# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:15:23 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: [(S)-hydroxy(naphthalen-1-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](c1cccc2ccccc12)[P](O)(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
 I59  I59  '[(S)-hydroxy(naphthalen-1-yl)methyl]phosphonic acid'  ligand  25  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I59
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
 I59  C1   C  CR16   0  -0.265  -1.8711   0.0797   3.3655
 I59  C2   C  CR16   0  -0.319  -0.5623  -0.2607   3.5693
 I59  C3   C  CR66   0   0.107   0.3842  -0.1768   2.5197
 I59  C4   C  CR66   0   0.094  -0.0308   0.2774   1.2383
 I59  C5   C  CR16   0  -0.334  -1.3990   0.5992   1.0564
 I59  C6   C  CR16   0  -0.264  -2.2919   0.5104   2.0913
 I59  C7   C  CR16   0  -0.349   1.7348  -0.5449   2.7275
 I59  C8   C  CR16   0  -0.241   2.6283  -0.4557   1.6980
 I59  C9   C  CR16   0  -0.357   2.2234   0.0163   0.4335
 I59  C10  C  CR6    0   0.109   0.9244   0.3854   0.1810
 I59  C11  C  CH1    0  -0.332   0.5139   0.9125  -1.1585
 I59  O12  O  OH1    0  -0.714   1.6226   1.2245  -1.9710
 I59  P13  P  P      0   1.169  -0.5517  -0.3289  -2.1667
 I59  O15  O  O      0  -0.860  -0.6589  -1.6263  -1.3767
 I59  O16  O  OP    -1  -0.880  -1.8806   0.3741  -2.4444
 I59  O17  O  OP    -1  -0.884   0.3723  -0.4264  -3.4114
 I59  H1   H  HCR6   0   0.250  -2.5858   0.0135   4.1756
 I59  H2   H  HCR6   0   0.247  -0.2302  -0.6032   4.5426
 I59  H5   H  HCR6   0   0.241  -1.7561   0.9020   0.0808
 I59  H6   H  HCR6   0   0.249  -3.3325   0.7607   1.9282
 I59  H7   H  HCR6   0   0.242   2.0445  -0.8948   3.7050
 I59  H8   H  HCR6   0   0.243   3.6629  -0.7375   1.8519
 I59  H9   H  HCR6   0   0.237   2.9589   0.1016  -0.3544
 I59  H11  H  HCH1   0   0.185  -0.0890   1.8185  -0.9978
 I59  H12  H  HOH1   0   0.426   1.4439   0.6427  -2.7578

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
 I59  C1   C2   aromatic  1.368  0.020  1.368
 I59  C1   C6   aromatic  1.409  0.020  1.409
 I59  C1   H1   single    0.930  0.020  1.080
 I59  C2   C3   aromatic  1.416  0.020  1.416
 I59  C2   H2   single    0.930  0.020  1.080
 I59  C3   C4   aromatic  1.421  0.020  1.421
 I59  C3   C7   aromatic  1.415  0.020  1.415
 I59  C4   C5   aromatic  1.417  0.020  1.417
 I59  C4   C10  aromatic  1.429  0.020  1.429
 I59  C5   C6   aromatic  1.370  0.020  1.370
 I59  C5   H5   single    0.930  0.020  1.080
 I59  C6   H6   single    0.930  0.020  1.080
 I59  C7   C8   aromatic  1.366  0.020  1.366
 I59  C7   H7   single    0.930  0.020  1.080
 I59  C8   C9   aromatic  1.409  0.020  1.409
 I59  C8   H8   single    0.930  0.020  1.080
 I59  C9   C10  aromatic  1.374  0.020  1.374
 I59  C9   H9   single    0.930  0.020  1.080
 I59  C10  C11  single    1.497  0.020  1.497
 I59  C11  O12  single    1.409  0.020  1.409
 I59  C11  P13  single    1.922  0.020  1.922
 I59  C11  H11  single    0.970  0.020  1.090
 I59  O12  H12  single    0.850  0.020  0.980
 I59  P13  O15  deloc     1.523  0.020  1.523
 I59  P13  O16  deloc     1.529  0.020  1.529
 I59  P13  O17  deloc     1.553  0.020  1.553

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
 I59  H1   C1   C6   119.89  3.000
 I59  H1   C1   C2   120.34  3.000
 I59  C6   C1   C2   119.78  3.000
 I59  H2   C2   C3   118.65  3.000
 I59  H2   C2   C1   120.38  3.000
 I59  C3   C2   C1   120.96  3.000
 I59  C7   C3   C4   119.61  3.000
 I59  C7   C3   C2   120.91  3.000
 I59  C4   C3   C2   119.48  3.000
 I59  C10  C4   C5   122.22  3.000
 I59  C10  C4   C3   119.74  3.000
 I59  C5   C4   C3   118.04  3.000
 I59  H5   C5   C6   118.96  3.000
 I59  H5   C5   C4   119.85  3.000
 I59  C6   C5   C4   121.17  3.000
 I59  H6   C6   C5   119.85  3.000
 I59  H6   C6   C1   119.59  3.000
 I59  C5   C6   C1   120.55  3.000
 I59  H7   C7   C8   120.94  3.000
 I59  H7   C7   C3   119.29  3.000
 I59  C8   C7   C3   119.77  3.000
 I59  H8   C8   C9   119.28  3.000
 I59  H8   C8   C7   120.04  3.000
 I59  C9   C8   C7   120.67  3.000
 I59  H9   C9   C10  119.22  3.000
 I59  H9   C9   C8   119.00  3.000
 I59  C10  C9   C8   121.78  3.000
 I59  C11  C10  C9   121.22  3.000
 I59  C11  C10  C4   120.36  3.000
 I59  C9   C10  C4   118.41  3.000
 I59  H11  C11  P13  107.74  3.000
 I59  H11  C11  O12  109.45  3.000
 I59  P13  C11  O12  106.06  3.000
 I59  H11  C11  C10  108.04  3.000
 I59  P13  C11  C10  113.21  3.000
 I59  O12  C11  C10  112.22  3.000
 I59  H12  O12  C11  100.68  3.000
 I59  O17  P13  O16  113.60  3.000
 I59  O17  P13  O15  113.83  3.000
 I59  O16  P13  O15  115.14  3.000
 I59  O17  P13  C11   97.54  3.000
 I59  O16  P13  C11  106.28  3.000
 I59  O15  P13  C11  108.50  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
 I59  CONST_01  C4   C3   C2   C1    0.00  0.0  0
 I59  CONST_02  C7   C3   C2   C1  180.00  0.0  0
 I59  CONST_03  C4   C5   C6   C1    0.00  0.0  0
 I59  CONST_04  C5   C6   C1   C2    0.00  0.0  0
 I59  CONST_05  C5   C4   C3   C2    0.00  0.0  0
 I59  CONST_06  C10  C4   C3   C2  180.00  0.0  0
 I59  CONST_07  C8   C7   C3   C2  180.00  0.0  0
 I59  CONST_08  C6   C1   C2   C3    0.00  0.0  0
 I59  CONST_09  C6   C5   C4   C3    0.00  0.0  0
 I59  CONST_10  C9   C10  C4   C3    0.00  0.0  0
 I59  CONST_11  C9   C8   C7   C3    0.00  0.0  0
 I59  CONST_12  C8   C7   C3   C4    0.00  0.0  0
 I59  CONST_13  C8   C9   C10  C4    0.00  0.0  0
 I59  CONST_14  C7   C3   C4   C5  180.00  0.0  0
 I59  CONST_15  C9   C10  C4   C5  180.00  0.0  0
 I59  CONST_16  C10  C4   C5   C6  180.00  0.0  0
 I59  CONST_17  C10  C4   C3   C7    0.00  0.0  0
 I59  CONST_18  C10  C9   C8   C7    0.00  0.0  0
 I59  CONST_19  C11  C10  C4   C3  180.00  0.0  0
 I59  CONST_20  C11  C10  C4   C5    0.00  0.0  0
 I59  CONST_21  C11  C10  C9   C8  180.00  0.0  0
 I59  CONST_22  H5   C5   C6   C1  180.00  0.0  0
 I59  CONST_23  H6   C6   C1   C2  180.00  0.0  0
 I59  CONST_24  H7   C7   C3   C2    0.00  0.0  0
 I59  CONST_25  H1   C1   C2   C3  180.00  0.0  0
 I59  CONST_26  H8   C8   C7   C3  180.00  0.0  0
 I59  CONST_27  H2   C2   C3   C4  180.00  0.0  0
 I59  CONST_28  H9   C9   C10  C4  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 I59  chir_01  C11  C10  O12  P13  negativ

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
 I59  plan-1  C1   0.020
 I59  plan-1  C2   0.020
 I59  plan-1  C3   0.020
 I59  plan-1  C4   0.020
 I59  plan-1  C5   0.020
 I59  plan-1  C6   0.020
 I59  plan-1  C7   0.020
 I59  plan-1  C8   0.020
 I59  plan-1  C9   0.020
 I59  plan-1  C10  0.020
 I59  plan-1  C11  0.020
 I59  plan-1  H1   0.020
 I59  plan-1  H2   0.020
 I59  plan-1  H5   0.020
 I59  plan-1  H6   0.020
 I59  plan-1  H7   0.020
 I59  plan-1  H8   0.020
 I59  plan-1  H9   0.020

