# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 20:21:37 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
#
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
 1S0  1S0  4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one  ligand  44  28  .  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_1S0
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
 1S0  OAE  O  OH1   0  -0.644  -33.1890  17.2290  12.0669
 1S0  OAG  O  O2    0  -0.626  -32.2029  22.4848   9.3539
 1S0  OAH  O  O     0  -0.716  -27.8766  15.7582  12.2159
 1S0  OAJ  O  OH1   0  -0.733  -33.7937  20.6523   8.7921
 1S0  OAK  O  O2    0  -0.615  -33.6855  24.4313   8.8105
 1S0  OAL  O  OH1   0  -0.640  -32.2572  24.4176  10.8190
 1S0  OAO  O  O     0  -0.728  -34.7218  25.4295   6.7423
 1S0  OAI  O  O     0  -0.680  -31.4561  20.7590   7.5979
 1S0  PAA  P  P     0   1.481  -32.2381  20.9536   8.8224
 1S0  PAB  P  P     0   1.441  -33.2623  23.4842  10.0377
 1S0  OAM  O  O     0  -0.667  -34.3628  22.8579  10.7764
 1S0  PAC  P  P     0   1.402  -34.5404  24.1550   7.4483
 1S0  OAP  O  OH1   0  -0.612  -33.7714  22.9804   6.7131
 1S0  OAN  O  OH1   0  -0.723  -35.8119  23.3325   7.9042
 1S0  OAF  O  O2    0  -0.535  -31.6375  20.1322  10.0390
 1S0  CAX  C  CH2   0  -0.250  -32.0915  20.2214  11.3910
 1S0  CAU  C  CH1   0  -0.009  -31.5503  19.0523  12.1713
 1S0  CAT  C  CH1   0   0.036  -31.9158  17.6526  11.6695
 1S0  CAV  C  CH2   0  -0.533  -30.8196  16.8346  12.3321
 1S0  CAW  C  CH1   0   0.190  -29.6162  17.7728  12.2643
 1S0  OAD  O  O2    0  -0.483  -30.1299  19.0753  12.1824
 1S0  NAQ  N  NR6   0  -0.464  -28.7632  17.5085  11.0913
 1S0  CAY  C  CR16  0   0.030  -28.8228  18.2505   9.9651
 1S0  CBA  C  CR16  0  -0.349  -28.0398  17.9744   8.9004
 1S0  CBB  C  CR6   0   0.403  -27.1449  16.8722   9.0334
 1S0  NAS  N  NH2   0  -0.841  -26.3324  16.5531   8.0249
 1S0  NAR  N  N     0  -0.410  -27.0852  16.1471  10.1339
 1S0  CAZ  C  CR6   0   0.555  -27.8828  16.4198  11.1839
 1S0  H1   H  HOH1  0   0.444  -33.8377  17.5471  11.4328
 1S0  H2   H  HOH1  0   0.499  -34.0749  20.0728   8.0708
 1S0  H3   H  HOH1  0   0.542  -32.5996  24.7561  11.6583
 1S0  H4   H  HOH1  0   0.561  -33.0197  23.2649   6.1753
 1S0  H5   H  HOH1  0   0.491  -36.4889  23.8500   8.3610
 1S0  H6   H  HCH2  0   0.196  -31.7493  21.1613  11.8309
 1S0  H7   H  HCH2  0   0.257  -33.1830  20.1980  11.4490
 1S0  H8   H  HCH1  0   0.242  -31.9365  19.1634  13.1942
 1S0  H9   H  HCH1  0   0.221  -31.8066  17.6057  10.5777
 1S0  H10  H  HCH2  0   0.261  -31.0841  16.6538  13.3770
 1S0  H11  H  HCH2  0   0.314  -30.6370  15.8717  11.8598
 1S0  H12  H  HCH1  0   0.311  -28.9738  17.6859  13.1400
 1S0  H13  H  HCR6  0   0.320  -29.5152  19.0767   9.9522
 1S0  H14  H  HCR6  0   0.308  -28.0894  18.5726   8.0031
 1S0  H15  H  HNH2  0   0.371  -25.7128  15.7655   8.1062
 1S0  H16  H  HNH2  0   0.383  -26.3484  17.0567   7.1561

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
 1S0  OAO  PAC  double  1.468  0.020  1.468
 1S0  OAI  PAA  double  1.466  0.020  1.466
 1S0  OAP  PAC  single  1.585  0.020  1.585
 1S0  PAC  OAN  single  1.581  0.020  1.581
 1S0  PAC  OAK  single  1.632  0.020  1.632
 1S0  NAS  CBB  single  1.334  0.020  1.334
 1S0  OAJ  PAA  single  1.585  0.020  1.585
 1S0  PAA  OAG  single  1.621  0.020  1.621
 1S0  PAA  OAF  single  1.586  0.020  1.586
 1S0  OAG  PAB  single  1.609  0.020  1.609
 1S0  CBA  CBB  single  1.426  0.020  1.426
 1S0  CBA  CAY  double  1.350  0.020  1.350
 1S0  OAK  PAB  single  1.607  0.020  1.607
 1S0  CBB  NAR  double  1.319  0.020  1.319
 1S0  PAB  OAM  double  1.466  0.020  1.466
 1S0  PAB  OAL  single  1.579  0.020  1.579
 1S0  CAY  NAQ  single  1.350  0.020  1.350
 1S0  OAF  CAX  single  1.429  0.020  1.429
 1S0  NAR  CAZ  single  1.347  0.020  1.347
 1S0  NAQ  CAZ  single  1.403  0.020  1.403
 1S0  NAQ  CAW  single  1.474  0.020  1.474
 1S0  CAX  CAU  single  1.506  0.020  1.506
 1S0  CAZ  OAH  double  1.226  0.020  1.226
 1S0  CAT  CAV  single  1.520  0.020  1.520
 1S0  CAT  CAU  single  1.531  0.020  1.531
 1S0  CAT  OAE  single  1.400  0.020  1.400
 1S0  CAV  CAW  single  1.527  0.020  1.527
 1S0  CAU  OAD  single  1.421  0.020  1.421
 1S0  OAD  CAW  single  1.402  0.020  1.402
 1S0  OAE  H1   single  0.850  0.020  0.980
 1S0  OAJ  H2   single  0.850  0.020  0.980
 1S0  OAL  H3   single  0.850  0.020  0.980
 1S0  OAP  H4   single  0.850  0.020  0.980
 1S0  OAN  H5   single  0.850  0.020  0.980
 1S0  CAX  H6   single  0.970  0.020  1.090
 1S0  CAX  H7   single  0.970  0.020  1.090
 1S0  CAU  H8   single  0.970  0.020  1.090
 1S0  CAT  H9   single  0.970  0.020  1.090
 1S0  CAV  H10  single  0.970  0.020  1.090
 1S0  CAV  H11  single  0.970  0.020  1.090
 1S0  CAW  H12  single  0.970  0.020  1.090
 1S0  CAY  H13  single  0.930  0.020  1.080
 1S0  CBA  H14  single  0.930  0.020  1.080
 1S0  NAS  H15  single  0.860  0.020  1.020
 1S0  NAS  H16  single  0.860  0.020  1.020

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
 1S0  H1   OAE  CAT  109.05  3.000
 1S0  PAB  OAG  PAA  135.37  3.000
 1S0  H2   OAJ  PAA  114.43  3.000
 1S0  PAC  OAK  PAB  132.51  3.000
 1S0  H3   OAL  PAB  114.25  3.000
 1S0  OAF  PAA  OAI  111.72  3.000
 1S0  OAF  PAA  OAJ  106.73  3.000
 1S0  OAI  PAA  OAJ  118.84  3.000
 1S0  OAF  PAA  OAG  103.27  3.000
 1S0  OAJ  PAA  OAG  101.96  3.000
 1S0  OAI  PAA  OAG  112.81  3.000
 1S0  OAM  PAB  OAL  118.77  3.000
 1S0  OAL  PAB  OAK  101.37  3.000
 1S0  OAM  PAB  OAK  116.04  3.000
 1S0  OAL  PAB  OAG   99.11  3.000
 1S0  OAM  PAB  OAG  116.30  3.000
 1S0  OAK  PAB  OAG  102.41  3.000
 1S0  OAN  PAC  OAP   97.95  3.000
 1S0  OAN  PAC  OAO  119.39  3.000
 1S0  OAP  PAC  OAO  118.70  3.000
 1S0  OAN  PAC  OAK  105.58  3.000
 1S0  OAP  PAC  OAK  104.98  3.000
 1S0  OAO  PAC  OAK  108.61  3.000
 1S0  H4   OAP  PAC  114.66  3.000
 1S0  H5   OAN  PAC  114.88  3.000
 1S0  CAX  OAF  PAA  124.97  3.000
 1S0  H7   CAX  H6   108.04  3.000
 1S0  H7   CAX  CAU  108.33  3.000
 1S0  H6   CAX  CAU  110.28  3.000
 1S0  H7   CAX  OAF  111.47  3.000
 1S0  H6   CAX  OAF  109.58  3.000
 1S0  CAU  CAX  OAF  109.12  3.000
 1S0  H8   CAU  OAD  110.03  3.000
 1S0  H8   CAU  CAT  108.28  3.000
 1S0  OAD  CAU  CAT  104.83  3.000
 1S0  H8   CAU  CAX  106.11  3.000
 1S0  OAD  CAU  CAX  110.53  3.000
 1S0  CAT  CAU  CAX  117.00  3.000
 1S0  H9   CAT  CAV  109.80  3.000
 1S0  H9   CAT  CAU  109.95  3.000
 1S0  CAV  CAT  CAU  100.19  3.000
 1S0  H9   CAT  OAE  111.09  3.000
 1S0  CAU  CAT  OAE  113.62  3.000
 1S0  CAV  CAT  OAE  111.68  3.000
 1S0  H11  CAV  H10  108.01  3.000
 1S0  H11  CAV  CAW  113.09  3.000
 1S0  H10  CAV  CAW  109.55  3.000
 1S0  H11  CAV  CAT  114.09  3.000
 1S0  H10  CAV  CAT  109.35  3.000
 1S0  CAW  CAV  CAT  102.61  3.000
 1S0  H12  CAW  NAQ  106.50  3.000
 1S0  H12  CAW  OAD  109.70  3.000
 1S0  NAQ  CAW  OAD  109.38  3.000
 1S0  H12  CAW  CAV  112.33  3.000
 1S0  OAD  CAW  CAV  106.53  3.000
 1S0  NAQ  CAW  CAV  112.40  3.000
 1S0  CAW  OAD  CAU  110.59  3.000
 1S0  CAZ  NAQ  CAY  120.61  3.000
 1S0  CAZ  NAQ  CAW  116.72  3.000
 1S0  CAY  NAQ  CAW  122.67  3.000
 1S0  H13  CAY  CBA  121.32  3.000
 1S0  H13  CAY  NAQ  117.35  3.000
 1S0  CBA  CAY  NAQ  121.33  3.000
 1S0  H14  CBA  CBB  122.32  3.000
 1S0  H14  CBA  CAY  121.03  3.000
 1S0  CBB  CBA  CAY  116.64  3.000
 1S0  NAR  CBB  NAS  118.14  3.000
 1S0  NAR  CBB  CBA  122.08  3.000
 1S0  NAS  CBB  CBA  119.78  3.000
 1S0  H16  NAS  H15  118.20  3.000
 1S0  H16  NAS  CBB  121.63  3.000
 1S0  H15  NAS  CBB  120.11  3.000
 1S0  CAZ  NAR  CBB  120.82  3.000
 1S0  NAR  CAZ  NAQ  118.51  3.000
 1S0  NAQ  CAZ  OAH  118.52  3.000
 1S0  NAR  CAZ  OAH  122.97  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
 1S0  CONST_01  NAR  CAZ  NAQ  CAW  180.00   0.0  0
 1S0  CONST_02  CBB  NAR  CAZ  NAQ    0.00   0.0  0
 1S0  CONST_03  NAR  CAZ  NAQ  CAY    0.00   0.0  0
 1S0  CONST_04  CAZ  NAR  CBB  CBA    0.00   0.0  0
 1S0  CONST_05  CBB  NAR  CAZ  OAH  180.00   0.0  0
 1S0  CONST_06  CAY  NAQ  CAZ  OAH  180.00   0.0  0
 1S0  CONST_07  CAW  NAQ  CAZ  OAH    0.00   0.0  0
 1S0  CONST_08  CAZ  NAR  CBB  NAS  180.00   0.0  0
 1S0  CONST_09  H15  NAS  CBB  CBA  180.00   0.0  0
 1S0  CONST_10  H16  NAS  CBB  CBA    0.00   0.0  0
 1S0  Var_01    CAU  CAX  OAF  PAA  164.96  30.0  3
 1S0  Var_02    OAM  PAB  OAG  PAA   25.17  30.0  3
 1S0  Var_03    OAF  PAA  OAG  PAB  -96.86  30.0  2
 1S0  Var_04    OAP  PAC  OAK  PAB  -57.27  30.0  2

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
 1S0  chir_03  CAU  CAX  CAT  OAD  negativ
 1S0  chir_04  CAT  OAE  CAU  CAV  negativ
 1S0  chir_05  CAW  OAD  NAQ  CAV  positiv
 1S0  chir_06  PAA  OAJ  OAG  OAF  both
 1S0  chir_07  PAB  OAK  OAM  OAL  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
 1S0  plan-1  OAH  0.020
 1S0  plan-1  CAW  0.020
 1S0  plan-1  NAQ  0.020
 1S0  plan-1  CAY  0.020
 1S0  plan-1  CBA  0.020
 1S0  plan-1  CBB  0.020
 1S0  plan-1  NAS  0.020
 1S0  plan-1  NAR  0.020
 1S0  plan-1  CAZ  0.020
 1S0  plan-1  H13  0.020
 1S0  plan-1  H14  0.020
 1S0  plan-1  H15  0.020
 1S0  plan-1  H16  0.020

