# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:34:56 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 7-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cc(C#N)c3C(=O)NC=Nc23
#
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
 7CI  7CI  7-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  33  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7CI
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
 7CI  C1    C  CH1   0   0.212   1.3226   0.7632  -0.4630
 7CI  N1    N  NR5   0  -0.549   0.0413   0.0812  -0.3502
 7CI  O1    O  O2    0  -0.489   2.2190  -0.0780  -1.1151
 7CI  C2    C  CR56  0   0.534  -1.1752   0.6944  -0.3509
 7CI  N2    N  N     0  -0.445  -1.3755   2.0171  -0.5245
 7CI  O2    O  OH1   0  -0.649   1.4769   2.3192   1.3518
 7CI  C3    C  CR16  0   0.166  -2.6220   2.3539  -0.4999
 7CI  N3    N  NR16  0  -0.662  -3.6495   1.4946  -0.3135
 7CI  O3    O  OH1   0  -0.666   3.8152   2.1966  -0.0608
 7CI  C4    C  CR6   0   0.516  -3.5251   0.1179  -0.1301
 7CI  N4    N  NS    0  -0.258  -2.5183  -3.8351   0.2885
 7CI  C5    C  CR56  0  -0.130  -2.1498  -0.2695  -0.1617
 7CI  O5    O  O     0  -0.459  -4.4961  -0.5998   0.0297
 7CI  C6    C  CR5   0  -0.109  -1.4748  -1.5173  -0.0465
 7CI  C7    C  CR15  0   0.028  -0.1312  -1.2558  -0.1696
 7CI  C8    C  CSP   0  -0.027  -2.0519  -2.7910   0.1369
 7CI  C9    C  CH1   0  -0.015   1.9471   1.0929   0.8980
 7CI  C10   C  CH1   0  -0.031   3.4398   1.0044   0.5736
 7CI  C11   C  CH1   0  -0.058   3.4407  -0.1916  -0.3764
 7CI  C12   C  CH2   0  -0.169   3.5298  -1.5119   0.3679
 7CI  O4    O  OH1   0  -0.666   3.2983  -2.5584  -0.5404
 7CI  H1    H  HCH1  0   0.272   1.1374   1.6784  -1.0344
 7CI  HO2   H  HOH1  0   0.464   1.7313   2.4246   2.2739
 7CI  H3    H  HCR6  0   0.306  -2.9026   3.3897  -0.6348
 7CI  HN3   H  HNR6  0   0.438  -4.5871   1.8764  -0.3126
 7CI  HO3   H  HOH1  0   0.458   4.7440   2.1320  -0.3050
 7CI  H7    H  HCR5  0   0.329   0.6959  -1.9470  -0.1729
 7CI  H9    H  HCH1  0   0.247   1.7078   0.2843   1.6023
 7CI  H10   H  HCH1  0   0.255   4.0444   0.8085   1.4686
 7CI  H11   H  HCH1  0   0.266   4.2615  -0.1344  -1.0975
 7CI  H122  H  HCH2  0   0.230   4.5302  -1.5674   0.8173
 7CI  H121  H  HCH2  0   0.202   2.8129  -1.5374   1.2005
 7CI  HO4   H  HOH1  0   0.461   3.3331  -3.3880  -0.0556

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
 7CI  N3   C3    single    1.352  0.020  1.352
 7CI  N3   C4    single    1.394  0.020  1.394
 7CI  O5   C4    double    1.218  0.020  1.218
 7CI  C3   N2    double    1.291  0.020  1.291
 7CI  C4   C5    single    1.429  0.020  1.429
 7CI  N2   C2    single    1.349  0.020  1.349
 7CI  C5   C2    aromatic  1.384  0.020  1.384
 7CI  C5   C6    aromatic  1.423  0.020  1.423
 7CI  C2   N1    aromatic  1.362  0.020  1.362
 7CI  C8   N4    triple    1.153  0.020  1.153
 7CI  C8   C6    single    1.410  0.020  1.410
 7CI  C6   C7    aromatic  1.374  0.020  1.374
 7CI  N1   C7    aromatic  1.360  0.020  1.360
 7CI  N1   C1    single    1.456  0.020  1.456
 7CI  C1   C9    single    1.533  0.020  1.533
 7CI  C1   O1    single    1.392  0.020  1.392
 7CI  C9   O2    single    1.390  0.020  1.390
 7CI  C9   C10   single    1.530  0.020  1.530
 7CI  O1   C11   single    1.432  0.020  1.432
 7CI  C10  C11   single    1.527  0.020  1.527
 7CI  C10  O3    single    1.402  0.020  1.402
 7CI  C11  C12   single    1.518  0.020  1.518
 7CI  O4   C12   single    1.405  0.020  1.405
 7CI  C1   H1    single    0.970  0.020  1.090
 7CI  O2   HO2   single    0.850  0.020  0.980
 7CI  C3   H3    single    0.930  0.020  1.080
 7CI  N3   HN3   single    0.860  0.020  1.020
 7CI  O3   HO3   single    0.850  0.020  0.980
 7CI  C7   H7    single    0.930  0.020  1.080
 7CI  C9   H9    single    0.970  0.020  1.090
 7CI  C10  H10   single    0.970  0.020  1.090
 7CI  C11  H11   single    0.970  0.020  1.090
 7CI  C12  H122  single    0.970  0.020  1.090
 7CI  C12  H121  single    0.970  0.020  1.090
 7CI  O4   HO4   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
 7CI  H1    C1   C9    110.64  3.000
 7CI  H1    C1   O1    111.70  3.000
 7CI  C9    C1   O1    106.47  3.000
 7CI  H1    C1   N1    106.45  3.000
 7CI  O1    C1   N1    108.67  3.000
 7CI  C9    C1   N1    112.98  3.000
 7CI  C7    N1   C2    109.22  3.000
 7CI  C7    N1   C1    125.62  3.000
 7CI  C2    N1   C1    125.10  3.000
 7CI  C11   O1   C1    110.84  3.000
 7CI  C5    C2   N2    126.59  3.000
 7CI  C5    C2   N1    108.38  3.000
 7CI  N2    C2   N1    125.03  3.000
 7CI  C3    N2   C2    113.36  3.000
 7CI  HO2   O2   C9    108.67  3.000
 7CI  H3    C3   N3    115.38  3.000
 7CI  H3    C3   N2    119.85  3.000
 7CI  N3    C3   N2    124.77  3.000
 7CI  HN3   N3   C4    117.06  3.000
 7CI  HN3   N3   C3    117.65  3.000
 7CI  C4    N3   C3    125.29  3.000
 7CI  HO3   O3   C10   108.43  3.000
 7CI  O5    C4   C5    127.62  3.000
 7CI  C5    C4   N3    110.52  3.000
 7CI  O5    C4   N3    121.86  3.000
 7CI  C6    C5   C4    133.80  3.000
 7CI  C6    C5   C2    106.73  3.000
 7CI  C4    C5   C2    119.47  3.000
 7CI  C8    C6   C7    125.70  3.000
 7CI  C7    C6   C5    106.83  3.000
 7CI  C8    C6   C5    127.46  3.000
 7CI  H7    C7   C6    128.93  3.000
 7CI  H7    C7   N1    122.18  3.000
 7CI  C6    C7   N1    108.84  3.000
 7CI  C6    C8   N4    180.00  3.000
 7CI  H9    C9   C10   107.81  3.000
 7CI  H9    C9   O2    111.50  3.000
 7CI  C10   C9   O2    116.77  3.000
 7CI  H9    C9   C1    108.79  3.000
 7CI  C10   C9   C1    101.34  3.000
 7CI  O2    C9   C1    109.99  3.000
 7CI  H10   C10  C11   111.54  3.000
 7CI  H10   C10  C9    112.01  3.000
 7CI  C11   C10  C9    100.24  3.000
 7CI  H10   C10  O3    111.92  3.000
 7CI  C11   C10  O3    112.61  3.000
 7CI  C9    C10  O3    107.94  3.000
 7CI  H11   C11  C12   108.94  3.000
 7CI  H11   C11  C10   111.69  3.000
 7CI  C12   C11  C10   112.09  3.000
 7CI  H11   C11  O1    107.21  3.000
 7CI  C12   C11  O1    111.83  3.000
 7CI  C10   C11  O1    104.96  3.000
 7CI  H121  C12  H122  106.44  3.000
 7CI  H121  C12  O4    111.41  3.000
 7CI  H122  C12  O4    112.15  3.000
 7CI  H121  C12  C11   110.69  3.000
 7CI  H122  C12  C11   107.34  3.000
 7CI  O4    C12  C11   108.73  3.000
 7CI  HO4   O4   C12   108.11  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
 7CI  CONST_01  C6   C5  C2  N1    0.00  0.0  0
 7CI  CONST_02  C5   C6  C7  N1    0.00  0.0  0
 7CI  CONST_03  C7   C6  C5  C2    0.00  0.0  0
 7CI  CONST_04  C6   C7  N1  C2    0.00  0.0  0
 7CI  CONST_05  C7   N1  C2  C5    0.00  0.0  0
 7CI  CONST_06  N2   C2  N1  C1    0.00  0.0  0
 7CI  CONST_07  C5   C2  N1  C1  180.00  0.0  0
 7CI  CONST_08  C6   C7  N1  C1  180.00  0.0  0
 7CI  CONST_09  N3   C3  N2  C2    0.00  0.0  0
 7CI  CONST_10  C4   N3  C3  N2    0.00  0.0  0
 7CI  CONST_11  C5   C4  N3  C3    0.00  0.0  0
 7CI  CONST_12  C8   C6  C7  N1  180.00  0.0  0
 7CI  CONST_13  C8   C6  C5  C2  180.00  0.0  0
 7CI  CONST_14  C8   C6  C5  C4    0.00  0.0  0
 7CI  CONST_15  O5   C4  N3  C3  180.00  0.0  0
 7CI  CONST_16  H7   C7  N1  C1    0.00  0.0  0
 7CI  CONST_17  H3   C3  N2  C2  180.00  0.0  0
 7CI  CONST_18  HN3  N3  C3  N2  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
 7CI  chir_01  C1   N1  C9   O1   negativ
 7CI  chir_02  C9   O2  C10  C1   positiv
 7CI  chir_03  C10  O3  C11  C9   positiv
 7CI  chir_04  C11  O1  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
 7CI  plan-1  C1   0.020
 7CI  plan-1  N1   0.020
 7CI  plan-1  C2   0.020
 7CI  plan-1  N2   0.020
 7CI  plan-1  C3   0.020
 7CI  plan-1  N3   0.020
 7CI  plan-1  C4   0.020
 7CI  plan-1  N4   0.020
 7CI  plan-1  C5   0.020
 7CI  plan-1  O5   0.020
 7CI  plan-1  C6   0.020
 7CI  plan-1  C7   0.020
 7CI  plan-1  C8   0.020
 7CI  plan-1  H3   0.020
 7CI  plan-1  HN3  0.020
 7CI  plan-1  H7   0.020

