# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:14:43 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  34  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 PERFECT
;

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  OP    -1  -0.890   0.8344  -3.0624  -0.5348
 KBK  P8   P  P      0   1.160  -0.1256  -2.2355   0.3267
 KBK  O11  O  O      0  -0.883  -1.5925  -2.6784   0.2062
 KBK  O10  O  OP    -1  -0.890   0.3357  -2.0199   1.7683
 KBK  C7   C  CH1    0  -0.261  -0.0613  -0.5262  -0.4731
 KBK  O12  O  O2     0  -0.503  -1.0268   0.3670   0.0735
 KBK  C13  C  CH2    0  -0.240  -2.2810   0.2469  -0.5174
 KBK  C14  C  C      0   0.474  -3.2263   1.1882   0.2033
 KBK  N16  N  NT     0  -0.201  -4.5176   1.1374  -0.2013
 KBK  C17  C  CH3    0  -0.514  -5.5377   2.0730   0.2012
 KBK  O18  O  OH1    0  -0.549  -4.7960   0.4399  -1.3502
 KBK  O15  O  O      0  -0.485  -2.8692   1.9274   1.1042
 KBK  C3   C  CR6    0   0.086   1.2937   0.0817  -0.3008
 KBK  C4   C  CR16   0  -0.297   1.5791   0.9879   0.7209
 KBK  C5   C  CR16   0  -0.336   2.8515   1.5085   0.8893
 KBK  C6   C  CR6    0   0.349   3.8918   1.1241   0.0442
 KBK  O19  O  O2     0  -0.479   5.1022   1.6842   0.2793
 KBK  C20  C  CH3    0  -0.432   6.1811   1.3131  -0.5504
 KBK  C1   C  CR16   0  -0.377   3.6286   0.2122  -0.9739
 KBK  C2   C  CR16   0  -0.278   2.3438  -0.2966  -1.1292
 KBK  H3   H  HCH1   0   0.182  -0.2462  -0.6495  -1.5528
 KBK  H4   H  HCH2   0   0.218  -2.2527   0.5180  -1.5852
 KBK  H5   H  HCH2   0   0.243  -2.6479  -0.7838  -0.4615
 KBK  H6   H  HCH3   0   0.255  -5.2569   2.5222   1.1484
 KBK  H7   H  HCH3   0   0.244  -5.6702   2.8650  -0.5389
 KBK  H8   H  HCH3   0   0.248  -6.4844   1.5512   0.3355
 KBK  H9   H  HOH1   0   0.478  -5.2090  -0.3881  -1.0691
 KBK  H10  H  HCR6   0   0.235   0.7941   1.3114   1.3907
 KBK  H11  H  HCR6   0   0.246   3.0474   2.2169   1.6857
 KBK  H12  H  HCH3   0   0.222   6.4046   0.2445  -0.4825
 KBK  H13  H  HCH3   0   0.222   6.0009   1.5645  -1.5996
 KBK  H14  H  HCH3   0   0.254   7.0476   1.8718  -0.2038
 KBK  H15  H  HCR6   0   0.265   4.4033  -0.1125  -1.6558
 KBK  H16  H  HCR6   0   0.232   2.1600  -1.0071  -1.9246

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   deloc     1.537  0.020  1.537
 KBK  C5   C4   aromatic  1.385  0.020  1.385
 KBK  C5   C6   aromatic  1.394  0.020  1.394
 KBK  C4   C3   aromatic  1.395  0.020  1.395
 KBK  O19  C6   single    1.354  0.020  1.354
 KBK  O19  C20  single    1.411  0.020  1.411
 KBK  P8   O10  deloc     1.529  0.020  1.529
 KBK  P8   O9   deloc     1.532  0.020  1.532
 KBK  P8   C7   single    1.888  0.020  1.888
 KBK  C6   C1   aromatic  1.392  0.020  1.392
 KBK  O18  N16  single    1.373  0.020  1.373
 KBK  C3   C7   single    1.495  0.020  1.495
 KBK  C3   C2   aromatic  1.390  0.020  1.390
 KBK  C7   O12  single    1.424  0.020  1.424
 KBK  C17  N16  single    1.441  0.020  1.441
 KBK  N16  C14  single    1.354  0.020  1.354
 KBK  C1   C2   aromatic  1.391  0.020  1.391
 KBK  O15  C14  double    1.219  0.020  1.219
 KBK  C14  C13  single    1.516  0.020  1.516
 KBK  O12  C13  single    1.392  0.020  1.392
 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  C7   P8   O10  105.16  3.000
 KBK  C7   P8   O11  105.08  3.000
 KBK  O10  P8   O11  113.74  3.000
 KBK  C7   P8   O9   103.24  3.000
 KBK  O10  P8   O9   114.66  3.000
 KBK  O11  P8   O9   113.47  3.000
 KBK  H3   C7   C3   108.08  3.000
 KBK  H3   C7   O12  109.41  3.000
 KBK  C3   C7   O12  108.37  3.000
 KBK  H3   C7   P8   107.93  3.000
 KBK  O12  C7   P8   112.46  3.000
 KBK  C3   C7   P8   110.49  3.000
 KBK  C13  O12  C7   113.19  3.000
 KBK  H5   C13  H4   106.83  3.000
 KBK  H5   C13  C14  110.54  3.000
 KBK  H4   C13  C14  108.89  3.000
 KBK  H5   C13  O12  111.19  3.000
 KBK  H4   C13  O12  111.54  3.000
 KBK  C14  C13  O12  107.84  3.000
 KBK  O15  C14  N16  121.53  3.000
 KBK  O15  C14  C13  123.04  3.000
 KBK  N16  C14  C13  115.42  3.000
 KBK  O18  N16  C17  114.84  3.000
 KBK  C17  N16  C14  124.55  3.000
 KBK  O18  N16  C14  117.55  3.000
 KBK  H8   C17  H7   109.00  3.000
 KBK  H8   C17  H6   108.39  3.000
 KBK  H7   C17  H6   108.83  3.000
 KBK  H8   C17  N16  109.79  3.000
 KBK  H7   C17  N16  111.55  3.000
 KBK  H6   C17  N16  109.22  3.000
 KBK  H9   O18  N16  106.17  3.000
 KBK  C2   C3   C4   117.30  3.000
 KBK  C2   C3   C7   120.35  3.000
 KBK  C4   C3   C7   122.27  3.000
 KBK  H10  C4   C5   118.63  3.000
 KBK  H10  C4   C3   119.96  3.000
 KBK  C5   C4   C3   121.40  3.000
 KBK  H11  C5   C6   119.39  3.000
 KBK  H11  C5   C4   120.07  3.000
 KBK  C6   C5   C4   120.54  3.000
 KBK  C1   C6   O19  124.54  3.000
 KBK  C1   C6   C5   118.87  3.000
 KBK  O19  C6   C5   116.59  3.000
 KBK  C20  O19  C6   118.21  3.000
 KBK  H14  C20  H13  108.59  3.000
 KBK  H14  C20  H12  108.61  3.000
 KBK  H13  C20  H12  108.52  3.000
 KBK  H14  C20  O19  106.67  3.000
 KBK  H13  C20  O19  112.19  3.000
 KBK  H12  C20  O19  112.13  3.000
 KBK  H15  C1   C2   118.77  3.000
 KBK  H15  C1   C6   121.48  3.000
 KBK  C2   C1   C6   119.75  3.000
 KBK  H16  C2   C1   118.63  3.000
 KBK  H16  C2   C3   119.24  3.000
 KBK  C1   C2   C3   122.13  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    -0.73  30.0  2
 KBK  Var_02    H12  C20  O19  C6    -61.57  30.0  3
 KBK  Var_03    C14  C13  O12  C7    176.83  30.0  3
 KBK  Var_04    N16  C14  C13  O12  -176.33  30.0  1
 KBK  Var_05    H6   C17  N16  C14   -24.15  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

