# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:50:29 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: [(1S)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N=Cc1c(O)c(C)ncc1CO[P](O)(O)=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
 EPC  EPC  '[(1S)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}ethyl]phosphonic acid'  ligand  38  22  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EPC
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
 EPC  C     C  CH1   0  -0.389  -0.9765   1.0173   2.9963
 EPC  N2    N  N     0  -0.457   0.0965   0.7160   2.0837
 EPC  N1    N  N     0  -0.393   3.0576  -0.1657  -1.8304
 EPC  C2    C  CR6   0   0.134   3.2544  -0.2638  -0.5329
 EPC  C2A   C  CH3   0  -0.720   4.5965  -0.6993  -0.0354
 EPC  C3    C  CR6   0   0.305   2.2256   0.0400   0.3818
 EPC  O1    O  OH1   0  -0.620   2.4909  -0.0792   1.6751
 EPC  C4    C  CR6   0  -0.020   0.9782   0.4555  -0.1063
 EPC  C4A   C  C1    0   0.067  -0.0927   0.7880   0.8286
 EPC  C5    C  CR6   0  -0.063   0.7967   0.5344  -1.4984
 EPC  C6    C  CR16  0  -0.155   1.8720   0.2198  -2.3054
 EPC  C5A   C  CH2   0  -0.250  -0.5134   0.9926  -2.0860
 EPC  O2    O  O2    0  -0.582  -0.5899   0.7070  -3.4787
 EPC  P1    P  P     0   1.446  -1.3640  -0.6073  -3.9713
 EPC  O3    O  O     0  -0.696  -2.8232  -0.6177  -3.7670
 EPC  O4    O  OH1   0  -0.726  -0.8157  -0.5927  -5.4642
 EPC  O5    O  OH1   0  -0.738  -0.7094  -1.8446  -3.2020
 EPC  P2    P  P     0   1.383  -1.3442  -0.5585   3.8483
 EPC  O7    O  O     0  -0.704  -0.2172  -1.1360   4.6144
 EPC  O8    O  OH1   0  -0.744  -2.6547  -0.1500   4.6769
 EPC  O6    O  OH1   0  -0.741  -1.8096  -1.5869   2.7060
 EPC  CA    C  CH3   0  -0.662  -0.5385   2.0903   3.9876
 EPC  H1C1  H  HCH1  0   0.279  -1.8805   1.3494   2.4684
 EPC  H2A1  H  HCH3  0   0.250   4.5320  -1.6299   0.5317
 EPC  H2A2  H  HCH3  0   0.250   5.2688  -0.8576  -0.8758
 EPC  H2A3  H  HCH3  0   0.250   5.0414   0.0459   0.6263
 EPC  HO1   H  HOH1  0   0.474   1.6705   0.1834   2.1788
 EPC  H4A1  H  H     0   0.265  -1.0556   1.1093   0.4289
 EPC  HC61  H  HCR6  0   0.265   1.7991   0.2857  -3.3836
 EPC  H5A1  H  HCH2  0   0.252  -1.3609   0.5507  -1.5556
 EPC  H5A2  H  HCH2  0   0.295  -0.6122   2.0750  -1.9856
 EPC  HO4   H  HOH1  0   0.507  -1.2754  -1.1984  -6.0615
 EPC  HO5   H  HOH1  0   0.495   0.2385  -1.9845  -3.3299
 EPC  HO8   H  HOH1  0   0.499  -2.9098  -0.7853   5.3607
 EPC  HO6   H  HOH1  0   0.492  -2.6347  -1.3719   2.2517
 EPC  HCA1  H  HCH3  0   0.244   0.3599   1.7861   4.5229
 EPC  HCA2  H  HCH3  0   0.258  -0.3235   3.0137   3.4514
 EPC  HCA3  H  HCH3  0   0.250  -1.3233   2.2976   4.7130

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
 EPC  C    N2    single    1.440  0.020  1.440
 EPC  C    P2    single    1.829  0.020  1.829
 EPC  C    CA    single    1.525  0.020  1.525
 EPC  C    H1C1  single    0.970  0.020  1.090
 EPC  N2   C4A   double    1.271  0.020  1.271
 EPC  N1   C2    aromatic  1.316  0.020  1.316
 EPC  N1   C6    aromatic  1.334  0.020  1.334
 EPC  C2   C2A   single    1.496  0.020  1.496
 EPC  C2   C3    aromatic  1.410  0.020  1.410
 EPC  C2A  H2A1  single    0.970  0.020  1.090
 EPC  C2A  H2A2  single    0.970  0.020  1.090
 EPC  C2A  H2A3  single    0.970  0.020  1.090
 EPC  C3   O1    single    1.326  0.020  1.326
 EPC  C3   C4    aromatic  1.402  0.020  1.402
 EPC  O1   HO1   single    0.850  0.020  0.980
 EPC  C4   C4A   single    1.460  0.020  1.460
 EPC  C4   C5    aromatic  1.406  0.020  1.406
 EPC  C4A  H4A1  single    0.930  0.020  1.080
 EPC  C5   C6    aromatic  1.381  0.020  1.381
 EPC  C5   C5A   single    1.507  0.020  1.507
 EPC  C6   HC61  single    0.930  0.020  1.080
 EPC  C5A  O2    single    1.424  0.020  1.424
 EPC  C5A  H5A1  single    0.970  0.020  1.090
 EPC  C5A  H5A2  single    0.970  0.020  1.090
 EPC  O2   P1    single    1.603  0.020  1.603
 EPC  P1   O3    double    1.473  0.020  1.473
 EPC  P1   O4    single    1.590  0.020  1.590
 EPC  P1   O5    single    1.597  0.020  1.597
 EPC  O4   HO4   single    0.850  0.020  0.980
 EPC  O5   HO5   single    0.850  0.020  0.980
 EPC  P2   O7    double    1.480  0.020  1.480
 EPC  P2   O8    single    1.603  0.020  1.603
 EPC  P2   O6    single    1.606  0.020  1.606
 EPC  O8   HO8   single    0.850  0.020  0.980
 EPC  O6   HO6   single    0.850  0.020  0.980
 EPC  CA   HCA1  single    0.970  0.020  1.090
 EPC  CA   HCA2  single    0.970  0.020  1.090
 EPC  CA   HCA3  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
 EPC  H1C1  C    CA    109.64  3.000
 EPC  H1C1  C    P2    108.60  3.000
 EPC  CA    C    P2    111.17  3.000
 EPC  H1C1  C    N2    111.83  3.000
 EPC  CA    C    N2    110.18  3.000
 EPC  P2    C    N2    105.35  3.000
 EPC  C4A   N2   C     120.18  3.000
 EPC  C6    N1   C2    120.36  3.000
 EPC  C3    C2   C2A   120.11  3.000
 EPC  C3    C2   N1    120.97  3.000
 EPC  C2A   C2   N1    118.93  3.000
 EPC  H2A3  C2A  H2A2  108.41  3.000
 EPC  H2A3  C2A  H2A1  106.93  3.000
 EPC  H2A2  C2A  H2A1  108.29  3.000
 EPC  H2A3  C2A  C2    111.62  3.000
 EPC  H2A2  C2A  C2    109.87  3.000
 EPC  H2A1  C2A  C2    111.58  3.000
 EPC  C4    C3   O1    122.97  3.000
 EPC  C4    C3   C2    119.15  3.000
 EPC  O1    C3   C2    117.88  3.000
 EPC  HO1   O1   C3    107.71  3.000
 EPC  C5    C4   C4A   121.77  3.000
 EPC  C5    C4   C3    118.42  3.000
 EPC  C4A   C4   C3    119.81  3.000
 EPC  H4A1  C4A  C4    118.68  3.000
 EPC  H4A1  C4A  N2    120.64  3.000
 EPC  C4    C4A  N2    120.67  3.000
 EPC  C5A   C5   C6    121.22  3.000
 EPC  C5A   C5   C4    121.01  3.000
 EPC  C6    C5   C4    117.73  3.000
 EPC  HC61  C6   C5    121.05  3.000
 EPC  HC61  C6   N1    115.59  3.000
 EPC  C5    C6   N1    123.36  3.000
 EPC  H5A2  C5A  H5A1  106.62  3.000
 EPC  H5A2  C5A  O2    106.51  3.000
 EPC  H5A1  C5A  O2    110.60  3.000
 EPC  H5A2  C5A  C5    110.14  3.000
 EPC  H5A1  C5A  C5    111.21  3.000
 EPC  O2    C5A  C5    111.54  3.000
 EPC  P1    O2   C5A   119.41  3.000
 EPC  O5    P1   O4    108.54  3.000
 EPC  O5    P1   O3    109.49  3.000
 EPC  O4    P1   O3    118.14  3.000
 EPC  O5    P1   O2    106.81  3.000
 EPC  O4    P1   O2     96.57  3.000
 EPC  O3    P1   O2    116.20  3.000
 EPC  HO4   O4   P1    114.21  3.000
 EPC  HO5   O5   P1    116.76  3.000
 EPC  O6    P2   O8    107.09  3.000
 EPC  O6    P2   O7    109.82  3.000
 EPC  O8    P2   O7    117.02  3.000
 EPC  O6    P2   C     106.18  3.000
 EPC  O8    P2   C     100.69  3.000
 EPC  O7    P2   C     115.10  3.000
 EPC  HO8   O8   P2    114.42  3.000
 EPC  HO6   O6   P2    116.07  3.000
 EPC  HCA3  CA   HCA2  108.00  3.000
 EPC  HCA3  CA   HCA1  108.69  3.000
 EPC  HCA2  CA   HCA1  108.41  3.000
 EPC  HCA3  CA   C     111.10  3.000
 EPC  HCA2  CA   C     109.46  3.000
 EPC  HCA1  CA   C     111.09  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
 EPC  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 EPC  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 EPC  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 EPC  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 EPC  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 EPC  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 EPC  CONST_07  O1    C3   C2   N1    180.00   0.0  0
 EPC  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 EPC  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 EPC  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 EPC  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 EPC  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 EPC  CONST_13  C5    C4   C3   O1    180.00   0.0  0
 EPC  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 EPC  CONST_15  HC61  C6   N1   C2    180.00   0.0  0
 EPC  Var_01    C3    C4   C4A  N2      0.61  30.0  1
 EPC  Var_02    O2    C5A  C5   C4   -166.44  30.0  2
 EPC  Var_03    H2A1  C2A  C2   N1   -118.55  30.0  2
 EPC  Var_04    C4    C4A  N2   C    -178.59   0.0  2
 EPC  Var_05    O3    P1   O2   C5A    67.61  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
 EPC  chir_01  C  N2  P2  CA  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
 EPC  plan-1  N1    0.020
 EPC  plan-1  C2    0.020
 EPC  plan-1  C2A   0.020
 EPC  plan-1  C3    0.020
 EPC  plan-1  O1    0.020
 EPC  plan-1  C4    0.020
 EPC  plan-1  C4A   0.020
 EPC  plan-1  C5    0.020
 EPC  plan-1  C6    0.020
 EPC  plan-1  C5A   0.020
 EPC  plan-1  HC61  0.020
 EPC  plan-2  C     0.020
 EPC  plan-2  N2    0.020
 EPC  plan-2  C4    0.020
 EPC  plan-2  C4A   0.020
 EPC  plan-2  H4A1  0.020

