# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:55:20 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCC(=NCc1c(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
 2LM  2LM  '(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid'  ligand  43  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_2LM
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
 2LM  C     C  C     0   0.527  -0.8812   4.3699  -0.8884
 2LM  N     N  N     0  -0.411   0.1854   2.2658  -0.6740
 2LM  O1    O  O     0  -0.410  -1.8841   5.0355  -0.9058
 2LM  P     P  P     0   1.464  -0.1054  -4.4382   0.3110
 2LM  N1    N  N     0  -0.407   4.1063  -0.7153   0.5484
 2LM  C2    C  CR6   0   0.128   3.9884   0.5745   0.2954
 2LM  C3    C  CR6   0   0.250   2.7553   1.1487  -0.0662
 2LM  O3    O  OH1   0  -0.645   2.7564   2.4655  -0.3103
 2LM  C4    C  CR6   0   0.027   1.6256   0.3343  -0.1526
 2LM  C5    C  CR6   0  -0.061   1.7832  -1.0319   0.1186
 2LM  C6    C  CR16  0  -0.145   3.0370  -1.5019   0.4622
 2LM  CA    C  C     0   0.201  -0.9216   2.8645  -0.7794
 2LM  CB    C  CH2   0  -0.557  -2.2812   2.2329  -0.7491
 2LM  SD    S  S2    0  -0.030  -4.4282   1.3832   0.7071
 2LM  CE    C  CH3   0  -0.764  -4.8201   1.5551   2.4612
 2LM  CG    C  CH2   0  -0.549  -2.8096   2.1987   0.6862
 2LM  C4A   C  CH2   0  -0.348   0.2510   0.8302  -0.5360
 2LM  C5A   C  CH2   0  -0.205   0.5880  -1.9372   0.0304
 2LM  OP1   O  O     0  -0.707  -1.1935  -4.4108  -0.6827
 2LM  OP2   O  OH1   0  -0.739  -0.7161  -4.3278   1.7819
 2LM  OP3   O  OH1   0  -0.728   0.9079  -5.6654   0.2870
 2LM  OP4   O  O2    0  -0.592   1.0001  -3.2895   0.1802
 2LM  O2    O  OH1   0  -0.575   0.3427   4.8512  -0.9494
 2LM  HO3   H  HOH1  0   0.476   1.8312   2.7366  -0.5182
 2LM  H6    H  HCR6  0   0.255   3.2003  -2.5494   0.6788
 2LM  HB    H  HCH2  0   0.294  -2.9674   2.7961  -1.3811
 2LM  HBA   H  HCH2  0   0.291  -2.2301   1.2212  -1.1541
 2LM  HE    H  HCH3  0   0.277  -5.7957   1.1020   2.6266
 2LM  HEA   H  HCH3  0   0.264  -4.0866   1.0412   3.0806
 2LM  HEB   H  HCH3  0   0.264  -4.8687   2.6040   2.7501
 2LM  HG    H  HCH2  0   0.273  -2.1235   1.6539   1.3386
 2LM  HGA   H  HCH2  0   0.281  -2.9142   3.2116   1.0780
 2LM  H2A   H  HCH3  0   0.245   5.4493   1.9120  -0.5530
 2LM  H2A1  H  HCH3  0   0.245   5.0744   2.2371   1.1287
 2LM  H2A2  H  HCH3  0   0.244   6.0624   0.8341   0.7050
 2LM  H4A   H  HCH2  0   0.270  -0.4769   0.4756   0.2022
 2LM  H5A   H  HCH2  0   0.256  -0.1379  -1.6725   0.8089
 2LM  H5A1  H  HCH2  0   0.260   0.0863  -1.8123  -0.9341
 2LM  HOP2  H  HOH1  0   0.497  -0.0851  -4.4086   2.5097
 2LM  HOP3  H  HOH1  0   0.506   0.4793  -6.5318   0.2648
 2LM  H4A1  H  HCH2  0   0.301  -0.0383   0.3723  -1.4907
 2LM  H2    H  HOH1  0   0.495   0.3198   5.8189  -1.0025
 2LM  C2A   C  CH3   0  -0.718   5.2091   1.4362   0.3997

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
 2LM  C    O1    double    1.204  0.020  1.204
 2LM  C    CA    single    1.510  0.020  1.510
 2LM  C    O2    single    1.317  0.020  1.317
 2LM  N    CA    double    1.263  0.020  1.263
 2LM  N    C4A   single    1.444  0.020  1.444
 2LM  P    OP1   double    1.474  0.020  1.474
 2LM  P    OP2   single    1.596  0.020  1.596
 2LM  P    OP3   single    1.592  0.020  1.592
 2LM  P    OP4   single    1.600  0.020  1.600
 2LM  N1   C2    aromatic  1.320  0.020  1.320
 2LM  N1   C6    aromatic  1.330  0.020  1.330
 2LM  C2   C3    aromatic  1.407  0.020  1.407
 2LM  C2   C2A   single    1.498  0.020  1.498
 2LM  C3   O3    single    1.339  0.020  1.339
 2LM  C3   C4    aromatic  1.395  0.020  1.395
 2LM  C4   C5    aromatic  1.402  0.020  1.402
 2LM  C4   C4A   single    1.511  0.020  1.511
 2LM  C5   C6    aromatic  1.382  0.020  1.382
 2LM  C5   C5A   single    1.502  0.020  1.502
 2LM  CA   CB    single    1.499  0.020  1.499
 2LM  CB   CG    single    1.530  0.020  1.530
 2LM  SD   CE    single    1.806  0.020  1.806
 2LM  SD   CG    single    1.813  0.020  1.813
 2LM  C5A  OP4   single    1.422  0.020  1.422
 2LM  O3   HO3   single    0.850  0.020  0.980
 2LM  C6   H6    single    0.930  0.020  1.080
 2LM  CB   HB    single    0.970  0.020  1.090
 2LM  CB   HBA   single    0.970  0.020  1.090
 2LM  CE   HE    single    0.970  0.020  1.090
 2LM  CE   HEA   single    0.970  0.020  1.090
 2LM  CE   HEB   single    0.970  0.020  1.090
 2LM  CG   HG    single    0.970  0.020  1.090
 2LM  CG   HGA   single    0.970  0.020  1.090
 2LM  C2A  H2A   single    0.970  0.020  1.090
 2LM  C2A  H2A1  single    0.970  0.020  1.090
 2LM  C2A  H2A2  single    0.970  0.020  1.090
 2LM  C4A  H4A   single    0.970  0.020  1.090
 2LM  C5A  H5A   single    0.970  0.020  1.090
 2LM  C5A  H5A1  single    0.970  0.020  1.090
 2LM  OP2  HOP2  single    0.850  0.020  0.980
 2LM  OP3  HOP3  single    0.850  0.020  0.980
 2LM  C4A  H4A1  single    0.970  0.020  1.090
 2LM  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
 2LM  O2    C    CA    113.12  3.000
 2LM  O2    C    O1    124.87  3.000
 2LM  CA    C    O1    122.01  3.000
 2LM  C4A   N    CA    121.28  3.000
 2LM  OP4   P    OP3    96.46  3.000
 2LM  OP4   P    OP2   106.86  3.000
 2LM  OP3   P    OP2   108.11  3.000
 2LM  OP4   P    OP1   116.22  3.000
 2LM  OP3   P    OP1   118.30  3.000
 2LM  OP2   P    OP1   109.72  3.000
 2LM  C6    N1   C2    119.58  3.000
 2LM  C2A   C2   C3    119.82  3.000
 2LM  C2A   C2   N1    118.43  3.000
 2LM  C3    C2   N1    121.75  3.000
 2LM  C4    C3   O3    124.28  3.000
 2LM  C4    C3   C2    119.16  3.000
 2LM  O3    C3   C2    116.56  3.000
 2LM  HO3   O3   C3    107.93  3.000
 2LM  C4A   C4   C5    118.12  3.000
 2LM  C4A   C4   C3    124.11  3.000
 2LM  C5    C4   C3    117.76  3.000
 2LM  C5A   C5   C6    122.10  3.000
 2LM  C5A   C5   C4    119.12  3.000
 2LM  C6    C5   C4    118.78  3.000
 2LM  H6    C6   C5    121.05  3.000
 2LM  H6    C6   N1    115.99  3.000
 2LM  C5    C6   N1    122.97  3.000
 2LM  CB    CA   N     126.40  3.000
 2LM  CB    CA   C     116.47  3.000
 2LM  N     CA   C     117.08  3.000
 2LM  HBA   CB   HB    107.07  3.000
 2LM  HBA   CB   CG    110.10  3.000
 2LM  HB    CB   CG    109.77  3.000
 2LM  HBA   CB   CA    109.91  3.000
 2LM  HB    CB   CA    109.97  3.000
 2LM  CG    CB   CA    109.97  3.000
 2LM  CG    SD   CE     99.33  3.000
 2LM  HEB   CE   HEA   109.49  3.000
 2LM  HEB   CE   HE    108.71  3.000
 2LM  HEA   CE   HE    108.71  3.000
 2LM  HEB   CE   SD    111.05  3.000
 2LM  HEA   CE   SD    111.19  3.000
 2LM  HE    CE   SD    107.61  3.000
 2LM  HGA   CG   HG    107.98  3.000
 2LM  HGA   CG   SD    109.15  3.000
 2LM  HG    CG   SD    109.25  3.000
 2LM  HGA   CG   CB    110.44  3.000
 2LM  HG    CG   CB    110.77  3.000
 2LM  SD    CG   CB    109.22  3.000
 2LM  H4A1  C4A  H4A   106.01  3.000
 2LM  H4A1  C4A  C4    108.89  3.000
 2LM  H4A   C4A  C4    109.10  3.000
 2LM  H4A1  C4A  N     108.65  3.000
 2LM  H4A   C4A  N     110.86  3.000
 2LM  C4    C4A  N     113.08  3.000
 2LM  H5A1  C5A  H5A   107.14  3.000
 2LM  H5A1  C5A  OP4   109.53  3.000
 2LM  H5A   C5A  OP4   110.28  3.000
 2LM  H5A1  C5A  C5    110.35  3.000
 2LM  H5A   C5A  C5    109.85  3.000
 2LM  OP4   C5A  C5    109.66  3.000
 2LM  HOP2  OP2  P     115.99  3.000
 2LM  HOP3  OP3  P     114.15  3.000
 2LM  C5A   OP4  P     119.43  3.000
 2LM  H2    O2   C     110.21  3.000
 2LM  H2A2  C2A  H2A1  108.39  3.000
 2LM  H2A2  C2A  H2A   108.27  3.000
 2LM  H2A1  C2A  H2A   106.88  3.000
 2LM  H2A2  C2A  C2    109.89  3.000
 2LM  H2A1  C2A  C2    111.60  3.000
 2LM  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
 2LM  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 2LM  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 2LM  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 2LM  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2LM  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 2LM  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 2LM  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 2LM  CONST_08  C5A  C5   C6   N1    180.00   0.0  0
 2LM  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 2LM  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 2LM  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 2LM  CONST_12  C2A  C2   C3   C4    180.00   0.0  0
 2LM  CONST_13  C2A  C2   N1   C6    180.00   0.0  0
 2LM  CONST_14  C4A  C4   C5   C6    180.00   0.0  0
 2LM  CONST_15  H6   C6   N1   C2    180.00   0.0  0
 2LM  CONST_16  H2   O2   C    O1      0.00   0.0  0
 2LM  Var_01    C3   C4   C4A  N      -6.02  30.0  3
 2LM  Var_02    OP4  C5A  C5   C4    172.90  30.0  2
 2LM  Var_03    H2A  C2A  C2   N1    119.13  30.0  2
 2LM  Var_04    C5   C5A  OP4  P     172.24  30.0  2
 2LM  Var_05    CG   CB   CA   C     -86.39  30.0  3
 2LM  Var_06    O1   C    CA   N    -175.12  30.0  2
 2LM  Var_07    SD   CG   CB   CA   -178.15  30.0  3
 2LM  Var_08    OP1  P    OP4  C5A    48.30  30.0  1
 2LM  Var_09    HE   CE   SD   CG    179.70  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
 2LM  plan-1  N1   0.020
 2LM  plan-1  C2   0.020
 2LM  plan-1  C3   0.020
 2LM  plan-1  O3   0.020
 2LM  plan-1  C4   0.020
 2LM  plan-1  C5   0.020
 2LM  plan-1  C6   0.020
 2LM  plan-1  C4A  0.020
 2LM  plan-1  C5A  0.020
 2LM  plan-1  H6   0.020
 2LM  plan-1  C2A  0.020
 2LM  plan-2  C    0.020
 2LM  plan-2  O1   0.020
 2LM  plan-2  CA   0.020
 2LM  plan-2  O2   0.020
 2LM  plan-2  H2   0.020
 2LM  plan-3  C    0.020
 2LM  plan-3  N    0.020
 2LM  plan-3  CA   0.020
 2LM  plan-3  CB   0.020
 2LM  plan-3  C4A  0.020

