# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:28:42 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2E)-2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C(N=Cc1c(O)c(C)ncc1CO[P](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
 4LM  4LM  '(2E)-2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid'  ligand  37  22  .  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_4LM
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
 4LM  C     C  C     0   0.466   3.0032  -2.3881   0.2349
 4LM  N     N  N     0  -0.529   2.5656   0.0487  -0.1083
 4LM  O1    O  O     0  -0.430   2.2992  -2.6138   1.1884
 4LM  P     P  P     0   1.452  -3.9467  -1.3385   0.0255
 4LM  N1    N  N     0  -0.398  -1.1518   3.3863  -0.0115
 4LM  C2    C  CR6   0   0.132   0.1481   3.5204  -0.1698
 4LM  C3    C  CR6   0   0.296   1.0014   2.3990  -0.1542
 4LM  O3    O  OH1   0  -0.623   2.3011   2.6061  -0.3247
 4LM  C4    C  CR6   0  -0.017   0.4523   1.1237   0.0372
 4LM  C5    C  CR6   0  -0.061  -0.9422   1.0176   0.2025
 4LM  C6    C  CR16  0  -0.142  -1.6882   2.1769   0.1681
 4LM  CA    C  C     0   0.221   3.4638  -1.0158  -0.1402
 4LM  CB    C  C1    0  -0.241   4.7393  -0.7290  -0.4458
 4LM  CG    C  CH3   0  -0.716   5.9203  -1.6262  -0.5230
 4LM  C4A   C  C1    0   0.043   1.3024  -0.0600   0.0571
 4LM  C5A   C  CH2   0  -0.231  -1.5725  -0.3320   0.4094
 4LM  OP1   O  O     0  -0.704  -3.5883  -2.7223   0.3845
 4LM  OP2   O  OH1   0  -0.737  -3.9721  -1.1844  -1.5639
 4LM  OP3   O  OH1   0  -0.726  -5.2995  -0.7339   0.6046
 4LM  OP4   O  O2    0  -0.591  -2.9777  -0.1924   0.5803
 4LM  O2    O  OH1   0  -0.575   3.4411  -3.3177  -0.5955
 4LM  HO3   H  HOH1  0   0.481   2.7514   1.7204  -0.2925
 4LM  H6    H  HCR6  0   0.261  -2.7629   2.1526   0.2876
 4LM  HB    H  H     0   0.280   4.9410   0.3183  -0.6476
 4LM  HG    H  HCH3  0   0.258   6.7616  -1.1567  -0.0122
 4LM  HGA   H  HCH3  0   0.252   5.7683  -2.6140  -0.0989
 4LM  HGB   H  HCH3  0   0.263   6.2253  -1.7478  -1.5655
 4LM  H2A   H  HCH3  0   0.249   1.4586   5.1355   0.3879
 4LM  H2A1  H  HCH3  0   0.249   1.2126   4.9770  -1.3406
 4LM  H2A2  H  HCH3  0   0.249  -0.0797   5.6309  -0.3278
 4LM  H4A   H  H     0   0.262   0.8176  -1.0213   0.2080
 4LM  H5A   H  HCH2  0   0.260  -1.3403  -0.9790  -0.4433
 4LM  H5A1  H  HCH2  0   0.273  -1.1628  -0.8137   1.3009
 4LM  HOP2  H  HOH1  0   0.497  -4.2524  -0.3227  -1.9014
 4LM  HOP3  H  HOH1  0   0.507  -6.0685  -1.3075   0.4821
 4LM  H2    H  HOH1  0   0.489   3.1589  -4.1958  -0.2936
 4LM  C2A   C  CH3   0  -0.720   0.7154   4.8903  -0.3727

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
 4LM  C    O1    double    1.206  0.020  1.206
 4LM  C    CA    single    1.495  0.020  1.495
 4LM  C    O2    single    1.321  0.020  1.321
 4LM  N    CA    single    1.393  0.020  1.393
 4LM  N    C4A   double    1.279  0.020  1.279
 4LM  P    OP1   double    1.474  0.020  1.474
 4LM  P    OP2   single    1.597  0.020  1.597
 4LM  P    OP3   single    1.591  0.020  1.591
 4LM  P    OP4   single    1.600  0.020  1.600
 4LM  N1   C2    aromatic  1.316  0.020  1.316
 4LM  N1   C6    aromatic  1.335  0.020  1.335
 4LM  C2   C3    aromatic  1.409  0.020  1.409
 4LM  C2   C2A   single    1.497  0.020  1.497
 4LM  C3   O3    single    1.327  0.020  1.327
 4LM  C3   C4    aromatic  1.402  0.020  1.402
 4LM  C4   C5    aromatic  1.408  0.020  1.408
 4LM  C4   C4A   single    1.457  0.020  1.457
 4LM  C5   C6    aromatic  1.379  0.020  1.379
 4LM  C5   C5A   single    1.504  0.020  1.504
 4LM  CA   CB    double    1.343  0.020  1.343
 4LM  CB   CG    single    1.485  0.020  1.485
 4LM  C5A  OP4   single    1.422  0.020  1.422
 4LM  O3   HO3   single    0.850  0.020  0.980
 4LM  C6   H6    single    0.930  0.020  1.080
 4LM  CB   HB    single    0.930  0.020  1.080
 4LM  CG   HG    single    0.970  0.020  1.090
 4LM  CG   HGA   single    0.970  0.020  1.090
 4LM  CG   HGB   single    0.970  0.020  1.090
 4LM  C2A  H2A   single    0.970  0.020  1.090
 4LM  C2A  H2A1  single    0.970  0.020  1.090
 4LM  C2A  H2A2  single    0.970  0.020  1.090
 4LM  C4A  H4A   single    0.930  0.020  1.080
 4LM  C5A  H5A   single    0.970  0.020  1.090
 4LM  C5A  H5A1  single    0.970  0.020  1.090
 4LM  OP2  HOP2  single    0.850  0.020  0.980
 4LM  OP3  HOP3  single    0.850  0.020  0.980
 4LM  O2   H2    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
 4LM  O2    C    CA    112.70  3.000
 4LM  O2    C    O1    123.95  3.000
 4LM  CA    C    O1    123.34  3.000
 4LM  C4A   N    CA    125.10  3.000
 4LM  OP4   P    OP3    96.69  3.000
 4LM  OP4   P    OP2   106.59  3.000
 4LM  OP3   P    OP2   108.18  3.000
 4LM  OP4   P    OP1   116.16  3.000
 4LM  OP3   P    OP1   118.35  3.000
 4LM  OP2   P    OP1   109.69  3.000
 4LM  C6    N1   C2    120.34  3.000
 4LM  C2A   C2   C3    120.03  3.000
 4LM  C2A   C2   N1    118.94  3.000
 4LM  C3    C2   N1    121.04  3.000
 4LM  C4    C3   O3    122.90  3.000
 4LM  C4    C3   C2    119.23  3.000
 4LM  O3    C3   C2    117.87  3.000
 4LM  HO3   O3   C3    107.49  3.000
 4LM  C4A   C4   C5    120.99  3.000
 4LM  C4A   C4   C3    120.82  3.000
 4LM  C5    C4   C3    118.19  3.000
 4LM  C5A   C5   C6    122.09  3.000
 4LM  C5A   C5   C4    119.91  3.000
 4LM  C6    C5   C4    118.00  3.000
 4LM  H6    C6   C5    121.06  3.000
 4LM  H6    C6   N1    115.75  3.000
 4LM  C5    C6   N1    123.19  3.000
 4LM  CB    CA   N     117.03  3.000
 4LM  CB    CA   C     123.08  3.000
 4LM  N     CA   C     119.79  3.000
 4LM  HB    CB   CG    115.18  3.000
 4LM  HB    CB   CA    115.15  3.000
 4LM  CG    CB   CA    129.66  3.000
 4LM  HGB   CG   HGA   108.09  3.000
 4LM  HGB   CG   HG    106.22  3.000
 4LM  HGA   CG   HG    108.47  3.000
 4LM  HGB   CG   CB    109.80  3.000
 4LM  HGA   CG   CB    114.71  3.000
 4LM  HG    CG   CB    109.21  3.000
 4LM  H4A   C4A  C4    117.38  3.000
 4LM  H4A   C4A  N     122.26  3.000
 4LM  C4    C4A  N     120.36  3.000
 4LM  H5A1  C5A  H5A   107.17  3.000
 4LM  H5A1  C5A  OP4   108.39  3.000
 4LM  H5A   C5A  OP4   111.16  3.000
 4LM  H5A1  C5A  C5    110.52  3.000
 4LM  H5A   C5A  C5    109.52  3.000
 4LM  OP4   C5A  C5    110.02  3.000
 4LM  HOP2  OP2  P     115.98  3.000
 4LM  HOP3  OP3  P     113.86  3.000
 4LM  C5A   OP4  P     119.09  3.000
 4LM  H2    O2   C     110.17  3.000
 4LM  H2A2  C2A  H2A1  108.39  3.000
 4LM  H2A2  C2A  H2A   108.43  3.000
 4LM  H2A1  C2A  H2A   106.86  3.000
 4LM  H2A2  C2A  C2    109.91  3.000
 4LM  H2A1  C2A  C2    111.44  3.000
 4LM  H2A   C2A  C2    111.67  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
 4LM  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 4LM  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 4LM  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 4LM  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 4LM  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 4LM  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 4LM  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 4LM  CONST_08  C5A  C5   C6   N1    180.00   0.0  0
 4LM  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 4LM  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 4LM  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 4LM  CONST_12  C2A  C2   C3   C4    180.00   0.0  0
 4LM  CONST_13  C2A  C2   N1   C6    180.00   0.0  0
 4LM  CONST_14  C4A  C4   C5   C6    180.00   0.0  0
 4LM  CONST_15  H6   C6   N1   C2    180.00   0.0  0
 4LM  CONST_16  H2   O2   C    O1      0.00   0.0  0
 4LM  Var_01    C3   C4   C4A  N      -0.41  30.0  2
 4LM  Var_02    OP4  C5A  C5   C4    178.75  30.0  2
 4LM  Var_03    H2A  C2A  C2   N1    122.16  30.0  2
 4LM  Var_04    C5   C5A  OP4  P     146.23  30.0  1
 4LM  Var_05    CG   CB   CA   C       1.78   0.0  2
 4LM  Var_06    O1   C    CA   N     -43.66  30.0  2
 4LM  Var_07    OP1  P    OP4  C5A    48.72  30.0  1
 4LM  Var_08    HG   CG   CB   CA   -134.36  30.0  3

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
 4LM  plan-1  N1   0.020
 4LM  plan-1  C2   0.020
 4LM  plan-1  C3   0.020
 4LM  plan-1  O3   0.020
 4LM  plan-1  C4   0.020
 4LM  plan-1  C5   0.020
 4LM  plan-1  C6   0.020
 4LM  plan-1  C4A  0.020
 4LM  plan-1  C5A  0.020
 4LM  plan-1  H6   0.020
 4LM  plan-1  C2A  0.020
 4LM  plan-2  C    0.020
 4LM  plan-2  O1   0.020
 4LM  plan-2  CA   0.020
 4LM  plan-2  O2   0.020
 4LM  plan-2  H2   0.020
 4LM  plan-3  N    0.020
 4LM  plan-3  C4   0.020
 4LM  plan-3  CA   0.020
 4LM  plan-3  C4A  0.020
 4LM  plan-3  H4A  0.020
 4LM  plan-4  C    0.020
 4LM  plan-4  N    0.020
 4LM  plan-4  CA   0.020
 4LM  plan-4  CB   0.020
 4LM  plan-4  CG   0.020
 4LM  plan-4  HB   0.020

