# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:11:50 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](c1cccc(n1)C(O)=O)[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
 60N  60N  '6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid'  ligand  20  15  .  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_60N
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
 60N  C10  C  CR16   0  -0.337   2.6663   1.1617  -0.3799
 60N  C11  C  CR6    0   0.024   2.1752   0.0974   0.3688
 60N  C12  C  C      0   0.374   3.1129  -1.0265   0.8159
 60N  O01  O  OH1    0  -0.717  -2.0830   2.0026   0.8509
 60N  C02  C  CH1    0  -0.326  -1.3826   0.7817   0.7551
 60N  P03  P  P      0   1.154  -2.3236  -0.2774  -0.5375
 60N  O04  O  O      0  -0.863  -1.3289  -0.7042  -1.6093
 60N  O05  O  OP    -1  -0.884  -2.9795  -1.4256   0.2250
 60N  O06  O  OP    -1  -0.891  -3.3266   0.8123  -1.0058
 60N  C07  C  CR6    0   0.258   0.0440   0.9695   0.3577
 60N  C08  C  CR16   0  -0.351   0.4577   2.0765  -0.3842
 60N  C09  C  CR16   0  -0.157   1.7870   2.1683  -0.7530
 60N  O13  O  OC    -1  -0.594   2.6275  -1.9147   1.5356
 60N  O14  O  O      0  -0.597   4.2913  -0.9474   0.4125
 60N  N15  N  N      0  -0.441   0.8973   0.0187   0.7289
 60N  H1   H  HCR6   0   0.241   3.7109   1.2014  -0.6522
 60N  H3   H  HCH1   0   0.188  -1.3942   0.2499   1.7165
 60N  H6   H  HCR6   0   0.241  -0.2506   2.8463  -0.6568
 60N  H7   H  HCR6   0   0.249   2.1387   3.0183  -1.3254
 60N  H2   H  HOH1   0   0.426  -2.7564   1.8864   0.1301

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
 60N  O04  P03  deloc     1.523  0.020  1.523
 60N  O05  P03  deloc     1.526  0.020  1.526
 60N  P03  O06  deloc     1.553  0.020  1.553
 60N  P03  C02  single    1.918  0.020  1.918
 60N  O01  C02  single    1.411  0.020  1.411
 60N  C02  C07  single    1.493  0.020  1.493
 60N  C08  C07  aromatic  1.395  0.020  1.395
 60N  C08  C09  aromatic  1.383  0.020  1.383
 60N  C07  N15  aromatic  1.330  0.020  1.330
 60N  C09  C10  aromatic  1.388  0.020  1.388
 60N  N15  C11  aromatic  1.330  0.020  1.330
 60N  C10  C11  aromatic  1.391  0.020  1.391
 60N  C11  C12  single    1.530  0.020  1.530
 60N  C12  O14  deloc     1.248  0.020  1.248
 60N  C12  O13  deloc     1.242  0.020  1.242
 60N  C10  H1   single    0.930  0.020  1.080
 60N  O01  H2   single    0.850  0.020  0.980
 60N  C02  H3   single    0.970  0.020  1.090
 60N  C08  H6   single    0.930  0.020  1.080
 60N  C09  H7   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
 60N  H1   C10  C09  121.22  3.000
 60N  H1   C10  C11  120.35  3.000
 60N  C09  C10  C11  118.43  3.000
 60N  N15  C11  C12  117.79  3.000
 60N  C12  C11  C10  120.19  3.000
 60N  N15  C11  C10  122.02  3.000
 60N  O14  C12  O13  126.98  3.000
 60N  O13  C12  C11  117.07  3.000
 60N  O14  C12  C11  115.95  3.000
 60N  H2   O01  C02  100.72  3.000
 60N  H3   C02  C07  107.69  3.000
 60N  H3   C02  P03  108.50  3.000
 60N  C07  C02  P03  111.03  3.000
 60N  H3   C02  O01  110.74  3.000
 60N  C07  C02  O01  112.56  3.000
 60N  P03  C02  O01  106.27  3.000
 60N  O06  P03  O05  113.63  3.000
 60N  O06  P03  O04  113.95  3.000
 60N  O05  P03  O04  114.92  3.000
 60N  O06  P03  C02   97.62  3.000
 60N  O05  P03  C02  106.84  3.000
 60N  O04  P03  C02  107.97  3.000
 60N  N15  C07  C08  121.68  3.000
 60N  N15  C07  C02  116.67  3.000
 60N  C08  C07  C02  121.65  3.000
 60N  H6   C08  C09  121.02  3.000
 60N  H6   C08  C07  120.32  3.000
 60N  C09  C08  C07  118.66  3.000
 60N  H7   C09  C08  120.34  3.000
 60N  H7   C09  C10  120.36  3.000
 60N  C08  C09  C10  119.30  3.000
 60N  C07  N15  C11  119.90  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
 60N  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 60N  CONST_02  C07  N15  C11  C10    0.00   0.0  0
 60N  CONST_03  C08  C07  N15  C11    0.00   0.0  0
 60N  CONST_04  C08  C09  C10  C11    0.00   0.0  0
 60N  CONST_05  N15  C07  C08  C09    0.00   0.0  0
 60N  CONST_06  N15  C11  C10  C09    0.00   0.0  0
 60N  CONST_07  C02  C07  N15  C11  180.00   0.0  0
 60N  CONST_08  C07  N15  C11  C12  180.00   0.0  0
 60N  CONST_09  C09  C10  C11  C12  180.00   0.0  0
 60N  CONST_10  C09  C08  C07  C02  180.00   0.0  0
 60N  CONST_11  H6   C08  C09  C10  180.00   0.0  0
 60N  CONST_12  H7   C09  C10  C11  180.00   0.0  0
 60N  CONST_13  H1   C10  C09  C08  180.00   0.0  0
 60N  Var_01    O14  C12  C11  C10   -3.37  30.0  2

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
 60N  chir_01  C02  P03  O01  C07  positiv

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
 60N  plan-1  C10  0.020
 60N  plan-1  C11  0.020
 60N  plan-1  C12  0.020
 60N  plan-1  C02  0.020
 60N  plan-1  C07  0.020
 60N  plan-1  C08  0.020
 60N  plan-1  C09  0.020
 60N  plan-1  N15  0.020
 60N  plan-1  H1   0.020
 60N  plan-1  H6   0.020
 60N  plan-1  H7   0.020
 60N  plan-2  C11  0.020
 60N  plan-2  C12  0.020
 60N  plan-2  O13  0.020
 60N  plan-2  O14  0.020

