# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:25:07 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[(2S)-2-{[4-(4-chlorophenoxy)phenoxy]methyl}pyrrolidin-1-yl]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-]C(=O)CCCN1CCC[C@H]1COc2ccc(Oc3ccc(Cl)cc3)cc2
#
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
 25P  25P  4-[(2S)-2-{[4-(4-chlorophenoxy)phenoxy]methyl}pyrrolidin-1-yl]butanoate  ligand  50  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_25P
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
 25P  CAD   C   CR16   0  -0.345  -4.8564   0.5164  -0.3284
 25P  CAC   C   CR16   0  -0.201  -5.9526   0.6124  -1.1756
 25P  CAB   C   CR6    0  -0.059  -7.1395  -0.0163  -0.8433
 25P  CLAG  CL  CL     0  -0.137  -8.5058   0.1057  -1.9055
 25P  CAA   C   CR16   0  -0.203  -7.2473  -0.7450   0.3326
 25P  CAF   C   CR16   0  -0.332  -6.1563  -0.8425   1.1778
 25P  CAE   C   CR6    0   0.375  -4.9581  -0.2124   0.8508
 25P  OAH   O   O2     0  -0.512  -3.9437  -0.3539   1.7430
 25P  CAI   C   CR6    0   0.274  -2.7026   0.1533   1.4310
 25P  CAN   C   CR16   0  -0.289  -2.3485   1.4223   1.8688
 25P  CAM   C   CR16   0  -0.349  -1.0852   1.9147   1.5987
 25P  CAJ   C   CR16   0  -0.287  -1.7993  -0.6150   0.7203
 25P  CAK   C   CR16   0  -0.379  -0.5280  -0.1247   0.4462
 25P  CAL   C   CR6    0   0.393  -0.1632   1.1467   0.8839
 25P  OAO   O   O2     0  -0.475   1.0406   1.7083   0.6700
 25P  CAP   C   CH2    0  -0.188   2.0565   0.9445   0.0421
 25P  CAQ   C   CH1    0  -0.128   3.3261   1.7978   0.0290
 25P  CAR   C   CH2    0  -0.445   3.2313   2.9611  -0.9527
 25P  CAS   C   CH2    0  -0.496   3.6104   2.3195  -2.2940
 25P  CAT   C   CH2    0  -0.266   4.4678   1.0985  -1.9156
 25P  NAU   N   NT     0  -0.430   4.4983   1.0967  -0.4595
 25P  CAV   C   CH2    0  -0.264   4.8319  -0.1605   0.1694
 25P  CAW   C   CH2    0  -0.421   6.2857  -0.5633  -0.0419
 25P  CAX   C   CH2    0  -0.583   6.6175  -1.8516   0.6930
 25P  CAY   C   C      0   0.412   8.0663  -2.3546   0.5638
 25P  OBA   O   OC    -1  -0.609   8.8579  -1.6869  -0.1301
 25P  OAZ   O   O      0  -0.634   8.3316  -3.4097   1.1788
 25P  HAD   H   HCR6   0   0.287  -3.9375   1.0155  -0.6051
 25P  HAC   H   HCR6   0   0.284  -5.8695   1.1820  -2.0914
 25P  HAA   H   HCR6   0   0.283  -8.1740  -1.2385   0.5921
 25P  HAF   H   HCR6   0   0.279  -6.2336  -1.4106   2.0961
 25P  HAN   H   HCR6   0   0.275  -3.0539   2.0222   2.4298
 25P  HAM   H   HCR6   0   0.269  -0.8032   2.9009   1.9451
 25P  HAJ   H   HCR6   0   0.277  -2.0748  -1.6047   0.3782
 25P  HAK   H   HCR6   0   0.286   0.1580  -0.7490  -0.1093
 25P  HAP   H   HCH2   0   0.237   2.2248   0.0158   0.5994
 25P  HAPA  H   HCH2   0   0.223   1.7561   0.6667  -0.9759
 25P  HAQ   H   HCH1   0   0.241   3.5095   2.1399   1.0539
 25P  HAR   H   HCH2   0   0.237   2.2486   3.4328  -0.9707
 25P  HARA  H   HCH2   0   0.240   3.9558   3.7280  -0.6732
 25P  HAS   H   HCH2   0   0.235   2.7183   2.0039  -2.8363
 25P  HASA  H   HCH2   0   0.244   4.1431   3.0152  -2.9415
 25P  HAT   H   HCH2   0   0.197   4.0285   0.1745  -2.3214
 25P  HATA  H   HCH2   0   0.225   5.4807   1.1628  -2.3205
 25P  HAV   H   HCH2   0   0.222   4.6474  -0.0583   1.2440
 25P  HAVA  H   HCH2   0   0.182   4.1831  -0.9838  -0.1786
 25P  HAW   H   HCH2   0   0.213   6.4888  -0.6846  -1.1091
 25P  HAWA  H   HCH2   0   0.205   6.9305   0.2485   0.3052
 25P  HAX   H   HCH2   0   0.218   6.3942  -1.7327   1.7600
 25P  HAXA  H   HCH2   0   0.218   5.9495  -2.6532   0.3556

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
 25P  CAD  CAC   aromatic  1.389  0.020  1.389
 25P  CAD  CAE   aromatic  1.390  0.020  1.390
 25P  CAC  CAB   aromatic  1.384  0.020  1.384
 25P  CAB  CLAG  single    1.735  0.020  1.735
 25P  CAB  CAA   aromatic  1.388  0.020  1.388
 25P  CAA  CAF   aromatic  1.384  0.020  1.384
 25P  CAF  CAE   aromatic  1.393  0.020  1.393
 25P  CAE  OAH   single    1.358  0.020  1.358
 25P  OAH  CAI   single    1.377  0.020  1.377
 25P  CAI  CAN   aromatic  1.388  0.020  1.388
 25P  CAI  CAJ   aromatic  1.383  0.020  1.383
 25P  CAN  CAM   aromatic  1.382  0.020  1.382
 25P  CAM  CAL   aromatic  1.397  0.020  1.397
 25P  CAJ  CAK   aromatic  1.390  0.020  1.390
 25P  CAK  CAL   aromatic  1.393  0.020  1.393
 25P  CAL  OAO   single    1.345  0.020  1.345
 25P  OAO  CAP   single    1.418  0.020  1.418
 25P  CAP  CAQ   single    1.530  0.020  1.530
 25P  CAQ  CAR   single    1.525  0.020  1.525
 25P  CAQ  NAU   single    1.451  0.020  1.451
 25P  CAR  CAS   single    1.535  0.020  1.535
 25P  CAS  CAT   single    1.539  0.020  1.539
 25P  CAT  NAU   single    1.456  0.020  1.456
 25P  NAU  CAV   single    1.445  0.020  1.445
 25P  CAV  CAW   single    1.523  0.020  1.523
 25P  CAW  CAX   single    1.520  0.020  1.520
 25P  CAX  CAY   single    1.539  0.020  1.539
 25P  CAY  OBA   deloc     1.247  0.020  1.247
 25P  CAY  OAZ   deloc     1.250  0.020  1.250
 25P  CAD  HAD   single    0.930  0.020  1.080
 25P  CAC  HAC   single    0.930  0.020  1.080
 25P  CAA  HAA   single    0.930  0.020  1.080
 25P  CAF  HAF   single    0.930  0.020  1.080
 25P  CAN  HAN   single    0.930  0.020  1.080
 25P  CAM  HAM   single    0.930  0.020  1.080
 25P  CAJ  HAJ   single    0.930  0.020  1.080
 25P  CAK  HAK   single    0.930  0.020  1.080
 25P  CAP  HAP   single    0.970  0.020  1.090
 25P  CAP  HAPA  single    0.970  0.020  1.090
 25P  CAQ  HAQ   single    0.970  0.020  1.090
 25P  CAR  HAR   single    0.970  0.020  1.090
 25P  CAR  HARA  single    0.970  0.020  1.090
 25P  CAS  HAS   single    0.970  0.020  1.090
 25P  CAS  HASA  single    0.970  0.020  1.090
 25P  CAT  HAT   single    0.970  0.020  1.090
 25P  CAT  HATA  single    0.970  0.020  1.090
 25P  CAV  HAV   single    0.970  0.020  1.090
 25P  CAV  HAVA  single    0.970  0.020  1.090
 25P  CAW  HAW   single    0.970  0.020  1.090
 25P  CAW  HAWA  single    0.970  0.020  1.090
 25P  CAX  HAX   single    0.970  0.020  1.090
 25P  CAX  HAXA  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
 25P  HAD   CAD  CAE   121.41  3.000
 25P  HAD   CAD  CAC   118.85  3.000
 25P  CAE   CAD  CAC   119.74  3.000
 25P  HAC   CAC  CAB   120.56  3.000
 25P  HAC   CAC  CAD   119.50  3.000
 25P  CAB   CAC  CAD   119.94  3.000
 25P  CAA   CAB  CLAG  119.64  3.000
 25P  CAA   CAB  CAC   120.59  3.000
 25P  CLAG  CAB  CAC   119.77  3.000
 25P  HAA   CAA  CAF   119.80  3.000
 25P  HAA   CAA  CAB   120.64  3.000
 25P  CAF   CAA  CAB   119.57  3.000
 25P  HAF   CAF  CAE   119.87  3.000
 25P  HAF   CAF  CAA   119.92  3.000
 25P  CAE   CAF  CAA   120.20  3.000
 25P  OAH   CAE  CAF   116.18  3.000
 25P  OAH   CAE  CAD   123.86  3.000
 25P  CAF   CAE  CAD   119.96  3.000
 25P  CAI   OAH  CAE   119.08  3.000
 25P  CAJ   CAI  CAN   120.23  3.000
 25P  CAJ   CAI  OAH   120.06  3.000
 25P  CAN   CAI  OAH   119.69  3.000
 25P  HAN   CAN  CAM   119.96  3.000
 25P  HAN   CAN  CAI   120.24  3.000
 25P  CAM   CAN  CAI   119.80  3.000
 25P  HAM   CAM  CAL   119.51  3.000
 25P  HAM   CAM  CAN   120.00  3.000
 25P  CAL   CAM  CAN   120.49  3.000
 25P  HAJ   CAJ  CAK   119.53  3.000
 25P  HAJ   CAJ  CAI   120.28  3.000
 25P  CAK   CAJ  CAI   120.19  3.000
 25P  HAK   CAK  CAL   121.48  3.000
 25P  HAK   CAK  CAJ   118.56  3.000
 25P  CAL   CAK  CAJ   119.97  3.000
 25P  OAO   CAL  CAK   124.42  3.000
 25P  OAO   CAL  CAM   116.26  3.000
 25P  CAK   CAL  CAM   119.32  3.000
 25P  CAP   OAO  CAL   119.12  3.000
 25P  HAPA  CAP  HAP   107.41  3.000
 25P  HAPA  CAP  CAQ   111.13  3.000
 25P  HAP   CAP  CAQ   110.46  3.000
 25P  HAPA  CAP  OAO   110.56  3.000
 25P  HAP   CAP  OAO   109.96  3.000
 25P  CAQ   CAP  OAO   107.34  3.000
 25P  HAQ   CAQ  NAU   109.30  3.000
 25P  HAQ   CAQ  CAR   111.98  3.000
 25P  NAU   CAQ  CAR   101.66  3.000
 25P  HAQ   CAQ  CAP   107.76  3.000
 25P  NAU   CAQ  CAP   113.83  3.000
 25P  CAR   CAQ  CAP   112.30  3.000
 25P  HARA  CAR  HAR   107.37  3.000
 25P  HARA  CAR  CAS   110.71  3.000
 25P  HAR   CAR  CAS   112.90  3.000
 25P  HARA  CAR  CAQ   109.26  3.000
 25P  HAR   CAR  CAQ   113.38  3.000
 25P  CAS   CAR  CAQ   103.20  3.000
 25P  HASA  CAS  HAS   106.81  3.000
 25P  HASA  CAS  CAT   112.35  3.000
 25P  HAS   CAS  CAT   110.39  3.000
 25P  HASA  CAS  CAR   111.92  3.000
 25P  HAS   CAS  CAR   110.70  3.000
 25P  CAT   CAS  CAR   104.74  3.000
 25P  HATA  CAT  HAT   106.42  3.000
 25P  HATA  CAT  NAU   110.56  3.000
 25P  HAT   CAT  NAU   112.08  3.000
 25P  HATA  CAT  CAS   112.25  3.000
 25P  HAT   CAT  CAS   110.67  3.000
 25P  NAU   CAT  CAS   104.98  3.000
 25P  CAV   NAU  CAT   116.18  3.000
 25P  CAV   NAU  CAQ   117.42  3.000
 25P  CAT   NAU  CAQ   108.61  3.000
 25P  HAVA  CAV  HAV   106.24  3.000
 25P  HAVA  CAV  CAW   108.65  3.000
 25P  HAV   CAV  CAW   108.76  3.000
 25P  HAVA  CAV  NAU   112.07  3.000
 25P  HAV   CAV  NAU   107.88  3.000
 25P  CAW   CAV  NAU   112.96  3.000
 25P  HAWA  CAW  HAW   106.42  3.000
 25P  HAWA  CAW  CAX   110.31  3.000
 25P  HAW   CAW  CAX   109.72  3.000
 25P  HAWA  CAW  CAV   108.81  3.000
 25P  HAW   CAW  CAV   110.01  3.000
 25P  CAX   CAW  CAV   111.44  3.000
 25P  HAXA  CAX  HAX   104.75  3.000
 25P  HAXA  CAX  CAY   107.98  3.000
 25P  HAX   CAX  CAY   107.99  3.000
 25P  HAXA  CAX  CAW   109.74  3.000
 25P  HAX   CAX  CAW   109.52  3.000
 25P  CAY   CAX  CAW   116.23  3.000
 25P  OAZ   CAY  OBA   126.26  3.000
 25P  OAZ   CAY  CAX   115.75  3.000
 25P  OBA   CAY  CAX   118.00  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
 25P  CONST_01  CAA   CAB  CAC  CAD      0.00   0.0  0
 25P  CONST_02  CAA   CAF  CAE  CAD      0.00   0.0  0
 25P  CONST_03  CAF   CAE  CAD  CAC      0.00   0.0  0
 25P  CONST_04  CAF   CAA  CAB  CAC      0.00   0.0  0
 25P  CONST_05  CAE   CAD  CAC  CAB      0.00   0.0  0
 25P  CONST_06  CAE   CAF  CAA  CAB      0.00   0.0  0
 25P  CONST_07  CAL   CAM  CAN  CAI      0.00   0.0  0
 25P  CONST_08  CAL   CAK  CAJ  CAI      0.00   0.0  0
 25P  CONST_09  CAK   CAJ  CAI  CAN      0.00   0.0  0
 25P  CONST_10  CAK   CAL  CAM  CAN      0.00   0.0  0
 25P  CONST_11  CAJ   CAI  CAN  CAM      0.00   0.0  0
 25P  CONST_12  CAJ   CAK  CAL  CAM      0.00   0.0  0
 25P  CONST_13  CLAG  CAB  CAC  CAD    180.00   0.0  0
 25P  CONST_14  OAH   CAE  CAD  CAC    180.00   0.0  0
 25P  CONST_15  CAF   CAA  CAB  CLAG   180.00   0.0  0
 25P  CONST_16  OAH   CAE  CAF  CAA    180.00   0.0  0
 25P  CONST_17  CAM   CAN  CAI  OAH    180.00   0.0  0
 25P  CONST_18  CAK   CAJ  CAI  OAH    180.00   0.0  0
 25P  CONST_19  OAO   CAL  CAM  CAN    180.00   0.0  0
 25P  CONST_20  OAO   CAL  CAK  CAJ    180.00   0.0  0
 25P  CONST_21  HAF   CAF  CAE  CAD    180.00   0.0  0
 25P  CONST_22  HAA   CAA  CAB  CAC    180.00   0.0  0
 25P  CONST_23  HAD   CAD  CAC  CAB    180.00   0.0  0
 25P  CONST_24  HAC   CAC  CAB  CAA    180.00   0.0  0
 25P  CONST_25  HAM   CAM  CAN  CAI    180.00   0.0  0
 25P  CONST_26  HAK   CAK  CAJ  CAI    180.00   0.0  0
 25P  CONST_27  HAJ   CAJ  CAI  CAN    180.00   0.0  0
 25P  CONST_28  HAN   CAN  CAI  CAJ    180.00   0.0  0
 25P  Var_01    CAT   CAS  CAR  CAQ    -24.61  30.0  1
 25P  Var_02    CAS   CAT  NAU  CAQ     24.48  30.0  1
 25P  Var_03    NAU   CAT  CAS  CAR      1.29  30.0  1
 25P  Var_04    CAN   CAI  OAH  CAE     94.66  30.0  2
 25P  Var_05    CAQ   CAP  OAO  CAL   -175.85  30.0  3
 25P  Var_06    CAW   CAV  NAU  CAQ   -159.61  30.0  3
 25P  Var_07    CAX   CAW  CAV  NAU    177.04  30.0  3
 25P  Var_08    CAY   CAX  CAW  CAV   -179.50  30.0  3
 25P  Var_09    OBA   CAY  CAX  CAW     -0.39  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 25P  chir_01  CAQ  CAP  CAR  NAU  positiv

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
 25P  plan-1  CAD   0.020
 25P  plan-1  CAC   0.020
 25P  plan-1  CAB   0.020
 25P  plan-1  CLAG  0.020
 25P  plan-1  CAA   0.020
 25P  plan-1  CAF   0.020
 25P  plan-1  CAE   0.020
 25P  plan-1  OAH   0.020
 25P  plan-1  HAD   0.020
 25P  plan-1  HAC   0.020
 25P  plan-1  HAA   0.020
 25P  plan-1  HAF   0.020
 25P  plan-2  OAH   0.020
 25P  plan-2  CAI   0.020
 25P  plan-2  CAN   0.020
 25P  plan-2  CAM   0.020
 25P  plan-2  CAJ   0.020
 25P  plan-2  CAK   0.020
 25P  plan-2  CAL   0.020
 25P  plan-2  OAO   0.020
 25P  plan-2  HAN   0.020
 25P  plan-2  HAM   0.020
 25P  plan-2  HAJ   0.020
 25P  plan-2  HAK   0.020
 25P  plan-3  CAX   0.020
 25P  plan-3  CAY   0.020
 25P  plan-3  OBA   0.020
 25P  plan-3  OAZ   0.020

