# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:01:42 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: [2-[(3-chlorophenyl)methylamino]-4-methoxy-1,3-benzoxazol-6-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc2oc(NCc3cccc(Cl)c3)nc12)C(=O)N4CC[C@@H](O)[C@H](C)C4
#
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
 QQN  QQN  '[2-[(3-chlorophenyl)methylamino]-4-methoxy-1,3-benzoxazol-6-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone'  ligand  54  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQN
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
 QQN  C4   C   CR56  0   0.367  12.4889  -13.4412  13.9799
 QQN  C5   C   CR16  0  -0.387  12.2401  -14.4936  13.1291
 QQN  C6   C   CR6   0  -0.075  10.8946  -14.7601  12.8965
 QQN  C7   C   C     0   0.511  10.5567  -15.9421  12.0437
 QQN  N12  N   N     0  -0.505  12.1230  -11.7133  15.3906
 QQN  C15  C   CR6   0   0.082  16.1845  -11.2011  14.0047
 QQN  C17  C   CR6   0  -0.024  16.0381   -9.8018  12.0639
 QQN  C20  C   CR16  0  -0.293  17.1156  -11.9904  13.3397
 QQN  C22  C   CH2   0  -0.321   9.0950  -16.9476  10.3721
 QQN  C24  C   CH1   0   0.084   6.9965  -15.6482   9.8889
 QQN  C26  C   CH2   0  -0.306   9.1143  -14.5351  10.5700
 QQN  C25  C   CH1   0  -0.284   7.5917  -14.4569  10.6456
 QQN  O27  O   OH1   0  -0.673   5.5925  -15.7223  10.0018
 QQN  C23  C   CH2   0  -0.458   7.5724  -16.9546  10.4131
 QQN  N9   N   NT    0  -0.453   9.6063  -15.7956  11.0958
 QQN  O8   O   O     0  -0.493  11.1344  -17.0047  12.2419
 QQN  C1   C   CR16  0  -0.420   9.8832  -14.0214  13.5288
 QQN  C2   C   CR6   0   0.316  10.1722  -12.9711  14.3936
 QQN  O29  O   O2    0  -0.458   9.2675  -12.2179  15.0369
 QQN  C30  C   CH3   0  -0.441   7.8976  -12.4524  14.7737
 QQN  C3   C   CR56  0   0.101  11.5204  -12.6776  14.6127
 QQN  O10  O   O     0  -0.461  13.6966  -12.9425  14.3742
 QQN  C11  C   CR5   0   0.725  13.3906  -11.9245  15.2067
 QQN  N13  N   NH1   0  -0.700  14.4162  -11.2647  15.7463
 QQN  C14  C   CH2   0  -0.348  15.7991  -11.5289  15.4289
 QQN  C16  C   CR16  0  -0.247  15.6417  -10.0960  13.3583
 QQN  CL1  CL  CL    0  -0.131  15.3511   -8.4231  11.2644
 QQN  C18  C   CR16  0  -0.228  16.9685  -10.5794  11.3921
 QQN  C19  C   CR16  0  -0.247  17.5063  -11.6785  12.0453
 QQN  H1   H   HCR6  0   0.276  13.0301  -15.0670  12.6645
 QQN  H2   H   HCR6  0   0.259  17.5343  -12.8587  13.8335
 QQN  H3   H   HCH2  0   0.270   9.4932  -17.8586  10.8092
 QQN  H4   H   HCH2  0   0.240   9.4424  -16.9036   9.3340
 QQN  H5   H   HCH1  0   0.191   7.2916  -15.5446   8.8312
 QQN  H6   H   HCH2  0   0.251   9.4298  -14.4521   9.5215
 QQN  H7   H   HCH2  0   0.277   9.5678  -13.6972  11.0925
 QQN  H11  H   HCH1  0   0.230   7.2942  -14.5447  11.6987
 QQN  H12  H   HOH1  0   0.450   5.2045  -14.9688   9.5472
 QQN  H13  H   HCH2  0   0.232   7.2387  -17.1179  11.4424
 QQN  H14  H   HCH2  0   0.248   7.2060  -17.7921   9.8148
 QQN  H15  H   HCR6  0   0.288   8.8536  -14.2997  13.3486
 QQN  H16  H   HCH3  0   0.266   7.3410  -11.7222  15.3550
 QQN  H17  H   HCH3  0   0.223   7.6593  -12.3137  13.7153
 QQN  H18  H   HCH3  0   0.234   7.5878  -13.4555  15.0772
 QQN  H19  H   HNH1  0   0.420  14.1868  -10.4802  16.3334
 QQN  H20  H   HCH2  0   0.270  16.0495  -12.5694  15.6454
 QQN  H21  H   HCH2  0   0.293  16.3905  -10.9230  16.1150
 QQN  H22  H   HCR6  0   0.273  14.9131   -9.4690  13.8567
 QQN  H23  H   HCR6  0   0.280  17.2640  -10.3377  10.3805
 QQN  H24  H   HCR6  0   0.269  18.2285  -12.3002  11.5329
 QQN  C28  C   CH3   0  -0.680   7.1082  -13.1169  10.1076
 QQN  H8   H   HCH3  0   0.239   7.5851  -12.2906  10.6373
 QQN  H9   H   HCH3  0   0.228   7.3411  -13.0072   9.0460
 QQN  H10  H   HCH3  0   0.236   6.0320  -12.9919  10.2310

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
 QQN  C24  O27  single    1.410  0.020  1.410
 QQN  C24  C23  single    1.521  0.020  1.521
 QQN  C24  C25  single    1.532  0.020  1.532
 QQN  C28  C25  single    1.523  0.020  1.523
 QQN  C23  C22  single    1.523  0.020  1.523
 QQN  C22  N9   single    1.453  0.020  1.453
 QQN  C25  C26  single    1.526  0.020  1.526
 QQN  C26  N9   single    1.452  0.020  1.452
 QQN  CL1  C17  single    1.736  0.020  1.736
 QQN  N9   C7   single    1.350  0.020  1.350
 QQN  C18  C17  aromatic  1.386  0.020  1.386
 QQN  C18  C19  aromatic  1.387  0.020  1.387
 QQN  C17  C16  aromatic  1.385  0.020  1.385
 QQN  C19  C20  aromatic  1.388  0.020  1.388
 QQN  C7   O8   double    1.226  0.020  1.226
 QQN  C7   C6   single    1.496  0.020  1.496
 QQN  C6   C5   aromatic  1.391  0.020  1.391
 QQN  C6   C1   aromatic  1.403  0.020  1.403
 QQN  C5   C4   aromatic  1.376  0.020  1.376
 QQN  C16  C15  aromatic  1.391  0.020  1.391
 QQN  C20  C15  aromatic  1.390  0.020  1.390
 QQN  C15  C14  single    1.511  0.020  1.511
 QQN  C4   O10  aromatic  1.365  0.020  1.365
 QQN  C4   C3   aromatic  1.386  0.020  1.386
 QQN  C1   C2   aromatic  1.391  0.020  1.391
 QQN  O10  C11  aromatic  1.350  0.020  1.350
 QQN  C2   C3   aromatic  1.397  0.020  1.397
 QQN  C2   O29  single    1.341  0.020  1.341
 QQN  C3   N12  aromatic  1.378  0.020  1.378
 QQN  C11  N12  aromatic  1.298  0.020  1.298
 QQN  C11  N13  single    1.334  0.020  1.334
 QQN  C14  N13  single    1.443  0.020  1.443
 QQN  O29  C30  single    1.415  0.020  1.415
 QQN  C5   H1   single    0.930  0.020  1.080
 QQN  C20  H2   single    0.930  0.020  1.080
 QQN  C22  H3   single    0.970  0.020  1.090
 QQN  C22  H4   single    0.970  0.020  1.090
 QQN  C24  H5   single    0.970  0.020  1.090
 QQN  C26  H6   single    0.970  0.020  1.090
 QQN  C26  H7   single    0.970  0.020  1.090
 QQN  C28  H8   single    0.970  0.020  1.090
 QQN  C28  H9   single    0.970  0.020  1.090
 QQN  C28  H10  single    0.970  0.020  1.090
 QQN  C25  H11  single    0.970  0.020  1.090
 QQN  O27  H12  single    0.850  0.020  0.980
 QQN  C23  H13  single    0.970  0.020  1.090
 QQN  C23  H14  single    0.970  0.020  1.090
 QQN  C1   H15  single    0.930  0.020  1.080
 QQN  C30  H16  single    0.970  0.020  1.090
 QQN  C30  H17  single    0.970  0.020  1.090
 QQN  C30  H18  single    0.970  0.020  1.090
 QQN  N13  H19  single    0.860  0.020  1.020
 QQN  C14  H20  single    0.970  0.020  1.090
 QQN  C14  H21  single    0.970  0.020  1.090
 QQN  C16  H22  single    0.930  0.020  1.080
 QQN  C18  H23  single    0.930  0.020  1.080
 QQN  C19  H24  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
 QQN  O10  C4   C3   106.56  3.000
 QQN  C3   C4   C5   125.26  3.000
 QQN  O10  C4   C5   128.18  3.000
 QQN  H1   C5   C6   122.23  3.000
 QQN  H1   C5   C4   122.63  3.000
 QQN  C6   C5   C4   115.14  3.000
 QQN  C1   C6   C7   120.66  3.000
 QQN  C1   C6   C5   121.40  3.000
 QQN  C7   C6   C5   117.71  3.000
 QQN  O8   C7   N9   122.64  3.000
 QQN  O8   C7   C6   119.10  3.000
 QQN  N9   C7   C6   118.25  3.000
 QQN  C11  N12  C3   103.48  3.000
 QQN  C16  C15  C14  120.72  3.000
 QQN  C14  C15  C20  119.90  3.000
 QQN  C16  C15  C20  119.36  3.000
 QQN  C18  C17  CL1  119.21  3.000
 QQN  C18  C17  C16  121.72  3.000
 QQN  CL1  C17  C16  119.07  3.000
 QQN  H2   C20  C19  119.77  3.000
 QQN  H2   C20  C15  119.74  3.000
 QQN  C19  C20  C15  120.48  3.000
 QQN  H4   C22  H3   107.38  3.000
 QQN  H4   C22  N9   109.17  3.000
 QQN  H3   C22  N9   109.61  3.000
 QQN  H4   C22  C23  110.03  3.000
 QQN  H3   C22  C23  110.60  3.000
 QQN  N9   C22  C23  110.00  3.000
 QQN  H5   C24  C23  108.05  3.000
 QQN  H5   C24  O27  110.37  3.000
 QQN  C23  C24  O27  107.71  3.000
 QQN  H5   C24  C25  107.26  3.000
 QQN  C23  C24  C25  110.52  3.000
 QQN  O27  C24  C25  112.84  3.000
 QQN  H7   C26  H6   106.31  3.000
 QQN  H7   C26  N9   110.73  3.000
 QQN  H6   C26  N9   108.30  3.000
 QQN  H7   C26  C25  110.67  3.000
 QQN  H6   C26  C25  109.27  3.000
 QQN  N9   C26  C25  111.39  3.000
 QQN  H11  C25  C28  108.86  3.000
 QQN  H11  C25  C26  108.29  3.000
 QQN  C28  C25  C26  110.14  3.000
 QQN  H11  C25  C24  107.84  3.000
 QQN  C26  C25  C24  108.86  3.000
 QQN  C28  C25  C24  112.73  3.000
 QQN  H12  O27  C24  108.82  3.000
 QQN  H14  C23  H13  107.37  3.000
 QQN  H14  C23  C24  110.04  3.000
 QQN  H13  C23  C24  109.69  3.000
 QQN  H14  C23  C22  108.91  3.000
 QQN  H13  C23  C22  109.31  3.000
 QQN  C24  C23  C22  111.43  3.000
 QQN  C26  N9   C22  112.87  3.000
 QQN  C26  N9   C7   125.95  3.000
 QQN  C22  N9   C7   120.74  3.000
 QQN  H15  C1   C2   119.71  3.000
 QQN  H15  C1   C6   118.40  3.000
 QQN  C2   C1   C6   121.87  3.000
 QQN  C3   C2   O29  117.23  3.000
 QQN  O29  C2   C1   125.60  3.000
 QQN  C3   C2   C1   117.17  3.000
 QQN  C30  O29  C2   118.08  3.000
 QQN  H18  C30  H17  108.87  3.000
 QQN  H18  C30  H16  108.85  3.000
 QQN  H17  C30  H16  108.71  3.000
 QQN  H18  C30  O29  112.03  3.000
 QQN  H17  C30  O29  111.72  3.000
 QQN  H16  C30  O29  106.56  3.000
 QQN  C2   C3   N12  131.13  3.000
 QQN  N12  C3   C4   109.74  3.000
 QQN  C2   C3   C4   119.14  3.000
 QQN  C11  O10  C4   104.66  3.000
 QQN  N13  C11  O10  116.63  3.000
 QQN  N13  C11  N12  127.81  3.000
 QQN  O10  C11  N12  115.56  3.000
 QQN  H19  N13  C14  119.30  3.000
 QQN  H19  N13  C11  116.52  3.000
 QQN  C14  N13  C11  123.87  3.000
 QQN  H21  C14  H20  106.29  3.000
 QQN  H21  C14  N13  106.25  3.000
 QQN  H20  C14  N13  110.52  3.000
 QQN  H21  C14  C15  109.53  3.000
 QQN  H20  C14  C15  109.57  3.000
 QQN  N13  C14  C15  114.33  3.000
 QQN  H22  C16  C17  119.98  3.000
 QQN  H22  C16  C15  120.59  3.000
 QQN  C17  C16  C15  119.43  3.000
 QQN  H23  C18  C19  120.78  3.000
 QQN  H23  C18  C17  120.76  3.000
 QQN  C19  C18  C17  118.46  3.000
 QQN  H24  C19  C18  119.41  3.000
 QQN  H24  C19  C20  120.04  3.000
 QQN  C18  C19  C20  120.54  3.000
 QQN  H10  C28  H9   107.99  3.000
 QQN  H10  C28  H8   106.83  3.000
 QQN  H9   C28  H8   107.61  3.000
 QQN  H10  C28  C25  111.98  3.000
 QQN  H9   C28  C25  111.35  3.000
 QQN  H8   C28  C25  110.86  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
 QQN  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 QQN  CONST_02  N12  C11  O10  C4      0.00   0.0  0
 QQN  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 QQN  CONST_04  C11  N12  C3   C4      0.00   0.0  0
 QQN  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 QQN  CONST_06  C11  O10  C4   C5    180.00   0.0  0
 QQN  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 QQN  CONST_08  N12  C3   C4   C5    180.00   0.0  0
 QQN  CONST_09  O10  C4   C5   C6    180.00   0.0  0
 QQN  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 QQN  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 QQN  CONST_12  O10  C4   C3   N12     0.00   0.0  0
 QQN  CONST_13  C1   C2   C3   N12   180.00   0.0  0
 QQN  CONST_14  C18  C17  C16  C15     0.00   0.0  0
 QQN  CONST_15  C18  C19  C20  C15     0.00   0.0  0
 QQN  CONST_16  C20  C19  C18  C17     0.00   0.0  0
 QQN  CONST_17  C20  C15  C16  C17     0.00   0.0  0
 QQN  CONST_18  O10  C4   C3   C2    180.00   0.0  0
 QQN  CONST_19  C11  N12  C3   C2    180.00   0.0  0
 QQN  CONST_20  C11  O10  C4   C3      0.00   0.0  0
 QQN  CONST_21  O10  C11  N12  C3      0.00   0.0  0
 QQN  CONST_22  C19  C18  C17  C16     0.00   0.0  0
 QQN  CONST_23  C19  C20  C15  C16     0.00   0.0  0
 QQN  CONST_24  C7   C6   C5   C4    180.00   0.0  0
 QQN  CONST_25  N13  C11  O10  C4    180.00   0.0  0
 QQN  CONST_26  O29  C2   C3   C4    180.00   0.0  0
 QQN  CONST_27  O29  C2   C1   C6    180.00   0.0  0
 QQN  CONST_28  C2   C1   C6   C7    180.00   0.0  0
 QQN  CONST_29  O29  C2   C3   N12     0.00   0.0  0
 QQN  CONST_30  CL1  C17  C16  C15   180.00   0.0  0
 QQN  CONST_31  C14  C15  C16  C17   180.00   0.0  0
 QQN  CONST_32  N13  C11  N12  C3    180.00   0.0  0
 QQN  CONST_33  C19  C20  C15  C14   180.00   0.0  0
 QQN  CONST_34  C19  C18  C17  CL1   180.00   0.0  0
 QQN  CONST_35  C22  N9   C7   C6    180.00   0.0  0
 QQN  CONST_37  H15  C1   C6   C5    180.00   0.0  0
 QQN  CONST_38  H24  C19  C20  C15   180.00   0.0  0
 QQN  CONST_39  H23  C18  C19  C20   180.00   0.0  0
 QQN  CONST_40  H22  C16  C15  C20   180.00   0.0  0
 QQN  CONST_41  H1   C5   C6   C1    180.00   0.0  0
 QQN  CONST_42  H2   C20  C15  C16   180.00   0.0  0
 QQN  CONST_43  O8   C7   N9   C22     0.00   0.0  0
 QQN  CONST_45  C14  N13  C11  N12   180.00   0.0  0
 QQN  CONST_46  C14  N13  C11  O10     0.00   0.0  0
 QQN  CONST_47  H19  N13  C11  N12     0.00   0.0  0
 QQN  Var_01    C25  C26  N9   C22    60.12  30.0  1
 QQN  Var_02    N9   C22  C23  C24    55.06  30.0  1
 QQN  Var_03    C23  C22  N9   C26   -58.07  30.0  1
 QQN  Var_04    N9   C7   C6   C5   -135.60  30.0  1
 QQN  Var_05    C11  N13  C14  C15    66.02  30.0  3
 QQN  Var_06    N13  C14  C15  C20  -144.82  30.0  2
 QQN  Var_07    C3   C2   O29  C30   176.69  30.0  1
 QQN  Var_08    H16  C30  O29  C2   -177.76  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
 QQN  chir_01  C24  O27  C23  C25  positiv
 QQN  chir_02  C25  C24  C28  C26  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
 QQN  plan-1  C15  0.020
 QQN  plan-1  C17  0.020
 QQN  plan-1  C20  0.020
 QQN  plan-1  C14  0.020
 QQN  plan-1  C16  0.020
 QQN  plan-1  CL1  0.020
 QQN  plan-1  C18  0.020
 QQN  plan-1  C19  0.020
 QQN  plan-1  H2   0.020
 QQN  plan-1  H22  0.020
 QQN  plan-1  H23  0.020
 QQN  plan-1  H24  0.020
 QQN  plan-2  C4   0.020
 QQN  plan-2  C5   0.020
 QQN  plan-2  C6   0.020
 QQN  plan-2  C7   0.020
 QQN  plan-2  N12  0.020
 QQN  plan-2  C1   0.020
 QQN  plan-2  C2   0.020
 QQN  plan-2  O29  0.020
 QQN  plan-2  C3   0.020
 QQN  plan-2  O10  0.020
 QQN  plan-2  C11  0.020
 QQN  plan-2  N13  0.020
 QQN  plan-2  H1   0.020
 QQN  plan-2  H15  0.020
 QQN  plan-3  C11  0.020
 QQN  plan-3  N13  0.020
 QQN  plan-3  C14  0.020
 QQN  plan-3  H19  0.020
 QQN  plan-4  C6   0.020
 QQN  plan-4  C7   0.020
 QQN  plan-4  C22  0.020
 QQN  plan-4  C26  0.020
 QQN  plan-4  N9   0.020
 QQN  plan-4  O8   0.020

