# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:33:53 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@@H]2O[P@](O)(=S)O[C@H]12)N3C=CC(=O)NC3=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
 UPT  UPT  1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione  ligand  31  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UPT
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
 UPT  S    S  S1    0  -0.458  -4.1251  -1.0625  -1.1071
 UPT  P    P  P     0   1.187  -2.8694  -1.0007   0.3310
 UPT  O    O  O2    0  -0.566  -2.6081   0.4158   1.0635
 UPT  O5   O  OH1   0  -0.697  -3.1761  -1.9519   1.5690
 UPT  O6   O  O2    0  -0.568  -1.3311  -1.2773  -0.0859
 UPT  C1   C  CR15  0  -0.061  -0.4194  -0.3800   0.5329
 UPT  C2   C  CR15  0  -0.029  -1.2541   0.8260   0.9888
 UPT  C3   C  CR15  0  -0.004  -0.9997   1.8605  -0.1096
 UPT  C4   C  CH2   0  -0.158  -1.1265   3.2847   0.3682
 UPT  O2   O  OH1   0  -0.664  -0.9156   4.1469  -0.7186
 UPT  O1   O  O     0  -0.479   0.3332   1.5978  -0.5072
 UPT  C    C  CR15  0   0.168   0.5484   0.2120  -0.5111
 UPT  N    N  NR6   0  -0.570   1.9420  -0.0199  -0.2074
 UPT  C8   C  CR6   0   0.747   2.7222  -0.7397  -1.0961
 UPT  O4   O  O     0  -0.470   2.2908  -1.2106  -2.1257
 UPT  N1   N  NR16  0  -0.735   4.0280  -0.8822  -0.7140
 UPT  C7   C  CR6   0   0.573   4.6450  -0.3972   0.4300
 UPT  O3   O  O     0  -0.454   5.8238  -0.6084   0.6344
 UPT  C5   C  CR16  0  -0.507   3.7564   0.3451   1.2938
 UPT  C6   C  CR16  0   0.105   2.4733   0.5019   0.9425
 UPT  H2   H  HCR5  0   0.319   0.0942  -0.8928   1.3484
 UPT  H3   H  HCR5  0   0.309  -0.9465   1.1893   1.9714
 UPT  H4   H  HCR5  0   0.258  -1.6950   1.6872  -0.9444
 UPT  H5   H  HCH2  0   0.217  -2.1288   3.4000   0.8007
 UPT  H6   H  HCH2  0   0.209  -0.4048   3.4538   1.1784
 UPT  H7   H  HOH1  0   0.462  -0.9874   5.0520  -0.4023
 UPT  H8   H  HCR5  0   0.302   0.3461  -0.2288  -1.4895
 UPT  H9   H  HNR6  0   0.430   4.6071  -1.4116  -1.3548
 UPT  H10  H  HCR6  0   0.299   4.1328   0.7717   2.2102
 UPT  H11  H  HCR6  0   0.325   1.7949   1.0649   1.5678
 UPT  H1   H  HOH1  0   0.507  -3.8221  -2.6474   1.3830

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
 UPT  O3  C7   double  1.215  0.020  1.215
 UPT  C7  N1   single  1.387  0.020  1.387
 UPT  C7  C5   single  1.445  0.020  1.445
 UPT  N1  C8   single  1.368  0.020  1.368
 UPT  C5  C6   double  1.339  0.020  1.339
 UPT  C8  O4   double  1.212  0.020  1.212
 UPT  C8  N    single  1.384  0.020  1.384
 UPT  O6  C1   single  1.421  0.020  1.421
 UPT  O6  P    single  1.618  0.020  1.618
 UPT  C6  N    single  1.370  0.020  1.370
 UPT  N   C    single  1.445  0.020  1.445
 UPT  O5  P    single  1.591  0.020  1.591
 UPT  C1  C    single  1.542  0.020  1.542
 UPT  C1  C2   single  1.536  0.020  1.536
 UPT  P   S    double  1.910  0.020  1.910
 UPT  P   O    single  1.616  0.020  1.616
 UPT  C   O1   single  1.402  0.020  1.402
 UPT  C2  O    single  1.417  0.020  1.417
 UPT  C2  C3   single  1.530  0.020  1.530
 UPT  O1  C3   single  1.416  0.020  1.416
 UPT  O2  C4   single  1.403  0.020  1.403
 UPT  C3  C4   single  1.507  0.020  1.507
 UPT  C1  H2   single  0.970  0.020  1.090
 UPT  C2  H3   single  0.970  0.020  1.090
 UPT  C3  H4   single  0.970  0.020  1.090
 UPT  C4  H5   single  0.970  0.020  1.090
 UPT  C4  H6   single  0.970  0.020  1.090
 UPT  O2  H7   single  0.850  0.020  0.980
 UPT  C   H8   single  0.970  0.020  1.090
 UPT  N1  H9   single  0.860  0.020  1.020
 UPT  C5  H10  single  0.930  0.020  1.080
 UPT  C6  H11  single  0.930  0.020  1.080
 UPT  O5  H1   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
 UPT  O6   P   O5  106.36  3.000
 UPT  O5   P   O   101.68  3.000
 UPT  O6   P   O    96.49  3.000
 UPT  O    P   S   118.42  3.000
 UPT  O5   P   S   116.09  3.000
 UPT  O6   P   S   115.19  3.000
 UPT  C2   O   P   112.61  3.000
 UPT  H1   O5  P   114.14  3.000
 UPT  C1   O6  P   112.95  3.000
 UPT  H2   C1  C   113.01  3.000
 UPT  H2   C1  C2  113.75  3.000
 UPT  C    C1  C2  103.92  3.000
 UPT  H2   C1  O6  109.31  3.000
 UPT  C2   C1  O6  106.05  3.000
 UPT  C    C1  O6  110.51  3.000
 UPT  H3   C2  C3  111.98  3.000
 UPT  H3   C2  C1  112.04  3.000
 UPT  C3   C2  C1  103.15  3.000
 UPT  H3   C2  O   108.55  3.000
 UPT  C3   C2  O   113.11  3.000
 UPT  C1   C2  O   107.92  3.000
 UPT  H4   C3  O1  110.65  3.000
 UPT  H4   C3  C4  109.65  3.000
 UPT  O1   C3  C4  110.09  3.000
 UPT  H4   C3  C2  109.46  3.000
 UPT  C4   C3  C2  113.40  3.000
 UPT  O1   C3  C2  103.46  3.000
 UPT  H6   C4  H5  107.05  3.000
 UPT  H6   C4  O2  112.21  3.000
 UPT  H5   C4  O2  112.20  3.000
 UPT  H6   C4  C3  108.91  3.000
 UPT  H5   C4  C3  107.51  3.000
 UPT  O2   C4  C3  108.81  3.000
 UPT  H7   O2  C4  108.20  3.000
 UPT  C    O1  C3  109.19  3.000
 UPT  H8   C   N   107.59  3.000
 UPT  H8   C   O1  111.90  3.000
 UPT  N    C   O1  107.82  3.000
 UPT  H8   C   C1  109.59  3.000
 UPT  O1   C   C1  106.33  3.000
 UPT  N    C   C1  113.67  3.000
 UPT  C6   N   C8  121.22  3.000
 UPT  C6   N   C   119.30  3.000
 UPT  C8   N   C   119.47  3.000
 UPT  N1   C8  O4  122.46  3.000
 UPT  O4   C8  N   123.16  3.000
 UPT  N1   C8  N   114.38  3.000
 UPT  H9   N1  C7  116.75  3.000
 UPT  H9   N1  C8  115.05  3.000
 UPT  C7   N1  C8  128.21  3.000
 UPT  C5   C7  O3  125.84  3.000
 UPT  C5   C7  N1  113.52  3.000
 UPT  O3   C7  N1  120.63  3.000
 UPT  H10  C5  C6  120.72  3.000
 UPT  H10  C5  C7  119.77  3.000
 UPT  C6   C5  C7  119.50  3.000
 UPT  H11  C6  C5  120.69  3.000
 UPT  H11  C6  N   116.14  3.000
 UPT  C5   C6  N   123.17  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
 UPT  CONST_01  N1  C8  N   C   180.00  0.0  0
 UPT  CONST_02  C7  N1  C8  N     0.00  0.0  0
 UPT  CONST_03  C5  C7  N1  C8    0.00  0.0  0
 UPT  CONST_04  C6  N   C8  N1    0.00  0.0  0
 UPT  CONST_05  O4  C8  N   C     0.00  0.0  0
 UPT  CONST_06  O3  C7  N1  C8  180.00  0.0  0
 UPT  CONST_07  C7  N1  C8  O4  180.00  0.0  0
 UPT  CONST_08  C6  N   C8  O4  180.00  0.0  0
 UPT  CONST_09  H9  N1  C8  N   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
 UPT  chir_02  C1  O6  C   C2  negativ
 UPT  chir_03  C2  O   C3  C1  positiv
 UPT  chir_04  C3  O1  C2  C4  negativ
 UPT  chir_05  C   O1  N   C1  negativ
 UPT  chir_06  P   O5  S   O   both

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
 UPT  plan-1  C    0.020
 UPT  plan-1  N    0.020
 UPT  plan-1  C8   0.020
 UPT  plan-1  O4   0.020
 UPT  plan-1  N1   0.020
 UPT  plan-1  C7   0.020
 UPT  plan-1  O3   0.020
 UPT  plan-1  C5   0.020
 UPT  plan-1  C6   0.020
 UPT  plan-1  H9   0.020
 UPT  plan-1  H10  0.020
 UPT  plan-1  H11  0.020

