# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 13:41:18 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC1=CC(=O)C(=CN1C)Oc2ccc(N)cc2C
#
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
 1S5  1S5  5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium  ligand  49  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1S5
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
 1S5  OAA   O  O     0  -0.504   1.5013  -0.5415   2.0211
 1S5  CAB   C  CR6   0   0.403   0.7218  -0.8515   1.1135
 1S5  CAC   C  CR6   0   0.104   1.1691  -1.1977  -0.2203
 1S5  OAD   O  O2    0  -0.506   2.5023  -1.2473  -0.4902
 1S5  CAE   C  CR6   0   0.309   3.2248  -0.0818  -0.3956
 1S5  CAF   C  CR6   0   0.026   4.5731  -0.2068  -0.0632
 1S5  CAG   C  CH3   0  -0.717   5.1625  -1.5504   0.2486
 1S5  CAH   C  CR16  0  -0.536  -0.7057  -0.9231   1.2509
 1S5  CAI   C  CR16  0  -0.064   0.2949  -1.5439  -1.1945
 1S5  CAJ   C  CR16  0  -0.322   2.6810   1.1618  -0.6669
 1S5  CAK   C  CR16  0  -0.369   5.3515   0.9425  -0.0186
 1S5  CAL   C  CR6   0   0.426  -1.5482  -1.2931   0.2426
 1S5  NAM   N  NR6   0  -0.497  -1.0464  -1.6022  -0.9845
 1S5  CAN   C  CR16  0  -0.336   3.4715   2.3011  -0.6062
 1S5  CAO   C  CR6   0   0.293   4.8257   2.2112  -0.2844
 1S5  NAP   N  NH2   0  -0.864   5.6428   3.3331  -0.2838
 1S5  CAQ   C  CH2   0  -0.546  -3.0314  -1.3265   0.4581
 1S5  CAR   C  CH3   0  -0.542  -1.9087  -2.0486  -2.0737
 1S5  CAS   C  CH2   0  -0.419  -3.7152  -0.0119   0.0700
 1S5  CAT   C  CH2   0  -0.417  -5.2191  -0.0643   0.3053
 1S5  CAU   C  CH2   0  -0.409  -5.9237   1.2368  -0.0548
 1S5  CAV   C  CH2   0  -0.419  -7.4264   1.1921   0.1958
 1S5  CAW   C  CH3   0  -0.663  -8.1251   2.4929  -0.1741
 1S5  HAG   H  HCH3  0   0.243   5.0842  -2.2352  -0.5969
 1S5  HAGA  H  HCH3  0   0.241   6.2168  -1.4609   0.5061
 1S5  HAGB  H  HCH3  0   0.243   4.6501  -2.0220   1.0889
 1S5  HAH   H  HCR6  0   0.263  -1.1395  -0.6899   2.2154
 1S5  HAI   H  HCR6  0   0.315   0.6396  -1.8084  -2.1846
 1S5  HAJ   H  HCR6  0   0.264   1.6344   1.2621  -0.9282
 1S5  HAK   H  HCR6  0   0.248   6.4015   0.8471   0.2372
 1S5  HAN   H  HCR6  0   0.255   3.0276   3.2664  -0.8184
 1S5  HNAP  H  HNH2  0   0.373   6.4517   3.2634   0.3139
 1S5  HNAA  H  HNH2  0   0.372   5.1597   4.2033  -0.1238
 1S5  HAQ   H  HCH2  0   0.267  -3.4898  -2.1587  -0.0812
 1S5  HAQA  H  HCH2  0   0.273  -3.2089  -1.5179   1.5176
 1S5  HAR   H  HCH3  0   0.277  -1.3162  -2.1304  -2.9793
 1S5  HARA  H  HCH3  0   0.273  -2.3414  -3.0225  -1.8533
 1S5  HARB  H  HCH3  0   0.267  -2.7064  -1.3335  -2.2562
 1S5  HAS   H  HCH2  0   0.235  -3.2756   0.8024   0.6533
 1S5  HASA  H  HCH2  0   0.227  -3.5196   0.2263  -0.9798
 1S5  HAT   H  HCH2  0   0.216  -5.6492  -0.8856  -0.2781
 1S5  HATA  H  HCH2  0   0.216  -5.4102  -0.3058   1.3564
 1S5  HAU   H  HCH2  0   0.209  -5.4843   2.0599   0.5194
 1S5  HAUA  H  HCH2  0   0.209  -5.7402   1.4720  -1.1090
 1S5  HAV   H  HCH2  0   0.211  -7.8627   0.3653  -0.3734
 1S5  HAVA  H  HCH2  0   0.211  -7.6085   0.9626   1.2500
 1S5  HAW   H  HCH3  0   0.216  -7.7199   3.3324   0.3942
 1S5  HAWA  H  HCH3  0   0.216  -7.9963   2.7214  -1.2339
 1S5  HAWB  H  HCH3  0   0.226  -9.1962   2.4451   0.0251

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
 1S5  OAA  CAB   double    1.236  0.020  1.236
 1S5  CAB  CAC   single    1.449  0.020  1.449
 1S5  CAB  CAH   single    1.436  0.020  1.436
 1S5  CAC  OAD   single    1.361  0.020  1.361
 1S5  CAC  CAI   double    1.354  0.020  1.354
 1S5  OAD  CAE   single    1.374  0.020  1.374
 1S5  CAE  CAF   aromatic  1.394  0.020  1.394
 1S5  CAE  CAJ   aromatic  1.384  0.020  1.384
 1S5  CAF  CAG   single    1.500  0.020  1.500
 1S5  CAF  CAK   aromatic  1.389  0.020  1.389
 1S5  CAH  CAL   double    1.365  0.020  1.365
 1S5  CAI  NAM   single    1.359  0.020  1.359
 1S5  CAJ  CAN   aromatic  1.388  0.020  1.388
 1S5  CAK  CAO   aromatic  1.399  0.020  1.399
 1S5  CAL  NAM   single    1.361  0.020  1.361
 1S5  CAL  CAQ   single    1.499  0.020  1.499
 1S5  NAM  CAR   single    1.459  0.020  1.459
 1S5  CAN  CAO   aromatic  1.395  0.020  1.395
 1S5  CAO  NAP   single    1.388  0.020  1.388
 1S5  CAQ  CAS   single    1.532  0.020  1.532
 1S5  CAS  CAT   single    1.523  0.020  1.523
 1S5  CAT  CAU   single    1.523  0.020  1.523
 1S5  CAU  CAV   single    1.524  0.020  1.524
 1S5  CAV  CAW   single    1.522  0.020  1.522
 1S5  CAG  HAG   single    0.970  0.020  1.090
 1S5  CAG  HAGA  single    0.970  0.020  1.090
 1S5  CAG  HAGB  single    0.970  0.020  1.090
 1S5  CAH  HAH   single    0.930  0.020  1.080
 1S5  CAI  HAI   single    0.930  0.020  1.080
 1S5  CAJ  HAJ   single    0.930  0.020  1.080
 1S5  CAK  HAK   single    0.930  0.020  1.080
 1S5  CAN  HAN   single    0.930  0.020  1.080
 1S5  NAP  HNAP  single    0.890  0.020  1.040
 1S5  NAP  HNAA  single    0.890  0.020  1.040
 1S5  CAQ  HAQ   single    0.970  0.020  1.090
 1S5  CAQ  HAQA  single    0.970  0.020  1.090
 1S5  CAR  HAR   single    0.970  0.020  1.090
 1S5  CAR  HARA  single    0.970  0.020  1.090
 1S5  CAR  HARB  single    0.970  0.020  1.090
 1S5  CAS  HAS   single    0.970  0.020  1.090
 1S5  CAS  HASA  single    0.970  0.020  1.090
 1S5  CAT  HAT   single    0.970  0.020  1.090
 1S5  CAT  HATA  single    0.970  0.020  1.090
 1S5  CAU  HAU   single    0.970  0.020  1.090
 1S5  CAU  HAUA  single    0.970  0.020  1.090
 1S5  CAV  HAV   single    0.970  0.020  1.090
 1S5  CAV  HAVA  single    0.970  0.020  1.090
 1S5  CAW  HAW   single    0.970  0.020  1.090
 1S5  CAW  HAWA  single    0.970  0.020  1.090
 1S5  CAW  HAWB  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
 1S5  CAH   CAB  CAC   112.53  3.000
 1S5  CAH   CAB  OAA   124.70  3.000
 1S5  CAC   CAB  OAA   122.77  3.000
 1S5  CAI   CAC  OAD   118.71  3.000
 1S5  CAI   CAC  CAB   121.61  3.000
 1S5  OAD   CAC  CAB   119.58  3.000
 1S5  CAE   OAD  CAC   118.06  3.000
 1S5  CAJ   CAE  CAF   120.47  3.000
 1S5  CAJ   CAE  OAD   122.81  3.000
 1S5  CAF   CAE  OAD   116.66  3.000
 1S5  CAK   CAF  CAG   120.95  3.000
 1S5  CAK   CAF  CAE   118.40  3.000
 1S5  CAG   CAF  CAE   120.65  3.000
 1S5  HAGB  CAG  HAGA  107.95  3.000
 1S5  HAGB  CAG  HAG   106.96  3.000
 1S5  HAGA  CAG  HAG   107.72  3.000
 1S5  HAGB  CAG  CAF   111.26  3.000
 1S5  HAGA  CAG  CAF   110.85  3.000
 1S5  HAG   CAG  CAF   111.90  3.000
 1S5  HAH   CAH  CAL   117.97  3.000
 1S5  HAH   CAH  CAB   118.21  3.000
 1S5  CAL   CAH  CAB   123.81  3.000
 1S5  HAI   CAI  NAM   116.47  3.000
 1S5  HAI   CAI  CAC   121.04  3.000
 1S5  NAM   CAI  CAC   122.48  3.000
 1S5  HAJ   CAJ  CAN   118.99  3.000
 1S5  HAJ   CAJ  CAE   120.66  3.000
 1S5  CAN   CAJ  CAE   120.35  3.000
 1S5  HAK   CAK  CAO   119.23  3.000
 1S5  HAK   CAK  CAF   118.51  3.000
 1S5  CAO   CAK  CAF   122.26  3.000
 1S5  CAQ   CAL  NAM   119.29  3.000
 1S5  CAQ   CAL  CAH   120.70  3.000
 1S5  NAM   CAL  CAH   119.99  3.000
 1S5  CAR   NAM  CAL   121.63  3.000
 1S5  CAR   NAM  CAI   118.76  3.000
 1S5  CAL   NAM  CAI   119.57  3.000
 1S5  HAN   CAN  CAO   120.03  3.000
 1S5  HAN   CAN  CAJ   119.30  3.000
 1S5  CAO   CAN  CAJ   120.67  3.000
 1S5  NAP   CAO  CAN   121.31  3.000
 1S5  NAP   CAO  CAK   120.78  3.000
 1S5  CAN   CAO  CAK   117.86  3.000
 1S5  HNAA  NAP  HNAP  110.49  3.000
 1S5  HNAA  NAP  CAO   114.57  3.000
 1S5  HNAP  NAP  CAO   114.63  3.000
 1S5  HAQA  CAQ  HAQ   106.11  3.000
 1S5  HAQA  CAQ  CAS   108.90  3.000
 1S5  HAQ   CAQ  CAS   109.96  3.000
 1S5  HAQA  CAQ  CAL   107.72  3.000
 1S5  HAQ   CAQ  CAL   111.17  3.000
 1S5  CAS   CAQ  CAL   112.71  3.000
 1S5  HARB  CAR  HARA  109.33  3.000
 1S5  HARB  CAR  HAR   108.07  3.000
 1S5  HARA  CAR  HAR   108.58  3.000
 1S5  HARB  CAR  NAM   110.97  3.000
 1S5  HARA  CAR  NAM   110.96  3.000
 1S5  HAR   CAR  NAM   108.86  3.000
 1S5  HASA  CAS  HAS   106.12  3.000
 1S5  HASA  CAS  CAT   109.40  3.000
 1S5  HAS   CAS  CAT   109.88  3.000
 1S5  HASA  CAS  CAQ   110.50  3.000
 1S5  HAS   CAS  CAQ   108.93  3.000
 1S5  CAT   CAS  CAQ   111.85  3.000
 1S5  HATA  CAT  HAT   106.10  3.000
 1S5  HATA  CAT  CAU   109.54  3.000
 1S5  HAT   CAT  CAU   109.45  3.000
 1S5  HATA  CAT  CAS   109.16  3.000
 1S5  HAT   CAT  CAS   109.34  3.000
 1S5  CAU   CAT  CAS   113.01  3.000
 1S5  HAUA  CAU  HAU   106.01  3.000
 1S5  HAUA  CAU  CAV   109.24  3.000
 1S5  HAU   CAU  CAV   109.35  3.000
 1S5  HAUA  CAU  CAT   109.48  3.000
 1S5  HAU   CAU  CAT   109.42  3.000
 1S5  CAV   CAU  CAT   113.10  3.000
 1S5  HAVA  CAV  HAV   106.04  3.000
 1S5  HAVA  CAV  CAW   109.69  3.000
 1S5  HAV   CAV  CAW   109.65  3.000
 1S5  HAVA  CAV  CAU   109.18  3.000
 1S5  HAV   CAV  CAU   109.25  3.000
 1S5  CAW   CAV  CAU   112.80  3.000
 1S5  HAWB  CAW  HAWA  107.60  3.000
 1S5  HAWB  CAW  HAW   107.65  3.000
 1S5  HAWA  CAW  HAW   107.49  3.000
 1S5  HAWB  CAW  CAV   111.65  3.000
 1S5  HAWA  CAW  CAV   111.14  3.000
 1S5  HAW   CAW  CAV   111.12  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
 1S5  CONST_01  CAO  CAK  CAF  CAE     0.00   0.0  0
 1S5  CONST_02  CAO  CAN  CAJ  CAE     0.00   0.0  0
 1S5  CONST_03  CAN  CAJ  CAE  CAF     0.00   0.0  0
 1S5  CONST_04  CAN  CAO  CAK  CAF     0.00   0.0  0
 1S5  CONST_05  CAK  CAF  CAE  CAJ     0.00   0.0  0
 1S5  CONST_06  CAK  CAO  CAN  CAJ     0.00   0.0  0
 1S5  CONST_07  CAK  CAF  CAE  OAD   180.00   0.0  0
 1S5  CONST_08  CAN  CAJ  CAE  OAD   180.00   0.0  0
 1S5  CONST_09  NAP  CAO  CAK  CAF   180.00   0.0  0
 1S5  CONST_10  CAJ  CAE  CAF  CAG   180.00   0.0  0
 1S5  CONST_11  CAO  CAK  CAF  CAG   180.00   0.0  0
 1S5  CONST_12  NAP  CAO  CAN  CAJ   180.00   0.0  0
 1S5  CONST_13  HAK  CAK  CAF  CAE   180.00   0.0  0
 1S5  CONST_14  HAN  CAN  CAJ  CAE   180.00   0.0  0
 1S5  CONST_15  HAJ  CAJ  CAE  CAF   180.00   0.0  0
 1S5  Var_01    CAF  CAE  OAD  CAC   151.35  30.0  2
 1S5  Var_02    CAI  CAC  OAD  CAE   119.39  30.0  1
 1S5  Var_03    CAS  CAQ  CAL  CAH    92.38  30.0  3
 1S5  Var_04    HAG  CAG  CAF  CAE    60.91  30.0  2
 1S5  Var_05    HAR  CAR  NAM  CAI    -8.67  30.0  3
 1S5  Var_06    CAT  CAS  CAQ  CAL  -179.62  30.0  3
 1S5  Var_07    CAU  CAT  CAS  CAQ   179.24  30.0  3
 1S5  Var_08    CAV  CAU  CAT  CAS  -179.31  30.0  3
 1S5  Var_09    CAW  CAV  CAU  CAT  -179.66  30.0  3
 1S5  Var_10    HAW  CAW  CAV  CAU   -59.02  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
 1S5  plan-1  OAA   0.020
 1S5  plan-1  CAB   0.020
 1S5  plan-1  CAC   0.020
 1S5  plan-1  OAD   0.020
 1S5  plan-1  CAH   0.020
 1S5  plan-1  CAI   0.020
 1S5  plan-1  CAL   0.020
 1S5  plan-1  NAM   0.020
 1S5  plan-1  CAQ   0.020
 1S5  plan-1  CAR   0.020
 1S5  plan-1  HAH   0.020
 1S5  plan-1  HAI   0.020
 1S5  plan-2  OAD   0.020
 1S5  plan-2  CAE   0.020
 1S5  plan-2  CAF   0.020
 1S5  plan-2  CAG   0.020
 1S5  plan-2  CAJ   0.020
 1S5  plan-2  CAK   0.020
 1S5  plan-2  CAN   0.020
 1S5  plan-2  CAO   0.020
 1S5  plan-2  NAP   0.020
 1S5  plan-2  HAJ   0.020
 1S5  plan-2  HAK   0.020
 1S5  plan-2  HAN   0.020
 1S5  plan-3  CAO   0.020
 1S5  plan-3  NAP   0.020
 1S5  plan-3  HNAP  0.020
 1S5  plan-3  HNAA  0.020

