# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:32:43 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  49  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  -6.6967  -0.0662   0.9719
 28P  CAR   C  CR16  0  -0.239  -7.2098  -1.1060   1.7365
 28P  CAS   C  CR16  0  -0.273  -7.1570  -2.4109   1.2640
 28P  CAT   C  CR16  0  -0.239  -6.5918  -2.6651   0.0208
 28P  CAU   C  CR16  0  -0.310  -6.0802  -1.6222  -0.7397
 28P  CAP   C  CR6   0   0.163  -6.1230  -0.3105  -0.2732
 28P  CAO   C  CH2   0  -0.622  -5.5183   0.8128  -1.0788
 28P  CAN   C  CR6   0   0.137  -4.0524   0.9854  -0.7680
 28P  CAV   C  CR16  0  -0.300  -3.0753   0.3320  -1.5058
 28P  CAW   C  CR16  0  -0.368  -1.7234   0.4445  -1.1963
 28P  CAM   C  CR16  0  -0.290  -3.6350   1.7742   0.3036
 28P  CAL   C  CR16  0  -0.333  -2.2969   1.9017   0.6270
 28P  CAK   C  CR6   0   0.370  -1.3254   1.2341  -0.1216
 28P  OAJ   O  O2    0  -0.478  -0.0460   1.4172   0.2617
 28P  CAI   C  CH2   0  -0.168   0.9851   0.7301  -0.4272
 28P  CAH   C  CH2   0  -0.485   2.3046   1.1180   0.2079
 28P  CAG   C  CH2   0  -0.263   3.4658   0.4077  -0.4762
 28P  N1    N  NT    0  -0.420   4.7382   0.6282   0.1925
 28P  CAX   C  CH3   0  -0.539   5.1737   2.0054   0.0636
 28P  CAB   C  CH2   0  -0.256   5.7485  -0.2962  -0.2945
 28P  CAC   C  CH2   0  -0.600   6.9187  -0.4167   0.6712
 28P  CAD   C  C     0   0.556   7.9358  -1.4316   0.2324
 28P  OAF   O  O     0  -0.447   7.8415  -2.1359  -0.7423
 28P  OAE   O  OH1   0  -0.596   8.9763  -1.4760   1.0591
 28P  HAQ   H  HCR6  0   0.245  -6.7479   0.9490   1.3481
 28P  HAR   H  HCR6  0   0.254  -7.6543  -0.8944   2.7007
 28P  HAS   H  HCR6  0   0.253  -7.5568  -3.2229   1.8577
 28P  HAT   H  HCR6  0   0.253  -6.5505  -3.6779  -0.3593
 28P  HAU   H  HCR6  0   0.245  -5.6450  -1.8331  -1.7099
 28P  HAO   H  HCH2  0   0.266  -5.6470   0.6112  -2.1445
 28P  HAOA  H  HCH2  0   0.266  -6.0513   1.7422  -0.8669
 28P  HAV   H  HCR6  0   0.248  -3.3615  -0.2824  -2.3518
 28P  HAW   H  HCR6  0   0.276  -1.0040  -0.0867  -1.8048
 28P  HAM   H  HCR6  0   0.247  -4.3688   2.3046   0.8996
 28P  HAL   H  HCR6  0   0.258  -1.9940   2.5210   1.4624
 28P  HAI   H  HCH2  0   0.221   0.8306  -0.3537  -0.3617
 28P  HAIA  H  HCH2  0   0.221   0.9814   0.9981  -1.4902
 28P  HAH   H  HCH2  0   0.240   2.4183   2.2025   0.1450
 28P  HAHA  H  HCH2  0   0.235   2.2987   0.8499   1.2675
 28P  HAG   H  HCH2  0   0.233   3.2673  -0.6678  -0.4668
 28P  HAGA  H  HCH2  0   0.194   3.5101   0.7056  -1.5383
 28P  HAX   H  HCH3  0   0.241   4.4558   2.6854   0.5198
 28P  HAXA  H  HCH3  0   0.238   6.1216   2.1632   0.5767
 28P  HAXB  H  HCH3  0   0.195   5.3063   2.3097  -0.9870
 28P  HAB   H  HCH2  0   0.240   5.2850  -1.2787  -0.4000
 28P  HABA  H  HCH2  0   0.203   6.1139  -0.0125  -1.2949
 28P  HAC   H  HCH2  0   0.279   7.4344   0.5371   0.8081
 28P  HACA  H  HCH2  0   0.282   6.5522  -0.7016   1.6622
 28P  HOAE  H  HOH1  0   0.478   9.6138  -2.1383   0.7530

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    1.523  0.020  1.523
 28P  CAH  HAH   single    0.970  0.020  1.090
 28P  CAH  HAHA  single    0.970  0.020  1.090
 28P  CAG  N1    single    1.454  0.020  1.454
 28P  CAG  HAG   single    0.970  0.020  1.090
 28P  CAG  HAGA  single    0.970  0.020  1.090
 28P  CAB  N1    single    1.453  0.020  1.453
 28P  N1   CAX   single    1.450  0.020  1.450
 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    1.522  0.020  1.522
 28P  CAB  HAB   single    0.970  0.020  1.090
 28P  CAB  HABA  single    0.970  0.020  1.090
 28P  CAD  CAC   single    1.502  0.020  1.502
 28P  CAC  HAC   single    0.970  0.020  1.090
 28P  CAC  HACA  single    0.970  0.020  1.090
 28P  OAF  CAD   double    1.206  0.020  1.206
 28P  OAE  CAD   single    1.330  0.020  1.330
 28P  OAE  HOAE  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
 28P  HAQ   CAQ  CAP   119.61  3.000
 28P  HAQ   CAQ  CAR   119.52  3.000
 28P  CAP   CAQ  CAR   120.87  3.000
 28P  HAR   CAR  CAS   120.15  3.000
 28P  HAR   CAR  CAQ   119.71  3.000
 28P  CAS   CAR  CAQ   120.14  3.000
 28P  HAS   CAS  CAT   120.26  3.000
 28P  HAS   CAS  CAR   120.28  3.000
 28P  CAT   CAS  CAR   119.46  3.000
 28P  HAT   CAT  CAU   119.76  3.000
 28P  HAT   CAT  CAS   120.06  3.000
 28P  CAU   CAT  CAS   120.18  3.000
 28P  HAU   CAU  CAP   119.69  3.000
 28P  HAU   CAU  CAT   119.47  3.000
 28P  CAP   CAU  CAT   120.84  3.000
 28P  CAO   CAP  CAU   120.66  3.000
 28P  CAO   CAP  CAQ   120.79  3.000
 28P  CAU   CAP  CAQ   118.51  3.000
 28P  HAOA  CAO  HAO   106.80  3.000
 28P  HAOA  CAO  CAN   109.69  3.000
 28P  HAO   CAO  CAN   109.68  3.000
 28P  HAOA  CAO  CAP   109.53  3.000
 28P  HAO   CAO  CAP   109.65  3.000
 28P  CAN   CAO  CAP   111.38  3.000
 28P  CAM   CAN  CAV   117.65  3.000
 28P  CAV   CAN  CAO   121.38  3.000
 28P  CAM   CAN  CAO   120.93  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   121.52  3.000
 28P  HAW   CAW  CAV   118.78  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   119.49  3.000
 28P  HAL   CAL  CAM   120.25  3.000
 28P  CAK   CAL  CAM   120.26  3.000
 28P  OAJ   CAK  CAL   116.29  3.000
 28P  OAJ   CAK  CAW   124.62  3.000
 28P  CAL   CAK  CAW   119.09  3.000
 28P  CAI   OAJ  CAK   119.09  3.000
 28P  HAIA  CAI  HAI   107.40  3.000
 28P  HAIA  CAI  CAH   110.29  3.000
 28P  HAI   CAI  CAH   110.53  3.000
 28P  HAIA  CAI  OAJ   110.51  3.000
 28P  HAI   CAI  OAJ   110.33  3.000
 28P  CAH   CAI  OAJ   107.80  3.000
 28P  HAHA  CAH  HAH   107.45  3.000
 28P  HAHA  CAH  CAG   108.97  3.000
 28P  HAH   CAH  CAG   110.96  3.000
 28P  HAHA  CAH  CAI   109.81  3.000
 28P  HAH   CAH  CAI   108.71  3.000
 28P  CAG   CAH  CAI   110.87  3.000
 28P  HAGA  CAG  HAG   106.31  3.000
 28P  HAGA  CAG  N1    111.49  3.000
 28P  HAG   CAG  N1    107.69  3.000
 28P  HAGA  CAG  CAH   109.68  3.000
 28P  HAG   CAG  CAH   108.44  3.000
 28P  N1    CAG  CAH   112.94  3.000
 28P  CAB   N1   CAX   111.44  3.000
 28P  CAX   N1   CAG   111.46  3.000
 28P  CAB   N1   CAG   110.96  3.000
 28P  HAXB  CAX  HAXA  107.72  3.000
 28P  HAXB  CAX  HAX   107.84  3.000
 28P  HAXA  CAX  HAX   106.61  3.000
 28P  HAXB  CAX  N1    112.54  3.000
 28P  HAXA  CAX  N1    110.92  3.000
 28P  HAX   CAX  N1    110.97  3.000
 28P  HABA  CAB  HAB   106.55  3.000
 28P  HABA  CAB  CAC   109.96  3.000
 28P  HAB   CAB  CAC   108.46  3.000
 28P  HABA  CAB  N1    111.77  3.000
 28P  HAB   CAB  N1    108.04  3.000
 28P  CAC   CAB  N1    111.85  3.000
 28P  HACA  CAC  HAC   105.77  3.000
 28P  HACA  CAC  CAD   108.38  3.000
 28P  HAC   CAC  CAD   107.86  3.000
 28P  HACA  CAC  CAB   109.74  3.000
 28P  HAC   CAC  CAB   111.91  3.000
 28P  CAD   CAC  CAB   112.87  3.000
 28P  OAE   CAD  OAF   122.96  3.000
 28P  OAE   CAD  CAC   111.76  3.000
 28P  OAF   CAD  CAC   125.28  3.000
 28P  HOAE  OAE  CAD   109.96  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  CONST_28  HOAE  OAE  CAD  CAC   180.00   0.0  0
 28P  Var_01    CAN   CAO  CAP  CAQ    90.67  30.0  2
 28P  Var_02    CAM   CAN  CAO  CAP   -85.94  30.0  2
 28P  Var_03    CAH   CAI  OAJ  CAK  -179.96  30.0  3
 28P  Var_04    CAG   CAH  CAI  OAJ   179.59  30.0  3
 28P  Var_05    N1    CAG  CAH  CAI  -173.44  30.0  1
 28P  Var_06    CAB   N1   CAG  CAH   166.85  30.0  3
 28P  Var_07    CAC   CAB  N1   CAG  -160.97  30.0  2
 28P  Var_08    CAD   CAC  CAB  N1    176.38  30.0  1
 28P  Var_09    OAF   CAD  CAC  CAB    -3.11  30.0  2
 28P  Var_10    HAX   CAX  N1   CAG    61.07  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
 28P  plan-3  HOAE  0.020

