# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:34:27 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-{4-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl}propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCN(CC1)c2ncnc3c(F)c(c(Cl)cc23)c4c(C)ccc5[nH]ncc45
#
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
 8YD  8YD  1-{4-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl}propan-1-one  ligand  54  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8YD
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
 8YD  C10   C   CR16  0  -0.284  -6.0517  -1.1417  -1.3397
 8YD  C13   C   CH3   0  -0.740  -3.0842   0.5606  -3.0089
 8YD  C20   C   CR6   0   0.534   1.7530   1.6971   0.7869
 8YD  C22   C   C     0  -0.301   4.1058   1.4542   1.3340
 8YD  C26   C   CH2   0  -0.601   6.7734  -1.5999  -1.1812
 8YD  C02   C   CR6   0  -0.090  -1.0161  -0.6563  -0.1330
 8YD  C03   C   CR6   0  -0.174  -2.1029   0.2377  -0.2521
 8YD  C04   C   CR6   0   0.051  -3.4544  -0.2170  -0.6436
 8YD  C05   C   CR56  0  -0.070  -4.2842  -0.8145   0.3176
 8YD  C06   C   CR15  0  -0.162  -4.1711  -1.1279   1.6977
 8YD  N07   N   N     0  -0.223  -5.2642  -1.7064   2.1312
 8YD  N08   N   NR15  0  -0.546  -6.0966  -1.7899   1.0938
 8YD  C09   C   CR56  0   0.411  -5.5636  -1.2677  -0.0359
 8YD  C11   C   CR16  0  -0.309  -5.2163  -0.5519  -2.2584
 8YD  C12   C   CR6   0   0.048  -3.9193  -0.0824  -1.9382
 8YD  C14   C   CR6   0   0.526  -1.8637   1.5502   0.0470
 8YD  F15   F   F     0  -0.281  -2.8692   2.4210  -0.0104
 8YD  C16   C   CR66  0   0.080  -0.6004   2.0378   0.4402
 8YD  N17   N   N     0  -0.441  -0.4793   3.3231   0.8437
 8YD  C18   C   CR16  0   0.052   0.6995   3.6587   1.2846
 8YD  N19   N   N     0  -0.463   1.8176   2.9213   1.2655
 8YD  N21   N   NR6   0  -0.497   2.9014   0.9812   0.6683
 8YD  C23   C   C     0  -0.309   5.0062   0.2666   1.6388
 8YD  N24   N   NR6   0  -0.469   5.2968  -0.4945   0.4391
 8YD  C25   C   C     0   0.571   6.5722  -0.7716   0.0744
 8YD  C27   C   CH3   0  -0.649   8.2376  -1.8457  -1.5014
 8YD  O28   O   O     0  -0.500   7.5270  -0.3770   0.7291
 8YD  C29   C   C     0  -0.308   4.1069  -0.9302  -0.2634
 8YD  C30   C   C     0  -0.339   3.2190   0.2633  -0.5628
 8YD  C31   C   CR66  0  -0.019   0.4743   1.1292   0.4451
 8YD  C32   C   CR16  0  -0.264   0.2410  -0.2367   0.2068
 8YD  H101  H   HCR6  0   0.274  -7.0349  -1.4956  -1.6189
 8YD  H132  H   HCH3  0   0.252  -3.1475   1.6496  -2.9594
 8YD  H131  H   HCH3  0   0.244  -2.0304   0.2956  -2.9233
 8YD  H133  H   HCH3  0   0.253  -3.4208   0.2619  -4.0006
 8YD  H222  H   H     0   0.241   4.6378   2.1813   0.7094
 8YD  H221  H   H     0   0.271   3.8379   1.9457   2.2665
 8YD  H261  H   HCH2  0   0.268   6.2542  -2.5557  -1.0648
 8YD  H262  H   HCH2  0   0.266   6.2888  -1.1028  -2.0260
 8YD  H061  H   HCR5  0   0.264  -3.3433  -0.9471   2.3664
 8YD  H081  H   HNR5  0   0.418  -7.0037  -2.2102   1.2133
 8YD  H111  H   HCR6  0   0.256  -5.5606  -0.4443  -3.2798
 8YD  H181  H   HCR6  0   0.261   0.8080   4.6604   1.6864
 8YD  H232  H   H     0   0.273   5.9331   0.6201   2.0814
 8YD  H231  H   H     0   0.247   4.5108  -0.3828   2.3685
 8YD  H271  H   HCH3  0   0.227   8.7477  -2.3655  -0.6918
 8YD  H273  H   HCH3  0   0.231   8.3174  -2.4637  -2.3953
 8YD  H272  H   HCH3  0   0.227   8.7714  -0.9158  -1.6933
 8YD  H291  H   H     0   0.284   4.3617  -1.4198  -1.1984
 8YD  H292  H   H     0   0.253   3.5608  -1.6542   0.3513
 8YD  H301  H   H     0   0.285   2.3212  -0.0631  -1.0788
 8YD  H302  H   H     0   0.266   3.7471   0.9442  -1.2424
 8YD  H321  H   HCR6  0   0.303   1.0309  -0.9647   0.3214
 8YD  CL    CL  CL    0  -0.098  -1.2967  -2.3331  -0.4294

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
 8YD  F15  C14   single    1.331  0.020  1.331
 8YD  N17  C18   aromatic  1.303  0.020  1.303
 8YD  N17  C16   aromatic  1.353  0.020  1.353
 8YD  C18  N19   aromatic  1.340  0.020  1.340
 8YD  C14  C16   aromatic  1.410  0.020  1.410
 8YD  C14  C03   aromatic  1.367  0.020  1.367
 8YD  C16  C31   aromatic  1.407  0.020  1.407
 8YD  N19  C20   aromatic  1.316  0.020  1.316
 8YD  N08  N07   aromatic  1.333  0.020  1.333
 8YD  N08  C09   aromatic  1.354  0.020  1.354
 8YD  C10  C09   aromatic  1.398  0.020  1.398
 8YD  C10  C11   aromatic  1.375  0.020  1.375
 8YD  N07  C06   aromatic  1.310  0.020  1.310
 8YD  C09  C05   aromatic  1.403  0.020  1.403
 8YD  C11  C12   aromatic  1.416  0.020  1.416
 8YD  C06  C05   aromatic  1.420  0.020  1.420
 8YD  C05  C04   aromatic  1.403  0.020  1.403
 8YD  C12  C04   aromatic  1.382  0.020  1.382
 8YD  C12  C13   single    1.502  0.020  1.502
 8YD  C04  C03   single    1.479  0.020  1.479
 8YD  C03  C02   aromatic  1.412  0.020  1.412
 8YD  C20  C31   aromatic  1.440  0.020  1.440
 8YD  C20  N21   single    1.358  0.020  1.358
 8YD  C31  C32   aromatic  1.406  0.020  1.406
 8YD  C30  N21   single    1.460  0.020  1.460
 8YD  C30  C29   single    1.517  0.020  1.517
 8YD  C02  C32   aromatic  1.368  0.020  1.368
 8YD  C02  CL    single    1.726  0.020  1.726
 8YD  N21  C22   single    1.455  0.020  1.455
 8YD  C29  N24   single    1.449  0.020  1.449
 8YD  C22  C23   single    1.521  0.020  1.521
 8YD  C23  N24   single    1.450  0.020  1.450
 8YD  N24  C25   single    1.355  0.020  1.355
 8YD  C25  C26   single    1.518  0.020  1.518
 8YD  C25  O28   double    1.223  0.020  1.223
 8YD  C27  C26   single    1.519  0.020  1.519
 8YD  C10  H101  single    0.930  0.020  1.080
 8YD  C13  H132  single    0.970  0.020  1.090
 8YD  C13  H131  single    0.970  0.020  1.090
 8YD  C13  H133  single    0.970  0.020  1.090
 8YD  C22  H222  single    0.970  0.020  1.090
 8YD  C22  H221  single    0.970  0.020  1.090
 8YD  C26  H261  single    0.970  0.020  1.090
 8YD  C26  H262  single    0.970  0.020  1.090
 8YD  C06  H061  single    0.930  0.020  1.080
 8YD  N08  H081  single    0.860  0.020  1.020
 8YD  C11  H111  single    0.930  0.020  1.080
 8YD  C18  H181  single    0.930  0.020  1.080
 8YD  C23  H232  single    0.970  0.020  1.090
 8YD  C23  H231  single    0.970  0.020  1.090
 8YD  C27  H271  single    0.970  0.020  1.090
 8YD  C27  H273  single    0.970  0.020  1.090
 8YD  C27  H272  single    0.970  0.020  1.090
 8YD  C29  H291  single    0.970  0.020  1.090
 8YD  C29  H292  single    0.970  0.020  1.090
 8YD  C30  H301  single    0.970  0.020  1.090
 8YD  C30  H302  single    0.970  0.020  1.090
 8YD  C32  H321  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
 8YD  H101  C10  C11   121.35  3.000
 8YD  H101  C10  C09   121.92  3.000
 8YD  C11   C10  C09   116.73  3.000
 8YD  H133  C13  H131  107.68  3.000
 8YD  H133  C13  H132  107.27  3.000
 8YD  H131  C13  H132  107.15  3.000
 8YD  H133  C13  C12   111.08  3.000
 8YD  H131  C13  C12   112.17  3.000
 8YD  H132  C13  C12   111.24  3.000
 8YD  C31   C20  N21   121.47  3.000
 8YD  N21   C20  N19   118.72  3.000
 8YD  C31   C20  N19   119.78  3.000
 8YD  H221  C22  H222  107.95  3.000
 8YD  H221  C22  C23   109.08  3.000
 8YD  H222  C22  C23   110.17  3.000
 8YD  H221  C22  N21   109.59  3.000
 8YD  H222  C22  N21   110.89  3.000
 8YD  C23   C22  N21   109.14  3.000
 8YD  H262  C26  H261  105.61  3.000
 8YD  H262  C26  C27   109.75  3.000
 8YD  H261  C26  C27   109.79  3.000
 8YD  H262  C26  C25   109.41  3.000
 8YD  H261  C26  C25   109.02  3.000
 8YD  C27   C26  C25   112.99  3.000
 8YD  C32   C02  C03   122.27  3.000
 8YD  C32   C02  CL    119.34  3.000
 8YD  C03   C02  CL    118.39  3.000
 8YD  C14   C03  C04   120.87  3.000
 8YD  C04   C03  C02   122.08  3.000
 8YD  C14   C03  C02   117.04  3.000
 8YD  C12   C04  C05   118.95  3.000
 8YD  C12   C04  C03   121.71  3.000
 8YD  C05   C04  C03   119.34  3.000
 8YD  C09   C05  C06   104.26  3.000
 8YD  C06   C05  C04   135.46  3.000
 8YD  C09   C05  C04   120.28  3.000
 8YD  H061  C06  N07   120.58  3.000
 8YD  H061  C06  C05   128.77  3.000
 8YD  N07   C06  C05   110.65  3.000
 8YD  N08   N07  C06   106.92  3.000
 8YD  H081  N08  C09   127.93  3.000
 8YD  H081  N08  N07   119.77  3.000
 8YD  C09   N08  N07   112.30  3.000
 8YD  N08   C09  C05   105.87  3.000
 8YD  C05   C09  C10   121.63  3.000
 8YD  N08   C09  C10   132.50  3.000
 8YD  H111  C11  C12   118.12  3.000
 8YD  H111  C11  C10   118.66  3.000
 8YD  C12   C11  C10   123.21  3.000
 8YD  C11   C12  C04   119.19  3.000
 8YD  C04   C12  C13   121.48  3.000
 8YD  C11   C12  C13   119.33  3.000
 8YD  C16   C14  F15   117.55  3.000
 8YD  C16   C14  C03   123.35  3.000
 8YD  F15   C14  C03   119.09  3.000
 8YD  C31   C16  N17   122.96  3.000
 8YD  C31   C16  C14   117.51  3.000
 8YD  N17   C16  C14   119.47  3.000
 8YD  C18   N17  C16   115.27  3.000
 8YD  H181  C18  N19   115.48  3.000
 8YD  H181  C18  N17   116.99  3.000
 8YD  N19   C18  N17   127.50  3.000
 8YD  C18   N19  C20   118.44  3.000
 8YD  C30   N21  C22   111.44  3.000
 8YD  C22   N21  C20   119.24  3.000
 8YD  C30   N21  C20   121.11  3.000
 8YD  H231  C23  H232  107.91  3.000
 8YD  H231  C23  N24   109.31  3.000
 8YD  H232  C23  N24   109.68  3.000
 8YD  H231  C23  C22   109.19  3.000
 8YD  H232  C23  C22   109.43  3.000
 8YD  N24   C23  C22   111.26  3.000
 8YD  C29   N24  C25   125.52  3.000
 8YD  C25   N24  C23   121.24  3.000
 8YD  C29   N24  C23   113.22  3.000
 8YD  O28   C25  N24   121.64  3.000
 8YD  O28   C25  C26   121.03  3.000
 8YD  N24   C25  C26   117.33  3.000
 8YD  H272  C27  H273  107.68  3.000
 8YD  H272  C27  H271  108.00  3.000
 8YD  H273  C27  H271  107.74  3.000
 8YD  H272  C27  C26   111.81  3.000
 8YD  H273  C27  C26   109.60  3.000
 8YD  H271  C27  C26   111.84  3.000
 8YD  H292  C29  H291  107.59  3.000
 8YD  H292  C29  C30   109.81  3.000
 8YD  H291  C29  C30   108.79  3.000
 8YD  H292  C29  N24   109.64  3.000
 8YD  H291  C29  N24   111.12  3.000
 8YD  C30   C29  N24   109.85  3.000
 8YD  H302  C30  H301  106.86  3.000
 8YD  H302  C30  C29   109.19  3.000
 8YD  H301  C30  C29   109.95  3.000
 8YD  H302  C30  N21   108.77  3.000
 8YD  H301  C30  N21   111.63  3.000
 8YD  C29   C30  N21   110.35  3.000
 8YD  C32   C31  C16   119.99  3.000
 8YD  C32   C31  C20   124.79  3.000
 8YD  C16   C31  C20   115.10  3.000
 8YD  H321  C32  C31   121.02  3.000
 8YD  H321  C32  C02   119.44  3.000
 8YD  C31   C32  C02   119.50  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
 8YD  CONST_01  N07   N08  C09  C10   180.00   0.0  0
 8YD  CONST_02  C06   C05  C09  C10   180.00   0.0  0
 8YD  CONST_03  C04   C05  C09  C10     0.00   0.0  0
 8YD  CONST_04  C04   C12  C11  C10     0.00   0.0  0
 8YD  CONST_05  N17   C18  N19  C20     0.00   0.0  0
 8YD  CONST_06  N17   C16  C31  C20     0.00   0.0  0
 8YD  CONST_07  C14   C16  C31  C20   180.00   0.0  0
 8YD  CONST_08  C02   C32  C31  C20   180.00   0.0  0
 8YD  CONST_09  C16   C14  C03  C02     0.00   0.0  0
 8YD  CONST_12  C16   C31  C32  C02     0.00   0.0  0
 8YD  CONST_13  N17   C16  C14  C03   180.00   0.0  0
 8YD  CONST_14  C31   C16  C14  C03     0.00   0.0  0
 8YD  CONST_15  C09   C05  C04  C03   180.00   0.0  0
 8YD  CONST_16  C06   C05  C04  C03     0.00   0.0  0
 8YD  CONST_17  C11   C12  C04  C03   180.00   0.0  0
 8YD  CONST_18  C31   C32  C02  C03     0.00   0.0  0
 8YD  CONST_19  N08   C09  C05  C04   180.00   0.0  0
 8YD  CONST_20  N07   C06  C05  C04   180.00   0.0  0
 8YD  CONST_21  C16   C14  C03  C04   180.00   0.0  0
 8YD  CONST_22  C32   C02  C03  C04   180.00   0.0  0
 8YD  CONST_23  N07   N08  C09  C05     0.00   0.0  0
 8YD  CONST_24  C11   C10  C09  C05     0.00   0.0  0
 8YD  CONST_25  N08   N07  C06  C05     0.00   0.0  0
 8YD  CONST_26  C11   C12  C04  C05     0.00   0.0  0
 8YD  CONST_28  C09   N08  N07  C06     0.00   0.0  0
 8YD  CONST_29  N08   C09  C05  C06     0.00   0.0  0
 8YD  CONST_30  C12   C04  C05  C06   180.00   0.0  0
 8YD  CONST_31  C09   C05  C06  N07     0.00   0.0  0
 8YD  CONST_32  C11   C10  C09  N08   180.00   0.0  0
 8YD  CONST_33  C12   C11  C10  C09     0.00   0.0  0
 8YD  CONST_34  C12   C04  C05  C09     0.00   0.0  0
 8YD  CONST_36  C18   N17  C16  C14   180.00   0.0  0
 8YD  CONST_37  C32   C31  C16  C14     0.00   0.0  0
 8YD  CONST_38  C32   C02  C03  C14     0.00   0.0  0
 8YD  CONST_39  N19   C18  N17  C16     0.00   0.0  0
 8YD  CONST_40  N19   C20  C31  C16     0.00   0.0  0
 8YD  CONST_41  C32   C31  C16  N17   180.00   0.0  0
 8YD  CONST_42  C31   C16  N17  C18     0.00   0.0  0
 8YD  CONST_43  C31   C20  N19  C18     0.00   0.0  0
 8YD  CONST_44  C32   C31  C20  N19   180.00   0.0  0
 8YD  CONST_45  N21   C20  C31  C16   180.00   0.0  0
 8YD  CONST_46  N21   C20  N19  C18   180.00   0.0  0
 8YD  CONST_47  C32   C31  C20  N21     0.00   0.0  0
 8YD  CONST_48  C13   C12  C11  C10   180.00   0.0  0
 8YD  CONST_49  C05   C04  C12  C13   180.00   0.0  0
 8YD  CONST_50  C03   C04  C12  C13     0.00   0.0  0
 8YD  CONST_51  C14   C03  C02  CL    180.00   0.0  0
 8YD  CONST_52  C04   C03  C02  CL      0.00   0.0  0
 8YD  CONST_53  C31   C32  C02  CL    180.00   0.0  0
 8YD  CONST_54  F15   C14  C03  C02   180.00   0.0  0
 8YD  CONST_55  F15   C14  C03  C04     0.00   0.0  0
 8YD  CONST_56  N17   C16  C14  F15     0.00   0.0  0
 8YD  CONST_57  C31   C16  C14  F15   180.00   0.0  0
 8YD  CONST_58  H081  N08  C09  C10     0.00   0.0  0
 8YD  CONST_59  H181  C18  N19  C20   180.00   0.0  0
 8YD  CONST_60  H321  C32  C31  C20     0.00   0.0  0
 8YD  CONST_61  H061  C06  C05  C04     0.00   0.0  0
 8YD  CONST_62  H111  C11  C12  C04   180.00   0.0  0
 8YD  CONST_63  H101  C10  C09  C05   180.00   0.0  0
 8YD  CONST_64  C29   N24  C25  C26     0.00   0.0  0
 8YD  CONST_65  C23   N24  C25  C26   180.00   0.0  0
 8YD  CONST_66  O28   C25  N24  C23     0.00   0.0  0
 8YD  CONST_67  C29   N24  C25  O28   180.00   0.0  0
 8YD  Var_01    C29   C30  N21  C20  -152.54  30.0  1
 8YD  Var_02    C23   C22  N21  C20   152.95  30.0  1
 8YD  Var_03    N19   C20  N21  C22    13.52  30.0  1
 8YD  Var_04    C29   N24  C23  C22   -54.98  30.0  1
 8YD  Var_05    N24   C29  C30  N21   -55.77  30.0  1
 8YD  Var_06    N24   C23  C22  N21    55.24  30.0  1
 8YD  Var_07    C30   C29  N24  C23    54.60  30.0  1
 8YD  Var_08    H132  C13  C12  C04   -81.68  30.0  2
 8YD  Var_09    C27   C26  C25  N24   179.73  30.0  3
 8YD  Var_10    H271  C27  C26  C25    59.19  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
 8YD  plan-1  C10   0.020
 8YD  plan-1  C13   0.020
 8YD  plan-1  C03   0.020
 8YD  plan-1  C04   0.020
 8YD  plan-1  C05   0.020
 8YD  plan-1  C06   0.020
 8YD  plan-1  N07   0.020
 8YD  plan-1  N08   0.020
 8YD  plan-1  C09   0.020
 8YD  plan-1  C11   0.020
 8YD  plan-1  C12   0.020
 8YD  plan-1  H101  0.020
 8YD  plan-1  H061  0.020
 8YD  plan-1  H081  0.020
 8YD  plan-1  H111  0.020
 8YD  plan-2  C20   0.020
 8YD  plan-2  C02   0.020
 8YD  plan-2  C03   0.020
 8YD  plan-2  C04   0.020
 8YD  plan-2  C14   0.020
 8YD  plan-2  F15   0.020
 8YD  plan-2  C16   0.020
 8YD  plan-2  N17   0.020
 8YD  plan-2  C18   0.020
 8YD  plan-2  N19   0.020
 8YD  plan-2  N21   0.020
 8YD  plan-2  C31   0.020
 8YD  plan-2  C32   0.020
 8YD  plan-2  H181  0.020
 8YD  plan-2  H321  0.020
 8YD  plan-2  CL    0.020
 8YD  plan-3  C26   0.020
 8YD  plan-3  C23   0.020
 8YD  plan-3  N24   0.020
 8YD  plan-3  C25   0.020
 8YD  plan-3  O28   0.020
 8YD  plan-3  C29   0.020

