# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:21:33 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2ccccc2c1c3ccc(cc3)C(=O)NCCN4CCOCC4
#
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
 7PQ  7PQ  4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide  ligand  56  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7PQ
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
 7PQ  C1   C  CR16  0  -0.267  -1.9976  -0.1048   1.4897
 7PQ  C2   C  CR16  0  -0.257  -0.6751   0.1624   1.8029
 7PQ  C3   C  CR6   0  -0.041   0.2762   0.2902   0.7947
 7PQ  C4   C  CR16  0  -0.279  -0.1283   0.1784  -0.5337
 7PQ  C5   C  CR16  0  -0.257  -1.4556  -0.0737  -0.8448
 7PQ  C6   C  CR6   0  -0.030  -2.4022  -0.2318   0.1631
 7PQ  C7   C  CR6   0   0.031  -3.8229  -0.5212  -0.1606
 7PQ  C8   C  C     0   0.530   1.6884   0.5850   1.1861
 7PQ  O9   O  O     0  -0.492   1.9460   1.1790   2.2253
 7PQ  N10  N  NH1   0  -0.655   2.6392   0.1637   0.3381
 7PQ  C11  C  CH2   0  -0.255   4.0481   0.3813   0.5877
 7PQ  C12  C  CH2   0  -0.306   4.8516   0.0581  -0.6653
 7PQ  N13  N  NT    0  -0.431   6.2654   0.2848  -0.4582
 7PQ  C14  C  CH2   0  -0.305   6.9863   0.4890  -1.7022
 7PQ  C15  C  CH2   0  -0.187   8.4351   0.8263  -1.4035
 7PQ  O16  O  O2    0  -0.486   9.0595  -0.1842  -0.6420
 7PQ  C17  C  CH2   0  -0.184   8.3583  -0.4122   0.5605
 7PQ  C18  C  CH2   0  -0.312   6.9085  -0.7739   0.3005
 7PQ  C19  C  CR66  0   0.123  -4.7091   0.5656  -0.4235
 7PQ  C20  C  CR66  0   0.100  -6.0716   0.2951  -0.7139
 7PQ  C21  C  CR16  0  -0.318  -6.5174  -1.0473  -0.7272
 7PQ  C22  C  CR16  0  -0.280  -5.6499  -2.0651  -0.4640
 7PQ  C23  C  CR6   0   0.072  -4.2832  -1.8177  -0.1883
 7PQ  C24  C  CR16  0  -0.338  -4.2822   1.9155  -0.3969
 7PQ  C25  C  CR16  0  -0.253  -5.1586   2.9361  -0.6537
 7PQ  C26  C  CR16  0  -0.262  -6.5086   2.6626  -0.9497
 7PQ  C27  C  CR16  0  -0.312  -6.9529   1.3688  -0.9772
 7PQ  C28  C  CH2   0  -0.387  -3.3975  -2.9963   0.1180
 7PQ  N29  N  NH2   0  -0.788  -3.6553  -3.4705   1.4725
 7PQ  H1   H  HCR6  0   0.258  -2.7264  -0.2049   2.2844
 7PQ  H2   H  HCR6  0   0.261  -0.3806   0.2651   2.8389
 7PQ  H3   H  HCR6  0   0.261   0.5794   0.3095  -1.3426
 7PQ  H4   H  HCR6  0   0.259  -1.7565  -0.1529  -1.8818
 7PQ  H5   H  HNH1  0   0.406   2.3865  -0.4622  -0.4100
 7PQ  H6   H  HCH2  0   0.243   4.2138   1.4250   0.8570
 7PQ  H7   H  HCH2  0   0.236   4.3792  -0.2259   1.4359
 7PQ  H8   H  HCH2  0   0.207   4.6421  -0.9745  -0.9934
 7PQ  H9   H  HCH2  0   0.248   4.5112   0.7150  -1.4697
 7PQ  H11  H  HCH2  0   0.200   6.9390  -0.3994  -2.3546
 7PQ  H12  H  HCH2  0   0.244   6.5378   1.3200  -2.2519
 7PQ  H13  H  HCH2  0   0.236   8.9978   0.9305  -2.3326
 7PQ  H14  H  HCH2  0   0.200   8.4759   1.7875  -0.8717
 7PQ  H15  H  HCH2  0   0.236   8.8611  -1.2274   1.0827
 7PQ  H16  H  HCH2  0   0.201   8.3982   0.4788   1.2030
 7PQ  H17  H  HCH2  0   0.244   6.4092  -0.9117   1.2611
 7PQ  H18  H  HCH2  0   0.202   6.8589  -1.7393  -0.2324
 7PQ  H19  H  HCR6  0   0.254  -7.5574  -1.2547  -0.9483
 7PQ  H20  H  HCR6  0   0.250  -5.9997  -3.0904  -0.4744
 7PQ  H21  H  HCR6  0   0.251  -3.2504   2.1455  -0.1659
 7PQ  H22  H  HCR6  0   0.259  -4.8134   3.9615  -0.6271
 7PQ  H23  H  HCR6  0   0.258  -7.1909   3.4782  -1.1505
 7PQ  H24  H  HCR6  0   0.256  -7.9907   1.1502  -1.1987
 7PQ  H25  H  HCH2  0   0.240  -3.6456  -3.8062  -0.5724
 7PQ  H26  H  HCH2  0   0.222  -2.3488  -2.7421  -0.0697
 7PQ  H27  H  HNH2  0   0.352  -3.0873  -4.2905   1.6474
 7PQ  H28  H  HNH2  0   0.340  -3.3381  -2.7727   2.1348

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
 7PQ  O16  C17  single    1.411  0.020  1.411
 7PQ  O16  C15  single    1.411  0.020  1.411
 7PQ  C25  C26  aromatic  1.409  0.020  1.409
 7PQ  C25  C24  aromatic  1.370  0.020  1.370
 7PQ  C18  C17  single    1.517  0.020  1.517
 7PQ  C18  N13  single    1.453  0.020  1.453
 7PQ  C26  C27  aromatic  1.368  0.020  1.368
 7PQ  C14  C15  single    1.517  0.020  1.517
 7PQ  C14  N13  single    1.452  0.020  1.452
 7PQ  C24  C19  aromatic  1.416  0.020  1.416
 7PQ  C12  N13  single    1.447  0.020  1.447
 7PQ  C12  C11  single    1.523  0.020  1.523
 7PQ  C27  C20  aromatic  1.414  0.020  1.414
 7PQ  C4   C5   aromatic  1.386  0.020  1.386
 7PQ  C4   C3   aromatic  1.393  0.020  1.393
 7PQ  C5   C6   aromatic  1.392  0.020  1.392
 7PQ  N10  C11  single    1.447  0.020  1.447
 7PQ  N10  C8   single    1.342  0.020  1.342
 7PQ  C19  C20  aromatic  1.419  0.020  1.419
 7PQ  C19  C7   aromatic  1.427  0.020  1.427
 7PQ  C20  C21  aromatic  1.415  0.020  1.415
 7PQ  C8   C3   single    1.495  0.020  1.495
 7PQ  C8   O9   double    1.224  0.020  1.224
 7PQ  C3   C2   aromatic  1.392  0.020  1.392
 7PQ  C6   C7   single    1.486  0.020  1.486
 7PQ  C6   C1   aromatic  1.393  0.020  1.393
 7PQ  C7   C23  aromatic  1.376  0.020  1.376
 7PQ  C21  C22  aromatic  1.363  0.020  1.363
 7PQ  C2   C1   aromatic  1.385  0.020  1.385
 7PQ  C23  C22  aromatic  1.416  0.020  1.416
 7PQ  C23  C28  single    1.506  0.020  1.506
 7PQ  C28  N29  single    1.458  0.020  1.458
 7PQ  C1   H1   single    0.930  0.020  1.080
 7PQ  C2   H2   single    0.930  0.020  1.080
 7PQ  C4   H3   single    0.930  0.020  1.080
 7PQ  C5   H4   single    0.930  0.020  1.080
 7PQ  N10  H5   single    0.860  0.020  1.020
 7PQ  C11  H6   single    0.970  0.020  1.090
 7PQ  C11  H7   single    0.970  0.020  1.090
 7PQ  C12  H8   single    0.970  0.020  1.090
 7PQ  C12  H9   single    0.970  0.020  1.090
 7PQ  C14  H11  single    0.970  0.020  1.090
 7PQ  C14  H12  single    0.970  0.020  1.090
 7PQ  C15  H13  single    0.970  0.020  1.090
 7PQ  C15  H14  single    0.970  0.020  1.090
 7PQ  C17  H15  single    0.970  0.020  1.090
 7PQ  C17  H16  single    0.970  0.020  1.090
 7PQ  C18  H17  single    0.970  0.020  1.090
 7PQ  C18  H18  single    0.970  0.020  1.090
 7PQ  C21  H19  single    0.930  0.020  1.080
 7PQ  C22  H20  single    0.930  0.020  1.080
 7PQ  C24  H21  single    0.930  0.020  1.080
 7PQ  C25  H22  single    0.930  0.020  1.080
 7PQ  C26  H23  single    0.930  0.020  1.080
 7PQ  C27  H24  single    0.930  0.020  1.080
 7PQ  C28  H25  single    0.970  0.020  1.090
 7PQ  C28  H26  single    0.970  0.020  1.090
 7PQ  N29  H27  single    0.890  0.020  1.040
 7PQ  N29  H28  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
 7PQ  H1   C1   C6   119.67  3.000
 7PQ  H1   C1   C2   119.64  3.000
 7PQ  C6   C1   C2   120.69  3.000
 7PQ  H2   C2   C3   119.92  3.000
 7PQ  H2   C2   C1   119.65  3.000
 7PQ  C3   C2   C1   120.43  3.000
 7PQ  C8   C3   C4   122.67  3.000
 7PQ  C8   C3   C2   118.30  3.000
 7PQ  C4   C3   C2   119.00  3.000
 7PQ  H3   C4   C5   118.69  3.000
 7PQ  H3   C4   C3   120.86  3.000
 7PQ  C5   C4   C3   120.44  3.000
 7PQ  H4   C5   C6   119.76  3.000
 7PQ  H4   C5   C4   119.62  3.000
 7PQ  C6   C5   C4   120.62  3.000
 7PQ  C7   C6   C5   120.98  3.000
 7PQ  C7   C6   C1   120.21  3.000
 7PQ  C5   C6   C1   118.80  3.000
 7PQ  C23  C7   C19  120.41  3.000
 7PQ  C23  C7   C6   120.52  3.000
 7PQ  C19  C7   C6   119.06  3.000
 7PQ  N10  C8   O9   122.65  3.000
 7PQ  O9   C8   C3   121.11  3.000
 7PQ  N10  C8   C3   116.24  3.000
 7PQ  H5   N10  C11  117.75  3.000
 7PQ  H5   N10  C8   119.10  3.000
 7PQ  C11  N10  C8   122.25  3.000
 7PQ  H7   C11  H6   107.08  3.000
 7PQ  H7   C11  C12  111.12  3.000
 7PQ  H6   C11  C12  109.03  3.000
 7PQ  H7   C11  N10  110.17  3.000
 7PQ  H6   C11  N10  109.53  3.000
 7PQ  C12  C11  N10  109.86  3.000
 7PQ  H9   C12  H8   106.53  3.000
 7PQ  H9   C12  N13  108.39  3.000
 7PQ  H8   C12  N13  112.01  3.000
 7PQ  H9   C12  C11  108.28  3.000
 7PQ  H8   C12  C11  110.06  3.000
 7PQ  N13  C12  C11  111.37  3.000
 7PQ  C18  N13  C14  109.28  3.000
 7PQ  C14  N13  C12  112.62  3.000
 7PQ  C18  N13  C12  113.15  3.000
 7PQ  H12  C14  H11  107.29  3.000
 7PQ  H12  C14  C15  108.78  3.000
 7PQ  H11  C14  C15  109.66  3.000
 7PQ  H12  C14  N13  109.52  3.000
 7PQ  H11  C14  N13  111.84  3.000
 7PQ  C15  C14  N13  109.67  3.000
 7PQ  H14  C15  H13  108.02  3.000
 7PQ  H14  C15  O16  110.41  3.000
 7PQ  H13  C15  O16  107.44  3.000
 7PQ  H14  C15  C14  108.97  3.000
 7PQ  H13  C15  C14  110.24  3.000
 7PQ  O16  C15  C14  111.68  3.000
 7PQ  C17  O16  C15  110.85  3.000
 7PQ  H16  C17  H15  108.01  3.000
 7PQ  H16  C17  C18  109.16  3.000
 7PQ  H15  C17  C18  110.14  3.000
 7PQ  H16  C17  O16  110.45  3.000
 7PQ  H15  C17  O16  107.44  3.000
 7PQ  C18  C17  O16  111.56  3.000
 7PQ  H18  C18  H17  107.10  3.000
 7PQ  H18  C18  C17  109.53  3.000
 7PQ  H17  C18  C17  108.45  3.000
 7PQ  H18  C18  N13  111.43  3.000
 7PQ  H17  C18  N13  110.44  3.000
 7PQ  C17  C18  N13  109.81  3.000
 7PQ  C24  C19  C20  118.36  3.000
 7PQ  C20  C19  C7   119.27  3.000
 7PQ  C24  C19  C7   122.37  3.000
 7PQ  C27  C20  C21  121.50  3.000
 7PQ  C21  C20  C19  119.03  3.000
 7PQ  C27  C20  C19  119.46  3.000
 7PQ  H19  C21  C22  120.50  3.000
 7PQ  H19  C21  C20  119.08  3.000
 7PQ  C22  C21  C20  120.42  3.000
 7PQ  H20  C22  C23  118.61  3.000
 7PQ  H20  C22  C21  119.96  3.000
 7PQ  C23  C22  C21  121.43  3.000
 7PQ  C28  C23  C22  118.07  3.000
 7PQ  C28  C23  C7   122.45  3.000
 7PQ  C22  C23  C7   119.44  3.000
 7PQ  H21  C24  C25  119.46  3.000
 7PQ  H21  C24  C19  119.62  3.000
 7PQ  C25  C24  C19  120.92  3.000
 7PQ  H22  C25  C26  119.65  3.000
 7PQ  H22  C25  C24  119.82  3.000
 7PQ  C26  C25  C24  120.53  3.000
 7PQ  H23  C26  C27  120.27  3.000
 7PQ  H23  C26  C25  119.80  3.000
 7PQ  C27  C26  C25  119.93  3.000
 7PQ  H24  C27  C26  120.39  3.000
 7PQ  H24  C27  C20  118.81  3.000
 7PQ  C26  C27  C20  120.80  3.000
 7PQ  H26  C28  H25  106.32  3.000
 7PQ  H26  C28  N29  113.83  3.000
 7PQ  H25  C28  N29  107.80  3.000
 7PQ  H26  C28  C23  110.29  3.000
 7PQ  H25  C28  C23  108.55  3.000
 7PQ  N29  C28  C23  109.85  3.000
 7PQ  H28  N29  H27  105.62  3.000
 7PQ  H28  N29  C28  109.14  3.000
 7PQ  H27  N29  C28  108.94  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
 7PQ  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 7PQ  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 7PQ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 7PQ  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 7PQ  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 7PQ  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 7PQ  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 7PQ  CONST_10  C7   C6   C5   C4    180.00   0.0  0
 7PQ  CONST_13  C24  C19  C7   C6      0.00   0.0  0
 7PQ  CONST_14  C20  C19  C7   C6    180.00   0.0  0
 7PQ  CONST_15  C22  C23  C7   C6    180.00   0.0  0
 7PQ  CONST_16  C25  C24  C19  C7    180.00   0.0  0
 7PQ  CONST_17  C27  C20  C19  C7    180.00   0.0  0
 7PQ  CONST_18  C21  C20  C19  C7      0.00   0.0  0
 7PQ  CONST_19  C21  C22  C23  C7      0.00   0.0  0
 7PQ  CONST_20  C26  C25  C24  C19     0.00   0.0  0
 7PQ  CONST_21  C26  C27  C20  C19     0.00   0.0  0
 7PQ  CONST_22  C22  C21  C20  C19     0.00   0.0  0
 7PQ  CONST_23  C22  C23  C7   C19     0.00   0.0  0
 7PQ  CONST_24  C25  C26  C27  C20     0.00   0.0  0
 7PQ  CONST_25  C25  C24  C19  C20     0.00   0.0  0
 7PQ  CONST_26  C23  C7   C19  C20     0.00   0.0  0
 7PQ  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 7PQ  CONST_28  C26  C27  C20  C21   180.00   0.0  0
 7PQ  CONST_29  C24  C19  C20  C21   180.00   0.0  0
 7PQ  CONST_30  C27  C20  C21  C22   180.00   0.0  0
 7PQ  CONST_31  C24  C19  C7   C23   180.00   0.0  0
 7PQ  CONST_32  C27  C26  C25  C24     0.00   0.0  0
 7PQ  CONST_33  C27  C20  C19  C24     0.00   0.0  0
 7PQ  CONST_34  C8   C3   C2   C1    180.00   0.0  0
 7PQ  CONST_35  C8   C3   C4   C5    180.00   0.0  0
 7PQ  CONST_36  C28  C23  C7   C6      0.00   0.0  0
 7PQ  CONST_37  C28  C23  C7   C19   180.00   0.0  0
 7PQ  CONST_38  C28  C23  C22  C21   180.00   0.0  0
 7PQ  CONST_39  H4   C5   C6   C1    180.00   0.0  0
 7PQ  CONST_40  H3   C4   C3   C2    180.00   0.0  0
 7PQ  CONST_41  H1   C1   C2   C3    180.00   0.0  0
 7PQ  CONST_42  H2   C2   C3   C4    180.00   0.0  0
 7PQ  CONST_43  H21  C24  C19  C7      0.00   0.0  0
 7PQ  CONST_44  H20  C22  C23  C7    180.00   0.0  0
 7PQ  CONST_45  H22  C25  C24  C19   180.00   0.0  0
 7PQ  CONST_46  H24  C27  C20  C19   180.00   0.0  0
 7PQ  CONST_47  H19  C21  C20  C19   180.00   0.0  0
 7PQ  CONST_48  H23  C26  C27  C20   180.00   0.0  0
 7PQ  CONST_49  C11  N10  C8   C3    180.00   0.0  0
 7PQ  CONST_50  H5   N10  C8   C3      0.00   0.0  0
 7PQ  CONST_51  C11  N10  C8   O9      0.00   0.0  0
 7PQ  Var_01    O16  C17  C18  N13   -57.70  30.0  1
 7PQ  Var_02    O16  C15  C14  N13    57.69  30.0  1
 7PQ  Var_03    C17  C18  N13  C14    57.81  30.0  1
 7PQ  Var_04    C18  C17  O16  C15    56.84  30.0  1
 7PQ  Var_05    C18  N13  C14  C15   -57.72  30.0  1
 7PQ  Var_06    N10  C8   C3   C2    152.97  30.0  2
 7PQ  Var_07    N29  C28  C23  C7    101.97  30.0  2
 7PQ  Var_08    N13  C12  C11  N10   179.10  30.0  1
 7PQ  Var_09    H27  N29  C28  C23   177.17  30.0  3
 7PQ  Var_10    C12  C11  N10  C8   -168.32  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
 7PQ  plan-1  C1   0.020
 7PQ  plan-1  C2   0.020
 7PQ  plan-1  C3   0.020
 7PQ  plan-1  C4   0.020
 7PQ  plan-1  C5   0.020
 7PQ  plan-1  C6   0.020
 7PQ  plan-1  C7   0.020
 7PQ  plan-1  C8   0.020
 7PQ  plan-1  H1   0.020
 7PQ  plan-1  H2   0.020
 7PQ  plan-1  H3   0.020
 7PQ  plan-1  H4   0.020
 7PQ  plan-2  C6   0.020
 7PQ  plan-2  C7   0.020
 7PQ  plan-2  C19  0.020
 7PQ  plan-2  C20  0.020
 7PQ  plan-2  C21  0.020
 7PQ  plan-2  C22  0.020
 7PQ  plan-2  C23  0.020
 7PQ  plan-2  C24  0.020
 7PQ  plan-2  C25  0.020
 7PQ  plan-2  C26  0.020
 7PQ  plan-2  C27  0.020
 7PQ  plan-2  C28  0.020
 7PQ  plan-2  H19  0.020
 7PQ  plan-2  H20  0.020
 7PQ  plan-2  H21  0.020
 7PQ  plan-2  H22  0.020
 7PQ  plan-2  H23  0.020
 7PQ  plan-2  H24  0.020
 7PQ  plan-3  C3   0.020
 7PQ  plan-3  C8   0.020
 7PQ  plan-3  O9   0.020
 7PQ  plan-3  N10  0.020
 7PQ  plan-3  C11  0.020
 7PQ  plan-3  H5   0.020

