# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:33:23 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-amino-7-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-3,5-dihydro-4H-pyrrolo[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@@H](O)[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
 IMG  IMG  2-amino-7-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  35  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IMG
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
 IMG  O5'   O  OH1   0  -0.674  -1.5294  -1.4120   4.8502
 IMG  C5'   C  CH2   0  -0.141  -0.8872  -0.1790   4.6093
 IMG  C4'   C  CH1   0  -0.118   0.0045  -0.3249   3.3987
 IMG  N4'   N  NH1   0  -0.622  -0.7491  -0.5579   2.1848
 IMG  C3'   C  CH1   0   0.015   0.7325   0.9602   3.0304
 IMG  O3'   O  OH1   0  -0.666   1.8387   1.1854   3.8699
 IMG  C2'   C  CH1   0   0.013   1.1364   0.7369   1.5507
 IMG  O2'   O  OH1   0  -0.681   2.4690   0.3052   1.4506
 IMG  C1'   C  CH1   0  -0.135   0.1641  -0.3691   1.0629
 IMG  C9    C  CR5   0  -0.047  -0.5837  -0.0293  -0.1819
 IMG  C8    C  CR15  0  -0.053  -1.8455   0.5236  -0.2630
 IMG  N7    N  NR15  0  -0.656  -2.1802   0.7229  -1.5583
 IMG  C5    C  CR56  0   0.127  -1.1467   0.3058  -2.3456
 IMG  C6    C  CR6   0   0.511  -1.0196   0.3024  -3.7584
 IMG  O6    O  O     0  -0.490  -1.8272   0.6867  -4.5944
 IMG  N1    N  NR16  0  -0.716   0.2125  -0.2252  -4.1310
 IMG  C2    C  CR6   0   0.630   1.1785  -0.6780  -3.2690
 IMG  N3    N  N     0  -0.500   1.0500  -0.6642  -1.9782
 IMG  C4    C  CR56  0   0.153  -0.1343  -0.1707  -1.5182
 IMG  HO'5  H  HOH1  0   0.456  -2.1007  -1.3106   5.6165
 IMG  H5'1  H  HCH2  0   0.197  -0.2765   0.1320   5.4663
 IMG  H5'2  H  HCH2  0   0.187  -1.6120   0.6228   4.4137
 IMG  H4'   H  HCH1  0   0.212   0.7564  -1.1092   3.5963
 IMG  HN'4  H  HNH1  0   0.353  -1.1850  -1.4698   2.1619
 IMG  H3'   H  HCH1  0   0.232   0.0226   1.7929   3.0840
 IMG  HO'3  H  HOH1  0   0.466   2.0044   2.1318   3.9197
 IMG  H2'   H  HCH1  0   0.213   0.9911   1.6559   0.9699
 IMG  HO'2  H  HOH1  0   0.440   2.9093   0.5755   2.2681
 IMG  H1'   H  HCH1  0   0.222   0.7834  -1.2586   0.8766
 IMG  H8    H  HCR5  0   0.280  -2.5271   0.7794   0.5315
 IMG  H7    H  HNR5  0   0.413  -3.0504   1.1095  -1.8834
 IMG  H1    H  HNR6  0   0.420   0.3831  -0.2869  -5.1260
 IMG  H21   H  HNH2  0   0.399   3.0674  -1.3466  -3.2266
 IMG  H22   H  HNH2  0   0.401   2.5501  -0.8876  -4.7676
 IMG  N2    N  NH2   0  -0.841   2.2882  -1.2035  -3.8478

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
 IMG  O5'  C5'   single    1.411  0.020  1.411
 IMG  O5'  HO'5  single    0.850  0.020  0.980
 IMG  C5'  C4'   single    1.511  0.020  1.511
 IMG  C5'  H5'1  single    0.970  0.020  1.090
 IMG  C5'  H5'2  single    0.970  0.020  1.090
 IMG  C4'  N4'   single    1.448  0.020  1.448
 IMG  C4'  C3'   single    1.522  0.020  1.522
 IMG  C4'  H4'   single    0.970  0.020  1.090
 IMG  N4'  C1'   single    1.459  0.020  1.459
 IMG  N4'  HN'4  single    0.890  0.020  1.040
 IMG  C3'  O3'   single    1.407  0.020  1.407
 IMG  C3'  C2'   single    1.550  0.020  1.550
 IMG  C3'  H3'   single    0.970  0.020  1.090
 IMG  O3'  HO'3  single    0.850  0.020  0.980
 IMG  C2'  O2'   single    1.404  0.020  1.404
 IMG  C2'  C1'   single    1.551  0.020  1.551
 IMG  C2'  H2'   single    0.970  0.020  1.090
 IMG  O2'  HO'2  single    0.850  0.020  0.980
 IMG  C1'  C9    single    1.491  0.020  1.491
 IMG  C1'  H1'   single    0.970  0.020  1.090
 IMG  C9   C8    aromatic  1.380  0.020  1.380
 IMG  C9   C4    aromatic  1.417  0.020  1.417
 IMG  C8   N7    aromatic  1.353  0.020  1.353
 IMG  C8   H8    single    0.930  0.020  1.080
 IMG  N7   C5    aromatic  1.365  0.020  1.365
 IMG  N7   H7    single    0.860  0.020  1.020
 IMG  C5   C6    single    1.418  0.020  1.418
 IMG  C5   C4    aromatic  1.392  0.020  1.392
 IMG  C6   O6    double    1.224  0.020  1.224
 IMG  C6   N1    single    1.391  0.020  1.391
 IMG  N1   C2    single    1.372  0.020  1.372
 IMG  N1   H1    single    0.860  0.020  1.020
 IMG  N2   C2    single    1.357  0.020  1.357
 IMG  N2   H21   single    0.890  0.020  1.040
 IMG  N2   H22   single    0.890  0.020  1.040
 IMG  C2   N3    double    1.297  0.020  1.297
 IMG  N3   C4    single    1.363  0.020  1.363

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
 IMG  HO'5  O5'  C5'   108.32  3.000
 IMG  H5'2  C5'  H5'1  107.42  3.000
 IMG  H5'2  C5'  C4'   108.50  3.000
 IMG  H5'1  C5'  C4'   108.95  3.000
 IMG  H5'2  C5'  O5'   111.59  3.000
 IMG  H5'1  C5'  O5'   111.57  3.000
 IMG  C4'   C5'  O5'   108.73  3.000
 IMG  H4'   C4'  C3'   108.50  3.000
 IMG  H4'   C4'  N4'   112.96  3.000
 IMG  C3'   C4'  N4'   100.48  3.000
 IMG  H4'   C4'  C5'   109.09  3.000
 IMG  C3'   C4'  C5'   113.24  3.000
 IMG  N4'   C4'  C5'   112.35  3.000
 IMG  HN'4  N4'  C1'   111.67  3.000
 IMG  HN'4  N4'  C4'   112.87  3.000
 IMG  C1'   N4'  C4'   107.35  3.000
 IMG  H3'   C3'  C2'   108.97  3.000
 IMG  H3'   C3'  O3'   111.02  3.000
 IMG  C2'   C3'  O3'   112.82  3.000
 IMG  H3'   C3'  C4'   108.66  3.000
 IMG  C2'   C3'  C4'   103.53  3.000
 IMG  O3'   C3'  C4'   111.52  3.000
 IMG  HO'3  O3'  C3'   108.89  3.000
 IMG  H2'   C2'  C1'   110.35  3.000
 IMG  H2'   C2'  O2'   110.22  3.000
 IMG  C1'   C2'  O2'   110.68  3.000
 IMG  H2'   C2'  C3'   110.50  3.000
 IMG  C1'   C2'  C3'   103.86  3.000
 IMG  O2'   C2'  C3'   111.08  3.000
 IMG  HO'2  O2'  C2'   106.61  3.000
 IMG  H1'   C1'  C9    108.98  3.000
 IMG  H1'   C1'  C2'   106.08  3.000
 IMG  C9    C1'  C2'   114.47  3.000
 IMG  H1'   C1'  N4'   112.22  3.000
 IMG  C9    C1'  N4'   110.95  3.000
 IMG  C2'   C1'  N4'   104.05  3.000
 IMG  C4    C9   C8    105.94  3.000
 IMG  C4    C9   C1'   127.26  3.000
 IMG  C8    C9   C1'   126.79  3.000
 IMG  H8    C8   N7    120.97  3.000
 IMG  H8    C8   C9    129.06  3.000
 IMG  N7    C8   C9    109.97  3.000
 IMG  H7    N7   C5    125.88  3.000
 IMG  H7    N7   C8    125.45  3.000
 IMG  C5    N7   C8    108.67  3.000
 IMG  C4    C5   C6    121.75  3.000
 IMG  C4    C5   N7    108.21  3.000
 IMG  C6    C5   N7    130.04  3.000
 IMG  N1    C6   O6    121.36  3.000
 IMG  N1    C6   C5    110.31  3.000
 IMG  O6    C6   C5    128.33  3.000
 IMG  H1    N1   C2    118.64  3.000
 IMG  H1    N1   C6    115.85  3.000
 IMG  C2    N1   C6    125.49  3.000
 IMG  N3    C2   N2    120.62  3.000
 IMG  N3    C2   N1    123.51  3.000
 IMG  N2    C2   N1    115.82  3.000
 IMG  C4    N3   C2    115.20  3.000
 IMG  N3    C4   C5    123.74  3.000
 IMG  N3    C4   C9    129.06  3.000
 IMG  C5    C4   C9    107.21  3.000
 IMG  H22   N2   H21   114.01  3.000
 IMG  H22   N2   C2    118.72  3.000
 IMG  H21   N2   C2    115.12  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
 IMG  CONST_01  C5   N7  C8  C9     0.00  0.0  0
 IMG  CONST_02  N7   C5  C4  C9     0.00  0.0  0
 IMG  CONST_03  C5   C4  C9  C8     0.00  0.0  0
 IMG  CONST_04  C4   C5  N7  C8     0.00  0.0  0
 IMG  CONST_05  C4   C9  C8  N7     0.00  0.0  0
 IMG  CONST_06  N7   C8  C9  C1'  180.00  0.0  0
 IMG  CONST_07  C5   C4  C9  C1'  180.00  0.0  0
 IMG  CONST_08  N3   C4  C9  C1'    0.00  0.0  0
 IMG  CONST_09  C2   N1  C6  C5     0.00  0.0  0
 IMG  CONST_10  N3   C2  N1  C6     0.00  0.0  0
 IMG  CONST_11  C4   N3  C2  N1     0.00  0.0  0
 IMG  CONST_12  N2   C2  N1  C6   180.00  0.0  0
 IMG  CONST_13  C2   N1  C6  O6   180.00  0.0  0
 IMG  CONST_14  C4   N3  C2  N2   180.00  0.0  0
 IMG  CONST_15  H8   C8  C9  C1'    0.00  0.0  0
 IMG  CONST_16  H7   N7  C8  C9   180.00  0.0  0
 IMG  CONST_17  H1   N1  C6  C5   180.00  0.0  0
 IMG  CONST_18  H21  N2  C2  N1   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
 IMG  chir_01  C4'  C5'  N4'  C3'  negativ
 IMG  chir_02  C3'  O3'  C4'  C2'  positiv
 IMG  chir_03  C2'  O2'  C3'  C1'  positiv
 IMG  chir_04  C1'  N4'  C2'  C9   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
 IMG  plan-1  C1'  0.020
 IMG  plan-1  C9   0.020
 IMG  plan-1  C8   0.020
 IMG  plan-1  N7   0.020
 IMG  plan-1  C5   0.020
 IMG  plan-1  C6   0.020
 IMG  plan-1  O6   0.020
 IMG  plan-1  N1   0.020
 IMG  plan-1  C2   0.020
 IMG  plan-1  N3   0.020
 IMG  plan-1  C4   0.020
 IMG  plan-1  H8   0.020
 IMG  plan-1  H7   0.020
 IMG  plan-1  H1   0.020
 IMG  plan-1  H21  0.020
 IMG  plan-1  H22  0.020
 IMG  plan-1  N2   0.020

