# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:42:18 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 7-{[(2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@@H](O)CN1Cc2c[nH]c3C(=O)NC=Nc23
#
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
 JMQ  JMQ  7-{[(2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  36  20  .  2022-07-25  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_JMQ
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
 JMQ  C1    C  CH2   0  -0.363   0.4637  -1.3615   0.2997
 JMQ  C2    C  CR16  0   0.118  -2.8096   0.5960  -2.0090
 JMQ  C8    C  CR15  0  -0.054  -1.4940  -0.9315   1.9105
 JMQ  C9    C  CR5   0  -0.017  -0.9042  -0.8863   0.6673
 JMQ  O6    O  O     0  -0.485  -5.1524   0.9936   0.6278
 JMQ  C6    C  CR6   0   0.516  -4.1208   0.6826   0.0486
 JMQ  N1    N  NR16  0  -0.660  -3.9273   0.9246  -1.3043
 JMQ  N3    N  N     0  -0.437  -1.7697   0.0225  -1.5160
 JMQ  C4    C  CR56  0   0.152  -1.8488  -0.2553  -0.1801
 JMQ  C5    C  CR56  0   0.144  -2.9676   0.0465   0.5917
 JMQ  N7    N  NR15  0  -0.652  -2.7293  -0.3741   1.8617
 JMQ  N4'   N  NR5   0  -0.434   1.3544  -0.2536   0.0634
 JMQ  C1'   C  CH2   0  -0.278   1.6566   0.5708   1.2119
 JMQ  C2'   C  CR15  0  -0.021   2.7876   1.4627   0.7257
 JMQ  O2'   O  OH1   0  -0.670   2.3574   2.4758  -0.1508
 JMQ  C3'   C  CR15  0   0.017   3.6038   0.4473  -0.0679
 JMQ  O3'   O  OH1   0  -0.670   4.5040   0.9687  -1.0060
 JMQ  C4'   C  CR15  0  -0.050   2.5420  -0.4090  -0.7715
 JMQ  C5'   C  CH2   0  -0.206   3.0238  -1.8259  -1.0297
 JMQ  O5'   O  OH1   0  -0.668   3.3147  -2.4767   0.1854
 JMQ  H11   H  HNR6  0   0.429  -4.6823   1.3757  -1.8036
 JMQ  H1    H  HCH2  0   0.204   0.8275  -2.0390   1.0871
 JMQ  H1A   H  HCH2  0   0.237   0.3932  -1.9576  -0.6130
 JMQ  H2    H  HCR6  0   0.289  -2.8434   0.8543  -3.0599
 JMQ  H8    H  HCR5  0   0.289  -1.1037  -1.3272   2.8350
 JMQ  HN7   H  HNR5  0   0.418  -3.3597  -0.2818   2.6412
 JMQ  H1'   H  HCH2  0   0.232   0.7842   1.1443   1.5418
 JMQ  H1'A  H  HCH2  0   0.188   1.9970  -0.0112   2.0857
 JMQ  H2'   H  HCR5  0   0.219   3.3569   1.8789   1.5679
 JMQ  HO2'  H  HOH1  0   0.448   1.7190   3.0230   0.3161
 JMQ  H3'   H  HCR5  0   0.216   4.1236  -0.1783   0.6697
 JMQ  HO3'  H  HOH1  0   0.451   5.2443   1.3605  -0.5334
 JMQ  H4'   H  HCR5  0   0.214   2.3574   0.0190  -1.7688
 JMQ  H5'   H  HCH2  0   0.211   2.2674  -2.3742  -1.6062
 JMQ  H5'A  H  HCH2  0   0.217   3.9094  -1.7544  -1.6765
 JMQ  HO5'  H  HOH1  0   0.456   3.6363  -3.3597  -0.0173

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
 JMQ  C1   C9    single    1.494  0.020  1.494
 JMQ  C1   N4'   single    1.441  0.020  1.441
 JMQ  C2   N1    single    1.362  0.020  1.362
 JMQ  C2   N3    double    1.286  0.020  1.286
 JMQ  C8   C9    aromatic  1.377  0.020  1.377
 JMQ  C8   N7    aromatic  1.356  0.020  1.356
 JMQ  C9   C4    aromatic  1.417  0.020  1.417
 JMQ  O6   C6    double    1.223  0.020  1.223
 JMQ  C6   N1    single    1.388  0.020  1.388
 JMQ  C6   C5    single    1.425  0.020  1.425
 JMQ  N3   C4    single    1.367  0.020  1.367
 JMQ  C4   C5    aromatic  1.392  0.020  1.392
 JMQ  C5   N7    aromatic  1.359  0.020  1.359
 JMQ  N4'  C1'   single    1.446  0.020  1.446
 JMQ  N4'  C4'   single    1.460  0.020  1.460
 JMQ  C1'  C2'   single    1.520  0.020  1.520
 JMQ  C2'  O2'   single    1.407  0.020  1.407
 JMQ  C2'  C3'   single    1.525  0.020  1.525
 JMQ  C3'  O3'   single    1.401  0.020  1.401
 JMQ  C3'  C4'   single    1.535  0.020  1.535
 JMQ  C4'  C5'   single    1.519  0.020  1.519
 JMQ  C5'  O5'   single    1.409  0.020  1.409
 JMQ  N1   H11   single    0.860  0.020  1.020
 JMQ  C1   H1    single    0.970  0.020  1.090
 JMQ  C1   H1A   single    0.970  0.020  1.090
 JMQ  C2   H2    single    0.930  0.020  1.080
 JMQ  C8   H8    single    0.930  0.020  1.080
 JMQ  N7   HN7   single    0.860  0.020  1.020
 JMQ  C1'  H1'   single    0.970  0.020  1.090
 JMQ  C1'  H1'A  single    0.970  0.020  1.090
 JMQ  C2'  H2'   single    0.970  0.020  1.090
 JMQ  O2'  HO2'  single    0.850  0.020  0.980
 JMQ  C3'  H3'   single    0.970  0.020  1.090
 JMQ  O3'  HO3'  single    0.850  0.020  0.980
 JMQ  C4'  H4'   single    0.970  0.020  1.090
 JMQ  C5'  H5'   single    0.970  0.020  1.090
 JMQ  C5'  H5'A  single    0.970  0.020  1.090
 JMQ  O5'  HO5'  single    0.850  0.020  0.980

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
 JMQ  H1A   C1   H1   106.45  3.000
 JMQ  H1A   C1   N4'  108.81  3.000
 JMQ  H1    C1   N4'  112.73  3.000
 JMQ  H1A   C1   C9   108.66  3.000
 JMQ  H1    C1   C9   108.80  3.000
 JMQ  N4'   C1   C9   111.21  3.000
 JMQ  H2    C2   N3   120.25  3.000
 JMQ  H2    C2   N1   114.78  3.000
 JMQ  N3    C2   N1   124.97  3.000
 JMQ  H8    C8   N7   120.75  3.000
 JMQ  H8    C8   C9   129.12  3.000
 JMQ  N7    C8   C9   110.13  3.000
 JMQ  C4    C9   C8   105.61  3.000
 JMQ  C4    C9   C1   127.21  3.000
 JMQ  C8    C9   C1   127.16  3.000
 JMQ  C5    C6   N1   109.67  3.000
 JMQ  C5    C6   O6   128.00  3.000
 JMQ  N1    C6   O6   122.33  3.000
 JMQ  H11   N1   C6   117.06  3.000
 JMQ  H11   N1   C2   117.70  3.000
 JMQ  C6    N1   C2   125.23  3.000
 JMQ  C4    N3   C2   114.75  3.000
 JMQ  C5    C4   N3   122.97  3.000
 JMQ  C5    C4   C9   107.50  3.000
 JMQ  N3    C4   C9   129.52  3.000
 JMQ  N7    C5   C4   108.06  3.000
 JMQ  N7    C5   C6   129.53  3.000
 JMQ  C4    C5   C6   122.41  3.000
 JMQ  HN7   N7   C5   125.83  3.000
 JMQ  HN7   N7   C8   125.46  3.000
 JMQ  C5    N7   C8   108.70  3.000
 JMQ  C4'   N4'  C1'  110.18  3.000
 JMQ  C4'   N4'  C1   120.97  3.000
 JMQ  C1'   N4'  C1   115.94  3.000
 JMQ  H1'A  C1'  H1'  106.46  3.000
 JMQ  H1'A  C1'  C2'  109.46  3.000
 JMQ  H1'   C1'  C2'  112.45  3.000
 JMQ  H1'A  C1'  N4'  113.12  3.000
 JMQ  H1'   C1'  N4'  111.81  3.000
 JMQ  C2'   C1'  N4'  103.65  3.000
 JMQ  H2'   C2'  C3'  111.95  3.000
 JMQ  H2'   C2'  O2'  111.30  3.000
 JMQ  C3'   C2'  O2'  108.59  3.000
 JMQ  H2'   C2'  C1'  111.26  3.000
 JMQ  C3'   C2'  C1'  100.01  3.000
 JMQ  O2'   C2'  C1'  113.21  3.000
 JMQ  HO2'  O2'  C2'  108.07  3.000
 JMQ  H3'   C3'  C4'  108.52  3.000
 JMQ  H3'   C3'  O3'  110.96  3.000
 JMQ  C4'   C3'  O3'  110.20  3.000
 JMQ  H3'   C3'  C2'  106.44  3.000
 JMQ  C4'   C3'  C2'  103.87  3.000
 JMQ  O3'   C3'  C2'  116.39  3.000
 JMQ  HO3'  O3'  C3'  108.50  3.000
 JMQ  H4'   C4'  C5'  105.18  3.000
 JMQ  H4'   C4'  C3'  108.32  3.000
 JMQ  C5'   C4'  C3'  112.27  3.000
 JMQ  H4'   C4'  N4'  109.89  3.000
 JMQ  C5'   C4'  N4'  117.04  3.000
 JMQ  C3'   C4'  N4'  103.96  3.000
 JMQ  H5'A  C5'  H5'  106.19  3.000
 JMQ  H5'A  C5'  O5'  111.79  3.000
 JMQ  H5'   C5'  O5'  111.38  3.000
 JMQ  H5'A  C5'  C4'  107.16  3.000
 JMQ  H5'   C5'  C4'  109.68  3.000
 JMQ  O5'   C5'  C4'  110.48  3.000
 JMQ  HO5'  O5'  C5'  108.15  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
 JMQ  CONST_01  C5   C4   C9   C8      0.00   0.0  0
 JMQ  CONST_02  C4   C5   N7   C8      0.00   0.0  0
 JMQ  CONST_03  C5   N7   C8   C9      0.00   0.0  0
 JMQ  CONST_04  N7   C5   C4   C9      0.00   0.0  0
 JMQ  CONST_05  N7   C8   C9   C4      0.00   0.0  0
 JMQ  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 JMQ  CONST_07  N3   C2   N1   C6      0.00   0.0  0
 JMQ  CONST_08  C4   N3   C2   N1      0.00   0.0  0
 JMQ  CONST_09  N7   C8   C9   C1    180.00   0.0  0
 JMQ  CONST_10  N3   C4   C9   C1      0.00   0.0  0
 JMQ  CONST_11  C5   C4   C9   C1    180.00   0.0  0
 JMQ  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 JMQ  CONST_13  HN7  N7   C8   C9    180.00   0.0  0
 JMQ  CONST_14  H8   C8   C9   C4    180.00   0.0  0
 JMQ  CONST_15  H2   C2   N1   C6    180.00   0.0  0
 JMQ  CONST_16  H11  N1   C2   N3    180.00   0.0  0
 JMQ  Var_01    C4'  N4'  C1'  C2'    27.77  30.0  1
 JMQ  Var_02    N4'  C1   C9   C8   -107.19  30.0  2
 JMQ  Var_03    C1'  N4'  C1   C9     65.80  30.0  3

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
 JMQ  chir_01  C2'  C1'  O2'  C3'  positiv
 JMQ  chir_02  C3'  O3'  C2'  C4'  negativ
 JMQ  chir_03  C4'  N4'  C3'  C5'  negativ

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
 JMQ  plan-1  C1   0.020
 JMQ  plan-1  C2   0.020
 JMQ  plan-1  C8   0.020
 JMQ  plan-1  C9   0.020
 JMQ  plan-1  O6   0.020
 JMQ  plan-1  C6   0.020
 JMQ  plan-1  N1   0.020
 JMQ  plan-1  N3   0.020
 JMQ  plan-1  C4   0.020
 JMQ  plan-1  C5   0.020
 JMQ  plan-1  N7   0.020
 JMQ  plan-1  H11  0.020
 JMQ  plan-1  H2   0.020
 JMQ  plan-1  H8   0.020
 JMQ  plan-1  HN7  0.020

