# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:55:40 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 5'-S-phosphono-5'-thioguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](CS[P](O)(O)=O)[C@@H](O)[C@H]3O)c2N1
#
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
 6CG  6CG  5'-S-phosphono-5'-thioguanosine  ligand  36  24  .  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_6CG
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
 6CG  C2   C  CR6    0   0.662   4.8428  -0.6382  -0.1648
 6CG  C4   C  CR56   0   0.621   2.6875   0.1742  -0.3245
 6CG  C5   C  CR56   0  -0.105   3.1411   1.4632  -0.2477
 6CG  C6   C  CR6    0   0.413   4.5626   1.7004  -0.1283
 6CG  N1   N  N      0  -0.539   5.3420   0.5670  -0.1068
 6CG  N2   N  NH2    0  -0.827   5.6545  -1.7029  -0.0740
 6CG  N3   N  NR16   0  -0.739   3.5091  -0.9071  -0.2854
 6CG  C8   C  CR15   0   0.086   1.0270   1.5669  -0.4319
 6CG  C1'  C  CR15   0   0.222   0.4447  -0.9122  -0.6302
 6CG  C3'  C  CR15   0   0.003  -1.0691  -2.2206   0.6555
 6CG  C4'  C  CR15   0  -0.018  -1.7245  -0.9299   0.1853
 6CG  C5'  C  CH2    0  -0.592  -1.9039   0.0895   1.2986
 6CG  O6   O  O      0  -0.496   5.0667   2.8155  -0.0545
 6CG  N7   N  N      0  -0.447   2.0768   2.3243  -0.3143
 6CG  N9   N  NR5    0  -0.540   1.3439   0.2280  -0.4440
 6CG  O4'  O  O      0  -0.485  -0.8405  -0.4525  -0.8411
 6CG  C2'  C  CR15   0  -0.068   0.4105  -1.8271   0.6036
 6CG  O2'  O  OH1    0  -0.662   1.3082  -2.8918   0.4220
 6CG  O3'  O  OH1    0  -0.667  -1.3553  -3.2351  -0.2714
 6CG  S5'  S  S2     0  -0.400  -2.5488   1.6811   0.7176
 6CG  P    P  P      0   1.122  -4.7173   1.1871   0.4635
 6CG  O1P  O  O      0  -0.851  -4.7425   0.1049  -0.6053
 6CG  O2P  O  OP    -1  -0.861  -5.1364   0.7242   1.8473
 6CG  O3P  O  OP    -1  -0.867  -5.2101   2.5555   0.0307
 6CG  H1   H  HNH2   0   0.411   5.3398  -2.6229  -0.3313
 6CG  H2   H  HNH2   0   0.410   6.6444  -1.5357  -0.1292
 6CG  H3   H  HNR6   0   0.429   3.1419  -1.8498  -0.2150
 6CG  H4   H  HCR5   0   0.291   0.0026   1.9024  -0.5016
 6CG  H5   H  HCR5   0   0.274   0.8049  -1.4619  -1.5080
 6CG  H6   H  HCR5   0   0.246  -1.3812  -2.4928   1.6717
 6CG  H7   H  HCR5   0   0.274  -2.6961  -1.1030  -0.2800
 6CG  H8   H  HCH2   0   0.261  -2.5980  -0.3196   2.0361
 6CG  H9   H  HCH2   0   0.248  -0.9614   0.2780   1.8197
 6CG  H10  H  HCR5   0   0.264   0.6632  -1.2513   1.5006
 6CG  H11  H  HOH1   0   0.477   1.5154  -3.2772   1.2804
 6CG  H12  H  HOH1   0   0.450  -0.7234  -3.9510  -0.1404

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
 6CG  O6   C6   double    1.226  0.020  1.226
 6CG  N1   C6   single    1.376  0.020  1.376
 6CG  N1   C2   double    1.306  0.020  1.306
 6CG  C6   C5   single    1.446  0.020  1.446
 6CG  N2   C2   single    1.342  0.020  1.342
 6CG  C2   N3   single    1.366  0.020  1.366
 6CG  C5   N7   aromatic  1.371  0.020  1.371
 6CG  C5   C4   aromatic  1.369  0.020  1.369
 6CG  N7   C8   aromatic  1.300  0.020  1.300
 6CG  N3   C4   single    1.359  0.020  1.359
 6CG  C4   N9   aromatic  1.350  0.020  1.350
 6CG  C8   N9   aromatic  1.376  0.020  1.376
 6CG  N9   C1'  single    1.464  0.020  1.464
 6CG  O2'  C2'  single    1.404  0.020  1.404
 6CG  C1'  C2'  single    1.536  0.020  1.536
 6CG  C1'  O4'  single    1.381  0.020  1.381
 6CG  C2'  C3'  single    1.532  0.020  1.532
 6CG  O4'  C4'  single    1.436  0.020  1.436
 6CG  C3'  C4'  single    1.522  0.020  1.522
 6CG  C3'  O3'  single    1.404  0.020  1.404
 6CG  C4'  C5'  single    1.520  0.020  1.520
 6CG  C5'  S5'  single    1.813  0.020  1.813
 6CG  S5'  P    single    2.238  0.020  2.238
 6CG  O1P  P    deloc     1.521  0.020  1.521
 6CG  P    O3P  deloc     1.517  0.020  1.517
 6CG  P    O2P  deloc     1.518  0.020  1.518
 6CG  N2   H1   single    0.890  0.020  1.040
 6CG  N2   H2   single    0.890  0.020  1.040
 6CG  N3   H3   single    0.860  0.020  1.020
 6CG  C8   H4   single    0.930  0.020  1.080
 6CG  C1'  H5   single    0.970  0.020  1.090
 6CG  C3'  H6   single    0.970  0.020  1.090
 6CG  C4'  H7   single    0.970  0.020  1.090
 6CG  C5'  H8   single    0.970  0.020  1.090
 6CG  C5'  H9   single    0.970  0.020  1.090
 6CG  C2'  H10  single    0.970  0.020  1.090
 6CG  O2'  H11  single    0.850  0.020  0.980
 6CG  O3'  H12  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
 6CG  N3   C2   N2   116.13  3.000
 6CG  N3   C2   N1   123.98  3.000
 6CG  N2   C2   N1   119.87  3.000
 6CG  N9   C4   N3   129.50  3.000
 6CG  N9   C4   C5   107.29  3.000
 6CG  N3   C4   C5   123.20  3.000
 6CG  N7   C5   C6   131.62  3.000
 6CG  N7   C5   C4   109.37  3.000
 6CG  C6   C5   C4   119.01  3.000
 6CG  O6   C6   N1   121.03  3.000
 6CG  N1   C6   C5   115.03  3.000
 6CG  O6   C6   C5   123.94  3.000
 6CG  C6   N1   C2   122.90  3.000
 6CG  H2   N2   H1   116.49  3.000
 6CG  H2   N2   C2   117.38  3.000
 6CG  H1   N2   C2   121.27  3.000
 6CG  H3   N3   C4   121.53  3.000
 6CG  H3   N3   C2   122.03  3.000
 6CG  C4   N3   C2   115.87  3.000
 6CG  H4   C8   N9   121.34  3.000
 6CG  H4   C8   N7   126.21  3.000
 6CG  N9   C8   N7   112.44  3.000
 6CG  H5   C1'  C2'  110.59  3.000
 6CG  H5   C1'  O4'  110.51  3.000
 6CG  C2'  C1'  O4'  107.46  3.000
 6CG  H5   C1'  N9   106.89  3.000
 6CG  O4'  C1'  N9   109.37  3.000
 6CG  C2'  C1'  N9   112.04  3.000
 6CG  H6   C3'  O3'  111.98  3.000
 6CG  H6   C3'  C2'  111.70  3.000
 6CG  O3'  C3'  C2'  111.11  3.000
 6CG  H6   C3'  C4'  111.96  3.000
 6CG  O3'  C3'  C4'  108.73  3.000
 6CG  C2'  C3'  C4'  100.82  3.000
 6CG  H7   C4'  O4'  107.22  3.000
 6CG  H7   C4'  C5'  108.28  3.000
 6CG  O4'  C4'  C5'  111.91  3.000
 6CG  H7   C4'  C3'  112.38  3.000
 6CG  C5'  C4'  C3'  113.16  3.000
 6CG  O4'  C4'  C3'  103.74  3.000
 6CG  H9   C5'  H8   106.90  3.000
 6CG  H9   C5'  S5'  107.94  3.000
 6CG  H8   C5'  S5'  108.61  3.000
 6CG  H9   C5'  C4'  111.28  3.000
 6CG  H8   C5'  C4'  108.56  3.000
 6CG  S5'  C5'  C4'  113.33  3.000
 6CG  C8   N7   C5   105.40  3.000
 6CG  C1'  N9   C8   128.14  3.000
 6CG  C1'  N9   C4   126.26  3.000
 6CG  C8   N9   C4   105.50  3.000
 6CG  C4'  O4'  C1'  110.68  3.000
 6CG  H10  C2'  O2'  110.92  3.000
 6CG  H10  C2'  C3'  109.27  3.000
 6CG  O2'  C2'  C3'  115.28  3.000
 6CG  H10  C2'  C1'  109.84  3.000
 6CG  C3'  C2'  C1'  101.63  3.000
 6CG  O2'  C2'  C1'  109.47  3.000
 6CG  H11  O2'  C2'  109.00  3.000
 6CG  H12  O3'  C3'  108.27  3.000
 6CG  P    S5'  C5'  100.79  3.000
 6CG  O3P  P    O2P  116.44  3.000
 6CG  O2P  P    O1P  114.76  3.000
 6CG  O3P  P    O1P  115.83  3.000
 6CG  O2P  P    S5'  103.37  3.000
 6CG  O3P  P    S5'   98.51  3.000
 6CG  O1P  P    S5'  104.64  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
 6CG  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 6CG  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 6CG  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 6CG  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 6CG  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 6CG  CONST_06  C1'  N9   C4   C5   180.00   0.0  0
 6CG  CONST_07  C1'  N9   C4   N3     0.00   0.0  0
 6CG  CONST_08  N7   C8   N9   C1'  180.00   0.0  0
 6CG  CONST_09  N1   C2   N3   C4     0.00   0.0  0
 6CG  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 6CG  CONST_11  N2   C2   N3   C4   180.00   0.0  0
 6CG  CONST_12  N2   C2   N1   C6   180.00   0.0  0
 6CG  CONST_13  H4   C8   N9   C4   180.00   0.0  0
 6CG  CONST_14  H3   N3   C2   N1   180.00   0.0  0
 6CG  CONST_15  H1   N2   C2   N1   180.00   0.0  0
 6CG  CONST_16  H2   N2   C2   N1     0.00   0.0  0
 6CG  Var_01    O1P  P    S5'  C5'  -62.37  30.0  3
 6CG  Var_02    H8   C5'  S5'  P    -42.95  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
 6CG  chir_01  C1'  N9   C2'  O4'  negativ
 6CG  chir_02  C3'  O3'  C4'  C2'  positiv
 6CG  chir_03  C4'  O4'  C3'  C5'  negativ
 6CG  chir_04  C2'  O2'  C3'  C1'  positiv

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
 6CG  plan-1  C2   0.020
 6CG  plan-1  C4   0.020
 6CG  plan-1  C5   0.020
 6CG  plan-1  C6   0.020
 6CG  plan-1  N1   0.020
 6CG  plan-1  N2   0.020
 6CG  plan-1  N3   0.020
 6CG  plan-1  C8   0.020
 6CG  plan-1  C1'  0.020
 6CG  plan-1  O6   0.020
 6CG  plan-1  N7   0.020
 6CG  plan-1  N9   0.020
 6CG  plan-1  H1   0.020
 6CG  plan-1  H2   0.020
 6CG  plan-1  H3   0.020
 6CG  plan-1  H4   0.020

