# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:29:24 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)\C=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
 KPR  KPR  '[(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate'  ligand  20  12  .  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_KPR
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
 KPR  O3P  O  OP    -1  -0.863   3.0340  -1.0811  -1.0774
 KPR  P    P  P      0   1.230   2.8565  -0.0428   0.0082
 KPR  O1P  O  O      0  -0.864   2.6454  -0.5749   1.4108
 KPR  O2P  O  OP    -1  -0.857   3.6759   1.2205  -0.1234
 KPR  O5   O  O2     0  -0.580   1.2308   0.6308  -0.4059
 KPR  C5   C  C1     0   0.158   0.1511   0.0612   0.0236
 KPR  C4   C  C1     0  -0.513  -1.1004   0.4213  -0.3702
 KPR  C3   C  C      0   0.329  -2.2711  -0.2541   0.1344
 KPR  O3   O  O      0  -0.471  -2.2484  -1.1810   0.9385
 KPR  C2   C  CH1    0  -0.198  -3.6160   0.2777  -0.3723
 KPR  N2   N  NH2    0  -0.780  -4.7012  -0.6819  -0.3226
 KPR  C1   C  CH3    0  -0.657  -3.9799   1.5205   0.4408
 KPR  H3   H  H      0   0.219   0.2662  -0.7492   0.7441
 KPR  H4   H  H      0   0.235  -1.2348   1.2222  -1.0894
 KPR  H5   H  HCH1   0   0.238  -3.4861   0.5844  -1.4153
 KPR  H6   H  HNH2   0   0.344  -4.4682  -1.4817  -0.8989
 KPR  H7   H  HNH2   0   0.335  -4.7767  -1.0475   0.6199
 KPR  H9   H  HCH3   0   0.234  -3.1984   2.2784   0.3889
 KPR  H10  H  HCH3   0   0.238  -4.9049   1.9589   0.0660
 KPR  H11  H  HCH3   0   0.224  -4.1279   1.2645   1.4922

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
 KPR  C1   C2   single  1.529  0.020  1.529
 KPR  O3   C3   double  1.227  0.020  1.227
 KPR  C3   C2   single  1.532  0.020  1.532
 KPR  C3   C4   single  1.443  0.020  1.443
 KPR  N2   C2   single  1.450  0.020  1.450
 KPR  C4   C5   double  1.361  0.020  1.361
 KPR  C5   O5   single  1.294  0.020  1.294
 KPR  O5   P    single  1.808  0.020  1.808
 KPR  O1P  P    deloc   1.515  0.020  1.515
 KPR  P    O2P  deloc   1.512  0.020  1.512
 KPR  P    O3P  deloc   1.513  0.020  1.513
 KPR  C5   H3   single  0.930  0.020  1.080
 KPR  C4   H4   single  0.930  0.020  1.080
 KPR  C2   H5   single  0.970  0.020  1.090
 KPR  N2   H6   single  0.890  0.020  1.040
 KPR  N2   H7   single  0.890  0.020  1.040
 KPR  C1   H9   single  0.970  0.020  1.090
 KPR  C1   H10  single  0.970  0.020  1.090
 KPR  C1   H11  single  0.970  0.020  1.090

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
 KPR  O5   P   O2P   98.98  3.000
 KPR  O2P  P   O1P  116.72  3.000
 KPR  O5   P   O1P  102.57  3.000
 KPR  O2P  P   O3P  116.59  3.000
 KPR  O1P  P   O3P  116.09  3.000
 KPR  O5   P   O3P  101.35  3.000
 KPR  C5   O5  P    120.68  3.000
 KPR  H3   C5  C4   119.01  3.000
 KPR  H3   C5  O5   117.28  3.000
 KPR  C4   C5  O5   123.70  3.000
 KPR  H4   C4  C3   118.49  3.000
 KPR  H4   C4  C5   120.08  3.000
 KPR  C3   C4  C5   121.42  3.000
 KPR  C2   C3  O3   119.66  3.000
 KPR  C2   C3  C4   115.73  3.000
 KPR  O3   C3  C4   124.59  3.000
 KPR  H5   C2  C1   107.89  3.000
 KPR  H5   C2  N2   107.87  3.000
 KPR  C1   C2  N2   109.98  3.000
 KPR  H5   C2  C3   107.94  3.000
 KPR  N2   C2  C3   114.58  3.000
 KPR  C1   C2  C3   108.37  3.000
 KPR  H7   N2  H6   105.15  3.000
 KPR  H7   N2  C2   109.05  3.000
 KPR  H6   N2  C2   109.33  3.000
 KPR  H11  C1  H10  108.07  3.000
 KPR  H11  C1  H9   107.82  3.000
 KPR  H10  C1  H9   108.20  3.000
 KPR  H11  C1  C2   110.71  3.000
 KPR  H10  C1  C2   110.24  3.000
 KPR  H9   C1  C2   111.67  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
 KPR  Var_01  C3  C4  C5  O5   179.59   0.0  2
 KPR  Var_02  C4  C5  O5  P   -172.29  30.0  1
 KPR  Var_03  O3  C3  C4  C5     0.14  30.0  1

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
 KPR  chir_01  C2  C1  C3  N2  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
 KPR  plan-1  C4  0.020
 KPR  plan-1  C3  0.020
 KPR  plan-1  O3  0.020
 KPR  plan-1  C2  0.020
 KPR  plan-2  O5  0.020
 KPR  plan-2  C5  0.020
 KPR  plan-2  C4  0.020
 KPR  plan-2  C3  0.020
 KPR  plan-2  H3  0.020
 KPR  plan-2  H4  0.020

