# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:27:42 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: {(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)CC[C@@H](c1ccc(F)c(F)c1)[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
 C0K  C0K  '{(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid'  ligand  34  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C0K
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
 C0K  C1    C  CR16  0  -0.371  -3.6271   0.0651   1.5967
 C0K  C2    C  CR16  0  -0.262  -2.3066  -0.3572   1.5918
 C0K  C3    C  CR6   0   0.145  -1.4508  -0.0364   0.5435
 C0K  C4    C  CR16  0  -0.469  -1.9482   0.7196  -0.5173
 C0K  C5    C  CR6   0   0.431  -3.2629   1.1345  -0.5090
 C0K  C6    C  CR6   0   0.394  -4.1046   0.8089   0.5390
 C0K  C7    C  CH1   0  -0.608  -0.0205  -0.5153   0.5538
 C0K  P8    P  P     0   1.386   0.1307  -2.0685  -0.3896
 C0K  O9    O  OH1   0  -0.734  -0.4527  -1.7549  -1.8593
 C0K  O10   O  O     0  -0.687   1.4946  -2.6314  -0.5137
 C0K  O11   O  OH1   0  -0.719  -0.9557  -2.9993   0.3395
 C0K  C12   C  CH2   0  -0.426   0.9791   0.5353   0.0359
 C0K  C13   C  CH2   0  -0.567   2.3987   0.2827   0.5223
 C0K  C14   C  C     0   0.568   3.3688   1.3068  -0.0266
 C0K  O15   O  O     0  -0.482   3.0156   2.2517  -0.7125
 C0K  N16   N  NT    0  -0.212   4.6755   1.1056   0.2675
 C0K  C17   C  CH3   0  -0.487   5.7509   2.0061  -0.0574
 C0K  O18   O  OH1   0  -0.530   5.0025   0.1165   1.1567
 C0K  F19   F  F     0  -0.309  -3.7395   1.8644  -1.5232
 C0K  F20   F  F     0  -0.298  -5.3697   1.2315   0.5180
 C0K  H1    H  HCR6  0   0.275  -4.2842  -0.1812   2.4194
 C0K  H2    H  HCR6  0   0.243  -1.9423  -0.9349   2.4304
 C0K  H4    H  HCR6  0   0.275  -1.3239   1.0253  -1.3473
 C0K  H7    H  HCH1  0   0.292   0.2430  -0.7702   1.5858
 C0K  HO9   H  HOH1  0   0.472  -1.3964  -1.5650  -1.9090
 C0K  HO11  H  HOH1  0   0.472  -0.9171  -3.9220   0.0612
 C0K  H12   H  HCH2  0   0.239   0.9606   0.5815  -1.0548
 C0K  H12A  H  HCH2  0   0.265   0.6420   1.5117   0.3865
 C0K  H13   H  HCH2  0   0.262   2.4275   0.3161   1.6152
 C0K  H13A  H  HCH2  0   0.275   2.7229  -0.7211   0.2464
 C0K  H17   H  HCH3  0   0.240   6.1717   2.4518   0.8443
 C0K  H17A  H  HCH3  0   0.226   6.5435   1.4806  -0.5916
 C0K  H17B  H  HCH3  0   0.253   5.3742   2.7981  -0.6956
 C0K  HO18  H  HOH1  0   0.450   5.3206  -0.6297   0.6328

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
 C0K  C2   C1    aromatic  1.386  0.020  1.386
 C0K  C6   C1    aromatic  1.378  0.020  1.378
 C0K  C1   H1    single    0.930  0.020  1.080
 C0K  C3   C2    aromatic  1.391  0.020  1.391
 C0K  C2   H2    single    0.930  0.020  1.080
 C0K  C7   C3    single    1.508  0.020  1.508
 C0K  C4   C3    aromatic  1.394  0.020  1.394
 C0K  C4   C5    aromatic  1.379  0.020  1.379
 C0K  C4   H4    single    0.930  0.020  1.080
 C0K  C5   F19   single    1.337  0.020  1.337
 C0K  C5   C6    aromatic  1.383  0.020  1.383
 C0K  C6   F20   single    1.334  0.020  1.334
 C0K  C12  C7    single    1.540  0.020  1.540
 C0K  C7   P8    single    1.824  0.020  1.824
 C0K  C7   H7    single    0.970  0.020  1.090
 C0K  O10  P8    double    1.481  0.020  1.481
 C0K  P8   O11   single    1.606  0.020  1.606
 C0K  P8   O9    single    1.612  0.020  1.612
 C0K  O9   HO9   single    0.850  0.020  0.980
 C0K  O11  HO11  single    0.850  0.020  0.980
 C0K  C13  C12   single    1.522  0.020  1.522
 C0K  C12  H12   single    0.970  0.020  1.090
 C0K  C12  H12A  single    0.970  0.020  1.090
 C0K  C14  C13   single    1.514  0.020  1.514
 C0K  C13  H13   single    0.970  0.020  1.090
 C0K  C13  H13A  single    0.970  0.020  1.090
 C0K  O15  C14   double    1.220  0.020  1.220
 C0K  N16  C14   single    1.354  0.020  1.354
 C0K  O18  N16   single    1.370  0.020  1.370
 C0K  N16  C17   single    1.440  0.020  1.440
 C0K  C17  H17   single    0.970  0.020  1.090
 C0K  C17  H17A  single    0.970  0.020  1.090
 C0K  C17  H17B  single    0.970  0.020  1.090
 C0K  O18  HO18  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
 C0K  H1    C1   C6    119.75  3.000
 C0K  H1    C1   C2    120.80  3.000
 C0K  C6    C1   C2    119.45  3.000
 C0K  H2    C2   C3    120.03  3.000
 C0K  H2    C2   C1    118.74  3.000
 C0K  C3    C2   C1    121.23  3.000
 C0K  C7    C3   C4    121.03  3.000
 C0K  C4    C3   C2    118.62  3.000
 C0K  C7    C3   C2    120.34  3.000
 C0K  H4    C4   C5    118.01  3.000
 C0K  H4    C4   C3    122.05  3.000
 C0K  C5    C4   C3    119.92  3.000
 C0K  F19   C5   C6    119.10  3.000
 C0K  C6    C5   C4    120.94  3.000
 C0K  F19   C5   C4    119.97  3.000
 C0K  F20   C6   C5    119.38  3.000
 C0K  F20   C6   C1    120.77  3.000
 C0K  C5    C6   C1    119.85  3.000
 C0K  H7    C7   C12   108.64  3.000
 C0K  H7    C7   P8    105.62  3.000
 C0K  C12   C7   P8    110.69  3.000
 C0K  H7    C7   C3    107.96  3.000
 C0K  P8    C7   C3    110.21  3.000
 C0K  C12   C7   C3    113.37  3.000
 C0K  O11   P8   O10   116.16  3.000
 C0K  O11   P8   O9    106.37  3.000
 C0K  O10   P8   O9    109.32  3.000
 C0K  O9    P8   C7    106.02  3.000
 C0K  O11   P8   C7    101.70  3.000
 C0K  O10   P8   C7    116.33  3.000
 C0K  HO9   O9   P8    116.08  3.000
 C0K  HO11  O11  P8    113.36  3.000
 C0K  H12A  C12  H12   106.14  3.000
 C0K  H12A  C12  C13   109.52  3.000
 C0K  H12   C12  C13   110.01  3.000
 C0K  H12A  C12  C7    107.58  3.000
 C0K  H12   C12  C7    110.72  3.000
 C0K  C13   C12  C7    112.63  3.000
 C0K  H13A  C13  H13   105.85  3.000
 C0K  H13A  C13  C14   109.91  3.000
 C0K  H13   C13  C14   108.95  3.000
 C0K  H13A  C13  C12   110.45  3.000
 C0K  H13   C13  C12   109.81  3.000
 C0K  C14   C13  C12   111.69  3.000
 C0K  N16   C14  O15   121.09  3.000
 C0K  N16   C14  C13   116.05  3.000
 C0K  O15   C14  C13   122.85  3.000
 C0K  O18   N16  C17   114.82  3.000
 C0K  C17   N16  C14   125.36  3.000
 C0K  O18   N16  C14   118.59  3.000
 C0K  H17B  C17  H17A  108.42  3.000
 C0K  H17B  C17  H17   108.79  3.000
 C0K  H17A  C17  H17   108.76  3.000
 C0K  H17B  C17  N16   109.27  3.000
 C0K  H17A  C17  N16   110.61  3.000
 C0K  H17   C17  N16   110.93  3.000
 C0K  HO18  O18  N16   106.53  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
 C0K  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 C0K  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 C0K  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 C0K  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 C0K  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 C0K  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 C0K  CONST_07  C7   C3   C2   C1   180.00   0.0  0
 C0K  CONST_08  F19  C5   C6   C1   180.00   0.0  0
 C0K  CONST_09  F20  C6   C1   C2   180.00   0.0  0
 C0K  CONST_10  F19  C5   C4   C3   180.00   0.0  0
 C0K  CONST_11  F20  C6   C5   C4   180.00   0.0  0
 C0K  CONST_12  C7   C3   C4   C5   180.00   0.0  0
 C0K  CONST_13  H4   C4   C3   C2   180.00   0.0  0
 C0K  CONST_14  H1   C1   C2   C3   180.00   0.0  0
 C0K  CONST_15  H2   C2   C3   C4   180.00   0.0  0
 C0K  CONST_16  O18  N16  C14  C13    0.00   0.0  0
 C0K  CONST_17  C17  N16  C14  C13  180.00   0.0  0
 C0K  CONST_18  O18  N16  C14  O15  180.00   0.0  0
 C0K  CONST_19  C17  N16  C14  O15    0.00   0.0  0
 C0K  Var_01    C14  C13  C12  C7   178.58  30.0  1
 C0K  Var_02    O15  C14  C13  C12    3.76  30.0  2
 C0K  Var_03    H17  C17  N16  C14  111.92  30.0  3

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
 C0K  chir_01  C7  C3  C12  P8  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
 C0K  plan-1  C1   0.020
 C0K  plan-1  C2   0.020
 C0K  plan-1  C3   0.020
 C0K  plan-1  C4   0.020
 C0K  plan-1  C5   0.020
 C0K  plan-1  C6   0.020
 C0K  plan-1  C7   0.020
 C0K  plan-1  F19  0.020
 C0K  plan-1  F20  0.020
 C0K  plan-1  H1   0.020
 C0K  plan-1  H2   0.020
 C0K  plan-1  H4   0.020
 C0K  plan-2  C13  0.020
 C0K  plan-2  C14  0.020
 C0K  plan-2  O15  0.020
 C0K  plan-2  N16  0.020
 C0K  plan-2  C17  0.020
 C0K  plan-2  O18  0.020

