# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 23:18:10 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  22  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  OH1   0  -0.719   3.1491  -0.8757  -1.4507
 KPR  P    P  P     0   1.464   2.6991  -0.2561  -0.0607
 KPR  O1P  O  O     0  -0.688   2.7474  -1.2590   1.0136
 KPR  O2P  O  OH1   0  -0.719   3.4552   1.1249   0.1324
 KPR  O5   O  O2    0  -0.560   1.2257   0.3762  -0.3352
 KPR  C5   C  C1    0   0.139   0.0929  -0.1677   0.1579
 KPR  C4   C  C1    0  -0.456  -1.1010   0.2396  -0.2729
 KPR  C3   C  C     0   0.348  -2.3313  -0.3565   0.2682
 KPR  O3   O  O     0  -0.415  -2.3259  -1.1945   1.1494
 KPR  C2   C  CH1   0  -0.204  -3.6335   0.1461  -0.3481
 KPR  N2   N  NH2   0  -0.777  -4.7898  -0.6737  -0.0699
 KPR  C1   C  CH3   0  -0.664  -3.8863   1.5808   0.1200
 KPR  H1   H  HOH1  0   0.505   3.2041  -0.2660  -2.1999
 KPR  H2   H  HOH1  0   0.512   4.4139   1.0490   0.2414
 KPR  H3   H  H     0   0.289   0.2073  -0.9342   0.9173
 KPR  H4   H  H     0   0.280  -1.1790   0.9945  -1.0460
 KPR  H5   H  HCH1  0   0.256  -3.4834   0.1690  -1.4338
 KPR  H6   H  HNH2  0   0.349  -4.6337  -1.6197  -0.3951
 KPR  H7   H  HNH2  0   0.341  -4.9266  -0.7452   0.9315
 KPR  H9   H  HCH3  0   0.240  -3.0535   2.2441  -0.1119
 KPR  H10  H  HCH3  0   0.249  -4.7750   1.9742  -0.3718
 KPR  H11  H  HCH3  0   0.232  -4.0513   1.6133   1.1987

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  1.530  0.020  1.530
 KPR  O3   C3   double  1.216  0.020  1.216
 KPR  C3   C2   single  1.526  0.020  1.526
 KPR  C3   C4   single  1.470  0.020  1.470
 KPR  N2   C2   single  1.444  0.020  1.444
 KPR  C4   C5   double  1.333  0.020  1.333
 KPR  C5   O5   single  1.350  0.020  1.350
 KPR  O5   P    single  1.627  0.020  1.627
 KPR  O1P  P    double  1.470  0.020  1.470
 KPR  P    O2P  single  1.586  0.020  1.586
 KPR  P    O3P  single  1.587  0.020  1.587
 KPR  O3P  H1   single  0.850  0.020  0.980
 KPR  O2P  H2   single  0.850  0.020  0.980
 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  H1   O3P  P    116.64  3.000
 KPR  O5   P    O2P   96.54  3.000
 KPR  O2P  P    O1P  119.29  3.000
 KPR  O5   P    O1P  114.72  3.000
 KPR  O2P  P    O3P  108.14  3.000
 KPR  O1P  P    O3P  111.37  3.000
 KPR  O5   P    O3P  105.12  3.000
 KPR  H2   O2P  P    114.69  3.000
 KPR  C5   O5   P    122.81  3.000
 KPR  H3   C5   C4   122.44  3.000
 KPR  H3   C5   O5   116.86  3.000
 KPR  C4   C5   O5   120.69  3.000
 KPR  H4   C4   C3   119.01  3.000
 KPR  H4   C4   C5   120.53  3.000
 KPR  C3   C4   C5   120.44  3.000
 KPR  C2   C3   O3   121.56  3.000
 KPR  C2   C3   C4   115.59  3.000
 KPR  O3   C3   C4   122.84  3.000
 KPR  H5   C2   C1   107.81  3.000
 KPR  H5   C2   N2   108.19  3.000
 KPR  C1   C2   N2   109.94  3.000
 KPR  H5   C2   C3   106.86  3.000
 KPR  N2   C2   C3   114.74  3.000
 KPR  C1   C2   C3   109.04  3.000
 KPR  H7   N2   H6   105.81  3.000
 KPR  H7   N2   C2   109.79  3.000
 KPR  H6   N2   C2   110.18  3.000
 KPR  H11  C1   H10  108.18  3.000
 KPR  H11  C1   H9   107.93  3.000
 KPR  H10  C1   H9   107.92  3.000
 KPR  H11  C1   C2   110.80  3.000
 KPR  H10  C1   C2   109.58  3.000
 KPR  H9   C1   C2   112.30  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  -180.00   0.0  2
 KPR  Var_02  C4  C5  O5  P   -168.41  30.0  1
 KPR  Var_03  O3  C3  C4  C5     2.76  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

