# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:35:37 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 5-methylnaphthalene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2c1cccc2C(O)=O
#
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
 5NE  5NE  '5-methylnaphthalene-1-carboxylic acid'  ligand  24  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NE
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
 5NE  O1N  O  O     0  -0.438   2.7100  -1.4542   0.7067
 5NE  C1L  C  C     0   0.489   2.5650  -0.4149   0.1088
 5NE  O1M  O  OH1   0  -0.589   3.5629   0.1936  -0.5207
 5NE  C1J  C  CR6   0  -0.094   1.2907   0.3463   0.0149
 5NE  C1E  C  CR66  0   0.137   0.0210  -0.3105   0.0176
 5NE  C1F  C  CR16  0  -0.352  -0.1290  -1.7194  -0.0243
 5NE  C1A  C  CR16  0  -0.227  -1.3735  -2.2829  -0.0478
 5NE  C1I  C  CR16  0  -0.269   1.3609   1.7204  -0.0096
 5NE  C1H  C  CR16  0  -0.240   0.1973   2.5024   0.0011
 5NE  C1G  C  CR16  0  -0.318  -1.0298   1.9013   0.0176
 5NE  C1D  C  CR66  0   0.065  -1.1572   0.4929   0.0140
 5NE  C1C  C  CR6   0   0.087  -2.4471  -0.1178  -0.0008
 5NE  C1O  C  CH3   0  -0.752  -3.6940   0.7170   0.0056
 5NE  C1B  C  CR16  0  -0.321  -2.5311  -1.4851  -0.0283
 5NE  H1   H  HOH1  0   0.487   4.3864  -0.2966  -0.3765
 5NE  H2   H  HCR6  0   0.258   0.7353  -2.3631  -0.0415
 5NE  H3   H  HCR6  0   0.260  -1.4722  -3.3601  -0.0831
 5NE  H4   H  HCR6  0   0.274   2.3195   2.2204  -0.0112
 5NE  H5   H  HCR6  0   0.267   0.2789   3.5807   0.0004
 5NE  H6   H  HCR6  0   0.266  -1.9163   2.5205   0.0286
 5NE  H7   H  HCH3  0   0.249  -3.7509   1.3707  -0.8667
 5NE  H8   H  HCH3  0   0.258  -4.5795   0.0834  -0.0006
 5NE  H9   H  HCH3  0   0.249  -3.7513   1.3549   0.8893
 5NE  H10  H  HCR6  0   0.253  -3.5034  -1.9619  -0.0433

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
 5NE  C1B  C1A  aromatic  1.406  0.020  1.406
 5NE  C1B  C1C  aromatic  1.370  0.020  1.370
 5NE  C1A  C1F  aromatic  1.366  0.020  1.366
 5NE  C1O  C1C  single    1.501  0.020  1.501
 5NE  C1C  C1D  aromatic  1.427  0.020  1.427
 5NE  C1F  C1E  aromatic  1.417  0.020  1.417
 5NE  C1D  C1E  aromatic  1.426  0.020  1.426
 5NE  C1D  C1G  aromatic  1.414  0.020  1.414
 5NE  C1E  C1J  aromatic  1.430  0.020  1.430
 5NE  C1G  C1H  aromatic  1.366  0.020  1.366
 5NE  C1J  C1L  single    1.487  0.020  1.487
 5NE  C1J  C1I  aromatic  1.376  0.020  1.376
 5NE  O1N  C1L  double    1.208  0.020  1.208
 5NE  C1L  O1M  single    1.328  0.020  1.328
 5NE  C1H  C1I  aromatic  1.402  0.020  1.402
 5NE  O1M  H1   single    0.850  0.020  0.980
 5NE  C1F  H2   single    0.930  0.020  1.080
 5NE  C1A  H3   single    0.930  0.020  1.080
 5NE  C1I  H4   single    0.930  0.020  1.080
 5NE  C1H  H5   single    0.930  0.020  1.080
 5NE  C1G  H6   single    0.930  0.020  1.080
 5NE  C1O  H7   single    0.970  0.020  1.090
 5NE  C1O  H8   single    0.970  0.020  1.090
 5NE  C1O  H9   single    0.970  0.020  1.090
 5NE  C1B  H10  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
 5NE  C1J  C1L  O1M  112.30  3.000
 5NE  O1M  C1L  O1N  122.61  3.000
 5NE  C1J  C1L  O1N  125.07  3.000
 5NE  H1   O1M  C1L  109.65  3.000
 5NE  C1I  C1J  C1E  120.28  3.000
 5NE  C1I  C1J  C1L  117.93  3.000
 5NE  C1E  C1J  C1L  121.71  3.000
 5NE  C1D  C1E  C1F  118.20  3.000
 5NE  C1D  C1E  C1J  118.35  3.000
 5NE  C1F  C1E  C1J  123.41  3.000
 5NE  H2   C1F  C1A  118.93  3.000
 5NE  H2   C1F  C1E  120.62  3.000
 5NE  C1A  C1F  C1E  120.45  3.000
 5NE  H3   C1A  C1B  119.35  3.000
 5NE  H3   C1A  C1F  119.62  3.000
 5NE  C1B  C1A  C1F  121.04  3.000
 5NE  H4   C1I  C1H  118.55  3.000
 5NE  H4   C1I  C1J  120.47  3.000
 5NE  C1H  C1I  C1J  120.96  3.000
 5NE  H5   C1H  C1G  120.43  3.000
 5NE  H5   C1H  C1I  119.57  3.000
 5NE  C1G  C1H  C1I  120.00  3.000
 5NE  H6   C1G  C1D  119.76  3.000
 5NE  H6   C1G  C1H  118.97  3.000
 5NE  C1D  C1G  C1H  121.26  3.000
 5NE  C1C  C1D  C1G  120.50  3.000
 5NE  C1G  C1D  C1E  119.12  3.000
 5NE  C1C  C1D  C1E  120.37  3.000
 5NE  C1B  C1C  C1O  120.28  3.000
 5NE  C1O  C1C  C1D  120.86  3.000
 5NE  C1B  C1C  C1D  118.86  3.000
 5NE  H9   C1O  H8   107.58  3.000
 5NE  H9   C1O  H7   107.11  3.000
 5NE  H8   C1O  H7   107.56  3.000
 5NE  H9   C1O  C1C  111.85  3.000
 5NE  H8   C1O  C1C  110.61  3.000
 5NE  H7   C1O  C1C  111.90  3.000
 5NE  H10  C1B  C1C  119.64  3.000
 5NE  H10  C1B  C1A  119.29  3.000
 5NE  C1C  C1B  C1A  121.07  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
 5NE  CONST_01  C1A  C1F  C1E  C1J  180.00   0.0  0
 5NE  CONST_02  C1C  C1D  C1E  C1J  180.00   0.0  0
 5NE  CONST_03  C1G  C1D  C1E  C1J    0.00   0.0  0
 5NE  CONST_04  C1G  C1H  C1I  C1J    0.00   0.0  0
 5NE  CONST_05  C1B  C1A  C1F  C1E    0.00   0.0  0
 5NE  CONST_06  C1B  C1C  C1D  C1E    0.00   0.0  0
 5NE  CONST_07  C1H  C1G  C1D  C1E    0.00   0.0  0
 5NE  CONST_08  C1H  C1I  C1J  C1E    0.00   0.0  0
 5NE  CONST_09  C1C  C1B  C1A  C1F    0.00   0.0  0
 5NE  CONST_10  C1C  C1D  C1E  C1F    0.00   0.0  0
 5NE  CONST_11  C1G  C1D  C1E  C1F  180.00   0.0  0
 5NE  CONST_12  C1I  C1J  C1E  C1F  180.00   0.0  0
 5NE  CONST_13  C1D  C1C  C1B  C1A    0.00   0.0  0
 5NE  CONST_14  C1D  C1E  C1F  C1A    0.00   0.0  0
 5NE  CONST_15  C1D  C1E  C1J  C1I    0.00   0.0  0
 5NE  CONST_16  C1D  C1G  C1H  C1I    0.00   0.0  0
 5NE  CONST_17  C1C  C1D  C1G  C1H  180.00   0.0  0
 5NE  CONST_18  C1B  C1C  C1D  C1G  180.00   0.0  0
 5NE  CONST_19  C1F  C1E  C1J  C1L    0.00   0.0  0
 5NE  CONST_20  C1D  C1E  C1J  C1L  180.00   0.0  0
 5NE  CONST_21  C1H  C1I  C1J  C1L  180.00   0.0  0
 5NE  CONST_22  C1O  C1C  C1D  C1E  180.00   0.0  0
 5NE  CONST_23  C1O  C1C  C1B  C1A  180.00   0.0  0
 5NE  CONST_24  C1O  C1C  C1D  C1G    0.00   0.0  0
 5NE  CONST_25  H2   C1F  C1E  C1J    0.00   0.0  0
 5NE  CONST_26  H5   C1H  C1I  C1J  180.00   0.0  0
 5NE  CONST_27  H3   C1A  C1F  C1E  180.00   0.0  0
 5NE  CONST_28  H6   C1G  C1D  C1E  180.00   0.0  0
 5NE  CONST_29  H4   C1I  C1J  C1E  180.00   0.0  0
 5NE  CONST_30  H10  C1B  C1A  C1F  180.00   0.0  0
 5NE  CONST_31  H1   O1M  C1L  C1J  180.00   0.0  0
 5NE  Var_01    C1E  C1J  C1L  O1N  -31.80  30.0  3
 5NE  Var_02    H7   C1O  C1C  C1D   60.49  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
 5NE  plan-1  C1L  0.020
 5NE  plan-1  C1J  0.020
 5NE  plan-1  C1E  0.020
 5NE  plan-1  C1F  0.020
 5NE  plan-1  C1A  0.020
 5NE  plan-1  C1I  0.020
 5NE  plan-1  C1H  0.020
 5NE  plan-1  C1G  0.020
 5NE  plan-1  C1D  0.020
 5NE  plan-1  C1C  0.020
 5NE  plan-1  C1O  0.020
 5NE  plan-1  C1B  0.020
 5NE  plan-1  H2   0.020
 5NE  plan-1  H3   0.020
 5NE  plan-1  H4   0.020
 5NE  plan-1  H5   0.020
 5NE  plan-1  H6   0.020
 5NE  plan-1  H10  0.020
 5NE  plan-2  O1N  0.020
 5NE  plan-2  C1L  0.020
 5NE  plan-2  O1M  0.020
 5NE  plan-2  C1J  0.020
 5NE  plan-2  H1   0.020

