# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 18:25:55 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (4-{[(4-aminobutyl)amino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNCCCCN)c1O
#
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
 P3T  P3T  '(4-{[(4-aminobutyl)amino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate'  ligand  43  21  .  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_P3T
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
 P3T  OAE   O  O     0  -0.708   2.2225  -3.6273   0.3100
 P3T  PAU   P  P     0   1.464   3.2200  -2.6157  -0.0824
 P3T  OAF   O  OH1   0  -0.729   4.5840  -2.5484   0.7355
 P3T  OAC   O  OH1   0  -0.741   3.5776  -2.7832  -1.6297
 P3T  OAP   O  O2    0  -0.592   2.8024  -1.0875   0.1347
 P3T  CAM   C  CH2   0  -0.208   1.5619  -0.6208  -0.3831
 P3T  CAS   C  CR6   0  -0.075   1.4404   0.8584  -0.1376
 P3T  CAH   C  CR16  0  -0.135   2.4653   1.5937   0.4392
 P3T  NAO   N  N     0  -0.407   2.3805   2.8982   0.6705
 P3T  CAQ   C  CR6   0   0.122   1.2754   3.5513   0.3498
 P3T  CAA   C  CH3   0  -0.785   1.2147   5.0234   0.6284
 P3T  CAR   C  CR6   0   0.265   0.1873   2.8881  -0.2338
 P3T  OAD   O  OH1   0  -0.615  -0.9473   3.5312  -0.5641
 P3T  CAT   C  CR6   0   0.067   0.2659   1.5237  -0.4972
 P3T  CAG   C  CH2   0  -0.343  -0.9063   0.8095  -1.1144
 P3T  NAN   N  NH1   0  -0.588  -1.9359   0.5576  -0.1216
 P3T  CAL   C  CH2   0  -0.254  -3.0688  -0.1603  -0.6782
 P3T  CAK   C  CH2   0  -0.445  -4.1539  -0.3824   0.3622
 P3T  CAJ   C  CH2   0  -0.428  -5.3463  -1.1464  -0.1995
 P3T  CAI   C  CH2   0  -0.272  -6.4668  -1.3141   0.8147
 P3T  NAB   N  NH2   0  -0.801  -7.5854  -2.0489   0.2405
 P3T  HOAF  H  HOH1  0   0.506   5.0060  -3.4076   0.8700
 P3T  HOAC  H  HOH1  0   0.497   4.2837  -2.2131  -1.9632
 P3T  HAM1  H  HCH2  0   0.260   1.5008  -0.8277  -1.4564
 P3T  HAM2  H  HCH2  0   0.257   0.7375  -1.1522   0.1018
 P3T  HAH   H  HCR6  0   0.257   3.3947   1.1227   0.7311
 P3T  HAA1  H  HCH3  0   0.256   1.0807   5.6109  -0.2838
 P3T  HAA2  H  HCH3  0   0.258   0.3965   5.2792   1.3064
 P3T  HAA3  H  HCH3  0   0.271   2.1424   5.3495   1.0927
 P3T  HOAD  H  HOH1  0   0.486  -0.8750   4.4764  -0.3906
 P3T  HAG1  H  HCH2  0   0.252  -1.3350   1.4312  -1.9040
 P3T  HAG2  H  HCH2  0   0.220  -0.5704  -0.1084  -1.6179
 P3T  HNAN  H  HNH1  0   0.341  -1.5400   0.0071   0.6323
 P3T  HAL1  H  HCH2  0   0.217  -3.4751   0.4375  -1.5006
 P3T  HAL2  H  HCH2  0   0.190  -2.7774  -1.1279  -1.1189
 P3T  HAK1  H  HCH2  0   0.216  -3.7392  -0.9319   1.2146
 P3T  HAK2  H  HCH2  0   0.217  -4.4819   0.5879   0.7474
 P3T  HAJ1  H  HCH2  0   0.214  -5.7374  -0.6282  -1.0807
 P3T  HAJ2  H  HCH2  0   0.213  -5.0166  -2.1337  -0.5415
 P3T  HAI1  H  HCH2  0   0.187  -6.0591  -1.7793   1.7245
 P3T  HAI2  H  HCH2  0   0.212  -6.8259  -0.3254   1.1140
 P3T  HAB1  H  HNH2  0   0.336  -7.3038  -3.0080   0.0774
 P3T  HAB2  H  HNH2  0   0.345  -8.3381  -2.0999   0.9150

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
 P3T  OAE  PAU   double    1.474  0.020  1.474
 P3T  PAU  OAP   single    1.599  0.020  1.599
 P3T  PAU  OAC   single    1.597  0.020  1.597
 P3T  PAU  OAF   single    1.592  0.020  1.592
 P3T  OAF  HOAF  single    0.850  0.020  0.980
 P3T  OAC  HOAC  single    0.850  0.020  0.980
 P3T  OAP  CAM   single    1.423  0.020  1.423
 P3T  CAM  CAS   single    1.504  0.020  1.504
 P3T  CAM  HAM1  single    0.970  0.020  1.090
 P3T  CAM  HAM2  single    0.970  0.020  1.090
 P3T  CAS  CAH   aromatic  1.387  0.020  1.387
 P3T  CAS  CAT   aromatic  1.397  0.020  1.397
 P3T  CAH  NAO   aromatic  1.328  0.020  1.328
 P3T  CAH  HAH   single    0.930  0.020  1.080
 P3T  NAO  CAQ   aromatic  1.323  0.020  1.323
 P3T  CAQ  CAA   single    1.499  0.020  1.499
 P3T  CAQ  CAR   aromatic  1.402  0.020  1.402
 P3T  CAA  HAA1  single    0.970  0.020  1.090
 P3T  CAA  HAA2  single    0.970  0.020  1.090
 P3T  CAA  HAA3  single    0.970  0.020  1.090
 P3T  CAR  OAD   single    1.345  0.020  1.345
 P3T  CAR  CAT   aromatic  1.392  0.020  1.392
 P3T  OAD  HOAD  single    0.850  0.020  0.980
 P3T  CAT  CAG   single    1.505  0.020  1.505
 P3T  CAG  NAN   single    1.452  0.020  1.452
 P3T  CAG  HAG1  single    0.970  0.020  1.090
 P3T  CAG  HAG2  single    0.970  0.020  1.090
 P3T  NAN  CAL   single    1.452  0.020  1.452
 P3T  NAN  HNAN  single    0.890  0.020  1.040
 P3T  CAL  CAK   single    1.520  0.020  1.520
 P3T  CAL  HAL1  single    0.970  0.020  1.090
 P3T  CAL  HAL2  single    0.970  0.020  1.090
 P3T  CAK  CAJ   single    1.523  0.020  1.523
 P3T  CAK  HAK1  single    0.970  0.020  1.090
 P3T  CAK  HAK2  single    0.970  0.020  1.090
 P3T  CAJ  CAI   single    1.521  0.020  1.521
 P3T  CAJ  HAJ1  single    0.970  0.020  1.090
 P3T  CAJ  HAJ2  single    0.970  0.020  1.090
 P3T  CAI  NAB   single    1.456  0.020  1.456
 P3T  CAI  HAI1  single    0.970  0.020  1.090
 P3T  CAI  HAI2  single    0.970  0.020  1.090
 P3T  NAB  HAB1  single    0.890  0.020  1.040
 P3T  NAB  HAB2  single    0.890  0.020  1.040

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
 P3T  OAP   PAU  OAC   106.88  3.000
 P3T  OAC   PAU  OAF   108.08  3.000
 P3T  OAP   PAU  OAF    96.52  3.000
 P3T  OAF   PAU  OAE   118.17  3.000
 P3T  OAC   PAU  OAE   109.73  3.000
 P3T  OAP   PAU  OAE   116.30  3.000
 P3T  HOAF  OAF  PAU   114.08  3.000
 P3T  HOAC  OAC  PAU   115.84  3.000
 P3T  CAM   OAP  PAU   119.46  3.000
 P3T  HAM2  CAM  HAM1  107.49  3.000
 P3T  HAM2  CAM  CAS   110.14  3.000
 P3T  HAM1  CAM  CAS   109.96  3.000
 P3T  HAM2  CAM  OAP   109.65  3.000
 P3T  HAM1  CAM  OAP   110.09  3.000
 P3T  CAS   CAM  OAP   109.49  3.000
 P3T  CAT   CAS  CAH   118.41  3.000
 P3T  CAT   CAS  CAM   119.62  3.000
 P3T  CAH   CAS  CAM   121.97  3.000
 P3T  HAH   CAH  NAO   115.82  3.000
 P3T  HAH   CAH  CAS   121.07  3.000
 P3T  NAO   CAH  CAS   123.11  3.000
 P3T  CAQ   NAO  CAH   119.74  3.000
 P3T  CAR   CAQ  CAA   120.70  3.000
 P3T  CAR   CAQ  NAO   121.05  3.000
 P3T  CAA   CAQ  NAO   118.25  3.000
 P3T  HAA3  CAA  HAA2  107.67  3.000
 P3T  HAA3  CAA  HAA1  107.44  3.000
 P3T  HAA2  CAA  HAA1  107.46  3.000
 P3T  HAA3  CAA  CAQ   109.83  3.000
 P3T  HAA2  CAA  CAQ   112.04  3.000
 P3T  HAA1  CAA  CAQ   112.18  3.000
 P3T  CAT   CAR  OAD   118.02  3.000
 P3T  CAT   CAR  CAQ   119.93  3.000
 P3T  OAD   CAR  CAQ   122.06  3.000
 P3T  HOAD  OAD  CAR   111.19  3.000
 P3T  CAG   CAT  CAR   119.93  3.000
 P3T  CAG   CAT  CAS   122.30  3.000
 P3T  CAR   CAT  CAS   117.75  3.000
 P3T  HAG2  CAG  HAG1  105.30  3.000
 P3T  HAG2  CAG  NAN   112.64  3.000
 P3T  HAG1  CAG  NAN   108.33  3.000
 P3T  HAG2  CAG  CAT   110.24  3.000
 P3T  HAG1  CAG  CAT   109.39  3.000
 P3T  NAN   CAG  CAT   110.74  3.000
 P3T  HNAN  NAN  CAL   108.74  3.000
 P3T  HNAN  NAN  CAG   109.00  3.000
 P3T  CAL   NAN  CAG   112.14  3.000
 P3T  HAL2  CAL  HAL1  106.08  3.000
 P3T  HAL2  CAL  CAK   109.52  3.000
 P3T  HAL1  CAL  CAK   109.21  3.000
 P3T  HAL2  CAL  NAN   112.39  3.000
 P3T  HAL1  CAL  NAN   107.91  3.000
 P3T  CAK   CAL  NAN   111.52  3.000
 P3T  HAK2  CAK  HAK1  106.52  3.000
 P3T  HAK2  CAK  CAJ   109.87  3.000
 P3T  HAK1  CAK  CAJ   109.37  3.000
 P3T  HAK2  CAK  CAL   108.99  3.000
 P3T  HAK1  CAK  CAL   109.61  3.000
 P3T  CAJ   CAK  CAL   112.31  3.000
 P3T  HAJ2  CAJ  HAJ1  106.43  3.000
 P3T  HAJ2  CAJ  CAI   109.30  3.000
 P3T  HAJ1  CAJ  CAI   109.02  3.000
 P3T  HAJ2  CAJ  CAK   109.36  3.000
 P3T  HAJ1  CAJ  CAK   109.82  3.000
 P3T  CAI   CAJ  CAK   112.71  3.000
 P3T  HAI2  CAI  HAI1  106.12  3.000
 P3T  HAI2  CAI  NAB   108.17  3.000
 P3T  HAI1  CAI  NAB   113.42  3.000
 P3T  HAI2  CAI  CAJ   108.95  3.000
 P3T  HAI1  CAI  CAJ   108.97  3.000
 P3T  NAB   CAI  CAJ   111.01  3.000
 P3T  HAB2  NAB  HAB1  105.44  3.000
 P3T  HAB2  NAB  CAI   109.51  3.000
 P3T  HAB1  NAB  CAI   109.13  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
 P3T  CONST_01  CAQ   NAO  CAH  CAS     0.00   0.0  0
 P3T  CONST_02  CAQ   CAR  CAT  CAS     0.00   0.0  0
 P3T  CONST_03  CAR   CAT  CAS  CAH     0.00   0.0  0
 P3T  CONST_04  CAR   CAQ  NAO  CAH     0.00   0.0  0
 P3T  CONST_05  CAT   CAS  CAH  NAO     0.00   0.0  0
 P3T  CONST_06  CAT   CAR  CAQ  NAO     0.00   0.0  0
 P3T  CONST_07  NAO   CAH  CAS  CAM   180.00   0.0  0
 P3T  CONST_08  CAR   CAT  CAS  CAM   180.00   0.0  0
 P3T  CONST_09  OAD   CAR  CAT  CAS   180.00   0.0  0
 P3T  CONST_10  CAG   CAT  CAS  CAH   180.00   0.0  0
 P3T  CONST_11  CAA   CAQ  NAO  CAH   180.00   0.0  0
 P3T  CONST_12  OAD   CAR  CAQ  NAO   180.00   0.0  0
 P3T  CONST_13  CAG   CAT  CAR  CAQ   180.00   0.0  0
 P3T  CONST_14  CAT   CAR  CAQ  CAA   180.00   0.0  0
 P3T  CONST_15  HAH   CAH  NAO  CAQ   180.00   0.0  0
 P3T  Var_01    CAH   CAS  CAM  OAP     3.55  30.0  2
 P3T  Var_02    NAN   CAG  CAT  CAS   100.81  30.0  2
 P3T  Var_03    HAA1  CAA  CAQ  NAO   118.65  30.0  2
 P3T  Var_04    CAS   CAM  OAP  PAU  -176.08  30.0  3
 P3T  Var_05    CAL   NAN  CAG  CAT  -178.60  30.0  3
 P3T  Var_06    CAK   CAL  NAN  CAG  -178.42  30.0  3
 P3T  Var_07    CAJ   CAK  CAL  NAN  -179.45  30.0  3
 P3T  Var_08    CAI   CAJ  CAK  CAL  -177.17  30.0  3
 P3T  Var_09    NAB   CAI  CAJ  CAK  -179.96  30.0  3
 P3T  Var_10    HAB1  NAB  CAI  CAJ    68.35  30.0  3

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
 P3T  plan-1  CAM  0.020
 P3T  plan-1  CAS  0.020
 P3T  plan-1  CAH  0.020
 P3T  plan-1  NAO  0.020
 P3T  plan-1  CAQ  0.020
 P3T  plan-1  CAA  0.020
 P3T  plan-1  CAR  0.020
 P3T  plan-1  OAD  0.020
 P3T  plan-1  CAT  0.020
 P3T  plan-1  CAG  0.020
 P3T  plan-1  HAH  0.020

