# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 13:07:07 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [5-hydroxy-4-({[6-(3-hydroxypropyl)-2-oxo-1,2-dihydropyridin-3-yl]amino}methyl)-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(CNC2=CC=C(CCCO)NC2=O)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
 PL8  PL8  '[5-hydroxy-4-({[6-(3-hydroxypropyl)-2-oxo-1,2-dihydropyridin-3-yl]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate'  ligand  49  27  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PL8
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
 PL8  CAA   C  CH3   0  -0.785   4.6310   4.1255  -1.2405
 PL8  OAB   O  O     0  -0.495  -1.2376  -0.7116   1.0587
 PL8  OAC   O  O     0  -0.708   1.7461  -3.6256   1.7509
 PL8  OAD   O  OH1   0  -0.673  -7.8665  -2.4815  -1.0526
 PL8  OAE   O  OH1   0  -0.622   1.8929   4.0479  -0.3186
 PL8  OAF   O  OH1   0  -0.730   3.8276  -4.0097   0.1888
 PL8  OAG   O  OH1   0  -0.739   1.4828  -3.4662  -0.7422
 PL8  CAH   C  CR16  0  -0.424  -3.9641   1.7736  -0.6321
 PL8  CAI   C  CR16  0  -0.207  -2.5846   2.0392  -0.7986
 PL8  CAJ   C  CR16  0  -0.134   4.0966   0.6486  -0.2419
 PL8  CAK   C  CH2   0  -0.140  -7.5820  -1.3421  -0.2717
 PL8  CAL   C  CH2   0  -0.457  -6.1354  -0.9470  -0.4957
 PL8  CAN   C  CH2   0  -0.376   0.5896   1.7748   0.6374
 PL8  CAO   C  CH2   0  -0.223   2.1696  -0.6800   0.7181
 PL8  NAP   N  NH1   0  -0.649  -0.2543   1.4236  -0.5050
 PL8  NAQ   N  NR16  0  -0.700  -3.3706  -0.0676   0.6708
 PL8  NAR   N  N     0  -0.407   4.6626   1.7658  -0.6849
 PL8  OAS   O  O2    0  -0.594   3.0270  -1.7788   0.4171
 PL8  CAT   C  CR6   0   0.128   3.9655   2.8891  -0.7135
 PL8  CAU   C  CR6   0   0.403  -4.3449   0.7071   0.1164
 PL8  CAV   C  CR6   0  -0.059   2.7865   0.5897   0.2064
 PL8  CAW   C  CR6   0   0.254   2.6331   2.9228  -0.2767
 PL8  CAX   C  CR6   0   0.095  -1.6188   1.2382  -0.2611
 PL8  CAY   C  CR6   0   0.065   2.0317   1.7648   0.2044
 PL8  CAZ   C  CR6   0   0.509  -2.0110   0.0881   0.5338
 PL8  PBA   P  P     0   1.460   2.4551  -3.2672   0.5094
 PL8  H1AA  H  HCH3  0   0.258   4.1325   4.5043  -2.1364
 PL8  H2AA  H  HCH3  0   0.256   4.6464   4.9341  -0.5053
 PL8  H3AA  H  HCH3  0   0.272   5.6616   3.9050  -1.5078
 PL8  HOAD  H  HOH1  0   0.454  -8.7877  -2.7183  -0.9134
 PL8  HOAE  H  HOH1  0   0.486   2.4006   4.7906  -0.6632
 PL8  HAH   H  HCR6  0   0.266  -4.7075   2.4121  -1.0862
 PL8  HAI   H  HCR6  0   0.270  -2.2872   2.9013  -1.3853
 PL8  HAJ   H  HCR6  0   0.257   4.7219  -0.2346  -0.2556
 PL8  H1AK  H  HCH2  0   0.194  -8.2320  -0.4983  -0.5396
 PL8  H2AK  H  HCH2  0   0.193  -7.7422  -1.5371   0.7973
 PL8  H1AL  H  HCH2  0   0.233  -5.4870  -1.7889  -0.2366
 PL8  H2AL  H  HCH2  0   0.240  -5.9709  -0.7306  -1.5545
 PL8  H1AM  H  HCH2  0   0.265  -6.4146   1.1174   0.0762
 PL8  H2AM  H  HCH2  0   0.261  -5.9253   0.0748   1.3981
 PL8  H1AN  H  HCH2  0   0.252   0.3227   2.7473   1.0629
 PL8  H2AN  H  HCH2  0   0.271   0.4298   1.0421   1.4249
 PL8  H1AO  H  HCH2  0   0.265   1.1803  -0.8187   0.2735
 PL8  H2AO  H  HCH2  0   0.260   2.0296  -0.6164   1.8018
 PL8  HNAP  H  HNH1  0   0.369  -0.1228   2.0984  -1.2476
 PL8  HNAQ  H  HNR6  0   0.413  -3.6526  -0.8692   1.2213
 PL8  H21   H  HOH1  0   0.505   3.7942  -4.9683   0.3081
 PL8  H22   H  HOH1  0   0.496   1.8771  -3.3112  -1.6111
 PL8  CAM   C  CH2   0  -0.528  -5.7611   0.2828   0.3359

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
 PL8  CAA  H1AA  single    0.970  0.020  1.090
 PL8  CAA  H2AA  single    0.970  0.020  1.090
 PL8  CAA  H3AA  single    0.970  0.020  1.090
 PL8  OAD  HOAD  single    0.850  0.020  0.980
 PL8  OAE  CAW   single    1.347  0.020  1.347
 PL8  OAE  HOAE  single    0.850  0.020  0.980
 PL8  OAF  PBA   single    1.593  0.020  1.593
 PL8  OAG  PBA   single    1.597  0.020  1.597
 PL8  CAH  CAI   single    1.415  0.020  1.415
 PL8  CAH  HAH   single    0.930  0.020  1.080
 PL8  CAI  CAX   double    1.365  0.020  1.365
 PL8  CAI  HAI   single    0.930  0.020  1.080
 PL8  CAJ  NAR   aromatic  1.328  0.020  1.328
 PL8  CAJ  HAJ   single    0.930  0.020  1.080
 PL8  CAK  CAL   single    1.516  0.020  1.516
 PL8  CAK  OAD   single    1.410  0.020  1.410
 PL8  CAK  H1AK  single    0.970  0.020  1.090
 PL8  CAK  H2AK  single    0.970  0.020  1.090
 PL8  CAL  H1AL  single    0.970  0.020  1.090
 PL8  CAL  H2AL  single    0.970  0.020  1.090
 PL8  CAM  CAU   single    1.495  0.020  1.495
 PL8  CAM  CAL   single    1.531  0.020  1.531
 PL8  CAM  H1AM  single    0.970  0.020  1.090
 PL8  CAM  H2AM  single    0.970  0.020  1.090
 PL8  CAN  CAY   single    1.506  0.020  1.506
 PL8  CAN  H1AN  single    0.970  0.020  1.090
 PL8  CAN  H2AN  single    0.970  0.020  1.090
 PL8  CAO  CAV   single    1.501  0.020  1.501
 PL8  CAO  OAS   single    1.426  0.020  1.426
 PL8  CAO  H1AO  single    0.970  0.020  1.090
 PL8  CAO  H2AO  single    0.970  0.020  1.090
 PL8  NAP  CAN   single    1.463  0.020  1.463
 PL8  NAP  HNAP  single    0.890  0.020  1.040
 PL8  NAQ  CAZ   single    1.375  0.020  1.375
 PL8  NAQ  HNAQ  single    0.860  0.020  1.020
 PL8  OAS  PBA   single    1.597  0.020  1.597
 PL8  CAT  CAA   single    1.500  0.020  1.500
 PL8  CAT  NAR   aromatic  1.322  0.020  1.322
 PL8  CAU  CAH   double    1.357  0.020  1.357
 PL8  CAU  NAQ   single    1.363  0.020  1.363
 PL8  CAV  CAJ   aromatic  1.386  0.020  1.386
 PL8  CAW  CAT   aromatic  1.403  0.020  1.403
 PL8  CAX  NAP   single    1.398  0.020  1.398
 PL8  CAY  CAW   aromatic  1.391  0.020  1.391
 PL8  CAY  CAV   aromatic  1.397  0.020  1.397
 PL8  CAZ  CAX   single    1.452  0.020  1.452
 PL8  CAZ  OAB   double    1.230  0.020  1.230
 PL8  PBA  OAC   double    1.474  0.020  1.474
 PL8  OAF  H21   single    0.850  0.020  0.980
 PL8  OAG  H22   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
 PL8  H3AA  CAA  H2AA  107.58  3.000
 PL8  H3AA  CAA  H1AA  107.52  3.000
 PL8  H2AA  CAA  H1AA  107.55  3.000
 PL8  H3AA  CAA  CAT   109.86  3.000
 PL8  H2AA  CAA  CAT   112.32  3.000
 PL8  H1AA  CAA  CAT   111.80  3.000
 PL8  HOAD  OAD  CAK   108.19  3.000
 PL8  HOAE  OAE  CAW   111.43  3.000
 PL8  H21   OAF  PBA   114.05  3.000
 PL8  H22   OAG  PBA   115.85  3.000
 PL8  HAH   CAH  CAU   120.21  3.000
 PL8  CAU   CAH  CAI   119.07  3.000
 PL8  HAH   CAH  CAI   120.71  3.000
 PL8  HAI   CAI  CAX   119.04  3.000
 PL8  HAI   CAI  CAH   118.71  3.000
 PL8  CAX   CAI  CAH   122.24  3.000
 PL8  HAJ   CAJ  CAV   121.03  3.000
 PL8  CAV   CAJ  NAR   123.12  3.000
 PL8  HAJ   CAJ  NAR   115.85  3.000
 PL8  H2AK  CAK  H1AK  106.71  3.000
 PL8  H2AK  CAK  CAL   109.22  3.000
 PL8  H1AK  CAK  CAL   109.17  3.000
 PL8  H2AK  CAK  OAD   111.47  3.000
 PL8  H1AK  CAK  OAD   111.48  3.000
 PL8  CAL   CAK  OAD   108.73  3.000
 PL8  H2AL  CAL  H1AL  107.01  3.000
 PL8  H2AL  CAL  CAM   109.29  3.000
 PL8  H1AL  CAL  CAM   110.16  3.000
 PL8  CAM   CAL  CAK   111.24  3.000
 PL8  H2AL  CAL  CAK   109.77  3.000
 PL8  H1AL  CAL  CAK   109.27  3.000
 PL8  H2AN  CAN  H1AN  106.34  3.000
 PL8  H2AN  CAN  CAY   110.15  3.000
 PL8  H1AN  CAN  CAY   110.56  3.000
 PL8  H2AN  CAN  NAP   108.60  3.000
 PL8  H1AN  CAN  NAP   112.10  3.000
 PL8  CAY   CAN  NAP   109.04  3.000
 PL8  H2AO  CAO  H1AO  107.11  3.000
 PL8  H2AO  CAO  CAV   109.93  3.000
 PL8  H1AO  CAO  CAV   109.91  3.000
 PL8  H2AO  CAO  OAS   109.31  3.000
 PL8  H1AO  CAO  OAS   111.13  3.000
 PL8  CAV   CAO  OAS   109.43  3.000
 PL8  HNAP  NAP  CAX   110.07  3.000
 PL8  CAX   NAP  CAN   117.29  3.000
 PL8  HNAP  NAP  CAN   109.76  3.000
 PL8  HNAQ  NAQ  CAZ   114.78  3.000
 PL8  HNAQ  NAQ  CAU   118.18  3.000
 PL8  CAZ   NAQ  CAU   127.01  3.000
 PL8  CAT   NAR  CAJ   119.80  3.000
 PL8  PBA   OAS  CAO   119.38  3.000
 PL8  CAW   CAT  NAR   120.96  3.000
 PL8  CAW   CAT  CAA   120.74  3.000
 PL8  NAR   CAT  CAA   118.30  3.000
 PL8  NAQ   CAU  CAM   117.15  3.000
 PL8  NAQ   CAU  CAH   118.06  3.000
 PL8  CAM   CAU  CAH   124.74  3.000
 PL8  CAY   CAV  CAO   119.34  3.000
 PL8  CAY   CAV  CAJ   118.33  3.000
 PL8  CAO   CAV  CAJ   122.32  3.000
 PL8  CAY   CAW  CAT   119.90  3.000
 PL8  CAY   CAW  OAE   117.94  3.000
 PL8  CAT   CAW  OAE   122.16  3.000
 PL8  CAZ   CAX  NAP   117.65  3.000
 PL8  CAZ   CAX  CAI   119.29  3.000
 PL8  NAP   CAX  CAI   122.95  3.000
 PL8  CAW   CAY  CAV   117.87  3.000
 PL8  CAV   CAY  CAN   121.52  3.000
 PL8  CAW   CAY  CAN   120.53  3.000
 PL8  CAX   CAZ  NAQ   114.28  3.000
 PL8  CAX   CAZ  OAB   125.36  3.000
 PL8  NAQ   CAZ  OAB   120.36  3.000
 PL8  OAS   PBA  OAG   106.79  3.000
 PL8  OAS   PBA  OAF    96.56  3.000
 PL8  OAG   PBA  OAF   107.98  3.000
 PL8  OAS   PBA  OAC   116.59  3.000
 PL8  OAG   PBA  OAC   109.68  3.000
 PL8  OAF   PBA  OAC   118.08  3.000
 PL8  H2AM  CAM  H1AM  106.64  3.000
 PL8  H2AM  CAM  CAU   109.79  3.000
 PL8  H1AM  CAM  CAU   108.38  3.000
 PL8  H2AM  CAM  CAL   109.74  3.000
 PL8  H1AM  CAM  CAL   109.79  3.000
 PL8  CAU   CAM  CAL   112.33  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
 PL8  CONST_01  CAW   CAT  NAR  CAJ     0.00   0.0  0
 PL8  CONST_02  CAW   CAY  CAV  CAJ     0.00   0.0  0
 PL8  CONST_03  CAY   CAV  CAJ  NAR     0.00   0.0  0
 PL8  CONST_04  CAY   CAW  CAT  NAR     0.00   0.0  0
 PL8  CONST_05  CAV   CAJ  NAR  CAT     0.00   0.0  0
 PL8  CONST_06  CAV   CAY  CAW  CAT     0.00   0.0  0
 PL8  CONST_07  CAX   CAZ  NAQ  CAU     0.00   0.0  0
 PL8  CONST_08  CAJ   NAR  CAT  CAA   180.00   0.0  0
 PL8  CONST_09  CAY   CAW  CAT  CAA   180.00   0.0  0
 PL8  CONST_10  NAR   CAT  CAW  OAE   180.00   0.0  0
 PL8  CONST_11  CAV   CAY  CAW  OAE   180.00   0.0  0
 PL8  CONST_12  CAN   CAY  CAV  CAJ   180.00   0.0  0
 PL8  CONST_13  CAT   CAW  CAY  CAN   180.00   0.0  0
 PL8  CONST_14  NAR   CAJ  CAV  CAO   180.00   0.0  0
 PL8  CONST_15  CAW   CAY  CAV  CAO   180.00   0.0  0
 PL8  CONST_16  CAU   NAQ  CAZ  OAB   180.00   0.0  0
 PL8  CONST_17  HAJ   CAJ  NAR  CAT   180.00   0.0  0
 PL8  CONST_18  HNAQ  NAQ  CAZ  CAX   180.00   0.0  0
 PL8  Var_01    CAL   CAM  CAU  CAH   103.98  30.0  2
 PL8  Var_02    CAN   NAP  CAX  CAI   115.87  30.0  2
 PL8  Var_03    OAS   CAO  CAV  CAJ   -11.22  30.0  2
 PL8  Var_04    CAW   CAY  CAN  NAP    90.94  30.0  2
 PL8  Var_05    CAY   CAN  NAP  CAX   173.19  30.0  3
 PL8  Var_06    H1AA  CAA  CAT  NAR   117.42  30.0  2
 PL8  Var_07    CAU   CAM  CAL  CAK  -179.07  30.0  1
 PL8  Var_08    CAM   CAL  CAK  OAD  -179.59  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
 PL8  plan-1  OAB   0.020
 PL8  plan-1  CAH   0.020
 PL8  plan-1  CAI   0.020
 PL8  plan-1  NAP   0.020
 PL8  plan-1  NAQ   0.020
 PL8  plan-1  CAU   0.020
 PL8  plan-1  CAX   0.020
 PL8  plan-1  CAZ   0.020
 PL8  plan-1  HAH   0.020
 PL8  plan-1  HAI   0.020
 PL8  plan-1  HNAQ  0.020
 PL8  plan-1  CAM   0.020
 PL8  plan-2  CAA   0.020
 PL8  plan-2  OAE   0.020
 PL8  plan-2  CAJ   0.020
 PL8  plan-2  CAN   0.020
 PL8  plan-2  CAO   0.020
 PL8  plan-2  NAR   0.020
 PL8  plan-2  CAT   0.020
 PL8  plan-2  CAV   0.020
 PL8  plan-2  CAW   0.020
 PL8  plan-2  CAY   0.020
 PL8  plan-2  HAJ   0.020

