# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:43:10 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 1,4-dihydroxynaphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(O)c2ccccc2c1O
#
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
 DNA  DNA  '1,4-dihydroxynaphthalene-2-carboxylic acid'  ligand  22  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DNA
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
 DNA  O1A   O  O      0  -0.636  -3.1669   1.4349   0.1914
 DNA  O1B   O  OC    -1  -0.550  -3.6308  -0.7338   0.0267
 DNA  O1D   O  OH1    0  -0.650  -0.8787   2.2517   0.2125
 DNA  C1E   C  CR16   0  -0.248   3.6842   0.2273  -0.1433
 DNA  C1F   C  CR16   0  -0.260   3.2210   1.5451   0.0189
 DNA  C1G   C  CR16   0  -0.315   2.7985  -0.8164  -0.2061
 DNA  C1H   C  CR16   0  -0.280   1.8761   1.7931   0.1018
 DNA  C1I   C  CR16   0  -0.403  -0.8761  -1.3836  -0.0793
 DNA  C1J   C  C      0   0.495  -2.8366   0.2083   0.0838
 DNA  C1K   C  CR6    0   0.284   0.4582  -1.6590  -0.1430
 DNA  C1L   C  CR6    0  -0.293  -1.3594  -0.0610   0.0261
 DNA  C1M   C  CR6    0   0.303  -0.4640   0.9947   0.0967
 DNA  C1N   C  CR66   0   0.015   1.4055  -0.5953  -0.1027
 DNA  C1O   C  CR66   0  -0.011   0.9390   0.7386   0.0373
 DNA  HO1C  H  HOH1   0   0.469   1.6508  -3.1227   0.2370
 DNA  HO1D  H  HOH1   0   0.463  -1.9095   2.1489   0.2235
 DNA  H1E   H  HCR6   0   0.259   4.7463   0.0370  -0.2253
 DNA  H1F   H  HCR6   0   0.257   3.9285   2.3619   0.0706
 DNA  H1G   H  HCR6   0   0.247   3.1849  -1.8174  -0.3517
 DNA  H1H   H  HCR6   0   0.254   1.5237   2.8090   0.2177
 DNA  H1I   H  HCR6   0   0.252  -1.5899  -2.1974  -0.1104
 DNA  O1C   O  OH1    0  -0.651   0.8596  -2.9551  -0.2855

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
 DNA  O1A  C1J   deloc     1.275  0.020  1.275
 DNA  C1J  O1B   deloc     1.234  0.020  1.234
 DNA  C1K  O1C   single    1.364  0.020  1.364
 DNA  O1C  HO1C  single    0.850  0.020  0.980
 DNA  O1D  C1M   single    1.329  0.020  1.329
 DNA  O1D  HO1D  single    0.850  0.020  0.980
 DNA  C1F  C1E   aromatic  1.406  0.020  1.406
 DNA  C1E  C1G   aromatic  1.370  0.020  1.370
 DNA  C1E  H1E   single    0.930  0.020  1.080
 DNA  C1F  C1H   aromatic  1.370  0.020  1.370
 DNA  C1F  H1F   single    0.930  0.020  1.080
 DNA  C1G  C1N   aromatic  1.414  0.020  1.414
 DNA  C1G  H1G   single    0.930  0.020  1.080
 DNA  C1H  C1O   aromatic  1.412  0.020  1.412
 DNA  C1H  H1H   single    0.930  0.020  1.080
 DNA  C1L  C1I   aromatic  1.412  0.020  1.412
 DNA  C1K  C1I   aromatic  1.364  0.020  1.364
 DNA  C1I  H1I   single    0.930  0.020  1.080
 DNA  C1L  C1J   single    1.503  0.020  1.503
 DNA  C1N  C1K   aromatic  1.425  0.020  1.425
 DNA  C1M  C1L   aromatic  1.386  0.020  1.386
 DNA  C1O  C1M   aromatic  1.428  0.020  1.428
 DNA  C1O  C1N   aromatic  1.420  0.020  1.420

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
 DNA  HO1D  O1D  C1M  102.57  3.000
 DNA  H1E   C1E  C1G  119.80  3.000
 DNA  H1E   C1E  C1F  119.79  3.000
 DNA  C1G   C1E  C1F  120.41  3.000
 DNA  H1F   C1F  C1H  120.16  3.000
 DNA  H1F   C1F  C1E  119.84  3.000
 DNA  C1H   C1F  C1E  120.00  3.000
 DNA  H1G   C1G  C1N  120.38  3.000
 DNA  H1G   C1G  C1E  118.66  3.000
 DNA  C1N   C1G  C1E  120.95  3.000
 DNA  H1H   C1H  C1O  119.35  3.000
 DNA  H1H   C1H  C1F  119.76  3.000
 DNA  C1O   C1H  C1F  120.89  3.000
 DNA  H1I   C1I  C1L  118.72  3.000
 DNA  H1I   C1I  C1K  119.45  3.000
 DNA  C1L   C1I  C1K  121.83  3.000
 DNA  C1L   C1J  O1B  119.62  3.000
 DNA  C1L   C1J  O1A  115.49  3.000
 DNA  O1B   C1J  O1A  124.89  3.000
 DNA  C1N   C1K  C1I  119.89  3.000
 DNA  C1N   C1K  O1C  121.10  3.000
 DNA  C1I   C1K  O1C  118.98  3.000
 DNA  C1M   C1L  C1J  119.77  3.000
 DNA  C1M   C1L  C1I  119.75  3.000
 DNA  C1J   C1L  C1I  120.47  3.000
 DNA  C1O   C1M  C1L  119.74  3.000
 DNA  C1O   C1M  O1D  118.69  3.000
 DNA  C1L   C1M  O1D  121.56  3.000
 DNA  C1O   C1N  C1K  119.06  3.000
 DNA  C1O   C1N  C1G  118.53  3.000
 DNA  C1K   C1N  C1G  122.41  3.000
 DNA  C1N   C1O  C1M  119.70  3.000
 DNA  C1N   C1O  C1H  119.21  3.000
 DNA  C1M   C1O  C1H  121.09  3.000
 DNA  HO1C  O1C  C1K  110.51  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
 DNA  CONST_01  C1O  C1H  C1F  C1E    0.00   0.0  0
 DNA  CONST_02  C1K  C1N  C1G  C1E  180.00   0.0  0
 DNA  CONST_03  C1O  C1N  C1G  C1E    0.00   0.0  0
 DNA  CONST_04  C1N  C1G  C1E  C1F    0.00   0.0  0
 DNA  CONST_05  C1M  C1O  C1H  C1F  180.00   0.0  0
 DNA  CONST_06  C1N  C1O  C1H  C1F    0.00   0.0  0
 DNA  CONST_07  C1H  C1F  C1E  C1G    0.00   0.0  0
 DNA  CONST_08  C1I  C1K  C1N  C1G  180.00   0.0  0
 DNA  CONST_09  C1H  C1O  C1N  C1G    0.00   0.0  0
 DNA  CONST_10  C1M  C1O  C1N  C1G  180.00   0.0  0
 DNA  CONST_11  C1L  C1M  C1O  C1H  180.00   0.0  0
 DNA  CONST_12  C1K  C1N  C1O  C1H  180.00   0.0  0
 DNA  CONST_13  C1O  C1M  C1L  C1I    0.00   0.0  0
 DNA  CONST_14  C1O  C1N  C1K  C1I    0.00   0.0  0
 DNA  CONST_15  C1M  C1L  C1I  C1K    0.00   0.0  0
 DNA  CONST_16  C1M  C1O  C1N  C1K    0.00   0.0  0
 DNA  CONST_17  C1N  C1K  C1I  C1L    0.00   0.0  0
 DNA  CONST_18  C1N  C1O  C1M  C1L    0.00   0.0  0
 DNA  CONST_19  C1L  C1I  C1K  O1C  180.00   0.0  0
 DNA  CONST_20  C1G  C1N  C1K  O1C    0.00   0.0  0
 DNA  CONST_21  C1O  C1N  C1K  O1C  180.00   0.0  0
 DNA  CONST_22  C1I  C1L  C1M  O1D  180.00   0.0  0
 DNA  CONST_23  C1H  C1O  C1M  O1D    0.00   0.0  0
 DNA  CONST_24  C1N  C1O  C1M  O1D  180.00   0.0  0
 DNA  CONST_25  C1K  C1I  C1L  C1J  180.00   0.0  0
 DNA  CONST_26  C1O  C1M  C1L  C1J  180.00   0.0  0
 DNA  CONST_27  H1H  C1H  C1F  C1E  180.00   0.0  0
 DNA  CONST_28  H1G  C1G  C1E  C1F  180.00   0.0  0
 DNA  CONST_29  H1F  C1F  C1E  C1G  180.00   0.0  0
 DNA  CONST_30  H1E  C1E  C1F  C1H  180.00   0.0  0
 DNA  CONST_31  H1I  C1I  C1L  C1M  180.00   0.0  0
 DNA  Var_01    C1I  C1L  C1J  O1A  179.36  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
 DNA  plan-1  O1D  0.020
 DNA  plan-1  C1E  0.020
 DNA  plan-1  C1F  0.020
 DNA  plan-1  C1G  0.020
 DNA  plan-1  C1H  0.020
 DNA  plan-1  C1I  0.020
 DNA  plan-1  C1J  0.020
 DNA  plan-1  C1K  0.020
 DNA  plan-1  C1L  0.020
 DNA  plan-1  C1M  0.020
 DNA  plan-1  C1N  0.020
 DNA  plan-1  C1O  0.020
 DNA  plan-1  H1E  0.020
 DNA  plan-1  H1F  0.020
 DNA  plan-1  H1G  0.020
 DNA  plan-1  H1H  0.020
 DNA  plan-1  H1I  0.020
 DNA  plan-1  O1C  0.020
 DNA  plan-2  O1A  0.020
 DNA  plan-2  O1B  0.020
 DNA  plan-2  C1J  0.020
 DNA  plan-2  C1L  0.020

