# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 14:43:52 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CN(C[C@H]3OC[C@@H](O)[P](O)(O)=O)C(=O)CC[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
 YPG  YPG  '[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid'  ligand  54  32  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YPG
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
 YPG  C4   C  CR56  0   0.507  31.7624   6.9829  23.9136
 YPG  C5   C  CR56  0  -0.097  31.8299   5.6701  24.3423
 YPG  C6   C  CR6   0   0.506  33.1111   5.0676  24.5002
 YPG  C8   C  CR15  0   0.084  29.7730   6.1409  24.2584
 YPG  N1   N  NR16  0  -0.728  34.1253   5.9746  24.1677
 YPG  N3   N  N     0  -0.514  32.7686   7.8120  23.6084
 YPG  PBF  P  P     0   1.365  27.6805   7.0975  17.8241
 YPG  OAJ  O  O     0  -0.714  28.7131   7.0873  16.7574
 YPG  OAE  O  OH1   0  -0.745  27.3180   5.6696  18.4614
 YPG  CAZ  C  CH1   0  -0.273  28.1236   8.0554  19.3195
 YPG  OAF  O  OH1   0  -0.647  28.3526   9.3869  18.9368
 YPG  CAN  C  CH2   0  -0.226  29.3173   7.4264  20.0391
 YPG  OAT  O  O2    0  -0.473  29.8307   8.2384  21.0651
 YPG  CBA  C  CR15  0   0.035  29.0105   8.4204  22.1797
 YPG  CAO  C  CH2   0  -0.293  28.2379   9.7427  22.1924
 YPG  NBC  N  NR5   0  -0.483  28.1084  10.0402  23.6151
 YPG  CAU  C  C     0   0.557  27.4070  11.0476  24.1617
 YPG  OAB  O  O     0  -0.501  27.3521  11.2055  25.3742
 YPG  CAL  C  CH2   0  -0.587  26.6802  11.9983  23.2320
 YPG  CAM  C  CH2   0  -0.738  27.1709  13.4381  23.4006
 YPG  PBE  P  P     0   1.367  28.8112  13.6894  22.7045
 YPG  OAG  O  OH1   0  -0.742  29.0454  15.2517  23.0004
 YPG  OAH  O  O     0  -0.716  28.9990  13.2821  21.2870
 YPG  OAD  O  OH1   0  -0.745  29.7574  12.8896  23.7348
 YPG  CAP  C  CH2   0  -0.245  28.9160   9.1690  24.4522
 YPG  CBB  C  CR15  0  -0.183  29.8598   8.5281  23.4422
 YPG  N9   N  NR5   0  -0.511  30.4358   7.2790  23.8680
 YPG  C2   C  CR6   0   0.694  33.9497   7.2615  23.7457
 YPG  O6   O  O     0  -0.473  33.3856   3.9369  24.8659
 YPG  N7   N  N     0  -0.441  30.5736   5.1634  24.5514
 YPG  H1   H  HCR5  0   0.294  28.6952   6.0974  24.3071
 YPG  H2   H  HNR6  0   0.426  35.0707   5.6249  24.2571
 YPG  H3   H  HNH2  0   0.413  34.9565   8.9439  23.2735
 YPG  H4   H  HNH2  0   0.415  35.9670   7.6274  23.6929
 YPG  H5   H  HOH1  0   0.496  26.1617   7.8295  16.4381
 YPG  H6   H  HOH1  0   0.497  27.2700   4.9416  17.8263
 YPG  H7   H  HCH1  0   0.286  27.2521   8.0639  19.9826
 YPG  H8   H  HOH1  0   0.457  29.1966   9.4485  18.4748
 YPG  H9   H  HCH2  0   0.238  29.0343   6.4381  20.4197
 YPG  H10  H  HCH2  0   0.254  30.1437   7.2861  19.3377
 YPG  H11  H  HCR5  0   0.248  28.3031   7.5860  22.2927
 YPG  H12  H  HCH2  0   0.260  28.8028  10.5157  21.6660
 YPG  H13  H  HCH2  0   0.265  27.2619   9.6460  21.7171
 YPG  H14  H  HCH2  0   0.299  25.6231  11.9658  23.5032
 YPG  H15  H  HCH2  0   0.274  26.7367  11.7092  22.1839
 YPG  H16  H  HCH2  0   0.304  26.4943  14.1123  22.8720
 YPG  H17  H  HCH2  0   0.294  27.1609  13.7363  24.4501
 YPG  H18  H  HOH1  0   0.493  29.7881  15.6390  22.5174
 YPG  H19  H  HOH1  0   0.490  30.5876  12.5851  23.3445
 YPG  H20  H  HCH2  0   0.253  28.2984   8.4246  24.9637
 YPG  H21  H  HCH2  0   0.274  29.4565   9.7311  25.2126
 YPG  H22  H  HCR5  0   0.302  30.6916   9.2079  23.2438
 YPG  N2   N  NH2   0  -0.832  35.0522   7.9559  23.4352
 YPG  OAI  O  OH1   0  -0.741  26.2799   7.7526  17.3943

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
 YPG  OAJ  PBF  double    1.485  0.020  1.485
 YPG  OAI  PBF  single    1.605  0.020  1.605
 YPG  OAF  CAZ  single    1.404  0.020  1.404
 YPG  PBF  CAZ  single    1.830  0.020  1.830
 YPG  PBF  OAE  single    1.605  0.020  1.605
 YPG  CAZ  CAN  single    1.529  0.020  1.529
 YPG  CAN  OAT  single    1.406  0.020  1.406
 YPG  OAT  CBA  single    1.396  0.020  1.396
 YPG  CBA  CAO  single    1.532  0.020  1.532
 YPG  CBA  CBB  single    1.525  0.020  1.525
 YPG  CAO  NBC  single    1.459  0.020  1.459
 YPG  OAH  PBE  double    1.487  0.020  1.487
 YPG  C8   N7   aromatic  1.297  0.020  1.297
 YPG  C8   N9   aromatic  1.374  0.020  1.374
 YPG  N7   C5   aromatic  1.371  0.020  1.371
 YPG  CBB  N9   single    1.440  0.020  1.440
 YPG  CBB  CAP  single    1.524  0.020  1.524
 YPG  N9   C4   aromatic  1.360  0.020  1.360
 YPG  CAL  CAM  single    1.530  0.020  1.530
 YPG  CAL  CAU  single    1.515  0.020  1.515
 YPG  NBC  CAU  single    1.344  0.020  1.344
 YPG  NBC  CAP  single    1.453  0.020  1.453
 YPG  C5   C4   aromatic  1.383  0.020  1.383
 YPG  C5   C6   single    1.425  0.020  1.425
 YPG  C4   N3   single    1.339  0.020  1.339
 YPG  CAM  PBE  single    1.800  0.020  1.800
 YPG  PBE  OAG  single    1.607  0.020  1.607
 YPG  PBE  OAD  single    1.611  0.020  1.611
 YPG  CAU  OAB  double    1.224  0.020  1.224
 YPG  O6   C6   double    1.220  0.020  1.220
 YPG  C6   N1   single    1.401  0.020  1.401
 YPG  N3   C2   double    1.310  0.020  1.310
 YPG  N1   C2   single    1.366  0.020  1.366
 YPG  C2   N2   single    1.340  0.020  1.340
 YPG  C8   H1   single    0.930  0.020  1.080
 YPG  N1   H2   single    0.860  0.020  1.020
 YPG  N2   H3   single    0.890  0.020  1.040
 YPG  N2   H4   single    0.890  0.020  1.040
 YPG  OAI  H5   single    0.850  0.020  0.980
 YPG  OAE  H6   single    0.850  0.020  0.980
 YPG  CAZ  H7   single    0.970  0.020  1.090
 YPG  OAF  H8   single    0.850  0.020  0.980
 YPG  CAN  H9   single    0.970  0.020  1.090
 YPG  CAN  H10  single    0.970  0.020  1.090
 YPG  CBA  H11  single    0.970  0.020  1.090
 YPG  CAO  H12  single    0.970  0.020  1.090
 YPG  CAO  H13  single    0.970  0.020  1.090
 YPG  CAL  H14  single    0.970  0.020  1.090
 YPG  CAL  H15  single    0.970  0.020  1.090
 YPG  CAM  H16  single    0.970  0.020  1.090
 YPG  CAM  H17  single    0.970  0.020  1.090
 YPG  OAG  H18  single    0.850  0.020  0.980
 YPG  OAD  H19  single    0.850  0.020  0.980
 YPG  CAP  H20  single    0.970  0.020  1.090
 YPG  CAP  H21  single    0.970  0.020  1.090
 YPG  CBB  H22  single    0.970  0.020  1.090

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
 YPG  N9   C4   N3   126.20  3.000
 YPG  N3   C4   C5   128.45  3.000
 YPG  N9   C4   C5   105.35  3.000
 YPG  N7   C5   C6   130.62  3.000
 YPG  C6   C5   C4   118.68  3.000
 YPG  N7   C5   C4   110.70  3.000
 YPG  O6   C6   N1   120.57  3.000
 YPG  N1   C6   C5   110.55  3.000
 YPG  O6   C6   C5   128.88  3.000
 YPG  H1   C8   N7   125.14  3.000
 YPG  H1   C8   N9   121.86  3.000
 YPG  N7   C8   N9   113.00  3.000
 YPG  H2   N1   C2   118.24  3.000
 YPG  H2   N1   C6   115.57  3.000
 YPG  C2   N1   C6   126.19  3.000
 YPG  C2   N3   C4   113.16  3.000
 YPG  CAZ  PBF  OAE  101.30  3.000
 YPG  OAE  PBF  OAJ  115.86  3.000
 YPG  CAZ  PBF  OAJ  114.98  3.000
 YPG  OAE  PBF  OAI  105.81  3.000
 YPG  CAZ  PBF  OAI  102.50  3.000
 YPG  OAJ  PBF  OAI  114.67  3.000
 YPG  H6   OAE  PBF  114.84  3.000
 YPG  H7   CAZ  CAN  109.85  3.000
 YPG  H7   CAZ  OAF  106.71  3.000
 YPG  CAN  CAZ  OAF  113.02  3.000
 YPG  H7   CAZ  PBF  107.83  3.000
 YPG  CAN  CAZ  PBF  110.98  3.000
 YPG  OAF  CAZ  PBF  108.24  3.000
 YPG  H8   OAF  CAZ  109.51  3.000
 YPG  H10  CAN  H9   107.60  3.000
 YPG  H10  CAN  OAT  105.45  3.000
 YPG  H9   CAN  OAT  111.21  3.000
 YPG  H10  CAN  CAZ  109.94  3.000
 YPG  H9   CAN  CAZ  109.43  3.000
 YPG  OAT  CAN  CAZ  113.01  3.000
 YPG  CBA  OAT  CAN  116.33  3.000
 YPG  H11  CBA  CBB  109.07  3.000
 YPG  H11  CBA  CAO  109.26  3.000
 YPG  CBB  CBA  CAO  102.30  3.000
 YPG  H11  CBA  OAT  111.17  3.000
 YPG  CBB  CBA  OAT  110.06  3.000
 YPG  CAO  CBA  OAT  114.56  3.000
 YPG  H13  CAO  H12  108.40  3.000
 YPG  H13  CAO  NBC  111.33  3.000
 YPG  H12  CAO  NBC  111.80  3.000
 YPG  H13  CAO  CBA  111.81  3.000
 YPG  H12  CAO  CBA  110.24  3.000
 YPG  NBC  CAO  CBA  103.23  3.000
 YPG  CAP  NBC  CAU  120.34  3.000
 YPG  CAP  NBC  CAO  112.96  3.000
 YPG  CAU  NBC  CAO  126.57  3.000
 YPG  CAL  CAU  OAB  120.35  3.000
 YPG  OAB  CAU  NBC  121.54  3.000
 YPG  CAL  CAU  NBC  118.11  3.000
 YPG  H15  CAL  H14  106.35  3.000
 YPG  H15  CAL  CAM  109.83  3.000
 YPG  H14  CAL  CAM  108.13  3.000
 YPG  H15  CAL  CAU  113.52  3.000
 YPG  H14  CAL  CAU  107.06  3.000
 YPG  CAM  CAL  CAU  111.65  3.000
 YPG  H17  CAM  H16  106.94  3.000
 YPG  H17  CAM  PBE  110.01  3.000
 YPG  H16  CAM  PBE  106.94  3.000
 YPG  H17  CAM  CAL  111.11  3.000
 YPG  H16  CAM  CAL  109.21  3.000
 YPG  PBE  CAM  CAL  112.39  3.000
 YPG  OAD  PBE  OAH  113.55  3.000
 YPG  OAD  PBE  OAG  106.21  3.000
 YPG  OAH  PBE  OAG  115.05  3.000
 YPG  OAD  PBE  CAM  102.63  3.000
 YPG  OAG  PBE  CAM  101.38  3.000
 YPG  OAH  PBE  CAM  116.47  3.000
 YPG  H18  OAG  PBE  114.16  3.000
 YPG  H19  OAD  PBE  113.73  3.000
 YPG  H21  CAP  H20  107.75  3.000
 YPG  H21  CAP  CBB  111.87  3.000
 YPG  H20  CAP  CBB  111.92  3.000
 YPG  H21  CAP  NBC  111.63  3.000
 YPG  H20  CAP  NBC  111.31  3.000
 YPG  CBB  CAP  NBC  102.39  3.000
 YPG  H22  CBB  N9   106.79  3.000
 YPG  H22  CBB  CAP  109.29  3.000
 YPG  N9   CBB  CAP  114.63  3.000
 YPG  H22  CBB  CBA  108.52  3.000
 YPG  CAP  CBB  CBA  103.50  3.000
 YPG  N9   CBB  CBA  113.97  3.000
 YPG  CBB  N9   C8   127.57  3.000
 YPG  CBB  N9   C4   126.09  3.000
 YPG  C8   N9   C4   106.31  3.000
 YPG  N3   C2   N2   119.99  3.000
 YPG  N2   C2   N1   117.02  3.000
 YPG  N3   C2   N1   122.97  3.000
 YPG  C8   N7   C5   104.64  3.000
 YPG  H4   N2   H3   116.66  3.000
 YPG  H4   N2   C2   121.34  3.000
 YPG  H3   N2   C2   117.91  3.000
 YPG  H5   OAI  PBF  113.84  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
 YPG  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 YPG  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 YPG  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 YPG  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 YPG  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 YPG  CONST_06  CBB  N9   C4   C5    180.00   0.0  0
 YPG  CONST_07  CBB  N9   C4   N3      0.00   0.0  0
 YPG  CONST_08  N7   C8   N9   CBB   180.00   0.0  0
 YPG  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 YPG  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 YPG  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 YPG  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 YPG  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 YPG  CONST_14  O6   C6   N1   C2    180.00   0.0  0
 YPG  CONST_15  H1   C8   N9   C4    180.00   0.0  0
 YPG  CONST_16  H2   N1   C6   C5    180.00   0.0  0
 YPG  CONST_17  CAL  CAU  NBC  CAO     0.00   0.0  0
 YPG  CONST_18  OAB  CAU  NBC  CAO   180.00   0.0  0
 YPG  CONST_19  CAP  NBC  CAU  OAB     0.00   0.0  0
 YPG  CONST_20  CAP  NBC  CAU  CAL   180.00   0.0  0
 YPG  CONST_21  H3   N2   C2   N1    180.00   0.0  0
 YPG  CONST_22  H4   N2   C2   N1      0.00   0.0  0
 YPG  Var_01    CAP  NBC  CAO  CBA    10.12  30.0  1
 YPG  Var_02    CBB  CAP  NBC  CAO    14.50  30.0  1
 YPG  Var_03    CAM  CAL  CAU  NBC  -119.92  30.0  1
 YPG  Var_04    H9   CAN  OAT  CBA   -55.61  30.0  2
 YPG  Var_05    PBE  CAM  CAL  CAU    72.89  30.0  3
 YPG  Var_06    OAH  PBE  CAM  CAL    53.52  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
 YPG  chir_01  CAZ  OAF  PBF  CAN  negativ
 YPG  chir_02  CBA  OAT  CBB  CAO  negativ
 YPG  chir_03  CBB  N9   CAP  CBA  positiv

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
 YPG  plan-1  C4   0.020
 YPG  plan-1  C5   0.020
 YPG  plan-1  C6   0.020
 YPG  plan-1  C8   0.020
 YPG  plan-1  N1   0.020
 YPG  plan-1  N3   0.020
 YPG  plan-1  CBB  0.020
 YPG  plan-1  N9   0.020
 YPG  plan-1  C2   0.020
 YPG  plan-1  O6   0.020
 YPG  plan-1  N7   0.020
 YPG  plan-1  H1   0.020
 YPG  plan-1  H2   0.020
 YPG  plan-1  H3   0.020
 YPG  plan-1  H4   0.020
 YPG  plan-1  N2   0.020
 YPG  plan-2  CAO  0.020
 YPG  plan-2  NBC  0.020
 YPG  plan-2  CAU  0.020
 YPG  plan-2  OAB  0.020
 YPG  plan-2  CAL  0.020
 YPG  plan-2  CAP  0.020

