# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 19:18:48 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: methyl 5-[(6-amino-8-oxo-7,8-dihydro-3H-imidazo[4,5-g]quinazolin-2-yl)amino]-5-deoxy-2,3-O-(1-methylethylidene)-beta-D-ribofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CNc2[nH]c3cc4N=C(N)NC(=O)c4cc3n2)[C@H]5OC(C)(C)O[C@@H]15
#
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
 6MQ  6MQ  'methyl 5-[(6-amino-8-oxo-7,8-dihydro-3H-imidazo[4,5-g]quinazolin-2-yl)amino]-5-deoxy-2,3-O-(1-methylethylidene)-beta-D-ribofuranoside'  ligand  51  29  .  2022-07-23  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_6MQ
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
 6MQ  C    C  CH3   0  -0.417  -1.8013   2.1522  -0.5757
 6MQ  C1   C  CR15  0   0.276  -3.7686   0.9472  -0.1053
 6MQ  C2   C  CR15  0  -0.056  -3.2788  -0.8846   1.1906
 6MQ  C3   C  CH2   0  -0.296  -1.8940  -1.3659   0.7652
 6MQ  C4   C  CR5   0   0.688   0.3978  -0.5271   1.1553
 6MQ  O    O  O2    0  -0.497  -2.6724   1.1037  -0.9477
 6MQ  C5   C  CR56  0   0.382   2.1025  -0.2558  -0.2198
 6MQ  C6   C  CR16  0  -0.410   2.9762  -0.1507  -1.2763
 6MQ  C7   C  CR66  0   0.259   4.3029   0.1999  -0.9854
 6MQ  C8   C  CR6   0   0.639   6.4063   0.6312  -1.7627
 6MQ  C9   C  CR6   0   0.546   6.0630   0.7834   0.6341
 6MQ  O1   O  O     0  -0.485  -3.4080   0.5259   1.1814
 6MQ  O2   O  O     0  -0.470   6.5348   1.0036   1.7388
 6MQ  C10  C  CR66  0  -0.138   4.6828   0.4266   0.3586
 6MQ  N    N  NH1   0  -0.690  -0.8663  -0.7431   1.5614
 6MQ  C11  C  CR16  0  -0.396   3.7719   0.3139   1.4177
 6MQ  C12  C  CR56  0   0.175   2.4708  -0.0296   1.1292
 6MQ  C13  C  CR15  0  -0.009  -4.3478  -1.3895   0.2250
 6MQ  N2   N  N     0  -0.526   5.1851   0.3045  -2.0305
 6MQ  N3   N  NH2   0  -0.834   7.3089   0.8070  -2.7521
 6MQ  N4   N  NR16  0  -0.719   6.8544   0.8652  -0.4904
 6MQ  N1   N  NR15  0  -0.751   0.7709  -0.5734  -0.1626
 6MQ  N5   N  N     0  -0.534   1.3849  -0.2107   1.9558
 6MQ  C17  C  CR15  0  -0.047  -4.6466  -0.1711  -0.6730
 6MQ  O4   O  O2    0  -0.506  -6.0031   0.1121  -0.4346
 6MQ  C14  C  CT    0   0.447  -6.6005  -1.0227   0.1582
 6MQ  C15  C  CH3   0  -0.673  -7.1265  -1.9752  -0.9098
 6MQ  C16  C  CH3   0  -0.679  -7.6886  -0.5708   1.1078
 6MQ  O3   O  O2    0  -0.503  -5.5608  -1.6236   0.8988
 6MQ  H1   H  HCH3  0   0.238  -1.0373   2.2298  -1.3469
 6MQ  H2   H  HCH3  0   0.218  -2.3320   3.1083  -0.5100
 6MQ  H3   H  HCH3  0   0.220  -1.3115   1.9632   0.3818
 6MQ  H4   H  HCR5  0   0.241  -4.3102   1.8956   0.0054
 6MQ  H5   H  HCR5  0   0.271  -3.4766  -1.2241   2.2110
 6MQ  H6   H  HCH2  0   0.258  -1.8706  -2.4575   0.8596
 6MQ  H7   H  HCH2  0   0.247  -1.7393  -1.1365  -0.2880
 6MQ  H8   H  HCR6  0   0.263   2.6740  -0.3274  -2.3001
 6MQ  H9   H  HNH1  0   0.399  -0.9671  -0.8092   2.5630
 6MQ  H10  H  HCR6  0   0.255   4.0913   0.4950   2.4356
 6MQ  H11  H  HCR5  0   0.263  -4.0224  -2.2736  -0.3332
 6MQ  H12  H  HNH2  0   0.406   8.2922   0.7438  -2.5461
 6MQ  H13  H  HNH2  0   0.403   7.0428   0.4643  -3.6601
 6MQ  H14  H  HNR6  0   0.421   7.8219   1.1234  -0.3448
 6MQ  H15  H  HNR5  0   0.423   0.1926  -0.8098  -0.9518
 6MQ  H17  H  HCR5  0   0.263  -4.4477  -0.3466  -1.7341
 6MQ  H18  H  HCH3  0   0.241  -6.3367  -2.3002  -1.5903
 6MQ  H19  H  HCH3  0   0.237  -7.5598  -2.8625  -0.4481
 6MQ  H20  H  HCH3  0   0.237  -7.9031  -1.4923  -1.5037
 6MQ  H21  H  HCH3  0   0.240  -8.4697  -0.0407   0.5639
 6MQ  H22  H  HCH3  0   0.240  -8.1483  -1.4303   1.5947
 6MQ  H23  H  HCH3  0   0.243  -7.2861   0.0912   1.8746

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
 6MQ  C16  C14  single    1.513  0.020  1.513
 6MQ  O4   C14  single    1.413  0.020  1.413
 6MQ  O4   C17  single    1.406  0.020  1.406
 6MQ  C14  C15  single    1.525  0.020  1.525
 6MQ  C14  O3   single    1.411  0.020  1.411
 6MQ  C1   C17  single    1.531  0.020  1.531
 6MQ  C1   O1   single    1.401  0.020  1.401
 6MQ  C1   O    single    1.391  0.020  1.391
 6MQ  O3   C13  single    1.407  0.020  1.407
 6MQ  C17  C13  single    1.543  0.020  1.543
 6MQ  O1   C2   single    1.416  0.020  1.416
 6MQ  C    O    single    1.413  0.020  1.413
 6MQ  C13  C2   single    1.526  0.020  1.526
 6MQ  C2   C3   single    1.526  0.020  1.526
 6MQ  C3   N    single    1.441  0.020  1.441
 6MQ  N    C4   single    1.345  0.020  1.345
 6MQ  C4   N1   aromatic  1.371  0.020  1.371
 6MQ  C4   N5   aromatic  1.310  0.020  1.310
 6MQ  N1   C5   aromatic  1.370  0.020  1.370
 6MQ  N5   C12  aromatic  1.377  0.020  1.377
 6MQ  C5   C12  aromatic  1.417  0.020  1.417
 6MQ  C5   C6   aromatic  1.375  0.020  1.375
 6MQ  C12  C11  aromatic  1.376  0.020  1.376
 6MQ  C6   C7   aromatic  1.403  0.020  1.403
 6MQ  C11  C10  aromatic  1.401  0.020  1.401
 6MQ  C7   C10  aromatic  1.415  0.020  1.415
 6MQ  C7   N2   single    1.372  0.020  1.372
 6MQ  C10  C9   single    1.452  0.020  1.452
 6MQ  N2   C8   double    1.292  0.020  1.292
 6MQ  C9   O2   double    1.221  0.020  1.221
 6MQ  C9   N4   single    1.377  0.020  1.377
 6MQ  C8   N4   single    1.369  0.020  1.369
 6MQ  C8   N3   single    1.351  0.020  1.351
 6MQ  C    H1   single    0.970  0.020  1.090
 6MQ  C    H2   single    0.970  0.020  1.090
 6MQ  C    H3   single    0.970  0.020  1.090
 6MQ  C1   H4   single    0.970  0.020  1.090
 6MQ  C2   H5   single    0.970  0.020  1.090
 6MQ  C3   H6   single    0.970  0.020  1.090
 6MQ  C3   H7   single    0.970  0.020  1.090
 6MQ  C6   H8   single    0.930  0.020  1.080
 6MQ  N    H9   single    0.890  0.020  1.040
 6MQ  C11  H10  single    0.930  0.020  1.080
 6MQ  C13  H11  single    0.970  0.020  1.090
 6MQ  N3   H12  single    0.890  0.020  1.040
 6MQ  N3   H13  single    0.890  0.020  1.040
 6MQ  N4   H14  single    0.860  0.020  1.020
 6MQ  N1   H15  single    0.860  0.020  1.020
 6MQ  C17  H17  single    0.970  0.020  1.090
 6MQ  C15  H18  single    0.970  0.020  1.090
 6MQ  C15  H19  single    0.970  0.020  1.090
 6MQ  C15  H20  single    0.970  0.020  1.090
 6MQ  C16  H21  single    0.970  0.020  1.090
 6MQ  C16  H22  single    0.970  0.020  1.090
 6MQ  C16  H23  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
 6MQ  H3   C    H2   108.40  3.000
 6MQ  H3   C    H1   108.59  3.000
 6MQ  H2   C    H1   108.69  3.000
 6MQ  H3   C    O    112.27  3.000
 6MQ  H2   C    O    111.39  3.000
 6MQ  H1   C    O    107.41  3.000
 6MQ  H4   C1   C17  112.68  3.000
 6MQ  H4   C1   O1   107.10  3.000
 6MQ  C17  C1   O1   105.57  3.000
 6MQ  H4   C1   O    110.64  3.000
 6MQ  O1   C1   O    112.77  3.000
 6MQ  C17  C1   O    108.03  3.000
 6MQ  H5   C2   C13  111.15  3.000
 6MQ  H5   C2   O1   107.38  3.000
 6MQ  C13  C2   O1   105.16  3.000
 6MQ  H5   C2   C3   109.04  3.000
 6MQ  C13  C2   C3   110.78  3.000
 6MQ  O1   C2   C3   113.27  3.000
 6MQ  H7   C3   H6   106.86  3.000
 6MQ  H7   C3   N    109.99  3.000
 6MQ  H6   C3   N    111.57  3.000
 6MQ  H7   C3   C2   109.38  3.000
 6MQ  H6   C3   C2   108.03  3.000
 6MQ  N    C3   C2   110.89  3.000
 6MQ  N5   C4   N1   113.00  3.000
 6MQ  N5   C4   N    124.23  3.000
 6MQ  N1   C4   N    122.73  3.000
 6MQ  C1   O    C    114.20  3.000
 6MQ  N1   C5   C12  104.47  3.000
 6MQ  C12  C5   C6   123.66  3.000
 6MQ  N1   C5   C6   131.86  3.000
 6MQ  H8   C6   C7   120.08  3.000
 6MQ  H8   C6   C5   122.48  3.000
 6MQ  C7   C6   C5   117.44  3.000
 6MQ  N2   C7   C10  122.60  3.000
 6MQ  N2   C7   C6   117.99  3.000
 6MQ  C10  C7   C6   119.40  3.000
 6MQ  N4   C8   N3   116.09  3.000
 6MQ  N3   C8   N2   120.84  3.000
 6MQ  N4   C8   N2   123.03  3.000
 6MQ  N4   C9   C10  113.94  3.000
 6MQ  N4   C9   O2   120.38  3.000
 6MQ  C10  C9   O2   125.68  3.000
 6MQ  C2   O1   C1   109.20  3.000
 6MQ  C11  C10  C9   119.62  3.000
 6MQ  C9   C10  C7   118.35  3.000
 6MQ  C11  C10  C7   122.03  3.000
 6MQ  H9   N    C4   113.83  3.000
 6MQ  H9   N    C3   116.67  3.000
 6MQ  C4   N    C3   124.94  3.000
 6MQ  H10  C11  C12  121.20  3.000
 6MQ  H10  C11  C10  120.36  3.000
 6MQ  C12  C11  C10  118.43  3.000
 6MQ  N5   C12  C11  130.74  3.000
 6MQ  C11  C12  C5   119.03  3.000
 6MQ  N5   C12  C5   110.22  3.000
 6MQ  H11  C13  O3   111.46  3.000
 6MQ  H11  C13  C17  113.48  3.000
 6MQ  O3   C13  C17  104.07  3.000
 6MQ  H11  C13  C2   112.42  3.000
 6MQ  C17  C13  C2   104.04  3.000
 6MQ  O3   C13  C2   110.85  3.000
 6MQ  C8   N2   C7   117.98  3.000
 6MQ  H13  N3   H12  114.94  3.000
 6MQ  H13  N3   C8   116.10  3.000
 6MQ  H12  N3   C8   119.65  3.000
 6MQ  H14  N4   C9   116.55  3.000
 6MQ  H14  N4   C8   119.35  3.000
 6MQ  C9   N4   C8   124.09  3.000
 6MQ  H15  N1   C5   125.46  3.000
 6MQ  H15  N1   C4   127.26  3.000
 6MQ  C5   N1   C4   107.27  3.000
 6MQ  C12  N5   C4   105.03  3.000
 6MQ  H17  C17  O4   111.85  3.000
 6MQ  H17  C17  C13  113.75  3.000
 6MQ  O4   C17  C13  104.31  3.000
 6MQ  H17  C17  C1   111.88  3.000
 6MQ  C13  C17  C1   104.48  3.000
 6MQ  O4   C17  C1   110.08  3.000
 6MQ  C14  O4   C17  108.50  3.000
 6MQ  O3   C14  C16  109.13  3.000
 6MQ  O3   C14  C15  110.85  3.000
 6MQ  C16  C14  C15  112.21  3.000
 6MQ  O3   C14  O4   104.52  3.000
 6MQ  C15  C14  O4   110.71  3.000
 6MQ  C16  C14  O4   109.12  3.000
 6MQ  H20  C15  H19  107.95  3.000
 6MQ  H20  C15  H18  107.90  3.000
 6MQ  H19  C15  H18  108.01  3.000
 6MQ  H20  C15  C14  110.53  3.000
 6MQ  H19  C15  C14  110.42  3.000
 6MQ  H18  C15  C14  111.90  3.000
 6MQ  H23  C16  H22  108.69  3.000
 6MQ  H23  C16  H21  108.69  3.000
 6MQ  H22  C16  H21  107.73  3.000
 6MQ  H23  C16  C14  110.93  3.000
 6MQ  H22  C16  C14  110.38  3.000
 6MQ  H21  C16  C14  110.34  3.000
 6MQ  C14  O3   C13  108.24  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
 6MQ  CONST_01  C12  C5   N1   C4      0.00   0.0  0
 6MQ  CONST_02  C6   C5   N1   C4    180.00   0.0  0
 6MQ  CONST_03  C5   C12  N5   C4      0.00   0.0  0
 6MQ  CONST_04  C11  C12  N5   C4    180.00   0.0  0
 6MQ  CONST_05  N5   C4   N1   C5      0.00   0.0  0
 6MQ  CONST_06  C10  C11  C12  C5      0.00   0.0  0
 6MQ  CONST_07  C10  C7   C6   C5      0.00   0.0  0
 6MQ  CONST_08  N5   C12  C5   C6    180.00   0.0  0
 6MQ  CONST_09  C11  C12  C5   C6      0.00   0.0  0
 6MQ  CONST_10  C11  C10  C7   C6      0.00   0.0  0
 6MQ  CONST_11  N1   C5   C6   C7    180.00   0.0  0
 6MQ  CONST_12  C12  C5   C6   C7      0.00   0.0  0
 6MQ  CONST_13  C12  C11  C10  C7      0.00   0.0  0
 6MQ  CONST_14  N5   C12  C11  C10   180.00   0.0  0
 6MQ  CONST_15  N1   C5   C12  C11   180.00   0.0  0
 6MQ  CONST_16  N1   C4   N5   C12     0.00   0.0  0
 6MQ  CONST_17  N5   C12  C5   N1      0.00   0.0  0
 6MQ  CONST_18  N4   C8   N2   C7      0.00   0.0  0
 6MQ  CONST_19  C10  C9   N4   C8      0.00   0.0  0
 6MQ  CONST_20  N2   C8   N4   C9      0.00   0.0  0
 6MQ  CONST_21  N    C4   N1   C5    180.00   0.0  0
 6MQ  CONST_22  C12  N5   C4   N     180.00   0.0  0
 6MQ  CONST_23  N3   C8   N2   C7    180.00   0.0  0
 6MQ  CONST_24  O2   C9   N4   C8    180.00   0.0  0
 6MQ  CONST_25  N3   C8   N4   C9    180.00   0.0  0
 6MQ  CONST_26  H10  C11  C12  C5    180.00   0.0  0
 6MQ  CONST_27  H15  N1   C5   C6      0.00   0.0  0
 6MQ  CONST_28  H8   C6   C7   C10   180.00   0.0  0
 6MQ  CONST_29  H14  N4   C9   C10   180.00   0.0  0
 6MQ  CONST_31  N5   C4   N    C3    180.00   0.0  0
 6MQ  CONST_32  H9   N    C4   N1    180.00   0.0  0
 6MQ  CONST_34  H13  N3   C8   N2      0.00   0.0  0
 6MQ  Var_01    O4   C14  O3   C13   -32.25  30.0  1
 6MQ  Var_02    O3   C14  O4   C17    30.95  30.0  1
 6MQ  Var_03    C4   N    C3   C2   -152.89  30.0  3
 6MQ  Var_04    H21  C16  C14  O4     62.36  30.0  3
 6MQ  Var_05    H18  C15  C14  O4     57.98  30.0  3
 6MQ  Var_06    H1   C    O    C1   -175.36  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
 6MQ  chir_01  C1   C17  O1   O    negativ
 6MQ  chir_02  C2   O1   C13  C3   negativ
 6MQ  chir_03  C13  O3   C17  C2   negativ
 6MQ  chir_04  C17  O4   C1   C13  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
 6MQ  plan-1  C4   0.020
 6MQ  plan-1  C5   0.020
 6MQ  plan-1  C6   0.020
 6MQ  plan-1  C7   0.020
 6MQ  plan-1  C8   0.020
 6MQ  plan-1  C9   0.020
 6MQ  plan-1  O2   0.020
 6MQ  plan-1  C10  0.020
 6MQ  plan-1  N    0.020
 6MQ  plan-1  C11  0.020
 6MQ  plan-1  C12  0.020
 6MQ  plan-1  N2   0.020
 6MQ  plan-1  N3   0.020
 6MQ  plan-1  N4   0.020
 6MQ  plan-1  N1   0.020
 6MQ  plan-1  N5   0.020
 6MQ  plan-1  H8   0.020
 6MQ  plan-1  H10  0.020
 6MQ  plan-1  H12  0.020
 6MQ  plan-1  H13  0.020
 6MQ  plan-1  H14  0.020
 6MQ  plan-1  H15  0.020
 6MQ  plan-2  C3   0.020
 6MQ  plan-2  C4   0.020
 6MQ  plan-2  N    0.020
 6MQ  plan-2  H9   0.020

