# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:43:00 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S,3S,4R,5R)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-(hydroxymethyl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c1[nH]cc2[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
 UA2  UA2  (2S,3S,4R,5R)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-(hydroxymethyl)pyrrolidine-3,4-diol  ligand  34  19  .  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_UA2
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
 UA2  C2    C  CR16  0   0.004  -3.3749  -1.5624   0.4110
 UA2  C4    C  CR56  0   0.156  -1.6102  -0.2000   0.3283
 UA2  C5    C  CR56  0   0.214  -2.3997   0.7842  -0.2774
 UA2  C6    C  CR6   0   0.454  -3.7508   0.4995  -0.5290
 UA2  O5'   O  OH1   0  -0.675   4.3958   2.1108   0.4494
 UA2  C5'   C  CH2   0  -0.130   3.6940   1.3292  -0.4911
 UA2  C4'   C  CH1   0  -0.101   3.0770   0.1442   0.2199
 UA2  N4'   N  NH1   0  -0.609   2.0386   0.5435   1.1648
 UA2  C3'   C  CH1   0  -0.011   2.3574  -0.7989  -0.7430
 UA2  O3'   O  OH1   0  -0.665   3.2748  -1.6551  -1.3768
 UA2  C2'   C  CH1   0   0.011   1.3628  -1.5161   0.1721
 UA2  O2'   O  OH1   0  -0.678   2.0235  -2.4707   0.9681
 UA2  C1'   C  CH1   0  -0.217   0.8916  -0.3627   1.0612
 UA2  C9    C  CR5   0  -0.021  -0.2973   0.3315   0.4683
 UA2  N3    N  N     0  -0.452  -2.1017  -1.4051   0.6848
 UA2  N1    N  N     0  -0.471  -4.2119  -0.6948  -0.1687
 UA2  C8    C  CR15  0  -0.054  -0.3544   1.6015  -0.0466
 UA2  N7    N  NR15  0  -0.678  -1.6094   1.8750  -0.4975
 UA2  N6    N  NH2   0  -0.826  -4.6057   1.3865  -1.0785
 UA2  H2    H  HCR6  0   0.237  -3.8162  -2.5166   0.6823
 UA2  HO5'  H  HOH1  0   0.453   4.7886   2.8560  -0.0131
 UA2  H5'1  H  HCH2  0   0.182   2.8925   1.9028  -0.9765
 UA2  H5'2  H  HCH2  0   0.191   4.3585   0.9634  -1.2852
 UA2  H4'   H  HCH1  0   0.223   3.8804  -0.4190   0.7149
 UA2  HN4'  H  HNH1  0   0.359   2.3925   0.5799   2.1079
 UA2  H3'   H  HCH1  0   0.223   1.7942  -0.2115  -1.4813
 UA2  HO3'  H  HOH1  0   0.461   2.8498  -2.0398  -2.1497
 UA2  H2'   H  HCH1  0   0.232   0.5361  -1.9720  -0.3873
 UA2  HO2'  H  HOH1  0   0.441   2.6528  -2.9332   0.4018
 UA2  H1'   H  HCH1  0   0.254   0.6113  -0.7540   2.0447
 UA2  H8    H  HCR5  0   0.285   0.4275   2.3395  -0.1161
 UA2  HN7   H  HNR5  0   0.414  -1.8881   2.7503  -0.9074
 UA2  HN61  H  HNH2  0   0.400  -4.2541   2.1796  -1.5864
 UA2  HN62  H  HNH2  0   0.396  -5.4994   1.0397  -1.3861

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
 UA2  C2   N1    aromatic  1.338  0.020  1.338
 UA2  C2   N3    aromatic  1.312  0.020  1.312
 UA2  C2   H2    single    0.930  0.020  1.080
 UA2  C4   N3    aromatic  1.349  0.020  1.349
 UA2  C4   C5    aromatic  1.400  0.020  1.400
 UA2  C4   C9    aromatic  1.423  0.020  1.423
 UA2  C5   C6    aromatic  1.404  0.020  1.404
 UA2  C5   N7    aromatic  1.365  0.020  1.365
 UA2  C6   N1    aromatic  1.330  0.020  1.330
 UA2  C6   N6    single    1.349  0.020  1.349
 UA2  O5'  C5'   single    1.410  0.020  1.410
 UA2  O5'  HO5'  single    0.850  0.020  0.980
 UA2  C5'  C4'   single    1.513  0.020  1.513
 UA2  C5'  H5'1  single    0.970  0.020  1.090
 UA2  C5'  H5'2  single    0.970  0.020  1.090
 UA2  C4'  C3'   single    1.528  0.020  1.528
 UA2  C4'  N4'   single    1.460  0.020  1.460
 UA2  C4'  H4'   single    0.970  0.020  1.090
 UA2  N4'  C1'   single    1.465  0.020  1.465
 UA2  N4'  HN4'  single    0.890  0.020  1.040
 UA2  C3'  O3'   single    1.406  0.020  1.406
 UA2  C3'  C2'   single    1.530  0.020  1.530
 UA2  C3'  H3'   single    0.970  0.020  1.090
 UA2  O3'  HO3'  single    0.850  0.020  0.980
 UA2  C2'  O2'   single    1.408  0.020  1.408
 UA2  C2'  C1'   single    1.531  0.020  1.531
 UA2  C2'  H2'   single    0.970  0.020  1.090
 UA2  O2'  HO2'  single    0.850  0.020  0.980
 UA2  C1'  C9    single    1.499  0.020  1.499
 UA2  C1'  H1'   single    0.970  0.020  1.090
 UA2  C9   C8    aromatic  1.372  0.020  1.372
 UA2  C8   N7    aromatic  1.361  0.020  1.361
 UA2  C8   H8    single    0.930  0.020  1.080
 UA2  N7   HN7   single    0.860  0.020  1.020
 UA2  N6   HN61  single    0.890  0.020  1.040
 UA2  N6   HN62  single    0.890  0.020  1.040

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
 UA2  H2    C2   N1    115.09  3.000
 UA2  H2    C2   N3    116.59  3.000
 UA2  N1    C2   N3    128.31  3.000
 UA2  N3    C4   C9    130.05  3.000
 UA2  C9    C4   C5    107.47  3.000
 UA2  N3    C4   C5    122.48  3.000
 UA2  N7    C5   C6    133.68  3.000
 UA2  N7    C5   C4    107.77  3.000
 UA2  C6    C5   C4    118.55  3.000
 UA2  N6    C6   N1    118.76  3.000
 UA2  N6    C6   C5    123.35  3.000
 UA2  N1    C6   C5    117.86  3.000
 UA2  HO5'  O5'  C5'   108.20  3.000
 UA2  H5'2  C5'  H5'1  107.21  3.000
 UA2  H5'2  C5'  C4'   109.00  3.000
 UA2  H5'1  C5'  C4'   108.60  3.000
 UA2  H5'2  C5'  O5'   111.46  3.000
 UA2  H5'1  C5'  O5'   111.62  3.000
 UA2  C4'   C5'  O5'   108.88  3.000
 UA2  H4'   C4'  C3'   108.17  3.000
 UA2  H4'   C4'  N4'   111.63  3.000
 UA2  C3'   C4'  N4'   103.99  3.000
 UA2  H4'   C4'  C5'   108.35  3.000
 UA2  N4'   C4'  C5'   112.33  3.000
 UA2  C3'   C4'  C5'   112.29  3.000
 UA2  HN4'  N4'  C1'   111.31  3.000
 UA2  HN4'  N4'  C4'   111.46  3.000
 UA2  C1'   N4'  C4'   109.99  3.000
 UA2  H3'   C3'  C2'   108.62  3.000
 UA2  H3'   C3'  O3'   110.93  3.000
 UA2  C2'   C3'  O3'   114.10  3.000
 UA2  H3'   C3'  C4'   109.56  3.000
 UA2  C2'   C3'  C4'   102.62  3.000
 UA2  O3'   C3'  C4'   110.65  3.000
 UA2  HO3'  O3'  C3'   108.51  3.000
 UA2  H2'   C2'  C1'   112.16  3.000
 UA2  H2'   C2'  O2'   111.11  3.000
 UA2  C1'   C2'  O2'   109.09  3.000
 UA2  H2'   C2'  C3'   112.31  3.000
 UA2  C1'   C2'  C3'   101.21  3.000
 UA2  O2'   C2'  C3'   110.54  3.000
 UA2  HO2'  O2'  C2'   107.42  3.000
 UA2  H1'   C1'  C9    108.53  3.000
 UA2  H1'   C1'  C2'   109.35  3.000
 UA2  C9    C1'  C2'   111.31  3.000
 UA2  H1'   C1'  N4'   110.97  3.000
 UA2  C9    C1'  N4'   111.25  3.000
 UA2  C2'   C1'  N4'   105.43  3.000
 UA2  C8    C9   C1'   127.61  3.000
 UA2  C8    C9   C4    105.69  3.000
 UA2  C1'   C9   C4    126.69  3.000
 UA2  C4    N3   C2    113.92  3.000
 UA2  C6    N1   C2    118.88  3.000
 UA2  H8    C8   N7    120.67  3.000
 UA2  H8    C8   C9    128.92  3.000
 UA2  N7    C8   C9    110.41  3.000
 UA2  HN7   N7   C8    124.42  3.000
 UA2  HN7   N7   C5    126.92  3.000
 UA2  C8    N7   C5    108.65  3.000
 UA2  HN62  N6   HN61  115.33  3.000
 UA2  HN62  N6   C6    117.42  3.000
 UA2  HN61  N6   C6    120.19  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
 UA2  CONST_01  C5    C6  N1  C2     0.00  0.0  0
 UA2  CONST_02  C5    C4  N3  C2     0.00  0.0  0
 UA2  CONST_03  C9    C4  N3  C2   180.00  0.0  0
 UA2  CONST_04  N1    C2  N3  C4     0.00  0.0  0
 UA2  CONST_05  N1    C6  C5  C4     0.00  0.0  0
 UA2  CONST_06  C8    N7  C5  C4     0.00  0.0  0
 UA2  CONST_07  N7    C8  C9  C4     0.00  0.0  0
 UA2  CONST_08  C8    C9  C4  C5     0.00  0.0  0
 UA2  CONST_09  C9    C8  N7  C5     0.00  0.0  0
 UA2  CONST_10  N3    C4  C5  C6     0.00  0.0  0
 UA2  CONST_11  C9    C4  C5  C6   180.00  0.0  0
 UA2  CONST_12  C8    N7  C5  C6   180.00  0.0  0
 UA2  CONST_13  N3    C2  N1  C6     0.00  0.0  0
 UA2  CONST_14  N7    C5  C4  C9     0.00  0.0  0
 UA2  CONST_15  N7    C5  C4  N3   180.00  0.0  0
 UA2  CONST_16  C8    C9  C4  N3   180.00  0.0  0
 UA2  CONST_17  N7    C5  C6  N1   180.00  0.0  0
 UA2  CONST_18  C1'   C9  C4  C5   180.00  0.0  0
 UA2  CONST_19  N3    C4  C9  C1'    0.00  0.0  0
 UA2  CONST_20  N7    C8  C9  C1'  180.00  0.0  0
 UA2  CONST_21  N6    C6  N1  C2   180.00  0.0  0
 UA2  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 UA2  CONST_23  N6    C6  C5  N7     0.00  0.0  0
 UA2  CONST_24  H2    C2  N3  C4   180.00  0.0  0
 UA2  CONST_25  HN7   N7  C5  C4   180.00  0.0  0
 UA2  CONST_26  H8    C8  C9  C4   180.00  0.0  0
 UA2  CONST_28  HN62  N6  C6  C5   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
 UA2  chir_01  C4'  C5'  C3'  N4'  positiv
 UA2  chir_02  C3'  O3'  C2'  C4'  negativ
 UA2  chir_03  C2'  O2'  C3'  C1'  positiv
 UA2  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
 UA2  plan-1  C2    0.020
 UA2  plan-1  C4    0.020
 UA2  plan-1  C5    0.020
 UA2  plan-1  C6    0.020
 UA2  plan-1  C1'   0.020
 UA2  plan-1  C9    0.020
 UA2  plan-1  N3    0.020
 UA2  plan-1  N1    0.020
 UA2  plan-1  C8    0.020
 UA2  plan-1  N7    0.020
 UA2  plan-1  N6    0.020
 UA2  plan-1  H2    0.020
 UA2  plan-1  H8    0.020
 UA2  plan-1  HN7   0.020
 UA2  plan-2  C6    0.020
 UA2  plan-2  N6    0.020
 UA2  plan-2  HN61  0.020
 UA2  plan-2  HN62  0.020

