# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:16:45 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[3-(4-benzylphenoxy)propyl]-N-methyl-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCOc1ccc(Cc2ccccc2)cc1)CCC(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
 28P  28P  N-[3-(4-benzylphenoxy)propyl]-N-methyl-beta-alanine  ligand  48  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_28P
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
 28P  CAQ   C  CR16   0  -0.314  -6.6510  -0.1370   0.9541
 28P  CAR   C  CR16   0  -0.238  -7.1249  -1.1890   1.7273
 28P  CAS   C  CR16   0  -0.274  -7.0433  -2.4928   1.2561
 28P  CAT   C  CR16   0  -0.239  -6.4886  -2.7338   0.0055
 28P  CAU   C  CR16   0  -0.310  -6.0164  -1.6787  -0.7636
 28P  CAP   C  CR6    0   0.162  -6.0885  -0.3678  -0.2987
 28P  CAO   C  CH2    0  -0.622  -5.5256   0.7700  -1.1146
 28P  CAN   C  CR6    0   0.137  -4.0630   0.9873  -0.8173
 28P  CAV   C  CR16   0  -0.300  -3.0733   0.3579  -1.5591
 28P  CAW   C  CR16   0  -0.367  -1.7231   0.5072  -1.2580
 28P  CAM   C  CR16   0  -0.290  -3.6604   1.7926   0.2477
 28P  CAL   C  CR16   0  -0.333  -2.3246   1.9553   0.5637
 28P  CAK   C  CR6    0   0.370  -1.3401   1.3083  -0.1861
 28P  OAJ   O  O2     0  -0.478  -0.0644   1.5197   0.1942
 28P  CAI   C  CH2    0  -0.168   0.9774   0.8280  -0.4744
 28P  CAH   C  CH2    0  -0.483   2.2834   1.1854   0.2048
 28P  CAG   C  CH2    0  -0.258   3.4548   0.4696  -0.4571
 28P  N1    N  NT     0  -0.417   4.7032   0.6261   0.2692
 28P  CAX   C  CH3    0  -0.535   5.1971   1.9853   0.1885
 28P  CAB   C  CH2    0  -0.248   5.6970  -0.3325  -0.1977
 28P  CAC   C  CH2    0  -0.610   6.8901  -0.4704   0.7335
 28P  CAD   C  C      0   0.417   7.8651  -1.6053   0.3663
 28P  OAF   O  O      0  -0.610   7.5584  -2.3535  -0.5827
 28P  OAE   O  OC    -1  -0.630   8.8954  -1.6861   1.0670
 28P  HAQ   H  HCR6   0   0.245  -6.7241   0.8770   1.3301
 28P  HAR   H  HCR6   0   0.253  -7.5614  -0.9876   2.6974
 28P  HAS   H  HCR6   0   0.253  -7.4120  -3.3144   1.8567
 28P  HAT   H  HCR6   0   0.253  -6.4248  -3.7458  -0.3737
 28P  HAU   H  HCR6   0   0.245  -5.5888  -1.8796  -1.7392
 28P  HAO   H  HCH2   0   0.266  -5.6580   0.5597  -2.1781
 28P  HAOA  H  HCH2   0   0.266  -6.0852   1.6836  -0.9021
 28P  HAV   H  HCR6   0   0.248  -3.3482  -0.2672  -2.4011
 28P  HAW   H  HCR6   0   0.277  -0.9928  -0.0051  -1.8698
 28P  HAM   H  HCR6   0   0.246  -4.4045   2.3062   0.8456
 28P  HAL   H  HCR6   0   0.258  -2.0333   2.5847   1.3958
 28P  HAI   H  HCH2   0   0.220   0.8070  -0.2544  -0.4273
 28P  HAIA  H  HCH2   0   0.221   1.0068   1.1090  -1.5338
 28P  HAH   H  HCH2   0   0.237   2.4150   2.2692   0.1685
 28P  HAHA  H  HCH2   0   0.233   2.2407   0.8962   1.2580
 28P  HAG   H  HCH2   0   0.227   3.2280  -0.5999  -0.4957
 28P  HAGA  H  HCH2   0   0.188   3.5488   0.8013  -1.5068
 28P  HAX   H  HCH3   0   0.235   4.4596   2.6915   0.5680
 28P  HAXA  H  HCH3   0   0.237   6.0922   2.1078   0.7971
 28P  HAXB  H  HCH3   0   0.187   5.4480   2.2840  -0.8427
 28P  HAB   H  HCH2   0   0.217   5.2079  -1.3054  -0.2747
 28P  HABA  H  HCH2   0   0.177   6.0442  -0.0823  -1.2153
 28P  HAC   H  HCH2   0   0.224   7.4656   0.4585   0.7832
 28P  HACA  H  HCH2   0   0.223   6.5266  -0.6438   1.7529

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
 28P  CAR  CAQ   aromatic  1.389  0.020  1.389
 28P  CAQ  CAP   aromatic  1.393  0.020  1.393
 28P  CAQ  HAQ   single    0.930  0.020  1.080
 28P  CAR  CAS   aromatic  1.389  0.020  1.389
 28P  CAR  HAR   single    0.930  0.020  1.080
 28P  CAS  CAT   aromatic  1.389  0.020  1.389
 28P  CAS  HAS   single    0.930  0.020  1.080
 28P  CAT  CAU   aromatic  1.388  0.020  1.388
 28P  CAT  HAT   single    0.930  0.020  1.080
 28P  CAP  CAU   aromatic  1.393  0.020  1.393
 28P  CAU  HAU   single    0.930  0.020  1.080
 28P  CAP  CAO   single    1.509  0.020  1.509
 28P  CAO  CAN   single    1.508  0.020  1.508
 28P  CAO  HAO   single    0.970  0.020  1.090
 28P  CAO  HAOA  single    0.970  0.020  1.090
 28P  CAM  CAN   aromatic  1.395  0.020  1.395
 28P  CAN  CAV   aromatic  1.388  0.020  1.388
 28P  CAV  CAW   aromatic  1.391  0.020  1.391
 28P  CAV  HAV   single    0.930  0.020  1.080
 28P  CAK  CAW   aromatic  1.392  0.020  1.392
 28P  CAW  HAW   single    0.930  0.020  1.080
 28P  CAM  CAL   aromatic  1.382  0.020  1.382
 28P  CAM  HAM   single    0.930  0.020  1.080
 28P  CAL  CAK   aromatic  1.396  0.020  1.396
 28P  CAL  HAL   single    0.930  0.020  1.080
 28P  CAK  OAJ   single    1.348  0.020  1.348
 28P  OAJ  CAI   single    1.418  0.020  1.418
 28P  CAI  CAH   single    1.515  0.020  1.515
 28P  CAI  HAI   single    0.970  0.020  1.090
 28P  CAI  HAIA  single    0.970  0.020  1.090
 28P  CAG  CAH   single    1.524  0.020  1.524
 28P  CAH  HAH   single    0.970  0.020  1.090
 28P  CAH  HAHA  single    0.970  0.020  1.090
 28P  CAG  N1    single    1.453  0.020  1.453
 28P  CAG  HAG   single    0.970  0.020  1.090
 28P  CAG  HAGA  single    0.970  0.020  1.090
 28P  CAB  N1    single    1.458  0.020  1.458
 28P  N1   CAX   single    1.448  0.020  1.448
 28P  CAX  HAX   single    0.970  0.020  1.090
 28P  CAX  HAXA  single    0.970  0.020  1.090
 28P  CAX  HAXB  single    0.970  0.020  1.090
 28P  CAC  CAB   single    1.520  0.020  1.520
 28P  CAB  HAB   single    0.970  0.020  1.090
 28P  CAB  HABA  single    0.970  0.020  1.090
 28P  CAD  CAC   single    1.541  0.020  1.541
 28P  CAC  HAC   single    0.970  0.020  1.090
 28P  CAC  HACA  single    0.970  0.020  1.090
 28P  OAF  CAD   deloc     1.247  0.020  1.247
 28P  OAE  CAD   deloc     1.249  0.020  1.249

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
 28P  HAQ   CAQ  CAP   119.63  3.000
 28P  HAQ   CAQ  CAR   119.50  3.000
 28P  CAP   CAQ  CAR   120.87  3.000
 28P  HAR   CAR  CAS   120.15  3.000
 28P  HAR   CAR  CAQ   119.70  3.000
 28P  CAS   CAR  CAQ   120.14  3.000
 28P  HAS   CAS  CAT   120.25  3.000
 28P  HAS   CAS  CAR   120.29  3.000
 28P  CAT   CAS  CAR   119.46  3.000
 28P  HAT   CAT  CAU   119.76  3.000
 28P  HAT   CAT  CAS   120.07  3.000
 28P  CAU   CAT  CAS   120.17  3.000
 28P  HAU   CAU  CAP   119.69  3.000
 28P  HAU   CAU  CAT   119.46  3.000
 28P  CAP   CAU  CAT   120.85  3.000
 28P  CAO   CAP  CAU   120.66  3.000
 28P  CAO   CAP  CAQ   120.81  3.000
 28P  CAU   CAP  CAQ   118.50  3.000
 28P  HAOA  CAO  HAO   106.76  3.000
 28P  HAOA  CAO  CAN   109.75  3.000
 28P  HAO   CAO  CAN   109.71  3.000
 28P  HAOA  CAO  CAP   109.53  3.000
 28P  HAO   CAO  CAP   109.64  3.000
 28P  CAN   CAO  CAP   111.33  3.000
 28P  CAM   CAN  CAV   117.66  3.000
 28P  CAV   CAN  CAO   121.39  3.000
 28P  CAM   CAN  CAO   120.91  3.000
 28P  HAV   CAV  CAW   118.42  3.000
 28P  HAV   CAV  CAN   119.73  3.000
 28P  CAW   CAV  CAN   121.85  3.000
 28P  HAW   CAW  CAK   121.49  3.000
 28P  HAW   CAW  CAV   118.81  3.000
 28P  CAK   CAW  CAV   119.70  3.000
 28P  HAM   CAM  CAL   118.78  3.000
 28P  HAM   CAM  CAN   119.78  3.000
 28P  CAL   CAM  CAN   121.44  3.000
 28P  HAL   CAL  CAK   119.48  3.000
 28P  HAL   CAL  CAM   120.25  3.000
 28P  CAK   CAL  CAM   120.26  3.000
 28P  OAJ   CAK  CAL   116.30  3.000
 28P  OAJ   CAK  CAW   124.61  3.000
 28P  CAL   CAK  CAW   119.09  3.000
 28P  CAI   OAJ  CAK   119.07  3.000
 28P  HAIA  CAI  HAI   107.38  3.000
 28P  HAIA  CAI  CAH   110.46  3.000
 28P  HAI   CAI  CAH   110.34  3.000
 28P  HAIA  CAI  OAJ   110.50  3.000
 28P  HAI   CAI  OAJ   110.31  3.000
 28P  CAH   CAI  OAJ   107.87  3.000
 28P  HAHA  CAH  HAH   107.41  3.000
 28P  HAHA  CAH  CAG   108.92  3.000
 28P  HAH   CAH  CAG   111.03  3.000
 28P  HAHA  CAH  CAI   109.63  3.000
 28P  HAH   CAH  CAI   108.85  3.000
 28P  CAG   CAH  CAI   110.93  3.000
 28P  HAGA  CAG  HAG   106.11  3.000
 28P  HAGA  CAG  N1    111.69  3.000
 28P  HAG   CAG  N1    107.53  3.000
 28P  HAGA  CAG  CAH   109.69  3.000
 28P  HAG   CAG  CAH   108.37  3.000
 28P  N1    CAG  CAH   113.13  3.000
 28P  CAB   N1   CAX   111.52  3.000
 28P  CAX   N1   CAG   111.49  3.000
 28P  CAB   N1   CAG   110.79  3.000
 28P  HAXB  CAX  HAXA  107.76  3.000
 28P  HAXB  CAX  HAX   107.72  3.000
 28P  HAXA  CAX  HAX   106.79  3.000
 28P  HAXB  CAX  N1    112.57  3.000
 28P  HAXA  CAX  N1    110.77  3.000
 28P  HAX   CAX  N1    110.98  3.000
 28P  HABA  CAB  HAB   106.14  3.000
 28P  HABA  CAB  CAC   109.78  3.000
 28P  HAB   CAB  CAC   108.31  3.000
 28P  HABA  CAB  N1    111.14  3.000
 28P  HAB   CAB  N1    107.65  3.000
 28P  CAC   CAB  N1    113.50  3.000
 28P  HACA  CAC  HAC   105.46  3.000
 28P  HACA  CAC  CAD   108.36  3.000
 28P  HAC   CAC  CAD   107.67  3.000
 28P  HACA  CAC  CAB   108.90  3.000
 28P  HAC   CAC  CAB   111.34  3.000
 28P  CAD   CAC  CAB   114.69  3.000
 28P  OAE   CAD  OAF   126.25  3.000
 28P  OAE   CAD  CAC   115.86  3.000
 28P  OAF   CAD  CAC   117.89  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
 28P  CONST_01  CAT  CAS  CAR  CAQ     0.00   0.0  0
 28P  CONST_02  CAT  CAU  CAP  CAQ     0.00   0.0  0
 28P  CONST_03  CAU  CAP  CAQ  CAR     0.00   0.0  0
 28P  CONST_04  CAU  CAT  CAS  CAR     0.00   0.0  0
 28P  CONST_05  CAP  CAQ  CAR  CAS     0.00   0.0  0
 28P  CONST_06  CAP  CAU  CAT  CAS     0.00   0.0  0
 28P  CONST_07  CAK  CAL  CAM  CAN     0.00   0.0  0
 28P  CONST_08  CAK  CAW  CAV  CAN     0.00   0.0  0
 28P  CONST_09  CAL  CAM  CAN  CAV     0.00   0.0  0
 28P  CONST_10  CAL  CAK  CAW  CAV     0.00   0.0  0
 28P  CONST_11  CAM  CAN  CAV  CAW     0.00   0.0  0
 28P  CONST_12  CAM  CAL  CAK  CAW     0.00   0.0  0
 28P  CONST_13  CAO  CAP  CAQ  CAR   180.00   0.0  0
 28P  CONST_14  CAO  CAP  CAU  CAT   180.00   0.0  0
 28P  CONST_15  CAL  CAM  CAN  CAO   180.00   0.0  0
 28P  CONST_16  CAW  CAV  CAN  CAO   180.00   0.0  0
 28P  CONST_17  OAJ  CAK  CAW  CAV   180.00   0.0  0
 28P  CONST_18  OAJ  CAK  CAL  CAM   180.00   0.0  0
 28P  CONST_19  HAS  CAS  CAR  CAQ   180.00   0.0  0
 28P  CONST_20  HAU  CAU  CAP  CAQ   180.00   0.0  0
 28P  CONST_21  HAT  CAT  CAS  CAR   180.00   0.0  0
 28P  CONST_22  HAQ  CAQ  CAR  CAS   180.00   0.0  0
 28P  CONST_23  HAR  CAR  CAS  CAT   180.00   0.0  0
 28P  CONST_24  HAL  CAL  CAM  CAN   180.00   0.0  0
 28P  CONST_25  HAW  CAW  CAV  CAN   180.00   0.0  0
 28P  CONST_26  HAM  CAM  CAN  CAV   180.00   0.0  0
 28P  CONST_27  HAV  CAV  CAN  CAM   180.00   0.0  0
 28P  Var_01    CAN  CAO  CAP  CAQ    90.30  30.0  2
 28P  Var_02    CAM  CAN  CAO  CAP   -85.93  30.0  2
 28P  Var_03    CAH  CAI  OAJ  CAK  -176.59  30.0  3
 28P  Var_04    CAG  CAH  CAI  OAJ   179.67  30.0  3
 28P  Var_05    N1   CAG  CAH  CAI  -171.78  30.0  2
 28P  Var_06    CAB  N1   CAG  CAH   165.58  30.0  3
 28P  Var_07    CAC  CAB  N1   CAG  -165.40  30.0  1
 28P  Var_08    CAD  CAC  CAB  N1    172.32  30.0  2
 28P  Var_09    OAF  CAD  CAC  CAB    -4.63  30.0  2
 28P  Var_10    HAX  CAX  N1   CAG    57.33  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
 28P  plan-1  CAQ  0.020
 28P  plan-1  CAR  0.020
 28P  plan-1  CAS  0.020
 28P  plan-1  CAT  0.020
 28P  plan-1  CAU  0.020
 28P  plan-1  CAP  0.020
 28P  plan-1  CAO  0.020
 28P  plan-1  HAQ  0.020
 28P  plan-1  HAR  0.020
 28P  plan-1  HAS  0.020
 28P  plan-1  HAT  0.020
 28P  plan-1  HAU  0.020
 28P  plan-2  CAO  0.020
 28P  plan-2  CAN  0.020
 28P  plan-2  CAV  0.020
 28P  plan-2  CAW  0.020
 28P  plan-2  CAM  0.020
 28P  plan-2  CAL  0.020
 28P  plan-2  CAK  0.020
 28P  plan-2  OAJ  0.020
 28P  plan-2  HAV  0.020
 28P  plan-2  HAW  0.020
 28P  plan-2  HAM  0.020
 28P  plan-2  HAL  0.020
 28P  plan-3  CAC  0.020
 28P  plan-3  CAD  0.020
 28P  plan-3  OAF  0.020
 28P  plan-3  OAE  0.020

