# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 13:29:04 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2c(c[nH]c2C(=O)N1)[C@@H]3N[C@H](CO)C[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
 5NT  5NT  2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one  ligand  34  19  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5NT
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
 5NT  O2   O  O     0  -0.490   3.7319  -2.3360  -0.5460
 5NT  C10  C  CR6   0   0.510   3.0710  -1.3370  -0.2930
 5NT  N4   N  NR16  0  -0.717   3.6531  -0.0736  -0.2620
 5NT  C    C  CR6   0   0.628   2.9968   1.0985   0.0129
 5NT  N    N  NH2   0  -0.841   3.7669   2.2148   0.0464
 5NT  C9   C  CR56  0   0.133   1.6868  -1.2498   0.0055
 5NT  C1   C  CR56  0   0.160   1.0721  -0.0319   0.2788
 5NT  N1   N  N     0  -0.509   1.7283   1.1629   0.2790
 5NT  N3   N  NR15  0  -0.658   0.7443  -2.2324   0.0973
 5NT  C8   C  CR15  0  -0.048  -0.4405  -1.6655   0.4220
 5NT  C2   C  CR5   0  -0.017  -0.2969  -0.2991   0.5392
 5NT  C3   C  CH1   0  -0.224  -1.3624   0.6918   0.9013
 5NT  C7   C  CH1   0   0.035  -1.5918   1.7074  -0.2251
 5NT  O1   O  OH1   0  -0.678  -2.1818   2.8528   0.3573
 5NT  C6   C  CH2   0  -0.515  -2.5731   0.9520  -1.1077
 5NT  C4   C  CH1   0  -0.091  -3.4884   0.2514  -0.0980
 5NT  N2   N  NH1   0  -0.601  -2.6548   0.0339   1.0924
 5NT  C5   C  CH2   0  -0.130  -4.0552  -1.0375  -0.6529
 5NT  O    O  OH1   0  -0.676  -4.9457  -1.5952   0.2873
 5NT  H1   H  HNR6  0   0.420   4.6492  -0.0415  -0.4356
 5NT  H2   H  HNH2  0   0.402   4.6155   2.2352  -0.4957
 5NT  H3   H  HNH2  0   0.399   3.2609   3.0852   0.0493
 5NT  H4   H  HNR5  0   0.412   0.9034  -3.2171  -0.0348
 5NT  H5   H  HCR5  0   0.281  -1.3235  -2.2665   0.5608
 5NT  H6   H  HCH1  0   0.249  -1.0638   1.2115   1.8179
 5NT  H7   H  HCH1  0   0.229  -0.6647   1.9668  -0.7489
 5NT  H8   H  HOH1  0   0.447  -2.5093   3.4150  -0.3514
 5NT  H9   H  HCH2  0   0.254  -3.1202   1.5981  -1.7970
 5NT  H10  H  HCH2  0   0.234  -2.0310   0.2199  -1.7145
 5NT  H11  H  HCH1  0   0.224  -4.3282   0.9120   0.1469
 5NT  H12  H  HNH1  0   0.355  -3.1135   0.4004   1.9123
 5NT  H14  H  HCH2  0   0.188  -4.5610  -0.8201  -1.6042
 5NT  H15  H  HCH2  0   0.182  -3.2251  -1.7202  -0.8795
 5NT  H16  H  HOH1  0   0.451  -5.2785  -2.4233  -0.0695

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
 5NT  O    C5   single    1.410  0.020  1.410
 5NT  C5   C4   single    1.513  0.020  1.513
 5NT  C4   C6   single    1.532  0.020  1.532
 5NT  C4   N2   single    1.469  0.020  1.469
 5NT  C6   C7   single    1.521  0.020  1.521
 5NT  N2   C3   single    1.463  0.020  1.463
 5NT  C7   O1   single    1.414  0.020  1.414
 5NT  C7   C3   single    1.534  0.020  1.534
 5NT  C3   C2   single    1.499  0.020  1.499
 5NT  C8   C2   aromatic  1.379  0.020  1.379
 5NT  C8   N3   aromatic  1.353  0.020  1.353
 5NT  C2   C1   aromatic  1.419  0.020  1.419
 5NT  N3   C9   aromatic  1.365  0.020  1.365
 5NT  C1   C9   aromatic  1.391  0.020  1.391
 5NT  C1   N1   single    1.363  0.020  1.363
 5NT  C9   C10  single    1.419  0.020  1.419
 5NT  N1   C    double    1.298  0.020  1.298
 5NT  C10  O2   double    1.224  0.020  1.224
 5NT  C10  N4   single    1.391  0.020  1.391
 5NT  C    N4   single    1.371  0.020  1.371
 5NT  C    N    single    1.357  0.020  1.357
 5NT  N4   H1   single    0.860  0.020  1.020
 5NT  N    H2   single    0.890  0.020  1.040
 5NT  N    H3   single    0.890  0.020  1.040
 5NT  N3   H4   single    0.860  0.020  1.020
 5NT  C8   H5   single    0.930  0.020  1.080
 5NT  C3   H6   single    0.970  0.020  1.090
 5NT  C7   H7   single    0.970  0.020  1.090
 5NT  O1   H8   single    0.850  0.020  0.980
 5NT  C6   H9   single    0.970  0.020  1.090
 5NT  C6   H10  single    0.970  0.020  1.090
 5NT  C4   H11  single    0.970  0.020  1.090
 5NT  N2   H12  single    0.890  0.020  1.040
 5NT  C5   H14  single    0.970  0.020  1.090
 5NT  C5   H15  single    0.970  0.020  1.090
 5NT  O    H16  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
 5NT  C9   C10  N4   110.35  3.000
 5NT  N4   C10  O2   121.31  3.000
 5NT  C9   C10  O2   128.34  3.000
 5NT  H1   N4   C    118.59  3.000
 5NT  H1   N4   C10  115.91  3.000
 5NT  C    N4   C10  125.48  3.000
 5NT  N1   C    N    120.60  3.000
 5NT  N    C    N4   115.89  3.000
 5NT  N1   C    N4   123.46  3.000
 5NT  H3   N    H2   114.04  3.000
 5NT  H3   N    C    115.22  3.000
 5NT  H2   N    C    118.80  3.000
 5NT  N3   C9   C1   108.18  3.000
 5NT  C1   C9   C10  121.75  3.000
 5NT  N3   C9   C10  130.07  3.000
 5NT  C2   C1   N1   129.01  3.000
 5NT  N1   C1   C9   123.68  3.000
 5NT  C2   C1   C9   107.31  3.000
 5NT  C1   N1   C    115.28  3.000
 5NT  H4   N3   C8   125.45  3.000
 5NT  H4   N3   C9   125.92  3.000
 5NT  C8   N3   C9   108.62  3.000
 5NT  H5   C8   C2   128.86  3.000
 5NT  H5   C8   N3   121.00  3.000
 5NT  C2   C8   N3   110.14  3.000
 5NT  C3   C2   C8   126.97  3.000
 5NT  C8   C2   C1   105.75  3.000
 5NT  C3   C2   C1   127.27  3.000
 5NT  H6   C3   N2   110.18  3.000
 5NT  H6   C3   C7   109.95  3.000
 5NT  N2   C3   C7   105.16  3.000
 5NT  H6   C3   C2   108.78  3.000
 5NT  C7   C3   C2   111.50  3.000
 5NT  N2   C3   C2   111.24  3.000
 5NT  H7   C7   C6   112.71  3.000
 5NT  H7   C7   O1   110.98  3.000
 5NT  C6   C7   O1   111.85  3.000
 5NT  H7   C7   C3   112.41  3.000
 5NT  O1   C7   C3   107.24  3.000
 5NT  C6   C7   C3   101.18  3.000
 5NT  H8   O1   C7   108.18  3.000
 5NT  H10  C6   H9   107.10  3.000
 5NT  H10  C6   C4   110.81  3.000
 5NT  H9   C6   C4   112.78  3.000
 5NT  H10  C6   C7   109.54  3.000
 5NT  H9   C6   C7   113.32  3.000
 5NT  C4   C6   C7   103.30  3.000
 5NT  H11  C4   C5   107.95  3.000
 5NT  H11  C4   N2   110.05  3.000
 5NT  C5   C4   N2   112.55  3.000
 5NT  H11  C4   C6   109.22  3.000
 5NT  N2   C4   C6   105.22  3.000
 5NT  C5   C4   C6   111.80  3.000
 5NT  H12  N2   C4   110.29  3.000
 5NT  H12  N2   C3   110.17  3.000
 5NT  C4   N2   C3   109.20  3.000
 5NT  H15  C5   H14  106.99  3.000
 5NT  H15  C5   O    111.66  3.000
 5NT  H14  C5   O    111.39  3.000
 5NT  H15  C5   C4   108.78  3.000
 5NT  H14  C5   C4   108.74  3.000
 5NT  O    C5   C4   109.20  3.000
 5NT  H16  O    C5   108.17  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
 5NT  CONST_01  C2  C8   N3   C9     0.00  0.0  0
 5NT  CONST_02  C8  C2   C1   C9     0.00  0.0  0
 5NT  CONST_03  N3  C8   C2   C1     0.00  0.0  0
 5NT  CONST_04  C8  N3   C9   C1     0.00  0.0  0
 5NT  CONST_05  C2  C1   C9   N3     0.00  0.0  0
 5NT  CONST_06  C3  C2   C1   C9   180.00  0.0  0
 5NT  CONST_07  C3  C2   C1   N1     0.00  0.0  0
 5NT  CONST_08  C3  C2   C8   N3   180.00  0.0  0
 5NT  CONST_09  N1  C    N4   C10    0.00  0.0  0
 5NT  CONST_10  C1  N1   C    N4     0.00  0.0  0
 5NT  CONST_11  C9  C10  N4   C      0.00  0.0  0
 5NT  CONST_12  C   N4   C10  O2   180.00  0.0  0
 5NT  CONST_13  N   C    N4   C10  180.00  0.0  0
 5NT  CONST_14  C1  N1   C    N    180.00  0.0  0
 5NT  CONST_15  H4  N3   C9   C10    0.00  0.0  0
 5NT  CONST_16  H5  C8   N3   C9   180.00  0.0  0
 5NT  CONST_17  H1  N4   C10  C9   180.00  0.0  0
 5NT  CONST_19  H3  N    C    N4   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
 5NT  chir_01  C3  N2  C7  C2  positiv
 5NT  chir_02  C7  O1  C3  C6  negativ
 5NT  chir_03  C4  N2  C5  C6  positiv

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
 5NT  plan-1  O2   0.020
 5NT  plan-1  C10  0.020
 5NT  plan-1  N4   0.020
 5NT  plan-1  C    0.020
 5NT  plan-1  N    0.020
 5NT  plan-1  C9   0.020
 5NT  plan-1  C1   0.020
 5NT  plan-1  N1   0.020
 5NT  plan-1  N3   0.020
 5NT  plan-1  C8   0.020
 5NT  plan-1  C2   0.020
 5NT  plan-1  C3   0.020
 5NT  plan-1  H1   0.020
 5NT  plan-1  H2   0.020
 5NT  plan-1  H3   0.020
 5NT  plan-1  H4   0.020
 5NT  plan-1  H5   0.020

