# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 18:45:43 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc2ccccc2c1c3ccc(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
 9PQ  9PQ  4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide  ligand  55  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9PQ
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
 9PQ  O24  O  O     0  -0.490  -1.9692  -1.9743   1.7639
 9PQ  C23  C  C     0   0.526  -1.7154  -1.0458   1.0080
 9PQ  N25  N  NH1   0  -0.652  -2.6662  -0.3291   0.3878
 9PQ  C26  C  CH2   0  -0.259  -4.0793  -0.5922   0.5571
 9PQ  C27  C  CH2   0  -0.303  -4.8589   0.0966  -0.5553
 9PQ  N7   N  NT    0  -0.430  -6.2846  -0.1124  -0.4237
 9PQ  C12  C  CH2   0  -0.305  -6.9833   0.1204  -1.6759
 9PQ  C11  C  CH2   0  -0.189  -8.4608  -0.1776  -1.5102
 9PQ  O10  O  O2    0  -0.485  -9.0352   0.6030  -0.4850
 9PQ  C9   C  CH2   0  -0.185  -8.3628   0.3970   0.7371
 9PQ  C8   C  CH2   0  -0.312  -6.8810   0.7009   0.6228
 9PQ  C16  C  CR6   0  -0.042  -0.3049  -0.6469   0.7156
 9PQ  C15  C  CR16  0  -0.278   0.0796  -0.1166  -0.5133
 9PQ  C14  C  CR16  0  -0.263   1.4064   0.2074  -0.7527
 9PQ  C17  C  CR16  0  -0.257   0.6627  -0.8560   1.6949
 9PQ  C18  C  CR16  0  -0.263   1.9836  -0.5149   1.4596
 9PQ  C13  C  CR6   0  -0.034   2.3719   0.0197   0.2320
 9PQ  C19  C  CR6   0   0.054   3.7900   0.3776  -0.0233
 9PQ  C2   C  CR66  0   0.120   4.7393  -0.6545  -0.2672
 9PQ  C20  C  CR6   0  -0.012   4.1782   1.7009  -0.0233
 9PQ  C28  C  CH2   0  -0.192   3.1664   2.7910   0.2322
 9PQ  O29  O  OH1   0  -0.667   3.8233   4.0083   0.4754
 9PQ  C21  C  CR16  0  -0.297   5.5302   2.0296  -0.2712
 9PQ  C22  C  CR16  0  -0.315   6.4605   1.0558  -0.4990
 9PQ  C1   C  CR66  0   0.102   6.0960  -0.3075  -0.5009
 9PQ  C6   C  CR16  0  -0.310   7.0471  -1.3283  -0.7356
 9PQ  C5   C  CR16  0  -0.264   6.6735  -2.6434  -0.7467
 9PQ  C4   C  CR16  0  -0.252   5.3251  -2.9924  -0.5266
 9PQ  C3   C  CR16  0  -0.339   4.3838  -2.0265  -0.2948
 9PQ  H1   H  HNH1  0   0.405  -2.4058   0.5364  -0.0583
 9PQ  H2   H  HCH2  0   0.245  -4.2551  -1.6667   0.5066
 9PQ  H3   H  HCH2  0   0.237  -4.4138  -0.2545   1.5426
 9PQ  H4   H  HCH2  0   0.205  -4.6031   1.1703  -0.5835
 9PQ  H5   H  HCH2  0   0.249  -4.5356  -0.3266  -1.5096
 9PQ  H7   H  HCH2  0   0.199  -6.8544   1.1576  -2.0298
 9PQ  H8   H  HCH2  0   0.244  -6.5736  -0.5358  -2.4476
 9PQ  H9   H  HCH2  0   0.237  -8.9949   0.0509  -2.4336
 9PQ  H10  H  HCH2  0   0.201  -8.5928  -1.2482  -1.2973
 9PQ  H11  H  HCH2  0   0.237  -8.8215   1.0529   1.4785
 9PQ  H12  H  HCH2  0   0.201  -8.4931  -0.6404   1.0768
 9PQ  H13  H  HCH2  0   0.243  -6.4155   0.4811   1.5853
 9PQ  H14  H  HCH2  0   0.201  -6.7343   1.7776   0.4283
 9PQ  H15  H  HCR6  0   0.262  -0.6429   0.0213  -1.3078
 9PQ  H16  H  HCR6  0   0.263   1.6958   0.5993  -1.7198
 9PQ  H17  H  HCR6  0   0.261   0.3798  -1.2780   2.6501
 9PQ  H18  H  HCR6  0   0.260   2.7232  -0.6666   2.2357
 9PQ  H19  H  HCH2  0   0.224   2.4979   2.8675  -0.6363
 9PQ  H20  H  HCH2  0   0.218   2.5317   2.5021   1.0800
 9PQ  H21  H  HOH1  0   0.464   3.1539   4.6910   0.5753
 9PQ  H22  H  HCR6  0   0.259   5.8364   3.0659  -0.2788
 9PQ  H23  H  HCR6  0   0.254   7.4934   1.3248  -0.6852
 9PQ  H24  H  HCR6  0   0.256   8.0795  -1.0497  -0.9097
 9PQ  H25  H  HCR6  0   0.258   7.4070  -3.4182  -0.9269
 9PQ  H26  H  HCR6  0   0.258   5.0334  -4.0346  -0.5426
 9PQ  H27  H  HCR6  0   0.252   3.3544  -2.3168  -0.1321

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
 9PQ  C4   C5   aromatic  1.410  0.020  1.410
 9PQ  C4   C3   aromatic  1.369  0.020  1.369
 9PQ  C5   C6   aromatic  1.367  0.020  1.367
 9PQ  C3   C2   aromatic  1.418  0.020  1.418
 9PQ  C6   C1   aromatic  1.415  0.020  1.415
 9PQ  C15  C14  aromatic  1.387  0.020  1.387
 9PQ  C15  C16  aromatic  1.392  0.020  1.392
 9PQ  C14  C13  aromatic  1.392  0.020  1.392
 9PQ  C2   C1   aromatic  1.420  0.020  1.420
 9PQ  C2   C19  aromatic  1.423  0.020  1.423
 9PQ  O24  C23  double    1.224  0.020  1.224
 9PQ  C1   C22  aromatic  1.411  0.020  1.411
 9PQ  C23  C16  single    1.495  0.020  1.495
 9PQ  C23  N25  single    1.342  0.020  1.342
 9PQ  C16  C17  aromatic  1.392  0.020  1.392
 9PQ  C13  C19  single    1.485  0.020  1.485
 9PQ  C13  C18  aromatic  1.394  0.020  1.394
 9PQ  C19  C20  aromatic  1.379  0.020  1.379
 9PQ  N25  C26  single    1.447  0.020  1.447
 9PQ  C26  C27  single    1.523  0.020  1.523
 9PQ  C22  C21  aromatic  1.366  0.020  1.366
 9PQ  C17  C18  aromatic  1.384  0.020  1.384
 9PQ  C20  C21  aromatic  1.413  0.020  1.413
 9PQ  C20  C28  single    1.509  0.020  1.509
 9PQ  C11  C12  single    1.516  0.020  1.516
 9PQ  C11  O10  single    1.411  0.020  1.411
 9PQ  N7   C12  single    1.453  0.020  1.453
 9PQ  N7   C27  single    1.447  0.020  1.447
 9PQ  N7   C8   single    1.453  0.020  1.453
 9PQ  C28  O29  single    1.404  0.020  1.404
 9PQ  C9   O10  single    1.410  0.020  1.410
 9PQ  C9   C8   single    1.517  0.020  1.517
 9PQ  N25  H1   single    0.860  0.020  1.020
 9PQ  C26  H2   single    0.970  0.020  1.090
 9PQ  C26  H3   single    0.970  0.020  1.090
 9PQ  C27  H4   single    0.970  0.020  1.090
 9PQ  C27  H5   single    0.970  0.020  1.090
 9PQ  C12  H7   single    0.970  0.020  1.090
 9PQ  C12  H8   single    0.970  0.020  1.090
 9PQ  C11  H9   single    0.970  0.020  1.090
 9PQ  C11  H10  single    0.970  0.020  1.090
 9PQ  C9   H11  single    0.970  0.020  1.090
 9PQ  C9   H12  single    0.970  0.020  1.090
 9PQ  C8   H13  single    0.970  0.020  1.090
 9PQ  C8   H14  single    0.970  0.020  1.090
 9PQ  C15  H15  single    0.930  0.020  1.080
 9PQ  C14  H16  single    0.930  0.020  1.080
 9PQ  C17  H17  single    0.930  0.020  1.080
 9PQ  C18  H18  single    0.930  0.020  1.080
 9PQ  C28  H19  single    0.970  0.020  1.090
 9PQ  C28  H20  single    0.970  0.020  1.090
 9PQ  O29  H21  single    0.850  0.020  0.980
 9PQ  C21  H22  single    0.930  0.020  1.080
 9PQ  C22  H23  single    0.930  0.020  1.080
 9PQ  C6   H24  single    0.930  0.020  1.080
 9PQ  C5   H25  single    0.930  0.020  1.080
 9PQ  C4   H26  single    0.930  0.020  1.080
 9PQ  C3   H27  single    0.930  0.020  1.080

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
 9PQ  C16  C23  N25  115.82  3.000
 9PQ  N25  C23  O24  122.91  3.000
 9PQ  C16  C23  O24  121.27  3.000
 9PQ  H1   N25  C26  117.39  3.000
 9PQ  H1   N25  C23  118.68  3.000
 9PQ  C26  N25  C23  122.72  3.000
 9PQ  H3   C26  H2   107.26  3.000
 9PQ  H3   C26  C27  111.21  3.000
 9PQ  H2   C26  C27  109.23  3.000
 9PQ  H3   C26  N25  110.35  3.000
 9PQ  H2   C26  N25  109.35  3.000
 9PQ  C27  C26  N25  109.40  3.000
 9PQ  H5   C27  H4   106.60  3.000
 9PQ  H5   C27  N7   108.36  3.000
 9PQ  H4   C27  N7   111.78  3.000
 9PQ  H5   C27  C26  108.14  3.000
 9PQ  H4   C27  C26  109.87  3.000
 9PQ  N7   C27  C26  111.88  3.000
 9PQ  C8   N7   C12  109.49  3.000
 9PQ  C8   N7   C27  112.89  3.000
 9PQ  C12  N7   C27  111.86  3.000
 9PQ  H8   C12  H7   107.10  3.000
 9PQ  H8   C12  C11  108.94  3.000
 9PQ  H7   C12  C11  109.49  3.000
 9PQ  H8   C12  N7   109.40  3.000
 9PQ  H7   C12  N7   111.77  3.000
 9PQ  C11  C12  N7   110.06  3.000
 9PQ  H10  C11  H9   108.00  3.000
 9PQ  H10  C11  O10  110.44  3.000
 9PQ  H9   C11  O10  107.45  3.000
 9PQ  H10  C11  C12  109.24  3.000
 9PQ  H9   C11  C12  110.08  3.000
 9PQ  O10  C11  C12  111.56  3.000
 9PQ  C9   O10  C11  110.78  3.000
 9PQ  H12  C9   H11  107.90  3.000
 9PQ  H12  C9   C8   109.16  3.000
 9PQ  H11  C9   C8   109.97  3.000
 9PQ  H12  C9   O10  110.43  3.000
 9PQ  H11  C9   O10  107.50  3.000
 9PQ  C8   C9   O10  111.80  3.000
 9PQ  H14  C8   H13  107.16  3.000
 9PQ  H14  C8   C9   109.79  3.000
 9PQ  H13  C8   C9   108.05  3.000
 9PQ  H14  C8   N7   111.37  3.000
 9PQ  H13  C8   N7   110.32  3.000
 9PQ  C9   C8   N7   110.06  3.000
 9PQ  C17  C16  C15  119.08  3.000
 9PQ  C17  C16  C23  118.56  3.000
 9PQ  C15  C16  C23  122.33  3.000
 9PQ  H15  C15  C14  118.82  3.000
 9PQ  H15  C15  C16  120.78  3.000
 9PQ  C14  C15  C16  120.37  3.000
 9PQ  H16  C14  C13  119.69  3.000
 9PQ  H16  C14  C15  119.63  3.000
 9PQ  C13  C14  C15  120.67  3.000
 9PQ  H17  C17  C18  119.71  3.000
 9PQ  H17  C17  C16  119.86  3.000
 9PQ  C18  C17  C16  120.43  3.000
 9PQ  H18  C18  C13  119.64  3.000
 9PQ  H18  C18  C17  119.70  3.000
 9PQ  C13  C18  C17  120.66  3.000
 9PQ  C19  C13  C18  120.66  3.000
 9PQ  C18  C13  C14  118.79  3.000
 9PQ  C19  C13  C14  120.56  3.000
 9PQ  C20  C19  C2   120.53  3.000
 9PQ  C20  C19  C13  120.01  3.000
 9PQ  C2   C19  C13  119.45  3.000
 9PQ  C3   C2   C1   118.23  3.000
 9PQ  C1   C2   C19  119.23  3.000
 9PQ  C3   C2   C19  122.54  3.000
 9PQ  C21  C20  C28  120.20  3.000
 9PQ  C28  C20  C19  120.29  3.000
 9PQ  C21  C20  C19  119.50  3.000
 9PQ  H20  C28  H19  106.08  3.000
 9PQ  H20  C28  O29  111.40  3.000
 9PQ  H19  C28  O29  111.17  3.000
 9PQ  H20  C28  C20  109.17  3.000
 9PQ  H19  C28  C20  108.93  3.000
 9PQ  O29  C28  C20  109.99  3.000
 9PQ  H21  O29  C28  107.93  3.000
 9PQ  H22  C21  C22  119.31  3.000
 9PQ  H22  C21  C20  119.69  3.000
 9PQ  C22  C21  C20  121.00  3.000
 9PQ  H23  C22  C1   119.07  3.000
 9PQ  H23  C22  C21  120.07  3.000
 9PQ  C1   C22  C21  120.87  3.000
 9PQ  C6   C1   C22  121.58  3.000
 9PQ  C22  C1   C2   118.86  3.000
 9PQ  C6   C1   C2   119.56  3.000
 9PQ  H24  C6   C5   120.43  3.000
 9PQ  H24  C6   C1   118.80  3.000
 9PQ  C5   C6   C1   120.78  3.000
 9PQ  H25  C5   C4   119.80  3.000
 9PQ  H25  C5   C6   120.32  3.000
 9PQ  C4   C5   C6   119.88  3.000
 9PQ  H26  C4   C3   119.79  3.000
 9PQ  H26  C4   C5   119.59  3.000
 9PQ  C3   C4   C5   120.63  3.000
 9PQ  H27  C3   C4   119.38  3.000
 9PQ  H27  C3   C2   119.70  3.000
 9PQ  C4   C3   C2   120.92  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
 9PQ  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 9PQ  CONST_02  C13  C18  C17  C16     0.00   0.0  0
 9PQ  CONST_03  C19  C13  C14  C15   180.00   0.0  0
 9PQ  CONST_04  C18  C13  C14  C15     0.00   0.0  0
 9PQ  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 9PQ  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 9PQ  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 9PQ  CONST_10  C19  C13  C18  C17   180.00   0.0  0
 9PQ  CONST_13  C3   C2   C19  C13     0.00   0.0  0
 9PQ  CONST_14  C1   C2   C19  C13   180.00   0.0  0
 9PQ  CONST_15  C21  C20  C19  C13   180.00   0.0  0
 9PQ  CONST_16  C4   C3   C2   C19   180.00   0.0  0
 9PQ  CONST_17  C6   C1   C2   C19   180.00   0.0  0
 9PQ  CONST_18  C22  C1   C2   C19     0.00   0.0  0
 9PQ  CONST_19  C22  C21  C20  C19     0.00   0.0  0
 9PQ  CONST_20  C5   C4   C3   C2      0.00   0.0  0
 9PQ  CONST_21  C5   C6   C1   C2      0.00   0.0  0
 9PQ  CONST_22  C21  C22  C1   C2      0.00   0.0  0
 9PQ  CONST_23  C21  C20  C19  C2      0.00   0.0  0
 9PQ  CONST_24  C3   C2   C19  C20   180.00   0.0  0
 9PQ  CONST_25  C1   C2   C19  C20     0.00   0.0  0
 9PQ  CONST_26  C1   C22  C21  C20     0.00   0.0  0
 9PQ  CONST_27  C6   C1   C22  C21   180.00   0.0  0
 9PQ  CONST_28  C5   C6   C1   C22   180.00   0.0  0
 9PQ  CONST_29  C3   C2   C1   C22   180.00   0.0  0
 9PQ  CONST_30  C4   C5   C6   C1      0.00   0.0  0
 9PQ  CONST_31  C4   C3   C2   C1      0.00   0.0  0
 9PQ  CONST_32  C3   C4   C5   C6      0.00   0.0  0
 9PQ  CONST_33  C3   C2   C1   C6      0.00   0.0  0
 9PQ  CONST_34  C14  C15  C16  C23   180.00   0.0  0
 9PQ  CONST_35  C18  C17  C16  C23   180.00   0.0  0
 9PQ  CONST_36  C28  C20  C19  C13     0.00   0.0  0
 9PQ  CONST_37  C28  C20  C19  C2    180.00   0.0  0
 9PQ  CONST_38  C22  C21  C20  C28   180.00   0.0  0
 9PQ  CONST_39  H16  C14  C15  C16   180.00   0.0  0
 9PQ  CONST_40  H18  C18  C17  C16   180.00   0.0  0
 9PQ  CONST_41  H17  C17  C16  C15   180.00   0.0  0
 9PQ  CONST_42  H15  C15  C16  C17   180.00   0.0  0
 9PQ  CONST_43  H27  C3   C2   C19     0.00   0.0  0
 9PQ  CONST_44  H22  C21  C20  C19   180.00   0.0  0
 9PQ  CONST_45  H26  C4   C3   C2    180.00   0.0  0
 9PQ  CONST_46  H24  C6   C1   C2    180.00   0.0  0
 9PQ  CONST_47  H23  C22  C1   C2    180.00   0.0  0
 9PQ  CONST_48  H25  C5   C6   C1    180.00   0.0  0
 9PQ  CONST_49  C16  C23  N25  C26   180.00   0.0  0
 9PQ  CONST_50  H1   N25  C23  C16     0.00   0.0  0
 9PQ  CONST_51  C26  N25  C23  O24     0.00   0.0  0
 9PQ  Var_01    O10  C11  C12  N7     57.62  30.0  1
 9PQ  Var_02    O10  C9   C8   N7    -57.08  30.0  1
 9PQ  Var_03    C9   C8   N7   C12    56.62  30.0  1
 9PQ  Var_04    C8   N7   C12  C11   -56.95  30.0  1
 9PQ  Var_05    C8   C9   O10  C11    56.96  30.0  1
 9PQ  Var_06    C15  C16  C23  O24   148.16  30.0  2
 9PQ  Var_07    C12  N7   C27  C26  -160.04  30.0  2
 9PQ  Var_08    O29  C28  C20  C19   167.09  30.0  2
 9PQ  Var_09    N7   C27  C26  N25  -178.98  30.0  3
 9PQ  Var_10    C27  C26  N25  C23  -163.74  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
 9PQ  plan-1  C23  0.020
 9PQ  plan-1  C16  0.020
 9PQ  plan-1  C15  0.020
 9PQ  plan-1  C14  0.020
 9PQ  plan-1  C17  0.020
 9PQ  plan-1  C18  0.020
 9PQ  plan-1  C13  0.020
 9PQ  plan-1  C19  0.020
 9PQ  plan-1  H15  0.020
 9PQ  plan-1  H16  0.020
 9PQ  plan-1  H17  0.020
 9PQ  plan-1  H18  0.020
 9PQ  plan-2  C13  0.020
 9PQ  plan-2  C19  0.020
 9PQ  plan-2  C2   0.020
 9PQ  plan-2  C20  0.020
 9PQ  plan-2  C28  0.020
 9PQ  plan-2  C21  0.020
 9PQ  plan-2  C22  0.020
 9PQ  plan-2  C1   0.020
 9PQ  plan-2  C6   0.020
 9PQ  plan-2  C5   0.020
 9PQ  plan-2  C4   0.020
 9PQ  plan-2  C3   0.020
 9PQ  plan-2  H22  0.020
 9PQ  plan-2  H23  0.020
 9PQ  plan-2  H24  0.020
 9PQ  plan-2  H25  0.020
 9PQ  plan-2  H26  0.020
 9PQ  plan-2  H27  0.020
 9PQ  plan-3  O24  0.020
 9PQ  plan-3  C23  0.020
 9PQ  plan-3  N25  0.020
 9PQ  plan-3  C26  0.020
 9PQ  plan-3  C16  0.020
 9PQ  plan-3  H1   0.020

