# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:30:01 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 7-(2-C-methyl-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(O)[C@H](O)[C@@H](CO)O[C@H]1n2ccc3c(N)ncnc23
#
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
 H5V  H5V  7-(2-C-methyl-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  36  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5V
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
 H5V  O3    O  OH1   0  -0.658   3.6183   1.1833   1.4936
 H5V  O4    O  OH1   0  -0.668   4.1436  -1.9752  -1.4616
 H5V  C9    C  CT    0   0.137   1.4137   1.3749   0.4228
 H5V  C10   C  CH1   0   0.196   0.8051   0.5120  -0.6995
 H5V  C11   C  CH1   0  -0.018   2.5681   0.4770   0.8948
 H5V  C12   C  CH1   0   0.017   3.0238  -0.1615  -0.4114
 H5V  C13   C  CH3   0  -0.687   0.4594   1.7749   1.5326
 H5V  C14   C  CH2   0  -0.160   3.6992  -1.4963  -0.2166
 H5V  C15   C  CR56  0   0.518  -1.6106   0.0443  -0.3657
 H5V  O1    O  O2    0  -0.496   1.8333  -0.3094  -1.1790
 H5V  O2    O  OH1   0  -0.673   1.9424   2.5061  -0.2330
 H5V  N5    N  NR5   0  -0.543  -0.3030  -0.3178  -0.2730
 H5V  N6    N  N     0  -0.467  -2.0765   1.1647  -0.9242
 H5V  N7    N  N     0  -0.479  -4.2515   0.3826  -0.3422
 H5V  C16   C  CR15  0  -0.022  -0.2328  -1.5331   0.3745
 H5V  C17   C  CR56  0  -0.077  -2.3829  -0.9567   0.2274
 H5V  C18   C  CR15  0  -0.437  -1.4851  -1.9608   0.6960
 H5V  C19   C  CR6   0   0.440  -3.7741  -0.7333   0.2154
 H5V  C20   C  CR16  0   0.037  -3.3902   1.2490  -0.8723
 H5V  HO3   H  HOH1  0   0.467   3.4335   1.2837   2.4325
 H5V  HO4   H  HOH1  0   0.458   4.5888  -2.8150  -1.3181
 H5V  HC10  H  HCH1  0   0.269   0.4148   1.1544  -1.4938
 H5V  HC11  H  HCH1  0   0.235   2.1738  -0.2943   1.5708
 H5V  HC12  H  HCH1  0   0.238   3.7145   0.5178  -0.9279
 H5V  H13A  H  HCH3  0   0.233   0.0502   0.9081   2.0519
 H5V  H13C  H  HCH3  0   0.245   0.9864   2.3810   2.2729
 H5V  H13B  H  HCH3  0   0.249  -0.3699   2.3687   1.1474
 H5V  H14A  H  HCH2  0   0.201   3.0009  -2.1939   0.2665
 H5V  H14B  H  HCH2  0   0.211   4.5300  -1.3432   0.4846
 H5V  HO2   H  HOH1  0   0.448   2.6627   2.8518   0.3091
 H5V  HN8A  H  HNH2  0   0.407  -4.3368  -2.4031   1.2613
 H5V  HN8B  H  HNH2  0   0.399  -5.6194  -1.3613   0.7926
 H5V  HC16  H  HCR5  0   0.296   0.7105  -2.0266   0.5381
 H5V  HC18  H  HCR5  0   0.257  -1.7234  -2.8869   1.1943
 H5V  HC20  H  HCR6  0   0.246  -3.8325   2.1362  -1.3135
 H5V  N8    N  NH2   0  -0.822  -4.6470  -1.6095   0.7293

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
 H5V  O3   C11   single    1.400  0.020  1.400
 H5V  O2   C9    single    1.410  0.020  1.410
 H5V  C11  C9    single    1.537  0.020  1.537
 H5V  C11  C12   single    1.524  0.020  1.524
 H5V  C13  C9    single    1.517  0.020  1.517
 H5V  C9   C10   single    1.541  0.020  1.541
 H5V  C14  C12   single    1.509  0.020  1.509
 H5V  C14  O4    single    1.406  0.020  1.406
 H5V  C12  O1    single    1.424  0.020  1.424
 H5V  C10  O1    single    1.401  0.020  1.401
 H5V  C10  N5    single    1.449  0.020  1.449
 H5V  N5   C16   aromatic  1.379  0.020  1.379
 H5V  N5   C15   aromatic  1.360  0.020  1.360
 H5V  C16  C18   aromatic  1.362  0.020  1.362
 H5V  N6   C15   aromatic  1.336  0.020  1.336
 H5V  N6   C20   aromatic  1.317  0.020  1.317
 H5V  C15  C17   aromatic  1.397  0.020  1.397
 H5V  C18  C17   aromatic  1.426  0.020  1.426
 H5V  C17  C19   aromatic  1.409  0.020  1.409
 H5V  C20  N7    aromatic  1.332  0.020  1.332
 H5V  C19  N7    aromatic  1.336  0.020  1.336
 H5V  C19  N8    single    1.339  0.020  1.339
 H5V  O3   HO3   single    0.850  0.020  0.980
 H5V  O4   HO4   single    0.850  0.020  0.980
 H5V  C10  HC10  single    0.970  0.020  1.090
 H5V  C11  HC11  single    0.970  0.020  1.090
 H5V  C12  HC12  single    0.970  0.020  1.090
 H5V  C13  H13A  single    0.970  0.020  1.090
 H5V  C13  H13C  single    0.970  0.020  1.090
 H5V  C13  H13B  single    0.970  0.020  1.090
 H5V  C14  H14A  single    0.970  0.020  1.090
 H5V  C14  H14B  single    0.970  0.020  1.090
 H5V  O2   HO2   single    0.850  0.020  0.980
 H5V  N8   HN8A  single    0.860  0.020  1.020
 H5V  N8   HN8B  single    0.860  0.020  1.020
 H5V  C16  HC16  single    0.930  0.020  1.080
 H5V  C18  HC18  single    0.930  0.020  1.080
 H5V  C20  HC20  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
 H5V  HO3   O3   C11   109.02  3.000
 H5V  HO4   O4   C14   108.17  3.000
 H5V  O2    C9   C13   111.37  3.000
 H5V  C13   C9   C11   113.69  3.000
 H5V  O2    C9   C11   109.26  3.000
 H5V  C13   C9   C10   115.59  3.000
 H5V  C11   C9   C10   101.14  3.000
 H5V  O2    C9   C10   104.98  3.000
 H5V  HC10  C10  N5    106.10  3.000
 H5V  HC10  C10  O1    110.97  3.000
 H5V  N5    C10  O1    109.05  3.000
 H5V  HC10  C10  C9    109.94  3.000
 H5V  N5    C10  C9    114.11  3.000
 H5V  O1    C10  C9    106.72  3.000
 H5V  HC11  C11  C12   109.91  3.000
 H5V  HC11  C11  C9    109.24  3.000
 H5V  C12   C11  C9    101.90  3.000
 H5V  HC11  C11  O3    111.11  3.000
 H5V  C12   C11  O3    110.72  3.000
 H5V  C9    C11  O3    113.58  3.000
 H5V  HC12  C12  O1    109.66  3.000
 H5V  HC12  C12  C14   109.06  3.000
 H5V  O1    C12  C14   110.61  3.000
 H5V  HC12  C12  C11   109.40  3.000
 H5V  O1    C12  C11   104.81  3.000
 H5V  C14   C12  C11   113.21  3.000
 H5V  H13B  C13  H13C  107.71  3.000
 H5V  H13B  C13  H13A  108.41  3.000
 H5V  H13C  C13  H13A  107.43  3.000
 H5V  H13B  C13  C9    111.32  3.000
 H5V  H13C  C13  C9    109.79  3.000
 H5V  H13A  C13  C9    112.01  3.000
 H5V  H14B  C14  H14A  106.78  3.000
 H5V  H14B  C14  C12   107.33  3.000
 H5V  H14A  C14  C12   109.50  3.000
 H5V  H14B  C14  O4    111.95  3.000
 H5V  H14A  C14  O4    111.96  3.000
 H5V  C12   C14  O4    109.18  3.000
 H5V  C17   C15  N6    125.87  3.000
 H5V  C17   C15  N5    108.18  3.000
 H5V  N6    C15  N5    125.96  3.000
 H5V  C12   O1   C10   111.61  3.000
 H5V  HO2   O2   C9    107.80  3.000
 H5V  C16   N5   C15   108.40  3.000
 H5V  C15   N5   C10   124.26  3.000
 H5V  C16   N5   C10   127.17  3.000
 H5V  C20   N6   C15   112.64  3.000
 H5V  C20   N7   C19   118.59  3.000
 H5V  HC16  C16  C18   128.73  3.000
 H5V  HC16  C16  N5    121.32  3.000
 H5V  C18   C16  N5    109.93  3.000
 H5V  C19   C17  C18   137.39  3.000
 H5V  C19   C17  C15   115.39  3.000
 H5V  C18   C17  C15   107.22  3.000
 H5V  HC18  C18  C17   128.13  3.000
 H5V  HC18  C18  C16   125.59  3.000
 H5V  C17   C18  C16   106.27  3.000
 H5V  C17   C19  N8    122.44  3.000
 H5V  N8    C19  N7    118.28  3.000
 H5V  C17   C19  N7    119.27  3.000
 H5V  HC20  C20  N7    115.48  3.000
 H5V  HC20  C20  N6    116.28  3.000
 H5V  N7    C20  N6    128.24  3.000
 H5V  HN8B  N8   HN8A  117.40  3.000
 H5V  HN8B  N8   C19   119.53  3.000
 H5V  HN8A  N8   C19   121.26  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
 H5V  CONST_01  C18   C16  N5   C15    0.00  0.0  0
 H5V  CONST_02  N7    C20  N6   C15    0.00  0.0  0
 H5V  CONST_03  C16   C18  C17  C15    0.00  0.0  0
 H5V  CONST_04  N7    C19  C17  C15    0.00  0.0  0
 H5V  CONST_05  C17   C18  C16  N5     0.00  0.0  0
 H5V  CONST_06  C20   N6   C15  N5   180.00  0.0  0
 H5V  CONST_07  C18   C17  C15  N5     0.00  0.0  0
 H5V  CONST_08  C19   C17  C15  N5   180.00  0.0  0
 H5V  CONST_09  C16   N5   C15  N6   180.00  0.0  0
 H5V  CONST_10  C18   C17  C15  N6   180.00  0.0  0
 H5V  CONST_11  C19   C17  C15  N6     0.00  0.0  0
 H5V  CONST_12  C19   N7   C20  N6     0.00  0.0  0
 H5V  CONST_13  C18   C17  C19  N7   180.00  0.0  0
 H5V  CONST_14  C17   C15  N5   C16    0.00  0.0  0
 H5V  CONST_15  C19   C17  C18  C16  180.00  0.0  0
 H5V  CONST_16  C20   N6   C15  C17    0.00  0.0  0
 H5V  CONST_17  C20   N7   C19  C17    0.00  0.0  0
 H5V  CONST_18  C18   C16  N5   C10  180.00  0.0  0
 H5V  CONST_19  N6    C15  N5   C10    0.00  0.0  0
 H5V  CONST_20  C17   C15  N5   C10  180.00  0.0  0
 H5V  CONST_21  N8    C19  C17  C15  180.00  0.0  0
 H5V  CONST_22  C18   C17  C19  N8     0.00  0.0  0
 H5V  CONST_23  C20   N7   C19  N8   180.00  0.0  0
 H5V  CONST_24  HC16  C16  N5   C10    0.00  0.0  0
 H5V  CONST_25  HC20  C20  N6   C15  180.00  0.0  0
 H5V  CONST_26  HC18  C18  C17  C15  180.00  0.0  0
 H5V  CONST_27  HN8A  N8   C19  N7   180.00  0.0  0
 H5V  CONST_28  HN8B  N8   C19  N7     0.00  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
 H5V  chir_01  C9   C11  C13  C10  positiv
 H5V  chir_02  C10  O1   N5   C9   negativ
 H5V  chir_03  C11  O3   C12  C9   positiv
 H5V  chir_04  C12  O1   C14  C11  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
 H5V  plan-1  C10   0.020
 H5V  plan-1  C15   0.020
 H5V  plan-1  N5    0.020
 H5V  plan-1  N6    0.020
 H5V  plan-1  N7    0.020
 H5V  plan-1  C16   0.020
 H5V  plan-1  C17   0.020
 H5V  plan-1  C18   0.020
 H5V  plan-1  C19   0.020
 H5V  plan-1  C20   0.020
 H5V  plan-1  HC16  0.020
 H5V  plan-1  HC18  0.020
 H5V  plan-1  HC20  0.020
 H5V  plan-1  N8    0.020
 H5V  plan-2  C19   0.020
 H5V  plan-2  HN8A  0.020
 H5V  plan-2  HN8B  0.020
 H5V  plan-2  N8    0.020

