# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:17:08 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-[(3S,4S)-3-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)quinazolin-2-yl]amino}oxan-4-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@H]1CCOC[C@H]1Nc2ncc3cc(ccc3n2)c4c(Cl)c(OC)cc(OC)c4Cl
#
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
 XL9  XL9  N-[(3S,4S)-3-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)quinazolin-2-yl]amino}oxan-4-yl]propanamide  ligand  60  34  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XL9
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
 XL9  C1   C   CR6   0   0.532   5.9625   1.1567   0.4721
 XL9  C2   C   CR6   0  -0.291   4.5727   1.1869   0.3438
 XL9  C3   C   CR6   0   0.243   3.8755   0.1211  -0.2133
 XL9  C4   C   CR6   0  -0.293   4.5930  -0.9854  -0.6524
 XL9  C5   C   CR6   0   0.531   5.9836  -1.0395  -0.5341
 XL9  C6   C   CR16  0  -0.573   6.6603   0.0371   0.0304
 XL9  O1   O   O2    0  -0.454   6.5394   2.2247   1.0281
 XL9  O2   O   O2    0  -0.454   6.5835  -2.1444  -0.9841
 XL9  C7   C   CH3   0  -0.444   7.9431   2.2212   1.2232
 XL9  C8   C   CH3   0  -0.444   7.9921  -2.2512  -0.8727
 XL9  C9   C   CR6   0   0.033   2.4006   0.1683  -0.3327
 XL9  C10  C   CR16  0  -0.314   1.6043  -0.5138   0.5485
 XL9  C11  C   CR66  0  -0.008   0.2050  -0.4520   0.4246
 XL9  C12  C   CR66  0   0.271  -0.4014   0.3056  -0.6020
 XL9  C13  C   CR16  0  -0.312   0.4392   0.9954  -1.5053
 XL9  C14  C   CR16  0  -0.247   1.7986   0.9255  -1.3645
 XL9  C15  C   CR16  0  -0.009  -0.6862  -1.1274   1.2862
 XL9  N1   N   N     0  -0.453  -1.9783  -1.0631   1.1634
 XL9  C16  C   CR6   0   0.587  -2.4624  -0.2913   0.1518
 XL9  N2   N   N     0  -0.505  -1.7395   0.3763  -0.7251
 XL9  N3   N   NH1   0  -0.667  -3.8038  -0.1973   0.0548
 XL9  C17  C   CH1   0  -0.093  -4.7501  -0.9406   0.8445
 XL9  C18  C   CH1   0  -0.136  -6.0435  -0.1397   1.0363
 XL9  C19  C   CH2   0  -0.454  -7.0557  -1.0170   1.7767
 XL9  C20  C   CH2   0  -0.195  -7.2202  -2.3637   1.0933
 XL9  O3   O   O2    0  -0.479  -5.9825  -3.0356   0.9728
 XL9  C21  C   CH2   0  -0.180  -5.0430  -2.3083   0.2197
 XL9  N4   N   NH1   0  -0.654  -6.5592   0.3272  -0.2359
 XL9  C22  C   C     0   0.561  -6.9843   1.5902  -0.4605
 XL9  C23  C   CH2   0  -0.576  -7.4953   1.8469  -1.8627
 XL9  C24  C   CH3   0  -0.661  -8.6051   2.8852  -1.9050
 XL9  O4   O   O     0  -0.493  -6.9326   2.4705   0.3845
 XL9  CL1  CL  CL    0  -0.102   3.7216   2.5772   0.9141
 XL9  CL2  CL  CL    0  -0.103   3.7769  -2.3253  -1.3748
 XL9  H1   H   HCR6  0   0.321   7.7361   0.0047   0.1249
 XL9  H2   H   HCH3  0   0.269   8.1848   3.1653   1.7033
 XL9  H3   H   HCH3  0   0.237   8.2580   1.4019   1.8737
 XL9  H4   H   HCH3  0   0.237   8.4854   2.1570   0.2770
 XL9  H5   H   HCH3  0   0.237   8.5040  -1.4682  -1.4368
 XL9  H6   H   HCH3  0   0.236   8.3190  -2.2145   0.1690
 XL9  H7   H   HCH3  0   0.269   8.2575  -3.2180  -1.2913
 XL9  H8   H   HCR6  0   0.264   2.0417  -1.1010   1.3475
 XL9  H9   H   HCR6  0   0.262  -0.0079   1.5745  -2.3029
 XL9  H10  H   HCR6  0   0.265   2.4338   1.4574  -2.0619
 XL9  H11  H   HCR6  0   0.278  -0.2944  -1.7379   2.0955
 XL9  H12  H   HNH1  0   0.390  -4.1516   0.3155  -0.7414
 XL9  H13  H   HCH1  0   0.274  -4.3220  -1.1043   1.8348
 XL9  H14  H   HCH1  0   0.280  -5.8190   0.7438   1.6328
 XL9  H15  H   HCH2  0   0.244  -6.7085  -1.1696   2.8021
 XL9  H16  H   HCH2  0   0.254  -8.0187  -0.5061   1.8356
 XL9  H17  H   HCH2  0   0.250  -7.8769  -3.0110   1.6757
 XL9  H18  H   HCH2  0   0.202  -7.6869  -2.2391   0.1045
 XL9  H19  H   HCH2  0   0.199  -5.3791  -2.1822  -0.8220
 XL9  H20  H   HCH2  0   0.249  -4.1256  -2.8989   0.1885
 XL9  H21  H   HNH1  0   0.400  -6.7412  -0.3535  -0.9571
 XL9  H22  H   HCH2  0   0.272  -6.6433   2.1916  -2.4575
 XL9  H23  H   HCH2  0   0.251  -7.8272   0.9152  -2.3256
 XL9  H24  H   HCH3  0   0.229  -9.4828   2.5539  -1.3496
 XL9  H25  H   HCH3  0   0.230  -8.2792   3.8346  -1.4839
 XL9  H26  H   HCH3  0   0.236  -8.9136   3.0653  -2.9340

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
 XL9  C24  C23  single    1.520  0.020  1.520
 XL9  C23  C22  single    1.514  0.020  1.514
 XL9  O4   C22  double    1.221  0.020  1.221
 XL9  C22  N4   single    1.351  0.020  1.351
 XL9  CL2  C4   single    1.727  0.020  1.727
 XL9  C8   O2   single    1.417  0.020  1.417
 XL9  N4   C18  single    1.450  0.020  1.450
 XL9  O2   C5   single    1.335  0.020  1.335
 XL9  C5   C4   aromatic  1.397  0.020  1.397
 XL9  C5   C6   aromatic  1.391  0.020  1.391
 XL9  C4   C3   aromatic  1.390  0.020  1.390
 XL9  C15  N1   aromatic  1.300  0.020  1.300
 XL9  C15  C11  aromatic  1.412  0.020  1.412
 XL9  C18  C17  single    1.533  0.020  1.533
 XL9  C18  C19  single    1.530  0.020  1.530
 XL9  N1   C16  aromatic  1.361  0.020  1.361
 XL9  C10  C11  aromatic  1.406  0.020  1.406
 XL9  C10  C9   aromatic  1.370  0.020  1.370
 XL9  C11  C12  aromatic  1.413  0.020  1.413
 XL9  C16  N3   single    1.348  0.020  1.348
 XL9  C16  N2   aromatic  1.318  0.020  1.318
 XL9  N3   C17  single    1.439  0.020  1.439
 XL9  C17  C21  single    1.532  0.020  1.532
 XL9  C6   C1   aromatic  1.391  0.020  1.391
 XL9  C3   C9   single    1.480  0.020  1.480
 XL9  C3   C2   aromatic  1.390  0.020  1.390
 XL9  C9   C14  aromatic  1.414  0.020  1.414
 XL9  C12  N2   aromatic  1.346  0.020  1.346
 XL9  C12  C13  aromatic  1.414  0.020  1.414
 XL9  C13  C14  aromatic  1.368  0.020  1.368
 XL9  C19  C20  single    1.519  0.020  1.519
 XL9  C1   C2   aromatic  1.396  0.020  1.396
 XL9  C1   O1   single    1.335  0.020  1.335
 XL9  C2   CL1  single    1.727  0.020  1.727
 XL9  C21  O3   single    1.407  0.020  1.407
 XL9  C7   O1   single    1.417  0.020  1.417
 XL9  C20  O3   single    1.413  0.020  1.413
 XL9  C6   H1   single    0.930  0.020  1.080
 XL9  C7   H2   single    0.970  0.020  1.090
 XL9  C7   H3   single    0.970  0.020  1.090
 XL9  C7   H4   single    0.970  0.020  1.090
 XL9  C8   H5   single    0.970  0.020  1.090
 XL9  C8   H6   single    0.970  0.020  1.090
 XL9  C8   H7   single    0.970  0.020  1.090
 XL9  C10  H8   single    0.930  0.020  1.080
 XL9  C13  H9   single    0.930  0.020  1.080
 XL9  C14  H10  single    0.930  0.020  1.080
 XL9  C15  H11  single    0.930  0.020  1.080
 XL9  N3   H12  single    0.860  0.020  1.020
 XL9  C17  H13  single    0.970  0.020  1.090
 XL9  C18  H14  single    0.970  0.020  1.090
 XL9  C19  H15  single    0.970  0.020  1.090
 XL9  C19  H16  single    0.970  0.020  1.090
 XL9  C20  H17  single    0.970  0.020  1.090
 XL9  C20  H18  single    0.970  0.020  1.090
 XL9  C21  H19  single    0.970  0.020  1.090
 XL9  C21  H20  single    0.970  0.020  1.090
 XL9  N4   H21  single    0.860  0.020  1.020
 XL9  C23  H22  single    0.970  0.020  1.090
 XL9  C23  H23  single    0.970  0.020  1.090
 XL9  C24  H24  single    0.970  0.020  1.090
 XL9  C24  H25  single    0.970  0.020  1.090
 XL9  C24  H26  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
 XL9  O1   C1   C6   124.01  3.000
 XL9  O1   C1   C2   116.82  3.000
 XL9  C6   C1   C2   119.18  3.000
 XL9  CL1  C2   C3   120.16  3.000
 XL9  CL1  C2   C1   118.53  3.000
 XL9  C3   C2   C1   121.31  3.000
 XL9  C9   C3   C4   120.94  3.000
 XL9  C9   C3   C2   120.50  3.000
 XL9  C4   C3   C2   118.56  3.000
 XL9  CL2  C4   C5   118.41  3.000
 XL9  C5   C4   C3   121.20  3.000
 XL9  CL2  C4   C3   120.38  3.000
 XL9  O2   C5   C6   123.95  3.000
 XL9  C6   C5   C4   119.25  3.000
 XL9  O2   C5   C4   116.79  3.000
 XL9  H1   C6   C5   119.78  3.000
 XL9  H1   C6   C1   119.72  3.000
 XL9  C5   C6   C1   120.51  3.000
 XL9  C7   O1   C1   118.90  3.000
 XL9  C8   O2   C5   118.85  3.000
 XL9  H4   C7   H3   109.18  3.000
 XL9  H4   C7   H2   108.87  3.000
 XL9  H3   C7   H2   108.93  3.000
 XL9  H4   C7   O1   111.88  3.000
 XL9  H3   C7   O1   111.68  3.000
 XL9  H2   C7   O1   106.21  3.000
 XL9  H7   C8   H6   108.92  3.000
 XL9  H7   C8   H5   108.94  3.000
 XL9  H6   C8   H5   109.15  3.000
 XL9  H7   C8   O2   106.24  3.000
 XL9  H6   C8   O2   111.71  3.000
 XL9  H5   C8   O2   111.78  3.000
 XL9  C14  C9   C10  119.24  3.000
 XL9  C14  C9   C3   120.00  3.000
 XL9  C10  C9   C3   120.76  3.000
 XL9  H8   C10  C11  119.37  3.000
 XL9  H8   C10  C9   120.63  3.000
 XL9  C11  C10  C9   120.00  3.000
 XL9  C15  C11  C12  115.41  3.000
 XL9  C12  C11  C10  120.99  3.000
 XL9  C15  C11  C10  123.60  3.000
 XL9  N2   C12  C13  120.48  3.000
 XL9  C13  C12  C11  118.08  3.000
 XL9  N2   C12  C11  121.43  3.000
 XL9  H9   C13  C14  120.89  3.000
 XL9  H9   C13  C12  119.10  3.000
 XL9  C14  C13  C12  120.00  3.000
 XL9  H10  C14  C13  119.43  3.000
 XL9  H10  C14  C9   118.88  3.000
 XL9  C13  C14  C9   121.69  3.000
 XL9  H11  C15  N1   117.17  3.000
 XL9  H11  C15  C11  119.72  3.000
 XL9  N1   C15  C11  123.11  3.000
 XL9  C16  N1   C15  116.86  3.000
 XL9  N3   C16  N2   117.55  3.000
 XL9  N2   C16  N1   125.91  3.000
 XL9  N3   C16  N1   116.54  3.000
 XL9  C16  N2   C12  117.26  3.000
 XL9  H12  N3   C17  117.95  3.000
 XL9  H12  N3   C16  115.80  3.000
 XL9  C17  N3   C16  125.36  3.000
 XL9  H13  C17  C21  108.13  3.000
 XL9  H13  C17  C18  107.21  3.000
 XL9  C21  C17  C18  110.86  3.000
 XL9  H13  C17  N3   108.51  3.000
 XL9  C21  C17  N3   111.29  3.000
 XL9  C18  C17  N3   110.70  3.000
 XL9  H14  C18  N4   107.01  3.000
 XL9  H14  C18  C19  109.65  3.000
 XL9  N4   C18  C19  111.96  3.000
 XL9  H14  C18  C17  108.55  3.000
 XL9  C19  C18  C17  108.60  3.000
 XL9  N4   C18  C17  111.00  3.000
 XL9  H16  C19  H15  107.15  3.000
 XL9  H16  C19  C20  110.09  3.000
 XL9  H15  C19  C20  109.43  3.000
 XL9  H16  C19  C18  109.95  3.000
 XL9  H15  C19  C18  108.89  3.000
 XL9  C20  C19  C18  111.23  3.000
 XL9  H18  C20  H17  106.95  3.000
 XL9  H18  C20  O3   110.40  3.000
 XL9  H17  C20  O3   106.90  3.000
 XL9  H18  C20  C19  110.47  3.000
 XL9  H17  C20  C19  110.56  3.000
 XL9  O3   C20  C19  111.41  3.000
 XL9  C21  O3   C20  112.62  3.000
 XL9  H20  C21  H19  106.93  3.000
 XL9  H20  C21  O3   107.27  3.000
 XL9  H19  C21  O3   111.20  3.000
 XL9  H20  C21  C17  109.52  3.000
 XL9  H19  C21  C17  109.98  3.000
 XL9  O3   C21  C17  111.78  3.000
 XL9  H21  N4   C22  117.08  3.000
 XL9  H21  N4   C18  118.32  3.000
 XL9  C22  N4   C18  123.96  3.000
 XL9  O4   C22  C23  122.19  3.000
 XL9  O4   C22  N4   123.05  3.000
 XL9  C23  C22  N4   114.73  3.000
 XL9  H23  C23  H22  105.96  3.000
 XL9  H23  C23  C24  110.43  3.000
 XL9  H22  C23  C24  109.75  3.000
 XL9  H23  C23  C22  110.51  3.000
 XL9  H22  C23  C22  107.08  3.000
 XL9  C24  C23  C22  112.82  3.000
 XL9  H26  C24  H25  107.83  3.000
 XL9  H26  C24  H24  107.66  3.000
 XL9  H25  C24  H24  108.00  3.000
 XL9  H26  C24  C23  110.24  3.000
 XL9  H25  C24  C23  111.49  3.000
 XL9  H24  C24  C23  111.46  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
 XL9  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 XL9  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 XL9  CONST_03  C9   C3   C2   C1    180.00   0.0  0
 XL9  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 XL9  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 XL9  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 XL9  CONST_09  C11  C10  C9   C3    180.00   0.0  0
 XL9  CONST_10  C13  C14  C9   C3    180.00   0.0  0
 XL9  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 XL9  CONST_14  C9   C3   C4   C5    180.00   0.0  0
 XL9  CONST_15  C15  C11  C10  C9    180.00   0.0  0
 XL9  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 XL9  CONST_17  C12  C13  C14  C9      0.00   0.0  0
 XL9  CONST_18  N1   C15  C11  C10   180.00   0.0  0
 XL9  CONST_19  N2   C12  C11  C10   180.00   0.0  0
 XL9  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 XL9  CONST_21  C13  C14  C9   C10     0.00   0.0  0
 XL9  CONST_22  C16  N1   C15  C11     0.00   0.0  0
 XL9  CONST_23  C14  C9   C10  C11     0.00   0.0  0
 XL9  CONST_24  C16  N2   C12  C11     0.00   0.0  0
 XL9  CONST_25  C14  C13  C12  C11     0.00   0.0  0
 XL9  CONST_26  N1   C15  C11  C12     0.00   0.0  0
 XL9  CONST_27  N1   C16  N2   C12     0.00   0.0  0
 XL9  CONST_28  C15  C11  C12  C13   180.00   0.0  0
 XL9  CONST_29  C16  N2   C12  C13   180.00   0.0  0
 XL9  CONST_30  N2   C12  C13  C14   180.00   0.0  0
 XL9  CONST_31  N2   C16  N1   C15     0.00   0.0  0
 XL9  CONST_32  N2   C12  C11  C15     0.00   0.0  0
 XL9  CONST_33  O2   C5   C6   C1    180.00   0.0  0
 XL9  CONST_34  CL2  C4   C3   C2    180.00   0.0  0
 XL9  CONST_35  O2   C5   C4   C3    180.00   0.0  0
 XL9  CONST_36  O1   C1   C2   C3    180.00   0.0  0
 XL9  CONST_37  CL1  C2   C3   C4    180.00   0.0  0
 XL9  CONST_38  O1   C1   C6   C5    180.00   0.0  0
 XL9  CONST_39  CL2  C4   C5   C6    180.00   0.0  0
 XL9  CONST_40  CL1  C2   C1   C6    180.00   0.0  0
 XL9  CONST_41  CL2  C4   C3   C9      0.00   0.0  0
 XL9  CONST_42  CL1  C2   C3   C9      0.00   0.0  0
 XL9  CONST_43  N3   C16  N2   C12   180.00   0.0  0
 XL9  CONST_44  N3   C16  N1   C15   180.00   0.0  0
 XL9  CONST_45  C17  N3   C16  N1      0.00   0.0  0
 XL9  CONST_46  C17  N3   C16  N2    180.00   0.0  0
 XL9  CONST_47  H1   C6   C1   C2    180.00   0.0  0
 XL9  CONST_48  H8   C10  C9   C3      0.00   0.0  0
 XL9  CONST_49  H10  C14  C9   C3      0.00   0.0  0
 XL9  CONST_50  H9   C13  C14  C9    180.00   0.0  0
 XL9  CONST_51  H11  C15  C11  C10     0.00   0.0  0
 XL9  CONST_52  H12  N3   C16  N1    180.00   0.0  0
 XL9  CONST_53  C23  C22  N4   C18   180.00   0.0  0
 XL9  CONST_54  O4   C22  N4   C18     0.00   0.0  0
 XL9  CONST_55  H21  N4   C22  C23     0.00   0.0  0
 XL9  Var_01    O3   C20  C19  C18    56.42  30.0  1
 XL9  Var_02    H19  C21  O3   C20   -63.80  30.0  1
 XL9  Var_03    H2   C7   O1   C1   -178.69  30.0  3
 XL9  Var_04    H5   C8   O2   C5    -61.54  30.0  3
 XL9  Var_05    C24  C23  C22  N4    148.03  30.0  1
 XL9  Var_06    H24  C24  C23  C22   -62.70  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
 XL9  chir_01  C17  C18  N3   C21  positiv
 XL9  chir_02  C18  N4   C19  C17  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
 XL9  plan-1  C1   0.020
 XL9  plan-1  C2   0.020
 XL9  plan-1  C3   0.020
 XL9  plan-1  C4   0.020
 XL9  plan-1  C5   0.020
 XL9  plan-1  C6   0.020
 XL9  plan-1  O1   0.020
 XL9  plan-1  O2   0.020
 XL9  plan-1  C9   0.020
 XL9  plan-1  CL1  0.020
 XL9  plan-1  CL2  0.020
 XL9  plan-1  H1   0.020
 XL9  plan-2  C3   0.020
 XL9  plan-2  C9   0.020
 XL9  plan-2  C10  0.020
 XL9  plan-2  C11  0.020
 XL9  plan-2  C12  0.020
 XL9  plan-2  C13  0.020
 XL9  plan-2  C14  0.020
 XL9  plan-2  C15  0.020
 XL9  plan-2  N1   0.020
 XL9  plan-2  C16  0.020
 XL9  plan-2  N2   0.020
 XL9  plan-2  N3   0.020
 XL9  plan-2  H8   0.020
 XL9  plan-2  H9   0.020
 XL9  plan-2  H10  0.020
 XL9  plan-2  H11  0.020
 XL9  plan-3  C16  0.020
 XL9  plan-3  N3   0.020
 XL9  plan-3  C17  0.020
 XL9  plan-3  H12  0.020
 XL9  plan-4  C18  0.020
 XL9  plan-4  N4   0.020
 XL9  plan-4  C22  0.020
 XL9  plan-4  C23  0.020
 XL9  plan-4  O4   0.020
 XL9  plan-4  H21  0.020

