# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:44:03 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c3ncnc(N)c13
#
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
 SGV  SGV  4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide  ligand  37  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SGV
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
 SGV  N1    N  N     0  -0.475   3.4322  -2.1122  -0.3202
 SGV  C2    C  CR16  0   0.042   2.3049  -2.8066  -0.4294
 SGV  N3    N  N     0  -0.458   1.0692  -2.3510  -0.4507
 SGV  C4    C  CR56  0   0.515   1.0136  -1.0231  -0.3531
 SGV  C5    C  CR56  0  -0.071   2.0977  -0.1510  -0.2429
 SGV  C6    C  CR6   0   0.423   3.3671  -0.7792  -0.2235
 SGV  N6    N  NH2   0  -0.837   4.5074  -0.0989  -0.0933
 SGV  C7    C  CR5   0  -0.199   1.5536   1.1765  -0.1596
 SGV  C8    C  CR15  0  -0.010   0.1918   1.0337  -0.2399
 SGV  N9    N  NR5   0  -0.556  -0.1335  -0.2843  -0.3525
 SGV  C1'   C  CH1   0   0.212  -1.4781  -0.8255  -0.4221
 SGV  C10   C  C     0   0.461   2.2815   2.4527  -0.0927
 SGV  N11   N  NH2   0  -0.810   1.5661   3.5330   0.2561
 SGV  O12   O  O     0  -0.501   3.4798   2.5318  -0.3638
 SGV  C2'   C  CH1   0  -0.014  -2.1275  -1.0259   0.9528
 SGV  O2'   O  OH1   0  -0.650  -1.8069  -2.2836   1.4524
 SGV  C3'   C  CH1   0  -0.032  -3.6040  -0.7720   0.6371
 SGV  O3'   O  OH1   0  -0.667  -4.1328  -1.9399   0.0706
 SGV  C4'   C  CH1   0  -0.053  -3.4771   0.3661  -0.3734
 SGV  O4'   O  O2    0  -0.490  -2.2881   0.0762  -1.1119
 SGV  C5'   C  CH2   0  -0.173  -3.4057   1.7225   0.3068
 SGV  O5'   O  OH1   0  -0.665  -3.0261   2.6873  -0.6426
 SGV  H2    H  HCR6  0   0.247   2.4233  -3.8824  -0.5095
 SGV  HN6   H  HNH2  0   0.392   5.3811  -0.5863  -0.1968
 SGV  HN6A  H  HNH2  0   0.418   4.4845   0.9089  -0.1824
 SGV  H8    H  HCR5  0   0.305  -0.5774   1.7892  -0.2831
 SGV  H1'   H  HCH1  0   0.264  -1.4017  -1.7816  -0.9503
 SGV  HN11  H  HNH2  0   0.406   0.6420   3.4700   0.6454
 SGV  HN1A  H  HNH2  0   0.408   2.0215   4.4291   0.3190
 SGV  H2'   H  HCH1  0   0.241  -1.7821  -0.2280   1.6236
 SGV  HO2'  H  HOH1  0   0.462  -2.0770  -2.3252   2.3750
 SGV  H3'   H  HCH1  0   0.253  -4.1650  -0.4586   1.5275
 SGV  HO3'  H  HOH1  0   0.457  -5.0548  -1.7788  -0.1534
 SGV  H4'   H  HCH1  0   0.263  -4.3084   0.3706  -1.0849
 SGV  H5'   H  HCH2  0   0.232  -4.3973   1.9287   0.7304
 SGV  H5'A  H  HCH2  0   0.199  -2.7048   1.6970   1.1535
 SGV  HO5'  H  HOH1  0   0.461  -3.0163   3.5452  -0.2084

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
 SGV  N1   C2    aromatic  1.328  0.020  1.328
 SGV  N1   C6    aromatic  1.338  0.020  1.338
 SGV  C2   N3    aromatic  1.317  0.020  1.317
 SGV  N3   C4    aromatic  1.333  0.020  1.333
 SGV  C4   C5    aromatic  1.396  0.020  1.396
 SGV  C4   N9    aromatic  1.364  0.020  1.364
 SGV  C5   C6    aromatic  1.417  0.020  1.417
 SGV  C5   C7    aromatic  1.437  0.020  1.437
 SGV  C6   N6    single    1.334  0.020  1.334
 SGV  C7   C8    aromatic  1.372  0.020  1.372
 SGV  C7   C10   single    1.471  0.020  1.471
 SGV  C8   N9    aromatic  1.362  0.020  1.362
 SGV  N9   C1'   single    1.451  0.020  1.451
 SGV  C1'  C2'   single    1.534  0.020  1.534
 SGV  C1'  O4'   single    1.395  0.020  1.395
 SGV  C10  N11   single    1.342  0.020  1.342
 SGV  C10  O12   double    1.231  0.020  1.231
 SGV  C2'  O2'   single    1.391  0.020  1.391
 SGV  C2'  C3'   single    1.531  0.020  1.531
 SGV  C3'  O3'   single    1.402  0.020  1.402
 SGV  C3'  C4'   single    1.527  0.020  1.527
 SGV  C4'  O4'   single    1.429  0.020  1.429
 SGV  C4'  C5'   single    1.519  0.020  1.519
 SGV  C5'  O5'   single    1.406  0.020  1.406
 SGV  C2   H2    single    0.930  0.020  1.080
 SGV  N6   HN6   single    0.860  0.020  1.020
 SGV  N6   HN6A  single    0.860  0.020  1.020
 SGV  C8   H8    single    0.930  0.020  1.080
 SGV  C1'  H1'   single    0.970  0.020  1.090
 SGV  N11  HN11  single    0.860  0.020  1.020
 SGV  N11  HN1A  single    0.860  0.020  1.020
 SGV  C2'  H2'   single    0.970  0.020  1.090
 SGV  O2'  HO2'  single    0.850  0.020  0.980
 SGV  C3'  H3'   single    0.970  0.020  1.090
 SGV  O3'  HO3'  single    0.850  0.020  0.980
 SGV  C4'  H4'   single    0.970  0.020  1.090
 SGV  C5'  H5'   single    0.970  0.020  1.090
 SGV  C5'  H5'A  single    0.970  0.020  1.090
 SGV  O5'  HO5'  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
 SGV  C6    N1   C2    119.04  3.000
 SGV  H2    C2   N3    116.36  3.000
 SGV  H2    C2   N1    115.57  3.000
 SGV  N3    C2   N1    128.06  3.000
 SGV  C4    N3   C2    112.50  3.000
 SGV  N9    C4   C5    108.34  3.000
 SGV  N9    C4   N3    125.08  3.000
 SGV  C5    C4   N3    126.58  3.000
 SGV  C7    C5   C6    138.43  3.000
 SGV  C7    C5   C4    106.72  3.000
 SGV  C6    C5   C4    114.84  3.000
 SGV  N6    C6   C5    122.76  3.000
 SGV  N6    C6   N1    118.26  3.000
 SGV  C5    C6   N1    118.97  3.000
 SGV  HN6A  N6   HN6   119.55  3.000
 SGV  HN6A  N6   C6    118.67  3.000
 SGV  HN6   N6   C6    119.03  3.000
 SGV  C10   C7   C8    125.76  3.000
 SGV  C10   C7   C5    128.08  3.000
 SGV  C8    C7   C5    106.04  3.000
 SGV  H8    C8   N9    120.26  3.000
 SGV  H8    C8   C7    129.58  3.000
 SGV  N9    C8   C7    110.04  3.000
 SGV  C1'   N9   C8    125.88  3.000
 SGV  C1'   N9   C4    125.24  3.000
 SGV  C8    N9   C4    108.85  3.000
 SGV  H1'   C1'  O4'   111.50  3.000
 SGV  H1'   C1'  C2'   110.36  3.000
 SGV  O4'   C1'  C2'   106.38  3.000
 SGV  H1'   C1'  N9    106.51  3.000
 SGV  O4'   C1'  N9    108.71  3.000
 SGV  C2'   C1'  N9    113.46  3.000
 SGV  O12   C10  N11   121.63  3.000
 SGV  O12   C10  C7    121.84  3.000
 SGV  N11   C10  C7    116.52  3.000
 SGV  HN1A  N11  HN11  116.58  3.000
 SGV  HN1A  N11  C10   119.44  3.000
 SGV  HN11  N11  C10   122.72  3.000
 SGV  H2'   C2'  C3'   107.98  3.000
 SGV  H2'   C2'  O2'   111.41  3.000
 SGV  C3'   C2'  O2'   116.51  3.000
 SGV  H2'   C2'  C1'   108.63  3.000
 SGV  C3'   C2'  C1'   101.64  3.000
 SGV  O2'   C2'  C1'   110.04  3.000
 SGV  HO2'  O2'  C2'   108.59  3.000
 SGV  H3'   C3'  C4'   111.49  3.000
 SGV  H3'   C3'  O3'   111.89  3.000
 SGV  C4'   C3'  O3'   112.63  3.000
 SGV  H3'   C3'  C2'   111.89  3.000
 SGV  C4'   C3'  C2'   100.36  3.000
 SGV  O3'   C3'  C2'   108.00  3.000
 SGV  HO3'  O3'  C3'   108.42  3.000
 SGV  H4'   C4'  C5'   108.85  3.000
 SGV  H4'   C4'  O4'   107.27  3.000
 SGV  C5'   C4'  O4'   111.92  3.000
 SGV  H4'   C4'  C3'   111.73  3.000
 SGV  C5'   C4'  C3'   111.90  3.000
 SGV  O4'   C4'  C3'   105.06  3.000
 SGV  C4'   O4'  C1'   111.02  3.000
 SGV  H5'A  C5'  H5'   106.44  3.000
 SGV  H5'A  C5'  O5'   111.34  3.000
 SGV  H5'   C5'  O5'   112.07  3.000
 SGV  H5'A  C5'  C4'   110.74  3.000
 SGV  H5'   C5'  C4'   107.34  3.000
 SGV  O5'   C5'  C4'   108.85  3.000
 SGV  HO5'  O5'  C5'   108.07  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
 SGV  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 SGV  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 SGV  CONST_03  C7    C5   C6   N1   180.00   0.0  0
 SGV  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 SGV  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 SGV  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 SGV  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 SGV  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 SGV  CONST_09  C7    C5   C4   N3   180.00   0.0  0
 SGV  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 SGV  CONST_11  C8    C7   C5   C4     0.00   0.0  0
 SGV  CONST_12  C7    C8   N9   C4     0.00   0.0  0
 SGV  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 SGV  CONST_14  N9    C8   C7   C5     0.00   0.0  0
 SGV  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 SGV  CONST_16  C8    C7   C5   C6   180.00   0.0  0
 SGV  CONST_17  N9    C4   C5   C7     0.00   0.0  0
 SGV  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 SGV  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 SGV  CONST_20  C1'   N9   C8   C7   180.00   0.0  0
 SGV  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 SGV  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 SGV  CONST_23  C10   C7   C5   C4   180.00   0.0  0
 SGV  CONST_24  C10   C7   C5   C6     0.00   0.0  0
 SGV  CONST_25  C7    C5   C6   N6     0.00   0.0  0
 SGV  CONST_26  C10   C7   C8   N9   180.00   0.0  0
 SGV  CONST_27  H2    C2   N3   C4   180.00   0.0  0
 SGV  CONST_28  H8    C8   N9   C4   180.00   0.0  0
 SGV  CONST_29  HN6   N6   C6   N1     0.00   0.0  0
 SGV  CONST_30  HN6A  N6   C6   N1   180.00   0.0  0
 SGV  CONST_31  HN11  N11  C10  C7     0.00   0.0  0
 SGV  CONST_32  HN1A  N11  C10  C7   180.00   0.0  0
 SGV  Var_01    N11   C10  C7   C5  -166.63  30.0  2

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
 SGV  chir_01  C1'  N9   C2'  O4'  negativ
 SGV  chir_02  C2'  O2'  C3'  C1'  positiv
 SGV  chir_03  C3'  O3'  C4'  C2'  positiv
 SGV  chir_04  C4'  O4'  C3'  C5'  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
 SGV  plan-1  N1    0.020
 SGV  plan-1  C2    0.020
 SGV  plan-1  N3    0.020
 SGV  plan-1  C4    0.020
 SGV  plan-1  C5    0.020
 SGV  plan-1  C6    0.020
 SGV  plan-1  N6    0.020
 SGV  plan-1  C7    0.020
 SGV  plan-1  C8    0.020
 SGV  plan-1  N9    0.020
 SGV  plan-1  C1'   0.020
 SGV  plan-1  C10   0.020
 SGV  plan-1  H2    0.020
 SGV  plan-1  H8    0.020
 SGV  plan-2  C6    0.020
 SGV  plan-2  N6    0.020
 SGV  plan-2  HN6   0.020
 SGV  plan-2  HN6A  0.020
 SGV  plan-3  C7    0.020
 SGV  plan-3  C10   0.020
 SGV  plan-3  N11   0.020
 SGV  plan-3  O12   0.020
 SGV  plan-3  HN11  0.020
 SGV  plan-3  HN1A  0.020

