# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:28:26 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  27  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  -0.261  -1.7824   0.0418   3.4802
 I59  C2   C  CR16  0  -0.309  -0.4680  -0.3205   3.5717
 I59  C3   C  CR66  0   0.111   0.3968  -0.2054   2.4576
 I59  C4   C  CR66  0   0.126  -0.1068   0.2926   1.2243
 I59  C5   C  CR16  0  -0.333  -1.4762   0.6526   1.1660
 I59  C6   C  CR16  0  -0.251  -2.2872   0.5368   2.2619
 I59  C7   C  CR16  0  -0.327   1.7561  -0.5799   2.5593
 I59  C8   C  CR16  0  -0.242   2.5855  -0.4621   1.4820
 I59  C9   C  CR16  0  -0.331   2.0927   0.0346   0.2603
 I59  C10  C  CR6   0   0.058   0.7817   0.4100   0.1139
 I59  C11  C  CH1   0  -0.305   0.2918   0.9366  -1.2179
 I59  O12  O  OH1   0  -0.641   1.2600   1.6040  -1.9803
 I59  P13  P  P     0   1.350  -0.4526  -0.4479  -2.1734
 I59  O15  O  O     0  -0.689  -1.4095  -1.2870  -1.4186
 I59  O16  O  OH1   0  -0.744  -1.0115   0.3209  -3.4646
 I59  O17  O  OH1   0  -0.750   0.8097  -1.3146  -2.6725
 I59  H1   H  HCR6  0   0.260  -2.4370  -0.0483   4.3371
 I59  H2   H  HCR6  0   0.257  -0.0672  -0.7022   4.5030
 I59  H5   H  HCR6  0   0.242  -1.9075   1.0269   0.2492
 I59  H6   H  HCR6  0   0.261  -3.3284   0.8229   2.1905
 I59  H7   H  HCR6  0   0.259   2.1279  -0.9596   3.5030
 I59  H8   H  HCR6  0   0.262   3.6266  -0.7462   1.5571
 I59  H9   H  HCR6  0   0.243   2.7934   0.1187  -0.5598
 I59  H11  H  HCH1  0   0.300  -0.5032   1.6680  -1.0515
 I59  H12  H  HOH1  0   0.459   1.9746   1.0044  -2.2185
 I59  H16  H  HOH1  0   0.499  -1.5927  -0.2092  -4.0281
 I59  H17  H  HOH1  0   0.496   1.1818  -1.0828  -3.5328

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  1.367  0.020  1.367
 I59  C1   C6   aromatic  1.409  0.020  1.409
 I59  C1   H1   single    0.930  0.020  1.080
 I59  C2   C3   aromatic  1.415  0.020  1.415
 I59  C2   H2   single    0.930  0.020  1.080
 I59  C3   C4   aromatic  1.422  0.020  1.422
 I59  C3   C7   aromatic  1.414  0.020  1.414
 I59  C4   C5   aromatic  1.417  0.020  1.417
 I59  C4   C10  aromatic  1.427  0.020  1.427
 I59  C5   C6   aromatic  1.368  0.020  1.368
 I59  C5   H5   single    0.930  0.020  1.080
 I59  C6   H6   single    0.930  0.020  1.080
 I59  C7   C8   aromatic  1.365  0.020  1.365
 I59  C7   H7   single    0.930  0.020  1.080
 I59  C8   C9   aromatic  1.408  0.020  1.408
 I59  C8   H8   single    0.930  0.020  1.080
 I59  C9   C10  aromatic  1.372  0.020  1.372
 I59  C9   H9   single    0.930  0.020  1.080
 I59  C10  C11  single    1.514  0.020  1.514
 I59  C11  O12  single    1.401  0.020  1.401
 I59  C11  P13  single    1.840  0.020  1.840
 I59  C11  H11  single    0.970  0.020  1.090
 I59  O12  H12  single    0.850  0.020  0.980
 I59  P13  O15  double    1.480  0.020  1.480
 I59  P13  O16  single    1.603  0.020  1.603
 I59  P13  O17  single    1.611  0.020  1.611
 I59  O16  H16  single    0.850  0.020  0.980
 I59  O17  H17  single    0.850  0.020  0.980

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   119.83  3.000
 I59  H1   C1   C2   120.45  3.000
 I59  C6   C1   C2   119.72  3.000
 I59  H2   C2   C3   118.65  3.000
 I59  H2   C2   C1   120.45  3.000
 I59  C3   C2   C1   120.90  3.000
 I59  C7   C3   C4   119.71  3.000
 I59  C7   C3   C2   120.63  3.000
 I59  C4   C3   C2   119.66  3.000
 I59  C10  C4   C5   123.28  3.000
 I59  C10  C4   C3   118.89  3.000
 I59  C5   C4   C3   117.83  3.000
 I59  H5   C5   C6   118.20  3.000
 I59  H5   C5   C4   120.59  3.000
 I59  C6   C5   C4   121.22  3.000
 I59  H6   C6   C5   119.67  3.000
 I59  H6   C6   C1   119.65  3.000
 I59  C5   C6   C1   120.67  3.000
 I59  H7   C7   C8   120.63  3.000
 I59  H7   C7   C3   119.06  3.000
 I59  C8   C7   C3   120.32  3.000
 I59  H8   C8   C9   119.32  3.000
 I59  H8   C8   C7   120.50  3.000
 I59  C9   C8   C7   120.18  3.000
 I59  H9   C9   C10  121.13  3.000
 I59  H9   C9   C8   117.29  3.000
 I59  C10  C9   C8   121.58  3.000
 I59  C11  C10  C9   119.90  3.000
 I59  C11  C10  C4   120.78  3.000
 I59  C9   C10  C4   119.32  3.000
 I59  H11  C11  P13  106.76  3.000
 I59  H11  C11  O12  105.46  3.000
 I59  P13  C11  O12  110.82  3.000
 I59  H11  C11  C10  109.53  3.000
 I59  P13  C11  C10  109.04  3.000
 I59  O12  C11  C10  114.88  3.000
 I59  H12  O12  C11  110.53  3.000
 I59  O17  P13  O16  106.36  3.000
 I59  O17  P13  O15  111.09  3.000
 I59  O16  P13  O15  117.22  3.000
 I59  O17  P13  C11  104.41  3.000
 I59  O16  P13  C11  101.45  3.000
 I59  O15  P13  C11  115.06  3.000
 I59  H16  O16  P13  114.56  3.000
 I59  H17  O17  P13  116.68  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

