# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 12:42:11 2021
#   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  45  28  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.561  36.3396  21.6940  10.4878
 UCP  C2    C  CR6   0   0.742  36.6133  21.7978   9.1360
 UCP  O2    O  O     0  -0.476  35.8135  22.2067   8.3214
 UCP  N3    N  NR16  0  -0.735  37.8710  21.3905   8.7753
 UCP  C4    C  CR6   0   0.570  38.8904  20.9280   9.5929
 UCP  O4    O  O     0  -0.460  39.9658  20.6088   9.1232
 UCP  C5    C  CR16  0  -0.508  38.5269  20.8796  10.9886
 UCP  C6    C  CR16  0   0.113  37.2969  21.2613  11.3619
 UCP  C1'   C  CH1   0   0.174  35.0594  22.1730  10.9942
 UCP  C2'   C  CH2   0  -0.573  34.3876  21.2414  12.0029
 UCP  C3'   C  CH1   0   0.012  34.5520  21.9452  13.3527
 UCP  O3'   O  OH1   0  -0.689  33.4858  21.7383  14.2295
 UCP  C4'   C  CH1   0   0.028  34.6601  23.4125  12.9306
 UCP  O4'   O  O2    0  -0.494  35.2794  23.3985  11.6570
 UCP  C5'   C  CH2   0  -0.211  35.5352  24.2801  13.8165
 UCP  O5'   O  O2    0  -0.568  34.8424  24.5353  15.0455
 UCP  PA    P  P     0   1.483  35.4370  24.3138  16.4905
 UCP  O1A   O  O     0  -0.670  34.5736  24.8469  17.5515
 UCP  O2A   O  OH1   0  -0.729  36.9133  24.8755  16.3503
 UCP  O3A   O  O2    0  -0.712  35.7034  22.7173  16.5969
 UCP  PB    P  P     0   1.403  34.9653  21.4732  17.3404
 UCP  O1B   O  O     0  -0.678  34.6746  20.3930  16.3674
 UCP  O2B   O  OH1   0  -0.746  33.6698  22.0336  18.0489
 UCP  CC    C  CH2   0  -1.019  36.1423  21.0502  18.6403
 UCP  PG    P  P     0   1.398  36.2403  22.3123  19.9280
 UCP  O1G   O  O     0  -0.711  34.8890  22.8291  20.2982
 UCP  O2G   O  OH1   0  -0.720  37.0568  21.6310  21.1118
 UCP  O3G   O  OH1   0  -0.736  37.2313  23.3792  19.2644
 UCP  HN3   H  HNR6  0   0.428  38.0732  21.4509   7.7845
 UCP  H5    H  HCR6  0   0.296  39.2436  20.5394  11.7197
 UCP  H6    H  HCR6  0   0.319  37.0088  21.2272  12.4027
 UCP  H1'   H  HCH1  0   0.281  34.4277  22.3274  10.1222
 UCP  H2'1  H  HCH2  0   0.285  33.3241  21.1753  11.7688
 UCP  H2'2  H  HCH2  0   0.287  34.7899  20.2286  11.9857
 UCP  H3'   H  HCH1  0   0.220  35.4994  21.6411  13.8191
 UCP  HO'3  H  HOH1  0   0.462  33.7713  21.1101  14.9117
 UCP  H4'   H  HCH1  0   0.246  33.6522  23.8448  12.8628
 UCP  H5'1  H  HCH2  0   0.245  36.4975  23.7900  13.9850
 UCP  H5'2  H  HCH2  0   0.274  35.7255  25.2439  13.3428
 UCP  HOA2  H  HOH1  0   0.503  37.4911  24.7384  17.1142
 UCP  HOB2  H  HOH1  0   0.499  33.8567  22.4822  18.9126
 UCP  HCC1  H  HCH2  0   0.354  35.7844  20.1287  19.1074
 UCP  HCC2  H  HCH2  0   0.358  37.1190  20.8394  18.2003
 UCP  HOG2  H  HOH1  0   0.510  36.6842  21.7746  21.9934
 UCP  HOG3  H  HOH1  0   0.509  37.4063  24.1581  19.8144

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  1.383  0.020  1.383
 UCP  N1   C6    single  1.367  0.020  1.367
 UCP  N1   C1'   single  1.458  0.020  1.458
 UCP  C2   O2    double  1.213  0.020  1.213
 UCP  C2   N3    single  1.370  0.020  1.370
 UCP  N3   C4    single  1.386  0.020  1.386
 UCP  N3   HN3   single  0.860  0.020  1.020
 UCP  C4   O4    double  1.216  0.020  1.216
 UCP  C4   C5    single  1.443  0.020  1.443
 UCP  C5   C6    double  1.341  0.020  1.341
 UCP  C5   H5    single  0.930  0.020  1.080
 UCP  C6   H6    single  0.930  0.020  1.080
 UCP  C1'  C2'   single  1.529  0.020  1.529
 UCP  C1'  O4'   single  1.411  0.020  1.411
 UCP  C1'  H1'   single  0.970  0.020  1.090
 UCP  C2'  C3'   single  1.531  0.020  1.531
 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  1.396  0.020  1.396
 UCP  C3'  C4'   single  1.531  0.020  1.531
 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  1.416  0.020  1.416
 UCP  C4'  C5'   single  1.518  0.020  1.518
 UCP  C4'  H4'   single  0.970  0.020  1.090
 UCP  C5'  O5'   single  1.434  0.020  1.434
 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  1.578  0.020  1.578
 UCP  PA   O1A   double  1.468  0.020  1.468
 UCP  PA   O2A   single  1.586  0.020  1.586
 UCP  PA   O3A   single  1.622  0.020  1.622
 UCP  O2A  HOA2  single  0.850  0.020  0.980
 UCP  O3A  PB    single  1.626  0.020  1.626
 UCP  PB   O1B   double  1.483  0.020  1.483
 UCP  PB   O2B   single  1.579  0.020  1.579
 UCP  PB   CC    single  1.804  0.020  1.804
 UCP  O2B  HOB2  single  0.850  0.020  0.980
 UCP  CC   PG    single  1.806  0.020  1.806
 UCP  CC   HCC1  single  0.970  0.020  1.090
 UCP  CC   HCC2  single  0.970  0.020  1.090
 UCP  PG   O1G   double  1.493  0.020  1.493
 UCP  PG   O2G   single  1.591  0.020  1.591
 UCP  PG   O3G   single  1.600  0.020  1.600
 UCP  O2G  HOG2  single  0.850  0.020  0.980
 UCP  O3G  HOG3  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
 UCP  C1'   N1   C6    119.81  3.000
 UCP  C1'   N1   C2    119.25  3.000
 UCP  C6    N1   C2    120.68  3.000
 UCP  N3    C2   O2    121.92  3.000
 UCP  N3    C2   N1    114.62  3.000
 UCP  O2    C2   N1    123.46  3.000
 UCP  HN3   N3   C4    116.74  3.000
 UCP  HN3   N3   C2    115.02  3.000
 UCP  C4    N3   C2    128.23  3.000
 UCP  C5    C4   O4    125.98  3.000
 UCP  C5    C4   N3    113.35  3.000
 UCP  O4    C4   N3    120.67  3.000
 UCP  H5    C5   C6    120.70  3.000
 UCP  H5    C5   C4    119.91  3.000
 UCP  C6    C5   C4    119.40  3.000
 UCP  H6    C6   C5    120.26  3.000
 UCP  H6    C6   N1    116.06  3.000
 UCP  C5    C6   N1    123.68  3.000
 UCP  H1'   C1'  O4'   110.12  3.000
 UCP  H1'   C1'  C2'   111.12  3.000
 UCP  O4'   C1'  C2'   106.74  3.000
 UCP  H1'   C1'  N1    106.15  3.000
 UCP  O4'   C1'  N1    108.16  3.000
 UCP  C2'   C1'  N1    114.51  3.000
 UCP  H2'2  C2'  H2'1  107.47  3.000
 UCP  H2'2  C2'  C3'   113.67  3.000
 UCP  H2'1  C2'  C3'   108.76  3.000
 UCP  H2'2  C2'  C1'   113.19  3.000
 UCP  H2'1  C2'  C1'   108.89  3.000
 UCP  C3'   C2'  C1'   104.74  3.000
 UCP  H3'   C3'  C4'   108.75  3.000
 UCP  H3'   C3'  O3'   110.54  3.000
 UCP  C4'   C3'  O3'   111.67  3.000
 UCP  H3'   C3'  C2'   109.85  3.000
 UCP  C4'   C3'  C2'   101.84  3.000
 UCP  O3'   C3'  C2'   113.81  3.000
 UCP  HO'3  O3'  C3'   108.23  3.000
 UCP  H4'   C4'  C5'   109.88  3.000
 UCP  H4'   C4'  O4'   110.46  3.000
 UCP  C5'   C4'  O4'   106.16  3.000
 UCP  H4'   C4'  C3'   109.23  3.000
 UCP  C5'   C4'  C3'   115.32  3.000
 UCP  O4'   C4'  C3'   105.63  3.000
 UCP  C4'   O4'  C1'   111.28  3.000
 UCP  H5'2  C5'  H5'1  108.03  3.000
 UCP  H5'2  C5'  O5'   107.42  3.000
 UCP  H5'1  C5'  O5'   111.91  3.000
 UCP  H5'2  C5'  C4'   110.63  3.000
 UCP  H5'1  C5'  C4'   109.96  3.000
 UCP  O5'   C5'  C4'   108.87  3.000
 UCP  PA    O5'  C5'   125.30  3.000
 UCP  O3A   PA   O2A   101.63  3.000
 UCP  O3A   PA   O1A   113.99  3.000
 UCP  O2A   PA   O1A   118.87  3.000
 UCP  O3A   PA   O5'   105.07  3.000
 UCP  O2A   PA   O5'   102.71  3.000
 UCP  O1A   PA   O5'   112.90  3.000
 UCP  HOA2  O2A  PA    115.84  3.000
 UCP  PB    O3A  PA    135.10  3.000
 UCP  CC    PB   O2B   107.17  3.000
 UCP  CC    PB   O1B   115.47  3.000
 UCP  O2B   PB   O1B   113.08  3.000
 UCP  CC    PB   O3A   102.28  3.000
 UCP  O2B   PB   O3A   107.81  3.000
 UCP  O1B   PB   O3A   110.26  3.000
 UCP  HOB2  O2B  PB    113.38  3.000
 UCP  HCC2  CC   HCC1  107.59  3.000
 UCP  HCC2  CC   PG    111.95  3.000
 UCP  HCC1  CC   PG    107.59  3.000
 UCP  HCC2  CC   PB    109.79  3.000
 UCP  HCC1  CC   PB    106.97  3.000
 UCP  PG    CC   PB    112.67  3.000
 UCP  O3G   PG   O2G   106.03  3.000
 UCP  O3G   PG   O1G   115.63  3.000
 UCP  O2G   PG   O1G   115.34  3.000
 UCP  O3G   PG   CC    101.77  3.000
 UCP  O2G   PG   CC    105.02  3.000
 UCP  O1G   PG   CC    111.69  3.000
 UCP  HOG2  O2G  PG    114.62  3.000
 UCP  HOG3  O3G  PG    114.34  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'  171.44  30.0  3
 UCP  Var_02    O1B   PB   O3A  PA   126.79  30.0  3
 UCP  Var_03    PG    CC   PB   O3A   69.53  30.0  3
 UCP  Var_04    O1G   PG   CC   PB    42.19  30.0  3
 UCP  Var_05    H5'1  C5'  O5'  PA     7.11  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
 UCP  chir_04  PA   O1A  O2A  O3A  both
 UCP  chir_05  PB   O1B  O3A  CC   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
 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

