# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:18:34 2022
#   Inital geometry file: a 158 line input string
#   Ligand name: (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=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
 12V  12V  '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  64  39  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_12V
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
 12V  N1    N  NR6    0  -0.568  112.2893  49.1377  61.5633
 12V  C2    C  CR6    0   0.734  112.3686  47.8717  61.0089
 12V  O2    O  O      0  -0.467  112.1558  47.6384  59.8390
 12V  N3    N  NR16   0  -0.736  112.7079  46.8830  61.8951
 12V  C4    C  CR6    0   0.567  112.9864  46.9996  63.2493
 12V  O4    O  O      0  -0.451  113.2681  46.0194  63.9101
 12V  C5    C  CR16   0  -0.511  112.9009  48.3565  63.7338
 12V  C6    C  CR16   0   0.102  112.5672  49.3415  62.8867
 12V  PA    P  P      0   1.351  111.5611  55.2179  63.2101
 12V  PB    P  P      0   1.368  109.0819  53.9635  64.2671
 12V  C1'   C  CH1    0  -0.117  107.6185  55.1788  62.4171
 12V  O1'   O  O2     0  -0.600  107.8800  54.0101  63.1291
 12V  O1A   O  O      0  -0.774  111.0199  56.5223  62.7236
 12V  C1B   C  CH1    0   0.192  111.9650  50.2657  60.7063
 12V  O1B   O  O      0  -0.765  109.0290  52.5771  64.8127
 12V  C2'   C  CH1    0  -0.079  106.1329  55.5264  62.5451
 12V  N2'   N  NH1    0  -0.622  105.7976  55.7084  63.9379
 12V  O2A   O  OP    -1  -0.790  112.3896  55.1127  64.4503
 12V  C2B   C  CH1    0  -0.015  110.7067  51.0328  61.1066
 12V  O2B   O  OP    -1  -0.784  109.0126  55.1784  65.1373
 12V  C3'   C  CH1    0   0.033  105.2254  54.4581  61.9394
 12V  O3'   O  OH1    0  -0.666  103.8997  54.8891  62.1341
 12V  O3A   O  O2     0  -0.754  110.3740  54.0743  63.2705
 12V  C3B   C  CH1    0  -0.064  110.9817  52.3791  60.4423
 12V  O3B   O  OH1    0  -0.668  110.7071  52.2416  59.0671
 12V  C4'   C  CH1    0   0.086  105.4824  54.2168  60.4497
 12V  O4'   O  OH1    0  -0.694  104.5297  53.2502  60.0674
 12V  C4B   C  CH1    0  -0.026  112.4845  52.5327  60.7039
 12V  O4B   O  O2     0  -0.497  113.0089  51.1997  60.7550
 12V  C5'   C  CH1    0  -0.468  106.9094  53.7593  60.1463
 12V  S5'   S  S2     0   0.016  108.0947  55.0355  60.6717
 12V  C5B   C  CH2    0  -0.173  112.8538  53.2500  61.9976
 12V  O5B   O  O2     0  -0.615  112.3732  54.5743  61.9305
 12V  C6'   C  CH2    0  -0.140  107.1639  53.5598  58.6547
 12V  O6'   O  OH1    0  -0.669  106.3145  52.5324  58.1756
 12V  C7'   C  C      0   0.524  106.1168  56.8215  64.6268
 12V  O7'   O  O      0  -0.498  106.5744  57.8220  64.0926
 12V  C8'   C  CH3    0  -0.779  105.8869  56.7373  66.1142
 12V  H5    H  HCR6   0   0.292  113.1083  48.5692  64.7709
 12V  H6    H  HCR6   0   0.329  112.5069  50.3629  63.2327
 12V  H1'   H  HCH1   0   0.281  108.2064  56.0281  62.7779
 12V  H1B   H  HCH1   0   0.271  111.8401  49.8599  59.7008
 12V  H2'   H  HCH1   0   0.263  105.9644  56.4700  62.0204
 12V  HN2'  H  HNH1   0   0.399  105.5243  54.8911  64.4609
 12V  HO2'  H  HOH1   0   0.463  108.7973  50.7485  61.0708
 12V  H2B   H  HCH1   0   0.241  110.6902  51.1933  62.1937
 12V  H3'   H  HCH1   0   0.211  105.4042  53.5051  62.4625
 12V  HO3'  H  HOH1   0   0.449  103.3172  54.2242  61.7519
 12V  H3B   H  HCH1   0   0.273  110.3938  53.1870  60.8837
 12V  HO3B  H  HOH1   0   0.455  110.8762  53.0883  58.6422
 12V  H4'   H  HCH1   0   0.199  105.3201  55.1666  59.9122
 12V  HO4'  H  HOH1   0   0.454  104.7998  52.8930  59.2077
 12V  H4B   H  HCH1   0   0.249  112.9564  53.0600  59.8673
 12V  H5'   H  HCH1   0   0.289  107.1373  52.8296  60.6785
 12V  H5B   H  HCH2   0   0.213  112.4549  52.7048  62.8588
 12V  H5BA  H  HCH2   0   0.231  113.9437  53.2513  62.1034
 12V  H6'   H  HCH2   0   0.219  106.9762  54.5039  58.1300
 12V  H6'A  H  HCH2   0   0.228  108.2162  53.2963  58.5010
 12V  HO6'  H  HOH1   0   0.469  106.3219  52.5503  57.2133
 12V  H8'   H  HCH3   0   0.256  105.5703  57.7032  66.5015
 12V  H8'A  H  HCH3   0   0.248  105.1511  55.9844  66.3925
 12V  H8'B  H  HCH3   0   0.266  106.8316  56.4753  66.5932
 12V  HN3   H  HNR6   0   0.424  112.7603  45.9524  61.4982
 12V  O2'   O  OH1    0  -0.653  109.5763  50.3386  60.6815

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
 12V  C1B  N1    single  1.453  0.020  1.453
 12V  C2   N1    single  1.384  0.020  1.384
 12V  N1   C6    single  1.367  0.020  1.367
 12V  O2   C2    double  1.212  0.020  1.212
 12V  C2   N3    single  1.370  0.020  1.370
 12V  N3   C4    single  1.387  0.020  1.387
 12V  C4   O4    double  1.215  0.020  1.215
 12V  C4   C5    single  1.443  0.020  1.443
 12V  C6   C5    double  1.341  0.020  1.341
 12V  C5   H5    single  0.930  0.020  1.080
 12V  C6   H6    single  0.930  0.020  1.080
 12V  O5B  PA    single  1.647  0.020  1.647
 12V  O1A  PA    deloc   1.494  0.020  1.494
 12V  PA   O3A   single  1.649  0.020  1.649
 12V  PA   O2A   deloc   1.495  0.020  1.495
 12V  O3A  PB    single  1.636  0.020  1.636
 12V  O1'  PB    single  1.656  0.020  1.656
 12V  PB   O1B   deloc   1.491  0.020  1.491
 12V  PB   O2B   deloc   1.496  0.020  1.496
 12V  S5'  C1'   single  1.815  0.020  1.815
 12V  C1'  C2'   single  1.531  0.020  1.531
 12V  C1'  O1'   single  1.393  0.020  1.393
 12V  C1'  H1'   single  0.970  0.020  1.090
 12V  C1B  O4B   single  1.402  0.020  1.402
 12V  C1B  C2B   single  1.527  0.020  1.527
 12V  C1B  H1B   single  0.970  0.020  1.090
 12V  C3'  C2'   single  1.527  0.020  1.527
 12V  C2'  N2'   single  1.444  0.020  1.444
 12V  C2'  H2'   single  0.970  0.020  1.090
 12V  N2'  C7'   single  1.347  0.020  1.347
 12V  N2'  HN2'  single  0.860  0.020  1.020
 12V  O2'  C2B   single  1.393  0.020  1.393
 12V  O2'  HO2'  single  0.850  0.020  0.980
 12V  C3B  C2B   single  1.526  0.020  1.526
 12V  C2B  H2B   single  0.970  0.020  1.090
 12V  C4'  C3'   single  1.531  0.020  1.531
 12V  C3'  O3'   single  1.408  0.020  1.408
 12V  C3'  H3'   single  0.970  0.020  1.090
 12V  O3'  HO3'  single  0.850  0.020  0.980
 12V  O3B  C3B   single  1.409  0.020  1.409
 12V  C3B  C4B   single  1.533  0.020  1.533
 12V  C3B  H3B   single  0.970  0.020  1.090
 12V  O3B  HO3B  single  0.850  0.020  0.980
 12V  C5'  C4'   single  1.529  0.020  1.529
 12V  O4'  C4'   single  1.410  0.020  1.410
 12V  C4'  H4'   single  0.970  0.020  1.090
 12V  O4'  HO4'  single  0.850  0.020  0.980
 12V  C4B  O4B   single  1.433  0.020  1.433
 12V  C4B  C5B   single  1.525  0.020  1.525
 12V  C4B  H4B   single  0.970  0.020  1.090
 12V  C6'  C5'   single  1.526  0.020  1.526
 12V  C5'  S5'   single  1.819  0.020  1.819
 12V  C5'  H5'   single  0.970  0.020  1.090
 12V  O5B  C5B   single  1.410  0.020  1.410
 12V  C5B  H5B   single  0.970  0.020  1.090
 12V  C5B  H5BA  single  0.970  0.020  1.090
 12V  O6'  C6'   single  1.417  0.020  1.417
 12V  C6'  H6'   single  0.970  0.020  1.090
 12V  C6'  H6'A  single  0.970  0.020  1.090
 12V  O6'  HO6'  single  0.850  0.020  0.980
 12V  O7'  C7'   double  1.223  0.020  1.223
 12V  C7'  C8'   single  1.507  0.020  1.507
 12V  C8'  H8'   single  0.970  0.020  1.090
 12V  C8'  H8'A  single  0.970  0.020  1.090
 12V  C8'  H8'B  single  0.970  0.020  1.090
 12V  N3   HN3   single  0.860  0.020  1.020

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
 12V  C1B   N1   C6    120.02  3.000
 12V  C6    N1   C2    120.81  3.000
 12V  C1B   N1   C2    119.10  3.000
 12V  N3    C2   O2    121.93  3.000
 12V  N3    C2   N1    114.51  3.000
 12V  O2    C2   N1    123.55  3.000
 12V  HN3   N3   C4    116.70  3.000
 12V  HN3   N3   C2    114.97  3.000
 12V  C4    N3   C2    128.33  3.000
 12V  C5    C4   O4    126.12  3.000
 12V  C5    C4   N3    113.25  3.000
 12V  O4    C4   N3    120.63  3.000
 12V  H5    C5   C6    120.67  3.000
 12V  H5    C5   C4    119.78  3.000
 12V  C6    C5   C4    119.54  3.000
 12V  H6    C6   C5    120.39  3.000
 12V  H6    C6   N1    116.08  3.000
 12V  C5    C6   N1    123.52  3.000
 12V  O5B   PA   O3A    96.45  3.000
 12V  O3A   PA   O2A   108.64  3.000
 12V  O5B   PA   O2A   110.11  3.000
 12V  O2A   PA   O1A   122.17  3.000
 12V  O3A   PA   O1A   110.89  3.000
 12V  O5B   PA   O1A   105.48  3.000
 12V  O3A   PB   O2B   109.63  3.000
 12V  O2B   PB   O1B   122.73  3.000
 12V  O3A   PB   O1B   108.31  3.000
 12V  O2B   PB   O1'   110.08  3.000
 12V  O1B   PB   O1'   104.59  3.000
 12V  O3A   PB   O1'    98.79  3.000
 12V  H1'   C1'  S5'   103.74  3.000
 12V  H1'   C1'  C2'   108.51  3.000
 12V  S5'   C1'  C2'   110.66  3.000
 12V  H1'   C1'  O1'   112.45  3.000
 12V  C2'   C1'  O1'   109.26  3.000
 12V  S5'   C1'  O1'   112.09  3.000
 12V  C1'   O1'  PB    120.73  3.000
 12V  H1B   C1B  O4B   111.41  3.000
 12V  H1B   C1B  C2B   109.51  3.000
 12V  O4B   C1B  C2B   105.66  3.000
 12V  H1B   C1B  N1    106.27  3.000
 12V  C2B   C1B  N1    114.78  3.000
 12V  O4B   C1B  N1    109.30  3.000
 12V  H2'   C2'  C3'   108.79  3.000
 12V  H2'   C2'  N2'   108.57  3.000
 12V  C3'   C2'  N2'   109.44  3.000
 12V  H2'   C2'  C1'   107.79  3.000
 12V  N2'   C2'  C1'   109.54  3.000
 12V  C3'   C2'  C1'   112.62  3.000
 12V  HN2'  N2'  C7'   117.95  3.000
 12V  HN2'  N2'  C2'   117.46  3.000
 12V  C7'   N2'  C2'   122.84  3.000
 12V  H2B   C2B  C3B   107.72  3.000
 12V  H2B   C2B  O2'   111.26  3.000
 12V  C3B   C2B  O2'   116.94  3.000
 12V  H2B   C2B  C1B   110.18  3.000
 12V  C3B   C2B  C1B   100.40  3.000
 12V  O2'   C2B  C1B   109.77  3.000
 12V  H3'   C3'  C4'   107.37  3.000
 12V  H3'   C3'  O3'   110.61  3.000
 12V  C4'   C3'  O3'   109.94  3.000
 12V  H3'   C3'  C2'   108.69  3.000
 12V  O3'   C3'  C2'   106.90  3.000
 12V  C4'   C3'  C2'   113.36  3.000
 12V  HO3'  O3'  C3'   107.66  3.000
 12V  PB    O3A  PA    129.64  3.000
 12V  H3B   C3B  C4B   112.62  3.000
 12V  H3B   C3B  O3B   111.20  3.000
 12V  C4B   C3B  O3B   111.55  3.000
 12V  H3B   C3B  C2B   112.30  3.000
 12V  C4B   C3B  C2B   101.00  3.000
 12V  O3B   C3B  C2B   107.67  3.000
 12V  HO3B  O3B  C3B   108.11  3.000
 12V  H4'   C4'  C5'   107.35  3.000
 12V  H4'   C4'  O4'   111.02  3.000
 12V  C5'   C4'  O4'   111.82  3.000
 12V  H4'   C4'  C3'   108.28  3.000
 12V  O4'   C4'  C3'   104.98  3.000
 12V  C5'   C4'  C3'   113.39  3.000
 12V  HO4'  O4'  C4'   107.75  3.000
 12V  H4B   C4B  C5B   108.50  3.000
 12V  H4B   C4B  O4B   108.49  3.000
 12V  C5B   C4B  O4B   108.58  3.000
 12V  H4B   C4B  C3B   109.88  3.000
 12V  C5B   C4B  C3B   115.42  3.000
 12V  O4B   C4B  C3B   105.76  3.000
 12V  C4B   O4B  C1B   110.24  3.000
 12V  H5'   C5'  C6'   109.22  3.000
 12V  H5'   C5'  S5'   108.64  3.000
 12V  C6'   C5'  S5'   105.39  3.000
 12V  H5'   C5'  C4'   110.59  3.000
 12V  S5'   C5'  C4'   109.93  3.000
 12V  C6'   C5'  C4'   112.87  3.000
 12V  C5'   S5'  C1'    99.34  3.000
 12V  H5BA  C5B  H5B   106.70  3.000
 12V  H5BA  C5B  O5B   110.04  3.000
 12V  H5B   C5B  O5B   112.39  3.000
 12V  H5BA  C5B  C4B   108.88  3.000
 12V  H5B   C5B  C4B   110.19  3.000
 12V  O5B   C5B  C4B   108.59  3.000
 12V  C5B   O5B  PA    119.88  3.000
 12V  H6'A  C6'  H6'   107.72  3.000
 12V  H6'A  C6'  O6'   110.73  3.000
 12V  H6'   C6'  O6'   111.10  3.000
 12V  H6'A  C6'  C5'   109.19  3.000
 12V  H6'   C6'  C5'   109.06  3.000
 12V  O6'   C6'  C5'   108.99  3.000
 12V  HO6'  O6'  C6'   108.67  3.000
 12V  C8'   C7'  O7'   122.26  3.000
 12V  C8'   C7'  N2'   114.98  3.000
 12V  O7'   C7'  N2'   122.76  3.000
 12V  H8'B  C8'  H8'A  107.87  3.000
 12V  H8'B  C8'  H8'   107.99  3.000
 12V  H8'A  C8'  H8'   109.04  3.000
 12V  H8'B  C8'  C7'   108.34  3.000
 12V  H8'A  C8'  C7'   113.19  3.000
 12V  H8'   C8'  C7'   110.25  3.000
 12V  HO2'  O2'  C2B   108.73  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
 12V  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 12V  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 12V  CONST_03  C1B   N1   C2   N3    180.00   0.0  0
 12V  CONST_04  C6    N1   C2   N3      0.00   0.0  0
 12V  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 12V  CONST_06  C1B   N1   C2   O2      0.00   0.0  0
 12V  CONST_07  C6    N1   C2   O2    180.00   0.0  0
 12V  CONST_08  C4    N3   C2   O2    180.00   0.0  0
 12V  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 12V  CONST_10  O7'   C7'  N2'  C2'     0.00   0.0  0
 12V  CONST_11  C8'   C7'  N2'  C2'   180.00   0.0  0
 12V  CONST_12  HN2'  N2'  C7'  O7'   180.00   0.0  0
 12V  Var_01    C4B   C5B  O5B  PA    133.44  30.0  3
 12V  Var_02    O3A   PB   O1'  C1'   -69.46  30.0  3
 12V  Var_03    O1'   PB   O3A  PA    119.98  30.0  3
 12V  Var_04    O5B   PA   O3A  PB   -178.47  30.0  1
 12V  Var_05    H8'   C8'  C7'  N2'  -145.46  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
 12V  chir_03  C1'  S5'  C2'  O1'  negativ
 12V  chir_04  C1B  N1   O4B  C2B  positiv
 12V  chir_05  C2'  C1'  C3'  N2'  negativ
 12V  chir_06  C2B  C1B  O2'  C3B  positiv
 12V  chir_07  C3'  C2'  C4'  O3'  positiv
 12V  chir_08  C3B  C2B  O3B  C4B  positiv
 12V  chir_09  C4'  C3'  C5'  O4'  negativ
 12V  chir_10  C4B  O4B  C3B  C5B  negativ
 12V  chir_11  C5'  C4'  C6'  S5'  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
 12V  plan-1  N1    0.020
 12V  plan-1  C2    0.020
 12V  plan-1  O2    0.020
 12V  plan-1  N3    0.020
 12V  plan-1  C4    0.020
 12V  plan-1  O4    0.020
 12V  plan-1  C5    0.020
 12V  plan-1  C6    0.020
 12V  plan-1  C1B   0.020
 12V  plan-1  H5    0.020
 12V  plan-1  H6    0.020
 12V  plan-1  HN3   0.020
 12V  plan-2  C2'   0.020
 12V  plan-2  N2'   0.020
 12V  plan-2  C7'   0.020
 12V  plan-2  O7'   0.020
 12V  plan-2  C8'   0.020
 12V  plan-2  HN2'  0.020

