# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:16:35 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: {5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NCCO[P](O)(O)=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
 EXT  EXT  '{5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate'  ligand  39  23  .  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_EXT
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
 EXT  CAA   C  CR6   0   0.004  -0.4065  -0.6144  -0.3163
 EXT  CAB   C  C1    0   0.073   0.2236   0.6218  -0.7797
 EXT  PAC   P  P     0   1.461  -5.1402   1.2342   0.0364
 EXT  OAD   O  OH1   0  -0.738  -5.4626   0.9714  -1.5050
 EXT  OAE   O  O     0  -0.706  -4.9254   2.6754   0.2579
 EXT  OAF   O  OH1   0  -0.727  -6.2429   0.4915   0.9102
 EXT  OAG   O  O2    0  -0.591  -3.9239   0.2685   0.4219
 EXT  CAH   C  CH2   0  -0.216  -2.6193   0.5613  -0.0586
 EXT  CAI   C  CR6   0  -0.078  -1.7583  -0.6656   0.0598
 EXT  NAJ   N  N     0  -0.400  -1.4989  -2.9656   0.6515
 EXT  CAK   C  CR16  0  -0.135  -2.2474  -1.8687   0.5299
 EXT  CAL   C  CR6   0   0.149  -0.2271  -2.9483   0.3057
 EXT  CAM   C  CH3   0  -0.721   0.5859  -4.1944   0.4611
 EXT  CAN   C  CR6   0   0.294   0.3622  -1.7784  -0.2023
 EXT  OAO   O  OH1   0  -0.662   1.6518  -1.8132  -0.5560
 EXT  OAP   O  OH1   0  -0.732   5.5139  -1.0177  -0.2016
 EXT  PAQ   P  P     0   1.437   4.7433   0.1433   0.5720
 EXT  OAR   O  OH1   0  -0.758   3.5046  -0.5168   1.3339
 EXT  OAS   O  O     0  -0.705   5.5161   0.9796   1.5087
 EXT  OAT   O  O2    0  -0.586   4.1705   0.8716  -0.7292
 EXT  CAU   C  CH2   0  -0.187   3.3039   2.0060  -0.6196
 EXT  CAV   C  CH2   0  -0.325   2.1178   1.8095  -1.5456
 EXT  NAW   N  N     0  -0.469   1.4248   0.6014  -1.1896
 EXT  HAB   H  H     0   0.270  -0.3447   1.5525  -0.7385
 EXT  HOAD  H  HOH1  0   0.497  -5.6746   0.0592  -1.7449
 EXT  HOAF  H  HOH1  0   0.507  -7.0932   0.9503   0.9474
 EXT  HAH   H  HCH2  0   0.262  -2.6528   0.8834  -1.1045
 EXT  HAHA  H  HCH2  0   0.269  -2.1953   1.3839   0.5240
 EXT  HAK   H  HCR6  0   0.265  -3.2822  -1.9712   0.8275
 EXT  HAM   H  HCH3  0   0.252   0.9900  -4.5309  -0.4951
 EXT  HAMA  H  HCH3  0   0.250   1.4354  -4.0374   1.1284
 EXT  HAMB  H  HCH3  0   0.252  -0.0299  -4.9904   0.8737
 EXT  HOAO  H  HOH1  0   0.477   1.8417  -0.9195  -0.9970
 EXT  HOAP  H  HOH1  0   0.504   6.0916  -1.5508   0.3611
 EXT  HOAR  H  HOH1  0   0.483   2.9481  -1.1267   0.8185
 EXT  HAU   H  HCH2  0   0.245   2.9532   2.1521   0.4050
 EXT  HAUA  H  HCH2  0   0.266   3.8555   2.8985  -0.9155
 EXT  HAV   H  HCH2  0   0.246   1.4778   2.6958  -1.4815
 EXT  HAVA  H  HCH2  0   0.271   2.4695   1.7205  -2.5758

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
 EXT  CAI  CAA   aromatic  1.404  0.020  1.404
 EXT  CAB  CAA   single    1.463  0.020  1.463
 EXT  CAA  CAN   aromatic  1.400  0.020  1.400
 EXT  NAW  CAB   double    1.269  0.020  1.269
 EXT  CAB  HAB   single    0.930  0.020  1.080
 EXT  OAE  PAC   double    1.474  0.020  1.474
 EXT  PAC  OAD   single    1.597  0.020  1.597
 EXT  PAC  OAF   single    1.591  0.020  1.591
 EXT  PAC  OAG   single    1.600  0.020  1.600
 EXT  OAD  HOAD  single    0.850  0.020  0.980
 EXT  OAF  HOAF  single    0.850  0.020  0.980
 EXT  OAG  CAH   single    1.421  0.020  1.421
 EXT  CAH  CAI   single    1.504  0.020  1.504
 EXT  CAH  HAH   single    0.970  0.020  1.090
 EXT  CAH  HAHA  single    0.970  0.020  1.090
 EXT  CAI  CAK   aromatic  1.381  0.020  1.381
 EXT  CAK  NAJ   aromatic  1.334  0.020  1.334
 EXT  NAJ  CAL   aromatic  1.318  0.020  1.318
 EXT  CAK  HAK   single    0.930  0.020  1.080
 EXT  CAN  CAL   aromatic  1.405  0.020  1.405
 EXT  CAL  CAM   single    1.496  0.020  1.496
 EXT  CAM  HAM   single    0.970  0.020  1.090
 EXT  CAM  HAMA  single    0.970  0.020  1.090
 EXT  CAM  HAMB  single    0.970  0.020  1.090
 EXT  CAN  OAO   single    1.338  0.020  1.338
 EXT  OAO  HOAO  single    0.850  0.020  0.980
 EXT  PAQ  OAP   single    1.594  0.020  1.594
 EXT  OAP  HOAP  single    0.850  0.020  0.980
 EXT  OAT  PAQ   single    1.597  0.020  1.597
 EXT  OAS  PAQ   double    1.474  0.020  1.474
 EXT  PAQ  OAR   single    1.597  0.020  1.597
 EXT  OAR  HOAR  single    0.850  0.020  0.980
 EXT  OAT  CAU   single    1.432  0.020  1.432
 EXT  CAU  CAV   single    1.518  0.020  1.518
 EXT  CAU  HAU   single    0.970  0.020  1.090
 EXT  CAU  HAUA  single    0.970  0.020  1.090
 EXT  CAV  NAW   single    1.437  0.020  1.437
 EXT  CAV  HAV   single    0.970  0.020  1.090
 EXT  CAV  HAVA  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
 EXT  CAN   CAA  CAI   118.46  3.000
 EXT  CAN   CAA  CAB   119.47  3.000
 EXT  CAI   CAA  CAB   122.03  3.000
 EXT  HAB   CAB  NAW   121.24  3.000
 EXT  HAB   CAB  CAA   118.98  3.000
 EXT  NAW   CAB  CAA   119.76  3.000
 EXT  OAG   PAC  OAF    96.47  3.000
 EXT  OAG   PAC  OAE   116.31  3.000
 EXT  OAF   PAC  OAE   118.36  3.000
 EXT  OAG   PAC  OAD   106.66  3.000
 EXT  OAF   PAC  OAD   108.26  3.000
 EXT  OAE   PAC  OAD   109.61  3.000
 EXT  HOAD  OAD  PAC   116.05  3.000
 EXT  HOAF  OAF  PAC   114.15  3.000
 EXT  CAH   OAG  PAC   119.47  3.000
 EXT  HAHA  CAH  HAH   107.43  3.000
 EXT  HAHA  CAH  CAI   110.48  3.000
 EXT  HAH   CAH  CAI   109.44  3.000
 EXT  HAHA  CAH  OAG   109.32  3.000
 EXT  HAH   CAH  OAG   110.83  3.000
 EXT  CAI   CAH  OAG   109.33  3.000
 EXT  CAK   CAI  CAH   122.33  3.000
 EXT  CAK   CAI  CAA   117.64  3.000
 EXT  CAH   CAI  CAA   120.03  3.000
 EXT  CAL   NAJ  CAK   120.46  3.000
 EXT  HAK   CAK  NAJ   115.72  3.000
 EXT  HAK   CAK  CAI   121.00  3.000
 EXT  NAJ   CAK  CAI   123.28  3.000
 EXT  CAN   CAL  CAM   120.22  3.000
 EXT  CAM   CAL  NAJ   119.09  3.000
 EXT  CAN   CAL  NAJ   120.69  3.000
 EXT  HAMB  CAM  HAMA  108.30  3.000
 EXT  HAMB  CAM  HAM   108.44  3.000
 EXT  HAMA  CAM  HAM   106.97  3.000
 EXT  HAMB  CAM  CAL   109.96  3.000
 EXT  HAMA  CAM  CAL   111.51  3.000
 EXT  HAM   CAM  CAL   111.54  3.000
 EXT  OAO   CAN  CAL   118.57  3.000
 EXT  OAO   CAN  CAA   121.98  3.000
 EXT  CAL   CAN  CAA   119.45  3.000
 EXT  HOAO  OAO  CAN   105.81  3.000
 EXT  HOAP  OAP  PAQ   114.09  3.000
 EXT  OAT   PAQ  OAS   116.54  3.000
 EXT  OAS   PAQ  OAR   109.75  3.000
 EXT  OAT   PAQ  OAR   107.39  3.000
 EXT  OAR   PAQ  OAP   107.79  3.000
 EXT  OAS   PAQ  OAP   117.91  3.000
 EXT  OAT   PAQ  OAP    96.32  3.000
 EXT  HOAR  OAR  PAQ   116.73  3.000
 EXT  CAU   OAT  PAQ   121.06  3.000
 EXT  HAUA  CAU  HAU   107.90  3.000
 EXT  HAUA  CAU  CAV   109.62  3.000
 EXT  HAU   CAU  CAV   109.79  3.000
 EXT  HAUA  CAU  OAT   108.77  3.000
 EXT  HAU   CAU  OAT   111.84  3.000
 EXT  CAV   CAU  OAT   108.90  3.000
 EXT  HAVA  CAV  HAV   108.02  3.000
 EXT  HAVA  CAV  NAW   108.68  3.000
 EXT  HAV   CAV  NAW   112.58  3.000
 EXT  HAVA  CAV  CAU   109.53  3.000
 EXT  HAV   CAV  CAU   108.44  3.000
 EXT  NAW   CAV  CAU   109.54  3.000
 EXT  CAV   NAW  CAB   121.51  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
 EXT  CONST_01  NAJ  CAK  CAI  CAA     0.00   0.0  0
 EXT  CONST_02  NAJ  CAL  CAN  CAA     0.00   0.0  0
 EXT  CONST_03  CAL  CAN  CAA  CAI     0.00   0.0  0
 EXT  CONST_04  CAL  NAJ  CAK  CAI     0.00   0.0  0
 EXT  CONST_05  CAN  CAA  CAI  CAK     0.00   0.0  0
 EXT  CONST_06  CAN  CAL  NAJ  CAK     0.00   0.0  0
 EXT  CONST_07  CAM  CAL  CAN  CAA   180.00   0.0  0
 EXT  CONST_08  CAK  CAI  CAA  CAB   180.00   0.0  0
 EXT  CONST_09  CAL  CAN  CAA  CAB   180.00   0.0  0
 EXT  CONST_10  CAN  CAA  CAI  CAH   180.00   0.0  0
 EXT  CONST_11  NAJ  CAK  CAI  CAH   180.00   0.0  0
 EXT  CONST_12  OAO  CAN  CAA  CAI   180.00   0.0  0
 EXT  CONST_13  OAO  CAN  CAL  NAJ   180.00   0.0  0
 EXT  CONST_14  CAM  CAL  NAJ  CAK   180.00   0.0  0
 EXT  CONST_15  HAK  CAK  CAI  CAA   180.00   0.0  0
 EXT  Var_01    OAG  CAH  CAI  CAA  -178.07  30.0  1
 EXT  Var_02    NAW  CAB  CAA  CAI  -175.52  30.0  3
 EXT  Var_03    HAM  CAM  CAL  NAJ   119.86  30.0  2
 EXT  Var_04    CAI  CAH  OAG  PAC  -162.59  30.0  3
 EXT  Var_05    CAU  CAV  NAW  CAB   117.07  30.0  2
 EXT  Var_06    CAV  CAU  OAT  PAQ  -132.85  30.0  3
 EXT  Var_07    NAW  CAV  CAU  OAT    58.68  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
 EXT  plan-1  CAA  0.020
 EXT  plan-1  CAB  0.020
 EXT  plan-1  CAH  0.020
 EXT  plan-1  CAI  0.020
 EXT  plan-1  NAJ  0.020
 EXT  plan-1  CAK  0.020
 EXT  plan-1  CAL  0.020
 EXT  plan-1  CAM  0.020
 EXT  plan-1  CAN  0.020
 EXT  plan-1  OAO  0.020
 EXT  plan-1  HAK  0.020
 EXT  plan-2  CAA  0.020
 EXT  plan-2  CAB  0.020
 EXT  plan-2  CAV  0.020
 EXT  plan-2  NAW  0.020
 EXT  plan-2  HAB  0.020

