# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 04:20:16 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)O[P@@](O)(=O)C[P](O)(O)=O)N2C=CC(=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
 UCP  UCP  2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]uridine  ligand  41  28  .  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_UCP
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
 UCP  N1    N  NR6    0  -0.565  -0.3448   0.3048   5.0552
 UCP  C2    C  CR6    0   0.717  -0.2263  -1.0701   5.0077
 UCP  O2    O  O      0  -0.496   0.6315  -1.6429   4.3719
 UCP  N3    N  NR16   0  -0.682  -1.1584  -1.7533   5.7450
 UCP  C4    C  CR6    0   0.525  -2.1928  -1.2371   6.5100
 UCP  O4    O  O      0  -0.508  -2.9440  -1.9784   7.1167
 UCP  C5    C  CR16   0  -0.398  -2.2569   0.2025   6.4823
 UCP  C6    C  CR16   0   0.034  -1.3523   0.8902   5.7664
 UCP  C1'   C  CH1    0   0.262   0.5697   1.1457   4.2796
 UCP  C2'   C  CH2    0  -0.567   2.0627   0.9425   4.5535
 UCP  C3'   C  CH1    0   0.039   2.6253   0.3638   3.2546
 UCP  O3'   O  OH1    0  -0.628   3.8735   0.8851   2.8708
 UCP  C4'   C  CH1    0  -0.029   1.5813   0.7816   2.2197
 UCP  O4'   O  O2     0  -0.520   0.3542   0.9261   2.9176
 UCP  C5'   C  CH2    0  -0.190   1.4141  -0.2148   1.0978
 UCP  O5'   O  O2     0  -0.627   0.5429   0.3190   0.1313
 UCP  PA    P  P      0   1.353  -0.0504  -0.7131  -1.0214
 UCP  O1A   O  O      0  -0.833  -1.0868  -1.5870  -0.3786
 UCP  O2A   O  OP    -1  -0.770   1.1024  -1.3440  -1.7452
 UCP  O3A   O  O2     0  -0.653  -0.7332   0.4800  -1.8836
 UCP  PB    P  P      0   1.136  -1.3166   0.2867  -3.4636
 UCP  O1B   O  O      0  -0.714  -2.4225   1.3077  -3.5460
 UCP  O2B   O  OP    -1  -0.911  -1.6627  -1.1687  -3.6242
 UCP  CC    C  CH2    0  -0.958   0.1234   0.7741  -4.4392
 UCP  PG    P  P      0   1.097   0.0272   0.4158  -6.2779
 UCP  O1G   O  O      0  -0.875  -1.3503   0.9199  -6.7212
 UCP  O2G   O  OP    -1  -0.990   1.1934   1.2315  -6.8618
 UCP  O3G   O  OP    -1  -0.816   0.2179  -1.0958  -6.4341
 UCP  HN3   H  HNR6   0   0.443  -1.0688  -2.7620   5.7182
 UCP  H5    H  HCR6   0   0.295  -3.0318   0.7178   7.0279
 UCP  H6    H  HCR6   0   0.315  -1.3820   1.9699   5.7222
 UCP  H1'   H  HCH1   0   0.282   0.2810   2.1645   4.5482
 UCP  H2'1  H  HCH2   0   0.276   2.2587   0.3259   5.4292
 UCP  H2'2  H  HCH2   0   0.229   2.5148   1.9195   4.7347
 UCP  H3'   H  HCH1   0   0.208   2.6697  -0.7266   3.3231
 UCP  HO'3  H  HOH1   0   0.455   4.5545   0.4526   3.3936
 UCP  H4'   H  HCH1   0   0.267   1.8845   1.7546   1.8052
 UCP  H5'1  H  HCH2   0   0.264   2.4032  -0.4212   0.6704
 UCP  H5'2  H  HCH2   0   0.207   1.0384  -1.1554   1.5205
 UCP  HCC1  H  HCH2   0   0.208   0.2764   1.8469  -4.2837
 UCP  HCC2  H  HCH2   0   0.117   1.0001   0.2668  -4.0248

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
 UCP  N1   C2    single  1.381  0.020  1.381
 UCP  N1   C6    single  1.365  0.020  1.365
 UCP  N1   C1'   single  1.465  0.020  1.465
 UCP  C2   O2    double  1.212  0.020  1.212
 UCP  C2   N3    single  1.371  0.020  1.371
 UCP  N3   C4    single  1.386  0.020  1.386
 UCP  N3   HN3   single  0.860  0.020  1.020
 UCP  C4   O4    double  1.217  0.020  1.217
 UCP  C4   C5    single  1.441  0.020  1.441
 UCP  C5   C6    double  1.343  0.020  1.343
 UCP  C5   H5    single  0.930  0.020  1.080
 UCP  C6   H6    single  0.930  0.020  1.080
 UCP  C1'  C2'   single  1.531  0.020  1.531
 UCP  C1'  O4'   single  1.396  0.020  1.396
 UCP  C1'  H1'   single  0.970  0.020  1.090
 UCP  C2'  C3'   single  1.529  0.020  1.529
 UCP  C2'  H2'1  single  0.970  0.020  1.090
 UCP  C2'  H2'2  single  0.970  0.020  1.090
 UCP  C3'  O3'   single  1.406  0.020  1.406
 UCP  C3'  C4'   single  1.528  0.020  1.528
 UCP  C3'  H3'   single  0.970  0.020  1.090
 UCP  O3'  HO'3  single  0.850  0.020  0.980
 UCP  C4'  O4'   single  1.419  0.020  1.419
 UCP  C4'  C5'   single  1.510  0.020  1.510
 UCP  C4'  H4'   single  0.970  0.020  1.090
 UCP  C5'  O5'   single  1.406  0.020  1.406
 UCP  C5'  H5'1  single  0.970  0.020  1.090
 UCP  C5'  H5'2  single  0.970  0.020  1.090
 UCP  O5'  PA    single  1.657  0.020  1.657
 UCP  PA   O1A   deloc   1.500  0.020  1.500
 UCP  PA   O2A   deloc   1.500  0.020  1.500
 UCP  PA   O3A   single  1.623  0.020  1.623
 UCP  O3A  PB    single  1.695  0.020  1.695
 UCP  PB   O1B   deloc   1.507  0.020  1.507
 UCP  PB   O2B   deloc   1.505  0.020  1.505
 UCP  PB   CC    single  1.806  0.020  1.806
 UCP  CC   PG    single  1.876  0.020  1.876
 UCP  CC   HCC1  single  0.970  0.020  1.090
 UCP  CC   HCC2  single  0.970  0.020  1.090
 UCP  PG   O1G   deloc   1.532  0.020  1.532
 UCP  PG   O2G   deloc   1.538  0.020  1.538
 UCP  PG   O3G   deloc   1.531  0.020  1.531

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
 UCP  C1'   N1   C6    119.37  3.000
 UCP  C1'   N1   C2    119.99  3.000
 UCP  C6    N1   C2    120.55  3.000
 UCP  N3    C2   O2    121.87  3.000
 UCP  N3    C2   N1    114.80  3.000
 UCP  O2    C2   N1    123.33  3.000
 UCP  HN3   N3   C4    116.83  3.000
 UCP  HN3   N3   C2    114.95  3.000
 UCP  C4    N3   C2    128.21  3.000
 UCP  C5    C4   O4    126.18  3.000
 UCP  C5    C4   N3    113.24  3.000
 UCP  O4    C4   N3    120.58  3.000
 UCP  H5    C5   C6    120.59  3.000
 UCP  H5    C5   C4    119.96  3.000
 UCP  C6    C5   C4    119.45  3.000
 UCP  H6    C6   C5    120.97  3.000
 UCP  H6    C6   N1    115.30  3.000
 UCP  C5    C6   N1    123.72  3.000
 UCP  H1'   C1'  O4'   110.23  3.000
 UCP  H1'   C1'  C2'   109.72  3.000
 UCP  O4'   C1'  C2'   107.70  3.000
 UCP  H1'   C1'  N1    103.90  3.000
 UCP  O4'   C1'  N1    109.27  3.000
 UCP  C2'   C1'  N1    115.96  3.000
 UCP  H2'2  C2'  H2'1  107.38  3.000
 UCP  H2'2  C2'  C3'   109.10  3.000
 UCP  H2'1  C2'  C3'   113.74  3.000
 UCP  H2'2  C2'  C1'   108.34  3.000
 UCP  H2'1  C2'  C1'   113.23  3.000
 UCP  C3'   C2'  C1'   104.89  3.000
 UCP  H3'   C3'  C4'   110.05  3.000
 UCP  H3'   C3'  O3'   110.54  3.000
 UCP  C4'   C3'  O3'   108.68  3.000
 UCP  H3'   C3'  C2'   109.82  3.000
 UCP  C4'   C3'  C2'   102.73  3.000
 UCP  O3'   C3'  C2'   114.72  3.000
 UCP  HO'3  O3'  C3'   108.27  3.000
 UCP  H4'   C4'  C5'   109.53  3.000
 UCP  H4'   C4'  O4'   109.48  3.000
 UCP  C5'   C4'  O4'   109.69  3.000
 UCP  H4'   C4'  C3'   107.98  3.000
 UCP  C5'   C4'  C3'   113.48  3.000
 UCP  O4'   C4'  C3'   106.59  3.000
 UCP  C4'   O4'  C1'   111.24  3.000
 UCP  H5'2  C5'  H5'1  107.31  3.000
 UCP  H5'2  C5'  O5'   112.20  3.000
 UCP  H5'1  C5'  O5'   111.23  3.000
 UCP  H5'2  C5'  C4'   108.50  3.000
 UCP  H5'1  C5'  C4'   108.29  3.000
 UCP  O5'   C5'  C4'   109.19  3.000
 UCP  PA    O5'  C5'   117.61  3.000
 UCP  O3A   PA   O2A   112.10  3.000
 UCP  O3A   PA   O1A   111.42  3.000
 UCP  O2A   PA   O1A   119.51  3.000
 UCP  O3A   PA   O5'    93.57  3.000
 UCP  O2A   PA   O5'   108.81  3.000
 UCP  O1A   PA   O5'   108.19  3.000
 UCP  PB    O3A  PA    123.79  3.000
 UCP  CC    PB   O2B   112.75  3.000
 UCP  CC    PB   O1B   111.88  3.000
 UCP  O2B   PB   O1B   118.73  3.000
 UCP  CC    PB   O3A   101.43  3.000
 UCP  O2B   PB   O3A   106.79  3.000
 UCP  O1B   PB   O3A   103.07  3.000
 UCP  HCC2  CC   HCC1  106.77  3.000
 UCP  HCC2  CC   PG    108.89  3.000
 UCP  HCC1  CC   PG    109.49  3.000
 UCP  HCC2  CC   PB    108.00  3.000
 UCP  HCC1  CC   PB    107.40  3.000
 UCP  PG    CC   PB    115.91  3.000
 UCP  O3G   PG   O2G   112.97  3.000
 UCP  O3G   PG   O1G   114.02  3.000
 UCP  O2G   PG   O1G   113.41  3.000
 UCP  O3G   PG   CC    106.39  3.000
 UCP  O2G   PG   CC    103.41  3.000
 UCP  O1G   PG   CC    105.47  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
 UCP  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 UCP  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 UCP  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 UCP  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 UCP  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 UCP  CONST_06  C6    N1   C2   O2   180.00   0.0  0
 UCP  CONST_07  C1'   N1   C2   O2     0.00   0.0  0
 UCP  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 UCP  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 UCP  Var_01    O1A   PA   O5'  C5'   73.99  30.0  3
 UCP  Var_02    O1B   PB   O3A  PA   151.29  30.0  3
 UCP  Var_03    PG    CC   PB   O3A  169.33  30.0  3
 UCP  Var_04    O1G   PG   CC   PB    47.26  30.0  3
 UCP  Var_05    H5'1  C5'  O5'  PA    73.60  30.0  1

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
 UCP  chir_01  C1'  N1   C2'  O4'  negativ
 UCP  chir_02  C3'  O3'  C4'  C2'  positiv
 UCP  chir_03  C4'  O4'  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
 UCP  plan-1  N1   0.020
 UCP  plan-1  C2   0.020
 UCP  plan-1  O2   0.020
 UCP  plan-1  N3   0.020
 UCP  plan-1  C4   0.020
 UCP  plan-1  O4   0.020
 UCP  plan-1  C5   0.020
 UCP  plan-1  C6   0.020
 UCP  plan-1  C1'  0.020
 UCP  plan-1  HN3  0.020
 UCP  plan-1  H5   0.020
 UCP  plan-1  H6   0.020

