# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 06:12:31 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}cyclopentyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NC2(CCCC2)[P](O)(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
 HCP  HCP  '(1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}cyclopentyl)phosphonic acid'  ligand  45  25  .  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_HCP
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
 HCP  C3    C  CR6   0   0.298   2.5665   0.7362  -0.2880
 HCP  C2    C  CR6   0   0.133   3.5609   1.0083   0.6736
 HCP  N1    N  N     0  -0.397   3.3716   0.7213   1.9440
 HCP  C6    C  CR16  0  -0.144   2.2278   0.1643   2.3488
 HCP  C4    C  CR6   0  -0.004   1.3616   0.1535   0.1254
 HCP  C4A   C  C1    0   0.064   0.3120  -0.1303  -0.8495
 HCP  N2    N  N     0  -0.472   0.5029   0.0974  -2.0844
 HCP  C     C  CT    0  -0.208  -0.4938  -0.1487  -3.1076
 HCP  CA1   C  CH2   0  -0.432   0.1246  -1.1148  -4.1320
 HCP  CB1   C  CH2   0  -0.451  -0.0029  -2.4722  -3.4349
 HCP  CB2   C  CH2   0  -0.446  -1.2987  -2.3849  -2.6002
 HCP  CA2   C  CH2   0  -0.518  -1.7498  -0.9126  -2.6719
 HCP  P2    P  P     0   1.408  -0.7832   1.5181  -3.8054
 HCP  O6    O  OH1   0  -0.744  -1.9245   1.2250  -4.8930
 HCP  O7    O  O     0  -0.701   0.4299   2.2128  -4.2931
 HCP  O8    O  OH1   0  -0.745  -1.4648   2.3755  -2.6285
 HCP  O1    O  OH1   0  -0.622   2.8197   1.0497  -1.5517
 HCP  C2A   C  CH3   0  -0.720   4.8566   1.6302   0.2569
 HCP  C5    C  CR6   0  -0.070   1.1921  -0.1412   1.4903
 HCP  C5A   C  CH2   0  -0.217  -0.0873  -0.7665   1.9737
 HCP  O2    O  O2    0  -0.591   0.0093  -1.0195   3.3684
 HCP  P1    P  P     0   1.460  -1.3134  -1.3731   4.1961
 HCP  O5    O  O     0  -0.705  -2.1956  -2.3965   3.6076
 HCP  O3    O  OH1   0  -0.727  -0.5817  -1.7012   5.5705
 HCP  O4    O  OH1   0  -0.738  -2.1226  -0.0090   4.3794
 HCP  HC6   H  HCR6  0   0.262   2.1527  -0.0382   3.4085
 HCP  HC4   H  H     0   0.258  -0.6269  -0.5378  -0.4776
 HCP  HA11  H  HCH2  0   0.251  -0.4639  -1.1017  -5.0513
 HCP  HA12  H  HCH2  0   0.262   1.1504  -0.8471  -4.3844
 HCP  HB11  H  HCH2  0   0.248  -0.0256  -3.2900  -4.1540
 HCP  HB12  H  HCH2  0   0.238   0.8593  -2.6400  -2.7879
 HCP  HB21  H  HCH2  0   0.250  -2.0783  -3.0359  -2.9948
 HCP  HB22  H  HCH2  0   0.238  -1.1226  -2.6987  -1.5703
 HCP  HA21  H  HCH2  0   0.265  -2.2012  -0.5499  -1.7464
 HCP  HA22  H  HCH2  0   0.278  -2.5121  -0.8000  -3.4431
 HCP  HO6   H  HOH1  0   0.499  -2.0961   1.9601  -5.4986
 HCP  HO8   H  HOH1  0   0.491  -2.3457   2.0948  -2.3488
 HCP  HO1   H  HOH1  0   0.476   2.0276   0.7748  -2.0935
 HCP  HC21  H  HCH3  0   0.249   5.3762   1.0168  -0.4814
 HCP  HC22  H  HCH3  0   0.249   4.7039   2.6118  -0.1957
 HCP  HC23  H  HCH3  0   0.249   5.5049   1.7499   1.1221
 HCP  HC51  H  HCH2  0   0.260  -0.9249  -0.0933   1.7617
 HCP  HC52  H  HCH2  0   0.264  -0.2798  -1.7065   1.4486
 HCP  HO3   H  HOH1  0   0.507  -1.1732  -2.0178   6.2669
 HCP  HO4   H  HOH1  0   0.497  -1.6534   0.7085   4.8262

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
 HCP  C3   C2    aromatic  1.410  0.020  1.410
 HCP  C3   C4    aromatic  1.401  0.020  1.401
 HCP  C3   O1    single    1.326  0.020  1.326
 HCP  C2   N1    aromatic  1.316  0.020  1.316
 HCP  C2   C2A   single    1.496  0.020  1.496
 HCP  N1   C6    aromatic  1.335  0.020  1.335
 HCP  C6   C5    aromatic  1.379  0.020  1.379
 HCP  C6   HC6   single    0.930  0.020  1.080
 HCP  C4   C4A   single    1.460  0.020  1.460
 HCP  C4   C5    aromatic  1.407  0.020  1.407
 HCP  C4A  N2    double    1.270  0.020  1.270
 HCP  C4A  HC4   single    0.930  0.020  1.080
 HCP  N2   C     single    1.449  0.020  1.449
 HCP  C    CA1   single    1.538  0.020  1.538
 HCP  C    CA2   single    1.533  0.020  1.533
 HCP  C    P2    single    1.830  0.020  1.830
 HCP  CA1  CB1   single    1.531  0.020  1.531
 HCP  CA1  HA11  single    0.970  0.020  1.090
 HCP  CA1  HA12  single    0.970  0.020  1.090
 HCP  CB1  CB2   single    1.544  0.020  1.544
 HCP  CB1  HB11  single    0.970  0.020  1.090
 HCP  CB1  HB12  single    0.970  0.020  1.090
 HCP  CB2  CA2   single    1.541  0.020  1.541
 HCP  CB2  HB21  single    0.970  0.020  1.090
 HCP  CB2  HB22  single    0.970  0.020  1.090
 HCP  CA2  HA21  single    0.970  0.020  1.090
 HCP  CA2  HA22  single    0.970  0.020  1.090
 HCP  P2   O6    single    1.604  0.020  1.604
 HCP  P2   O7    double    1.481  0.020  1.481
 HCP  P2   O8    single    1.608  0.020  1.608
 HCP  O6   HO6   single    0.850  0.020  0.980
 HCP  O8   HO8   single    0.850  0.020  0.980
 HCP  O1   HO1   single    0.850  0.020  0.980
 HCP  C2A  HC21  single    0.970  0.020  1.090
 HCP  C2A  HC22  single    0.970  0.020  1.090
 HCP  C2A  HC23  single    0.970  0.020  1.090
 HCP  C5   C5A   single    1.504  0.020  1.504
 HCP  C5A  O2    single    1.421  0.020  1.421
 HCP  C5A  HC51  single    0.970  0.020  1.090
 HCP  C5A  HC52  single    0.970  0.020  1.090
 HCP  O2   P1    single    1.600  0.020  1.600
 HCP  P1   O5    double    1.474  0.020  1.474
 HCP  P1   O3    single    1.591  0.020  1.591
 HCP  P1   O4    single    1.597  0.020  1.597
 HCP  O3   HO3   single    0.850  0.020  0.980
 HCP  O4   HO4   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
 HCP  O1    C3   C4    122.93  3.000
 HCP  O1    C3   C2    118.01  3.000
 HCP  C4    C3   C2    119.06  3.000
 HCP  C2A   C2   N1    118.95  3.000
 HCP  C2A   C2   C3    120.07  3.000
 HCP  N1    C2   C3    120.99  3.000
 HCP  C6    N1   C2    120.46  3.000
 HCP  HC6   C6   C5    121.08  3.000
 HCP  HC6   C6   N1    115.77  3.000
 HCP  C5    C6   N1    123.16  3.000
 HCP  C5    C4   C4A   121.37  3.000
 HCP  C5    C4   C3    118.50  3.000
 HCP  C4A   C4   C3    120.13  3.000
 HCP  HC4   C4A  N2    121.92  3.000
 HCP  HC4   C4A  C4    117.67  3.000
 HCP  N2    C4A  C4    120.41  3.000
 HCP  C     N2   C4A   123.54  3.000
 HCP  P2    C    CA2   115.64  3.000
 HCP  P2    C    CA1   112.44  3.000
 HCP  CA2   C    CA1   101.87  3.000
 HCP  P2    C    N2    102.91  3.000
 HCP  CA2   C    N2    116.57  3.000
 HCP  CA1   C    N2    107.48  3.000
 HCP  HA12  CA1  HA11  108.03  3.000
 HCP  HA12  CA1  CB1   113.68  3.000
 HCP  HA11  CA1  CB1   110.43  3.000
 HCP  HA12  CA1  C     112.24  3.000
 HCP  HA11  CA1  C     109.67  3.000
 HCP  CB1   CA1  C     102.72  3.000
 HCP  HB12  CB1  HB11  107.01  3.000
 HCP  HB12  CB1  CB2   110.57  3.000
 HCP  HB11  CB1  CB2   112.45  3.000
 HCP  HB12  CB1  CA1   109.91  3.000
 HCP  HB11  CB1  CA1   111.52  3.000
 HCP  CB2   CB1  CA1   105.42  3.000
 HCP  HB22  CB2  HB21  106.59  3.000
 HCP  HB22  CB2  CA2   111.46  3.000
 HCP  HB21  CB2  CA2   110.14  3.000
 HCP  HB22  CB2  CB1   111.02  3.000
 HCP  HB21  CB2  CB1   111.77  3.000
 HCP  CA2   CB2  CB1   105.93  3.000
 HCP  HA22  CA2  HA21  106.03  3.000
 HCP  HA22  CA2  CB2   109.65  3.000
 HCP  HA21  CA2  CB2   113.51  3.000
 HCP  HA22  CA2  C     108.68  3.000
 HCP  HA21  CA2  C     114.46  3.000
 HCP  CB2   CA2  C     104.44  3.000
 HCP  O8    P2   O7    109.77  3.000
 HCP  O8    P2   O6    106.99  3.000
 HCP  O7    P2   O6    116.45  3.000
 HCP  O8    P2   C     105.88  3.000
 HCP  O7    P2   C     115.05  3.000
 HCP  O6    P2   C     101.81  3.000
 HCP  HO6   O6   P2    114.32  3.000
 HCP  HO8   O8   P2    116.33  3.000
 HCP  HO1   O1   C3    107.49  3.000
 HCP  HC23  C2A  HC22  108.31  3.000
 HCP  HC23  C2A  HC21  108.43  3.000
 HCP  HC22  C2A  HC21  106.95  3.000
 HCP  HC23  C2A  C2    109.89  3.000
 HCP  HC22  C2A  C2    111.59  3.000
 HCP  HC21  C2A  C2    111.53  3.000
 HCP  C5A   C5   C4    120.10  3.000
 HCP  C5A   C5   C6    122.06  3.000
 HCP  C4    C5   C6    117.85  3.000
 HCP  HC52  C5A  HC51  107.50  3.000
 HCP  HC52  C5A  O2    109.28  3.000
 HCP  HC51  C5A  O2    110.58  3.000
 HCP  HC52  C5A  C5    110.65  3.000
 HCP  HC51  C5A  C5    109.44  3.000
 HCP  O2    C5A  C5    109.38  3.000
 HCP  P1    O2   C5A   119.41  3.000
 HCP  O4    P1   O3    108.06  3.000
 HCP  O4    P1   O5    109.62  3.000
 HCP  O3    P1   O5    118.49  3.000
 HCP  O4    P1   O2    106.83  3.000
 HCP  O3    P1   O2     96.45  3.000
 HCP  O5    P1   O2    116.22  3.000
 HCP  HO3   O3   P1    114.10  3.000
 HCP  HO4   O4   P1    116.18  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
 HCP  CONST_01  C6    N1   C2   C3     0.00   0.0  0
 HCP  CONST_02  C6    C5   C4   C3     0.00   0.0  0
 HCP  CONST_03  C5    C4   C3   C2     0.00   0.0  0
 HCP  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 HCP  CONST_05  C4    C3   C2   N1     0.00   0.0  0
 HCP  CONST_06  C4    C5   C6   N1     0.00   0.0  0
 HCP  CONST_07  C5A   C5   C4   C3   180.00   0.0  0
 HCP  CONST_08  C4A   C4   C3   C2   180.00   0.0  0
 HCP  CONST_09  O1    C3   C2   N1   180.00   0.0  0
 HCP  CONST_10  C5A   C5   C6   N1   180.00   0.0  0
 HCP  CONST_11  C2A   C2   N1   C6   180.00   0.0  0
 HCP  CONST_12  C4A   C4   C5   C6   180.00   0.0  0
 HCP  CONST_13  C2A   C2   C3   C4   180.00   0.0  0
 HCP  CONST_14  C5    C4   C3   O1   180.00   0.0  0
 HCP  CONST_15  HC6   C6   N1   C2   180.00   0.0  0
 HCP  Var_01    CB2   CB1  CA1  C     32.66  30.0  1
 HCP  Var_02    CB1   CB2  CA2  C    -18.81  30.0  1
 HCP  Var_03    CA2   CB2  CB1  CA1   -8.65  30.0  1
 HCP  Var_04    N2    C4A  C4   C3     2.89  30.0  2
 HCP  Var_05    O2    C5A  C5   C6    -2.74  30.0  2
 HCP  Var_06    HC21  C2A  C2   C3   -58.73  30.0  2
 HCP  Var_07    O5    P1   O2   C5A   47.71  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
 HCP  chir_01  C  CA1  CA2  P2  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
 HCP  plan-1  C3   0.020
 HCP  plan-1  C2   0.020
 HCP  plan-1  N1   0.020
 HCP  plan-1  C6   0.020
 HCP  plan-1  C4   0.020
 HCP  plan-1  C4A  0.020
 HCP  plan-1  O1   0.020
 HCP  plan-1  C2A  0.020
 HCP  plan-1  C5   0.020
 HCP  plan-1  C5A  0.020
 HCP  plan-1  HC6  0.020
 HCP  plan-2  C4   0.020
 HCP  plan-2  C4A  0.020
 HCP  plan-2  N2   0.020
 HCP  plan-2  C    0.020
 HCP  plan-2  HC4  0.020

