8886  -0.6689
 E82  C20  C  CR16  0  -0.257   5.6910   2.8263  -0.8577
 E82  C22  C  CR16  0  -0.301   6.3651   1.6514  -0.5721
 E82  C26  C  CR6   0  -0.022  -0.1585  -0.9033  -0.1454
 E82  C27  C  CR16  0  -0.341  -1.3457  -0.2834   0.2314
 E82  C29  C  CR6   0   0.106  -2.5303  -0.5123  -0.4634
 E82  C30  C  CR16  0  -0.307  -2.5096  -1.4012  -1.5400
 E82  O25  O  O     0  -0.486   0.9782  -0.3524   1.8595
 E82  N1   N  NH1   0  -0.650   2.2341  -0.7149   0.0120
 E82  C8   C  CH2   0  -0.455   5.7215  -1.7313   1.0378
 E82  C5   C  CH2   0  -0.438   4.3077  -1.9089   0.5099
 E82  C34  C  CR16  0  -0.308  -0.1579  -1.7897  -1.2192
 E82  C32  C  CR16  0  -0.226  -1.3353  -2.0368  -1.9094
 E82  C36  C  CR6   0   0.106  -3.7813   0.1642  -0.0657
 E82  C40  C  CR16  0  -0.296  -6.1641   1.4287   0.6595
 E82  C39  C  CR6   0   0.127  -6.1880   0.0880   0.2782
 E82  C37  C  CR16  0  -0.377  -4.9963  -0.5240  -0.0874
 E82  N49  N  NH2   0  -0.791  -8.5331   0.0235  -0.4169
 E82  H1   H  HCH1  0   0.271   3.3523  -0.4152   1.6969
 E82  H2   H  HCR6  0   0.255  -4.9528   3.1662   0.9845
 E82  H3   H  HCR6  0   0.254  -2.8536   2.0628   0.3429
 E82  H4   H  HCH2  0   0.215  -7.2804  -1.6971  -0.1145
 E82  H5   H  HCH2  0   0.239  -7.8003  -0.8345   1.3162
 E82  H6   H  HCH2  0   0.246   6.7332  -1.2066  -0.7815
 E82  H7   H  HCH2  0   0.251   7.4338  -0.4747   0.6394
 E82  H8   H  HCR6  0   0.246   2.5670   1.8317  -0.0571
 E82  H9   H  HCR6  0   0.252   3.7735   3.7996  -0.8865
 E82  H10  H  HCR6  0   0.252   6.2330   3.6895  -1.2221
 E82  H11  H  HCR6  0   0.246   7.4385   1.6018  -0.7165
 E82  H12  H  HCR6  0   0.259  -1.3454   0.3790   1.0878
 E82  H13  H  HCR6  0   0.261  -3.4159  -1.5879  -2.1024
 E82  H14  H  HNH1  0   0.404   2.2217  -0.8659  -0.9850
 E82  H15  H  HCH2  0   0.244   6.2479  -2.6869   1.0556
 E82  H16  H  HCH2  0   0.227   5.6824  -1.3765   2.0723
 E82  H17  H  HCH2  0   0.248   3.7754  -2.6881   1.0584
 E82  H18  H  HCH2  0   0.227   4.3396  -2.2203  -0.5398
 E82  H19  H  HCR6  0   0.260   0.7424  -2.3167  -1.5090
 E82  H20  H  HCR6  0   0.266  -1.3366  -2.7293  -2.7404
 E82  H21  H  HCR6  0   0.248  -7.0875   1.9235   0.9325
 E82  H22  H  HCR6  0   0.249  -5.0128  -1.5690  -0.3774
 E82  H23  H  HNH2  0   0.343  -8.3268   0.0438  -1.4078
 E82  H24  H  HNH2  0   0.352  -9.4001  -0.4900  -0.3233
 E82  C24  C  C     0   0.540   1.0657  -0.6339   0.6718

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
 E82  C5   C8   single    1.520  0.020  1.520
 E82  C5   C3   single    1.525  0.020  1.525
 E82  C8   C11  single    1.521  0.020  1.521
 E82  O25  C24  double    1.224  0.020  1.224
 E82  C34  C32  aromatic  1.387  0.020  1.387
 E82  C34  C26  aromatic  1.392  0.020  1.392
 E82  C32  C30  aromatic  1.385  0.020  1.385
 E82  C24  C26  single    1.496  0.020  1.496
 E82  C24  N1   single    1.344  0.020  1.344
 E82  C11  C14  single    1.508  0.020  1.508
 E82  C3   N1   single    1.448  0.020  1.448
 E82  C3   C15  single    1.520  0.020  1.520
 E82  C26  C27  aromatic  1.391  0.020  1.391
 E82  C30  C29  aromatic  1.396  0.020  1.396
 E82  C15  C14  aromatic  1.398  0.020  1.398
 E82  C15  C16  aromatic  1.395  0.020  1.395
 E82  C14  C22  aromatic  1.396  0.020  1.396
 E82  C27  C29  aromatic  1.392  0.020  1.392
 E82  C29  C36  single    1.477  0.020  1.477
 E82  C16  C18  aromatic  1.385  0.020  1.385
 E82  C22  C20  aromatic  1.384  0.020  1.384
 E82  C36  C37  aromatic  1.396  0.020  1.396
 E82  C36  C44  aromatic  1.393  0.020  1.393
 E82  C37  C39  aromatic  1.389  0.020  1.389
 E82  C20  C18  aromatic  1.389  0.020  1.389
 E82  C44  C42  aromatic  1.389  0.020  1.389
 E82  N49  C46  single    1.454  0.020  1.454
 E82  C39  C46  single    1.507  0.020  1.507
 E82  C39  C40  aromatic  1.394  0.020  1.394
 E82  C42  C40  aromatic  1.386  0.020  1.386
 E82  C3   H1   single    0.970  0.020  1.090
 E82  C42  H2   single    0.930  0.020  1.080
 E82  C44  H3   single    0.930  0.020  1.080
 E82  C46  H4   single    0.970  0.020  1.090
 E82  C46  H5   single    0.970  0.020  1.090
 E82  C11  H6   single    0.970  0.020  1.090
 E82  C11  H7   single    0.970  0.020  1.090
 E82  C16  H8   single    0.930  0.020  1.080
 E82  C18  H9   single    0.930  0.020  1.080
 E82  C20  H10  single    0.930  0.020  1.080
 E82  C22  H11  single    0.930  0.020  1.080
 E82  C27  H12  single    0.930  0.020  1.080
 E82  C30  H13  single    0.930  0.020  1.080
 E82  N1   H14  single    0.860  0.020  1.020
 E82  C8   H15  single    0.970  0.020  1.090
 E82  C8   H16  single    0.970  0.020  1.090
 E82  C5   H17  single    0.970  0.020  1.090
 E82  C5   H18  single    0.970  0.020  1.090
 E82  C34  H19  single    0.930  0.020  1.080
 E82  C32  H20  single    0.930  0.020  1.080
 E82  C40  H21  single    0.930  0.020  1.080
 E82  C37  H22  single    0.930  0.020  1.080
 E82  N49  H23  single    0.890  0.020  1.040
 E82  N49  H24  single    0.890  0.020  1.040

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
 E82  H1   C3   C5   108.07  3.000
 E82  H1   C3   N1   106.33  3.000
 E82  C5   C3   N1   110.58  3.000
 E82  H1   C3   C15  107.76  3.000
 E82  N1   C3   C15  111.39  3.000
 E82  C5   C3   C15  112.42  3.000
 E82  H2   C42  C40  119.96  3.000
 E82  H2   C42  C44  119.55  3.000
 E82  C40  C42  C44  120.49  3.000
 E82  H3   C44  C36  120.21  3.000
 E82  H3   C44  C42  119.56  3.000
 E82  C36  C44  C42  120.22  3.000
 E82  H5   C46  H4   105.93  3.000
 E82  H5   C46  N49  107.70  3.000
 E82  H4   C46  N49  114.06  3.000
 E82  H5   C46  C39  108.78  3.000
 E82  H4   C46  C39  108.65  3.000
 E82  N49  C46  C39  111.46  3.000
 E82  H7   C11  H6   105.82  3.000
 E82  H7   C11  C8   110.52  3.000
 E82  H6   C11  C8   109.22  3.000
 E82  H7   C11  C14  109.43  3.000
 E82  H6   C11  C14  108.66  3.000
 E82  C8   C11  C14  112.92  3.000
 E82  C22  C14  C15  118.92  3.000
 E82  C22  C14  C11  119.11  3.000
 E82  C15  C14  C11  121.97  3.000
 E82  C16  C15  C14  119.21  3.000
 E82  C16  C15  C3   119.58  3.000
 E82  C14  C15  C3   121.18  3.000
 E82  H8   C16  C18  119.08  3.000
 E82  H8   C16  C15  119.60  3.000
 E82  C18  C16  C15  121.32  3.000
 E82  H9   C18  C20  120.42  3.000
 E82  H9   C18  C16  120.01  3.000
 E82  C20  C18  C16  119.57  3.000
 E82  H10  C20  C22  120.16  3.000
 E82  H10  C20  C18  120.37  3.000
 E82  C22  C20  C18  119.47  3.000
 E82  H11  C22  C20  119.56  3.000
 E82  H11  C22  C14  118.91  3.000
 E82  C20  C22  C14  121.52  3.000
 E82  C34  C26  C27  119.53  3.000
 E82  C27  C26  C24  118.03  3.000
 E82  C34  C26  C24  122.37  3.000
 E82  H12  C27  C29  119.70  3.000
 E82  H12  C27  C26  119.12  3.000
 E82  C29  C27  C26  121.17  3.000
 E82  C36  C29  C30  120.78  3.000
 E82  C36  C29  C27  120.74  3.000
 E82  C30  C29  C27  118.48  3.000
 E82  H13  C30  C32  119.45  3.000
 E82  H13  C30  C29  119.86  3.000
 E82  C32  C30  C29  120.68  3.000
 E82  H14  N1   C24  118.92  3.000
 E82  H14  N1   C3   116.67  3.000
 E82  C24  N1   C3   124.41  3.000
 E82  H16  C8   H15  106.60  3.000
 E82  H16  C8   C5   109.46  3.000
 E82  H15  C8   C5   110.62  3.000
 E82  H16  C8   C11  110.01  3.000
 E82  H15  C8   C11  109.99  3.000
 E82  C5   C8   C11  110.10  3.000
 E82  H18  C5   H17  107.03  3.000
 E82  H18  C5   C8   109.82  3.000
 E82  H17  C5   C8   111.26  3.000
 E82  H18  C5   C3   109.75  3.000
 E82  H17  C5   C3   108.92  3.000
 E82  C8   C5   C3   110.01  3.000
 E82  H19  C34  C32  119.07  3.000
 E82  H19  C34  C26  121.11  3.000
 E82  C32  C34  C26  119.79  3.000
 E82  H20  C32  C34  119.83  3.000
 E82  H20  C32  C30  119.84  3.000
 E82  C34  C32  C30  120.33  3.000
 E82  C37  C36  C29  120.47  3.000
 E82  C37  C36  C44  118.59  3.000
 E82  C29  C36  C44  120.94  3.000
 E82  H21  C40  C39  119.59  3.000
 E82  H21  C40  C42  120.16  3.000
 E82  C39  C40  C42  120.24  3.000
 E82  C37  C39  C40  118.76  3.000
 E82  C40  C39  C46  120.79  3.000
 E82  C37  C39  C46  120.44  3.000
 E82  H22  C37  C39  118.81  3.000
 E82  H22  C37  C36  119.49  3.000
 E82  C39  C37  C36  121.69  3.000
 E82  H24  N49  H23  105.98  3.000
 E82  H24  N49  C46  109.16  3.000
 E82  H23  N49  C46  109.38  3.000
 E82  N1   C24  O25  123.53  3.000
 E82  N1   C24  C26  115.61  3.000
 E82  O25  C24  C26  120.86  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
 E82  CONST_01  C29  C36  C44  C42  180.00   0.0  0
 E82  CONST_02  C37  C36  C44  C42    0.00   0.0  0
 E82  CONST_03  C37  C39  C40  C42    0.00   0.0  0
 E82  CONST_06  C39  C37  C36  C44    0.00   0.0  0
 E82  CONST_07  C39  C40  C42  C44    0.00   0.0  0
 E82  CONST_08  C18  C16  C15  C14    0.00   0.0  0
 E82  CONST_09  C18  C20  C22  C14    0.00   0.0  0
 E82  CONST_10  C20  C22  C14  C15    0.00   0.0  0
 E82  CONST_11  C20  C18  C16  C15    0.00   0.0  0
 E82  CONST_12  C22  C14  C15  C16    0.00   0.0  0
 E82  CONST_13  C22  C20  C18  C16    0.00   0.0  0
 E82  CONST_14  C30  C32  C34  C26    0.00   0.0  0
 E82  CONST_15  C30  C29  C27  C26    0.00   0.0  0
 E82  CONST_16  C36  C29  C27  C26  180.00   0.0  0
 E82  CONST_17  C32  C34  C26  C27    0.00   0.0  0
 E82  CONST_18  C32  C30  C29  C27    0.00   0.0  0
 E82  CONST_20  C34  C32  C30  C29    0.00   0.0  0
 E82  CONST_21  C34  C26  C27  C29    0.00   0.0  0
 E82  CONST_22  C39  C37  C36  C29  180.00   0.0  0
 E82  CONST_24  C36  C29  C30  C32  180.00   0.0  0
 E82  CONST_25  C40  C39  C37  C36    0.00   0.0  0
 E82  CONST_26  C40  C42  C44  C36    0.00   0.0  0
 E82  CONST_27  C46  C39  C40  C42  180.00   0.0  0
 E82  CONST_28  C36  C37  C39  C46  180.00   0.0  0
 E82  CONST_29  C32  C34  C26  C24  180.00   0.0  0
 E82  CONST_30  C29  C27  C26  C24  180.00   0.0  0
 E82  CONST_31  H8   C16  C15  C3     0.00   0.0  0
 E82  CONST_32  H22  C37  C36  C44  180.00   0.0  0
 E82  CONST_33  H21  C40  C42  C44  180.00   0.0  0
 E82  CONST_34  H11  C22  C14  C11    0.00   0.0  0
 E82  CONST_35  H10  C20  C22  C14  180.00   0.0  0
 E82  CONST_36  H9   C18  C16  C15  180.00   0.0  0
 E82  CONST_37  H20  C32  C34  C26  180.00   0.0  0
 E82  CONST_38  H19  C34  C26  C27  180.00   0.0  0
 E82  CONST_39  H13  C30  C29  C27  180.00   0.0  0
 E82  CONST_40  H3   C44  C36  C29    0.00   0.0  0
 E82  CONST_41  H12  C27  C29  C30  180.00   0.0  0
 E82  CONST_42  H2   C42  C44  C36  180.00   0.0  0
 E82  CONST_43  C26  C24  N1   C3   180.00   0.0  0
 E82  CONST_44  O25  C24  N1   C3     0.00   0.0  0
 E82  CONST_45  H14  N1   C24  C26    0.00   0.0  0
 E82  Var_01    C11  C8   C5   C3   -64.49  30.0  1
 E82  Var_02    C5   C8   C11  C14   47.52  30.0  1
 E82  Var_03    C8   C11  C14  C15  -17.33  30.0  1
 E82  Var_04    O25  C24  C26  C27   28.24  30.0  2
 E82  Var_05    N49  C46  C39  C40   49.73  30.0  2
 E82  Var_06    H23  N49  C46  C39   69.47  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
 E82  chir_01  C3  C5  N1  C15  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
 E82  plan-1  C26  0.020
 E82  plan-1  C27  0.020
 E82  plan-1  C29  0.020
 E82  plan-1  C30  0.020
 E82  plan-1  C34  0.020
 E82  plan-1  C32  0.020
 E82  plan-1  C36  0.020
 E82  plan-1  H12  0.020
 E82  plan-1  H13  0.020
 E82  plan-1  H19  0.020
 E82  plan-1  H20  0.020
 E82  plan-1  C24  0.020
 E82  plan-2  C42  0.020
 E82  plan-2  C44  0.020
 E82  plan-2  C46  0.020
 E82  plan-2  C29  0.020
 E82  plan-2  C36  0.020
 E82  plan-2  C40  0.020
 E82  plan-2  C39  0.020
 E82  plan-2  C37  0.020
 E82  plan-2  H2   0.020
 E82  plan-2  H3   0.020
 E82  plan-2  H21  0.020
 E82  plan-2  H22  0.020
 E82  plan-3  C3   0.020
 E82  plan-3  C11  0.020
 E82  plan-3  C14  0.020
 E82  plan-3  C15  0.020
 E82  plan-3  C16  0.020
 E82  plan-3  C18  0.020
 E82  plan-3  C20  0.020
 E82  plan-3  C22  0.020
 E82  plan-3  H8   0.020
 E82  plan-3  H9   0.020
 E82  plan-3  H10  0.020
 E82  plan-3  H11  0.020
 E82  plan-4  C3   0.020
 E82  plan-4  C26  0.020
 E82  plan-4  O25  0.020
 E82  plan-4  N1   0.020
 E82  plan-4  H14  0.020
 E82  plan-4  C24  0.020

