# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 12:19:27 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3ccccc3
#
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
 5GW  5GW  '5-phenyluridine 5'-(trihydrogen diphosphate)'  ligand  49  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5GW
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
 5GW  CAM  C  CR16  0  -0.292  35.4474  54.9828   1.3919
 5GW  CAK  C  CR16  0  -0.241  36.5965  55.5896   1.8754
 5GW  CAJ  C  CR16  0  -0.265  36.8274  55.6690   3.2429
 5GW  CAL  C  CR16  0  -0.234  35.8984  55.1368   4.1254
 5GW  CAN  C  CR16  0  -0.304  34.7456  54.5356   3.6427
 5GW  CAU  C  CR6   0   0.110  34.5074  54.4432   2.2713
 5GW  CAV  C  CR6   0  -0.235  33.2974  53.7624   1.7794
 5GW  CAO  C  CR16  0   0.057  32.9043  52.5850   2.3118
 5GW  CAW  C  CR6   0   0.554  32.4695  54.3595   0.7477
 5GW  OAA  O  O     0  -0.445  32.6730  55.4212   0.1908
 5GW  NAQ  N  NR16  0  -0.733  31.3531  53.6072   0.4212
 5GW  CAX  C  CR6   0   0.739  30.9531  52.4133   0.9527
 5GW  OAB  O  O     0  -0.480  29.9520  51.8310   0.5865
 5GW  NBC  N  NR6   0  -0.570  31.7776  51.9190   1.9380
 5GW  C1'  C  CR15  0   0.177  31.3506  50.6518   2.5652
 5GW  O4'  O  O     0  -0.495  32.0131  50.4912   3.7814
 5GW  C2'  C  CR15  0  -0.053  31.6908  49.4248   1.6962
 5GW  O2'  O  OH1   0  -0.658  30.7726  48.3916   1.9103
 5GW  C3'  C  CR15  0  -0.002  33.0300  49.0129   2.2931
 5GW  O3'  O  OH1   0  -0.653  33.3559  47.6888   2.0064
 5GW  C4'  C  CR15  0   0.005  32.7918  49.2983   3.7776
 5GW  C5'  C  CH2   0  -0.231  34.0131  49.4648   4.6446
 5GW  O5'  O  O2    0  -0.576  34.8877  50.4680   4.1098
 5GW  PBE  P  P     0   1.506  36.3986  50.1914   3.7175
 5GW  OAI  O  OH1   0  -0.760  36.3901  48.8485   2.8470
 5GW  OAD  O  O     0  -0.640  37.0676  51.3615   3.1442
 5GW  OAT  O  O2    0  -0.698  36.9902  49.6447   5.1181
 5GW  PBD  P  P     0   1.464  38.1554  48.5240   5.3292
 5GW  OAG  O  OH1   0  -0.725  37.3523  47.1539   5.3515
 5GW  OAH  O  O     0  -0.687  39.2708  48.6466   4.3786
 5GW  OAC  O  OH1   0  -0.715  38.4259  48.7482   6.8712
 5GW  H1   H  HCR6  0   0.248  35.2927  54.9152   0.3236
 5GW  H2   H  HCR6  0   0.254  37.3178  55.9991   1.1799
 5GW  H3   H  HCR6  0   0.255  37.7248  56.1440   3.6173
 5GW  H4   H  HCR6  0   0.254  36.0641  55.1992   5.1932
 5GW  H5   H  HCR6  0   0.249  34.0135  54.1497   4.3421
 5GW  H6   H  HCR6  0   0.325  33.4995  52.1136   3.0786
 5GW  H7   H  HNR6  0   0.429  30.7459  53.9888  -0.2942
 5GW  H8   H  HCR5  0   0.289  30.2745  50.7339   2.7331
 5GW  H9   H  HCR5  0   0.272  31.7740  49.6876   0.6369
 5GW  H10  H  HOH1  0   0.463  29.9443  48.6256   1.4790
 5GW  H11  H  HCR5  0   0.243  33.7843  49.7068   1.8993
 5GW  H12  H  HOH1  0   0.455  34.3030  47.5724   2.1316
 5GW  H13  H  HCR5  0   0.264  32.2153  48.4747   4.2176
 5GW  H14  H  HCH2  0   0.287  33.7310  49.7760   5.6507
 5GW  H15  H  HCH2  0   0.254  34.5040  48.4919   4.7307
 5GW  H16  H  HOH1  0   0.515  36.7114  48.9561   1.9400
 5GW  H17  H  HOH1  0   0.505  37.2762  46.7098   4.4955
 5GW  H18  H  HOH1  0   0.515  39.3609  48.8414   7.0991

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
 5GW  OAA  CAW  double    1.216  0.020  1.216
 5GW  NAQ  CAW  single    1.385  0.020  1.385
 5GW  NAQ  CAX  single    1.367  0.020  1.367
 5GW  OAB  CAX  double    1.215  0.020  1.215
 5GW  CAW  CAV  single    1.451  0.020  1.451
 5GW  CAX  NBC  single    1.377  0.020  1.377
 5GW  CAM  CAK  aromatic  1.387  0.020  1.387
 5GW  CAM  CAU  aromatic  1.396  0.020  1.396
 5GW  C2'  O2'  single    1.399  0.020  1.399
 5GW  C2'  C3'  single    1.523  0.020  1.523
 5GW  C2'  C1'  single    1.542  0.020  1.542
 5GW  CAV  CAU  single    1.473  0.020  1.473
 5GW  CAV  CAO  double    1.351  0.020  1.351
 5GW  NBC  CAO  single    1.361  0.020  1.361
 5GW  NBC  C1'  single    1.477  0.020  1.477
 5GW  CAK  CAJ  aromatic  1.389  0.020  1.389
 5GW  O3'  C3'  single    1.393  0.020  1.393
 5GW  CAU  CAN  aromatic  1.395  0.020  1.395
 5GW  C3'  C4'  single    1.530  0.020  1.530
 5GW  C1'  O4'  single    1.394  0.020  1.394
 5GW  OAD  PBE  double    1.465  0.020  1.465
 5GW  OAI  PBE  single    1.600  0.020  1.600
 5GW  CAJ  CAL  aromatic  1.387  0.020  1.387
 5GW  CAN  CAL  aromatic  1.387  0.020  1.387
 5GW  PBE  O5'  single    1.585  0.020  1.585
 5GW  PBE  OAT  single    1.616  0.020  1.616
 5GW  C4'  O4'  single    1.425  0.020  1.425
 5GW  C4'  C5'  single    1.507  0.020  1.507
 5GW  O5'  C5'  single    1.434  0.020  1.434
 5GW  OAH  PBD  double    1.471  0.020  1.471
 5GW  OAT  PBD  single    1.630  0.020  1.630
 5GW  OAG  PBD  single    1.588  0.020  1.588
 5GW  PBD  OAC  single    1.581  0.020  1.581
 5GW  CAM  H1   single    0.930  0.020  1.080
 5GW  CAK  H2   single    0.930  0.020  1.080
 5GW  CAJ  H3   single    0.930  0.020  1.080
 5GW  CAL  H4   single    0.930  0.020  1.080
 5GW  CAN  H5   single    0.930  0.020  1.080
 5GW  CAO  H6   single    0.930  0.020  1.080
 5GW  NAQ  H7   single    0.860  0.020  1.020
 5GW  C1'  H8   single    0.970  0.020  1.090
 5GW  C2'  H9   single    0.970  0.020  1.090
 5GW  O2'  H10  single    0.850  0.020  0.980
 5GW  C3'  H11  single    0.970  0.020  1.090
 5GW  O3'  H12  single    0.850  0.020  0.980
 5GW  C4'  H13  single    0.970  0.020  1.090
 5GW  C5'  H14  single    0.970  0.020  1.090
 5GW  C5'  H15  single    0.970  0.020  1.090
 5GW  OAI  H16  single    0.850  0.020  0.980
 5GW  OAG  H17  single    0.850  0.020  0.980
 5GW  OAC  H18  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
 5GW  H1   CAM  CAU  120.13  3.000
 5GW  H1   CAM  CAK  119.36  3.000
 5GW  CAU  CAM  CAK  120.50  3.000
 5GW  H2   CAK  CAJ  120.01  3.000
 5GW  H2   CAK  CAM  119.58  3.000
 5GW  CAJ  CAK  CAM  120.40  3.000
 5GW  H3   CAJ  CAL  120.24  3.000
 5GW  H3   CAJ  CAK  120.23  3.000
 5GW  CAL  CAJ  CAK  119.53  3.000
 5GW  H4   CAL  CAN  119.70  3.000
 5GW  H4   CAL  CAJ  120.19  3.000
 5GW  CAN  CAL  CAJ  120.10  3.000
 5GW  H5   CAN  CAU  119.71  3.000
 5GW  H5   CAN  CAL  119.43  3.000
 5GW  CAU  CAN  CAL  120.85  3.000
 5GW  CAV  CAU  CAN  119.95  3.000
 5GW  CAN  CAU  CAM  118.61  3.000
 5GW  CAV  CAU  CAM  121.43  3.000
 5GW  CAW  CAV  CAO  118.22  3.000
 5GW  CAO  CAV  CAU  120.68  3.000
 5GW  CAW  CAV  CAU  121.06  3.000
 5GW  H6   CAO  NBC  115.98  3.000
 5GW  H6   CAO  CAV  120.02  3.000
 5GW  NBC  CAO  CAV  124.00  3.000
 5GW  NAQ  CAW  OAA  120.07  3.000
 5GW  NAQ  CAW  CAV  113.82  3.000
 5GW  OAA  CAW  CAV  126.11  3.000
 5GW  H7   NAQ  CAX  115.36  3.000
 5GW  H7   NAQ  CAW  116.42  3.000
 5GW  CAX  NAQ  CAW  128.22  3.000
 5GW  NBC  CAX  OAB  122.50  3.000
 5GW  NBC  CAX  NAQ  114.63  3.000
 5GW  OAB  CAX  NAQ  122.87  3.000
 5GW  C1'  NBC  CAX  116.03  3.000
 5GW  C1'  NBC  CAO  122.85  3.000
 5GW  CAX  NBC  CAO  121.11  3.000
 5GW  H8   C1'  C2'  111.34  3.000
 5GW  H8   C1'  O4'  110.05  3.000
 5GW  C2'  C1'  O4'  107.17  3.000
 5GW  H8   C1'  NBC  106.60  3.000
 5GW  O4'  C1'  NBC  109.38  3.000
 5GW  C2'  C1'  NBC  112.32  3.000
 5GW  C4'  O4'  C1'  110.73  3.000
 5GW  H9   C2'  C3'  112.17  3.000
 5GW  H9   C2'  O2'  112.05  3.000
 5GW  C3'  C2'  O2'  108.52  3.000
 5GW  H9   C2'  C1'  111.79  3.000
 5GW  C3'  C2'  C1'  100.86  3.000
 5GW  O2'  C2'  C1'  110.90  3.000
 5GW  H10  O2'  C2'  108.46  3.000
 5GW  H11  C3'  C4'  109.69  3.000
 5GW  H11  C3'  O3'  111.47  3.000
 5GW  C4'  C3'  O3'  114.41  3.000
 5GW  H11  C3'  C2'  107.02  3.000
 5GW  C4'  C3'  C2'  101.12  3.000
 5GW  O3'  C3'  C2'  112.46  3.000
 5GW  H12  O3'  C3'  108.56  3.000
 5GW  H13  C4'  C5'  106.14  3.000
 5GW  H13  C4'  C3'  109.32  3.000
 5GW  C5'  C4'  C3'  116.91  3.000
 5GW  H13  C4'  O4'  109.89  3.000
 5GW  C5'  C4'  O4'  110.43  3.000
 5GW  C3'  C4'  O4'  104.11  3.000
 5GW  H15  C5'  H14  107.31  3.000
 5GW  H15  C5'  O5'  112.21  3.000
 5GW  H14  C5'  O5'  107.58  3.000
 5GW  H15  C5'  C4'  108.12  3.000
 5GW  H14  C5'  C4'  110.66  3.000
 5GW  O5'  C5'  C4'  110.91  3.000
 5GW  PBE  O5'  C5'  123.46  3.000
 5GW  OAT  PBE  OAD  116.25  3.000
 5GW  OAT  PBE  OAI  100.92  3.000
 5GW  OAD  PBE  OAI  117.38  3.000
 5GW  OAT  PBE  O5'  101.15  3.000
 5GW  OAI  PBE  O5'  106.02  3.000
 5GW  OAD  PBE  O5'  113.13  3.000
 5GW  H16  OAI  PBE  114.49  3.000
 5GW  PBD  OAT  PBE  127.34  3.000
 5GW  OAC  PBD  OAH  119.25  3.000
 5GW  OAC  PBD  OAG  101.25  3.000
 5GW  OAH  PBD  OAG  117.68  3.000
 5GW  OAC  PBD  OAT   98.69  3.000
 5GW  OAG  PBD  OAT  103.50  3.000
 5GW  OAH  PBD  OAT  113.64  3.000
 5GW  H17  OAG  PBD  115.05  3.000
 5GW  H18  OAC  PBD  114.14  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
 5GW  CONST_01  CAL  CAJ  CAK  CAM    0.00   0.0  0
 5GW  CONST_02  CAL  CAN  CAU  CAM    0.00   0.0  0
 5GW  CONST_03  CAN  CAU  CAM  CAK    0.00   0.0  0
 5GW  CONST_04  CAN  CAL  CAJ  CAK    0.00   0.0  0
 5GW  CONST_05  CAU  CAM  CAK  CAJ    0.00   0.0  0
 5GW  CONST_06  CAU  CAN  CAL  CAJ    0.00   0.0  0
 5GW  CONST_07  CAV  CAU  CAM  CAK  180.00   0.0  0
 5GW  CONST_08  CAV  CAU  CAN  CAL  180.00   0.0  0
 5GW  CONST_09  CAX  NAQ  CAW  CAV    0.00   0.0  0
 5GW  CONST_10  NAQ  CAX  NBC  CAO    0.00   0.0  0
 5GW  CONST_11  NBC  CAX  NAQ  CAW    0.00   0.0  0
 5GW  CONST_12  C1'  NBC  CAX  NAQ  180.00   0.0  0
 5GW  CONST_13  OAB  CAX  NBC  CAO  180.00   0.0  0
 5GW  CONST_14  OAB  CAX  NAQ  CAW  180.00   0.0  0
 5GW  CONST_15  CAX  NAQ  CAW  OAA  180.00   0.0  0
 5GW  CONST_16  C1'  NBC  CAX  OAB    0.00   0.0  0
 5GW  CONST_17  H3   CAJ  CAK  CAM  180.00   0.0  0
 5GW  CONST_18  H5   CAN  CAU  CAM  180.00   0.0  0
 5GW  CONST_19  H4   CAL  CAJ  CAK  180.00   0.0  0
 5GW  CONST_20  H1   CAM  CAK  CAJ  180.00   0.0  0
 5GW  CONST_21  H2   CAK  CAJ  CAL  180.00   0.0  0
 5GW  CONST_22  H7   NAQ  CAW  CAV  180.00   0.0  0
 5GW  Var_01    CAW  CAV  CAU  CAM  -47.72  30.0  2
 5GW  Var_02    OAD  PBE  O5'  C5'  177.72  30.0  1
 5GW  Var_03    OAH  PBD  OAT  PBE   40.47  30.0  3
 5GW  Var_04    H14  C5'  O5'  PBE  116.77  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
 5GW  chir_01  C1'  C2'  NBC  O4'  positiv
 5GW  chir_02  C2'  O2'  C3'  C1'  positiv
 5GW  chir_03  C3'  O3'  C2'  C4'  negativ
 5GW  chir_04  C4'  O4'  C3'  C5'  negativ
 5GW  chir_05  PBE  OAI  O5'  OAT  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
 5GW  plan-1  CAM  0.020
 5GW  plan-1  CAK  0.020
 5GW  plan-1  CAJ  0.020
 5GW  plan-1  CAL  0.020
 5GW  plan-1  CAN  0.020
 5GW  plan-1  CAU  0.020
 5GW  plan-1  CAV  0.020
 5GW  plan-1  H1   0.020
 5GW  plan-1  H2   0.020
 5GW  plan-1  H3   0.020
 5GW  plan-1  H4   0.020
 5GW  plan-1  H5   0.020
 5GW  plan-2  CAU  0.020
 5GW  plan-2  CAV  0.020
 5GW  plan-2  CAO  0.020
 5GW  plan-2  CAW  0.020
 5GW  plan-2  OAA  0.020
 5GW  plan-2  NAQ  0.020
 5GW  plan-2  CAX  0.020
 5GW  plan-2  OAB  0.020
 5GW  plan-2  NBC  0.020
 5GW  plan-2  C1'  0.020
 5GW  plan-2  H6   0.020
 5GW  plan-2  H7   0.020

