# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:10:26 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: N-[(2R,3R)-1-benzyl-2-methylpyrrolidin-3-yl]-5-chloro-2-methoxy-4-(methylamino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(OC)c(cc1Cl)C(=O)N[C@@H]2CCN(Cc3ccccc3)[C@@H]2C
#
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
 AQD  AQD  N-[(2R,3R)-1-benzyl-2-methylpyrrolidin-3-yl]-5-chloro-2-methoxy-4-(methylamino)benzamide  ligand  53  27  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AQD
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
 AQD  CAB  C   CH3   0  -0.442   4.7747  -3.3066   0.2969
 AQD  OAR  O   O2    0  -0.459   3.5934  -2.5417   0.4411
 AQD  CAW  C   CR6   0   0.426   3.6390  -1.2210   0.2210
 AQD  CAK  C   CR16  0  -0.534   4.8070  -0.5516  -0.1169
 AQD  CAV  C   CR6   0   0.507   4.8174   0.8314  -0.3675
 AQD  NAP  N   NH1   0  -0.682   5.9605   1.4804  -0.6714
 AQD  CAA  C   CH3   0  -0.533   7.2347   0.8311  -0.8257
 AQD  CAU  C   CR6   0  -0.173   3.5846   1.5051  -0.2835
 AQD  CLA  CL  CL    0  -0.136   3.5275   3.2182  -0.5803
 AQD  CAL  C   CR16  0  -0.218   2.4245   0.8356   0.0375
 AQD  CAX  C   CR6   0  -0.216   2.4204  -0.5287   0.3052
 AQD  CAS  C   C     0   0.519   1.1619  -1.2082   0.7214
 AQD  OAD  O   O     0  -0.488   1.0988  -1.9375   1.7014
 AQD  NAQ  N   NH1   0  -0.639   0.0980  -0.9398  -0.0600
 AQD  CAZ  C   CH1   0  -0.090  -1.2338  -1.4172   0.2121
 AQD  CAY  C   CH1   0  -0.039  -2.1159  -0.5003   1.1150
 AQD  CAC  C   CH3   0  -0.665  -1.4886   0.8300   1.4880
 AQD  CAM  C   CH2   0  -0.468  -2.0457  -1.5926  -1.0715
 AQD  CAN  C   CH2   0  -0.269  -3.4674  -1.4185  -0.5801
 AQD  NBA  N   NT    0  -0.429  -3.3447  -0.3088   0.3444
 AQD  CAO  C   CH2   0  -0.334  -4.5198  -0.0785   1.1480
 AQD  CAT  C   CR6   0   0.101  -5.6835   0.4111   0.3252
 AQD  CAI  C   CR16  0  -0.284  -5.5201   1.4716  -0.5648
 AQD  CAG  C   CR16  0  -0.243  -6.5928   1.9429  -1.3065
 AQD  CAF  C   CR16  0  -0.272  -7.8480   1.3585  -1.1720
 AQD  CAH  C   CR16  0  -0.241  -8.0194   0.3008  -0.2910
 AQD  CAJ  C   CR16  0  -0.320  -6.9404  -0.1696   0.4495
 AQD  H1   H   HCH3  0   0.232   5.5444  -3.0094   1.0133
 AQD  H2   H   HCH3  0   0.264   4.4951  -4.3386   0.4925
 AQD  H3   H   HCH3  0   0.232   5.1845  -3.2378  -0.7139
 AQD  H4   H   HCR6  0   0.303   5.7358  -1.0984  -0.1956
 AQD  H5   H   HNH1  0   0.389   5.9050   2.4554  -0.9067
 AQD  H6   H   HCH3  0   0.266   7.9754   1.5868  -1.0713
 AQD  H7   H   HCH3  0   0.237   7.5534   0.3355   0.0941
 AQD  H8   H   HCH3  0   0.234   7.2303   0.0875  -1.6275
 AQD  H9   H   HCR6  0   0.277   1.5012   1.3987   0.1029
 AQD  H10  H   HNH1  0   0.401   0.2350  -0.3625  -0.8744
 AQD  H11  H   HCH1  0   0.264  -1.1396  -2.3845   0.7056
 AQD  H12  H   HCH1  0   0.210  -2.3298  -1.0543   2.0425
 AQD  H13  H   HCH3  0   0.237  -2.2007   1.4462   2.0393
 AQD  H14  H   HCH3  0   0.225  -0.6199   0.6945   2.1332
 AQD  H15  H   HCH3  0   0.218  -1.1810   1.3893   0.6037
 AQD  H16  H   HCH2  0   0.236  -1.8080  -0.8050  -1.7920
 AQD  H17  H   HCH2  0   0.250  -1.8665  -2.5546  -1.5499
 AQD  H18  H   HCH2  0   0.240  -4.1704  -1.1897  -1.3827
 AQD  H19  H   HCH2  0   0.194  -3.8199  -2.3396  -0.0853
 AQD  H21  H   HCH2  0   0.212  -4.8217  -0.9826   1.7041
 AQD  H22  H   HCH2  0   0.252  -4.2840   0.6779   1.9026
 AQD  H23  H   HCR6  0   0.243  -4.5410   1.9206  -0.6794
 AQD  H24  H   HCR6  0   0.252  -6.4529   2.7680  -1.9934
 AQD  H25  H   HCR6  0   0.253  -8.6836   1.7238  -1.7552
 AQD  H26  H   HCR6  0   0.252  -8.9905  -0.1654  -0.1833
 AQD  H27  H   HCR6  0   0.246  -7.0768  -1.0036   1.1286

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
 AQD  CAG  CAI  aromatic  1.387  0.020  1.387
 AQD  CAG  CAF  aromatic  1.391  0.020  1.391
 AQD  CAI  CAT  aromatic  1.394  0.020  1.394
 AQD  CAF  CAH  aromatic  1.387  0.020  1.387
 AQD  CAT  CAO  single    1.507  0.020  1.507
 AQD  CAT  CAJ  aromatic  1.390  0.020  1.390
 AQD  CAO  NBA  single    1.442  0.020  1.442
 AQD  CAH  CAJ  aromatic  1.391  0.020  1.391
 AQD  CAC  CAY  single    1.517  0.020  1.517
 AQD  CAY  NBA  single    1.463  0.020  1.463
 AQD  CAY  CAZ  single    1.560  0.020  1.560
 AQD  NBA  CAN  single    1.450  0.020  1.450
 AQD  CAN  CAM  single    1.514  0.020  1.514
 AQD  CAZ  CAM  single    1.529  0.020  1.529
 AQD  CAZ  NAQ  single    1.441  0.020  1.441
 AQD  NAQ  CAS  single    1.347  0.020  1.347
 AQD  CAB  OAR  single    1.415  0.020  1.415
 AQD  OAR  CAW  single    1.340  0.020  1.340
 AQD  CAS  OAD  double    1.223  0.020  1.223
 AQD  CAS  CAX  single    1.489  0.020  1.489
 AQD  CAW  CAX  aromatic  1.404  0.020  1.404
 AQD  CAW  CAK  aromatic  1.388  0.020  1.388
 AQD  CAX  CAL  aromatic  1.390  0.020  1.390
 AQD  CAK  CAV  aromatic  1.406  0.020  1.406
 AQD  CAL  CAU  aromatic  1.377  0.020  1.377
 AQD  CAV  CAU  aromatic  1.407  0.020  1.407
 AQD  CAV  NAP  single    1.349  0.020  1.349
 AQD  CAU  CLA  single    1.739  0.020  1.739
 AQD  NAP  CAA  single    1.438  0.020  1.438
 AQD  CAB  H1   single    0.970  0.020  1.090
 AQD  CAB  H2   single    0.970  0.020  1.090
 AQD  CAB  H3   single    0.970  0.020  1.090
 AQD  CAK  H4   single    0.930  0.020  1.080
 AQD  NAP  H5   single    0.860  0.020  1.020
 AQD  CAA  H6   single    0.970  0.020  1.090
 AQD  CAA  H7   single    0.970  0.020  1.090
 AQD  CAA  H8   single    0.970  0.020  1.090
 AQD  CAL  H9   single    0.930  0.020  1.080
 AQD  NAQ  H10  single    0.860  0.020  1.020
 AQD  CAZ  H11  single    0.970  0.020  1.090
 AQD  CAY  H12  single    0.970  0.020  1.090
 AQD  CAC  H13  single    0.970  0.020  1.090
 AQD  CAC  H14  single    0.970  0.020  1.090
 AQD  CAC  H15  single    0.970  0.020  1.090
 AQD  CAM  H16  single    0.970  0.020  1.090
 AQD  CAM  H17  single    0.970  0.020  1.090
 AQD  CAN  H18  single    0.970  0.020  1.090
 AQD  CAN  H19  single    0.970  0.020  1.090
 AQD  CAO  H21  single    0.970  0.020  1.090
 AQD  CAO  H22  single    0.970  0.020  1.090
 AQD  CAI  H23  single    0.930  0.020  1.080
 AQD  CAG  H24  single    0.930  0.020  1.080
 AQD  CAF  H25  single    0.930  0.020  1.080
 AQD  CAH  H26  single    0.930  0.020  1.080
 AQD  CAJ  H27  single    0.930  0.020  1.080

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
 AQD  H3   CAB  H2   108.83  3.000
 AQD  H3   CAB  H1   108.97  3.000
 AQD  H2   CAB  H1   108.75  3.000
 AQD  H3   CAB  OAR  111.93  3.000
 AQD  H2   CAB  OAR  106.27  3.000
 AQD  H1   CAB  OAR  111.98  3.000
 AQD  CAW  OAR  CAB  119.20  3.000
 AQD  CAX  CAW  CAK  120.48  3.000
 AQD  CAK  CAW  OAR  122.96  3.000
 AQD  CAX  CAW  OAR  116.53  3.000
 AQD  H4   CAK  CAV  118.58  3.000
 AQD  H4   CAK  CAW  119.80  3.000
 AQD  CAV  CAK  CAW  121.61  3.000
 AQD  CAU  CAV  NAP  121.69  3.000
 AQD  NAP  CAV  CAK  121.32  3.000
 AQD  CAU  CAV  CAK  116.99  3.000
 AQD  H5   NAP  CAA  117.51  3.000
 AQD  H5   NAP  CAV  118.22  3.000
 AQD  CAA  NAP  CAV  123.89  3.000
 AQD  H8   CAA  H7   108.06  3.000
 AQD  H8   CAA  H6   108.06  3.000
 AQD  H7   CAA  H6   107.88  3.000
 AQD  H8   CAA  NAP  112.47  3.000
 AQD  H7   CAA  NAP  111.89  3.000
 AQD  H6   CAA  NAP  108.32  3.000
 AQD  CAL  CAU  CLA  119.39  3.000
 AQD  CLA  CAU  CAV  119.34  3.000
 AQD  CAL  CAU  CAV  121.27  3.000
 AQD  H9   CAL  CAX  119.72  3.000
 AQD  H9   CAL  CAU  118.64  3.000
 AQD  CAX  CAL  CAU  121.63  3.000
 AQD  CAS  CAX  CAL  120.26  3.000
 AQD  CAL  CAX  CAW  118.01  3.000
 AQD  CAS  CAX  CAW  121.68  3.000
 AQD  NAQ  CAS  OAD  122.87  3.000
 AQD  OAD  CAS  CAX  122.65  3.000
 AQD  NAQ  CAS  CAX  114.48  3.000
 AQD  H10  NAQ  CAZ  117.92  3.000
 AQD  H10  NAQ  CAS  118.40  3.000
 AQD  CAZ  NAQ  CAS  123.68  3.000
 AQD  H11  CAZ  CAM  108.92  3.000
 AQD  H11  CAZ  CAY  107.96  3.000
 AQD  CAM  CAZ  CAY  104.66  3.000
 AQD  H11  CAZ  NAQ  107.44  3.000
 AQD  CAM  CAZ  NAQ  111.74  3.000
 AQD  CAY  CAZ  NAQ  115.93  3.000
 AQD  H12  CAY  NBA  110.26  3.000
 AQD  H12  CAY  CAC  108.32  3.000
 AQD  NBA  CAY  CAC  111.22  3.000
 AQD  H12  CAY  CAZ  107.55  3.000
 AQD  NBA  CAY  CAZ  104.30  3.000
 AQD  CAC  CAY  CAZ  115.07  3.000
 AQD  H15  CAC  H14  108.59  3.000
 AQD  H15  CAC  H13  107.70  3.000
 AQD  H14  CAC  H13  106.92  3.000
 AQD  H15  CAC  CAY  111.52  3.000
 AQD  H14  CAC  CAY  111.46  3.000
 AQD  H13  CAC  CAY  110.46  3.000
 AQD  H17  CAM  H16  108.11  3.000
 AQD  H17  CAM  CAN  113.49  3.000
 AQD  H16  CAM  CAN  109.57  3.000
 AQD  H17  CAM  CAZ  112.50  3.000
 AQD  H16  CAM  CAZ  110.80  3.000
 AQD  CAN  CAM  CAZ  102.30  3.000
 AQD  H19  CAN  H18  107.40  3.000
 AQD  H19  CAN  NBA  112.34  3.000
 AQD  H18  CAN  NBA  111.29  3.000
 AQD  H19  CAN  CAM  110.45  3.000
 AQD  H18  CAN  CAM  112.98  3.000
 AQD  NBA  CAN  CAM  102.45  3.000
 AQD  CAO  NBA  CAN  114.12  3.000
 AQD  CAN  NBA  CAY  107.87  3.000
 AQD  CAO  NBA  CAY  114.32  3.000
 AQD  H22  CAO  H21  106.13  3.000
 AQD  H22  CAO  CAT  108.56  3.000
 AQD  H21  CAO  CAT  109.27  3.000
 AQD  H22  CAO  NBA  108.61  3.000
 AQD  H21  CAO  NBA  111.89  3.000
 AQD  CAT  CAO  NBA  112.14  3.000
 AQD  CAJ  CAT  CAI  118.74  3.000
 AQD  CAJ  CAT  CAO  120.91  3.000
 AQD  CAI  CAT  CAO  120.35  3.000
 AQD  H23  CAI  CAG  120.11  3.000
 AQD  H23  CAI  CAT  119.26  3.000
 AQD  CAG  CAI  CAT  120.62  3.000
 AQD  H24  CAG  CAF  119.87  3.000
 AQD  H24  CAG  CAI  119.90  3.000
 AQD  CAF  CAG  CAI  120.23  3.000
 AQD  H25  CAF  CAH  120.27  3.000
 AQD  H25  CAF  CAG  120.18  3.000
 AQD  CAH  CAF  CAG  119.55  3.000
 AQD  H26  CAH  CAJ  119.82  3.000
 AQD  H26  CAH  CAF  120.15  3.000
 AQD  CAJ  CAH  CAF  120.02  3.000
 AQD  H27  CAJ  CAH  119.75  3.000
 AQD  H27  CAJ  CAT  119.42  3.000
 AQD  CAH  CAJ  CAT  120.83  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
 AQD  CONST_01  CAU  CAL  CAX  CAW     0.00   0.0  0
 AQD  CONST_02  CAU  CAV  CAK  CAW     0.00   0.0  0
 AQD  CONST_03  CAL  CAX  CAW  CAK     0.00   0.0  0
 AQD  CONST_04  CAL  CAU  CAV  CAK     0.00   0.0  0
 AQD  CONST_05  CAX  CAW  CAK  CAV     0.00   0.0  0
 AQD  CONST_06  CAX  CAL  CAU  CAV     0.00   0.0  0
 AQD  CONST_07  CAF  CAG  CAI  CAT     0.00   0.0  0
 AQD  CONST_08  CAF  CAH  CAJ  CAT     0.00   0.0  0
 AQD  CONST_09  CAH  CAF  CAG  CAI     0.00   0.0  0
 AQD  CONST_10  CAH  CAJ  CAT  CAI     0.00   0.0  0
 AQD  CONST_11  CAJ  CAT  CAI  CAG     0.00   0.0  0
 AQD  CONST_12  CAJ  CAH  CAF  CAG     0.00   0.0  0
 AQD  CONST_13  CAL  CAX  CAW  OAR   180.00   0.0  0
 AQD  CONST_14  CAV  CAK  CAW  OAR   180.00   0.0  0
 AQD  CONST_15  NAP  CAV  CAK  CAW   180.00   0.0  0
 AQD  CONST_16  CAS  CAX  CAW  CAK   180.00   0.0  0
 AQD  CONST_17  CLA  CAU  CAV  CAK   180.00   0.0  0
 AQD  CONST_18  CAL  CAU  CAV  NAP   180.00   0.0  0
 AQD  CONST_19  CAS  CAX  CAL  CAU   180.00   0.0  0
 AQD  CONST_20  CAX  CAL  CAU  CLA   180.00   0.0  0
 AQD  CONST_21  CAG  CAI  CAT  CAO   180.00   0.0  0
 AQD  CONST_22  CAH  CAJ  CAT  CAO   180.00   0.0  0
 AQD  CONST_23  H9   CAL  CAX  CAW   180.00   0.0  0
 AQD  CONST_24  H4   CAK  CAV  CAU   180.00   0.0  0
 AQD  CONST_25  H24  CAG  CAI  CAT   180.00   0.0  0
 AQD  CONST_26  H26  CAH  CAJ  CAT   180.00   0.0  0
 AQD  CONST_27  H25  CAF  CAG  CAI   180.00   0.0  0
 AQD  CONST_28  H27  CAJ  CAT  CAI   180.00   0.0  0
 AQD  CONST_29  H23  CAI  CAG  CAF   180.00   0.0  0
 AQD  CONST_30  CAZ  NAQ  CAS  CAX   180.00   0.0  0
 AQD  CONST_31  CAA  NAP  CAV  CAK     0.00   0.0  0
 AQD  CONST_32  CAU  CAV  NAP  CAA   180.00   0.0  0
 AQD  CONST_33  H5   NAP  CAV  CAK   180.00   0.0  0
 AQD  CONST_34  CAZ  NAQ  CAS  OAD     0.00   0.0  0
 AQD  CONST_35  H10  NAQ  CAS  CAX     0.00   0.0  0
 AQD  Var_01    NBA  CAN  CAM  CAZ    41.54  30.0  1
 AQD  Var_02    CAM  CAN  NBA  CAY   -41.24  30.0  1
 AQD  Var_03    CAT  CAO  NBA  CAY   167.33  30.0  1
 AQD  Var_04    CAI  CAT  CAO  NBA   -49.40  30.0  2
 AQD  Var_05    CAX  CAW  OAR  CAB   176.48  30.0  2
 AQD  Var_06    NAQ  CAS  CAX  CAW  -133.32  30.0  2
 AQD  Var_07    H1   CAB  OAR  CAW    63.04  30.0  3
 AQD  Var_08    H6   CAA  NAP  CAV   179.80  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
 AQD  chir_01  CAZ  CAY  CAM  NAQ  negativ
 AQD  chir_02  CAY  NBA  CAZ  CAC  negativ

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
 AQD  plan-1  OAR  0.020
 AQD  plan-1  CAW  0.020
 AQD  plan-1  CAK  0.020
 AQD  plan-1  CAV  0.020
 AQD  plan-1  NAP  0.020
 AQD  plan-1  CAU  0.020
 AQD  plan-1  CLA  0.020
 AQD  plan-1  CAL  0.020
 AQD  plan-1  CAX  0.020
 AQD  plan-1  CAS  0.020
 AQD  plan-1  H4   0.020
 AQD  plan-1  H9   0.020
 AQD  plan-2  CAO  0.020
 AQD  plan-2  CAT  0.020
 AQD  plan-2  CAI  0.020
 AQD  plan-2  CAG  0.020
 AQD  plan-2  CAF  0.020
 AQD  plan-2  CAH  0.020
 AQD  plan-2  CAJ  0.020
 AQD  plan-2  H23  0.020
 AQD  plan-2  H24  0.020
 AQD  plan-2  H25  0.020
 AQD  plan-2  H26  0.020
 AQD  plan-2  H27  0.020
 AQD  plan-3  CAV  0.020
 AQD  plan-3  NAP  0.020
 AQD  plan-3  CAA  0.020
 AQD  plan-3  H5   0.020
 AQD  plan-4  CAX  0.020
 AQD  plan-4  CAS  0.020
 AQD  plan-4  OAD  0.020
 AQD  plan-4  NAQ  0.020
 AQD  plan-4  CAZ  0.020
 AQD  plan-4  H10  0.020

