# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:54:35 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: [(R)-{2-[hydroxy(methyl)amino]-2-oxoethoxy}(4-methoxyphenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H](OCC(=O)N(C)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
 KBK  KBK  '[(R)-{2-[hydroxy(methyl)amino]-2-oxoethoxy}(4-methoxyphenyl)methyl]phosphonic acid'  ligand  36  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KBK
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
 KBK  O9   O  OH1   0  -0.735   1.1878  -3.0968  -0.0667
 KBK  P8   P  P     0   1.355  -0.1372  -2.3213   0.3897
 KBK  O11  O  O     0  -0.700  -1.4256  -3.0249   0.1721
 KBK  O10  O  OH1   0  -0.741   0.2933  -2.0755   1.9151
 KBK  C7   C  CH1   0  -0.283  -0.0770  -0.6629  -0.4088
 KBK  O12  O  O2    0  -0.483  -1.0762   0.1289   0.1879
 KBK  C13  C  CH2   0  -0.251  -2.3285   0.0834  -0.4435
 KBK  C14  C  C     0   0.486  -3.1612   1.2139   0.1397
 KBK  N16  N  NT    0  -0.198  -4.3861   1.3608  -0.4074
 KBK  C17  C  CH3   0  -0.514  -5.4073   2.2529   0.0815
 KBK  O18  O  OH1   0  -0.547  -4.8238   0.3822  -1.2615
 KBK  O15  O  O     0  -0.475  -2.7483   1.9468   1.0195
 KBK  C3   C  CR6   0   0.075   1.2644  -0.0073  -0.2460
 KBK  C4   C  CR16  0  -0.273   1.5712   0.7626   0.8757
 KBK  C5   C  CR16  0  -0.329   2.8187   1.3387   1.0187
 KBK  C6   C  CR6   0   0.374   3.8016   1.1514   0.0438
 KBK  O19  O  O2    0  -0.470   4.9857   1.7511   0.2662
 KBK  C20  C  CH3   0  -0.437   6.0009   1.6253  -0.7097
 KBK  C1   C  CR16  0  -0.372   3.5072   0.3814  -1.0784
 KBK  C2   C  CR16  0  -0.275   2.2464  -0.1870  -1.2088
 KBK  H1   H  HOH1  0   0.501   1.0865  -3.5920  -0.8898
 KBK  H2   H  HOH1  0   0.498  -0.4000  -1.6763   2.4566
 KBK  H3   H  HCH1  0   0.280  -0.2701  -0.8177  -1.4798
 KBK  H4   H  HCH2  0   0.251  -2.2268   0.2167  -1.5284
 KBK  H5   H  HCH2  0   0.256  -2.8335  -0.8740  -0.2822
 KBK  H6   H  HCH3  0   0.258  -4.9475   3.0112   0.7071
 KBK  H7   H  HCH3  0   0.251  -5.8986   2.7477  -0.7556
 KBK  H8   H  HCH3  0   0.249  -6.1551   1.7162   0.6677
 KBK  H9   H  HOH1  0   0.481  -4.7570   0.7497  -2.1542
 KBK  H10  H  HCR6  0   0.255   0.8293   0.9324   1.6446
 KBK  H11  H  HCR6  0   0.262   3.0433   1.9412   1.8902
 KBK  H12  H  HCH3  0   0.229   6.3071   0.5856  -0.8519
 KBK  H13  H  HCH3  0   0.229   5.6930   2.0374  -1.6741
 KBK  H14  H  HCH3  0   0.260   6.8533   2.1922  -0.3441
 KBK  H15  H  HCR6  0   0.280   4.2357   0.2184  -1.8604
 KBK  H16  H  HCR6  0   0.255   2.0327  -0.7758  -2.0932

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
 KBK  O11  P8   double    1.484  0.020  1.484
 KBK  C5   C4   aromatic  1.382  0.020  1.382
 KBK  C5   C6   aromatic  1.397  0.020  1.397
 KBK  C4   C3   aromatic  1.395  0.020  1.395
 KBK  O19  C6   single    1.346  0.020  1.346
 KBK  O19  C20  single    1.414  0.020  1.414
 KBK  P8   O10  single    1.604  0.020  1.604
 KBK  P8   O9   single    1.602  0.020  1.602
 KBK  P8   C7   single    1.842  0.020  1.842
 KBK  C6   C1   aromatic  1.392  0.020  1.392
 KBK  O18  N16  single    1.371  0.020  1.371
 KBK  C3   C7   single    1.502  0.020  1.502
 KBK  C3   C2   aromatic  1.387  0.020  1.387
 KBK  C7   O12  single    1.408  0.020  1.408
 KBK  C17  N16  single    1.441  0.020  1.441
 KBK  N16  C14  single    1.350  0.020  1.350
 KBK  C1   C2   aromatic  1.389  0.020  1.389
 KBK  O15  C14  double    1.217  0.020  1.217
 KBK  C14  C13  single    1.520  0.020  1.520
 KBK  O12  C13  single    1.403  0.020  1.403
 KBK  O9   H1   single    0.850  0.020  0.980
 KBK  O10  H2   single    0.850  0.020  0.980
 KBK  C7   H3   single    0.970  0.020  1.090
 KBK  C13  H4   single    0.970  0.020  1.090
 KBK  C13  H5   single    0.970  0.020  1.090
 KBK  C17  H6   single    0.970  0.020  1.090
 KBK  C17  H7   single    0.970  0.020  1.090
 KBK  C17  H8   single    0.970  0.020  1.090
 KBK  O18  H9   single    0.850  0.020  0.980
 KBK  C4   H10  single    0.930  0.020  1.080
 KBK  C5   H11  single    0.930  0.020  1.080
 KBK  C20  H12  single    0.970  0.020  1.090
 KBK  C20  H13  single    0.970  0.020  1.090
 KBK  C20  H14  single    0.970  0.020  1.090
 KBK  C1   H15  single    0.930  0.020  1.080
 KBK  C2   H16  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
 KBK  H1   O9   P8   113.84  3.000
 KBK  C7   P8   O10  105.40  3.000
 KBK  C7   P8   O11  113.07  3.000
 KBK  O10  P8   O11  116.43  3.000
 KBK  C7   P8   O9   106.58  3.000
 KBK  O10  P8   O9    97.07  3.000
 KBK  O11  P8   O9   116.54  3.000
 KBK  H2   O10  P8   113.81  3.000
 KBK  H3   C7   C3   108.91  3.000
 KBK  H3   C7   O12  111.56  3.000
 KBK  C3   C7   O12  110.03  3.000
 KBK  H3   C7   P8   106.85  3.000
 KBK  O12  C7   P8   107.43  3.000
 KBK  C3   C7   P8   112.05  3.000
 KBK  C13  O12  C7   115.12  3.000
 KBK  H5   C13  H4   107.13  3.000
 KBK  H5   C13  C14  109.96  3.000
 KBK  H4   C13  C14  109.85  3.000
 KBK  H5   C13  O12  111.95  3.000
 KBK  H4   C13  O12  110.98  3.000
 KBK  C14  C13  O12  106.98  3.000
 KBK  O15  C14  N16  122.37  3.000
 KBK  O15  C14  C13  122.63  3.000
 KBK  N16  C14  C13  114.99  3.000
 KBK  O18  N16  C17  115.27  3.000
 KBK  C17  N16  C14  124.95  3.000
 KBK  O18  N16  C14  117.70  3.000
 KBK  H8   C17  H7   109.09  3.000
 KBK  H8   C17  H6   108.92  3.000
 KBK  H7   C17  H6   108.46  3.000
 KBK  H8   C17  N16  111.30  3.000
 KBK  H7   C17  N16  109.88  3.000
 KBK  H6   C17  N16  109.14  3.000
 KBK  H9   O18  N16  106.36  3.000
 KBK  C2   C3   C4   118.30  3.000
 KBK  C2   C3   C7   120.04  3.000
 KBK  C4   C3   C7   121.64  3.000
 KBK  H10  C4   C5   118.70  3.000
 KBK  H10  C4   C3   120.49  3.000
 KBK  C5   C4   C3   120.80  3.000
 KBK  H11  C5   C6   119.36  3.000
 KBK  H11  C5   C4   120.17  3.000
 KBK  C6   C5   C4   120.48  3.000
 KBK  C1   C6   O19  124.45  3.000
 KBK  C1   C6   C5   119.20  3.000
 KBK  O19  C6   C5   116.35  3.000
 KBK  C20  O19  C6   118.56  3.000
 KBK  H14  C20  H13  108.73  3.000
 KBK  H14  C20  H12  108.67  3.000
 KBK  H13  C20  H12  108.83  3.000
 KBK  H14  C20  O19  106.53  3.000
 KBK  H13  C20  O19  111.92  3.000
 KBK  H12  C20  O19  112.06  3.000
 KBK  H15  C1   C2   118.81  3.000
 KBK  H15  C1   C6   121.60  3.000
 KBK  C2   C1   C6   119.59  3.000
 KBK  H16  C2   C1   118.55  3.000
 KBK  H16  C2   C3   119.82  3.000
 KBK  C1   C2   C3   121.63  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
 KBK  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 KBK  CONST_02  C6   C1   C2   C3      0.00   0.0  0
 KBK  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 KBK  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 KBK  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 KBK  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 KBK  CONST_07  C5   C4   C3   C7    180.00   0.0  0
 KBK  CONST_08  C1   C2   C3   C7    180.00   0.0  0
 KBK  CONST_09  O19  C6   C5   C4    180.00   0.0  0
 KBK  CONST_10  C2   C1   C6   O19   180.00   0.0  0
 KBK  CONST_11  H11  C5   C4   C3    180.00   0.0  0
 KBK  CONST_12  H15  C1   C2   C3    180.00   0.0  0
 KBK  CONST_13  H16  C2   C3   C4    180.00   0.0  0
 KBK  CONST_14  H10  C4   C5   C6    180.00   0.0  0
 KBK  CONST_15  O18  N16  C14  C13     0.00   0.0  0
 KBK  CONST_16  C17  N16  C14  C13   180.00   0.0  0
 KBK  CONST_17  O15  C14  N16  C17     0.00   0.0  0
 KBK  CONST_18  O15  C14  N16  O18   180.00   0.0  0
 KBK  Var_01    C1   C6   O19  C20     1.48  30.0  2
 KBK  Var_02    H12  C20  O19  C6    -62.31  30.0  3
 KBK  Var_03    C14  C13  O12  C7   -167.57  30.0  3
 KBK  Var_04    N16  C14  C13  O12   176.83  30.0  2
 KBK  Var_05    H6   C17  N16  C14    19.49  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
 KBK  chir_01  C7  P8  C3  O12  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
 KBK  plan-1  C7   0.020
 KBK  plan-1  C3   0.020
 KBK  plan-1  C4   0.020
 KBK  plan-1  C5   0.020
 KBK  plan-1  C6   0.020
 KBK  plan-1  O19  0.020
 KBK  plan-1  C1   0.020
 KBK  plan-1  C2   0.020
 KBK  plan-1  H10  0.020
 KBK  plan-1  H11  0.020
 KBK  plan-1  H15  0.020
 KBK  plan-1  H16  0.020
 KBK  plan-2  C13  0.020
 KBK  plan-2  C14  0.020
 KBK  plan-2  N16  0.020
 KBK  plan-2  C17  0.020
 KBK  plan-2  O18  0.020
 KBK  plan-2  O15  0.020

