# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:28:43 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(C#N)c12)[C@@H]3O[C@H](CO)[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
 TO1  TO1  4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  34  21  .  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_TO1
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
 TO1  C     C  CH1   0   0.173   1.2370  -0.8551   0.8266
 TO1  N     N  NR5   0  -0.555   0.0015  -0.1270   0.5231
 TO1  O     O  O2    0  -0.494   2.2242   0.0542   1.1949
 TO1  C2    C  CR56  0   0.526  -1.2152  -0.7310   0.3668
 TO1  N2    N  N     0  -0.463  -1.4438  -2.0387   0.4682
 TO1  O2    O  OH1   0  -0.663   2.5163  -2.6864   0.0606
 TO1  C3    C  CR16  0   0.048  -2.7120  -2.3443   0.2693
 TO1  N3    N  N     0  -0.469  -3.7193  -1.5230  -0.0094
 TO1  O3    O  OH1   0  -0.655   3.6670  -1.0502  -1.8430
 TO1  C4    C  CR6   0   0.452  -3.4799  -0.2124  -0.1095
 TO1  N4    N  NS    0  -0.256  -2.4484   3.8228  -0.3352
 TO1  C5    C  CR56  0  -0.035  -2.1615   0.2489   0.0869
 TO1  N5    N  NH2   0  -0.828  -4.5010   0.5968  -0.3974
 TO1  C6    C  CR5   0  -0.123  -1.4596   1.4964   0.0853
 TO1  C7    C  CR15  0   0.036  -0.1437   1.2121   0.3608
 TO1  C8    C  CSP   0  -0.051  -1.9868   2.7820  -0.1430
 TO1  C9    C  CH1   0  -0.038   1.7560  -1.6039  -0.3993
 TO1  C10   C  CH1   0  -0.042   2.6493  -0.5330  -1.0346
 TO1  C11   C  CH1   0   0.005   3.2442   0.1459   0.1965
 TO1  C12   C  CH2   0  -0.155   3.6323   1.5833  -0.0458
 TO1  H     H  HCH1  0   0.290   1.0131  -1.5367   1.6512
 TO1  HO2   H  HOH1  0   0.453   3.2060  -2.8595  -0.5921
 TO1  H3    H  HCR6  0   0.257  -2.9698  -3.3953   0.3395
 TO1  HO3   H  HOH1  0   0.470   3.3159  -1.2042  -2.7262
 TO1  HO4   H  HOH1  0   0.460   4.4613   3.0187   0.9520
 TO1  HN5   H  HNH2  0   0.408  -5.4263   0.2149  -0.4962
 TO1  HN5A  H  HNH2  0   0.414  -4.4025   1.5950  -0.4487
 TO1  H7    H  HCR5  0   0.333   0.6816   1.8968   0.4580
 TO1  H9    H  HCH1  0   0.263   0.9451  -1.9261  -1.0625
 TO1  H10   H  HCH1  0   0.246   2.0187   0.1776  -1.5857
 TO1  H11   H  HCH1  0   0.250   4.1249  -0.4135   0.5356
 TO1  H12   H  HCH2  0   0.197   2.7550   2.1511  -0.3866
 TO1  H12A  H  HCH2  0   0.218   4.3515   1.5889  -0.8750
 TO1  O4    O  OH1   0  -0.668   4.1804   2.1172   1.1329

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
 TO1  C    N     single    1.466  0.020  1.466
 TO1  C    O     single    1.392  0.020  1.392
 TO1  C    C9    single    1.527  0.020  1.527
 TO1  N    C2    aromatic  1.367  0.020  1.367
 TO1  N    C7    aromatic  1.357  0.020  1.357
 TO1  O    C11   single    1.430  0.020  1.430
 TO1  C2   N2    aromatic  1.331  0.020  1.331
 TO1  C2   C5    aromatic  1.391  0.020  1.391
 TO1  N2   C3    aromatic  1.320  0.020  1.320
 TO1  O2   C9    single    1.400  0.020  1.400
 TO1  C3   N3    aromatic  1.329  0.020  1.329
 TO1  N3   C4    aromatic  1.336  0.020  1.336
 TO1  O3   C10   single    1.399  0.020  1.399
 TO1  C4   C5    aromatic  1.410  0.020  1.410
 TO1  C4   N5    single    1.334  0.020  1.334
 TO1  N4   C8    triple    1.155  0.020  1.155
 TO1  O4   C12   single    1.405  0.020  1.405
 TO1  C5   C6    aromatic  1.431  0.020  1.431
 TO1  C6   C7    aromatic  1.374  0.020  1.374
 TO1  C6   C8    single    1.408  0.020  1.408
 TO1  C9   C10   single    1.532  0.020  1.532
 TO1  C10  C11   single    1.527  0.020  1.527
 TO1  C11  C12   single    1.509  0.020  1.509
 TO1  C    H     single    0.970  0.020  1.090
 TO1  O2   HO2   single    0.850  0.020  0.980
 TO1  C3   H3    single    0.930  0.020  1.080
 TO1  O3   HO3   single    0.850  0.020  0.980
 TO1  O4   HO4   single    0.850  0.020  0.980
 TO1  N5   HN5   single    0.860  0.020  1.020
 TO1  N5   HN5A  single    0.860  0.020  1.020
 TO1  C7   H7    single    0.930  0.020  1.080
 TO1  C9   H9    single    0.970  0.020  1.090
 TO1  C10  H10   single    0.970  0.020  1.090
 TO1  C11  H11   single    0.970  0.020  1.090
 TO1  C12  H12   single    0.970  0.020  1.090
 TO1  C12  H12A  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
 TO1  H     C    C9   111.68  3.000
 TO1  H     C    O    110.67  3.000
 TO1  C9    C    O    106.96  3.000
 TO1  H     C    N    107.05  3.000
 TO1  C9    C    N    111.33  3.000
 TO1  O     C    N    109.16  3.000
 TO1  C7    N    C2   109.10  3.000
 TO1  C7    N    C    127.24  3.000
 TO1  C2    N    C    123.66  3.000
 TO1  C11   O    C    111.29  3.000
 TO1  C5    C2   N2   126.20  3.000
 TO1  C5    C2   N    108.50  3.000
 TO1  N2    C2   N    125.31  3.000
 TO1  C3    N2   C2   112.40  3.000
 TO1  HO2   O2   C9   107.73  3.000
 TO1  H3    C3   N3   115.61  3.000
 TO1  H3    C3   N2   116.31  3.000
 TO1  N3    C3   N2   128.08  3.000
 TO1  C4    N3   C3   119.08  3.000
 TO1  HO3   O3   C10  108.91  3.000
 TO1  N5    C4   C5   123.16  3.000
 TO1  N5    C4   N3   118.29  3.000
 TO1  C5    C4   N3   118.54  3.000
 TO1  C6    C5   C4   138.00  3.000
 TO1  C6    C5   C2   106.30  3.000
 TO1  C4    C5   C2   115.70  3.000
 TO1  HN5A  N5   HN5  117.55  3.000
 TO1  HN5A  N5   C4   122.59  3.000
 TO1  HN5   N5   C4   119.67  3.000
 TO1  C8    C6   C7   125.45  3.000
 TO1  C8    C6   C5   127.75  3.000
 TO1  C7    C6   C5   106.80  3.000
 TO1  H7    C7   C6   128.35  3.000
 TO1  H7    C7   N    122.34  3.000
 TO1  C6    C7   N    109.31  3.000
 TO1  C6    C8   N4   180.00  3.000
 TO1  H9    C9   C10  112.70  3.000
 TO1  H9    C9   O2   111.91  3.000
 TO1  C10   C9   O2   111.09  3.000
 TO1  H9    C9   C    112.23  3.000
 TO1  C10   C9   C    100.85  3.000
 TO1  O2    C9   C    107.45  3.000
 TO1  H10   C10  C11  109.92  3.000
 TO1  H10   C10  C9   108.99  3.000
 TO1  C11   C10  C9   101.75  3.000
 TO1  H10   C10  O3   111.53  3.000
 TO1  C11   C10  O3   110.30  3.000
 TO1  C9    C10  O3   113.91  3.000
 TO1  H11   C11  C12  109.20  3.000
 TO1  H11   C11  C10  109.60  3.000
 TO1  C12   C11  C10  113.23  3.000
 TO1  H11   C11  O    108.91  3.000
 TO1  C12   C11  O    110.90  3.000
 TO1  C10   C11  O    104.86  3.000
 TO1  H12A  C12  H12  106.62  3.000
 TO1  H12A  C12  C11  107.14  3.000
 TO1  H12   C12  C11  109.68  3.000
 TO1  H12A  C12  O4   112.10  3.000
 TO1  H12   C12  O4   112.03  3.000
 TO1  C11   C12  O4   109.13  3.000
 TO1  HO4   O4   C12  108.20  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
 TO1  CONST_01  C3    N2  C2  N   180.00  0.0  0
 TO1  CONST_02  C4    C5  C2  N   180.00  0.0  0
 TO1  CONST_03  C6    C5  C2  N     0.00  0.0  0
 TO1  CONST_04  C5    C6  C7  N     0.00  0.0  0
 TO1  CONST_05  C6    C7  N   C2    0.00  0.0  0
 TO1  CONST_06  N3    C3  N2  C2    0.00  0.0  0
 TO1  CONST_07  N3    C4  C5  C2    0.00  0.0  0
 TO1  CONST_08  C7    C6  C5  C2    0.00  0.0  0
 TO1  CONST_09  C7    N   C2  N2  180.00  0.0  0
 TO1  CONST_10  C4    C5  C2  N2    0.00  0.0  0
 TO1  CONST_11  C6    C5  C2  N2  180.00  0.0  0
 TO1  CONST_12  C4    N3  C3  N2    0.00  0.0  0
 TO1  CONST_13  C5    C2  N2  C3    0.00  0.0  0
 TO1  CONST_14  C5    C4  N3  C3    0.00  0.0  0
 TO1  CONST_15  C6    C5  C4  N3  180.00  0.0  0
 TO1  CONST_16  C7    C6  C5  C4  180.00  0.0  0
 TO1  CONST_17  C7    N   C2  C5    0.00  0.0  0
 TO1  CONST_18  N2    C2  N   C     0.00  0.0  0
 TO1  CONST_19  C5    C2  N   C   180.00  0.0  0
 TO1  CONST_20  C6    C7  N   C   180.00  0.0  0
 TO1  CONST_21  C8    C6  C7  N   180.00  0.0  0
 TO1  CONST_22  N5    C4  C5  C2  180.00  0.0  0
 TO1  CONST_23  C8    C6  C5  C2  180.00  0.0  0
 TO1  CONST_24  N5    C4  N3  C3  180.00  0.0  0
 TO1  CONST_25  C8    C6  C5  C4    0.00  0.0  0
 TO1  CONST_26  C6    C5  C4  N5    0.00  0.0  0
 TO1  CONST_27  H7    C7  N   C     0.00  0.0  0
 TO1  CONST_28  H3    C3  N2  C2  180.00  0.0  0
 TO1  CONST_29  HN5   N5  C4  N3    0.00  0.0  0
 TO1  CONST_30  HN5A  N5  C4  N3  180.00  0.0  0

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
 TO1  chir_01  C    N   O    C9   positiv
 TO1  chir_02  C9   O2  C    C10  negativ
 TO1  chir_03  C10  O3  C11  C9   positiv
 TO1  chir_04  C11  O   C10  C12  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
 TO1  plan-1  C     0.020
 TO1  plan-1  N     0.020
 TO1  plan-1  C2    0.020
 TO1  plan-1  N2    0.020
 TO1  plan-1  C3    0.020
 TO1  plan-1  N3    0.020
 TO1  plan-1  C4    0.020
 TO1  plan-1  N4    0.020
 TO1  plan-1  C5    0.020
 TO1  plan-1  N5    0.020
 TO1  plan-1  C6    0.020
 TO1  plan-1  C7    0.020
 TO1  plan-1  C8    0.020
 TO1  plan-1  H3    0.020
 TO1  plan-1  H7    0.020
 TO1  plan-2  C4    0.020
 TO1  plan-2  N5    0.020
 TO1  plan-2  HN5   0.020
 TO1  plan-2  HN5A  0.020

