# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:58:32 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(6-amino-2-iodo-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nc(I)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
 NEI  NEI  '(2S,3S,4R,5R)-5-(6-amino-2-iodo-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)'  ligand  38  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NEI
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
 NEI  C52   C  CH3   0  -0.704   8.1825   0.2102   0.5351
 NEI  C51   C  CH2   0  -0.260   7.0634  -0.5179  -0.1833
 NEI  N5'   N  NH1   0  -0.625   5.8816   0.3219  -0.2599
 NEI  C5'   C  C     0   0.528   4.7181  -0.1061  -0.7578
 NEI  O5'   O  O     0  -0.482   4.5528  -1.2214  -1.2283
 NEI  C4'   C  CR15  0  -0.068   3.5955   0.9157  -0.6478
 NEI  O4'   O  O     0  -0.484   2.4975   0.5324  -1.4472
 NEI  C3'   C  CR15  0  -0.039   3.0511   1.0272   0.7825
 NEI  O3'   O  OH1   0  -0.652   3.7997   1.9557   1.5091
 NEI  C2'   C  CR15  0  -0.043   1.6060   1.4638   0.5148
 NEI  O2'   O  OH1   0  -0.660   1.5448   2.8220   0.1854
 NEI  C1'   C  CR15  0   0.170   1.2938   0.6761  -0.7553
 NEI  N9    N  NR5   0  -0.541   0.7527  -0.6455  -0.4488
 NEI  C8    C  CR15  0   0.093   1.3461  -1.8723  -0.5923
 NEI  N7    N  N     0  -0.448   0.5676  -2.8596  -0.2526
 NEI  C5    C  CR56  0   0.007  -0.6002  -2.2604   0.1300
 NEI  C4    C  CR56  0   0.497  -0.5051  -0.8840   0.0112
 NEI  N3    N  N     0  -0.426  -1.4603   0.0068   0.2937
 NEI  C2    C  CR6   0   0.089  -2.5437  -0.5945   0.7159
 NEI  I2    I  I     0   0.053  -4.1533   0.6980   1.2070
 NEI  N1    N  N     0  -0.445  -2.7953  -1.8747   0.8863
 NEI  C6    C  CR6   0   0.470  -1.8296  -2.7621   0.5976
 NEI  N6    N  NH2   0  -0.809  -2.0693  -4.0575   0.7659
 NEI  H521  H  HCH3  0   0.236   7.8959   0.4740   1.5536
 NEI  H522  H  HCH3  0   0.248   9.0636  -0.4270   0.5914
 NEI  H523  H  HCH3  0   0.237   8.4647   1.1235   0.0101
 NEI  H511  H  HCH2  0   0.239   7.3837  -0.7970  -1.1896
 NEI  H512  H  HCH2  0   0.239   6.8196  -1.4438   0.3416
 NEI  HN5'  H  HNH1  0   0.403   5.9382   1.2575   0.1119
 NEI  H4'   H  HCR5  0   0.279   3.9646   1.8973  -0.9701
 NEI  H3'   H  HCR5  0   0.264   3.0482   0.0436   1.2682
 NEI  HO3'  H  HOH1  0   0.474   3.7480   1.7391   2.4453
 NEI  H2'   H  HCR5  0   0.269   0.9300   1.2078   1.3395
 NEI  HO2'  H  HOH1  0   0.455   2.0973   3.3062   0.8112
 NEI  H1'   H  HCR5  0   0.294   0.5604   1.1916  -1.3808
 NEI  H8    H  HCR5  0   0.311   2.3574  -1.9742  -0.9545
 NEI  HN61  H  HNH2  0   0.418  -1.3751  -4.7472   0.5354
 NEI  HN62  H  HNH2  0   0.411  -2.9678  -4.3741   1.0882

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
 NEI  C52  C51   single    1.516  0.020  1.516
 NEI  C52  H521  single    0.970  0.020  1.090
 NEI  C52  H522  single    0.970  0.020  1.090
 NEI  C52  H523  single    0.970  0.020  1.090
 NEI  C51  N5'   single    1.452  0.020  1.452
 NEI  C51  H511  single    0.970  0.020  1.090
 NEI  C51  H512  single    0.970  0.020  1.090
 NEI  N5'  C5'   single    1.336  0.020  1.336
 NEI  N5'  HN5'  single    0.860  0.020  1.020
 NEI  C5'  O5'   double    1.222  0.020  1.222
 NEI  C5'  C4'   single    1.522  0.020  1.522
 NEI  C4'  O4'   single    1.411  0.020  1.411
 NEI  C4'  C3'   single    1.534  0.020  1.534
 NEI  C4'  H4'   single    0.970  0.020  1.090
 NEI  O4'  C1'   single    1.396  0.020  1.396
 NEI  C3'  O3'   single    1.397  0.020  1.397
 NEI  C3'  C2'   single    1.533  0.020  1.533
 NEI  C3'  H3'   single    0.970  0.020  1.090
 NEI  O3'  HO3'  single    0.850  0.020  0.980
 NEI  C2'  O2'   single    1.399  0.020  1.399
 NEI  C2'  C1'   single    1.527  0.020  1.527
 NEI  C2'  H2'   single    0.970  0.020  1.090
 NEI  O2'  HO2'  single    0.850  0.020  0.980
 NEI  C1'  N9    single    1.461  0.020  1.461
 NEI  C1'  H1'   single    0.970  0.020  1.090
 NEI  N9   C8    aromatic  1.370  0.020  1.370
 NEI  N9   C4    aromatic  1.360  0.020  1.360
 NEI  C8   N7    aromatic  1.302  0.020  1.302
 NEI  C8   H8    single    0.930  0.020  1.080
 NEI  N7   C5    aromatic  1.367  0.020  1.367
 NEI  C5   C4    aromatic  1.385  0.020  1.385
 NEI  C5   C6    aromatic  1.408  0.020  1.408
 NEI  C4   N3    aromatic  1.336  0.020  1.336
 NEI  N3   C2    aromatic  1.309  0.020  1.309
 NEI  C2   I2    single    2.122  0.020  2.122
 NEI  C2   N1    aromatic  1.316  0.020  1.316
 NEI  N1   C6    aromatic  1.343  0.020  1.343
 NEI  C6   N6    single    1.328  0.020  1.328
 NEI  N6   HN61  single    0.860  0.020  1.020
 NEI  N6   HN62  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
 NEI  H523  C52  H522  107.79  3.000
 NEI  H523  C52  H521  108.36  3.000
 NEI  H522  C52  H521  107.82  3.000
 NEI  H523  C52  C51   111.41  3.000
 NEI  H522  C52  C51   109.93  3.000
 NEI  H521  C52  C51   111.39  3.000
 NEI  H512  C51  H511  106.95  3.000
 NEI  H512  C51  N5'   109.51  3.000
 NEI  H511  C51  N5'   109.75  3.000
 NEI  H512  C51  C52   110.14  3.000
 NEI  H511  C51  C52   110.05  3.000
 NEI  N5'   C51  C52   110.37  3.000
 NEI  HN5'  N5'  C5'   118.92  3.000
 NEI  HN5'  N5'  C51   118.13  3.000
 NEI  C5'   N5'  C51   122.91  3.000
 NEI  C4'   C5'  O5'   122.74  3.000
 NEI  C4'   C5'  N5'   113.60  3.000
 NEI  O5'   C5'  N5'   123.63  3.000
 NEI  H4'   C4'  C3'   109.16  3.000
 NEI  H4'   C4'  O4'   109.78  3.000
 NEI  C3'   C4'  O4'   105.77  3.000
 NEI  H4'   C4'  C5'   109.34  3.000
 NEI  C3'   C4'  C5'   112.20  3.000
 NEI  O4'   C4'  C5'   110.52  3.000
 NEI  C1'   O4'  C4'   111.23  3.000
 NEI  H3'   C3'  C2'   109.28  3.000
 NEI  H3'   C3'  O3'   111.54  3.000
 NEI  C2'   C3'  O3'   114.00  3.000
 NEI  H3'   C3'  C4'   110.39  3.000
 NEI  C2'   C3'  C4'   101.09  3.000
 NEI  O3'   C3'  C4'   110.07  3.000
 NEI  HO3'  O3'  C3'   109.13  3.000
 NEI  H2'   C2'  C1'   112.28  3.000
 NEI  H2'   C2'  O2'   112.13  3.000
 NEI  C1'   C2'  O2'   107.22  3.000
 NEI  H2'   C2'  C3'   112.54  3.000
 NEI  C1'   C2'  C3'   101.01  3.000
 NEI  O2'   C2'  C3'   111.03  3.000
 NEI  HO2'  O2'  C2'   108.02  3.000
 NEI  H1'   C1'  N9    107.35  3.000
 NEI  H1'   C1'  C2'   111.71  3.000
 NEI  N9    C1'  C2'   111.60  3.000
 NEI  H1'   C1'  O4'   110.09  3.000
 NEI  N9    C1'  O4'   109.29  3.000
 NEI  C2'   C1'  O4'   106.81  3.000
 NEI  C4    N9   C8    106.19  3.000
 NEI  C4    N9   C1'   124.90  3.000
 NEI  C8    N9   C1'   128.88  3.000
 NEI  H8    C8   N7    125.18  3.000
 NEI  H8    C8   N9    121.71  3.000
 NEI  N7    C8   N9    113.11  3.000
 NEI  C5    N7   C8    104.56  3.000
 NEI  C6    C5   C4    116.28  3.000
 NEI  C6    C5   N7    133.05  3.000
 NEI  C4    C5   N7    110.67  3.000
 NEI  N3    C4   C5    126.54  3.000
 NEI  N3    C4   N9    127.99  3.000
 NEI  C5    C4   N9    105.47  3.000
 NEI  C2    N3   C4    110.70  3.000
 NEI  N1    C2   I2    114.68  3.000
 NEI  N1    C2   N3    130.32  3.000
 NEI  I2    C2   N3    115.00  3.000
 NEI  C6    N1   C2    118.53  3.000
 NEI  N6    C6   N1    119.18  3.000
 NEI  N6    C6   C5    123.18  3.000
 NEI  N1    C6   C5    117.64  3.000
 NEI  HN62  N6   HN61  118.33  3.000
 NEI  HN62  N6   C6    120.59  3.000
 NEI  HN61  N6   C6    121.03  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
 NEI  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 NEI  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 NEI  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 NEI  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 NEI  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 NEI  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 NEI  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 NEI  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 NEI  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 NEI  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 NEI  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 NEI  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 NEI  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 NEI  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 NEI  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 NEI  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 NEI  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 NEI  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 NEI  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 NEI  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 NEI  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 NEI  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 NEI  CONST_23  I2    C2   N3   C4    180.00   0.0  0
 NEI  CONST_24  N6    C6   N1   C2    180.00   0.0  0
 NEI  CONST_25  C6    N1   C2   I2    180.00   0.0  0
 NEI  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 NEI  CONST_27  HN61  N6   C6   C5      0.00   0.0  0
 NEI  CONST_28  HN62  N6   C6   C5    180.00   0.0  0
 NEI  CONST_29  C4'   C5'  N5'  C51   180.00   0.0  0
 NEI  CONST_30  HN5'  N5'  C5'  C4'     0.00   0.0  0
 NEI  CONST_31  O5'   C5'  N5'  C51     0.00   0.0  0
 NEI  Var_01    C5'   N5'  C51  C52  -175.12  30.0  3
 NEI  Var_02    H521  C52  C51  N5'    60.36  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
 NEI  chir_01  C4'  C5'  O4'  C3'  negativ
 NEI  chir_02  C3'  O3'  C4'  C2'  positiv
 NEI  chir_03  C2'  O2'  C3'  C1'  positiv
 NEI  chir_04  C1'  O4'  N9   C2'  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
 NEI  plan-1  C1'   0.020
 NEI  plan-1  N9    0.020
 NEI  plan-1  C8    0.020
 NEI  plan-1  N7    0.020
 NEI  plan-1  C5    0.020
 NEI  plan-1  C4    0.020
 NEI  plan-1  N3    0.020
 NEI  plan-1  C2    0.020
 NEI  plan-1  I2    0.020
 NEI  plan-1  N1    0.020
 NEI  plan-1  C6    0.020
 NEI  plan-1  N6    0.020
 NEI  plan-1  H8    0.020
 NEI  plan-2  C6    0.020
 NEI  plan-2  N6    0.020
 NEI  plan-2  HN61  0.020
 NEI  plan-2  HN62  0.020
 NEI  plan-3  C51   0.020
 NEI  plan-3  N5'   0.020
 NEI  plan-3  C5'   0.020
 NEI  plan-3  O5'   0.020
 NEI  plan-3  C4'   0.020
 NEI  plan-3  HN5'  0.020

