# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 23:47:04 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCC(=[NH+]\C=C1/C(=C(C)NC=C1CO[P](O)(O)=O)[O-])C(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
 PN9  PN9  "(4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate"  ligand  43  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PN9
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
 PN9  N1   N  NC1    1  -0.563   -9.7686  -1.8662  3.7482
 PN9  C4   C  CH3    0  -0.771  -14.4514  -3.8169  4.8385
 PN9  C5   C  C      0   0.199   -5.8575  -0.4896  4.4850
 PN9  C6   C  CH3    0  -0.720   -5.4721   0.9454  4.5435
 PN9  C7   C  C      0   0.300   -7.1924  -0.8789  4.2506
 PN9  C8   C  C      0  -0.032   -7.4646  -2.2930  4.1843
 PN9  C10  C  C      0  -0.044   -6.4124  -3.2105  4.3961
 PN9  C13  C  C      0   0.135  -11.0464  -2.0947  3.4471
 PN9  C1   C  C      0   0.469  -11.9354  -0.9711  3.3044
 PN9  C11  C  CH2    0  -0.316   -6.6361  -4.6897  4.3854
 PN9  C12  C  C1     0  -0.049   -5.1437  -2.7458  4.6277
 PN9  C2   C  CH2    0  -0.535  -11.5404  -3.4863  3.2600
 PN9  C3   C  CH2    0  -0.567  -11.7214  -4.2760  4.5607
 PN9  C9   C  C1     0  -0.065   -8.7862  -2.7414  3.9173
 PN9  N2   N  NH1    0  -0.593   -4.9130  -1.4273  4.6603
 PN9  O1   O  OH1    0  -0.626  -11.3520   0.2136  3.5490
 PN9  O2   O  O      0  -0.474  -13.1090  -1.0529  2.9859
 PN9  O3   O  O      0  -0.685   -7.5515  -6.7363  1.2342
 PN9  O4   O  OH1    0  -0.741   -6.7570  -7.5952  3.5974
 PN9  O6   O  OH1    0  -0.745   -8.9315  -6.6231  3.4595
 PN9  O7   O  O2     0  -0.582   -6.9050  -5.1009  3.0365
 PN9  P1   P  P      0   1.470   -7.5330  -6.5341  2.6928
 PN9  S1   S  S2     0  -0.031  -12.9002  -3.5471  5.7235
 PN9  H8   H  HCH3   0   0.271  -15.2597  -3.4894  5.4903
 PN9  H6   H  HCH3   0   0.263  -14.4908  -3.2351  3.9204
 PN9  H7   H  HCH3   0   0.257  -14.5939  -4.8730  4.6130
 PN9  H11  H  HCH3   0   0.256   -4.4017   1.0714  4.6995
 PN9  H9   H  HCH3   0   0.263   -5.7430   1.4547  3.6180
 PN9  H10  H  HCH3   0   0.263   -5.9954   1.4562  5.3530
 PN9  H14  H  HCH2   0   0.256   -7.4683  -4.9537  5.0448
 PN9  H13  H  HCH2   0   0.276   -5.7474  -5.2055  4.7538
 PN9  H15  H  H      0   0.316   -4.2936  -3.3900  4.7935
 PN9  H3   H  HCH2   0   0.277  -12.4833  -3.4632  2.7154
 PN9  H2   H  HCH2   0   0.260  -10.8476  -4.0507  2.6223
 PN9  H4   H  HCH2   0   0.275  -12.0294  -5.2988  4.3330
 PN9  H5   H  HCH2   0   0.276  -10.7835  -4.3473  5.1142
 PN9  H12  H  H      0   0.269   -9.0130  -3.7911  3.8235
 PN9  H16  H  HNH1   0   0.439   -3.9640  -1.1187  4.8289
 PN9  H20  H  HOH1   0   0.477  -11.9986   0.9199  3.4131
 PN9  H21  H  HOH1   0   0.501   -5.8413  -7.7578  3.3317
 PN9  H22  H  HOH1   0   0.505   -9.6845  -6.3199  2.9344
 PN9  H1   H  HNC1   0   0.466   -9.3838  -0.8794  3.8603
 PN9  O5   O  OC    -1  -0.599   -8.1091  -0.0062  4.1030

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
 PN9  O3   P1   double  1.473  0.020  1.473
 PN9  P1   O6   single  1.597  0.020  1.597
 PN9  P1   O7   single  1.602  0.020  1.602
 PN9  P1   O4   single  1.596  0.020  1.596
 PN9  O2   C1   double  1.219  0.020  1.219
 PN9  O7   C11  single  1.436  0.020  1.436
 PN9  C1   C13  single  1.440  0.020  1.440
 PN9  C1   O1   single  1.343  0.020  1.343
 PN9  C2   C13  single  1.488  0.020  1.488
 PN9  C2   C3   single  1.532  0.020  1.532
 PN9  C13  N1   double  1.333  0.020  1.333
 PN9  N1   C9   single  1.327  0.020  1.327
 PN9  C9   C8   double  1.421  0.020  1.421
 PN9  O5   C7   single  1.274  0.020  1.274
 PN9  C8   C7   single  1.442  0.020  1.442
 PN9  C8   C10  single  1.412  0.020  1.412
 PN9  C7   C5   double  1.410  0.020  1.410
 PN9  C10  C11  single  1.496  0.020  1.496
 PN9  C10  C12  double  1.371  0.020  1.371
 PN9  C5   C6   single  1.487  0.020  1.487
 PN9  C5   N2   single  1.342  0.020  1.342
 PN9  C3   S1   single  1.809  0.020  1.809
 PN9  C12  N2   single  1.339  0.020  1.339
 PN9  C4   S1   single  1.806  0.020  1.806
 PN9  C4   H8   single  0.970  0.020  1.090
 PN9  C4   H6   single  0.970  0.020  1.090
 PN9  C4   H7   single  0.970  0.020  1.090
 PN9  C6   H11  single  0.970  0.020  1.090
 PN9  C6   H9   single  0.970  0.020  1.090
 PN9  C6   H10  single  0.970  0.020  1.090
 PN9  C11  H14  single  0.970  0.020  1.090
 PN9  C11  H13  single  0.970  0.020  1.090
 PN9  C12  H15  single  0.930  0.020  1.080
 PN9  C2   H3   single  0.970  0.020  1.090
 PN9  C2   H2   single  0.970  0.020  1.090
 PN9  C3   H4   single  0.970  0.020  1.090
 PN9  C3   H5   single  0.970  0.020  1.090
 PN9  C9   H12  single  0.930  0.020  1.080
 PN9  N2   H16  single  0.860  0.020  1.020
 PN9  O1   H20  single  0.850  0.020  0.980
 PN9  O4   H21  single  0.850  0.020  0.980
 PN9  O6   H22  single  0.850  0.020  0.980
 PN9  N1   H1   single  0.860  0.020  1.020

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
 PN9  H1   N1   C9   109.28  3.000
 PN9  H1   N1   C13  121.95  3.000
 PN9  C9   N1   C13  128.74  3.000
 PN9  H7   C4   H6   109.82  3.000
 PN9  H7   C4   H8   108.56  3.000
 PN9  H6   C4   H8   108.52  3.000
 PN9  H7   C4   S1   111.02  3.000
 PN9  H6   C4   S1   111.40  3.000
 PN9  H8   C4   S1   107.42  3.000
 PN9  N2   C5   C7   119.67  3.000
 PN9  N2   C5   C6   119.12  3.000
 PN9  C7   C5   C6   121.22  3.000
 PN9  H10  C6   H9   106.97  3.000
 PN9  H10  C6   H11  108.12  3.000
 PN9  H9   C6   H11  108.16  3.000
 PN9  H10  C6   C5   110.90  3.000
 PN9  H9   C6   C5   110.67  3.000
 PN9  H11  C6   C5   111.85  3.000
 PN9  O5   C7   C8   122.05  3.000
 PN9  C8   C7   C5   117.21  3.000
 PN9  O5   C7   C5   120.75  3.000
 PN9  C9   C8   C10  121.08  3.000
 PN9  C10  C8   C7   119.33  3.000
 PN9  C9   C8   C7   119.59  3.000
 PN9  C12  C10  C11  118.34  3.000
 PN9  C12  C10  C8   119.65  3.000
 PN9  C11  C10  C8   122.01  3.000
 PN9  C2   C13  C1   120.81  3.000
 PN9  C2   C13  N1   120.46  3.000
 PN9  C1   C13  N1   118.73  3.000
 PN9  O2   C1   O1   121.67  3.000
 PN9  O1   C1   C13  113.71  3.000
 PN9  O2   C1   C13  124.62  3.000
 PN9  H13  C11  H14  107.57  3.000
 PN9  H13  C11  O7   109.53  3.000
 PN9  H14  C11  O7   110.77  3.000
 PN9  H13  C11  C10  110.06  3.000
 PN9  H14  C11  C10  110.36  3.000
 PN9  O7   C11  C10  108.53  3.000
 PN9  H15  C12  N2   116.63  3.000
 PN9  H15  C12  C10  123.54  3.000
 PN9  N2   C12  C10  119.83  3.000
 PN9  H2   C2   H3   105.48  3.000
 PN9  H2   C2   C3   107.62  3.000
 PN9  H3   C2   C3   109.46  3.000
 PN9  H2   C2   C13  110.13  3.000
 PN9  H3   C2   C13  109.28  3.000
 PN9  C3   C2   C13  114.48  3.000
 PN9  H5   C3   H4   106.67  3.000
 PN9  H5   C3   S1   105.09  3.000
 PN9  H4   C3   S1   109.12  3.000
 PN9  H5   C3   C2   111.26  3.000
 PN9  H4   C3   C2   109.81  3.000
 PN9  S1   C3   C2   114.51  3.000
 PN9  H12  C9   C8   121.28  3.000
 PN9  H12  C9   N1   118.39  3.000
 PN9  C8   C9   N1   120.31  3.000
 PN9  H16  N2   C12  117.77  3.000
 PN9  H16  N2   C5   117.94  3.000
 PN9  C12  N2   C5   124.29  3.000
 PN9  H20  O1   C1   109.16  3.000
 PN9  H21  O4   P1   114.61  3.000
 PN9  H22  O6   P1   113.81  3.000
 PN9  P1   O7   C11  122.09  3.000
 PN9  O7   P1   O6   106.86  3.000
 PN9  O7   P1   O4   106.41  3.000
 PN9  O6   P1   O4    96.70  3.000
 PN9  O4   P1   O3   118.44  3.000
 PN9  O7   P1   O3   109.89  3.000
 PN9  O6   P1   O3   117.18  3.000
 PN9  C3   S1   C4   100.63  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
 PN9  CONST_01  H20  O1   C1   C13   180.00   0.0  0
 PN9  CONST_02  H20  O1   C1   O2      0.00   0.0  0
 PN9  Var_01    C10  C8   C7   C5      2.02  30.0  1
 PN9  Var_02    C10  C12  N2   C5      0.35  30.0  1
 PN9  Var_03    C12  C10  C8   C7     -1.64  30.0  1
 PN9  Var_04    C12  N2   C5   C7      0.09  30.0  1
 PN9  Var_05    N2   C5   C7   C8     -1.27  30.0  1
 PN9  Var_06    N2   C12  C10  C8      0.45  30.0  1
 PN9  Var_07    C9   C8   C7   C5   -178.45  30.0  1
 PN9  Var_08    C8   C7   C5   C6    178.78  30.0  1
 PN9  Var_09    C12  N2   C5   C6   -179.95  30.0  1
 PN9  Var_10    C11  C10  C8   C7    177.97  30.0  1
 PN9  Var_11    O5   C7   C8   C10  -178.11  30.0  1
 PN9  Var_12    N2   C12  C10  C11  -179.17  30.0  1
 PN9  Var_13    C9   C8   C10  C12   178.83  30.0  1
 PN9  Var_14    O5   C7   C5   N2    178.86  30.0  1
 PN9  Var_15    H15  C12  N2   C5   -179.45  30.0  1
 PN9  Var_16    H16  N2   C5   C7   -179.86  30.0  1
 PN9  Var_17    H15  C12  C10  C8   -179.76  30.0  1
 PN9  Var_18    H16  N2   C12  C10  -179.69  30.0  1
 PN9  Var_19    C7   C8   C9   N1     -0.93   0.0  2
 PN9  Var_20    C10  C8   C9   N1    178.59   0.0  2
 PN9  Var_21    O5   C7   C5   C6     -1.10  30.0  1
 PN9  Var_22    O7   C11  C10  C8     70.91  30.0  3
 PN9  Var_23    C9   C8   C10  C11    -1.56  30.0  1
 PN9  Var_24    O7   C11  C10  C12  -109.48  30.0  3
 PN9  Var_25    O5   C7   C8   C9      1.43  30.0  1
 PN9  Var_26    H12  C9   C8   C7    177.57   0.0  2
 PN9  Var_27    H12  C9   C8   C10    -2.90   0.0  2
 PN9  Var_28    H16  N2   C5   C6      0.09  30.0  1
 PN9  Var_29    H11  C6   C5   C7   -178.14  30.0  3
 PN9  Var_30    H9   C6   C5   C7    -57.48  30.0  3
 PN9  Var_31    H10  C6   C5   C7     61.08  30.0  3
 PN9  Var_32    H14  C11  C10  C8    -50.65  30.0  3
 PN9  Var_33    H13  C11  C10  C8   -169.23  30.0  3
 PN9  Var_34    H15  C12  C10  C11     0.62  30.0  1
 PN9  Var_35    H14  C11  C10  C12   128.96  30.0  3
 PN9  Var_36    H13  C11  C10  C12    10.37  30.0  3
 PN9  Var_37    H11  C6   C5   N2      1.91  30.0  3
 PN9  Var_38    H9   C6   C5   N2    122.57  30.0  3
 PN9  Var_39    H10  C6   C5   N2   -118.88  30.0  3
 PN9  Var_40    C13  N1   C9   C8    177.40  30.0  1
 PN9  Var_41    P1   O7   C11  C10  -164.97  30.0  2
 PN9  Var_42    H1   N1   C9   C8     -0.75  30.0  1
 PN9  Var_43    C9   N1   C13  C1   -179.58   0.0  2
 PN9  Var_44    C9   N1   C13  C2      0.30   0.0  2
 PN9  Var_45    O2   C1   C13  N1    177.30  30.0  1
 PN9  Var_46    O1   C1   C13  N1     -2.31  30.0  1
 PN9  Var_47    C3   C2   C13  N1     75.21  30.0  2
 PN9  Var_48    C2   C3   S1   C4     69.44  30.0  2
 PN9  Var_49    S1   C3   C2   C13    60.07  30.0  3
 PN9  Var_50    C3   C2   C13  C1   -104.91  30.0  2
 PN9  Var_51    O3   P1   O7   C11  -173.50  30.0  2
 PN9  Var_52    O6   P1   O7   C11    58.38  30.0  2
 PN9  Var_53    O4   P1   O7   C11   -44.11  30.0  2
 PN9  Var_54    O2   C1   C13  C2     -2.58  30.0  1
 PN9  Var_55    O1   C1   C13  C2    177.81  30.0  1
 PN9  Var_56    H1   N1   C13  C1     -1.64   0.0  2
 PN9  Var_57    H1   N1   C13  C2    178.25   0.0  2
 PN9  Var_58    H3   C2   C13  N1   -161.62  30.0  2
 PN9  Var_59    H2   C2   C13  N1    -46.20  30.0  2
 PN9  Var_60    H4   C3   S1   C4    -54.09  30.0  2
 PN9  Var_61    H5   C3   S1   C4   -168.17  30.0  2
 PN9  Var_62    H4   C3   C2   C13  -176.77  30.0  3
 PN9  Var_63    H5   C3   C2   C13   -58.90  30.0  3
 PN9  Var_64    H12  C9   N1   C13    -1.15  30.0  2
 PN9  Var_65    H3   C2   C13  C1     18.26  30.0  2
 PN9  Var_66    H2   C2   C13  C1    133.69  30.0  2
 PN9  Var_67    H8   C4   S1   C3    175.19  30.0  3
 PN9  Var_68    H6   C4   S1   C3    -66.10  30.0  3
 PN9  Var_69    H7   C4   S1   C3     56.63  30.0  3
 PN9  Var_70    H14  C11  O7   P1    -43.66  30.0  3
 PN9  Var_71    H13  C11  O7   P1     74.84  30.0  3
 PN9  Var_72    H3   C2   C3   S1    -63.00  30.0  1
 PN9  Var_73    H2   C2   C3   S1   -177.15  30.0  1

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
 PN9  plan-1  C5   0.020
 PN9  plan-1  C7   0.020
 PN9  plan-1  C8   0.020
 PN9  plan-1  O5   0.020
 PN9  plan-2  C5   0.020
 PN9  plan-2  C12  0.020
 PN9  plan-2  N2   0.020
 PN9  plan-2  H16  0.020
 PN9  plan-3  C13  0.020
 PN9  plan-3  C1   0.020
 PN9  plan-3  O1   0.020
 PN9  plan-3  O2   0.020
 PN9  plan-3  H20  0.020
 PN9  plan-4  N1   0.020
 PN9  plan-4  C13  0.020
 PN9  plan-4  C1   0.020
 PN9  plan-4  C2   0.020
 PN9  plan-4  C9   0.020
 PN9  plan-4  H1   0.020
 PN9  plan-5  N1   0.020
 PN9  plan-5  C7   0.020
 PN9  plan-5  C8   0.020
 PN9  plan-5  C10  0.020
 PN9  plan-5  C9   0.020
 PN9  plan-5  H12  0.020

