# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 12:54:29 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-[(5E)-5,6-dideoxy-2-O-methyl-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-2,4-dihydroxypyrimidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)[C@H](O[C@H]1[n+]2ccc(O)nc2O)\C=C\[P](O)(O)=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
 UVP  UVP  1-[(5E)-5,6-dideoxy-2-O-methyl-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-2,4-dihydroxypyrimidin-1-ium  ligand  36  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UVP
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
 UVP  OP   O  O      0  -0.894   3.8730  -2.5174  -0.4366
 UVP  P    P  P      0   1.152   2.8918  -1.7598   0.4595
 UVP  OP1  O  OP    -1  -0.870   1.6508  -2.5833   0.8491
 UVP  OP2  O  OP    -1  -0.885   3.5371  -1.0121   1.6258
 UVP  C6'  C  C1     0  -0.561   2.1242  -0.4790  -0.6172
 UVP  C5'  C  C1     0  -0.276   1.8930   0.7854  -0.2693
 UVP  C4'  C  CH1    0  -0.044   0.9968   1.7280  -1.0256
 UVP  O4'  O  O2     0  -0.479  -0.1124   1.0245  -1.6300
 UVP  C3'  C  CH1    0  -0.033   0.3287   2.7555  -0.1088
 UVP  O3'  O  OH1    0  -0.668  -0.2245   3.8377  -0.8044
 UVP  C2'  C  CH1    0  -0.007  -0.8268   1.9083   0.4232
 UVP  O2'  O  O2     0  -0.477  -1.9233   2.5720   0.9492
 UVP  CB'  C  CH3    0  -0.414  -1.6706   3.1868   2.1940
 UVP  C1'  C  CH1    0   0.189  -1.2470   1.1677  -0.8486
 UVP  N1   N  NR6    1  -0.530  -1.8277  -0.1674  -0.5418
 UVP  C2   C  CR6    0   0.764  -3.1316  -0.4536  -0.7479
 UVP  O2   O  OH1    0  -0.559  -3.8692   0.5118  -1.2138
 UVP  N3   N  N      0  -0.484  -3.6583  -1.6222  -0.5013
 UVP  C4   C  CR6    0   0.579  -2.8920  -2.5847  -0.0185
 UVP  O4   O  OH1    0  -0.540  -3.5032  -3.7170   0.1938
 UVP  C5   C  CR16   0  -0.504  -1.5256  -2.3774   0.2428
 UVP  C6   C  CR16   0   0.122  -1.0371  -1.1456  -0.0324
 UVP  H3   H  H      0   0.224   1.6725  -0.8398  -1.5425
 UVP  H5   H  H      0   0.237   2.3376   1.1708   0.6457
 UVP  H7   H  HCH1   0   0.274   1.5358   2.2231  -1.8397
 UVP  H8   H  HCH1   0   0.265   1.0116   3.0805   0.6851
 UVP  H9   H  HOH1   0   0.460   0.4935   4.3725  -1.1581
 UVP  H10  H  HCH1   0   0.258  -0.4052   1.1978   1.1536
 UVP  H11  H  HCH3   0   0.216  -1.2830   2.4708   2.9266
 UVP  H12  H  HCH3   0   0.221  -0.9598   4.0142   2.1108
 UVP  H13  H  HCH3   0   0.244  -2.6161   3.5814   2.5609
 UVP  H14  H  HCH1   0   0.299  -2.0169   1.7240  -1.3827
 UVP  H16  H  HCR6   0   0.326  -0.8629  -3.1356   0.6340
 UVP  H17  H  HCR6   0   0.371   0.0043  -0.9192   0.1507
 UVP  H4   H  HOH1   0   0.516  -4.7811   0.2053  -1.3392
 UVP  H6   H  HOH1   0   0.510  -2.9064  -4.3896   0.5509

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
 UVP  OP   P    deloc     1.530  0.020  1.530
 UVP  OP1  P    deloc     1.539  0.020  1.539
 UVP  P    OP2  deloc     1.528  0.020  1.528
 UVP  P    C6'  single    1.841  0.020  1.841
 UVP  C5'  C6'  double    1.332  0.020  1.332
 UVP  C5'  C4'  single    1.505  0.020  1.505
 UVP  C3'  O3'  single    1.400  0.020  1.400
 UVP  C3'  C4'  single    1.531  0.020  1.531
 UVP  C3'  C2'  single    1.528  0.020  1.528
 UVP  C4'  O4'  single    1.446  0.020  1.446
 UVP  C2'  O2'  single    1.385  0.020  1.385
 UVP  C2'  C1'  single    1.531  0.020  1.531
 UVP  O2'  CB'  single    1.411  0.020  1.411
 UVP  O4'  C1'  single    1.385  0.020  1.385
 UVP  C1'  N1   single    1.488  0.020  1.488
 UVP  C6   N1   aromatic  1.357  0.020  1.357
 UVP  C6   C5   aromatic  1.353  0.020  1.353
 UVP  N1   C2   aromatic  1.351  0.020  1.351
 UVP  C5   C4   aromatic  1.407  0.020  1.407
 UVP  C2   O2   single    1.301  0.020  1.301
 UVP  C2   N3   aromatic  1.305  0.020  1.305
 UVP  C4   N3   aromatic  1.322  0.020  1.322
 UVP  C4   O4   single    1.304  0.020  1.304
 UVP  C6'  H3   single    0.930  0.020  1.080
 UVP  C5'  H5   single    0.930  0.020  1.080
 UVP  C4'  H7   single    0.970  0.020  1.090
 UVP  C3'  H8   single    0.970  0.020  1.090
 UVP  O3'  H9   single    0.850  0.020  0.980
 UVP  C2'  H10  single    0.970  0.020  1.090
 UVP  CB'  H11  single    0.970  0.020  1.090
 UVP  CB'  H12  single    0.970  0.020  1.090
 UVP  CB'  H13  single    0.970  0.020  1.090
 UVP  C1'  H14  single    0.970  0.020  1.090
 UVP  C5   H16  single    0.930  0.020  1.080
 UVP  C6   H17  single    0.930  0.020  1.080
 UVP  O2   H4   single    0.850  0.020  0.980
 UVP  O4   H6   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
 UVP  C6'  P    OP2  106.38  3.000
 UVP  C6'  P    OP1  100.61  3.000
 UVP  OP2  P    OP1  114.14  3.000
 UVP  C6'  P    OP   105.63  3.000
 UVP  OP2  P    OP   114.74  3.000
 UVP  OP1  P    OP   113.61  3.000
 UVP  H3   C6'  C5'  117.62  3.000
 UVP  H3   C6'  P    116.01  3.000
 UVP  C5'  C6'  P    125.47  3.000
 UVP  H5   C5'  C4'  116.38  3.000
 UVP  H5   C5'  C6'  119.02  3.000
 UVP  C4'  C5'  C6'  124.54  3.000
 UVP  H7   C4'  C3'  110.90  3.000
 UVP  H7   C4'  O4'  106.68  3.000
 UVP  C3'  C4'  O4'  104.02  3.000
 UVP  H7   C4'  C5'  111.34  3.000
 UVP  O4'  C4'  C5'  111.24  3.000
 UVP  C3'  C4'  C5'  112.30  3.000
 UVP  C1'  O4'  C4'  110.02  3.000
 UVP  H8   C3'  C2'  112.54  3.000
 UVP  H8   C3'  O3'  112.12  3.000
 UVP  C2'  C3'  O3'  107.61  3.000
 UVP  H8   C3'  C4'  111.15  3.000
 UVP  C2'  C3'  C4'   99.58  3.000
 UVP  O3'  C3'  C4'  113.18  3.000
 UVP  H9   O3'  C3'  108.49  3.000
 UVP  H10  C2'  C1'  110.09  3.000
 UVP  H10  C2'  O2'  111.09  3.000
 UVP  C1'  C2'  O2'  109.27  3.000
 UVP  H10  C2'  C3'  107.37  3.000
 UVP  C1'  C2'  C3'  100.75  3.000
 UVP  O2'  C2'  C3'  117.71  3.000
 UVP  CB'  O2'  C2'  113.70  3.000
 UVP  H13  CB'  H12  108.42  3.000
 UVP  H13  CB'  H11  108.61  3.000
 UVP  H12  CB'  H11  108.38  3.000
 UVP  H13  CB'  O2'  107.44  3.000
 UVP  H12  CB'  O2'  112.26  3.000
 UVP  H11  CB'  O2'  111.63  3.000
 UVP  H14  C1'  N1   106.47  3.000
 UVP  H14  C1'  C2'  110.74  3.000
 UVP  N1   C1'  C2'  111.72  3.000
 UVP  H14  C1'  O4'  110.80  3.000
 UVP  N1   C1'  O4'  110.08  3.000
 UVP  C2'  C1'  O4'  107.09  3.000
 UVP  C6   N1   C2   117.83  3.000
 UVP  C2   N1   C1'  122.37  3.000
 UVP  C6   N1   C1'  119.80  3.000
 UVP  N3   C2   O2   120.21  3.000
 UVP  N3   C2   N1   123.39  3.000
 UVP  O2   C2   N1   116.40  3.000
 UVP  H4   O2   C2   110.17  3.000
 UVP  C4   N3   C2   119.15  3.000
 UVP  C5   C4   O4   123.58  3.000
 UVP  O4   C4   N3   114.84  3.000
 UVP  C5   C4   N3   121.58  3.000
 UVP  H6   O4   C4   112.00  3.000
 UVP  H16  C5   C6   119.41  3.000
 UVP  H16  C5   C4   124.03  3.000
 UVP  C6   C5   C4   116.55  3.000
 UVP  H17  C6   C5   120.25  3.000
 UVP  H17  C6   N1   118.27  3.000
 UVP  C5   C6   N1   121.48  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
 UVP  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 UVP  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 UVP  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 UVP  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 UVP  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 UVP  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 UVP  CONST_07  C5   C6   N1   C1'   180.00   0.0  0
 UVP  CONST_08  N3   C2   N1   C1'   180.00   0.0  0
 UVP  CONST_09  O2   C2   N1   C1'     0.00   0.0  0
 UVP  CONST_10  O4   C4   N3   C2    180.00   0.0  0
 UVP  CONST_11  C6   N1   C2   O2    180.00   0.0  0
 UVP  CONST_12  C4   N3   C2   O2    180.00   0.0  0
 UVP  CONST_13  C6   C5   C4   O4    180.00   0.0  0
 UVP  CONST_14  H17  C6   N1   C1'     0.00   0.0  0
 UVP  CONST_15  H16  C5   C6   N1    180.00   0.0  0
 UVP  Var_01    C4'  C5'  C6'  P    -165.42   0.0  2
 UVP  Var_02    H11  CB'  O2'  C2'   -55.07  30.0  3
 UVP  Var_03    C5'  C6'  P    OP   -137.51  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
 UVP  chir_01  C4'  C5'  C3'  O4'  positiv
 UVP  chir_02  C3'  O3'  C2'  C4'  negativ
 UVP  chir_03  C2'  O2'  C1'  C3'  negativ
 UVP  chir_04  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
 UVP  plan-1  C1'  0.020
 UVP  plan-1  N1   0.020
 UVP  plan-1  C2   0.020
 UVP  plan-1  O2   0.020
 UVP  plan-1  N3   0.020
 UVP  plan-1  C4   0.020
 UVP  plan-1  O4   0.020
 UVP  plan-1  C5   0.020
 UVP  plan-1  C6   0.020
 UVP  plan-1  H16  0.020
 UVP  plan-1  H17  0.020
 UVP  plan-2  P    0.020
 UVP  plan-2  C6'  0.020
 UVP  plan-2  C5'  0.020
 UVP  plan-2  C4'  0.020
 UVP  plan-2  H3   0.020
 UVP  plan-2  H5   0.020

