# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:59:45 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: [5-hydroxy-6-methyl-4-({[(4R)-3-oxoisoxazolidin-4-yl]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[C@@H]2CONC2=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
 DCS  DCS  '[5-hydroxy-6-methyl-4-({[(4R)-3-oxoisoxazolidin-4-yl]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate'  ligand  38  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_DCS
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
 DCS  N1    N  N     0  -0.369   3.5019   0.5024   0.9764
 DCS  C2    C  CR6   0   0.161   3.5270   0.4571  -0.3449
 DCS  C2A   C  CH3   0  -0.704   4.8044   0.7951  -1.0497
 DCS  C3    C  CR6   0   0.161   2.3880   0.0949  -1.0798
 DCS  O3    O  OH1   0  -0.660   2.4782   0.0621  -2.4172
 DCS  C4    C  CR6   0   0.012   1.2088  -0.2289  -0.4083
 DCS  C4A   C  CH2   0  -0.366  -0.0000  -0.6814  -1.1901
 DCS  C5    C  CR6   0   0.162   1.2069  -0.1606   0.9880
 DCS  C6    C  CR16  0  -0.190   2.3798   0.2082   1.6266
 DCS  C5A   C  CH2   0  -0.320  -0.0496  -0.4913   1.7448
 DCS  O4P   O  O2    0  -0.620   0.1773  -0.3744   3.1465
 DCS  P     P  P     0   1.489  -1.0483   0.0135   4.0974
 DCS  O1P   O  O     0  -0.744  -2.2991  -0.7372   3.8868
 DCS  O2P   O  OH1   0  -0.673  -0.2817  -0.1766   5.4791
 DCS  O3P   O  OH1   0  -0.748  -1.3171   1.5742   3.8877
 DCS  N     N  NH1   0  -0.602  -0.1610   0.1139  -2.4065
 DCS  CA    C  CH1   0  -0.283  -1.0581  -0.4342  -3.3943
 DCS  C     C  C     0   0.451  -2.5519  -0.3230  -3.0880
 DCS  O     O  O     0  -0.317  -3.1157  -0.5279  -2.0307
 DCS  ND    N  NH1   0  -0.361  -3.1266   0.1061  -4.2243
 DCS  OG    O  O2    0  -0.363  -2.2629   0.0982  -5.3127
 DCS  CB    C  CH2   0  -0.161  -0.9788   0.2969  -4.7277
 DCS  H2A1  H  HCH3  0   0.241   5.2049  -0.0640  -1.5917
 DCS  H2A2  H  HCH3  0   0.238   4.6612   1.5918  -1.7813
 DCS  H2A3  H  HCH3  0   0.239   5.5521   1.1187  -0.3285
 DCS  HO3   H  HOH1  0   0.463   1.5458   0.0927  -2.7605
 DCS  H4A1  H  HCH2  0   0.282   0.1509  -1.7219  -1.4943
 DCS  H4A2  H  HCH2  0   0.262  -0.8991  -0.6681  -0.5725
 DCS  H6    H  HCR6  0   0.240   2.4272   0.2769   2.7055
 DCS  H5A1  H  HCH2  0   0.251  -0.8525   0.1792   1.4195
 DCS  H5A2  H  HCH2  0   0.270  -0.3743  -1.5117   1.5259
 DCS  HOP2  H  HOH1  0   0.548  -0.8520  -0.0819   6.2546
 DCS  HOP3  H  HOH1  0   0.484  -0.5627   2.1582   4.0441
 DCS  HN    H  HNH1  0   0.366  -0.4226   1.0653  -2.1695
 DCS  HA    H  HCH1  0   0.285  -0.8248  -1.4968  -3.5232
 DCS  HND   H  HNH1  0   0.420  -4.1018   0.0197  -4.4761
 DCS  HB1   H  HCH2  0   0.216  -0.7884   1.3653  -4.5684
 DCS  HB2   H  HCH2  0   0.242  -0.2372  -0.1065  -5.4131

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
 DCS  N1   C2    aromatic  1.322  0.020  1.322
 DCS  N1   C6    aromatic  1.330  0.020  1.330
 DCS  C2   C2A   single    1.498  0.020  1.498
 DCS  C2   C3    aromatic  1.403  0.020  1.403
 DCS  C2A  H2A1  single    0.970  0.020  1.090
 DCS  C2A  H2A2  single    0.970  0.020  1.090
 DCS  C2A  H2A3  single    0.970  0.020  1.090
 DCS  C3   O3    single    1.341  0.020  1.341
 DCS  C3   C4    aromatic  1.395  0.020  1.395
 DCS  O3   HO3   single    0.850  0.020  0.980
 DCS  C4   C4A   single    1.509  0.020  1.509
 DCS  C4   C5    aromatic  1.398  0.020  1.398
 DCS  C4A  N     single    1.462  0.020  1.462
 DCS  C4A  H4A1  single    0.970  0.020  1.090
 DCS  C4A  H4A2  single    0.970  0.020  1.090
 DCS  C5   C6    aromatic  1.386  0.020  1.386
 DCS  C5   C5A   single    1.504  0.020  1.504
 DCS  C6   H6    single    0.930  0.020  1.080
 DCS  C5A  O4P   single    1.425  0.020  1.425
 DCS  C5A  H5A1  single    0.970  0.020  1.090
 DCS  C5A  H5A2  single    0.970  0.020  1.090
 DCS  O4P  P     single    1.599  0.020  1.599
 DCS  P    O1P   double    1.474  0.020  1.474
 DCS  P    O2P   single    1.591  0.020  1.591
 DCS  P    O3P   single    1.597  0.020  1.597
 DCS  O2P  HOP2  single    0.850  0.020  0.980
 DCS  O3P  HOP3  single    0.850  0.020  0.980
 DCS  N    CA    single    1.442  0.020  1.442
 DCS  N    HN    single    0.890  0.020  1.040
 DCS  CA   C     single    1.529  0.020  1.529
 DCS  CA   CB    single    1.523  0.020  1.523
 DCS  CA   HA    single    0.970  0.020  1.090
 DCS  C    O     double    1.216  0.020  1.216
 DCS  C    ND    single    1.344  0.020  1.344
 DCS  ND   OG    single    1.390  0.020  1.390
 DCS  ND   HND   single    0.890  0.020  1.040
 DCS  OG   CB    single    1.425  0.020  1.425
 DCS  CB   HB1   single    0.970  0.020  1.090
 DCS  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
 DCS  C6    N1   C2    119.80  3.000
 DCS  C3    C2   C2A   120.28  3.000
 DCS  C3    C2   N1    121.12  3.000
 DCS  C2A   C2   N1    118.60  3.000
 DCS  H2A3  C2A  H2A2  108.51  3.000
 DCS  H2A3  C2A  H2A1  108.12  3.000
 DCS  H2A2  C2A  H2A1  106.84  3.000
 DCS  H2A3  C2A  C2    109.96  3.000
 DCS  H2A2  C2A  C2    111.62  3.000
 DCS  H2A1  C2A  C2    111.65  3.000
 DCS  C4    C3   O3    122.09  3.000
 DCS  C4    C3   C2    119.60  3.000
 DCS  O3    C3   C2    118.31  3.000
 DCS  HO3   O3   C3    106.30  3.000
 DCS  C5    C4   C4A   122.07  3.000
 DCS  C5    C4   C3    118.08  3.000
 DCS  C4A   C4   C3    119.82  3.000
 DCS  H4A2  C4A  H4A1  106.41  3.000
 DCS  H4A2  C4A  N     111.94  3.000
 DCS  H4A1  C4A  N     107.52  3.000
 DCS  H4A2  C4A  C4    111.30  3.000
 DCS  H4A1  C4A  C4    108.58  3.000
 DCS  N     C4A  C4    110.86  3.000
 DCS  C5A   C5   C6    122.27  3.000
 DCS  C5A   C5   C4    119.55  3.000
 DCS  C6    C5   C4    118.17  3.000
 DCS  H6    C6   C5    120.90  3.000
 DCS  H6    C6   N1    115.88  3.000
 DCS  C5    C6   N1    123.22  3.000
 DCS  H5A2  C5A  H5A1  107.11  3.000
 DCS  H5A2  C5A  O4P   108.72  3.000
 DCS  H5A1  C5A  O4P   111.02  3.000
 DCS  H5A2  C5A  C5    110.65  3.000
 DCS  H5A1  C5A  C5    109.18  3.000
 DCS  O4P   C5A  C5    110.13  3.000
 DCS  P     O4P  C5A   118.88  3.000
 DCS  O3P   P    O2P   108.16  3.000
 DCS  O3P   P    O1P   109.63  3.000
 DCS  O2P   P    O1P   118.16  3.000
 DCS  O3P   P    O4P   106.74  3.000
 DCS  O2P   P    O4P    96.79  3.000
 DCS  O1P   P    O4P   116.23  3.000
 DCS  HOP2  O2P  P     113.60  3.000
 DCS  HOP3  O3P  P     115.95  3.000
 DCS  HN    N    CA    110.85  3.000
 DCS  HN    N    C4A   110.12  3.000
 DCS  CA    N    C4A   115.56  3.000
 DCS  HA    CA   CB    110.58  3.000
 DCS  HA    CA   C     107.59  3.000
 DCS  CB    CA   C     101.03  3.000
 DCS  HA    CA   N     108.47  3.000
 DCS  CB    CA   N     112.63  3.000
 DCS  C     CA   N     116.28  3.000
 DCS  ND    C    O     126.22  3.000
 DCS  ND    C    CA    105.77  3.000
 DCS  O     C    CA    127.96  3.000
 DCS  HND   ND   OG    113.83  3.000
 DCS  HND   ND   C     126.58  3.000
 DCS  OG    ND   C     113.25  3.000
 DCS  CB    OG   ND    103.76  3.000
 DCS  HB2   CB   HB1   109.54  3.000
 DCS  HB2   CB   OG    107.70  3.000
 DCS  HB1   CB   OG    110.60  3.000
 DCS  HB2   CB   CA    114.16  3.000
 DCS  HB1   CB   CA    110.45  3.000
 DCS  OG    CB   CA    104.22  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
 DCS  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 DCS  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 DCS  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 DCS  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 DCS  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 DCS  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 DCS  CONST_07  OG    ND   C    CA     0.00   0.0  0
 DCS  CONST_08  O3    C3   C2   N1   180.00   0.0  0
 DCS  CONST_09  C5A   C5   C6   N1   180.00   0.0  0
 DCS  CONST_10  C4A   C4   C3   C2   180.00   0.0  0
 DCS  CONST_11  C6    N1   C2   C2A  180.00   0.0  0
 DCS  CONST_12  C4    C3   C2   C2A  180.00   0.0  0
 DCS  CONST_13  C5A   C5   C4   C3   180.00   0.0  0
 DCS  CONST_14  C5    C4   C3   O3   180.00   0.0  0
 DCS  CONST_15  C6    C5   C4   C4A  180.00   0.0  0
 DCS  CONST_16  OG    ND   C    O    180.00   0.0  0
 DCS  CONST_17  H6    C6   N1   C2   180.00   0.0  0
 DCS  Var_01    HB1   CB   OG   ND   -83.99  30.0  1
 DCS  Var_02    N     C4A  C4   C3   -41.13  30.0  2
 DCS  Var_03    CA    N    C4A  C4   164.72  30.0  3
 DCS  Var_04    O4P   C5A  C5   C4   179.23  30.0  2
 DCS  Var_05    H2A1  C2A  C2   N1   115.66  30.0  2
 DCS  Var_06    O1P   P    O4P  C5A   47.48  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
 DCS  chir_01  CA  N  C  CB  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
 DCS  plan-1  N1   0.020
 DCS  plan-1  C2   0.020
 DCS  plan-1  C2A  0.020
 DCS  plan-1  C3   0.020
 DCS  plan-1  O3   0.020
 DCS  plan-1  C4   0.020
 DCS  plan-1  C4A  0.020
 DCS  plan-1  C5   0.020
 DCS  plan-1  C6   0.020
 DCS  plan-1  C5A  0.020
 DCS  plan-1  H6   0.020
 DCS  plan-2  CA   0.020
 DCS  plan-2  C    0.020
 DCS  plan-2  O    0.020
 DCS  plan-2  ND   0.020
 DCS  plan-2  OG   0.020
 DCS  plan-2  HND  0.020

