# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 05:16:28 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-(2-pyren-1-ylethynyl)pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C#Cc3ccc4ccc5cccc6ccc3c4c56)C(=O)NC2=O
#
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
 UTB  UTB  1-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-(2-pyren-1-ylethynyl)pyrimidine-2,4-dione  ligand  54  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UTB
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
 UTB  C4    C  CR6   0   0.537  -2.6483   9.8333   3.2843
 UTB  C5    C  CR6   0  -0.422  -1.2402   9.5401   3.5122
 UTB  C2    C  CR6   0   0.749  -1.9224  11.8562   2.0473
 UTB  N1    N  NR6   0  -0.569  -0.6060  11.4951   2.2877
 UTB  C5'   C  CH2   0  -0.199   0.2777  15.9178   1.9863
 UTB  C4'   C  CH1   0  -0.015   0.8242  14.5890   1.5067
 UTB  O4'   O  O2    0  -0.490   0.4481  13.5729   2.4264
 UTB  C3'   C  CH1   0   0.046   0.3265  14.0975   0.1423
 UTB  C2'   C  CH2   0  -0.559   0.4952  12.5889   0.2722
 UTB  O3'   O  OH1   0  -0.663   1.0835  14.5932  -0.9322
 UTB  C1'   C  CH1   0   0.228   0.4866  12.3313   1.7854
 UTB  C6    C  CR16  0   0.061  -0.3073  10.3835   3.0073
 UTB  C7    C  CSP   0   0.141  -0.8928   8.3917   4.2564
 UTB  O4    O  O     0  -0.419  -3.5767   9.1585   3.6734
 UTB  N3    N  NR16  0  -0.736  -2.8551  10.9924   2.5609
 UTB  O2    O  O     0  -0.449  -2.2347  12.8466   1.4291
 UTB  C11   C  CSP   0   0.154  -0.6216   7.4068   4.9013
 UTB  C12   C  CR6   0  -0.123  -0.3406   6.2407   5.6567
 UTB  C13   C  CR66  0   0.078   0.9725   5.9338   6.0659
 UTB  C14   C  CR16  0  -0.319  -1.3937   5.3863   6.0005
 UTB  C15   C  CR16  0  -0.343  -1.1697   4.2432   6.7386
 UTB  C16   C  C     0   0.134   1.1978   4.7584   6.8236
 UTB  C17   C  CR66  0   0.069   0.1180   3.9072   7.1630
 UTB  C18   C  CR16  0  -0.356   2.0895   6.7676   5.7445
 UTB  C19   C  CR16  0  -0.319   3.3413   6.4516   6.1491
 UTB  C20   C  C     0   0.115   2.5133   4.4292   7.2494
 UTB  C21   C  CR66  0   0.088   3.6002   5.2719   6.9160
 UTB  C22   C  CR16  0  -0.337   4.8851   4.9312   7.3420
 UTB  C23   C  CR16  0  -0.248   5.0994   3.7813   8.0859
 UTB  C24   C  CR66  0   0.094   2.7408   3.2557   8.0100
 UTB  C25   C  CR16  0  -0.336   4.0401   2.9505   8.4182
 UTB  C26   C  CR16  0  -0.330   1.6275   2.4170   8.3369
 UTB  C27   C  CR16  0  -0.322   0.3753   2.7286   7.9313
 UTB  HO5'  H  HOH1  0   0.446  -1.4477  15.2616   2.5665
 UTB  H5'   H  HCH2  0   0.228   0.6242  16.6910   1.2965
 UTB  H5''  H  HCH2  0   0.217   0.7188  16.1499   2.9648
 UTB  H4'   H  HCH1  0   0.226   1.9209  14.6740   1.4626
 UTB  H3'   H  HCH1  0   0.231  -0.7306  14.3480   0.0249
 UTB  H2''  H  HCH2  0   0.279  -0.2568  12.0157  -0.2669
 UTB  H2'   H  HCH2  0   0.269   1.4708  12.3004  -0.1238
 UTB  H1    H  HOH1  0   0.453   0.7802  15.4837  -1.1325
 UTB  H1'   H  HCH1  0   0.259   1.3921  11.7887   2.0696
 UTB  H6    H  HCR6  0   0.335   0.7459  10.1913   3.1599
 UTB  H3    H  HNR6  0   0.432  -3.8194  11.2491   2.3825
 UTB  H19   H  HCR6  0   0.262  -2.3972   5.6327   5.6796
 UTB  H20   H  HCR6  0   0.263  -2.0001   3.5969   6.9945
 UTB  H12   H  HCR6  0   0.254   1.9213   7.6664   5.1651
 UTB  H13   H  HCR6  0   0.260   4.1731   7.0969   5.8939
 UTB  H14   H  HCR6  0   0.261   5.7169   5.5759   7.0856
 UTB  H15   H  HCR6  0   0.261   6.1009   3.5295   8.4091
 UTB  H16   H  HCR6  0   0.261   4.2158   2.0541   9.0004
 UTB  H17   H  HCR6  0   0.259   1.8084   1.5223   8.9201
 UTB  H18   H  HCR6  0   0.259  -0.4583   2.0853   8.1854
 UTB  O5'   O  OH1   0  -0.655  -1.1251  15.9827   2.0166

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
 UTB  O3'  C3'   single    1.405  0.020  1.405
 UTB  C3'  C2'   single    1.524  0.020  1.524
 UTB  C3'  C4'   single    1.533  0.020  1.533
 UTB  C2'  C1'   single    1.535  0.020  1.535
 UTB  O5'  C5'   single    1.405  0.020  1.405
 UTB  O2   C2    double    1.209  0.020  1.209
 UTB  C4'  C5'   single    1.515  0.020  1.515
 UTB  C4'  O4'   single    1.421  0.020  1.421
 UTB  C2   N1    single    1.386  0.020  1.386
 UTB  C2   N3    single    1.371  0.020  1.371
 UTB  C1'  N1    single    1.465  0.020  1.465
 UTB  C1'  O4'   single    1.398  0.020  1.398
 UTB  N1   C6    single    1.357  0.020  1.357
 UTB  N3   C4    single    1.382  0.020  1.382
 UTB  C6   C5    double    1.355  0.020  1.355
 UTB  C4   O4    double    1.212  0.020  1.212
 UTB  C4   C5    single    1.456  0.020  1.456
 UTB  C5   C7    single    1.412  0.020  1.412
 UTB  C7   C11   triple    1.208  0.020  1.208
 UTB  C11  C12   single    1.418  0.020  1.418
 UTB  C18  C19   aromatic  1.353  0.020  1.353
 UTB  C18  C13   aromatic  1.431  0.020  1.431
 UTB  C12  C13   aromatic  1.409  0.020  1.409
 UTB  C12  C14   aromatic  1.399  0.020  1.399
 UTB  C19  C21   aromatic  1.431  0.020  1.431
 UTB  C13  C16   aromatic  1.416  0.020  1.416
 UTB  C14  C15   aromatic  1.379  0.020  1.379
 UTB  C21  C22   aromatic  1.396  0.020  1.396
 UTB  C21  C20   aromatic  1.415  0.020  1.415
 UTB  C16  C20   aromatic  1.421  0.020  1.421
 UTB  C16  C17   aromatic  1.416  0.020  1.416
 UTB  C22  C23   aromatic  1.386  0.020  1.386
 UTB  C15  C17   aromatic  1.397  0.020  1.397
 UTB  C20  C24   aromatic  1.417  0.020  1.417
 UTB  C17  C27   aromatic  1.430  0.020  1.430
 UTB  C23  C25   aromatic  1.387  0.020  1.387
 UTB  C24  C25   aromatic  1.396  0.020  1.396
 UTB  C24  C26   aromatic  1.432  0.020  1.432
 UTB  C27  C26   aromatic  1.353  0.020  1.353
 UTB  O5'  HO5'  single    0.850  0.020  0.980
 UTB  C5'  H5'   single    0.970  0.020  1.090
 UTB  C5'  H5''  single    0.970  0.020  1.090
 UTB  C4'  H4'   single    0.970  0.020  1.090
 UTB  C3'  H3'   single    0.970  0.020  1.090
 UTB  C2'  H2''  single    0.970  0.020  1.090
 UTB  C2'  H2'   single    0.970  0.020  1.090
 UTB  O3'  H1    single    0.850  0.020  0.980
 UTB  C1'  H1'   single    0.970  0.020  1.090
 UTB  C6   H6    single    0.930  0.020  1.080
 UTB  N3   H3    single    0.860  0.020  1.020
 UTB  C14  H19   single    0.930  0.020  1.080
 UTB  C15  H20   single    0.930  0.020  1.080
 UTB  C18  H12   single    0.930  0.020  1.080
 UTB  C19  H13   single    0.930  0.020  1.080
 UTB  C22  H14   single    0.930  0.020  1.080
 UTB  C23  H15   single    0.930  0.020  1.080
 UTB  C25  H16   single    0.930  0.020  1.080
 UTB  C26  H17   single    0.930  0.020  1.080
 UTB  C27  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
 UTB  N3    C4   O4    121.36  3.000
 UTB  O4    C4   C5    125.34  3.000
 UTB  N3    C4   C5    113.30  3.000
 UTB  C7    C5   C6    122.22  3.000
 UTB  C7    C5   C4    118.96  3.000
 UTB  C6    C5   C4    118.82  3.000
 UTB  O2    C2   N3    122.15  3.000
 UTB  N3    C2   N1    114.64  3.000
 UTB  O2    C2   N1    123.21  3.000
 UTB  C6    N1   C1'   119.03  3.000
 UTB  C6    N1   C2    120.95  3.000
 UTB  C1'   N1   C2    120.01  3.000
 UTB  H5''  C5'  H5'   106.59  3.000
 UTB  H5''  C5'  C4'   108.82  3.000
 UTB  H5'   C5'  C4'   107.84  3.000
 UTB  H5''  C5'  O5'   111.85  3.000
 UTB  H5'   C5'  O5'   107.32  3.000
 UTB  C4'   C5'  O5'   114.06  3.000
 UTB  H4'   C4'  C3'   108.21  3.000
 UTB  H4'   C4'  O4'   110.17  3.000
 UTB  C3'   C4'  O4'   105.12  3.000
 UTB  H4'   C4'  C5'   107.72  3.000
 UTB  O4'   C4'  C5'   109.08  3.000
 UTB  C3'   C4'  C5'   116.47  3.000
 UTB  C1'   O4'  C4'   109.33  3.000
 UTB  H3'   C3'  O3'   110.99  3.000
 UTB  H3'   C3'  C2'   110.08  3.000
 UTB  O3'   C3'  C2'   110.79  3.000
 UTB  H3'   C3'  C4'   109.65  3.000
 UTB  C2'   C3'  C4'   101.86  3.000
 UTB  O3'   C3'  C4'   113.12  3.000
 UTB  H2'   C2'  H2''  107.37  3.000
 UTB  H2'   C2'  C1'   108.56  3.000
 UTB  H2''  C2'  C1'   113.33  3.000
 UTB  H2'   C2'  C3'   109.25  3.000
 UTB  H2''  C2'  C3'   113.74  3.000
 UTB  C1'   C2'  C3'   104.45  3.000
 UTB  H1    O3'  C3'   108.43  3.000
 UTB  H1'   C1'  C2'   109.57  3.000
 UTB  H1'   C1'  O4'   110.15  3.000
 UTB  C2'   C1'  O4'   107.65  3.000
 UTB  H1'   C1'  N1    104.20  3.000
 UTB  O4'   C1'  N1    109.23  3.000
 UTB  C2'   C1'  N1    115.98  3.000
 UTB  H6    C6   N1    115.76  3.000
 UTB  H6    C6   C5    120.48  3.000
 UTB  N1    C6   C5    123.76  3.000
 UTB  C11   C7   C5    180.00  3.000
 UTB  H3    N3   C2    114.94  3.000
 UTB  H3    N3   C4    116.54  3.000
 UTB  C2    N3   C4    128.52  3.000
 UTB  C12   C11  C7    180.00  3.000
 UTB  C14   C12  C13   119.80  3.000
 UTB  C14   C12  C11   118.96  3.000
 UTB  C13   C12  C11   121.24  3.000
 UTB  C18   C13  C16   118.66  3.000
 UTB  C16   C13  C12   118.97  3.000
 UTB  C18   C13  C12   122.37  3.000
 UTB  H19   C14  C15   119.88  3.000
 UTB  H19   C14  C12   119.09  3.000
 UTB  C15   C14  C12   121.03  3.000
 UTB  H20   C15  C17   119.44  3.000
 UTB  H20   C15  C14   119.78  3.000
 UTB  C17   C15  C14   120.78  3.000
 UTB  C20   C16  C17   119.65  3.000
 UTB  C17   C16  C13   120.37  3.000
 UTB  C20   C16  C13   119.98  3.000
 UTB  C27   C17  C16   119.13  3.000
 UTB  C27   C17  C15   121.82  3.000
 UTB  C16   C17  C15   119.05  3.000
 UTB  H12   C18  C19   119.85  3.000
 UTB  H12   C18  C13   118.88  3.000
 UTB  C19   C18  C13   121.27  3.000
 UTB  H13   C19  C21   118.59  3.000
 UTB  H13   C19  C18   120.06  3.000
 UTB  C21   C19  C18   121.36  3.000
 UTB  C24   C20  C21   119.76  3.000
 UTB  C24   C20  C16   120.09  3.000
 UTB  C21   C20  C16   120.15  3.000
 UTB  C22   C21  C20   119.32  3.000
 UTB  C20   C21  C19   118.58  3.000
 UTB  C22   C21  C19   122.10  3.000
 UTB  H14   C22  C23   120.14  3.000
 UTB  H14   C22  C21   119.30  3.000
 UTB  C23   C22  C21   120.56  3.000
 UTB  H15   C23  C25   119.74  3.000
 UTB  H15   C23  C22   119.76  3.000
 UTB  C25   C23  C22   120.50  3.000
 UTB  C26   C24  C25   121.94  3.000
 UTB  C26   C24  C20   118.88  3.000
 UTB  C25   C24  C20   119.18  3.000
 UTB  H16   C25  C24   119.29  3.000
 UTB  H16   C25  C23   120.05  3.000
 UTB  C24   C25  C23   120.67  3.000
 UTB  H17   C26  C27   120.41  3.000
 UTB  H17   C26  C24   118.49  3.000
 UTB  C27   C26  C24   121.10  3.000
 UTB  H18   C27  C26   120.35  3.000
 UTB  H18   C27  C17   118.49  3.000
 UTB  C26   C27  C17   121.16  3.000
 UTB  HO5'  O5'  C5'   108.21  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
 UTB  CONST_01  C19  C18  C13  C12  180.00  0.0  0
 UTB  CONST_02  C20  C16  C13  C12  180.00  0.0  0
 UTB  CONST_03  C17  C16  C13  C12    0.00  0.0  0
 UTB  CONST_04  C17  C15  C14  C12    0.00  0.0  0
 UTB  CONST_05  C21  C19  C18  C13    0.00  0.0  0
 UTB  CONST_06  C15  C14  C12  C13    0.00  0.0  0
 UTB  CONST_07  C21  C20  C16  C13    0.00  0.0  0
 UTB  CONST_08  C24  C20  C16  C13  180.00  0.0  0
 UTB  CONST_09  C15  C17  C16  C13    0.00  0.0  0
 UTB  CONST_10  C27  C17  C16  C13  180.00  0.0  0
 UTB  CONST_11  C18  C13  C12  C14  180.00  0.0  0
 UTB  CONST_12  C16  C13  C12  C14    0.00  0.0  0
 UTB  CONST_13  C16  C17  C15  C14    0.00  0.0  0
 UTB  CONST_14  C27  C17  C15  C14  180.00  0.0  0
 UTB  CONST_15  C20  C16  C17  C15  180.00  0.0  0
 UTB  CONST_16  C26  C27  C17  C15  180.00  0.0  0
 UTB  CONST_17  C19  C18  C13  C16    0.00  0.0  0
 UTB  CONST_18  C19  C21  C20  C16    0.00  0.0  0
 UTB  CONST_19  C22  C21  C20  C16  180.00  0.0  0
 UTB  CONST_20  C25  C24  C20  C16  180.00  0.0  0
 UTB  CONST_21  C26  C24  C20  C16    0.00  0.0  0
 UTB  CONST_22  C26  C27  C17  C16    0.00  0.0  0
 UTB  CONST_23  C18  C13  C16  C17  180.00  0.0  0
 UTB  CONST_24  C21  C20  C16  C17  180.00  0.0  0
 UTB  CONST_25  C24  C20  C16  C17    0.00  0.0  0
 UTB  CONST_26  C24  C26  C27  C17    0.00  0.0  0
 UTB  CONST_27  C22  C21  C19  C18  180.00  0.0  0
 UTB  CONST_28  C20  C21  C19  C18    0.00  0.0  0
 UTB  CONST_29  C20  C16  C13  C18    0.00  0.0  0
 UTB  CONST_30  C23  C22  C21  C19  180.00  0.0  0
 UTB  CONST_31  C24  C20  C21  C19  180.00  0.0  0
 UTB  CONST_32  C23  C22  C21  C20    0.00  0.0  0
 UTB  CONST_33  C27  C17  C16  C20    0.00  0.0  0
 UTB  CONST_34  C23  C25  C24  C20    0.00  0.0  0
 UTB  CONST_35  C27  C26  C24  C20    0.00  0.0  0
 UTB  CONST_36  C25  C23  C22  C21    0.00  0.0  0
 UTB  CONST_37  C25  C24  C20  C21    0.00  0.0  0
 UTB  CONST_38  C26  C24  C20  C21  180.00  0.0  0
 UTB  CONST_39  C24  C20  C21  C22    0.00  0.0  0
 UTB  CONST_40  C24  C25  C23  C22    0.00  0.0  0
 UTB  CONST_41  C26  C24  C25  C23  180.00  0.0  0
 UTB  CONST_42  C27  C26  C24  C25  180.00  0.0  0
 UTB  CONST_43  N1   C2   N3   C4     0.00  0.0  0
 UTB  CONST_44  C2   N3   C4   C5     0.00  0.0  0
 UTB  CONST_45  N3   C2   N1   C1'  180.00  0.0  0
 UTB  CONST_46  N3   C2   N1   C6     0.00  0.0  0
 UTB  CONST_47  C18  C13  C12  C11    0.00  0.0  0
 UTB  CONST_48  C16  C13  C12  C11  180.00  0.0  0
 UTB  CONST_49  C15  C14  C12  C11  180.00  0.0  0
 UTB  CONST_50  O2   C2   N3   C4   180.00  0.0  0
 UTB  CONST_51  O4   C4   N3   C2   180.00  0.0  0
 UTB  CONST_52  O2   C2   N1   C1'    0.00  0.0  0
 UTB  CONST_53  O2   C2   N1   C6   180.00  0.0  0
 UTB  CONST_54  H12  C18  C13  C12    0.00  0.0  0
 UTB  CONST_55  H20  C15  C14  C12  180.00  0.0  0
 UTB  CONST_56  H13  C19  C18  C13  180.00  0.0  0
 UTB  CONST_57  H19  C14  C12  C13  180.00  0.0  0
 UTB  CONST_58  H18  C27  C17  C15    0.00  0.0  0
 UTB  CONST_59  H17  C26  C27  C17  180.00  0.0  0
 UTB  CONST_60  H14  C22  C21  C19    0.00  0.0  0
 UTB  CONST_61  H16  C25  C24  C20  180.00  0.0  0
 UTB  CONST_62  H15  C23  C22  C21  180.00  0.0  0
 UTB  CONST_63  H3   N3   C4   C5   180.00  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
 UTB  chir_01  C4'  C3'  C5'  O4'  negativ
 UTB  chir_02  C3'  O3'  C2'  C4'  negativ
 UTB  chir_03  C1'  O4'  N1   C2'  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
 UTB  plan-1  C4   0.020
 UTB  plan-1  C5   0.020
 UTB  plan-1  C2   0.020
 UTB  plan-1  N1   0.020
 UTB  plan-1  C1'  0.020
 UTB  plan-1  C6   0.020
 UTB  plan-1  C7   0.020
 UTB  plan-1  O4   0.020
 UTB  plan-1  N3   0.020
 UTB  plan-1  O2   0.020
 UTB  plan-1  C11  0.020
 UTB  plan-1  H6   0.020
 UTB  plan-1  H3   0.020
 UTB  plan-2  C7   0.020
 UTB  plan-2  C11  0.020
 UTB  plan-2  C12  0.020
 UTB  plan-2  C13  0.020
 UTB  plan-2  C14  0.020
 UTB  plan-2  C15  0.020
 UTB  plan-2  C16  0.020
 UTB  plan-2  C17  0.020
 UTB  plan-2  C18  0.020
 UTB  plan-2  C19  0.020
 UTB  plan-2  C20  0.020
 UTB  plan-2  C21  0.020
 UTB  plan-2  C22  0.020
 UTB  plan-2  C23  0.020
 UTB  plan-2  C24  0.020
 UTB  plan-2  C25  0.020
 UTB  plan-2  C26  0.020
 UTB  plan-2  C27  0.020
 UTB  plan-2  H19  0.020
 UTB  plan-2  H20  0.020
 UTB  plan-2  H12  0.020
 UTB  plan-2  H13  0.020
 UTB  plan-2  H14  0.020
 UTB  plan-2  H15  0.020
 UTB  plan-2  H16  0.020
 UTB  plan-2  H17  0.020
 UTB  plan-2  H18  0.020

