# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:12:15 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: (3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(hydroxymethyl)pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CO)C3)c[nH]c12
#
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
 223  223  (3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(hydroxymethyl)pyrrolidin-3-ol  ligand  36  19  .  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_223
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
 223  N1    N  N      0  -0.470  -1.9861   3.5463   0.9701
 223  C2    C  CR16   0   0.005  -1.0989   3.1343   0.0576
 223  C4    C  CR56   0   0.162  -2.2634   1.3257  -0.5317
 223  C5    C  CR56   0   0.206  -3.2620   1.6729   0.3856
 223  C6    C  CR6    0   0.451  -3.0899   2.8304   1.1600
 223  C8    C  CR15   0  -0.052  -3.8991  -0.1839  -0.6342
 223  N6    N  NH2    0  -0.825  -4.0037   3.2698   2.0516
 223  N3    N  N      0  -0.444  -1.1535   2.0706  -0.7079
 223  C9    C  CR5    0  -0.040  -2.6811   0.1301  -1.1824
 223  N7    N  NR15   0  -0.677  -4.2511   0.7350   0.3042
 223  C10   C  CH2    0  -0.365  -1.9340  -0.6291  -2.2253
 223  N1'   N  NT    -1  -0.411  -0.7543  -1.2717  -1.6889
 223  C6'   C  CH2    0  -0.268   0.0759  -1.8988  -2.6964
 223  C4'   C  CH1    0  -0.330   1.0684  -2.7309  -1.8806
 223  C5'   C  CH2    0  -0.160   1.5262  -3.9758  -2.6203
 223  O5'   O  OH1    0  -0.666   2.4281  -4.7632  -1.8762
 223  C3'   C  CH1    0   0.056   0.3302  -3.0205  -0.5580
 223  O3'   O  OH1    0  -0.678   1.0838  -2.4809   0.5081
 223  C2'   C  CH2    0  -0.299  -1.0258  -2.3377  -0.7466
 223  H2    H  HCR6   0   0.237  -0.2229   3.7671  -0.0494
 223  H8    H  HCR5   0   0.289  -4.5520  -1.0137  -0.8563
 223  HN61  H  HNH2   0   0.399  -4.6883   2.6325   2.4212
 223  HN62  H  HNH2   0   0.395  -3.7105   3.9935   2.6872
 223  HN7   H  HNR5   0   0.416  -5.1125   0.7163   0.8241
 223  H101  H  HCH2   0   0.204  -2.6116  -1.3598  -2.7018
 223  H102  H  HCH2   0   0.238  -1.6137   0.0559  -3.0157
 223  H6'1  H  HCH2   0   0.240   0.5643  -1.1558  -3.3306
 223  H6'2  H  HCH2   0   0.187  -0.5147  -2.5598  -3.3595
 223  H4'   H  HCH1   0   0.249   1.9446  -2.1150  -1.6490
 223  H5'1  H  HCH2   0   0.208   1.9531  -3.6852  -3.5900
 223  H5'2  H  HCH2   0   0.213   0.6630  -4.6119  -2.8353
 223  HO5'  H  HOH1   0   0.446   3.1991  -4.2241  -1.6752
 223  H3'   H  HCH1   0   0.211   0.1849  -4.0978  -0.4114
 223  HO3'  H  HOH1   0   0.446   0.6229  -2.6801   1.3286
 223  H2'1  H  HCH2   0   0.187  -1.7448  -3.0664  -1.1631
 223  H2'2  H  HCH2   0   0.240  -1.4476  -1.9653   0.1897

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
 223  N1   C6    aromatic  1.329  0.020  1.329
 223  N1   C2    aromatic  1.338  0.020  1.338
 223  C2   N3    aromatic  1.312  0.020  1.312
 223  C2   H2    single    0.930  0.020  1.080
 223  C4   C5    aromatic  1.400  0.020  1.400
 223  C4   C9    aromatic  1.424  0.020  1.424
 223  C4   N3    aromatic  1.348  0.020  1.348
 223  C5   N7    aromatic  1.366  0.020  1.366
 223  C5   C6    aromatic  1.403  0.020  1.403
 223  C6   N6    single    1.350  0.020  1.350
 223  C8   N7    aromatic  1.360  0.020  1.360
 223  C8   C9    aromatic  1.372  0.020  1.372
 223  C8   H8    single    0.930  0.020  1.080
 223  N6   HN61  single    0.890  0.020  1.040
 223  N6   HN62  single    0.890  0.020  1.040
 223  C9   C10   single    1.491  0.020  1.491
 223  N7   HN7   single    0.860  0.020  1.020
 223  C10  N1'   single    1.447  0.020  1.447
 223  C10  H101  single    0.970  0.020  1.090
 223  C10  H102  single    0.970  0.020  1.090
 223  N1'  C6'   single    1.448  0.020  1.448
 223  N1'  C2'   single    1.448  0.020  1.448
 223  C6'  C4'   single    1.531  0.020  1.531
 223  C6'  H6'1  single    0.970  0.020  1.090
 223  C6'  H6'2  single    0.970  0.020  1.090
 223  C4'  C3'   single    1.542  0.020  1.542
 223  C4'  C5'   single    1.519  0.020  1.519
 223  C4'  H4'   single    0.970  0.020  1.090
 223  C5'  O5'   single    1.410  0.020  1.410
 223  C5'  H5'1  single    0.970  0.020  1.090
 223  C5'  H5'2  single    0.970  0.020  1.090
 223  O5'  HO5'  single    0.850  0.020  0.980
 223  C3'  C2'   single    1.530  0.020  1.530
 223  C3'  O3'   single    1.413  0.020  1.413
 223  C3'  H3'   single    0.970  0.020  1.090
 223  O3'  HO3'  single    0.850  0.020  0.980
 223  C2'  H2'1  single    0.970  0.020  1.090
 223  C2'  H2'2  single    0.970  0.020  1.090

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
 223  C6    N1   C2    118.84  3.000
 223  H2    C2   N3    116.66  3.000
 223  H2    C2   N1    115.01  3.000
 223  N3    C2   N1    128.33  3.000
 223  C9    C4   N3    130.22  3.000
 223  N3    C4   C5    122.40  3.000
 223  C9    C4   C5    107.37  3.000
 223  N7    C5   C6    133.49  3.000
 223  C6    C5   C4    118.61  3.000
 223  N7    C5   C4    107.90  3.000
 223  N6    C6   C5    123.36  3.000
 223  N6    C6   N1    118.76  3.000
 223  C5    C6   N1    117.85  3.000
 223  H8    C8   N7    120.34  3.000
 223  H8    C8   C9    129.12  3.000
 223  N7    C8   C9    110.54  3.000
 223  HN62  N6   HN61  114.94  3.000
 223  HN62  N6   C6    116.98  3.000
 223  HN61  N6   C6    119.82  3.000
 223  C4    N3   C2    113.96  3.000
 223  C10   C9   C8    127.43  3.000
 223  C10   C9   C4    126.90  3.000
 223  C8    C9   C4    105.67  3.000
 223  HN7   N7   C8    124.45  3.000
 223  HN7   N7   C5    127.01  3.000
 223  C8    N7   C5    108.53  3.000
 223  H102  C10  H101  106.39  3.000
 223  H102  C10  N1'   107.90  3.000
 223  H101  C10  N1'   111.49  3.000
 223  H102  C10  C9    109.47  3.000
 223  H101  C10  C9    109.35  3.000
 223  N1'   C10  C9    112.06  3.000
 223  C2'   N1'  C6'   103.97  3.000
 223  C2'   N1'  C10   114.54  3.000
 223  C6'   N1'  C10   113.70  3.000
 223  H6'2  C6'  H6'1  107.28  3.000
 223  H6'2  C6'  C4'   109.91  3.000
 223  H6'1  C6'  C4'   112.92  3.000
 223  H6'2  C6'  N1'   111.67  3.000
 223  H6'1  C6'  N1'   111.45  3.000
 223  C4'   C6'  N1'   103.67  3.000
 223  H4'   C4'  C3'   107.89  3.000
 223  H4'   C4'  C5'   108.82  3.000
 223  C3'   C4'  C5'   114.09  3.000
 223  H4'   C4'  C6'   109.00  3.000
 223  C5'   C4'  C6'   112.42  3.000
 223  C3'   C4'  C6'   104.41  3.000
 223  H5'2  C5'  H5'1  106.69  3.000
 223  H5'2  C5'  O5'   106.49  3.000
 223  H5'1  C5'  O5'   111.41  3.000
 223  H5'2  C5'  C4'   109.55  3.000
 223  H5'1  C5'  C4'   109.28  3.000
 223  O5'   C5'  C4'   113.18  3.000
 223  HO5'  O5'  C5'   108.07  3.000
 223  H3'   C3'  C2'   109.72  3.000
 223  H3'   C3'  O3'   110.18  3.000
 223  C2'   C3'  O3'   113.29  3.000
 223  H3'   C3'  C4'   111.26  3.000
 223  O3'   C3'  C4'   108.67  3.000
 223  C2'   C3'  C4'   103.58  3.000
 223  HO3'  O3'  C3'   108.00  3.000
 223  H2'2  C2'  H2'1  107.25  3.000
 223  H2'2  C2'  C3'   112.88  3.000
 223  H2'1  C2'  C3'   109.20  3.000
 223  H2'2  C2'  N1'   112.28  3.000
 223  H2'1  C2'  N1'   111.22  3.000
 223  C3'   C2'  N1'   104.04  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
 223  CONST_01  C4    C5   C6  N1    0.00   0.0  0
 223  CONST_02  N7    C5   C6  N1  180.00   0.0  0
 223  CONST_03  C4    N3   C2  N1    0.00   0.0  0
 223  CONST_04  C5    C6   N1  C2    0.00   0.0  0
 223  CONST_05  C5    C4   N3  C2    0.00   0.0  0
 223  CONST_06  C9    C4   N3  C2  180.00   0.0  0
 223  CONST_07  C8    N7   C5  C4    0.00   0.0  0
 223  CONST_08  N7    C8   C9  C4    0.00   0.0  0
 223  CONST_09  C8    C9   C4  C5    0.00   0.0  0
 223  CONST_10  C9    C8   N7  C5    0.00   0.0  0
 223  CONST_11  N3    C2   N1  C6    0.00   0.0  0
 223  CONST_12  C9    C4   C5  C6  180.00   0.0  0
 223  CONST_13  N3    C4   C5  C6    0.00   0.0  0
 223  CONST_14  C8    N7   C5  C6  180.00   0.0  0
 223  CONST_15  N3    C4   C9  C8  180.00   0.0  0
 223  CONST_16  N7    C5   C4  N3  180.00   0.0  0
 223  CONST_17  N7    C5   C4  C9    0.00   0.0  0
 223  CONST_18  N6    C6   N1  C2  180.00   0.0  0
 223  CONST_19  N6    C6   C5  C4  180.00   0.0  0
 223  CONST_20  C10   C9   C4  C5  180.00   0.0  0
 223  CONST_21  N7    C5   C6  N6    0.00   0.0  0
 223  CONST_22  C10   C9   C4  N3    0.00   0.0  0
 223  CONST_23  C10   C9   C8  N7  180.00   0.0  0
 223  CONST_24  HN7   N7   C5  C4  180.00   0.0  0
 223  CONST_25  H8    C8   C9  C4  180.00   0.0  0
 223  CONST_26  H2    C2   N3  C4  180.00   0.0  0
 223  CONST_28  HN62  N6   C6  N1    0.00   0.0  0
 223  Var_01    N1'   C10  C9  C4   69.37  30.0  2

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
 223  chir_01  N1'  C10  C6'  C2'  positiv
 223  chir_02  C4'  C6'  C3'  C5'  negativ
 223  chir_03  C3'  O3'  C4'  C2'  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
 223  plan-1  N1    0.020
 223  plan-1  C2    0.020
 223  plan-1  C4    0.020
 223  plan-1  C5    0.020
 223  plan-1  C6    0.020
 223  plan-1  C8    0.020
 223  plan-1  N6    0.020
 223  plan-1  N3    0.020
 223  plan-1  C9    0.020
 223  plan-1  N7    0.020
 223  plan-1  C10   0.020
 223  plan-1  H2    0.020
 223  plan-1  H8    0.020
 223  plan-1  HN7   0.020
 223  plan-2  C6    0.020
 223  plan-2  N6    0.020
 223  plan-2  HN61  0.020
 223  plan-2  HN62  0.020

