# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:44:28 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(6-amino-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)ncnc23
#
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
 NEC  NEC  '(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)'  ligand  38  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NEC
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
 NEC  C5'   C  C     0   0.537   0.6580   0.2696   2.9899
 NEC  O5'   O  O     0  -0.485   1.7550   0.1178   2.4711
 NEC  N5'   N  NH1   0  -0.628   0.4404   0.1784   4.3036
 NEC  C51   C  CH2   0  -0.262   1.4866  -0.1427   5.2569
 NEC  C52   C  CH3   0  -0.701   0.8993  -0.3591   6.6380
 NEC  C4'   C  CR15  0  -0.081  -0.5968   0.4919   2.1644
 NEC  O4'   O  O     0  -0.486  -0.2977   1.3049   1.0480
 NEC  C3'   C  CR15  0  -0.011  -1.1257  -0.8234   1.5657
 NEC  O3'   O  OH1   0  -0.657  -1.9642  -1.5404   2.4160
 NEC  C2'   C  CR15  0  -0.052  -1.8774  -0.2947   0.3459
 NEC  O2'   O  OH1   0  -0.660  -3.1036   0.2807   0.7017
 NEC  C1'   C  CR15  0   0.171  -0.9574   0.8429  -0.0973
 NEC  N9    N  NR5   0  -0.536   0.0273   0.4030  -1.0725
 NEC  C8    C  CR15  0   0.087   1.3247   0.0131  -0.8705
 NEC  N7    N  N     0  -0.453   1.9321  -0.3300  -1.9697
 NEC  C5    C  CR56  0  -0.003   0.9902  -0.1615  -2.9504
 NEC  C6    C  CR6   0   0.455   1.0080  -0.3523  -4.3445
 NEC  N6    N  NH2   0  -0.817   2.0834  -0.7933  -4.9991
 NEC  N1    N  N     0  -0.474  -0.1104  -0.0838  -5.0282
 NEC  C2    C  CR16  0   0.041  -1.1851   0.3476  -4.3733
 NEC  N3    N  N     0  -0.459  -1.3249   0.5629  -3.0764
 NEC  C4    C  CR56  0   0.486  -0.2024   0.2941  -2.4123
 NEC  HN5   H  HNH1  0   0.407  -0.4756   0.3997   4.6616
 NEC  H511  H  HCH2  0   0.240   2.2259   0.6616   5.2843
 NEC  H512  H  HCH2  0   0.241   2.0068  -1.0431   4.9260
 NEC  H521  H  HCH3  0   0.248   1.6937  -0.6018   7.3422
 NEC  H522  H  HCH3  0   0.236   0.3948   0.5366   7.0026
 NEC  H523  H  HCH3  0   0.236   0.1846  -1.1826   6.6425
 NEC  H4'   H  HCR5  0   0.267  -1.3827   0.9577   2.7710
 NEC  H3'   H  HCR5  0   0.255  -0.2795  -1.4303   1.2194
 NEC  HO3'  H  HOH1  0   0.470  -1.4477  -2.1865   2.9055
 NEC  H2'   H  HCR5  0   0.271  -1.9897  -1.0553  -0.4357
 NEC  HO2'  H  HOH1  0   0.461  -3.6434  -0.3913   1.1319
 NEC  H1'   H  HCR5  0   0.286  -1.5288   1.6494  -0.5649
 NEC  H8    H  HCR5  0   0.306   1.7656   0.0072   0.1151
 NEC  HN61  H  HNH2  0   0.403   2.0711  -0.8668  -6.0016
 NEC  HN62  H  HNH2  0   0.411   2.9508  -0.9581  -4.5197
 NEC  H2    H  HCR6  0   0.252  -2.0566   0.5466  -4.9881

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
 NEC  C5'  O5'   double    1.223  0.020  1.223
 NEC  C5'  N5'   single    1.335  0.020  1.335
 NEC  C5'  C4'   single    1.518  0.020  1.518
 NEC  N5'  C51   single    1.451  0.020  1.451
 NEC  N5'  HN5   single    0.860  0.020  1.020
 NEC  C51  C52   single    1.516  0.020  1.516
 NEC  C51  H511  single    0.970  0.020  1.090
 NEC  C51  H512  single    0.970  0.020  1.090
 NEC  C52  H521  single    0.970  0.020  1.090
 NEC  C52  H522  single    0.970  0.020  1.090
 NEC  C52  H523  single    0.970  0.020  1.090
 NEC  C4'  O4'   single    1.413  0.020  1.413
 NEC  C4'  C3'   single    1.539  0.020  1.539
 NEC  C4'  H4'   single    0.970  0.020  1.090
 NEC  O4'  C1'   single    1.400  0.020  1.400
 NEC  C3'  O3'   single    1.393  0.020  1.393
 NEC  C3'  C2'   single    1.527  0.020  1.527
 NEC  C3'  H3'   single    0.970  0.020  1.090
 NEC  O3'  HO3'  single    0.850  0.020  0.980
 NEC  C2'  O2'   single    1.400  0.020  1.400
 NEC  C2'  C1'   single    1.529  0.020  1.529
 NEC  C2'  H2'   single    0.970  0.020  1.090
 NEC  O2'  HO2'  single    0.850  0.020  0.980
 NEC  C1'  N9    single    1.454  0.020  1.454
 NEC  C1'  H1'   single    0.970  0.020  1.090
 NEC  N9   C8    aromatic  1.370  0.020  1.370
 NEC  N9   C4    aromatic  1.364  0.020  1.364
 NEC  C8   N7    aromatic  1.302  0.020  1.302
 NEC  C8   H8    single    0.930  0.020  1.080
 NEC  N7   C5    aromatic  1.370  0.020  1.370
 NEC  C5   C6    aromatic  1.407  0.020  1.407
 NEC  C5   C4    aromatic  1.385  0.020  1.385
 NEC  C6   N6    single    1.334  0.020  1.334
 NEC  C6   N1    aromatic  1.338  0.020  1.338
 NEC  N6   HN61  single    0.860  0.020  1.020
 NEC  N6   HN62  single    0.860  0.020  1.020
 NEC  N1   C2    aromatic  1.330  0.020  1.330
 NEC  C2   N3    aromatic  1.322  0.020  1.322
 NEC  C2   H2    single    0.930  0.020  1.080
 NEC  N3   C4    aromatic  1.332  0.020  1.332

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
 NEC  C4'   C5'  N5'   114.23  3.000
 NEC  C4'   C5'  O5'   121.92  3.000
 NEC  N5'   C5'  O5'   123.73  3.000
 NEC  HN5   N5'  C51   118.05  3.000
 NEC  HN5   N5'  C5'   118.86  3.000
 NEC  C51   N5'  C5'   122.96  3.000
 NEC  H512  C51  H511  107.00  3.000
 NEC  H512  C51  C52   110.06  3.000
 NEC  H511  C51  C52   110.13  3.000
 NEC  H512  C51  N5'   109.09  3.000
 NEC  H511  C51  N5'   109.96  3.000
 NEC  C52   C51  N5'   110.53  3.000
 NEC  H523  C52  H522  108.40  3.000
 NEC  H523  C52  H521  107.89  3.000
 NEC  H522  C52  H521  107.71  3.000
 NEC  H523  C52  C51   111.43  3.000
 NEC  H522  C52  C51   111.49  3.000
 NEC  H521  C52  C51   109.78  3.000
 NEC  H4'   C4'  C3'   109.38  3.000
 NEC  H4'   C4'  O4'   110.14  3.000
 NEC  C3'   C4'  O4'   104.90  3.000
 NEC  H4'   C4'  C5'   110.71  3.000
 NEC  C3'   C4'  C5'   111.74  3.000
 NEC  O4'   C4'  C5'   109.81  3.000
 NEC  C1'   O4'  C4'   110.90  3.000
 NEC  H3'   C3'  C2'   108.60  3.000
 NEC  H3'   C3'  O3'   111.85  3.000
 NEC  C2'   C3'  O3'   111.68  3.000
 NEC  H3'   C3'  C4'   109.29  3.000
 NEC  C2'   C3'  C4'   100.60  3.000
 NEC  O3'   C3'  C4'   114.17  3.000
 NEC  HO3'  O3'  C3'   109.48  3.000
 NEC  H2'   C2'  C1'   111.79  3.000
 NEC  H2'   C2'  O2'   112.12  3.000
 NEC  C1'   C2'  O2'   107.15  3.000
 NEC  H2'   C2'  C3'   112.31  3.000
 NEC  C1'   C2'  C3'   101.12  3.000
 NEC  O2'   C2'  C3'   111.73  3.000
 NEC  HO2'  O2'  C2'   108.51  3.000
 NEC  H1'   C1'  N9    106.87  3.000
 NEC  H1'   C1'  C2'   111.00  3.000
 NEC  N9    C1'  C2'   112.13  3.000
 NEC  H1'   C1'  O4'   110.65  3.000
 NEC  N9    C1'  O4'   109.23  3.000
 NEC  C2'   C1'  O4'   106.98  3.000
 NEC  C4    N9   C8    106.36  3.000
 NEC  C4    N9   C1'   124.68  3.000
 NEC  C8    N9   C1'   128.95  3.000
 NEC  H8    C8   N7    125.36  3.000
 NEC  H8    C8   N9    121.53  3.000
 NEC  N7    C8   N9    113.11  3.000
 NEC  C5    N7   C8    104.55  3.000
 NEC  C4    C5   C6    116.12  3.000
 NEC  C4    C5   N7    110.75  3.000
 NEC  C6    C5   N7    133.14  3.000
 NEC  N1    C6   N6    119.30  3.000
 NEC  N1    C6   C5    117.93  3.000
 NEC  N6    C6   C5    122.76  3.000
 NEC  HN62  N6   HN61  118.32  3.000
 NEC  HN62  N6   C6    121.07  3.000
 NEC  HN61  N6   C6    120.24  3.000
 NEC  C2    N1   C6    119.26  3.000
 NEC  H2    C2   N3    116.18  3.000
 NEC  H2    C2   N1    115.42  3.000
 NEC  N3    C2   N1    128.40  3.000
 NEC  C4    N3   C2    111.54  3.000
 NEC  N3    C4   C5    126.75  3.000
 NEC  N3    C4   N9    128.01  3.000
 NEC  C5    C4   N9    105.24  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
 NEC  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 NEC  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 NEC  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 NEC  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 NEC  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 NEC  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 NEC  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 NEC  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 NEC  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 NEC  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 NEC  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 NEC  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 NEC  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 NEC  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 NEC  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 NEC  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 NEC  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 NEC  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 NEC  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 NEC  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 NEC  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 NEC  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 NEC  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 NEC  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 NEC  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 NEC  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 NEC  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 NEC  CONST_28  C4'   C5'  N5'  C51   180.00   0.0  0
 NEC  CONST_29  HN5   N5'  C5'  C4'     0.00   0.0  0
 NEC  CONST_30  C51   N5'  C5'  O5'     0.00   0.0  0
 NEC  Var_01    C52   C51  N5'  C5'  -172.26  30.0  3
 NEC  Var_02    H521  C52  C51  N5'   179.84  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
 NEC  chir_01  C4'  C5'  O4'  C3'  negativ
 NEC  chir_02  C3'  O3'  C4'  C2'  positiv
 NEC  chir_03  C2'  O2'  C3'  C1'  positiv
 NEC  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
 NEC  plan-1  C1'   0.020
 NEC  plan-1  N9    0.020
 NEC  plan-1  C8    0.020
 NEC  plan-1  N7    0.020
 NEC  plan-1  C5    0.020
 NEC  plan-1  C6    0.020
 NEC  plan-1  N6    0.020
 NEC  plan-1  N1    0.020
 NEC  plan-1  C2    0.020
 NEC  plan-1  N3    0.020
 NEC  plan-1  C4    0.020
 NEC  plan-1  H8    0.020
 NEC  plan-1  H2    0.020
 NEC  plan-2  C6    0.020
 NEC  plan-2  N6    0.020
 NEC  plan-2  HN61  0.020
 NEC  plan-2  HN62  0.020
 NEC  plan-3  C5'   0.020
 NEC  plan-3  O5'   0.020
 NEC  plan-3  N5'   0.020
 NEC  plan-3  C51   0.020
 NEC  plan-3  C4'   0.020
 NEC  plan-3  HN5   0.020

