# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:38:11 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)c3ccncc3)[C@@H](O)[C@H]2O
#
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
 829  829  5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine  ligand  42  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_829
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
 829  N1    N  NR6   0  -0.554  -2.5773   0.3331   0.4196
 829  C2    C  CR6   0   0.612  -2.6363   0.4182  -0.9807
 829  O2    O  O     0  -0.509  -2.2072  -0.5092  -1.6521
 829  N3    N  N     0  -0.542  -3.1774   1.5222  -1.5328
 829  C4    C  CR6   0   0.515  -3.6530   2.4970  -0.7828
 829  N4    N  NH2   0  -0.808  -4.1769   3.5611  -1.3881
 829  C5    C  CR16  0  -0.478  -3.6189   2.4421   0.6446
 829  C6    C  CR16  0   0.102  -3.0602   1.3425   1.1851
 829  C07   C  C     0   0.537   2.3239   0.1994  -0.5691
 829  C08   C  CR16  0  -0.361   4.0848   0.3556   1.2608
 829  C09   C  CR16  0  -0.055   5.2169   0.9851   1.7586
 829  C1'   C  CH1   0   0.202  -1.9192  -0.7894   1.0717
 829  N10   N  N     0  -0.398   5.8379   1.9769   1.1343
 829  C11   C  CR16  0  -0.057   5.3300   2.3885  -0.0223
 829  C12   C  CR16  0  -0.340   4.1960   1.8390  -0.5984
 829  C13   C  CR6   0   0.052   3.5608   0.7857   0.0479
 829  O15   O  O     0  -0.471   1.6017   0.8873  -1.2724
 829  C2'   C  CH1   0  -0.041  -2.4412  -2.1939   0.7252
 829  O2'   O  OH1   0  -0.678  -2.6340  -2.8846   1.9340
 829  C3'   C  CH1   0  -0.034  -1.2866  -2.8290  -0.0743
 829  O3'   O  OH1   0  -0.665  -1.0912  -4.1861   0.2437
 829  C4'   C  CH1   0   0.053  -0.0688  -2.0183   0.3705
 829  O4'   O  O2    0  -0.482  -0.5493  -0.7579   0.7925
 829  C5'   C  CH2   0  -0.312   0.9472  -1.8302  -0.7412
 829  N5'   N  NH1   0  -0.647   2.1148  -1.0998  -0.3094
 829  HN4   H  HNH2  0   0.403  -4.1976   3.6135  -2.3923
 829  HN4A  H  HNH2  0   0.414  -4.5544   4.3319  -0.8662
 829  H5    H  HCR6  0   0.289  -4.0064   3.2372   1.2630
 829  H6    H  HCR6  0   0.319  -2.9764   1.2162   2.2559
 829  H09   H  HCR6  0   0.272   5.6344   0.6696   2.7079
 829  H1'   H  HCH1  0   0.251  -2.0889  -0.6292   2.1409
 829  H11   H  HCR6  0   0.271   5.8495   3.1994  -0.5199
 829  H12   H  HCR6  0   0.275   3.8264   2.2230  -1.5390
 829  H2'   H  HCH1  0   0.245  -3.3710  -2.1547   0.1477
 829  HO2'  H  HOH1  0   0.447  -2.2974  -3.7813   1.7969
 829  H3'   H  HCH1  0   0.261  -1.4644  -2.6997  -1.1414
 829  HO3'  H  HOH1  0   0.469  -1.5901  -4.7253  -0.3780
 829  H4'   H  HCH1  0   0.232   0.4105  -2.5321   1.2167
 829  H5'   H  HCH2  0   0.263   1.2615  -2.8134  -1.0961
 829  H5'A  H  HCH2  0   0.263   0.4851  -1.3025  -1.5739
 829  HN5'  H  HNH1  0   0.411   2.8081  -1.6109   0.2122
 829  H08   H  HCR6  0   0.275   3.6269  -0.4354   1.8404

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
 829  C6   N1    single    1.356  0.020  1.356
 829  N1   C1'   single    1.455  0.020  1.455
 829  N1   C2    single    1.404  0.020  1.404
 829  N3   C2    single    1.348  0.020  1.348
 829  C2   O2    double    1.223  0.020  1.223
 829  C4   N3    double    1.319  0.020  1.319
 829  C5   C4    single    1.429  0.020  1.429
 829  N4   C4    single    1.332  0.020  1.332
 829  N4   HN4   single    0.860  0.020  1.020
 829  N4   HN4A  single    0.860  0.020  1.020
 829  C5   C6    double    1.347  0.020  1.347
 829  C5   H5    single    0.930  0.020  1.080
 829  C6   H6    single    0.930  0.020  1.080
 829  O15  C07   double    1.220  0.020  1.220
 829  C13  C07   single    1.501  0.020  1.501
 829  C07  N5'   single    1.341  0.020  1.341
 829  C09  C08   aromatic  1.388  0.020  1.388
 829  C13  C08   aromatic  1.390  0.020  1.390
 829  C08  H08   single    0.930  0.020  1.080
 829  N10  C09   aromatic  1.326  0.020  1.326
 829  C09  H09   single    0.930  0.020  1.080
 829  C2'  C1'   single    1.538  0.020  1.538
 829  C1'  O4'   single    1.398  0.020  1.398
 829  C1'  H1'   single    0.970  0.020  1.090
 829  C11  N10   aromatic  1.329  0.020  1.329
 829  C11  C12   aromatic  1.386  0.020  1.386
 829  C11  H11   single    0.930  0.020  1.080
 829  C12  C13   aromatic  1.390  0.020  1.390
 829  C12  H12   single    0.930  0.020  1.080
 829  C3'  C2'   single    1.541  0.020  1.541
 829  C2'  O2'   single    1.405  0.020  1.405
 829  C2'  H2'   single    0.970  0.020  1.090
 829  O2'  HO2'  single    0.850  0.020  0.980
 829  O3'  C3'   single    1.407  0.020  1.407
 829  C3'  C4'   single    1.529  0.020  1.529
 829  C3'  H3'   single    0.970  0.020  1.090
 829  O3'  HO3'  single    0.850  0.020  0.980
 829  C5'  C4'   single    1.518  0.020  1.518
 829  C4'  O4'   single    1.413  0.020  1.413
 829  C4'  H4'   single    0.970  0.020  1.090
 829  N5'  C5'   single    1.443  0.020  1.443
 829  C5'  H5'   single    0.970  0.020  1.090
 829  C5'  H5'A  single    0.970  0.020  1.090
 829  N5'  HN5'  single    0.860  0.020  1.020

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
 829  C1'   N1   C6   118.83  3.000
 829  C1'   N1   C2   120.84  3.000
 829  C6    N1   C2   120.20  3.000
 829  N3    C2   O2   122.50  3.000
 829  O2    C2   N1   119.14  3.000
 829  N3    C2   N1   118.36  3.000
 829  C4    N3   C2   121.15  3.000
 829  C5    C4   N4   119.62  3.000
 829  N4    C4   N3   118.30  3.000
 829  C5    C4   N3   122.09  3.000
 829  HN4A  N4   HN4  118.10  3.000
 829  HN4A  N4   C4   121.66  3.000
 829  HN4   N4   C4   120.23  3.000
 829  H5    C5   C6   121.37  3.000
 829  H5    C5   C4   122.38  3.000
 829  C6    C5   C4   116.25  3.000
 829  H6    C6   C5   121.66  3.000
 829  H6    C6   N1   116.39  3.000
 829  C5    C6   N1   121.94  3.000
 829  N5'   C07  O15  124.42  3.000
 829  N5'   C07  C13  115.28  3.000
 829  O15   C07  C13  120.28  3.000
 829  H08   C08  C13  122.29  3.000
 829  H08   C08  C09  118.99  3.000
 829  C13   C08  C09  118.71  3.000
 829  H09   C09  N10  116.71  3.000
 829  H09   C09  C08  119.76  3.000
 829  N10   C09  C08  123.53  3.000
 829  H1'   C1'  O4'  110.11  3.000
 829  H1'   C1'  C2'  107.53  3.000
 829  O4'   C1'  C2'  107.94  3.000
 829  H1'   C1'  N1   104.76  3.000
 829  O4'   C1'  N1   109.64  3.000
 829  C2'   C1'  N1   116.73  3.000
 829  C11   N10  C09  117.55  3.000
 829  H11   C11  C12  119.87  3.000
 829  H11   C11  N10  116.62  3.000
 829  C12   C11  N10  123.50  3.000
 829  H12   C12  C13  121.17  3.000
 829  H12   C12  C11  120.05  3.000
 829  C13   C12  C11  118.78  3.000
 829  C12   C13  C08  117.92  3.000
 829  C12   C13  C07  118.78  3.000
 829  C08   C13  C07  123.27  3.000
 829  H2'   C2'  C3'  112.16  3.000
 829  H2'   C2'  O2'  110.77  3.000
 829  C3'   C2'  O2'  110.26  3.000
 829  H2'   C2'  C1'  111.98  3.000
 829  O2'   C2'  C1'  107.55  3.000
 829  C3'   C2'  C1'  103.82  3.000
 829  HO2'  O2'  C2'  106.61  3.000
 829  H3'   C3'  C4'  110.60  3.000
 829  H3'   C3'  O3'  111.00  3.000
 829  C4'   C3'  O3'  109.57  3.000
 829  H3'   C3'  C2'  109.69  3.000
 829  C4'   C3'  C2'  103.14  3.000
 829  O3'   C3'  C2'  112.59  3.000
 829  HO3'  O3'  C3'  108.80  3.000
 829  H4'   C4'  C5'  109.25  3.000
 829  H4'   C4'  O4'  109.58  3.000
 829  C5'   C4'  O4'  109.62  3.000
 829  H4'   C4'  C3'  108.85  3.000
 829  O4'   C4'  C3'  106.79  3.000
 829  C5'   C4'  C3'  112.70  3.000
 829  C4'   O4'  C1'  111.88  3.000
 829  H5'A  C5'  H5'  108.07  3.000
 829  H5'A  C5'  N5'  109.07  3.000
 829  H5'   C5'  N5'  108.67  3.000
 829  H5'A  C5'  C4'  109.64  3.000
 829  H5'   C5'  C4'  108.62  3.000
 829  N5'   C5'  C4'  112.66  3.000
 829  HN5'  N5'  C5'  117.06  3.000
 829  HN5'  N5'  C07  118.99  3.000
 829  C5'   N5'  C07  123.94  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
 829  CONST_01  C11   N10  C09  C08     0.00   0.0  0
 829  CONST_02  C11   C12  C13  C08     0.00   0.0  0
 829  CONST_03  C12   C13  C08  C09     0.00   0.0  0
 829  CONST_04  C12   C11  N10  C09     0.00   0.0  0
 829  CONST_05  C13   C08  C09  N10     0.00   0.0  0
 829  CONST_06  C13   C12  C11  N10     0.00   0.0  0
 829  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 829  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 829  CONST_09  C6    N1   C2   N3      0.00   0.0  0
 829  CONST_10  C1'   N1   C2   N3    180.00   0.0  0
 829  CONST_11  C09   C08  C13  C07   180.00   0.0  0
 829  CONST_12  C11   C12  C13  C07   180.00   0.0  0
 829  CONST_13  N4    C4   N3   C2    180.00   0.0  0
 829  CONST_14  C6    N1   C2   O2    180.00   0.0  0
 829  CONST_15  C1'   N1   C2   O2      0.00   0.0  0
 829  CONST_16  C4    N3   C2   O2    180.00   0.0  0
 829  CONST_17  H12   C12  C13  C08   180.00   0.0  0
 829  CONST_18  H11   C11  N10  C09   180.00   0.0  0
 829  CONST_19  H08   C08  C09  N10   180.00   0.0  0
 829  CONST_20  H09   C09  N10  C11   180.00   0.0  0
 829  CONST_21  HN4   N4   C4   N3      0.00   0.0  0
 829  CONST_22  HN4A  N4   C4   N3    180.00   0.0  0
 829  CONST_23  C5'   N5'  C07  C13   180.00   0.0  0
 829  CONST_24  HN5'  N5'  C07  C13     0.00   0.0  0
 829  CONST_25  C5'   N5'  C07  O15     0.00   0.0  0
 829  Var_01    O15   C07  C13  C08   149.81  30.0  2
 829  Var_02    C4'   C5'  N5'  C07  -101.38  30.0  3

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
 829  chir_01  C1'  N1   C2'  O4'  negativ
 829  chir_02  C2'  O2'  C3'  C1'  positiv
 829  chir_03  C3'  O3'  C2'  C4'  negativ
 829  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
 829  plan-1  N1    0.020
 829  plan-1  C2    0.020
 829  plan-1  O2    0.020
 829  plan-1  N3    0.020
 829  plan-1  C4    0.020
 829  plan-1  N4    0.020
 829  plan-1  C5    0.020
 829  plan-1  C6    0.020
 829  plan-1  C1'   0.020
 829  plan-1  HN4   0.020
 829  plan-1  HN4A  0.020
 829  plan-1  H5    0.020
 829  plan-1  H6    0.020
 829  plan-2  C07   0.020
 829  plan-2  C08   0.020
 829  plan-2  C09   0.020
 829  plan-2  N10   0.020
 829  plan-2  C11   0.020
 829  plan-2  C12   0.020
 829  plan-2  C13   0.020
 829  plan-2  H09   0.020
 829  plan-2  H11   0.020
 829  plan-2  H12   0.020
 829  plan-2  H08   0.020
 829  plan-3  C07   0.020
 829  plan-3  C13   0.020
 829  plan-3  O15   0.020
 829  plan-3  C5'   0.020
 829  plan-3  N5'   0.020
 829  plan-3  HN5'  0.020

