# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 07:06:30 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=C2CONC2=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
 LCS  LCS  '[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate'  ligand  36  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_LCS
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
 LCS  N1    N  N     0  -0.406   0.7235  -3.2471  -0.7900
 LCS  C2    C  CR6   0   0.130  -0.5354  -3.3445  -0.3987
 LCS  C2A   C  CH3   0  -0.785  -1.2796  -4.6106  -0.7007
 LCS  C3    C  CR6   0   0.263  -1.1648  -2.2890   0.2771
 LCS  O3    O  OH1   0  -0.622  -2.4515  -2.3536   0.6668
 LCS  C4    C  CR6   0   0.108  -0.4525  -1.1297   0.5588
 LCS  C4A   C  CH2   0  -0.445  -1.1187   0.0162   1.2793
 LCS  C5    C  CR6   0  -0.069   0.8699  -1.0459   0.1186
 LCS  C6    C  CR16  0  -0.135   1.4085  -2.1349  -0.5479
 LCS  C5A   C  CH2   0  -0.205   1.6504   0.2099   0.3798
 LCS  O4P   O  O2    0  -0.593   2.9184   0.1268  -0.2607
 LCS  P     P  P     0   1.463   4.0395   1.2129   0.0874
 LCS  O1P   O  O     0  -0.707   3.6091   2.6226   0.0679
 LCS  O2P   O  OH1   0  -0.739   4.6032   0.8430   1.5352
 LCS  O3P   O  OH1   0  -0.728   5.1038   0.7319  -0.9938
 LCS  N     N  N     0  -0.324  -1.5809   0.9760   0.2965
 LCS  CA    C  CR5   0   0.052  -2.8010   1.2661   0.2387
 LCS  C     C  CR5   0   0.505  -3.3158   2.2552  -0.7663
 LCS  O     O  O     0  -0.462  -2.6817   2.8652  -1.6065
 LCS  ND    N  NR15  0  -0.350  -4.6267   2.3096  -0.5356
 LCS  OG    O  O     0  -0.381  -5.0991   1.5468   0.5120
 LCS  CB    C  CH2   0  -0.206  -3.9908   0.8074   1.0274
 LCS  H2A1  H  HCH3  0   0.257  -1.6655  -5.0893   0.2030
 LCS  H2A2  H  HCH3  0   0.260  -2.1259  -4.4386  -1.3706
 LCS  H2A3  H  HCH3  0   0.273  -0.6157  -5.3200  -1.1889
 LCS  HO3   H  HOH1  0   0.488  -2.8468  -3.2025   0.4397
 LCS  H4A1  H  HCH2  0   0.271  -1.8988  -0.3548   1.9473
 LCS  H4A2  H  HCH2  0   0.285  -0.3899   0.5273   1.9134
 LCS  H6    H  HCR6  0   0.259   2.4305  -2.1215  -0.9037
 LCS  H5A1  H  HCH2  0   0.265   1.1006   1.0751   0.0004
 LCS  H5A2  H  HCH2  0   0.258   1.7735   0.3482   1.4599
 LCS  HOP2  H  HOH1  0   0.497   4.9705  -0.0459   1.6315
 LCS  HOP3  H  HOH1  0   0.506   5.8603   1.3250  -1.0951
 LCS  HND   H  HNR5  0   0.440  -5.3196   2.9165  -0.9501
 LCS  HB1   H  HCH2  0   0.287  -4.1730  -0.2622   0.8946
 LCS  HB2   H  HCH2  0   0.290  -3.8937   1.0173   2.0951

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
 LCS  N1   C2    aromatic  1.322  0.020  1.322
 LCS  N1   C6    aromatic  1.329  0.020  1.329
 LCS  C2   C2A   single    1.499  0.020  1.499
 LCS  C2   C3    aromatic  1.402  0.020  1.402
 LCS  C3   O3    single    1.346  0.020  1.346
 LCS  C3   C4    aromatic  1.390  0.020  1.390
 LCS  C4   C4A   single    1.509  0.020  1.509
 LCS  C4   C5    aromatic  1.396  0.020  1.396
 LCS  C4A  N     single    1.449  0.020  1.449
 LCS  C5   C6    aromatic  1.386  0.020  1.386
 LCS  C5   C5A   single    1.502  0.020  1.502
 LCS  C5A  O4P   single    1.423  0.020  1.423
 LCS  O4P  P     single    1.599  0.020  1.599
 LCS  P    O1P   double    1.474  0.020  1.474
 LCS  P    O2P   single    1.597  0.020  1.597
 LCS  P    O3P   single    1.592  0.020  1.592
 LCS  N    CA    double    1.255  0.020  1.255
 LCS  CA   C     single    1.501  0.020  1.501
 LCS  CA   CB    single    1.499  0.020  1.499
 LCS  C    O     double    1.217  0.020  1.217
 LCS  C    ND    single    1.332  0.020  1.332
 LCS  ND   OG    single    1.379  0.020  1.379
 LCS  OG   CB    single    1.429  0.020  1.429
 LCS  C2A  H2A1  single    0.970  0.020  1.090
 LCS  C2A  H2A2  single    0.970  0.020  1.090
 LCS  C2A  H2A3  single    0.970  0.020  1.090
 LCS  O3   HO3   single    0.850  0.020  0.980
 LCS  C4A  H4A1  single    0.970  0.020  1.090
 LCS  C4A  H4A2  single    0.970  0.020  1.090
 LCS  C6   H6    single    0.930  0.020  1.080
 LCS  C5A  H5A1  single    0.970  0.020  1.090
 LCS  C5A  H5A2  single    0.970  0.020  1.090
 LCS  O2P  HOP2  single    0.850  0.020  0.980
 LCS  O3P  HOP3  single    0.850  0.020  0.980
 LCS  ND   HND   single    0.860  0.020  1.020
 LCS  CB   HB1   single    0.970  0.020  1.090
 LCS  CB   HB2   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
 LCS  C6    N1   C2    119.92  3.000
 LCS  C3    C2   C2A   120.65  3.000
 LCS  C3    C2   N1    120.97  3.000
 LCS  C2A   C2   N1    118.38  3.000
 LCS  H2A3  C2A  H2A2  107.47  3.000
 LCS  H2A3  C2A  H2A1  107.52  3.000
 LCS  H2A2  C2A  H2A1  107.59  3.000
 LCS  H2A3  C2A  C2    109.78  3.000
 LCS  H2A2  C2A  C2    112.02  3.000
 LCS  H2A1  C2A  C2    112.24  3.000
 LCS  C4    C3   O3    118.13  3.000
 LCS  C4    C3   C2    119.71  3.000
 LCS  O3    C3   C2    122.17  3.000
 LCS  HO3   O3   C3    111.48  3.000
 LCS  C5    C4   C4A   121.55  3.000
 LCS  C5    C4   C3    118.14  3.000
 LCS  C4A   C4   C3    120.28  3.000
 LCS  H4A2  C4A  H4A1  106.28  3.000
 LCS  H4A2  C4A  N     107.24  3.000
 LCS  H4A1  C4A  N     114.33  3.000
 LCS  H4A2  C4A  C4    109.75  3.000
 LCS  H4A1  C4A  C4    110.46  3.000
 LCS  N     C4A  C4    108.66  3.000
 LCS  C5A   C5   C6    122.61  3.000
 LCS  C5A   C5   C4    119.19  3.000
 LCS  C6    C5   C4    118.21  3.000
 LCS  H6    C6   C5    121.03  3.000
 LCS  H6    C6   N1    115.94  3.000
 LCS  C5    C6   N1    123.03  3.000
 LCS  H5A2  C5A  H5A1  107.38  3.000
 LCS  H5A2  C5A  O4P   110.54  3.000
 LCS  H5A1  C5A  O4P   109.77  3.000
 LCS  H5A2  C5A  C5    109.59  3.000
 LCS  H5A1  C5A  C5    109.89  3.000
 LCS  O4P   C5A  C5    109.63  3.000
 LCS  P     O4P  C5A   119.14  3.000
 LCS  O3P   P    O2P   108.05  3.000
 LCS  O3P   P    O1P   118.38  3.000
 LCS  O2P   P    O1P   109.66  3.000
 LCS  O3P   P    O4P    96.64  3.000
 LCS  O2P   P    O4P   106.70  3.000
 LCS  O1P   P    O4P   116.23  3.000
 LCS  HOP2  O2P  P     115.94  3.000
 LCS  HOP3  O3P  P     114.15  3.000
 LCS  CA    N    C4A   119.62  3.000
 LCS  CB    CA   C     106.35  3.000
 LCS  CB    CA   N     132.55  3.000
 LCS  C     CA   N     121.09  3.000
 LCS  ND    C    O     127.74  3.000
 LCS  ND    C    CA    104.39  3.000
 LCS  O     C    CA    127.87  3.000
 LCS  HND   ND   OG    114.14  3.000
 LCS  HND   ND   C     128.94  3.000
 LCS  OG    ND   C     116.49  3.000
 LCS  CB    OG   ND    107.13  3.000
 LCS  HB2   CB   HB1   108.76  3.000
 LCS  HB2   CB   OG    108.79  3.000
 LCS  HB1   CB   OG    109.47  3.000
 LCS  HB2   CB   CA    112.63  3.000
 LCS  HB1   CB   CA    111.57  3.000
 LCS  OG    CB   CA    105.52  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
 LCS  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 LCS  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 LCS  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 LCS  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 LCS  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 LCS  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 LCS  CONST_07  OG    ND   C    CA      0.00   0.0  0
 LCS  CONST_08  O3    C3   C2   N1    180.00   0.0  0
 LCS  CONST_09  C5A   C5   C6   N1    180.00   0.0  0
 LCS  CONST_10  C4A   C4   C3   C2    180.00   0.0  0
 LCS  CONST_11  C6    N1   C2   C2A   180.00   0.0  0
 LCS  CONST_12  C4    C3   C2   C2A   180.00   0.0  0
 LCS  CONST_13  C5A   C5   C4   C3    180.00   0.0  0
 LCS  CONST_14  C5    C4   C3   O3    180.00   0.0  0
 LCS  CONST_15  C6    C5   C4   C4A   180.00   0.0  0
 LCS  CONST_16  OG    ND   C    O     180.00   0.0  0
 LCS  CONST_17  H6    C6   N1   C2    180.00   0.0  0
 LCS  CONST_18  HND   ND   C    CA    180.00   0.0  0
 LCS  Var_01    OG    CB   CA   C      -1.98  30.0  1
 LCS  Var_02    CB    CA   C    ND     -0.11  30.0  1
 LCS  Var_03    N     C4A  C4   C3    -96.33  30.0  2
 LCS  Var_04    O4P   C5A  C5   C4   -174.49  30.0  2
 LCS  Var_05    C     CA   N    C4A  -179.98  30.0  2
 LCS  Var_06    H2A1  C2A  C2   N1    122.15  30.0  2
 LCS  Var_07    O1P   P    O4P  C5A   -47.89  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
 LCS  plan-1  N1   0.020
 LCS  plan-1  C2   0.020
 LCS  plan-1  C2A  0.020
 LCS  plan-1  C3   0.020
 LCS  plan-1  O3   0.020
 LCS  plan-1  C4   0.020
 LCS  plan-1  C4A  0.020
 LCS  plan-1  C5   0.020
 LCS  plan-1  C6   0.020
 LCS  plan-1  C5A  0.020
 LCS  plan-1  H6   0.020
 LCS  plan-2  CA   0.020
 LCS  plan-2  C    0.020
 LCS  plan-2  O    0.020
 LCS  plan-2  ND   0.020
 LCS  plan-2  OG   0.020
 LCS  plan-2  HND  0.020

