# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:42:21 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethoxy}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCCn1ccc2ncnc(Nc3cnc(Oc4cccc(c4)C(F)(F)F)c(Cl)c3)c12
#
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
 03Q  03Q  2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethoxy}ethanol  ligand  53  34  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_03Q
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
 03Q  O1    O   OH1   0  -0.671  -4.8135   4.3415  -0.8929
 03Q  C2    C   CH2   0  -0.185  -5.6623   3.7308  -1.8371
 03Q  C3    C   CH2   0  -0.165  -5.2509   2.2940  -2.0273
 03Q  O4    O   O2    0  -0.484  -5.4604   1.5746  -0.8345
 03Q  C5    C   CH2   0  -0.125  -5.0920   0.2286  -0.9398
 03Q  C6    C   CH2   0  -0.395  -5.3218  -0.4177   0.4196
 03Q  N7    N   NR5   0  -0.517  -4.9412  -1.8140   0.4176
 03Q  C8    C   CR15  0  -0.008  -5.8371  -2.8325   0.2884
 03Q  C9    C   CR15  0  -0.415  -5.1980  -4.0357   0.1755
 03Q  C10   C   CR56  0   0.181  -3.8110  -3.7473   0.2228
 03Q  N11   N   N     0  -0.443  -2.7564  -4.5783   0.1342
 03Q  C12   C   CR16  0   0.016  -1.5937  -3.9773   0.1944
 03Q  N13   N   N     0  -0.466  -1.3555  -2.6726   0.3502
 03Q  C14   C   CR6   0   0.514  -2.3738  -1.8359   0.4550
 03Q  N15   N   NH1   0  -0.787  -2.1145  -0.5036   0.6256
 03Q  C16   C   CR6   0   0.253  -0.8439   0.0754   0.6611
 03Q  C17   C   CR16  0  -0.066   0.1534  -0.2331  -0.2556
 03Q  N18   N   N     0  -0.436   1.3478   0.3437  -0.2292
 03Q  C19   C   CR6   0   0.565   1.6138   1.2554   0.6698
 03Q  O20   O   O2    0  -0.511   2.8225   1.8499   0.6964
 03Q  C21   C   CR6   0   0.380   3.7770   1.4330  -0.2013
 03Q  C22   C   CR16  0  -0.296   3.9322   2.1179  -1.3959
 03Q  C23   C   CR16  0  -0.241   4.9419   1.7367  -2.2643
 03Q  C24   C   CR16  0  -0.287   5.7841   0.6788  -1.9491
 03Q  C25   C   CR6   0  -0.192   5.6115   0.0036  -0.7491
 03Q  C26   C   CR16  0  -0.323   4.6039   0.3778   0.1337
 03Q  C27   C   CT    0   1.054   6.4961  -1.1410  -0.3629
 03Q  F28   F   F     0  -0.313   7.1585  -0.8905   0.7754
 03Q  F29   F   F     0  -0.313   5.7890  -2.2604  -0.1523
 03Q  F30   F   F     0  -0.300   7.4095  -1.4239  -1.2940
 03Q  C31   C   CR6   0  -0.185   0.6743   1.6577   1.6186
 03Q  CL32  CL  CL    0  -0.092   1.0671   2.8709   2.7731
 03Q  C33   C   CR16  0  -0.163  -0.5620   1.0499   1.6175
 03Q  C34   C   CR56  0   0.212  -3.6777  -2.3542   0.3747
 03Q  HO1   H   HOH1  0   0.456  -5.1060   5.2489  -0.7721
 03Q  H2    H   HCH2  0   0.203  -6.7144   3.7696  -1.5265
 03Q  H2A   H   HCH2  0   0.204  -5.6038   4.2185  -2.8184
 03Q  H3    H   HCH2  0   0.210  -5.8422   1.8703  -2.8501
 03Q  H3A   H   HCH2  0   0.208  -4.1958   2.2401  -2.3315
 03Q  H5    H   HCH2  0   0.218  -5.6886  -0.2974  -1.6981
 03Q  H5A   H   HCH2  0   0.207  -4.0390   0.1281  -1.2399
 03Q  H6    H   HCH2  0   0.269  -4.7921   0.1199   1.2081
 03Q  H6A   H   HCH2  0   0.292  -6.3788  -0.3678   0.6793
 03Q  H8    H   HCR5  0   0.298  -6.8945  -2.6181   0.2875
 03Q  H9    H   HCR5  0   0.259  -5.6617  -5.0028   0.0703
 03Q  H12   H   HCR6  0   0.246  -0.7117  -4.6044   0.1162
 03Q  HN15  H   HNH1  0   0.418  -2.8463   0.0569   1.0289
 03Q  H17   H   HCR6  0   0.284  -0.0106  -0.9650  -1.0336
 03Q  H22   H   HCR6  0   0.284   3.2756   2.9429  -1.6405
 03Q  H23   H   HCR6  0   0.278   5.0736   2.2653  -3.1983
 03Q  H24   H   HCR6  0   0.277   6.5626   0.3985  -2.6445
 03Q  H26   H   HCR6  0   0.290   4.4585  -0.1349   1.0768
 03Q  H33   H   HCR6  0   0.306  -1.3044   1.3281   2.3547

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
 03Q  O1    C2    single    1.409  0.020  1.409
 03Q  O1    HO1   single    0.850  0.020  0.980
 03Q  C2    C3    single    1.507  0.020  1.507
 03Q  C2    H2    single    0.970  0.020  1.090
 03Q  C2    H2A   single    0.970  0.020  1.090
 03Q  O4    C3    single    1.409  0.020  1.409
 03Q  C3    H3    single    0.970  0.020  1.090
 03Q  C3    H3A   single    0.970  0.020  1.090
 03Q  O4    C5    single    1.399  0.020  1.399
 03Q  C6    C5    single    1.523  0.020  1.523
 03Q  C5    H5    single    0.970  0.020  1.090
 03Q  C5    H5A   single    0.970  0.020  1.090
 03Q  C6    N7    single    1.447  0.020  1.447
 03Q  C6    H6    single    0.970  0.020  1.090
 03Q  C6    H6A   single    0.970  0.020  1.090
 03Q  C34   N7    aromatic  1.375  0.020  1.375
 03Q  N7    C8    aromatic  1.363  0.020  1.363
 03Q  C8    C9    aromatic  1.367  0.020  1.367
 03Q  C8    H8    single    0.930  0.020  1.080
 03Q  C10   C9    aromatic  1.417  0.020  1.417
 03Q  C9    H9    single    0.930  0.020  1.080
 03Q  C34   C10   aromatic  1.408  0.020  1.408
 03Q  N11   C10   aromatic  1.346  0.020  1.346
 03Q  C12   N11   aromatic  1.310  0.020  1.310
 03Q  N13   C12   aromatic  1.335  0.020  1.335
 03Q  C12   H12   single    0.930  0.020  1.080
 03Q  N13   C14   aromatic  1.322  0.020  1.322
 03Q  N15   C14   single    1.368  0.020  1.368
 03Q  C14   C34   aromatic  1.405  0.020  1.405
 03Q  C16   N15   single    1.397  0.020  1.397
 03Q  N15   HN15  single    0.890  0.020  1.040
 03Q  C33   C16   aromatic  1.394  0.020  1.394
 03Q  C16   C17   aromatic  1.389  0.020  1.389
 03Q  N18   C17   aromatic  1.327  0.020  1.327
 03Q  C17   H17   single    0.930  0.020  1.080
 03Q  C19   N18   aromatic  1.308  0.020  1.308
 03Q  O20   C19   single    1.347  0.020  1.347
 03Q  C31   C19   aromatic  1.395  0.020  1.395
 03Q  O20   C21   single    1.375  0.020  1.375
 03Q  C26   C21   aromatic  1.382  0.020  1.382
 03Q  C21   C22   aromatic  1.386  0.020  1.386
 03Q  C22   C23   aromatic  1.385  0.020  1.385
 03Q  C22   H22   single    0.930  0.020  1.080
 03Q  C24   C23   aromatic  1.388  0.020  1.388
 03Q  C23   H23   single    0.930  0.020  1.080
 03Q  C25   C24   aromatic  1.388  0.020  1.388
 03Q  C24   H24   single    0.930  0.020  1.080
 03Q  C27   C25   single    1.497  0.020  1.497
 03Q  C26   C25   aromatic  1.391  0.020  1.391
 03Q  C26   H26   single    0.930  0.020  1.080
 03Q  F29   C27   single    1.341  0.020  1.341
 03Q  F28   C27   single    1.341  0.020  1.341
 03Q  C27   F30   single    1.335  0.020  1.335
 03Q  CL32  C31   single    1.720  0.020  1.720
 03Q  C31   C33   aromatic  1.378  0.020  1.378
 03Q  C33   H33   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
 03Q  HO1   O1   C2    108.07  3.000
 03Q  H2A   C2   H2    106.76  3.000
 03Q  H2A   C2   C3    107.24  3.000
 03Q  H2    C2   C3    109.34  3.000
 03Q  H2A   C2   O1    111.99  3.000
 03Q  H2    C2   O1    111.87  3.000
 03Q  C3    C2   O1    109.48  3.000
 03Q  H3A   C3   H3    106.89  3.000
 03Q  H3A   C3   O4    110.61  3.000
 03Q  H3    C3   O4    110.94  3.000
 03Q  H3A   C3   C2    110.10  3.000
 03Q  H3    C3   C2    108.39  3.000
 03Q  O4    C3   C2    109.85  3.000
 03Q  C5    O4   C3    112.85  3.000
 03Q  H5A   C5   H5    106.73  3.000
 03Q  H5A   C5   C6    110.46  3.000
 03Q  H5    C5   C6    109.33  3.000
 03Q  H5A   C5   O4    111.14  3.000
 03Q  H5    C5   O4    111.67  3.000
 03Q  C6    C5   O4    107.54  3.000
 03Q  H6A   C6   H6    106.02  3.000
 03Q  H6A   C6   N7    107.43  3.000
 03Q  H6    C6   N7    110.40  3.000
 03Q  H6A   C6   C5    109.87  3.000
 03Q  H6    C6   C5    111.26  3.000
 03Q  N7    C6   C5    111.63  3.000
 03Q  C34   N7   C8    107.91  3.000
 03Q  C8    N7   C6    123.26  3.000
 03Q  C34   N7   C6    128.38  3.000
 03Q  H8    C8   C9    129.28  3.000
 03Q  H8    C8   N7    119.73  3.000
 03Q  C9    C8   N7    111.00  3.000
 03Q  H9    C9   C10   127.37  3.000
 03Q  H9    C9   C8    126.63  3.000
 03Q  C10   C9   C8    106.00  3.000
 03Q  C34   C10  N11   122.96  3.000
 03Q  N11   C10  C9    129.72  3.000
 03Q  C34   C10  C9    107.31  3.000
 03Q  C12   N11  C10   114.16  3.000
 03Q  H12   C12  N13   115.35  3.000
 03Q  H12   C12  N11   116.94  3.000
 03Q  N13   C12  N11   127.72  3.000
 03Q  C14   N13  C12   119.35  3.000
 03Q  C34   C14  N15   122.84  3.000
 03Q  C34   C14  N13   118.46  3.000
 03Q  N15   C14  N13   118.70  3.000
 03Q  HN15  N15  C16   114.87  3.000
 03Q  HN15  N15  C14   117.04  3.000
 03Q  C16   N15  C14   125.41  3.000
 03Q  C33   C16  C17   117.56  3.000
 03Q  C17   C16  N15   122.97  3.000
 03Q  C33   C16  N15   119.42  3.000
 03Q  H17   C17  N18   116.45  3.000
 03Q  H17   C17  C16   121.10  3.000
 03Q  N18   C17  C16   122.45  3.000
 03Q  C19   N18  C17   120.00  3.000
 03Q  C31   C19  O20   117.63  3.000
 03Q  C31   C19  N18   122.13  3.000
 03Q  O20   C19  N18   120.25  3.000
 03Q  C21   O20  C19   118.43  3.000
 03Q  C26   C21  C22   121.29  3.000
 03Q  C22   C21  O20   119.39  3.000
 03Q  C26   C21  O20   119.25  3.000
 03Q  H22   C22  C23   120.68  3.000
 03Q  H22   C22  C21   120.24  3.000
 03Q  C23   C22  C21   119.08  3.000
 03Q  H23   C23  C24   119.64  3.000
 03Q  H23   C23  C22   119.73  3.000
 03Q  C24   C23  C22   120.63  3.000
 03Q  H24   C24  C25   121.32  3.000
 03Q  H24   C24  C23   119.24  3.000
 03Q  C25   C24  C23   119.44  3.000
 03Q  C27   C25  C26   118.03  3.000
 03Q  C26   C25  C24   120.54  3.000
 03Q  C27   C25  C24   121.44  3.000
 03Q  H26   C26  C25   121.50  3.000
 03Q  H26   C26  C21   119.49  3.000
 03Q  C25   C26  C21   119.02  3.000
 03Q  F30   C27  F29   107.07  3.000
 03Q  F30   C27  F28   107.09  3.000
 03Q  F29   C27  F28   106.45  3.000
 03Q  F30   C27  C25   112.73  3.000
 03Q  F28   C27  C25   111.60  3.000
 03Q  F29   C27  C25   111.55  3.000
 03Q  C33   C31  CL32  121.11  3.000
 03Q  C33   C31  C19   118.47  3.000
 03Q  CL32  C31  C19   120.41  3.000
 03Q  H33   C33  C31   120.09  3.000
 03Q  H33   C33  C16   120.54  3.000
 03Q  C31   C33  C16   119.37  3.000
 03Q  C14   C34  C10   117.32  3.000
 03Q  C14   C34  N7    134.90  3.000
 03Q  C10   C34  N7    107.77  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
 03Q  CONST_01  C9    C10  C34  N7      0.00   0.0  0
 03Q  CONST_02  N11   C10  C34  N7    180.00   0.0  0
 03Q  CONST_03  N13   C14  C34  N7    180.00   0.0  0
 03Q  CONST_04  C10   C9   C8   N7      0.00   0.0  0
 03Q  CONST_05  C10   C34  N7   C8      0.00   0.0  0
 03Q  CONST_06  C14   C34  N7   C8    180.00   0.0  0
 03Q  CONST_07  C34   C10  C9   C8      0.00   0.0  0
 03Q  CONST_08  N11   C10  C9   C8    180.00   0.0  0
 03Q  CONST_09  C34   N7   C8   C9      0.00   0.0  0
 03Q  CONST_10  C14   C34  C10  C9    180.00   0.0  0
 03Q  CONST_11  C12   N11  C10  C9    180.00   0.0  0
 03Q  CONST_12  N13   C14  C34  C10     0.00   0.0  0
 03Q  CONST_13  N13   C12  N11  C10     0.00   0.0  0
 03Q  CONST_14  C14   C34  C10  N11     0.00   0.0  0
 03Q  CONST_15  C14   N13  C12  N11     0.00   0.0  0
 03Q  CONST_16  C34   C10  N11  C12     0.00   0.0  0
 03Q  CONST_17  C34   C14  N13  C12     0.00   0.0  0
 03Q  CONST_18  C19   C31  C33  C16     0.00   0.0  0
 03Q  CONST_19  C19   N18  C17  C16     0.00   0.0  0
 03Q  CONST_20  C31   C33  C16  C17     0.00   0.0  0
 03Q  CONST_21  C31   C19  N18  C17     0.00   0.0  0
 03Q  CONST_22  C33   C16  C17  N18     0.00   0.0  0
 03Q  CONST_23  C33   C31  C19  N18     0.00   0.0  0
 03Q  CONST_24  C24   C25  C26  C21     0.00   0.0  0
 03Q  CONST_25  C24   C23  C22  C21     0.00   0.0  0
 03Q  CONST_26  C25   C26  C21  C22     0.00   0.0  0
 03Q  CONST_27  C25   C24  C23  C22     0.00   0.0  0
 03Q  CONST_28  C26   C21  C22  C23     0.00   0.0  0
 03Q  CONST_29  C26   C25  C24  C23     0.00   0.0  0
 03Q  CONST_30  C10   C34  N7   C6    180.00   0.0  0
 03Q  CONST_31  C14   C34  N7   C6      0.00   0.0  0
 03Q  CONST_32  C9    C8   N7   C6    180.00   0.0  0
 03Q  CONST_33  N15   C14  C34  N7      0.00   0.0  0
 03Q  CONST_34  N15   C14  C34  C10   180.00   0.0  0
 03Q  CONST_35  N15   C14  N13  C12   180.00   0.0  0
 03Q  CONST_36  C31   C33  C16  N15   180.00   0.0  0
 03Q  CONST_37  N18   C17  C16  N15   180.00   0.0  0
 03Q  CONST_38  CL32  C31  C33  C16   180.00   0.0  0
 03Q  CONST_39  O20   C19  N18  C17   180.00   0.0  0
 03Q  CONST_40  CL32  C31  C19  N18   180.00   0.0  0
 03Q  CONST_41  C33   C31  C19  O20   180.00   0.0  0
 03Q  CONST_42  C25   C26  C21  O20   180.00   0.0  0
 03Q  CONST_43  C23   C22  C21  O20   180.00   0.0  0
 03Q  CONST_44  C27   C25  C26  C21   180.00   0.0  0
 03Q  CONST_45  C27   C25  C24  C23   180.00   0.0  0
 03Q  CONST_46  H9    C9   C8   N7    180.00   0.0  0
 03Q  CONST_47  H8    C8   C9   C10   180.00   0.0  0
 03Q  CONST_48  H12   C12  N11  C10   180.00   0.0  0
 03Q  CONST_49  H33   C33  C16  C17   180.00   0.0  0
 03Q  CONST_50  H17   C17  N18  C19   180.00   0.0  0
 03Q  CONST_51  H23   C23  C22  C21   180.00   0.0  0
 03Q  CONST_52  H26   C26  C21  C22   180.00   0.0  0
 03Q  CONST_53  H24   C24  C23  C22   180.00   0.0  0
 03Q  CONST_54  H22   C22  C23  C24   180.00   0.0  0
 03Q  Var_01    C16   N15  C14  N13     2.04  30.0  1
 03Q  Var_02    C33   C16  N15  C14  -137.10  30.0  3
 03Q  Var_03    C26   C21  O20  C19   -87.91  30.0  2
 03Q  Var_04    C31   C19  O20  C21   177.75  30.0  2
 03Q  Var_05    C34   N7   C6   C5     71.71  30.0  2
 03Q  Var_06    F29   C27  C25  C24  -121.64  30.0  2
 03Q  Var_07    N7    C6   C5   O4   -178.83  30.0  2
 03Q  Var_08    O4    C3   C2   O1     65.36  30.0  3
 03Q  Var_09    C6    C5   O4   C3    178.10  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
 03Q  plan-1  O20   0.020
 03Q  plan-1  C21   0.020
 03Q  plan-1  C22   0.020
 03Q  plan-1  C23   0.020
 03Q  plan-1  C24   0.020
 03Q  plan-1  C25   0.020
 03Q  plan-1  C26   0.020
 03Q  plan-1  C27   0.020
 03Q  plan-1  H22   0.020
 03Q  plan-1  H23   0.020
 03Q  plan-1  H24   0.020
 03Q  plan-1  H26   0.020
 03Q  plan-2  N15   0.020
 03Q  plan-2  C16   0.020
 03Q  plan-2  C17   0.020
 03Q  plan-2  N18   0.020
 03Q  plan-2  C19   0.020
 03Q  plan-2  O20   0.020
 03Q  plan-2  C31   0.020
 03Q  plan-2  CL32  0.020
 03Q  plan-2  C33   0.020
 03Q  plan-2  H17   0.020
 03Q  plan-2  H33   0.020
 03Q  plan-3  C6    0.020
 03Q  plan-3  N7    0.020
 03Q  plan-3  C8    0.020
 03Q  plan-3  C9    0.020
 03Q  plan-3  C10   0.020
 03Q  plan-3  N11   0.020
 03Q  plan-3  C12   0.020
 03Q  plan-3  N13   0.020
 03Q  plan-3  C14   0.020
 03Q  plan-3  N15   0.020
 03Q  plan-3  C34   0.020
 03Q  plan-3  H8    0.020
 03Q  plan-3  H9    0.020
 03Q  plan-3  H12   0.020

