# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 19:00:19 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(R)-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 GAV  GAV  5'-O-[(R)-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]guanosine  ligand  48  32  .  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_GAV
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
 GAV  O6    O  O     0  -0.472  74.1080  38.8876  47.7698
 GAV  C6    C  CR6   0   0.507  73.7109  38.7693  46.6233
 GAV  C5    C  CR56  0  -0.097  72.9694  39.6948  45.8333
 GAV  C4    C  CR56  0   0.513  72.6282  39.3403  44.5418
 GAV  N3    N  N     0  -0.513  72.9052  38.2055  43.8894
 GAV  C2    C  CR6   0   0.696  73.5842  37.3478  44.6113
 GAV  N2    N  NH2   0  -0.831  73.8994  36.1496  44.1027
 GAV  N1    N  NR16  0  -0.727  73.9685  37.5994  45.8970
 GAV  N7    N  N     0  -0.440  72.5078  40.9521  46.1299
 GAV  C8    C  CR15  0   0.097  71.9020  41.3437  45.0541
 GAV  N9    N  NR5   0  -0.539  71.9379  40.4060  44.0486
 GAV  C1'   C  CH1   0   0.202  71.3809  40.5218  42.7282
 GAV  C2'   C  CH1   0  -0.011  69.8589  40.6566  42.7004
 GAV  O2'   O  OH1   0  -0.649  69.2800  39.3991  42.8176
 GAV  C3'   C  CH1   0  -0.034  69.6506  41.3879  41.3737
 GAV  O3'   O  OH1   0  -0.663  69.7341  40.4424  40.3444
 GAV  O4'   O  O2    0  -0.492  71.8769  41.6846  42.1165
 GAV  C4'   C  CH1   0  -0.034  70.8507  42.3406  41.3778
 GAV  C5'   C  CH2   0  -0.209  70.5852  43.6796  42.0477
 GAV  O5'   O  O2    0  -0.551  69.6984  44.4215  41.1990
 GAV  PA    P  P     0   1.300  68.5235  45.3415  41.7245
 GAV  S1A   S  S2    0  -0.312  67.3837  44.3037  43.0970
 GAV  O2A   O  O     0  -0.665  67.7980  45.9381  40.5803
 GAV  O3A   O  O2    0  -0.697  69.1887  46.3856  42.7587
 GAV  PB    P  P     0   1.511  70.1847  47.6639  42.5666
 GAV  O1B   O  OH1   0  -0.712  71.4620  47.0676  41.8544
 GAV  O2B   O  O     0  -0.646  70.3418  48.3805  43.8325
 GAV  O3B   O  O2    0  -0.695  69.5590  48.4439  41.3218
 GAV  PG    P  P     0   1.444  68.0592  49.1260  41.2039
 GAV  O1G   O  OH1   0  -0.706  68.3631  50.5741  40.6529
 GAV  O3G   O  O     0  -0.685  67.3290  48.9871  42.4739
 GAV  O2G   O  OH1   0  -0.740  67.4966  48.4509  39.9015
 GAV  H1    H  HNR6  0   0.426  74.4871  36.8846  46.3917
 GAV  H2N1  H  HNH2  0   0.414  73.7502  36.0063  43.1183
 GAV  H2N2  H  HNH2  0   0.416  74.5806  35.5562  44.5448
 GAV  H8    H  HCR5  0   0.288  71.4215  42.3021  44.9261
 GAV  H1'   H  HCH1  0   0.270  71.6879  39.6228  42.1845
 GAV  H2'   H  HCH1  0   0.237  69.5369  41.3226  43.5144
 GAV  HA    H  HOH1  0   0.465  68.3342  39.5018  42.9616
 GAV  H3'   H  HCH1  0   0.243  68.6984  41.9321  41.3460
 GAV  HB    H  HOH1  0   0.460  69.6485  40.8999  39.5016
 GAV  H4'   H  HCH1  0   0.279  71.2067  42.5237  40.3587
 GAV  H5'1  H  HCH2  0   0.234  70.1534  43.5462  43.0440
 GAV  H5'2  H  HCH2  0   0.285  71.5133  44.2403  42.1540
 GAV  H1A   H  HSH1  0   0.290  66.7006  43.6292  42.1607
 GAV  H1B   H  HOH1  0   0.519  72.2364  46.9730  42.4280
 GAV  H1G   H  HOH1  0   0.514  68.4179  51.2621  41.3306
 GAV  H2G   H  HOH1  0   0.509  67.4836  47.4636  39.9893

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
 GAV  O6   C6    double    1.219  0.020  1.219
 GAV  C6   C5    single    1.425  0.020  1.425
 GAV  C5   C4    aromatic  1.382  0.020  1.382
 GAV  C4   N3    single    1.338  0.020  1.338
 GAV  N3   C2    double    1.311  0.020  1.311
 GAV  C2   N2    single    1.339  0.020  1.339
 GAV  C6   N1    single    1.401  0.020  1.401
 GAV  C2   N1    single    1.365  0.020  1.365
 GAV  C5   N7    aromatic  1.372  0.020  1.372
 GAV  N7   C8    aromatic  1.295  0.020  1.295
 GAV  C4   N9    aromatic  1.362  0.020  1.362
 GAV  C8   N9    aromatic  1.375  0.020  1.375
 GAV  N9   C1'   single    1.438  0.020  1.438
 GAV  C1'  C2'   single    1.528  0.020  1.528
 GAV  C2'  O2'   single    1.389  0.020  1.389
 GAV  C2'  C3'   single    1.529  0.020  1.529
 GAV  C3'  O3'   single    1.400  0.020  1.400
 GAV  C1'  O4'   single    1.404  0.020  1.404
 GAV  C3'  C4'   single    1.532  0.020  1.532
 GAV  O4'  C4'   single    1.424  0.020  1.424
 GAV  C4'  C5'   single    1.521  0.020  1.521
 GAV  C5'  O5'   single    1.434  0.020  1.434
 GAV  O5'  PA    single    1.582  0.020  1.582
 GAV  PA   S1A   single    2.064  0.020  2.064
 GAV  PA   O2A   double    1.480  0.020  1.480
 GAV  PA   O3A   single    1.613  0.020  1.613
 GAV  O3A  PB    single    1.632  0.020  1.632
 GAV  PB   O1B   single    1.579  0.020  1.579
 GAV  PB   O2B   double    1.463  0.020  1.463
 GAV  PB   O3B   single    1.597  0.020  1.597
 GAV  O3B  PG    single    1.652  0.020  1.652
 GAV  PG   O1G   single    1.579  0.020  1.579
 GAV  PG   O3G   double    1.472  0.020  1.472
 GAV  PG   O2G   single    1.571  0.020  1.571
 GAV  N1   H1    single    0.860  0.020  1.020
 GAV  N2   H2N1  single    0.890  0.020  1.040
 GAV  N2   H2N2  single    0.890  0.020  1.040
 GAV  C8   H8    single    0.930  0.020  1.080
 GAV  C1'  H1'   single    0.970  0.020  1.090
 GAV  C2'  H2'   single    0.970  0.020  1.090
 GAV  O2'  HA    single    0.850  0.020  0.980
 GAV  C3'  H3'   single    0.970  0.020  1.090
 GAV  O3'  HB    single    0.850  0.020  0.980
 GAV  C4'  H4'   single    0.970  0.020  1.090
 GAV  C5'  H5'1  single    0.970  0.020  1.090
 GAV  C5'  H5'2  single    0.970  0.020  1.090
 GAV  S1A  H1A   single    1.200  0.020  1.300
 GAV  O1B  H1B   single    0.850  0.020  0.980
 GAV  O1G  H1G   single    0.850  0.020  0.980
 GAV  O2G  H2G   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
 GAV  N1    C6   C5    110.53  3.000
 GAV  N1    C6   O6    120.58  3.000
 GAV  C5    C6   O6    128.89  3.000
 GAV  N7    C5   C4    110.74  3.000
 GAV  N7    C5   C6    130.58  3.000
 GAV  C4    C5   C6    118.68  3.000
 GAV  N9    C4   N3    126.29  3.000
 GAV  N9    C4   C5    105.24  3.000
 GAV  N3    C4   C5    128.47  3.000
 GAV  C2    N3   C4    113.19  3.000
 GAV  N1    C2   N2    117.14  3.000
 GAV  N1    C2   N3    122.95  3.000
 GAV  N2    C2   N3    119.88  3.000
 GAV  H2N2  N2   H2N1  116.53  3.000
 GAV  H2N2  N2   C2    121.35  3.000
 GAV  H2N1  N2   C2    117.65  3.000
 GAV  H1    N1   C2    118.32  3.000
 GAV  H1    N1   C6    115.51  3.000
 GAV  C2    N1   C6    126.18  3.000
 GAV  C8    N7   C5    104.77  3.000
 GAV  H8    C8   N9    122.01  3.000
 GAV  H8    C8   N7    125.10  3.000
 GAV  N9    C8   N7    112.88  3.000
 GAV  C1'   N9   C8    127.33  3.000
 GAV  C1'   N9   C4    126.29  3.000
 GAV  C8    N9   C4    106.37  3.000
 GAV  H1'   C1'  O4'   111.38  3.000
 GAV  H1'   C1'  C2'   110.04  3.000
 GAV  O4'   C1'  C2'   105.71  3.000
 GAV  H1'   C1'  N9    106.34  3.000
 GAV  O4'   C1'  N9    109.27  3.000
 GAV  C2'   C1'  N9    114.18  3.000
 GAV  H2'   C2'  C3'   108.22  3.000
 GAV  H2'   C2'  O2'   111.32  3.000
 GAV  C3'   C2'  O2'   116.70  3.000
 GAV  H2'   C2'  C1'   109.36  3.000
 GAV  C3'   C2'  C1'   101.16  3.000
 GAV  O2'   C2'  C1'   109.49  3.000
 GAV  HA    O2'  C2'   109.00  3.000
 GAV  H3'   C3'  C4'   111.81  3.000
 GAV  H3'   C3'  O3'   111.60  3.000
 GAV  C4'   C3'  O3'   112.03  3.000
 GAV  H3'   C3'  C2'   112.17  3.000
 GAV  C4'   C3'  C2'   100.86  3.000
 GAV  O3'   C3'  C2'   107.86  3.000
 GAV  HB    O3'  C3'   108.51  3.000
 GAV  C4'   O4'  C1'   110.66  3.000
 GAV  H4'   C4'  C5'   108.64  3.000
 GAV  H4'   C4'  O4'   108.99  3.000
 GAV  C5'   C4'  O4'   107.63  3.000
 GAV  H4'   C4'  C3'   110.87  3.000
 GAV  C5'   C4'  C3'   114.32  3.000
 GAV  O4'   C4'  C3'   106.22  3.000
 GAV  H5'2  C5'  H5'1  108.06  3.000
 GAV  H5'2  C5'  O5'   108.55  3.000
 GAV  H5'1  C5'  O5'   110.97  3.000
 GAV  H5'2  C5'  C4'   110.33  3.000
 GAV  H5'1  C5'  C4'   111.27  3.000
 GAV  O5'   C5'  C4'   107.63  3.000
 GAV  PA    O5'  C5'   124.30  3.000
 GAV  O3A   PA   O2A   115.90  3.000
 GAV  O3A   PA   S1A    97.29  3.000
 GAV  O2A   PA   S1A   116.49  3.000
 GAV  O3A   PA   O5'   106.44  3.000
 GAV  O2A   PA   O5'   109.98  3.000
 GAV  S1A   PA   O5'   109.79  3.000
 GAV  H1A   S1A  PA     94.01  3.000
 GAV  PB    O3A  PA    133.10  3.000
 GAV  O3B   PB   O2B   118.51  3.000
 GAV  O3B   PB   O1B    98.61  3.000
 GAV  O2B   PB   O1B   119.23  3.000
 GAV  O3B   PB   O3A   103.61  3.000
 GAV  O2B   PB   O3A   110.33  3.000
 GAV  O1B   PB   O3A   104.54  3.000
 GAV  H1B   O1B  PB    114.61  3.000
 GAV  PG    O3B  PB    127.82  3.000
 GAV  O2G   PG   O3G   119.81  3.000
 GAV  O2G   PG   O1G   100.00  3.000
 GAV  O3G   PG   O1G   118.90  3.000
 GAV  O2G   PG   O3B   101.94  3.000
 GAV  O3G   PG   O3B   110.49  3.000
 GAV  O1G   PG   O3B   103.23  3.000
 GAV  H1G   O1G  PG    114.76  3.000
 GAV  H2G   O2G  PG    111.05  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
 GAV  CONST_01  C8    N9   C4   C5     0.00   0.0  0
 GAV  CONST_02  N9    C8   N7   C5     0.00   0.0  0
 GAV  CONST_03  C8    N7   C5   C4     0.00   0.0  0
 GAV  CONST_04  N7    C8   N9   C4     0.00   0.0  0
 GAV  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 GAV  CONST_06  C1'   N9   C4   C5   180.00   0.0  0
 GAV  CONST_07  C1'   N9   C4   N3     0.00   0.0  0
 GAV  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 GAV  CONST_09  N3    C2   N1   C6     0.00   0.0  0
 GAV  CONST_10  C2    N1   C6   C5     0.00   0.0  0
 GAV  CONST_11  N1    C2   N3   C4     0.00   0.0  0
 GAV  CONST_12  C2    N1   C6   O6   180.00   0.0  0
 GAV  CONST_13  N2    C2   N1   C6   180.00   0.0  0
 GAV  CONST_14  N2    C2   N3   C4   180.00   0.0  0
 GAV  CONST_15  H8    C8   N7   C5   180.00   0.0  0
 GAV  CONST_16  H1    N1   C6   C5   180.00   0.0  0
 GAV  CONST_17  H2N1  N2   C2   N3     0.00   0.0  0
 GAV  CONST_18  H2N2  N2   C2   N3   180.00   0.0  0
 GAV  Var_01    S1A   PA   O5'  C5'  -49.68  30.0  3
 GAV  Var_02    O1B   PB   O3A  PA   -58.29  30.0  3
 GAV  Var_03    O1G   PG   O3B  PB   130.99  30.0  3
 GAV  Var_04    H5'1  C5'  O5'  PA    19.68  30.0  1

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
 GAV  chir_01  C1'  N9   C2'  O4'  negativ
 GAV  chir_02  C2'  O2'  C3'  C1'  positiv
 GAV  chir_03  C3'  O3'  C4'  C2'  positiv
 GAV  chir_04  C4'  O4'  C3'  C5'  negativ
 GAV  chir_05  PA   S1A  O2A  O3A  both
 GAV  chir_06  PB   O1B  O2B  O3B  both

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
 GAV  plan-1  O6    0.020
 GAV  plan-1  C6    0.020
 GAV  plan-1  C5    0.020
 GAV  plan-1  C4    0.020
 GAV  plan-1  N3    0.020
 GAV  plan-1  C2    0.020
 GAV  plan-1  N2    0.020
 GAV  plan-1  N1    0.020
 GAV  plan-1  N7    0.020
 GAV  plan-1  C8    0.020
 GAV  plan-1  N9    0.020
 GAV  plan-1  C1'   0.020
 GAV  plan-1  H1    0.020
 GAV  plan-1  H2N1  0.020
 GAV  plan-1  H2N2  0.020
 GAV  plan-1  H8    0.020

