# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 03:28:11 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CO)C(O)=O)c1O
#
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
 KOU  KOU  (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine  ligand  37  22  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KOU
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
 KOU  C     C  C     0   0.557  -4.3050   1.4404   0.6403
 KOU  N     N  N     0  -0.289  -2.3556   0.3157  -0.2158
 KOU  O     O  O     0  -0.422  -4.7338   0.4004   1.0622
 KOU  P     P  P     0   1.463   3.9413   1.4077  -0.3906
 KOU  N1    N  N     0  -0.400   1.0739  -3.3926   0.1418
 KOU  C2    C  CR6   0   0.125  -0.2381  -3.4848   0.2520
 KOU  C3    C  CR6   0   0.263  -1.0493  -2.3382   0.3137
 KOU  O3    O  OH1   0  -0.591  -2.3787  -2.4240   0.4451
 KOU  C4    C  CR6   0   0.037  -0.4514  -1.0800   0.2613
 KOU  C5    C  CR6   0  -0.056   0.9456  -1.0128   0.1579
 KOU  C6    C  CR16  0  -0.137   1.6557  -2.1981   0.0952
 KOU  CA    C  CH1   0  -0.291  -2.9803   1.6061  -0.0843
 KOU  CB    C  CH2   0  -0.145  -3.2034   2.2221  -1.4621
 KOU  OG    O  OH1   0  -0.664  -4.1735   1.4600  -2.1337
 KOU  O1P   O  OH1   0  -0.738   3.7411   1.6544  -1.9550
 KOU  O2P   O  OH1   0  -0.727   5.3418   0.6820  -0.1794
 KOU  O3P   O  O     0  -0.706   3.6825   2.6568   0.3473
 KOU  C4A   C  C1    0  -0.076  -1.2321   0.1678   0.3379
 KOU  O4P   O  O2    0  -0.591   3.0250   0.1549  -0.0013
 KOU  C5A   C  CH2   0  -0.211   1.6180   0.3303   0.0965
 KOU  OXT   O  OH1   0  -0.594  -4.9227   2.6063   0.7796
 KOU  HO3   H  HOH1  0   0.486  -2.6507  -3.3363   0.5957
 KOU  H6    H  HCR6  0   0.262   2.7334  -2.2006   0.0021
 KOU  HA    H  HCH1  0   0.277  -2.3707   2.3148   0.4992
 KOU  HB    H  HCH2  0   0.221  -3.5091   3.2659  -1.3364
 KOU  HBA   H  HCH2  0   0.221  -2.2421   2.2321  -1.9906
 KOU  HOG   H  HOH1  0   0.462  -4.3843   1.8997  -2.9623
 KOU  HO1P  H  HOH1  0   0.498   3.9505   0.9072  -2.5317
 KOU  H2A   H  HCH3  0   0.260  -1.3516  -5.0319   1.2697
 KOU  H2AA  H  HCH3  0   0.260  -1.5856  -5.0125  -0.4783
 KOU  H2AB  H  HCH3  0   0.274  -0.0758  -5.6063   0.2051
 KOU  HO2P  H  HOH1  0   0.506   6.1058   1.2676  -0.2725
 KOU  H4A   H  H     0   0.243  -0.7653   0.9803   0.9074
 KOU  H5A   H  HCH2  0   0.259   1.2364   0.8894  -0.7646
 KOU  H5AA  H  HCH2  0   0.268   1.3855   0.9139   0.9919
 KOU  HOXT  H  HOH1  0   0.484  -5.7599   2.4848   1.2522
 KOU  C2A   C  CH3   0  -0.788  -0.8509  -4.8519   0.3144

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
 KOU  C    CA    single    1.519  0.020  1.519
 KOU  C    OXT   single    1.327  0.020  1.327
 KOU  N    C4A   double    1.261  0.020  1.261
 KOU  N    CA    single    1.440  0.020  1.440
 KOU  O    C     double    1.201  0.020  1.201
 KOU  P    O2P   single    1.591  0.020  1.591
 KOU  P    O1P   single    1.596  0.020  1.596
 KOU  N1   C6    aromatic  1.329  0.020  1.329
 KOU  C2   N1    aromatic  1.320  0.020  1.320
 KOU  C2   C3    aromatic  1.406  0.020  1.406
 KOU  C3   C4    aromatic  1.394  0.020  1.394
 KOU  O3   C3    single    1.339  0.020  1.339
 KOU  O3   HO3   single    0.850  0.020  0.980
 KOU  C4   C5    aromatic  1.402  0.020  1.402
 KOU  C4   C4A   single    1.474  0.020  1.474
 KOU  C5   C5A   single    1.503  0.020  1.503
 KOU  C6   C5    aromatic  1.383  0.020  1.383
 KOU  C6   H6    single    0.930  0.020  1.080
 KOU  CA   CB    single    1.526  0.020  1.526
 KOU  CA   HA    single    0.970  0.020  1.090
 KOU  CB   OG    single    1.405  0.020  1.405
 KOU  CB   HB    single    0.970  0.020  1.090
 KOU  CB   HBA   single    0.970  0.020  1.090
 KOU  OG   HOG   single    0.850  0.020  0.980
 KOU  O1P  HO1P  single    0.850  0.020  0.980
 KOU  C2A  C2    single    1.499  0.020  1.499
 KOU  C2A  H2A   single    0.970  0.020  1.090
 KOU  C2A  H2AA  single    0.970  0.020  1.090
 KOU  C2A  H2AB  single    0.970  0.020  1.090
 KOU  O2P  HO2P  single    0.850  0.020  0.980
 KOU  O3P  P     double    1.474  0.020  1.474
 KOU  C4A  H4A   single    0.930  0.020  1.080
 KOU  O4P  P     single    1.600  0.020  1.600
 KOU  C5A  O4P   single    1.421  0.020  1.421
 KOU  C5A  H5A   single    0.970  0.020  1.090
 KOU  C5A  H5AA  single    0.970  0.020  1.090
 KOU  OXT  HOXT  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
 KOU  OXT   C    CA    111.11  3.000
 KOU  OXT   C    O     123.89  3.000
 KOU  CA    C    O     124.98  3.000
 KOU  C4A   N    CA    116.84  3.000
 KOU  O4P   P    O3P   116.18  3.000
 KOU  O4P   P    O2P    96.58  3.000
 KOU  O3P   P    O2P   118.33  3.000
 KOU  O4P   P    O1P   106.72  3.000
 KOU  O3P   P    O1P   109.73  3.000
 KOU  O2P   P    O1P   108.11  3.000
 KOU  C6    N1   C2    120.05  3.000
 KOU  C2A   C2   C3    120.40  3.000
 KOU  C2A   C2   N1    118.25  3.000
 KOU  C3    C2   N1    121.35  3.000
 KOU  C4    C3   O3    119.17  3.000
 KOU  O3    C3   C2    121.67  3.000
 KOU  C4    C3   C2    119.14  3.000
 KOU  HO3   O3   C3    110.87  3.000
 KOU  C4A   C4   C5    119.40  3.000
 KOU  C4A   C4   C3    122.34  3.000
 KOU  C5    C4   C3    118.24  3.000
 KOU  C5A   C5   C6    122.29  3.000
 KOU  C6    C5   C4    118.28  3.000
 KOU  C5A   C5   C4    119.43  3.000
 KOU  H6    C6   C5    121.16  3.000
 KOU  H6    C6   N1    115.91  3.000
 KOU  C5    C6   N1    122.93  3.000
 KOU  HA    CA   CB    107.42  3.000
 KOU  HA    CA   N     112.63  3.000
 KOU  CB    CA   N     110.05  3.000
 KOU  HA    CA   C     107.46  3.000
 KOU  CB    CA   C     110.32  3.000
 KOU  N     CA   C     108.91  3.000
 KOU  HBA   CB   HB    106.94  3.000
 KOU  HBA   CB   OG    112.32  3.000
 KOU  HB    CB   OG    112.29  3.000
 KOU  HBA   CB   CA    108.10  3.000
 KOU  HB    CB   CA    108.79  3.000
 KOU  OG    CB   CA    108.28  3.000
 KOU  HOG   OG   CB    108.38  3.000
 KOU  HO1P  O1P  P     115.97  3.000
 KOU  HO2P  O2P  P     113.98  3.000
 KOU  H4A   C4A  C4    115.40  3.000
 KOU  H4A   C4A  N     121.35  3.000
 KOU  C4    C4A  N     123.25  3.000
 KOU  C5A   O4P  P     119.14  3.000
 KOU  H5AA  C5A  H5A   107.29  3.000
 KOU  H5AA  C5A  O4P   109.42  3.000
 KOU  H5A   C5A  O4P   110.72  3.000
 KOU  H5AA  C5A  C5    110.38  3.000
 KOU  H5A   C5A  C5    109.41  3.000
 KOU  O4P   C5A  C5    109.59  3.000
 KOU  HOXT  OXT  C     110.08  3.000
 KOU  H2AB  C2A  H2AA  107.73  3.000
 KOU  H2AB  C2A  H2A   107.46  3.000
 KOU  H2AA  C2A  H2A   107.56  3.000
 KOU  H2AB  C2A  C2    109.71  3.000
 KOU  H2AA  C2A  C2    112.25  3.000
 KOU  H2A   C2A  C2    111.93  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
 KOU  CONST_01  C4    C5   C6   N1    0.00   0.0  0
 KOU  CONST_02  C4    C3   C2   N1    0.00   0.0  0
 KOU  CONST_03  C5    C6   N1   C2    0.00   0.0  0
 KOU  CONST_04  C5    C4   C3   C2    0.00   0.0  0
 KOU  CONST_05  C6    N1   C2   C3    0.00   0.0  0
 KOU  CONST_06  C6    C5   C4   C3    0.00   0.0  0
 KOU  CONST_07  C5A   C5   C6   N1  180.00   0.0  0
 KOU  CONST_08  O3    C3   C2   N1  180.00   0.0  0
 KOU  CONST_09  C4A   C4   C3   C2  180.00   0.0  0
 KOU  CONST_10  C5A   C5   C4   C3  180.00   0.0  0
 KOU  CONST_11  C5    C4   C3   O3  180.00   0.0  0
 KOU  CONST_12  C2A   C2   C3   C4  180.00   0.0  0
 KOU  CONST_13  C2A   C2   N1   C6  180.00   0.0  0
 KOU  CONST_14  C4A   C4   C5   C6  180.00   0.0  0
 KOU  CONST_15  H6    C6   N1   C2  180.00   0.0  0
 KOU  CONST_16  HOXT  OXT  C    O     0.00   0.0  0
 KOU  Var_01    C3    C4   C4A  N   -38.49  30.0  1
 KOU  Var_02    O4P   C5A  C5   C4  179.82  30.0  2
 KOU  Var_03    H2A   C2A  C2   N1  116.36  30.0  2
 KOU  Var_04    C5    C5A  O4P  P   167.15  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
 KOU  chir_01  CA  C  N  CB  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
 KOU  plan-1  N1    0.020
 KOU  plan-1  C2    0.020
 KOU  plan-1  C3    0.020
 KOU  plan-1  O3    0.020
 KOU  plan-1  C4    0.020
 KOU  plan-1  C5    0.020
 KOU  plan-1  C6    0.020
 KOU  plan-1  C4A   0.020
 KOU  plan-1  C5A   0.020
 KOU  plan-1  H6    0.020
 KOU  plan-1  C2A   0.020
 KOU  plan-2  C     0.020
 KOU  plan-2  O     0.020
 KOU  plan-2  CA    0.020
 KOU  plan-2  OXT   0.020
 KOU  plan-2  HOXT  0.020
 KOU  plan-3  N     0.020
 KOU  plan-3  C4    0.020
 KOU  plan-3  CA    0.020
 KOU  plan-3  C4A   0.020
 KOU  plan-3  H4A   0.020

