# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:20:49 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 3-(naphthalen-1-ylmethoxy)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1OCc2cccc3ccccc23
#
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
 LI4  LI4  3-(naphthalen-1-ylmethoxy)pyridin-2-amine  ligand  33  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LI4
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
 LI4  C1    C  CR16  0  -0.341  -1.9842  -0.0538   4.1163
 LI4  C2    C  CR16  0  -0.286  -1.5372  -0.0444   2.7902
 LI4  C3    C  CR6   0   0.282  -0.1845  -0.0214   2.5398
 LI4  C4    C  CR6   0   0.352   0.7089   0.0052   3.6418
 LI4  C6    C  CR16  0  -0.092  -1.0441  -0.0327   5.1187
 LI4  O10   O  O2    0  -0.487   0.3992  -0.0181   1.3220
 LI4  N12   N  NH2   0  -0.829   2.0597  -0.0137   3.4298
 LI4  C13   C  CR16  0  -0.345  -1.6500   0.0538  -2.4493
 LI4  C15   C  CR66  0   0.119  -0.2397   0.0068  -2.3225
 LI4  C16   C  CR66  0   0.110   0.5408  -0.0011  -3.5090
 LI4  C17   C  CR16  0  -0.310  -0.1052   0.0393  -4.7664
 LI4  C18   C  CR16  0  -0.260  -1.4694   0.0847  -4.8546
 LI4  C19   C  CR16  0  -0.246  -2.2477   0.0910  -3.6809
 LI4  C23   C  CR6   0   0.023   0.4170  -0.0325  -1.0570
 LI4  C24   C  CR16  0  -0.341   1.7853  -0.0821  -1.0095
 LI4  C25   C  CR16  0  -0.243   2.5555  -0.0890  -2.1915
 LI4  C26   C  CR16  0  -0.325   1.9515  -0.0491  -3.4142
 LI4  N3    N  N     0  -0.445   0.2710   0.0008   4.8874
 LI4  C9    C  CH2   0  -0.219  -0.4293  -0.0239   0.1857
 LI4  H1    H  HCR6  0   0.261  -3.0412  -0.0744   4.3408
 LI4  H2    H  HCR6  0   0.291  -2.2601  -0.0594   1.9857
 LI4  H6    H  HCR6  0   0.252  -1.3443  -0.0387   6.1604
 LI4  H121  H  HNH2  0   0.383   2.6164   0.2539   4.2255
 LI4  H122  H  HNH2  0   0.393   2.4025   0.3571   2.5592
 LI4  H17   H  HCR6  0   0.257   0.5031   0.0332  -5.6631
 LI4  H18   H  HCR6  0   0.259  -1.9534   0.1162  -5.8220
 LI4  H19   H  HCR6  0   0.261  -3.3268   0.1249  -3.7537
 LI4  H24   H  HCR6  0   0.261   2.3028  -0.1185  -0.0613
 LI4  H25   H  HCR6  0   0.259   3.6342  -0.1262  -2.1164
 LI4  H26   H  HCR6  0   0.256   2.5418  -0.0550  -4.3224
 LI4  H9C1  H  HCH2  0   0.247  -1.0828  -0.9057   0.1955
 LI4  H9C2  H  HCH2  0   0.246  -1.0802   0.8595   0.1872
 LI4  H13   H  HCR6  0   0.256  -2.2794   0.0595  -1.5690

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
 LI4  C1   C2    aromatic  1.399  0.020  1.399
 LI4  C1   C6    aromatic  1.374  0.020  1.374
 LI4  C1   H1    single    0.930  0.020  1.080
 LI4  C2   C3    aromatic  1.376  0.020  1.376
 LI4  C2   H2    single    0.930  0.020  1.080
 LI4  C3   C4    aromatic  1.419  0.020  1.419
 LI4  C3   O10   single    1.351  0.020  1.351
 LI4  C4   N12   single    1.367  0.020  1.367
 LI4  C4   N3    aromatic  1.320  0.020  1.320
 LI4  C6   N3    aromatic  1.336  0.020  1.336
 LI4  C6   H6    single    0.930  0.020  1.080
 LI4  O10  C9    single    1.406  0.020  1.406
 LI4  N12  H121  single    0.890  0.020  1.040
 LI4  N12  H122  single    0.890  0.020  1.040
 LI4  C13  C15   aromatic  1.417  0.020  1.417
 LI4  C13  C19   aromatic  1.369  0.020  1.369
 LI4  C13  H13   single    0.930  0.020  1.080
 LI4  C15  C16   aromatic  1.420  0.020  1.420
 LI4  C15  C23   aromatic  1.426  0.020  1.426
 LI4  C16  C17   aromatic  1.414  0.020  1.414
 LI4  C16  C26   aromatic  1.415  0.020  1.415
 LI4  C17  C18   aromatic  1.368  0.020  1.368
 LI4  C17  H17   single    0.930  0.020  1.080
 LI4  C18  C19   aromatic  1.408  0.020  1.408
 LI4  C18  H18   single    0.930  0.020  1.080
 LI4  C19  H19   single    0.930  0.020  1.080
 LI4  C23  C24   aromatic  1.370  0.020  1.370
 LI4  C23  C9    single    1.503  0.020  1.503
 LI4  C24  C25   aromatic  1.411  0.020  1.411
 LI4  C24  H24   single    0.930  0.020  1.080
 LI4  C25  C26   aromatic  1.364  0.020  1.364
 LI4  C25  H25   single    0.930  0.020  1.080
 LI4  C26  H26   single    0.930  0.020  1.080
 LI4  C9   H9C1  single    0.970  0.020  1.090
 LI4  C9   H9C2  single    0.970  0.020  1.090

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
 LI4  H1    C1   C6    121.18  3.000
 LI4  H1    C1   C2    120.62  3.000
 LI4  C6    C1   C2    118.20  3.000
 LI4  H2    C2   C3    121.46  3.000
 LI4  H2    C2   C1    119.43  3.000
 LI4  C3    C2   C1    119.11  3.000
 LI4  O10   C3   C4    115.35  3.000
 LI4  O10   C3   C2    126.09  3.000
 LI4  C4    C3   C2    118.56  3.000
 LI4  N3    C4   N12   118.28  3.000
 LI4  N3    C4   C3    121.59  3.000
 LI4  N12   C4   C3    120.09  3.000
 LI4  H6    C6   N3    116.05  3.000
 LI4  H6    C6   C1    120.76  3.000
 LI4  N3    C6   C1    123.20  3.000
 LI4  C9    O10  C3    118.29  3.000
 LI4  H122  N12  H121  113.40  3.000
 LI4  H122  N12  C4    117.74  3.000
 LI4  H121  N12  C4    114.82  3.000
 LI4  H13   C13  C19   118.53  3.000
 LI4  H13   C13  C15   120.42  3.000
 LI4  C19   C13  C15   121.06  3.000
 LI4  C23   C15  C16   119.22  3.000
 LI4  C23   C15  C13   122.59  3.000
 LI4  C16   C15  C13   118.19  3.000
 LI4  C26   C16  C17   121.07  3.000
 LI4  C26   C16  C15   119.49  3.000
 LI4  C17   C16  C15   119.45  3.000
 LI4  H17   C17  C18   120.45  3.000
 LI4  H17   C17  C16   118.63  3.000
 LI4  C18   C17  C16   120.92  3.000
 LI4  H18   C18  C19   119.85  3.000
 LI4  H18   C18  C17   120.31  3.000
 LI4  C19   C18  C17   119.84  3.000
 LI4  H19   C19  C18   119.68  3.000
 LI4  H19   C19  C13   119.77  3.000
 LI4  C18   C19  C13   120.55  3.000
 LI4  C9    C23  C24   122.26  3.000
 LI4  C9    C23  C15   118.30  3.000
 LI4  C24   C23  C15   119.44  3.000
 LI4  H24   C24  C25   118.25  3.000
 LI4  H24   C24  C23   120.66  3.000
 LI4  C25   C24  C23   121.09  3.000
 LI4  H25   C25  C26   120.30  3.000
 LI4  H25   C25  C24   119.10  3.000
 LI4  C26   C25  C24   120.60  3.000
 LI4  H26   C26  C25   120.66  3.000
 LI4  H26   C26  C16   119.18  3.000
 LI4  C25   C26  C16   120.16  3.000
 LI4  C6    N3   C4    119.34  3.000
 LI4  H9C2  C9   H9C1  107.07  3.000
 LI4  H9C2  C9   C23   109.85  3.000
 LI4  H9C1  C9   C23   109.75  3.000
 LI4  H9C2  C9   O10   110.18  3.000
 LI4  H9C1  C9   O10   110.29  3.000
 LI4  C23   C9   O10   109.65  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
 LI4  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 LI4  CONST_02  C4   N3   C6   C1      0.00   0.0  0
 LI4  CONST_03  N3   C6   C1   C2      0.00   0.0  0
 LI4  CONST_04  N3   C4   C3   C2      0.00   0.0  0
 LI4  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 LI4  CONST_06  C6   N3   C4   C3      0.00   0.0  0
 LI4  CONST_07  C17  C16  C15  C13     0.00   0.0  0
 LI4  CONST_08  C26  C16  C15  C13   180.00   0.0  0
 LI4  CONST_09  C24  C23  C15  C13   180.00   0.0  0
 LI4  CONST_10  C17  C18  C19  C13     0.00   0.0  0
 LI4  CONST_11  C18  C19  C13  C15     0.00   0.0  0
 LI4  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 LI4  CONST_13  C25  C26  C16  C15     0.00   0.0  0
 LI4  CONST_14  C25  C24  C23  C15     0.00   0.0  0
 LI4  CONST_15  C19  C13  C15  C16     0.00   0.0  0
 LI4  CONST_16  C24  C23  C15  C16     0.00   0.0  0
 LI4  CONST_17  C19  C18  C17  C16     0.00   0.0  0
 LI4  CONST_18  C24  C25  C26  C16     0.00   0.0  0
 LI4  CONST_19  C23  C15  C16  C17   180.00   0.0  0
 LI4  CONST_20  C25  C26  C16  C17   180.00   0.0  0
 LI4  CONST_21  C26  C16  C17  C18   180.00   0.0  0
 LI4  CONST_22  C23  C15  C13  C19   180.00   0.0  0
 LI4  CONST_23  C26  C16  C15  C23     0.00   0.0  0
 LI4  CONST_24  C26  C25  C24  C23     0.00   0.0  0
 LI4  CONST_25  O10  C3   C2   C1    180.00   0.0  0
 LI4  CONST_26  N12  C4   C3   C2    180.00   0.0  0
 LI4  CONST_27  N12  C4   N3   C6    180.00   0.0  0
 LI4  CONST_28  N3   C4   C3   O10   180.00   0.0  0
 LI4  CONST_29  C9   C23  C15  C13     0.00   0.0  0
 LI4  CONST_30  C9   C23  C15  C16   180.00   0.0  0
 LI4  CONST_31  C9   C23  C24  C25   180.00   0.0  0
 LI4  CONST_32  H6   C6   C1   C2    180.00   0.0  0
 LI4  CONST_33  H1   C1   C2   C3    180.00   0.0  0
 LI4  CONST_34  H2   C2   C3   C4    180.00   0.0  0
 LI4  CONST_35  H18  C18  C19  C13   180.00   0.0  0
 LI4  CONST_36  H19  C19  C13  C15   180.00   0.0  0
 LI4  CONST_37  H17  C17  C16  C15   180.00   0.0  0
 LI4  CONST_38  H26  C26  C16  C15   180.00   0.0  0
 LI4  CONST_39  H24  C24  C23  C15   180.00   0.0  0
 LI4  CONST_40  H13  C13  C15  C16   180.00   0.0  0
 LI4  CONST_41  H25  C25  C26  C16   180.00   0.0  0
 LI4  Var_01    C23  C9   O10  C3   -179.45  30.0  3
 LI4  Var_02    C15  C23  C9   O10  -177.90  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
 LI4  plan-1  C1    0.020
 LI4  plan-1  C2    0.020
 LI4  plan-1  C3    0.020
 LI4  plan-1  C4    0.020
 LI4  plan-1  C6    0.020
 LI4  plan-1  O10   0.020
 LI4  plan-1  N12   0.020
 LI4  plan-1  N3    0.020
 LI4  plan-1  H1    0.020
 LI4  plan-1  H2    0.020
 LI4  plan-1  H6    0.020
 LI4  plan-2  C13   0.020
 LI4  plan-2  C15   0.020
 LI4  plan-2  C16   0.020
 LI4  plan-2  C17   0.020
 LI4  plan-2  C18   0.020
 LI4  plan-2  C19   0.020
 LI4  plan-2  C23   0.020
 LI4  plan-2  C24   0.020
 LI4  plan-2  C25   0.020
 LI4  plan-2  C26   0.020
 LI4  plan-2  C9    0.020
 LI4  plan-2  H17   0.020
 LI4  plan-2  H18   0.020
 LI4  plan-2  H19   0.020
 LI4  plan-2  H24   0.020
 LI4  plan-2  H25   0.020
 LI4  plan-2  H26   0.020
 LI4  plan-2  H13   0.020
 LI4  plan-3  C4    0.020
 LI4  plan-3  N12   0.020
 LI4  plan-3  H121  0.020
 LI4  plan-3  H122  0.020

