# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 04:48:55 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: N-(naphthalen-1-yl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cccc2ccccc12)c3cccnc3
#
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
 L30  L30  "N-(naphthalen-1-yl)pyridine-3-carboxamide"
  ligand  31  19  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L30
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
 L30  O18  O  O     0  -0.447  -0.9996  69.1970  40.3459
 L30  C6   C  C     0   0.519  -0.9254  69.6257  39.2095
 L30  C7   C  CR6   0  -0.145  -1.9840  70.5163  38.6493
 L30  C8   C  CR16  0  -0.150  -3.2828  70.4062  39.1364
 L30  C10  C  CR16  0  -0.316  -4.2613  71.2401  38.6275
 L30  C12  C  CR16  0  -0.053  -3.9007  72.1716  37.6638
 L30  N13  N  N     0  -0.395  -2.6611  72.3069  37.2097
 L30  C15  C  CR16  0  -0.076  -1.7304  71.4950  37.6919
 L30  N5   N  NH1   0  -0.763   0.0929  69.3306  38.3644
 L30  C4   C  CR6   0   0.308   1.1791  68.4999  38.7102
 L30  C3   C  CR16  0  -0.289   2.0271  68.8544  39.7258
 L30  C2   C  CR16  0  -0.264   3.1228  68.0373  40.0609
 L30  C1   C  CR16  0  -0.316   3.3700  66.8892  39.3614
 L30  C22  C  CR66  0   0.096   2.5162  66.4959  38.3058
 L30  C24  C  CR16  0  -0.308   2.7499  65.3077  37.5744
 L30  C26  C  CR16  0  -0.254   1.9029  64.9227  36.5726
 L30  C28  C  CR16  0  -0.248   0.7753  65.7089  36.2616
 L30  C20  C  CR16  0  -0.309   0.5230  66.8660  36.9476
 L30  C21  C  CR66  0   0.083   1.3902  67.2980  37.9793
 L30  H1   H  HCR6  0   0.279  -3.5231  69.6715  39.8935
 L30  H2   H  HCR6  0   0.278  -5.2848  71.1757  38.9695
 L30  H3   H  HCR6  0   0.273  -4.6451  72.8398  37.2454
 L30  H4   H  HCR6  0   0.269  -0.7264  71.6541  37.3115
 L30  H5   H  HNH1  0   0.416   0.0032  69.5894  37.3935
 L30  H6   H  HCR6  0   0.267   1.8649  69.7782  40.2649
 L30  H7   H  HCR6  0   0.261   3.7770  68.3369  40.8688
 L30  H8   H  HCR6  0   0.258   4.2213  66.2670  39.6093
 L30  H9   H  HCR6  0   0.258   3.6126  64.7029  37.8265
 L30  H10  H  HCR6  0   0.259   2.0911  64.0115  36.0201
 L30  H11  H  HCR6  0   0.260   0.1011  65.3906  35.4773
 L30  H12  H  HCR6  0   0.248  -0.3561  67.4460  36.6992

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
 L30  C28  C26  aromatic  1.409  0.020  1.409
 L30  C28  C20  aromatic  1.369  0.020  1.369
 L30  C26  C24  aromatic  1.367  0.020  1.367
 L30  C20  C21  aromatic  1.415  0.020  1.415
 L30  C24  C22  aromatic  1.415  0.020  1.415
 L30  C12  N13  aromatic  1.327  0.020  1.327
 L30  C12  C10  aromatic  1.388  0.020  1.388
 L30  N13  C15  aromatic  1.326  0.020  1.326
 L30  C21  C22  aromatic  1.421  0.020  1.421
 L30  C21  C4   aromatic  1.423  0.020  1.423
 L30  C10  C8   aromatic  1.383  0.020  1.383
 L30  C15  C7   aromatic  1.392  0.020  1.392
 L30  C22  C1   aromatic  1.414  0.020  1.414
 L30  N5   C4   single    1.410  0.020  1.410
 L30  N5   C6   single    1.356  0.020  1.356
 L30  C8   C7   aromatic  1.392  0.020  1.392
 L30  C7   C6   single    1.493  0.020  1.493
 L30  C4   C3   aromatic  1.370  0.020  1.370
 L30  C6   O18  double    1.217  0.020  1.217
 L30  C1   C2   aromatic  1.367  0.020  1.367
 L30  C3   C2   aromatic  1.407  0.020  1.407
 L30  C8   H1   single    0.930  0.020  1.080
 L30  C10  H2   single    0.930  0.020  1.080
 L30  C12  H3   single    0.930  0.020  1.080
 L30  C15  H4   single    0.930  0.020  1.080
 L30  N5   H5   single    0.860  0.020  1.020
 L30  C3   H6   single    0.930  0.020  1.080
 L30  C2   H7   single    0.930  0.020  1.080
 L30  C1   H8   single    0.930  0.020  1.080
 L30  C24  H9   single    0.930  0.020  1.080
 L30  C26  H10  single    0.930  0.020  1.080
 L30  C28  H11  single    0.930  0.020  1.080
 L30  C20  H12  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
 L30  N5   C6   C7   115.38  3.000
 L30  C7   C6   O18  121.17  3.000
 L30  N5   C6   O18  123.45  3.000
 L30  C15  C7   C8   117.80  3.000
 L30  C8   C7   C6   118.91  3.000
 L30  C15  C7   C6   123.25  3.000
 L30  H1   C8   C10  120.65  3.000
 L30  H1   C8   C7   120.40  3.000
 L30  C10  C8   C7   118.95  3.000
 L30  H2   C10  C12  120.37  3.000
 L30  H2   C10  C8   121.18  3.000
 L30  C12  C10  C8   118.45  3.000
 L30  H3   C12  N13  116.51  3.000
 L30  H3   C12  C10  120.21  3.000
 L30  N13  C12  C10  123.28  3.000
 L30  C15  N13  C12  117.95  3.000
 L30  H4   C15  N13  115.59  3.000
 L30  H4   C15  C7   120.84  3.000
 L30  N13  C15  C7   123.55  3.000
 L30  H5   N5   C4   117.10  3.000
 L30  H5   N5   C6   118.51  3.000
 L30  C4   N5   C6   123.62  3.000
 L30  C21  C4   C3   120.51  3.000
 L30  C3   C4   N5   120.41  3.000
 L30  C21  C4   N5   119.07  3.000
 L30  H6   C3   C2   119.59  3.000
 L30  H6   C3   C4   119.84  3.000
 L30  C2   C3   C4   120.55  3.000
 L30  H7   C2   C1   120.36  3.000
 L30  H7   C2   C3   119.20  3.000
 L30  C1   C2   C3   120.44  3.000
 L30  H8   C1   C22  119.06  3.000
 L30  H8   C1   C2   120.50  3.000
 L30  C22  C1   C2   120.44  3.000
 L30  C21  C22  C24  119.10  3.000
 L30  C21  C22  C1   119.56  3.000
 L30  C24  C22  C1   121.34  3.000
 L30  H9   C24  C26  120.44  3.000
 L30  H9   C24  C22  118.70  3.000
 L30  C26  C24  C22  120.86  3.000
 L30  H10  C26  C28  119.75  3.000
 L30  H10  C26  C24  120.23  3.000
 L30  C28  C26  C24  120.02  3.000
 L30  H11  C28  C20  119.81  3.000
 L30  H11  C28  C26  119.63  3.000
 L30  C20  C28  C26  120.56  3.000
 L30  H12  C20  C21  120.10  3.000
 L30  H12  C20  C28  119.20  3.000
 L30  C21  C20  C28  120.70  3.000
 L30  C20  C21  C22  118.74  3.000
 L30  C22  C21  C4   118.47  3.000
 L30  C20  C21  C4   122.79  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
 L30  CONST_01  C12  N13  C15  C7     0.00   0.0  0
 L30  CONST_02  C12  C10  C8   C7     0.00   0.0  0
 L30  CONST_03  N13  C12  C10  C8     0.00   0.0  0
 L30  CONST_04  N13  C15  C7   C8     0.00   0.0  0
 L30  CONST_05  C15  N13  C12  C10    0.00   0.0  0
 L30  CONST_06  C15  C7   C8   C10    0.00   0.0  0
 L30  CONST_07  C28  C20  C21  C4   180.00   0.0  0
 L30  CONST_08  C24  C22  C21  C4   180.00   0.0  0
 L30  CONST_09  C1   C22  C21  C4     0.00   0.0  0
 L30  CONST_10  C1   C2   C3   C4     0.00   0.0  0
 L30  CONST_11  C20  C21  C4   C3   180.00   0.0  0
 L30  CONST_12  C22  C21  C4   C3     0.00   0.0  0
 L30  CONST_13  C22  C1   C2   C3     0.00   0.0  0
 L30  CONST_14  C24  C22  C1   C2   180.00   0.0  0
 L30  CONST_15  C21  C22  C1   C2     0.00   0.0  0
 L30  CONST_16  C21  C4   C3   C2     0.00   0.0  0
 L30  CONST_17  C26  C24  C22  C1   180.00   0.0  0
 L30  CONST_18  C20  C21  C22  C1   180.00   0.0  0
 L30  CONST_19  C28  C26  C24  C22    0.00   0.0  0
 L30  CONST_20  C28  C20  C21  C22    0.00   0.0  0
 L30  CONST_21  C20  C28  C26  C24    0.00   0.0  0
 L30  CONST_22  C20  C21  C22  C24    0.00   0.0  0
 L30  CONST_23  C21  C20  C28  C26    0.00   0.0  0
 L30  CONST_24  C21  C22  C24  C26    0.00   0.0  0
 L30  CONST_25  N13  C15  C7   C6   180.00   0.0  0
 L30  CONST_26  C10  C8   C7   C6   180.00   0.0  0
 L30  CONST_27  C20  C21  C4   N5     0.00   0.0  0
 L30  CONST_28  C22  C21  C4   N5   180.00   0.0  0
 L30  CONST_29  C2   C3   C4   N5   180.00   0.0  0
 L30  CONST_30  H2   C10  C8   C7   180.00   0.0  0
 L30  CONST_31  H3   C12  C10  C8   180.00   0.0  0
 L30  CONST_32  H4   C15  C7   C8   180.00   0.0  0
 L30  CONST_33  H4   C15  N13  C12  180.00   0.0  0
 L30  CONST_34  H1   C8   C10  C12  180.00   0.0  0
 L30  CONST_35  H2   C10  C12  N13  180.00   0.0  0
 L30  CONST_36  H3   C12  N13  C15  180.00   0.0  0
 L30  CONST_37  H1   C8   C7   C15  180.00   0.0  0
 L30  CONST_38  H12  C20  C21  C4     0.00   0.0  0
 L30  CONST_39  H7   C2   C3   C4   180.00   0.0  0
 L30  CONST_40  H8   C1   C2   C3   180.00   0.0  0
 L30  CONST_41  H9   C24  C22  C1     0.00   0.0  0
 L30  CONST_42  H6   C3   C2   C1   180.00   0.0  0
 L30  CONST_43  H10  C26  C24  C22  180.00   0.0  0
 L30  CONST_44  H12  C20  C21  C22  180.00   0.0  0
 L30  CONST_45  H7   C2   C1   C22  180.00   0.0  0
 L30  CONST_46  H11  C28  C26  C24  180.00   0.0  0
 L30  CONST_47  H8   C1   C22  C24    0.00   0.0  0
 L30  CONST_48  H12  C20  C28  C26  180.00   0.0  0
 L30  CONST_49  H9   C24  C26  C28  180.00   0.0  0
 L30  CONST_50  H10  C26  C28  C20  180.00   0.0  0
 L30  CONST_51  H11  C28  C20  C21  180.00   0.0  0
 L30  CONST_52  H9   C24  C22  C21  180.00   0.0  0
 L30  CONST_53  H8   C1   C22  C21  180.00   0.0  0
 L30  CONST_54  H6   C3   C4   C21  180.00   0.0  0
 L30  CONST_55  C4   N5   C6   C7   180.00   0.0  0
 L30  CONST_60  C4   N5   C6   O18    0.00   0.0  0
 L30  CONST_61  H5   N5   C6   C7     0.00   0.0  0
 L30  CONST_62  H5   N5   C6   O18  180.00   0.0  0
 L30  Var_01    C15  C7   C6   O18  149.59  30.0  2
 L30  Var_02    C8   C7   C6   O18  -27.92  30.0  2
 L30  Var_03    N5   C6   C7   C8   151.46  30.0  2
 L30  Var_04    N5   C6   C7   C15  -31.03  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
 L30  plan-1  C6   0.020
 L30  plan-1  C7   0.020
 L30  plan-1  C8   0.020
 L30  plan-1  C10  0.020
 L30  plan-1  C12  0.020
 L30  plan-1  N13  0.020
 L30  plan-1  C15  0.020
 L30  plan-1  H1   0.020
 L30  plan-1  H2   0.020
 L30  plan-1  H3   0.020
 L30  plan-1  H4   0.020
 L30  plan-2  N5   0.020
 L30  plan-2  C4   0.020
 L30  plan-2  C3   0.020
 L30  plan-2  C2   0.020
 L30  plan-2  C1   0.020
 L30  plan-2  C22  0.020
 L30  plan-2  C24  0.020
 L30  plan-2  C26  0.020
 L30  plan-2  C28  0.020
 L30  plan-2  C20  0.020
 L30  plan-2  C21  0.020
 L30  plan-2  H6   0.020
 L30  plan-2  H7   0.020
 L30  plan-2  H8   0.020
 L30  plan-2  H9   0.020
 L30  plan-2  H10  0.020
 L30  plan-2  H11  0.020
 L30  plan-2  H12  0.020
 L30  plan-3  O18  0.020
 L30  plan-3  C6   0.020
 L30  plan-3  C7   0.020
 L30  plan-3  N5   0.020
 L30  plan-3  C4   0.020
 L30  plan-3  H5   0.020

