# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:15:42 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: {2-[(3S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)pyrrolidin-1-yl]-2-oxoethyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3CCN(C3)C(=O)C[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
 3ZF  3ZF  '{2-[(3S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)pyrrolidin-1-yl]-2-oxoethyl}phosphonic acid'  ligand  36  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3ZF
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
 3ZF  N1    N  NH1    0  -0.727  -5.2409   1.1713  -0.1964
 3ZF  C2    C  C      0   0.688  -4.0902   1.8996  -0.0942
 3ZF  N2    N  NH2    0  -0.832  -4.2117   3.2358  -0.1245
 3ZF  N3    N  N      0  -0.512  -2.9112   1.3529   0.0627
 3ZF  C4    C  CR5    0   0.500  -2.9523   0.0141   0.1143
 3ZF  C5    C  CR5    0  -0.096  -4.0567  -0.8140   0.0200
 3ZF  C6    C  C      0   0.503  -5.3420  -0.2250  -0.1507
 3ZF  O6    O  O      0  -0.476  -6.4278  -0.7717  -0.2530
 3ZF  N7    N  N      0  -0.446  -3.6840  -2.1294   0.1149
 3ZF  C8    C  CR15   0   0.086  -2.3948  -2.0929   0.2629
 3ZF  N9    N  NR5    0  -0.510  -1.8890  -0.8174   0.2707
 3ZF  OAB   O  O      0  -0.539   2.7842  -1.1709  -1.9862
 3ZF  OAD   O  OP    -1  -0.901   6.0293   0.7161   0.9335
 3ZF  OAE   O  OP    -1  -0.878   3.6447   1.6468   0.6814
 3ZF  OAF   O  O      0  -0.893   5.0846   1.2251  -1.4003
 3ZF  CAH   C  CH2    0  -0.472   0.1479  -0.9381   1.7116
 3ZF  CAI   C  CH2    0  -0.275   1.6301  -0.7751   1.4130
 3ZF  CAJ   C  CH2    0  -0.857   4.1435  -0.9407  -0.0362
 3ZF  CAK   C  CH2    0  -0.233   0.4134  -0.9458  -0.6743
 3ZF  CAT   C  CH1    0  -0.152  -0.5062  -0.4259   0.4329
 3ZF  NAU   N  NT     0  -0.466   1.7123  -0.9696  -0.0325
 3ZF  PAW   P  P      0   1.177   4.7858   0.8447   0.0489
 3ZF  HN2   H  HNH2   0   0.413  -5.0552   3.6685  -0.4613
 3ZF  HN2A  H  HNH2   0   0.412  -3.3676   3.7731  -0.2282
 3ZF  HN1   H  HNH1   0   0.424  -6.1132   1.6698  -0.3170
 3ZF  H8    H  HCR5   0   0.294  -1.7557  -2.9565   0.3700
 3ZF  HAH   H  HCH2   0   0.249  -0.0941  -1.9920   1.8651
 3ZF  HAHA  H  HCH2   0   0.266  -0.1686  -0.3871   2.5963
 3ZF  HAI   H  HCH2   0   0.254   2.0059   0.2140   1.6763
 3ZF  HAIA  H  HCH2   0   0.242   2.2234  -1.5157   1.9508
 3ZF  HAJ   H  HCH2   0   0.221   4.0745  -1.3267   0.9814
 3ZF  HAJA  H  HCH2   0   0.227   4.8846  -1.5417  -0.5671
 3ZF  HAK   H  HCH2   0   0.234   0.1060  -1.9449  -1.0037
 3ZF  HAKA  H  HCH2   0   0.253   0.4043  -0.2946  -1.5486
 3ZF  HAT   H  HCH1   0   0.290  -0.4927   0.6650   0.4294
 3ZF  CAO   C  C      0   0.530   2.8492  -1.0429  -0.7629

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
 3ZF  N1   C6    single    1.401  0.020  1.401
 3ZF  N1   C2    single    1.366  0.020  1.366
 3ZF  N2   C2    single    1.342  0.020  1.342
 3ZF  C2   N3    double    1.309  0.020  1.309
 3ZF  N2   HN2   single    0.890  0.020  1.040
 3ZF  N2   HN2A  single    0.890  0.020  1.040
 3ZF  N3   C4    single    1.340  0.020  1.340
 3ZF  N1   HN1   single    0.860  0.020  1.020
 3ZF  C5   C4    aromatic  1.384  0.020  1.384
 3ZF  C4   N9    aromatic  1.359  0.020  1.359
 3ZF  C6   C5    single    1.424  0.020  1.424
 3ZF  C5   N7    aromatic  1.370  0.020  1.370
 3ZF  O6   C6    double    1.220  0.020  1.220
 3ZF  N7   C8    aromatic  1.298  0.020  1.298
 3ZF  C8   N9    aromatic  1.372  0.020  1.372
 3ZF  C8   H8    single    0.930  0.020  1.080
 3ZF  N9   CAT   single    1.446  0.020  1.446
 3ZF  CAO  OAB   double    1.232  0.020  1.232
 3ZF  OAD  PAW   deloc     1.531  0.020  1.531
 3ZF  PAW  OAE   deloc     1.532  0.020  1.532
 3ZF  OAF  PAW   deloc     1.528  0.020  1.528
 3ZF  CAT  CAH   single    1.525  0.020  1.525
 3ZF  CAH  CAI   single    1.521  0.020  1.521
 3ZF  CAH  HAH   single    0.970  0.020  1.090
 3ZF  CAH  HAHA  single    0.970  0.020  1.090
 3ZF  CAI  NAU   single    1.461  0.020  1.461
 3ZF  CAI  HAI   single    0.970  0.020  1.090
 3ZF  CAI  HAIA  single    0.970  0.020  1.090
 3ZF  CAO  CAJ   single    1.488  0.020  1.488
 3ZF  CAJ  PAW   single    1.899  0.020  1.899
 3ZF  CAJ  HAJ   single    0.970  0.020  1.090
 3ZF  CAJ  HAJA  single    0.970  0.020  1.090
 3ZF  CAT  CAK   single    1.530  0.020  1.530
 3ZF  CAK  NAU   single    1.449  0.020  1.449
 3ZF  CAK  HAK   single    0.970  0.020  1.090
 3ZF  CAK  HAKA  single    0.970  0.020  1.090
 3ZF  NAU  CAO   single    1.353  0.020  1.353
 3ZF  CAT  HAT   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
 3ZF  HN1   N1   C6   115.64  3.000
 3ZF  HN1   N1   C2   118.21  3.000
 3ZF  C6    N1   C2   126.15  3.000
 3ZF  N3    C2   N2   120.00  3.000
 3ZF  N3    C2   N1   123.04  3.000
 3ZF  N2    C2   N1   116.93  3.000
 3ZF  HN2A  N2   HN2  116.06  3.000
 3ZF  HN2A  N2   C2   117.26  3.000
 3ZF  HN2   N2   C2   120.78  3.000
 3ZF  C4    N3   C2   113.21  3.000
 3ZF  N9    C4   C5   105.44  3.000
 3ZF  N9    C4   N3   126.27  3.000
 3ZF  C5    C4   N3   128.29  3.000
 3ZF  N7    C5   C6   130.60  3.000
 3ZF  N7    C5   C4   110.65  3.000
 3ZF  C6    C5   C4   118.75  3.000
 3ZF  O6    C6   C5   128.90  3.000
 3ZF  O6    C6   N1   120.55  3.000
 3ZF  C5    C6   N1   110.55  3.000
 3ZF  C8    N7   C5   104.53  3.000
 3ZF  H8    C8   N9   121.65  3.000
 3ZF  H8    C8   N7   125.21  3.000
 3ZF  N9    C8   N7   113.13  3.000
 3ZF  CAT   N9   C8   127.21  3.000
 3ZF  CAT   N9   C4   126.54  3.000
 3ZF  C8    N9   C4   106.24  3.000
 3ZF  HAHA  CAH  HAH  108.03  3.000
 3ZF  HAHA  CAH  CAT  112.74  3.000
 3ZF  HAH   CAH  CAT  110.30  3.000
 3ZF  HAHA  CAH  CAI  112.86  3.000
 3ZF  HAH   CAH  CAI  110.30  3.000
 3ZF  CAT   CAH  CAI  102.56  3.000
 3ZF  HAIA  CAI  HAI  108.02  3.000
 3ZF  HAIA  CAI  NAU  111.52  3.000
 3ZF  HAI   CAI  NAU  109.90  3.000
 3ZF  HAIA  CAI  CAH  111.14  3.000
 3ZF  HAI   CAI  CAH  112.69  3.000
 3ZF  NAU   CAI  CAH  103.59  3.000
 3ZF  HAJA  CAJ  HAJ  107.56  3.000
 3ZF  HAJA  CAJ  PAW  108.04  3.000
 3ZF  HAJ   CAJ  PAW  108.20  3.000
 3ZF  HAJA  CAJ  CAO  108.37  3.000
 3ZF  HAJ   CAJ  CAO  112.11  3.000
 3ZF  PAW   CAJ  CAO  112.37  3.000
 3ZF  HAKA  CAK  HAK  107.52  3.000
 3ZF  HAKA  CAK  NAU  111.87  3.000
 3ZF  HAK   CAK  NAU  111.69  3.000
 3ZF  HAKA  CAK  CAT  111.86  3.000
 3ZF  HAK   CAK  CAT  111.02  3.000
 3ZF  NAU   CAK  CAT  102.94  3.000
 3ZF  HAT   CAT  CAK  109.27  3.000
 3ZF  HAT   CAT  CAH  109.46  3.000
 3ZF  CAK   CAT  CAH  103.58  3.000
 3ZF  HAT   CAT  N9   106.39  3.000
 3ZF  CAK   CAT  N9   113.67  3.000
 3ZF  CAH   CAT  N9   114.41  3.000
 3ZF  CAO   NAU  CAK  120.99  3.000
 3ZF  CAO   NAU  CAI  126.06  3.000
 3ZF  CAK   NAU  CAI  112.68  3.000
 3ZF  CAJ   PAW  OAF  104.93  3.000
 3ZF  CAJ   PAW  OAE  105.00  3.000
 3ZF  OAF   PAW  OAE  114.02  3.000
 3ZF  CAJ   PAW  OAD  102.80  3.000
 3ZF  OAF   PAW  OAD  114.21  3.000
 3ZF  OAE   PAW  OAD  114.23  3.000
 3ZF  NAU   CAO  CAJ  117.61  3.000
 3ZF  NAU   CAO  OAB  119.82  3.000
 3ZF  CAJ   CAO  OAB  122.56  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
 3ZF  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 3ZF  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 3ZF  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 3ZF  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 3ZF  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 3ZF  CONST_06  CAT   N9   C4   N3     0.00   0.0  0
 3ZF  CONST_07  CAT   N9   C4   C5   180.00   0.0  0
 3ZF  CONST_08  CAT   N9   C8   N7   180.00   0.0  0
 3ZF  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 3ZF  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 3ZF  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 3ZF  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 3ZF  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 3ZF  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 3ZF  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 3ZF  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 3ZF  CONST_17  CAI   NAU  CAO  OAB  180.00   0.0  0
 3ZF  CONST_18  CAK   NAU  CAO  OAB    0.00   0.0  0
 3ZF  CONST_19  CAJ   CAO  NAU  CAI    0.00   0.0  0
 3ZF  CONST_20  CAK   NAU  CAO  CAJ  180.00   0.0  0
 3ZF  CONST_22  HN2A  N2   C2   N1   180.00   0.0  0
 3ZF  Var_01    CAK   NAU  CAI  CAH   12.51  30.0  1
 3ZF  Var_02    CAT   CAK  NAU  CAI   11.48  30.0  1
 3ZF  Var_03    NAU   CAI  CAH  CAT  -31.15  30.0  1
 3ZF  Var_04    PAW   CAJ  CAO  NAU  -92.28  30.0  3
 3ZF  Var_05    CAO   CAJ  PAW  OAD  175.04  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
 3ZF  chir_01  CAT  N9  CAH  CAK  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
 3ZF  plan-1  N1    0.020
 3ZF  plan-1  C2    0.020
 3ZF  plan-1  N2    0.020
 3ZF  plan-1  N3    0.020
 3ZF  plan-1  C4    0.020
 3ZF  plan-1  C5    0.020
 3ZF  plan-1  C6    0.020
 3ZF  plan-1  O6    0.020
 3ZF  plan-1  N7    0.020
 3ZF  plan-1  C8    0.020
 3ZF  plan-1  N9    0.020
 3ZF  plan-1  CAT   0.020
 3ZF  plan-1  HN2   0.020
 3ZF  plan-1  HN2A  0.020
 3ZF  plan-1  HN1   0.020
 3ZF  plan-1  H8    0.020
 3ZF  plan-2  OAB   0.020
 3ZF  plan-2  CAI   0.020
 3ZF  plan-2  CAJ   0.020
 3ZF  plan-2  CAK   0.020
 3ZF  plan-2  NAU   0.020
 3ZF  plan-2  CAO   0.020

