# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:50:12 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2R,3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@H](O)[C@H]3CO)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
 AGV  AGV  (2R,3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidine-3,4-diol  ligand  37  20  .  2022-07-24  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_AGV
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
 AGV  O5'  O  OH1   0  -0.672  -4.5044   2.0389   0.6882
 AGV  C5'  C  CH2   0  -0.173  -3.2255   1.6157   1.1019
 AGV  C4'  C  CR15  0  -0.082  -2.6003   0.8164  -0.0389
 AGV  C3'  C  CR15  0   0.025  -3.4665  -0.4139  -0.3885
 AGV  O3'  O  OH1   0  -0.668  -4.2040  -0.1883  -1.5578
 AGV  N4'  N  NR5   0  -0.424  -1.2948   0.2531   0.2735
 AGV  C1'  C  CH2   0  -0.302  -1.4558  -1.1476   0.5817
 AGV  C2'  C  CR15  0  -0.001  -2.4791  -1.5854  -0.4521
 AGV  O2'  O  OH1   0  -0.667  -1.9471  -1.6605  -1.7518
 AGV  C7   C  CH2   0  -0.370  -0.3908   1.0210   1.0946
 AGV  C9   C  CR5   0  -0.040   0.9810   0.4347   1.0899
 AGV  C8   C  CR15  0  -0.053   1.6354  -0.1360   2.1517
 AGV  N7   N  NR15  0  -0.676   2.8583  -0.5915   1.7707
 AGV  C5   C  CR56  0   0.204   3.0247  -0.3250   0.4417
 AGV  C4   C  CR56  0   0.171   1.8689   0.3186  -0.0176
 AGV  C6   C  CR6   0   0.450   4.0670  -0.5681  -0.4657
 AGV  N6   N  NH2   0  -0.826   5.2307  -1.1587  -0.1181
 AGV  N1   N  N     0  -0.470   3.9066  -0.1579  -1.7196
 AGV  C2   C  CR16  0   0.002   2.7696   0.4642  -2.0530
 AGV  N3   N  N     0  -0.438   1.7339   0.7305  -1.2941
 AGV  H1   H  HOH1  0   0.455  -4.8928   2.5562   1.3991
 AGV  H2   H  HCH2  0   0.209  -2.5915   2.4752   1.3533
 AGV  H3   H  HCH2  0   0.191  -3.2777   0.9848   2.0011
 AGV  H4   H  HCR5  0   0.225  -2.5226   1.4785  -0.9120
 AGV  H5   H  HCR5  0   0.213  -4.1355  -0.6172   0.4599
 AGV  H6   H  HOH1  0   0.449  -4.7983  -0.9333  -1.6904
 AGV  H8   H  HCH2  0   0.243  -0.5106  -1.6901   0.4953
 AGV  H9   H  HCH2  0   0.194  -1.8390  -1.3459   1.5984
 AGV  H10  H  HCR5  0   0.211  -2.9576  -2.5315  -0.1644
 AGV  H11  H  HOH1  0   0.446  -1.1533  -2.2023  -1.7189
 AGV  H12  H  HCH2  0   0.239  -0.3509   2.0381   0.6921
 AGV  H13  H  HCH2  0   0.204  -0.7238   1.1152   2.1418
 AGV  H14  H  HCR5  0   0.289   1.3043  -0.2513   3.1722
 AGV  H15  H  HNR5  0   0.415   3.5218  -1.0258   2.3898
 AGV  H16  H  HNH2  0   0.399   5.2806  -1.7140   0.7189
 AGV  H17  H  HNH2  0   0.396   5.8312  -1.4628  -0.8670
 AGV  H18  H  HCR6  0   0.236   2.7072   0.7812  -3.0897

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
 AGV  O5'  C5'  single    1.409  0.020  1.409
 AGV  C5'  C4'  single    1.527  0.020  1.527
 AGV  O3'  C3'  single    1.401  0.020  1.401
 AGV  C3'  C4'  single    1.545  0.020  1.545
 AGV  C3'  C2'  single    1.533  0.020  1.533
 AGV  C4'  N4'  single    1.456  0.020  1.456
 AGV  C2'  O2'  single    1.406  0.020  1.406
 AGV  C2'  C1'  single    1.519  0.020  1.519
 AGV  N4'  C1'  single    1.443  0.020  1.443
 AGV  N4'  C7   single    1.443  0.020  1.443
 AGV  C8   C9   aromatic  1.372  0.020  1.372
 AGV  C8   N7   aromatic  1.359  0.020  1.359
 AGV  C7   C9   single    1.492  0.020  1.492
 AGV  C9   C4   aromatic  1.424  0.020  1.424
 AGV  N7   C5   aromatic  1.366  0.020  1.366
 AGV  C4   C5   aromatic  1.400  0.020  1.400
 AGV  C4   N3   aromatic  1.348  0.020  1.348
 AGV  C5   C6   aromatic  1.403  0.020  1.403
 AGV  N3   C2   aromatic  1.311  0.020  1.311
 AGV  C6   N6   single    1.351  0.020  1.351
 AGV  C6   N1   aromatic  1.329  0.020  1.329
 AGV  C2   N1   aromatic  1.338  0.020  1.338
 AGV  O5'  H1   single    0.850  0.020  0.980
 AGV  C5'  H2   single    0.970  0.020  1.090
 AGV  C5'  H3   single    0.970  0.020  1.090
 AGV  C4'  H4   single    0.970  0.020  1.090
 AGV  C3'  H5   single    0.970  0.020  1.090
 AGV  O3'  H6   single    0.850  0.020  0.980
 AGV  C1'  H8   single    0.970  0.020  1.090
 AGV  C1'  H9   single    0.970  0.020  1.090
 AGV  C2'  H10  single    0.970  0.020  1.090
 AGV  O2'  H11  single    0.850  0.020  0.980
 AGV  C7   H12  single    0.970  0.020  1.090
 AGV  C7   H13  single    0.970  0.020  1.090
 AGV  C8   H14  single    0.930  0.020  1.080
 AGV  N7   H15  single    0.860  0.020  1.020
 AGV  N6   H16  single    0.890  0.020  1.040
 AGV  N6   H17  single    0.890  0.020  1.040
 AGV  C2   H18  single    0.930  0.020  1.080

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
 AGV  H1   O5'  C5'  108.13  3.000
 AGV  H3   C5'  H2   106.83  3.000
 AGV  H3   C5'  C4'  109.27  3.000
 AGV  H2   C5'  C4'  110.17  3.000
 AGV  H3   C5'  O5'  111.67  3.000
 AGV  H2   C5'  O5'  110.88  3.000
 AGV  C4'  C5'  O5'  108.03  3.000
 AGV  H4   C4'  N4'  109.90  3.000
 AGV  H4   C4'  C3'  109.87  3.000
 AGV  N4'  C4'  C3'  104.08  3.000
 AGV  H4   C4'  C5'  107.89  3.000
 AGV  N4'  C4'  C5'  114.17  3.000
 AGV  C3'  C4'  C5'  110.88  3.000
 AGV  H5   C3'  C2'  106.42  3.000
 AGV  H5   C3'  O3'  110.70  3.000
 AGV  C2'  C3'  O3'  115.31  3.000
 AGV  H5   C3'  C4'  108.30  3.000
 AGV  C2'  C3'  C4'  104.88  3.000
 AGV  O3'  C3'  C4'  110.85  3.000
 AGV  H6   O3'  C3'  108.39  3.000
 AGV  C7   N4'  C1'  117.71  3.000
 AGV  C7   N4'  C4'  118.56  3.000
 AGV  C1'  N4'  C4'  108.74  3.000
 AGV  H9   C1'  H8   106.48  3.000
 AGV  H9   C1'  C2'  109.93  3.000
 AGV  H8   C1'  C2'  112.68  3.000
 AGV  H9   C1'  N4'  114.18  3.000
 AGV  H8   C1'  N4'  111.62  3.000
 AGV  C2'  C1'  N4'  102.10  3.000
 AGV  H10  C2'  O2'  111.15  3.000
 AGV  H10  C2'  C1'  111.31  3.000
 AGV  O2'  C2'  C1'  112.92  3.000
 AGV  H10  C2'  C3'  111.51  3.000
 AGV  C1'  C2'  C3'  100.68  3.000
 AGV  O2'  C2'  C3'  108.83  3.000
 AGV  H11  O2'  C2'  108.11  3.000
 AGV  H13  C7   H12  106.31  3.000
 AGV  H13  C7   C9   108.31  3.000
 AGV  H12  C7   C9   109.30  3.000
 AGV  H13  C7   N4'  113.37  3.000
 AGV  H12  C7   N4'  107.95  3.000
 AGV  C9   C7   N4'  111.42  3.000
 AGV  C4   C9   C8   105.70  3.000
 AGV  C4   C9   C7   127.42  3.000
 AGV  C8   C9   C7   126.86  3.000
 AGV  H14  C8   N7   120.35  3.000
 AGV  H14  C8   C9   129.06  3.000
 AGV  N7   C8   C9   110.59  3.000
 AGV  H15  N7   C5   127.07  3.000
 AGV  H15  N7   C8   124.43  3.000
 AGV  C5   N7   C8   108.48  3.000
 AGV  C6   C5   C4   118.72  3.000
 AGV  C6   C5   N7   133.32  3.000
 AGV  C4   C5   N7   107.96  3.000
 AGV  N3   C4   C5   122.25  3.000
 AGV  N3   C4   C9   130.47  3.000
 AGV  C5   C4   C9   107.27  3.000
 AGV  N1   C6   N6   118.80  3.000
 AGV  N1   C6   C5   117.84  3.000
 AGV  N6   C6   C5   123.32  3.000
 AGV  H17  N6   H16  115.00  3.000
 AGV  H17  N6   C6   117.03  3.000
 AGV  H16  N6   C6   119.90  3.000
 AGV  C2   N1   C6   118.75  3.000
 AGV  H18  C2   N3   116.61  3.000
 AGV  H18  C2   N1   114.98  3.000
 AGV  N3   C2   N1   128.41  3.000
 AGV  C2   N3   C4   114.01  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
 AGV  CONST_01  C5   N7   C8   C9      0.00   0.0  0
 AGV  CONST_02  N7   C5   C4   C9      0.00   0.0  0
 AGV  CONST_03  C6   C5   C4   C9    180.00   0.0  0
 AGV  CONST_04  C2   N3   C4   C9    180.00   0.0  0
 AGV  CONST_05  C5   C4   C9   C8      0.00   0.0  0
 AGV  CONST_06  N3   C4   C9   C8    180.00   0.0  0
 AGV  CONST_07  C4   C5   N7   C8      0.00   0.0  0
 AGV  CONST_08  C6   C5   N7   C8    180.00   0.0  0
 AGV  CONST_09  C4   C9   C8   N7      0.00   0.0  0
 AGV  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 AGV  CONST_11  N1   C6   C5   N7    180.00   0.0  0
 AGV  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 AGV  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 AGV  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 AGV  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 AGV  CONST_16  N3   C4   C5   C6      0.00   0.0  0
 AGV  CONST_17  N3   C2   N1   C6      0.00   0.0  0
 AGV  CONST_18  N7   C8   C9   C7    180.00   0.0  0
 AGV  CONST_19  C5   C4   C9   C7    180.00   0.0  0
 AGV  CONST_20  N3   C4   C9   C7      0.00   0.0  0
 AGV  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 AGV  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 AGV  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 AGV  CONST_24  H15  N7   C8   C9    180.00   0.0  0
 AGV  CONST_25  H14  C8   N7   C5    180.00   0.0  0
 AGV  CONST_26  H18  C2   N3   C4    180.00   0.0  0
 AGV  CONST_28  H17  N6   C6   C5    180.00   0.0  0
 AGV  Var_01    C2'  C1'  N4'  C4'    40.32  30.0  1
 AGV  Var_02    C9   C7   N4'  C4'  -168.57  30.0  3
 AGV  Var_03    C8   C9   C7   N4'  -113.68  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
 AGV  chir_01  C4'  C5'  C3'  N4'  positiv
 AGV  chir_02  C3'  O3'  C4'  C2'  positiv
 AGV  chir_03  C2'  O2'  C3'  C1'  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
 AGV  plan-1  C7   0.020
 AGV  plan-1  C9   0.020
 AGV  plan-1  C8   0.020
 AGV  plan-1  N7   0.020
 AGV  plan-1  C5   0.020
 AGV  plan-1  C4   0.020
 AGV  plan-1  C6   0.020
 AGV  plan-1  N6   0.020
 AGV  plan-1  N1   0.020
 AGV  plan-1  C2   0.020
 AGV  plan-1  N3   0.020
 AGV  plan-1  H14  0.020
 AGV  plan-1  H15  0.020
 AGV  plan-1  H18  0.020
 AGV  plan-2  C6   0.020
 AGV  plan-2  N6   0.020
 AGV  plan-2  H16  0.020
 AGV  plan-2  H17  0.020

