# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 04:16:06 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 7-(cyclopentylamino)-5-fluoro-2-{[(piperidin-4-yl)sulfanyl]methyl}quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(NC2CCCC2)cc3N=C(CSC4CCNCC4)NC(=O)c13
#
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
 XRM  XRM  7-(cyclopentylamino)-5-fluoro-2-{[(piperidin-4-yl)sulfanyl]methyl}quinazolin-4(3H)-one  ligand  51  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XRM
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
 XRM  C4   C  CR66  0  -0.360  -24.2596  -13.2411  11.5516
 XRM  C5   C  CR66  0   0.315  -23.5202  -14.4026  11.2324
 XRM  C6   C  CR16  0  -0.473  -23.5381  -14.9398   9.9502
 XRM  C7   C  CR6   0   0.547  -24.2209  -12.7129  12.8995
 XRM  C13  C  CH2   0  -0.442  -24.5034  -17.3115   7.5728
 XRM  C15  C  CH2   0  -0.445  -23.4169  -17.6166   5.4041
 XRM  C20  C  CH2   0  -0.406  -21.5796  -13.6784  17.3872
 XRM  C21  C  CH2   0  -0.291  -20.7459  -13.3602  18.6227
 XRM  C24  C  CH2   0  -0.415  -22.3371  -15.7686  18.5386
 XRM  C1   C  CR6   0   0.449  -24.2828  -14.3365   8.9318
 XRM  C2   C  CR16  0  -0.535  -25.0318  -13.1764   9.2448
 XRM  C3   C  CR6   0   0.572  -25.0064  -12.6703  10.5111
 XRM  N8   N  NR16  0  -0.689  -23.4188  -13.4647  13.7418
 XRM  C9   C  CR6   0   0.492  -22.7380  -14.5779  13.3689
 XRM  N10  N  N     0  -0.475  -22.7623  -15.0579  12.1788
 XRM  N11  N  NH1   0  -0.703  -24.3027  -14.8004   7.6640
 XRM  C12  C  CR15  0  -0.077  -23.7178  -16.0435   7.2275
 XRM  C14  C  CH2   0  -0.455  -23.8480  -18.3689   6.6863
 XRM  C16  C  CH2   0  -0.453  -23.6020  -16.1197   5.7053
 XRM  S18  S  S2    0  -0.002  -22.8853  -15.6521  15.8963
 XRM  C19  C  CH1   0  -0.388  -21.7594  -15.1843  17.2527
 XRM  N22  N  NH1   0  -0.592  -21.3823  -13.9174  19.8019
 XRM  C23  C  CH2   0  -0.291  -21.4733  -15.3632  19.7260
 XRM  F25  F  F     0  -0.295  -25.7357  -11.5791  10.7554
 XRM  O26  O  O     0  -0.447  -24.7969  -11.7288  13.3277
 XRM  H1   H  HCR6  0   0.270  -22.9602  -15.8358   9.7735
 XRM  H2   H  HCH2  0   0.222  -25.5508  -17.1632   7.2932
 XRM  H3   H  HCH2  0   0.241  -24.4766  -17.5619   8.6344
 XRM  H4   H  HCH2  0   0.233  -24.0148  -17.9160   4.5434
 XRM  H5   H  HCH2  0   0.232  -22.3795  -17.8411   5.1555
 XRM  H6   H  HCH2  0   0.309  -21.4656  -16.1457  13.9857
 XRM  H7   H  HCH2  0   0.312  -21.0894  -14.5817  14.7098
 XRM  H9   H  HCH2  0   0.226  -22.5607  -13.2043  17.4775
 XRM  H10  H  HCH2  0   0.191  -19.7231  -13.7441  18.4715
 XRM  H11  H  HCH2  0   0.237  -20.6642  -12.2780  18.7399
 XRM  H12  H  HCH2  0   0.230  -23.3550  -15.3959  18.6896
 XRM  H13  H  HCH2  0   0.246  -22.3902  -16.8570  18.4733
 XRM  H14  H  HCR6  0   0.284  -25.6258  -12.6865   8.4826
 XRM  H15  H  HNR6  0   0.421  -23.3836  -13.1760  14.7123
 XRM  H16  H  HNH1  0   0.390  -24.9717  -14.3790   7.0382
 XRM  H17  H  HCR5  0   0.242  -22.7119  -16.1246   7.6529
 XRM  H18  H  HCH2  0   0.235  -24.5153  -19.2046   6.4766
 XRM  H19  H  HCH2  0   0.229  -22.9733  -18.7832   7.1914
 XRM  H20  H  HCH2  0   0.246  -22.7924  -15.5008   5.3179
 XRM  H21  H  HCH2  0   0.230  -24.5320  -15.7546   5.2584
 XRM  H22  H  HCH1  0   0.272  -20.7908  -15.6557  17.0569
 XRM  H23  H  HNH1  0   0.352  -20.8578  -13.6538  20.6257
 XRM  H25  H  HCH2  0   0.238  -21.9195  -15.7419  20.6474
 XRM  H26  H  HCH2  0   0.192  -20.4866  -15.8441  19.6232
 XRM  C17  C  CH2   0  -0.660  -21.9039  -15.2484  14.4166
 XRM  H8   H  HCH2  0   0.241  -21.0908  -13.2613  16.5038

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
 XRM  C15  C16  single    1.538  0.020  1.538
 XRM  C15  C14  single    1.548  0.020  1.548
 XRM  C16  C12  single    1.528  0.020  1.528
 XRM  C14  C13  single    1.528  0.020  1.528
 XRM  C12  N11  single    1.441  0.020  1.441
 XRM  C12  C13  single    1.531  0.020  1.531
 XRM  N11  C1   single    1.350  0.020  1.350
 XRM  C2   C1   aromatic  1.416  0.020  1.416
 XRM  C2   C3   aromatic  1.364  0.020  1.364
 XRM  C1   C6   aromatic  1.398  0.020  1.398
 XRM  F25  C3   single    1.335  0.020  1.335
 XRM  C3   C4   aromatic  1.402  0.020  1.402
 XRM  C6   C5   aromatic  1.390  0.020  1.390
 XRM  C4   C5   aromatic  1.413  0.020  1.413
 XRM  C4   C7   single    1.448  0.020  1.448
 XRM  C5   N10  single    1.378  0.020  1.378
 XRM  O26  C7   double    1.218  0.020  1.218
 XRM  C7   N8   single    1.385  0.020  1.385
 XRM  N10  C9   double    1.283  0.020  1.283
 XRM  N8   C9   single    1.357  0.020  1.357
 XRM  C9   C17  single    1.498  0.020  1.498
 XRM  C17  S18  single    1.821  0.020  1.821
 XRM  S18  C19  single    1.824  0.020  1.824
 XRM  C19  C20  single    1.522  0.020  1.522
 XRM  C19  C24  single    1.526  0.020  1.526
 XRM  C20  C21  single    1.524  0.020  1.524
 XRM  C24  C23  single    1.523  0.020  1.523
 XRM  C21  N22  single    1.451  0.020  1.451
 XRM  C23  N22  single    1.451  0.020  1.451
 XRM  C6   H1   single    0.930  0.020  1.080
 XRM  C13  H2   single    0.970  0.020  1.090
 XRM  C13  H3   single    0.970  0.020  1.090
 XRM  C15  H4   single    0.970  0.020  1.090
 XRM  C15  H5   single    0.970  0.020  1.090
 XRM  C17  H6   single    0.970  0.020  1.090
 XRM  C17  H7   single    0.970  0.020  1.090
 XRM  C20  H8   single    0.970  0.020  1.090
 XRM  C20  H9   single    0.970  0.020  1.090
 XRM  C21  H10  single    0.970  0.020  1.090
 XRM  C21  H11  single    0.970  0.020  1.090
 XRM  C24  H12  single    0.970  0.020  1.090
 XRM  C24  H13  single    0.970  0.020  1.090
 XRM  C2   H14  single    0.930  0.020  1.080
 XRM  N8   H15  single    0.860  0.020  1.020
 XRM  N11  H16  single    0.860  0.020  1.020
 XRM  C12  H17  single    0.970  0.020  1.090
 XRM  C14  H18  single    0.970  0.020  1.090
 XRM  C14  H19  single    0.970  0.020  1.090
 XRM  C16  H20  single    0.970  0.020  1.090
 XRM  C16  H21  single    0.970  0.020  1.090
 XRM  C19  H22  single    0.970  0.020  1.090
 XRM  N22  H23  single    0.890  0.020  1.040
 XRM  C23  H25  single    0.970  0.020  1.090
 XRM  C23  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
 XRM  C3   C4   C7   123.81  3.000
 XRM  C7   C4   C5   119.73  3.000
 XRM  C3   C4   C5   116.45  3.000
 XRM  N10  C5   C6   117.18  3.000
 XRM  N10  C5   C4   121.55  3.000
 XRM  C6   C5   C4   121.27  3.000
 XRM  H1   C6   C1   121.56  3.000
 XRM  H1   C6   C5   117.66  3.000
 XRM  C1   C6   C5   120.78  3.000
 XRM  O26  C7   N8   119.91  3.000
 XRM  N8   C7   C4   112.56  3.000
 XRM  O26  C7   C4   127.53  3.000
 XRM  H3   C13  H2   107.66  3.000
 XRM  H3   C13  C14  113.28  3.000
 XRM  H2   C13  C14  110.88  3.000
 XRM  H3   C13  C12  113.38  3.000
 XRM  H2   C13  C12  108.74  3.000
 XRM  C14  C13  C12  102.84  3.000
 XRM  H5   C15  H4   106.58  3.000
 XRM  H5   C15  C16  111.08  3.000
 XRM  H4   C15  C16  110.86  3.000
 XRM  H5   C15  C14  110.72  3.000
 XRM  H4   C15  C14  111.59  3.000
 XRM  C16  C15  C14  106.10  3.000
 XRM  H9   C20  H8   107.62  3.000
 XRM  H9   C20  C19  109.29  3.000
 XRM  H8   C20  C19  111.04  3.000
 XRM  H9   C20  C21  109.47  3.000
 XRM  H8   C20  C21  109.33  3.000
 XRM  C19  C20  C21  110.04  3.000
 XRM  H11  C21  H10  106.89  3.000
 XRM  H11  C21  N22  109.04  3.000
 XRM  H10  C21  N22  112.61  3.000
 XRM  H11  C21  C20  109.57  3.000
 XRM  H10  C21  C20  108.87  3.000
 XRM  N22  C21  C20  109.79  3.000
 XRM  H13  C24  H12  107.61  3.000
 XRM  H13  C24  C23  109.85  3.000
 XRM  H12  C24  C23  109.22  3.000
 XRM  H13  C24  C19  110.47  3.000
 XRM  H12  C24  C19  109.75  3.000
 XRM  C23  C24  C19  109.89  3.000
 XRM  N11  C1   C2   118.77  3.000
 XRM  C2   C1   C6   118.31  3.000
 XRM  N11  C1   C6   122.92  3.000
 XRM  H14  C2   C3   119.71  3.000
 XRM  H14  C2   C1   120.34  3.000
 XRM  C3   C2   C1   119.96  3.000
 XRM  F25  C3   C2   117.58  3.000
 XRM  F25  C3   C4   119.20  3.000
 XRM  C2   C3   C4   123.22  3.000
 XRM  H15  N8   C9   118.65  3.000
 XRM  H15  N8   C7   116.62  3.000
 XRM  C9   N8   C7   124.66  3.000
 XRM  N10  C9   N8   123.50  3.000
 XRM  N8   C9   C17  117.03  3.000
 XRM  N10  C9   C17  119.46  3.000
 XRM  C9   N10  C5   118.00  3.000
 XRM  H16  N11  C12  116.21  3.000
 XRM  H16  N11  C1   116.67  3.000
 XRM  C12  N11  C1   125.07  3.000
 XRM  H17  C12  C16  108.28  3.000
 XRM  H17  C12  N11  108.60  3.000
 XRM  C16  C12  N11  112.04  3.000
 XRM  H17  C12  C13  108.80  3.000
 XRM  N11  C12  C13  115.96  3.000
 XRM  C16  C12  C13  102.84  3.000
 XRM  H19  C14  H18  106.77  3.000
 XRM  H19  C14  C15  110.16  3.000
 XRM  H18  C14  C15  112.57  3.000
 XRM  H19  C14  C13  109.75  3.000
 XRM  H18  C14  C13  112.31  3.000
 XRM  C15  C14  C13  105.30  3.000
 XRM  H21  C16  H20  107.25  3.000
 XRM  H21  C16  C12  109.00  3.000
 XRM  H20  C16  C12  112.45  3.000
 XRM  H21  C16  C15  110.30  3.000
 XRM  H20  C16  C15  113.17  3.000
 XRM  C12  C16  C15  104.64  3.000
 XRM  C19  S18  C17  102.40  3.000
 XRM  H22  C19  S18  107.62  3.000
 XRM  H22  C19  C24  108.71  3.000
 XRM  S18  C19  C24  107.14  3.000
 XRM  H22  C19  C20  109.71  3.000
 XRM  C24  C19  C20  110.43  3.000
 XRM  S18  C19  C20  113.09  3.000
 XRM  H23  N22  C23  109.56  3.000
 XRM  H23  N22  C21  109.53  3.000
 XRM  C23  N22  C21  111.58  3.000
 XRM  H26  C23  H25  107.05  3.000
 XRM  H26  C23  N22  112.55  3.000
 XRM  H25  C23  N22  109.11  3.000
 XRM  H26  C23  C24  108.58  3.000
 XRM  H25  C23  C24  109.51  3.000
 XRM  N22  C23  C24  109.98  3.000
 XRM  H7   C17  H6   108.01  3.000
 XRM  H7   C17  S18  108.60  3.000
 XRM  H6   C17  S18  110.87  3.000
 XRM  H7   C17  C9   109.26  3.000
 XRM  H6   C17  C9   108.46  3.000
 XRM  S18  C17  C9   111.56  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
 XRM  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 XRM  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 XRM  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 XRM  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 XRM  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 XRM  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 XRM  CONST_07  C9   N8   C7   C4     0.00   0.0  0
 XRM  CONST_08  N8   C9   N10  C5     0.00   0.0  0
 XRM  CONST_09  N10  C9   N8   C7     0.00   0.0  0
 XRM  CONST_10  N11  C1   C6   C5   180.00   0.0  0
 XRM  CONST_11  F25  C3   C4   C5   180.00   0.0  0
 XRM  CONST_12  F25  C3   C4   C7     0.00   0.0  0
 XRM  CONST_13  F25  C3   C2   C1   180.00   0.0  0
 XRM  CONST_14  N11  C1   C2   C3   180.00   0.0  0
 XRM  CONST_15  C12  N11  C1   C6     0.00   0.0  0
 XRM  CONST_16  C12  N11  C1   C2   180.00   0.0  0
 XRM  CONST_17  C17  C9   N10  C5   180.00   0.0  0
 XRM  CONST_18  C17  C9   N8   C7   180.00   0.0  0
 XRM  CONST_19  O26  C7   N8   C9   180.00   0.0  0
 XRM  CONST_20  H14  C2   C3   C4   180.00   0.0  0
 XRM  CONST_21  H1   C6   C5   C4   180.00   0.0  0
 XRM  CONST_22  H15  N8   C7   C4   180.00   0.0  0
 XRM  CONST_23  H16  N11  C1   C6   180.00   0.0  0
 XRM  Var_01    C16  C15  C14  C13   10.21  30.0  1
 XRM  Var_02    C12  C13  C14  C15  -32.76  30.0  1
 XRM  Var_03    C23  N22  C21  C20   62.11  30.0  1
 XRM  Var_04    C24  C23  N22  C21  -62.16  30.0  1
 XRM  Var_05    C14  C15  C16  C12   16.38  30.0  1
 XRM  Var_06    N22  C21  C20  C19  -57.43  30.0  1
 XRM  Var_07    N22  C23  C24  C19   57.29  30.0  1
 XRM  Var_08    S18  C17  C9   N8    54.70  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
 XRM  chir_01  C12  C16  N11  C13  negativ
 XRM  chir_02  C19  S18  C20  C24  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
 XRM  plan-1  C1   0.020
 XRM  plan-1  N11  0.020
 XRM  plan-1  C12  0.020
 XRM  plan-1  H16  0.020
 XRM  plan-2  C4   0.020
 XRM  plan-2  C5   0.020
 XRM  plan-2  C6   0.020
 XRM  plan-2  C7   0.020
 XRM  plan-2  C1   0.020
 XRM  plan-2  C2   0.020
 XRM  plan-2  C3   0.020
 XRM  plan-2  N8   0.020
 XRM  plan-2  C9   0.020
 XRM  plan-2  N10  0.020
 XRM  plan-2  N11  0.020
 XRM  plan-2  F25  0.020
 XRM  plan-2  O26  0.020
 XRM  plan-2  H1   0.020
 XRM  plan-2  H14  0.020
 XRM  plan-2  H15  0.020
 XRM  plan-2  C17  0.020

