# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 19:51:49 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: [(1R)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-1-methylpropyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@](C)(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
 MPM  MPM  '[(1R)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-1-methylpropyl]phosphonic acid'  ligand  44  24  .  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_MPM
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
 MPM  C4    C  CR6   0  -0.010  -0.2850   1.0800   0.1287
 MPM  C3    C  CR6   0   0.299   0.2450   2.3396   0.4350
 MPM  C5    C  CR6   0  -0.067  -1.6642   0.9774  -0.1276
 MPM  C4A   C  C1    0   0.059   0.5853  -0.0933   0.0809
 MPM  C2    C  CR6   0   0.134  -0.6180   3.4529   0.4846
 MPM  C6    C  CR16  0  -0.142  -2.4209   2.1286  -0.0545
 MPM  O1    O  OH1   0  -0.623   1.5326   2.5384   0.6872
 MPM  C5A   C  CH2   0  -0.222  -2.2689  -0.3558  -0.4728
 MPM  N2    N  N     0  -0.468   1.8335   0.0189   0.2851
 MPM  N1    N  N     0  -0.397  -1.9056   3.3232   0.2441
 MPM  C2A   C  CH3   0  -0.721  -0.0764   4.8072   0.8190
 MPM  O2    O  O2    0  -0.591  -3.6452  -0.1880  -0.7837
 MPM  C     C  CT    0  -0.189   2.7418  -1.1148   0.2804
 MPM  P1    P  P     0   1.457  -4.6464  -1.4250  -0.6187
 MPM  CA2   C  CH2   0  -0.486   2.2267  -2.4029  -0.3814
 MPM  CA1   C  CH3   0  -0.663   3.0945  -1.4151   1.7438
 MPM  P2    P  P     0   1.400   4.2027  -0.4221  -0.6064
 MPM  O3    O  O     0  -0.705  -4.2101  -2.7030  -1.2094
 MPM  O5    O  OH1   0  -0.737  -4.8833  -1.6119   0.9493
 MPM  O4    O  OH1   0  -0.726  -5.9249  -0.7057  -1.2347
 MPM  O8    O  OH1   0  -0.743   4.8211   0.7166   0.3471
 MPM  O6    O  OH1   0  -0.745   5.2088  -1.6700  -0.5584
 MPM  O7    O  O     0  -0.702   3.9283   0.1659  -1.9374
 MPM  CA3   C  CH3   0  -0.673   1.8857  -2.3526  -1.8669
 MPM  H4AC  H  H     0   0.263   0.1208  -1.0571  -0.1224
 MPM  HC6   H  HCR6  0   0.262  -3.4864   2.1089  -0.2394
 MPM  HO1   H  HOH1  0   0.474   1.9926   1.6587   0.6058
 MPM  H5A1  H  HCH2  0   0.266  -1.7627  -0.7925  -1.3379
 MPM  H5A2  H  HCH2  0   0.261  -2.1363  -1.0462   0.3672
 MPM  H2A1  H  HCH3  0   0.249   0.6996   5.1163   0.1167
 MPM  H2A2  H  HCH3  0   0.250  -0.8765   5.5432   0.7914
 MPM  H2A3  H  HCH3  0   0.250   0.3726   4.8232   1.8137
 MPM  HA21  H  HCH2  0   0.252   1.3545  -2.7379   0.1886
 MPM  HA22  H  HCH2  0   0.269   2.9781  -3.1768  -0.2154
 MPM  HA11  H  HCH3  0   0.256   3.8930  -2.1522   1.8211
 MPM  HA12  H  HCH3  0   0.249   3.3908  -0.5195   2.2889
 MPM  HA13  H  HCH3  0   0.262   2.2143  -1.8223   2.2427
 MPM  HO5   H  HOH1  0   0.497  -5.2186  -0.8383   1.4226
 MPM  HO4   H  HOH1  0   0.507  -6.6781  -1.2952  -1.3758
 MPM  HO8   H  HOH1  0   0.491   5.1855   0.4215   1.1913
 MPM  HO6   H  HOH1  0   0.498   5.9984  -1.5733  -1.1092
 MPM  HA31  H  HCH3  0   0.237   2.7689  -2.2157  -2.4875
 MPM  HA32  H  HCH3  0   0.242   1.4253  -3.2953  -2.1612
 MPM  HA33  H  HCH3  0   0.226   1.1843  -1.5568  -2.1182

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
 MPM  C4   C3    aromatic  1.400  0.020  1.400
 MPM  C4   C5    aromatic  1.407  0.020  1.407
 MPM  C4   C4A   single    1.462  0.020  1.462
 MPM  C3   C2    aromatic  1.409  0.020  1.409
 MPM  C3   O1    single    1.327  0.020  1.327
 MPM  C5   C6    aromatic  1.380  0.020  1.380
 MPM  C5   C5A   single    1.504  0.020  1.504
 MPM  C4A  N2    double    1.270  0.020  1.270
 MPM  C4A  H4AC  single    0.930  0.020  1.080
 MPM  C2   N1    aromatic  1.316  0.020  1.316
 MPM  C2   C2A   single    1.496  0.020  1.496
 MPM  C6   N1    aromatic  1.335  0.020  1.335
 MPM  C6   HC6   single    0.930  0.020  1.080
 MPM  O1   HO1   single    0.850  0.020  0.980
 MPM  C5A  O2    single    1.421  0.020  1.421
 MPM  C5A  H5A1  single    0.970  0.020  1.090
 MPM  C5A  H5A2  single    0.970  0.020  1.090
 MPM  N2   C     single    1.453  0.020  1.453
 MPM  C2A  H2A1  single    0.970  0.020  1.090
 MPM  C2A  H2A2  single    0.970  0.020  1.090
 MPM  C2A  H2A3  single    0.970  0.020  1.090
 MPM  O2   P1    single    1.600  0.020  1.600
 MPM  C    CA2   single    1.537  0.020  1.537
 MPM  C    CA1   single    1.535  0.020  1.535
 MPM  C    P2    single    1.844  0.020  1.844
 MPM  P1   O3    double    1.474  0.020  1.474
 MPM  P1   O5    single    1.597  0.020  1.597
 MPM  P1   O4    single    1.591  0.020  1.591
 MPM  CA2  CA3   single    1.525  0.020  1.525
 MPM  CA2  HA21  single    0.970  0.020  1.090
 MPM  CA2  HA22  single    0.970  0.020  1.090
 MPM  CA1  HA11  single    0.970  0.020  1.090
 MPM  CA1  HA12  single    0.970  0.020  1.090
 MPM  CA1  HA13  single    0.970  0.020  1.090
 MPM  P2   O8    single    1.609  0.020  1.609
 MPM  P2   O6    single    1.604  0.020  1.604
 MPM  P2   O7    double    1.481  0.020  1.481
 MPM  O5   HO5   single    0.850  0.020  0.980
 MPM  O4   HO4   single    0.850  0.020  0.980
 MPM  O8   HO8   single    0.850  0.020  0.980
 MPM  O6   HO6   single    0.850  0.020  0.980
 MPM  CA3  HA31  single    0.970  0.020  1.090
 MPM  CA3  HA32  single    0.970  0.020  1.090
 MPM  CA3  HA33  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
 MPM  C4A   C4   C5    121.28  3.000
 MPM  C4A   C4   C3    120.25  3.000
 MPM  C5    C4   C3    118.46  3.000
 MPM  O1    C3   C2    117.97  3.000
 MPM  O1    C3   C4    122.92  3.000
 MPM  C2    C3   C4    119.11  3.000
 MPM  C5A   C5   C6    122.09  3.000
 MPM  C5A   C5   C4    120.05  3.000
 MPM  C6    C5   C4    117.86  3.000
 MPM  H4AC  C4A  N2    121.84  3.000
 MPM  H4AC  C4A  C4    117.56  3.000
 MPM  N2    C4A  C4    120.60  3.000
 MPM  C2A   C2   N1    118.95  3.000
 MPM  C2A   C2   C3    120.08  3.000
 MPM  N1    C2   C3    120.97  3.000
 MPM  HC6   C6   N1    115.77  3.000
 MPM  HC6   C6   C5    121.08  3.000
 MPM  N1    C6   C5    123.15  3.000
 MPM  HO1   O1   C3    107.47  3.000
 MPM  H5A2  C5A  H5A1  107.40  3.000
 MPM  H5A2  C5A  O2    111.07  3.000
 MPM  H5A1  C5A  O2    108.81  3.000
 MPM  H5A2  C5A  C5    109.51  3.000
 MPM  H5A1  C5A  C5    110.46  3.000
 MPM  O2    C5A  C5    109.57  3.000
 MPM  C     N2   C4A   123.03  3.000
 MPM  C6    N1   C2    120.44  3.000
 MPM  H2A3  C2A  H2A2  108.42  3.000
 MPM  H2A3  C2A  H2A1  106.84  3.000
 MPM  H2A2  C2A  H2A1  108.37  3.000
 MPM  H2A3  C2A  C2    111.46  3.000
 MPM  H2A2  C2A  C2    109.91  3.000
 MPM  H2A1  C2A  C2    111.71  3.000
 MPM  P1    O2   C5A   119.49  3.000
 MPM  P2    C    CA1   110.48  3.000
 MPM  P2    C    CA2   111.92  3.000
 MPM  CA1   C    CA2   108.88  3.000
 MPM  P2    C    N2    101.76  3.000
 MPM  CA1   C    N2    107.05  3.000
 MPM  CA2   C    N2    116.48  3.000
 MPM  O4    P1   O5    108.29  3.000
 MPM  O4    P1   O3    118.34  3.000
 MPM  O5    P1   O3    109.63  3.000
 MPM  O4    P1   O2     96.51  3.000
 MPM  O5    P1   O2    106.54  3.000
 MPM  O3    P1   O2    116.35  3.000
 MPM  HA22  CA2  HA21  104.63  3.000
 MPM  HA22  CA2  CA3   109.00  3.000
 MPM  HA21  CA2  CA3   109.83  3.000
 MPM  HA22  CA2  C     107.34  3.000
 MPM  HA21  CA2  C     107.42  3.000
 MPM  CA3   CA2  C     117.82  3.000
 MPM  HA13  CA1  HA12  107.32  3.000
 MPM  HA13  CA1  HA11  107.85  3.000
 MPM  HA12  CA1  HA11  108.75  3.000
 MPM  HA13  CA1  C     108.89  3.000
 MPM  HA12  CA1  C     112.25  3.000
 MPM  HA11  CA1  C     111.61  3.000
 MPM  O7    P2   O6    116.88  3.000
 MPM  O7    P2   O8    108.83  3.000
 MPM  O6    P2   O8    106.97  3.000
 MPM  O7    P2   C     115.76  3.000
 MPM  O6    P2   C     100.97  3.000
 MPM  O8    P2   C     106.58  3.000
 MPM  HO5   O5   P1    116.01  3.000
 MPM  HO4   O4   P1    114.01  3.000
 MPM  HO8   O8   P2    116.54  3.000
 MPM  HO6   O6   P2    114.66  3.000
 MPM  HA33  CA3  HA32  107.30  3.000
 MPM  HA33  CA3  HA31  107.39  3.000
 MPM  HA32  CA3  HA31  107.32  3.000
 MPM  HA33  CA3  CA2   113.11  3.000
 MPM  HA32  CA3  CA2   109.21  3.000
 MPM  HA31  CA3  CA2   112.23  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
 MPM  CONST_01  N1    C2   C3   C4      0.00   0.0  0
 MPM  CONST_02  N1    C6   C5   C4      0.00   0.0  0
 MPM  CONST_03  C6    C5   C4   C3      0.00   0.0  0
 MPM  CONST_04  C6    N1   C2   C3      0.00   0.0  0
 MPM  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 MPM  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 MPM  CONST_07  C2A   C2   C3   C4    180.00   0.0  0
 MPM  CONST_08  C5A   C5   C4   C3    180.00   0.0  0
 MPM  CONST_09  O1    C3   C4   C5    180.00   0.0  0
 MPM  CONST_10  C2    C3   C4   C4A   180.00   0.0  0
 MPM  CONST_11  C6    C5   C4   C4A   180.00   0.0  0
 MPM  CONST_12  C2A   C2   N1   C6    180.00   0.0  0
 MPM  CONST_13  N1    C2   C3   O1    180.00   0.0  0
 MPM  CONST_14  N1    C6   C5   C5A   180.00   0.0  0
 MPM  CONST_15  HC6   C6   C5   C4    180.00   0.0  0
 MPM  Var_01    O2    C5A  C5   C4   -175.68  30.0  2
 MPM  Var_02    N2    C4A  C4   C3     -1.64  30.0  2
 MPM  Var_03    H2A1  C2A  C2   C3     58.53  30.0  2
 MPM  Var_04    O3    P1   O2   C5A   -48.21  30.0  3
 MPM  Var_05    HA31  CA3  CA2  C      67.87  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
 MPM  chir_01  C  CA2  CA1  P2  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
 MPM  plan-1  C4    0.020
 MPM  plan-1  C3    0.020
 MPM  plan-1  C5    0.020
 MPM  plan-1  C4A   0.020
 MPM  plan-1  C2    0.020
 MPM  plan-1  C6    0.020
 MPM  plan-1  O1    0.020
 MPM  plan-1  C5A   0.020
 MPM  plan-1  N1    0.020
 MPM  plan-1  C2A   0.020
 MPM  plan-1  HC6   0.020
 MPM  plan-2  C4    0.020
 MPM  plan-2  C4A   0.020
 MPM  plan-2  N2    0.020
 MPM  plan-2  C     0.020
 MPM  plan-2  H4AC  0.020

