# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:53:59 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: naphthalene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2ccccc2c1O
#
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
 D1N  D1N  'naphthalene-1,2-diol     '  ligand  20  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D1N
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
 D1N  O2   O  OH1   0  -0.648   5.2145  -4.4036  -0.7981
 D1N  C2   C  CR6   0   0.250   3.9121  -4.1952  -0.4873
 D1N  C3   C  CR16  0  -0.371   3.0396  -5.2351  -0.1218
 D1N  C4   C  CR16  0  -0.335   1.7320  -4.9747   0.1868
 D1N  C5   C  CR66  0   0.098   1.2377  -3.6540   0.1434
 D1N  C10  C  CR66  0   0.005   2.1121  -2.5957  -0.2264
 D1N  C1   C  CR6   0   0.238   3.4591  -2.8931  -0.5418
 D1N  O1   O  OH1   0  -0.625   4.2655  -1.8682  -0.8907
 D1N  C9   C  CR16  0  -0.290   1.6052  -1.2724  -0.2726
 D1N  C8   C  CR16  0  -0.256   0.2962  -1.0183   0.0336
 D1N  C7   C  CR16  0  -0.262  -0.5737  -2.0669   0.4012
 D1N  C6   C  CR16  0  -0.311  -0.1102  -3.3517   0.4537
 D1N  HO2  H  HOH1  0   0.482   5.4148  -5.3452  -0.8217
 D1N  H3   H  HCR6  0   0.277   3.4150  -6.2518  -0.0872
 D1N  H4   H  HCR6  0   0.256   1.0693  -5.7845   0.4646
 D1N  HO1  H  HOH1  0   0.475   5.1384  -2.1947  -1.1392
 D1N  H9   H  HCR6  0   0.253   2.2548  -0.4541  -0.5523
 D1N  H8   H  HCR6  0   0.256  -0.0766  -0.0028  -0.0058
 D1N  H7   H  HCR6  0   0.255  -1.6066  -1.8495   0.6397
 D1N  H6   H  HCR6  0   0.253  -0.7733  -4.1620   0.7334

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
 D1N  O2   C2   single    1.355  0.020  1.355
 D1N  O2   HO2  single    0.850  0.020  0.980
 D1N  C2   C3   aromatic  1.406  0.020  1.406
 D1N  C2   C1   aromatic  1.380  0.020  1.380
 D1N  C3   C4   aromatic  1.369  0.020  1.369
 D1N  C3   H3   single    0.930  0.020  1.080
 D1N  C4   C5   aromatic  1.411  0.020  1.411
 D1N  C4   H4   single    0.930  0.020  1.080
 D1N  C5   C10  aromatic  1.422  0.020  1.422
 D1N  C5   C6   single    1.416  0.020  1.416
 D1N  C10  C1   aromatic  1.415  0.020  1.415
 D1N  C10  C9   single    1.418  0.020  1.418
 D1N  C1   O1   single    1.350  0.020  1.350
 D1N  O1   HO1  single    0.850  0.020  0.980
 D1N  C9   C8   double    1.368  0.020  1.368
 D1N  C9   H9   single    0.930  0.020  1.080
 D1N  C8   C7   single    1.411  0.020  1.411
 D1N  C8   H8   single    0.930  0.020  1.080
 D1N  C7   C6   double    1.367  0.020  1.367
 D1N  C7   H7   single    0.930  0.020  1.080
 D1N  C6   H6   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
 D1N  HO2  O2   C2   110.85  3.000
 D1N  C1   C2   C3   120.31  3.000
 D1N  C1   C2   O2   116.85  3.000
 D1N  C3   C2   O2   122.84  3.000
 D1N  H3   C3   C4   120.13  3.000
 D1N  H3   C3   C2   119.14  3.000
 D1N  C4   C3   C2   120.72  3.000
 D1N  H4   C4   C5   119.58  3.000
 D1N  H4   C4   C3   120.03  3.000
 D1N  C5   C4   C3   120.39  3.000
 D1N  C6   C5   C10  118.92  3.000
 D1N  C6   C5   C4   121.78  3.000
 D1N  C10  C5   C4   119.30  3.000
 D1N  C9   C10  C1   121.96  3.000
 D1N  C9   C10  C5   118.90  3.000
 D1N  C1   C10  C5   119.14  3.000
 D1N  O1   C1   C10  117.82  3.000
 D1N  O1   C1   C2   122.04  3.000
 D1N  C10  C1   C2   120.14  3.000
 D1N  HO1  O1   C1   110.50  3.000
 D1N  H9   C9   C8   119.47  3.000
 D1N  H9   C9   C10  119.99  3.000
 D1N  C8   C9   C10  120.54  3.000
 D1N  H8   C8   C7   119.62  3.000
 D1N  H8   C8   C9   119.71  3.000
 D1N  C7   C8   C9   120.67  3.000
 D1N  H7   C7   C6   120.27  3.000
 D1N  H7   C7   C8   119.77  3.000
 D1N  C6   C7   C8   119.96  3.000
 D1N  H6   C6   C7   120.34  3.000
 D1N  H6   C6   C5   118.65  3.000
 D1N  C7   C6   C5   121.01  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
 D1N  CONST_01  C5   C4   C3   C2    0.00  0.0  0
 D1N  CONST_02  C5   C10  C1   C2    0.00  0.0  0
 D1N  CONST_03  C10  C1   C2   C3    0.00  0.0  0
 D1N  CONST_04  C10  C5   C4   C3    0.00  0.0  0
 D1N  CONST_05  C1   C2   C3   C4    0.00  0.0  0
 D1N  CONST_06  C1   C10  C5   C4    0.00  0.0  0
 D1N  CONST_07  C4   C3   C2   O2  180.00  0.0  0
 D1N  CONST_08  C10  C1   C2   O2  180.00  0.0  0
 D1N  CONST_09  O1   C1   C2   C3  180.00  0.0  0
 D1N  CONST_10  O1   C1   C10  C5  180.00  0.0  0
 D1N  CONST_11  C9   C10  C1   O1    0.00  0.0  0
 D1N  CONST_12  H4   C4   C3   C2  180.00  0.0  0
 D1N  CONST_13  H3   C3   C4   C5  180.00  0.0  0

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
 D1N  plan-1  O2   0.020
 D1N  plan-1  C2   0.020
 D1N  plan-1  C3   0.020
 D1N  plan-1  C4   0.020
 D1N  plan-1  C5   0.020
 D1N  plan-1  C10  0.020
 D1N  plan-1  C1   0.020
 D1N  plan-1  O1   0.020
 D1N  plan-1  C9   0.020
 D1N  plan-1  C8   0.020
 D1N  plan-1  C7   0.020
 D1N  plan-1  C6   0.020
 D1N  plan-1  H3   0.020
 D1N  plan-1  H4   0.020
 D1N  plan-1  H9   0.020
 D1N  plan-1  H8   0.020
 D1N  plan-1  H7   0.020
 D1N  plan-1  H6   0.020

