# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 02:21:34 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-amino-N-(naphthalen-1-yl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cncc(c1)C(=O)Nc2cccc3ccccc23
#
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
 9EI  9EI  "5-amino-N-(naphthalen-1-yl)pyridine-3-carboxamide"
  ligand  33  20  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9EI
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
 9EI  C4   C  CR6   0   0.292   0.2158  69.4197  37.5870
 9EI  C6   C  C     0   0.498  -1.4317  70.8259  38.6880
 9EI  C7   C  CR6   0  -0.117  -2.3040  72.0263  38.5324
 9EI  C8   C  CR16  0  -0.265  -1.9263  73.1294  37.7799
 9EI  C10  C  CR6   0   0.267  -2.7813  74.2302  37.6957
 9EI  C1   C  CR16  0  -0.314   1.9323  67.2174  37.4745
 9EI  C2   C  CR16  0  -0.263   0.7667  67.2193  36.7611
 9EI  C3   C  CR16  0  -0.300  -0.1010  68.3265  36.8258
 9EI  C12  C  CR16  0  -0.138  -3.9931  74.1396  38.3967
 9EI  O18  O  O     0  -0.446  -1.4213  70.1693  39.7135
 9EI  N30  N  NH2   0  -0.858  -2.4799  75.3274  36.9347
 9EI  N13  N  N     0  -0.381  -4.3503  73.0894  39.1153
 9EI  C15  C  CR16  0  -0.104  -3.5282  72.0533  39.1938
 9EI  N5   N  NH1   0  -0.755  -0.6624  70.5284  37.6127
 9EI  C22  C  CR66  0   0.094   2.2922  68.3325  38.2666
 9EI  C21  C  CR66  0   0.114   1.4339  69.4630  38.3182
 9EI  C24  C  CR16  0  -0.310   3.5035  68.3523  38.9979
 9EI  C26  C  CR16  0  -0.254   3.8565  69.4467  39.7377
 9EI  C28  C  CR16  0  -0.251   3.0152  70.5776  39.7690
 9EI  C20  C  CR16  0  -0.312   1.8339  70.5871  39.0782
 9EI  H1   H  HCR6  0   0.278  -0.9660  73.1630  37.2772
 9EI  H2   H  HCR6  0   0.258   2.5988  66.3642  37.4370
 9EI  H3   H  HCR6  0   0.261   0.4959  66.3682  36.1506
 9EI  H4   H  HCR6  0   0.267  -1.0317  68.3146  36.2727
 9EI  H5   H  HCR6  0   0.265  -4.6900  74.9724  38.3645
 9EI  H6   H  HNH2  0   0.387  -2.9585  76.1833  37.1654
 9EI  H7   H  HNH2  0   0.388  -1.5077  75.4726  36.7149
 9EI  H8   H  HCR6  0   0.259  -3.8531  71.2103  39.7916
 9EI  H9   H  HNH1  0   0.415  -0.8623  70.9799  36.7328
 9EI  H10  H  HCR6  0   0.257   4.1493  67.4834  38.9575
 9EI  H11  H  HCR6  0   0.258   4.7853  69.4524  40.2930
 9EI  H12  H  HCR6  0   0.258   3.3096  71.4467  40.3428
 9EI  H13  H  HCR6  0   0.251   1.2125  71.4720  39.0993

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
 9EI  C3   C2   aromatic  1.408  0.020  1.408
 9EI  C3   C4   aromatic  1.369  0.020  1.369
 9EI  C2   C1   aromatic  1.367  0.020  1.367
 9EI  N30  C10  single    1.369  0.020  1.369
 9EI  C4   N5   single    1.415  0.020  1.415
 9EI  C4   C21  aromatic  1.421  0.020  1.421
 9EI  N5   C6   single    1.355  0.020  1.355
 9EI  C1   C22  aromatic  1.414  0.020  1.414
 9EI  C10  C8   aromatic  1.396  0.020  1.396
 9EI  C10  C12  aromatic  1.403  0.020  1.403
 9EI  C8   C7   aromatic  1.388  0.020  1.388
 9EI  C22  C21  aromatic  1.420  0.020  1.420
 9EI  C22  C24  aromatic  1.415  0.020  1.415
 9EI  C12  N13  aromatic  1.322  0.020  1.322
 9EI  C21  C20  aromatic  1.415  0.020  1.415
 9EI  C7   C6   single    1.492  0.020  1.492
 9EI  C7   C15  aromatic  1.392  0.020  1.392
 9EI  C6   O18  double    1.218  0.020  1.218
 9EI  C24  C26  aromatic  1.367  0.020  1.367
 9EI  C20  C28  aromatic  1.368  0.020  1.368
 9EI  N13  C15  aromatic  1.325  0.020  1.325
 9EI  C26  C28  aromatic  1.410  0.020  1.410
 9EI  C8   H1   single    0.930  0.020  1.080
 9EI  C1   H2   single    0.930  0.020  1.080
 9EI  C2   H3   single    0.930  0.020  1.080
 9EI  C3   H4   single    0.930  0.020  1.080
 9EI  C12  H5   single    0.930  0.020  1.080
 9EI  N30  H6   single    0.890  0.020  1.040
 9EI  N30  H7   single    0.890  0.020  1.040
 9EI  C15  H8   single    0.930  0.020  1.080
 9EI  N5   H9   single    0.860  0.020  1.020
 9EI  C24  H10  single    0.930  0.020  1.080
 9EI  C26  H11  single    0.930  0.020  1.080
 9EI  C28  H12  single    0.930  0.020  1.080
 9EI  C20  H13  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
 9EI  C21  C4   N5   119.92  3.000
 9EI  C21  C4   C3   120.57  3.000
 9EI  N5   C4   C3   119.49  3.000
 9EI  N5   C6   O18  123.02  3.000
 9EI  O18  C6   C7   121.78  3.000
 9EI  N5   C6   C7   115.20  3.000
 9EI  C15  C7   C8   118.80  3.000
 9EI  C15  C7   C6   118.71  3.000
 9EI  C8   C7   C6   122.47  3.000
 9EI  H1   C8   C10  119.33  3.000
 9EI  H1   C8   C7   121.14  3.000
 9EI  C10  C8   C7   119.52  3.000
 9EI  N30  C10  C12  121.31  3.000
 9EI  C12  C10  C8   116.61  3.000
 9EI  N30  C10  C8   122.04  3.000
 9EI  H2   C1   C22  118.94  3.000
 9EI  H2   C1   C2   120.51  3.000
 9EI  C22  C1   C2   120.55  3.000
 9EI  H3   C2   C3   119.35  3.000
 9EI  H3   C2   C1   120.47  3.000
 9EI  C3   C2   C1   120.18  3.000
 9EI  H4   C3   C2   119.84  3.000
 9EI  H4   C3   C4   119.45  3.000
 9EI  C2   C3   C4   120.71  3.000
 9EI  H5   C12  N13  116.86  3.000
 9EI  H5   C12  C10  119.33  3.000
 9EI  N13  C12  C10  123.81  3.000
 9EI  H7   N30  H6   112.71  3.000
 9EI  H7   N30  C10  116.71  3.000
 9EI  H6   N30  C10  116.69  3.000
 9EI  C15  N13  C12  119.07  3.000
 9EI  H8   C15  N13  117.07  3.000
 9EI  H8   C15  C7   120.73  3.000
 9EI  N13  C15  C7   122.19  3.000
 9EI  H9   N5   C6   118.76  3.000
 9EI  H9   N5   C4   117.25  3.000
 9EI  C6   N5   C4   122.61  3.000
 9EI  C24  C22  C21  119.17  3.000
 9EI  C24  C22  C1   121.22  3.000
 9EI  C21  C22  C1   119.61  3.000
 9EI  C20  C21  C22  118.76  3.000
 9EI  C20  C21  C4   122.88  3.000
 9EI  C22  C21  C4   118.35  3.000
 9EI  H10  C24  C26  120.55  3.000
 9EI  H10  C24  C22  118.67  3.000
 9EI  C26  C24  C22  120.78  3.000
 9EI  H11  C26  C28  119.77  3.000
 9EI  H11  C26  C24  120.23  3.000
 9EI  C28  C26  C24  120.00  3.000
 9EI  H12  C28  C20  119.80  3.000
 9EI  H12  C28  C26  119.58  3.000
 9EI  C20  C28  C26  120.63  3.000
 9EI  H13  C20  C28  119.46  3.000
 9EI  H13  C20  C21  119.88  3.000
 9EI  C28  C20  C21  120.65  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
 9EI  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 9EI  CONST_02  C1   C22  C21  C4     0.00   0.0  0
 9EI  CONST_03  C24  C22  C21  C4   180.00   0.0  0
 9EI  CONST_04  C28  C20  C21  C4   180.00   0.0  0
 9EI  CONST_05  C12  C10  C8   C7     0.00   0.0  0
 9EI  CONST_06  C12  N13  C15  C7     0.00   0.0  0
 9EI  CONST_07  N13  C12  C10  C8     0.00   0.0  0
 9EI  CONST_08  N13  C15  C7   C8     0.00   0.0  0
 9EI  CONST_09  C15  C7   C8   C10    0.00   0.0  0
 9EI  CONST_10  C15  N13  C12  C10    0.00   0.0  0
 9EI  CONST_11  C20  C21  C22  C1   180.00   0.0  0
 9EI  CONST_12  C26  C24  C22  C1   180.00   0.0  0
 9EI  CONST_13  C21  C4   C3   C2     0.00   0.0  0
 9EI  CONST_14  C21  C22  C1   C2     0.00   0.0  0
 9EI  CONST_15  C24  C22  C1   C2   180.00   0.0  0
 9EI  CONST_16  C22  C1   C2   C3     0.00   0.0  0
 9EI  CONST_17  C22  C21  C4   C3     0.00   0.0  0
 9EI  CONST_18  C20  C21  C4   C3   180.00   0.0  0
 9EI  CONST_19  C28  C20  C21  C22    0.00   0.0  0
 9EI  CONST_20  C28  C26  C24  C22    0.00   0.0  0
 9EI  CONST_21  C26  C24  C22  C21    0.00   0.0  0
 9EI  CONST_22  C26  C28  C20  C21    0.00   0.0  0
 9EI  CONST_23  C20  C21  C22  C24    0.00   0.0  0
 9EI  CONST_24  C20  C28  C26  C24    0.00   0.0  0
 9EI  CONST_25  C10  C8   C7   C6   180.00   0.0  0
 9EI  CONST_26  N13  C15  C7   C6   180.00   0.0  0
 9EI  CONST_27  N30  C10  C8   C7   180.00   0.0  0
 9EI  CONST_28  N5   C4   C3   C2   180.00   0.0  0
 9EI  CONST_29  N13  C12  C10  N30  180.00   0.0  0
 9EI  CONST_30  C22  C21  C4   N5   180.00   0.0  0
 9EI  CONST_31  C20  C21  C4   N5     0.00   0.0  0
 9EI  CONST_32  H3   C2   C3   C4   180.00   0.0  0
 9EI  CONST_33  H13  C20  C21  C4     0.00   0.0  0
 9EI  CONST_34  H5   C12  C10  C8   180.00   0.0  0
 9EI  CONST_35  H8   C15  C7   C8   180.00   0.0  0
 9EI  CONST_36  H4   C3   C2   C1   180.00   0.0  0
 9EI  CONST_37  H10  C24  C22  C1     0.00   0.0  0
 9EI  CONST_38  H2   C1   C2   C3   180.00   0.0  0
 9EI  CONST_39  H1   C8   C10  C12  180.00   0.0  0
 9EI  CONST_40  H8   C15  N13  C12  180.00   0.0  0
 9EI  CONST_41  H1   C8   C7   C15  180.00   0.0  0
 9EI  CONST_42  H5   C12  N13  C15  180.00   0.0  0
 9EI  CONST_43  H3   C2   C1   C22  180.00   0.0  0
 9EI  CONST_44  H13  C20  C21  C22  180.00   0.0  0
 9EI  CONST_45  H11  C26  C24  C22  180.00   0.0  0
 9EI  CONST_46  H4   C3   C4   C21  180.00   0.0  0
 9EI  CONST_47  H2   C1   C22  C21  180.00   0.0  0
 9EI  CONST_48  H10  C24  C22  C21  180.00   0.0  0
 9EI  CONST_49  H12  C28  C20  C21  180.00   0.0  0
 9EI  CONST_50  H2   C1   C22  C24    0.00   0.0  0
 9EI  CONST_51  H12  C28  C26  C24  180.00   0.0  0
 9EI  CONST_52  H13  C20  C28  C26  180.00   0.0  0
 9EI  CONST_53  H10  C24  C26  C28  180.00   0.0  0
 9EI  CONST_54  H11  C26  C28  C20  180.00   0.0  0
 9EI  CONST_55  C7   C6   N5   C4   180.00   0.0  0
 9EI  CONST_64  O18  C6   N5   C4     0.00   0.0  0
 9EI  CONST_65  H9   N5   C6   C7     0.00   0.0  0
 9EI  CONST_66  H9   N5   C6   O18  180.00   0.0  0
 9EI  Var_01    N5   C6   C7   C8   -33.18  30.0  2
 9EI  Var_02    O18  C6   C7   C8   146.81  30.0  2
 9EI  Var_03    C15  C7   C6   O18  -31.57  30.0  2
 9EI  Var_04    N5   C6   C7   C15  148.44  30.0  2

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
 9EI  plan-1  C6   0.020
 9EI  plan-1  C7   0.020
 9EI  plan-1  C8   0.020
 9EI  plan-1  C10  0.020
 9EI  plan-1  C12  0.020
 9EI  plan-1  N30  0.020
 9EI  plan-1  N13  0.020
 9EI  plan-1  C15  0.020
 9EI  plan-1  H1   0.020
 9EI  plan-1  H5   0.020
 9EI  plan-1  H8   0.020
 9EI  plan-2  C4   0.020
 9EI  plan-2  C1   0.020
 9EI  plan-2  C2   0.020
 9EI  plan-2  C3   0.020
 9EI  plan-2  N5   0.020
 9EI  plan-2  C22  0.020
 9EI  plan-2  C21  0.020
 9EI  plan-2  C24  0.020
 9EI  plan-2  C26  0.020
 9EI  plan-2  C28  0.020
 9EI  plan-2  C20  0.020
 9EI  plan-2  H2   0.020
 9EI  plan-2  H3   0.020
 9EI  plan-2  H4   0.020
 9EI  plan-2  H10  0.020
 9EI  plan-2  H11  0.020
 9EI  plan-2  H12  0.020
 9EI  plan-2  H13  0.020
 9EI  plan-3  C4   0.020
 9EI  plan-3  C6   0.020
 9EI  plan-3  C7   0.020
 9EI  plan-3  O18  0.020
 9EI  plan-3  N5   0.020
 9EI  plan-3  H9   0.020
 9EI  plan-4  C10  0.020
 9EI  plan-4  N30  0.020
 9EI  plan-4  H6   0.020
 9EI  plan-4  H7   0.020

