# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 11:30:16 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-2-methyl-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@](C)(CO)C(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
 MMM  MMM  (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-2-methyl-L-serine  ligand  40  23  .  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_MMM
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
 MMM  N1    N  N     0  -0.398   1.1638  -3.4241   0.2214
 MMM  C2    C  CR6   0   0.132  -0.1382  -3.4453   0.4153
 MMM  C2A   C  CH3   0  -0.721  -0.8113  -4.7562   0.6759
 MMM  C3    C  CR6   0   0.298  -0.8959  -2.2572   0.3835
 MMM  O3    O  OH1   0  -0.624  -2.2030  -2.3437   0.5945
 MMM  C4    C  CR6   0  -0.011  -0.2478  -1.0417   0.1312
 MMM  C4A   C  C1    0   0.070  -1.0123   0.2041   0.0794
 MMM  C5    C  CR6   0  -0.069   1.1438  -1.0548  -0.0718
 MMM  C6    C  CR16  0  -0.145   1.7935  -2.2706  -0.0129
 MMM  C5A   C  CH2   0  -0.219   1.8754   0.2298  -0.3464
 MMM  OP4   O  O2    0  -0.592   3.2662  -0.0339  -0.4767
 MMM  P     P  P     0   1.463   4.2881   1.1973  -0.5135
 MMM  OP1   O  O     0  -0.707   3.9557   2.2898  -1.4455
 MMM  OP2   O  OH1   0  -0.739   4.3720   1.7678   0.9753
 MMM  OP3   O  OH1   0  -0.727   5.5997   0.3410  -0.7924
 MMM  NA    N  N     0  -0.465  -2.2603   0.2000   0.3104
 MMM  CAA   C  CT    0  -0.083  -3.0770   1.3947   0.3183
 MMM  CBA   C  CH2   0  -0.186  -2.4268   2.6508  -0.2592
 MMM  OGA   O  OH1   0  -0.667  -2.1556   2.4207  -1.6185
 MMM  CAB   C  CH3   0  -0.638  -3.4807   1.6604   1.7727
 MMM  CA    C  C     0   0.580  -4.3462   1.1377  -0.4996
 MMM  OXT   O  OH1   0  -0.571  -4.3531  -0.0173  -1.1366
 MMM  OA    O  O     0  -0.441  -5.2489   1.9344  -0.5467
 MMM  H2A1  H  HCH3  0   0.249  -1.3016  -4.7675   1.6510
 MMM  H2A2  H  HCH3  0   0.249  -1.5811  -4.9675  -0.0683
 MMM  H2A3  H  HCH3  0   0.249  -0.0795  -5.5604   0.6498
 MMM  H6    H  HCR6  0   0.261   2.8633  -2.3402  -0.1565
 MMM  H5A1  H  HCH2  0   0.266   1.5040   0.6886  -1.2675
 MMM  H5A2  H  HCH2  0   0.258   1.6975   0.9384   0.4692
 MMM  HP2   H  HOH1  0   0.498   4.6235   1.1316   1.6585
 MMM  HP3   H  HOH1  0   0.507   6.3899   0.8746  -0.9538
 MMM  H4A   H  H     0   0.261  -0.4664   1.1145  -0.1607
 MMM  HAB1  H  HCH3  0   0.253  -2.5966   1.9107   2.3592
 MMM  HAB2  H  HCH3  0   0.249  -4.1813   2.4908   1.8374
 MMM  HAB3  H  HCH3  0   0.257  -3.9447   0.7803   2.2162
 MMM  HBA1  H  HCH2  0   0.247  -3.1180   3.4874  -0.1128
 MMM  HBA2  H  HCH2  0   0.228  -1.5221   2.8918   0.3146
 MMM  HGA   H  HOH1  0   0.465  -1.8124   3.2314  -2.0060
 MMM  HOA   H  HOH1  0   0.485  -5.1805  -0.1097  -1.6342
 MMM  HO3   H  HOH1  0   0.475  -2.5713  -1.4163   0.5468

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
 MMM  N1   C2    aromatic  1.317  0.020  1.317
 MMM  N1   C6    aromatic  1.335  0.020  1.335
 MMM  C2   C2A   single    1.496  0.020  1.496
 MMM  C2   C3    aromatic  1.409  0.020  1.409
 MMM  C2A  H2A1  single    0.970  0.020  1.090
 MMM  C2A  H2A2  single    0.970  0.020  1.090
 MMM  C2A  H2A3  single    0.970  0.020  1.090
 MMM  C3   C4    aromatic  1.400  0.020  1.400
 MMM  C3   O3    single    1.327  0.020  1.327
 MMM  O3   HO3   single    0.850  0.020  0.980
 MMM  C4   C5    aromatic  1.406  0.020  1.406
 MMM  C4   C4A   single    1.463  0.020  1.463
 MMM  C4A  NA    double    1.269  0.020  1.269
 MMM  C4A  H4A   single    0.930  0.020  1.080
 MMM  C5   C6    aromatic  1.380  0.020  1.380
 MMM  C5   C5A   single    1.504  0.020  1.504
 MMM  C6   H6    single    0.930  0.020  1.080
 MMM  C5A  OP4   single    1.422  0.020  1.422
 MMM  C5A  H5A1  single    0.970  0.020  1.090
 MMM  C5A  H5A2  single    0.970  0.020  1.090
 MMM  OP4  P     single    1.601  0.020  1.601
 MMM  P    OP1   double    1.474  0.020  1.474
 MMM  P    OP2   single    1.597  0.020  1.597
 MMM  P    OP3   single    1.591  0.020  1.591
 MMM  OP2  HP2   single    0.850  0.020  0.980
 MMM  OP3  HP3   single    0.850  0.020  0.980
 MMM  NA   CAA   single    1.447  0.020  1.447
 MMM  CAA  CAB   single    1.533  0.020  1.533
 MMM  CAA  CBA   single    1.528  0.020  1.528
 MMM  CAA  CA    single    1.532  0.020  1.532
 MMM  CBA  OGA   single    1.405  0.020  1.405
 MMM  CBA  HBA1  single    0.970  0.020  1.090
 MMM  CBA  HBA2  single    0.970  0.020  1.090
 MMM  OGA  HGA   single    0.850  0.020  0.980
 MMM  CAB  HAB1  single    0.970  0.020  1.090
 MMM  CAB  HAB2  single    0.970  0.020  1.090
 MMM  CAB  HAB3  single    0.970  0.020  1.090
 MMM  CA   OXT   single    1.319  0.020  1.319
 MMM  CA   OA    double    1.205  0.020  1.205
 MMM  OXT  HOA   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
 MMM  C6    N1   C2    120.42  3.000
 MMM  C3    C2   C2A   120.04  3.000
 MMM  C3    C2   N1    120.98  3.000
 MMM  C2A   C2   N1    118.98  3.000
 MMM  H2A3  C2A  H2A2  108.37  3.000
 MMM  H2A3  C2A  H2A1  108.42  3.000
 MMM  H2A2  C2A  H2A1  106.87  3.000
 MMM  H2A3  C2A  C2    109.94  3.000
 MMM  H2A2  C2A  C2    111.60  3.000
 MMM  H2A1  C2A  C2    111.51  3.000
 MMM  C4    C3   O3    122.76  3.000
 MMM  O3    C3   C2    118.10  3.000
 MMM  C4    C3   C2    119.14  3.000
 MMM  HO3   O3   C3    107.17  3.000
 MMM  C5    C4   C4A   121.33  3.000
 MMM  C4A   C4   C3    120.25  3.000
 MMM  C5    C4   C3    118.42  3.000
 MMM  H4A   C4A  NA    122.42  3.000
 MMM  H4A   C4A  C4    117.26  3.000
 MMM  NA    C4A  C4    120.32  3.000
 MMM  C5A   C5   C6    122.11  3.000
 MMM  C5A   C5   C4    119.99  3.000
 MMM  C6    C5   C4    117.90  3.000
 MMM  H6    C6   C5    121.11  3.000
 MMM  H6    C6   N1    115.74  3.000
 MMM  C5    C6   N1    123.15  3.000
 MMM  H5A2  C5A  H5A1  107.49  3.000
 MMM  H5A2  C5A  OP4   110.32  3.000
 MMM  H5A1  C5A  OP4   109.44  3.000
 MMM  H5A2  C5A  C5    109.74  3.000
 MMM  H5A1  C5A  C5    110.30  3.000
 MMM  OP4   C5A  C5    109.53  3.000
 MMM  P     OP4  C5A   118.95  3.000
 MMM  OP3   P    OP2   108.21  3.000
 MMM  OP3   P    OP1   118.29  3.000
 MMM  OP2   P    OP1   109.67  3.000
 MMM  OP3   P    OP4    96.68  3.000
 MMM  OP2   P    OP4   106.68  3.000
 MMM  OP1   P    OP4   116.15  3.000
 MMM  HP2   OP2  P     115.94  3.000
 MMM  HP3   OP3  P     113.94  3.000
 MMM  CAA   NA   C4A   123.59  3.000
 MMM  CA    CAA  CAB   108.52  3.000
 MMM  CA    CAA  CBA   106.78  3.000
 MMM  CAB   CAA  CBA   109.17  3.000
 MMM  CA    CAA  NA    109.04  3.000
 MMM  CBA   CAA  NA    115.88  3.000
 MMM  CAB   CAA  NA    107.27  3.000
 MMM  HBA2  CBA  HBA1  106.41  3.000
 MMM  HBA2  CBA  OGA   112.49  3.000
 MMM  HBA1  CBA  OGA   112.11  3.000
 MMM  HBA2  CBA  CAA   109.48  3.000
 MMM  HBA1  CBA  CAA   108.00  3.000
 MMM  OGA   CBA  CAA   108.25  3.000
 MMM  HGA   OGA  CBA   108.70  3.000
 MMM  HAB3  CAB  HAB2  108.54  3.000
 MMM  HAB3  CAB  HAB1  108.18  3.000
 MMM  HAB2  CAB  HAB1  108.35  3.000
 MMM  HAB3  CAB  CAA   111.01  3.000
 MMM  HAB2  CAB  CAA   110.99  3.000
 MMM  HAB1  CAB  CAA   109.68  3.000
 MMM  OA    CA   OXT   123.79  3.000
 MMM  OA    CA   CAA   122.06  3.000
 MMM  OXT   CA   CAA   114.15  3.000
 MMM  HOA   OXT  CA    109.61  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
 MMM  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 MMM  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 MMM  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 MMM  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 MMM  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 MMM  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 MMM  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 MMM  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 MMM  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 MMM  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 MMM  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 MMM  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 MMM  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 MMM  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 MMM  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 MMM  CONST_16  HOA   OXT  CA   CAA  180.00   0.0  0
 MMM  Var_01    NA    C4A  C4   C3     2.55  30.0  2
 MMM  Var_02    OP4   C5A  C5   C4   178.32  30.0  2
 MMM  Var_03    H2A1  C2A  C2   N1   119.31  30.0  2
 MMM  Var_04    OP1   P    OP4  C5A  -49.17  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
 MMM  chir_01  CAA  CAB  CBA  CA  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
 MMM  plan-1  N1   0.020
 MMM  plan-1  C2   0.020
 MMM  plan-1  C2A  0.020
 MMM  plan-1  C3   0.020
 MMM  plan-1  O3   0.020
 MMM  plan-1  C4   0.020
 MMM  plan-1  C4A  0.020
 MMM  plan-1  C5   0.020
 MMM  plan-1  C6   0.020
 MMM  plan-1  C5A  0.020
 MMM  plan-1  H6   0.020
 MMM  plan-2  CAA  0.020
 MMM  plan-2  CA   0.020
 MMM  plan-2  OXT  0.020
 MMM  plan-2  OA   0.020
 MMM  plan-2  HOA  0.020
 MMM  plan-3  C4   0.020
 MMM  plan-3  C4A  0.020
 MMM  plan-3  NA   0.020
 MMM  plan-3  CAA  0.020
 MMM  plan-3  H4A  0.020

