# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:07:17 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-[[2,4-bis(oxidanylidene)quinazolin-1-yl]methyl]-~{N}-[(3~{R})-1-(cyclopropylmethyl)pyrrolidin-3-yl]-2-fluoranyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CN2C(=O)NC(=O)c3ccccc23)cc1C(=O)N[C@@H]4CCN(CC5CC5)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
 4YR  4YR  5-[[2,4-bis(oxidanylidene)quinazolin-1-yl]methyl]-~{N}-[(3~{R})-1-(cyclopropylmethyl)pyrrolidin-3-yl]-2-fluoranyl-benzamide  ligand  57  32  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4YR
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
 4YR  C49  C  CH2   0  -0.481  -7.5721  -1.9595   0.0198
 4YR  C50  C  CH2   0  -0.498  -7.2515  -3.3227  -0.5118
 4YR  C48  C  CH1   0  -0.254  -6.4937  -2.1298  -1.0073
 4YR  C45  C  CH2   0  -0.269  -5.0441  -1.9776  -0.6321
 4YR  N27  N  NR5   0  -0.432  -4.5675  -0.6205  -0.7739
 4YR  C28  C  CH2   0  -0.271  -3.1444  -0.4832  -0.5617
 4YR  C26  C  CH2   0  -0.274  -5.1755   0.3442   0.1300
 4YR  C25  C  CH2   0  -0.470  -4.2647   1.5724   0.0361
 4YR  C24  C  CR15  0  -0.092  -2.9442   1.0308  -0.5570
 4YR  N22  N  NH1   0  -0.638  -1.7535   1.4106   0.1648
 4YR  C21  C  C     0   0.528  -0.9151   2.3841  -0.2251
 4YR  O23  O  O     0  -0.478  -1.0727   3.0684  -1.2239
 4YR  C19  C  CR6   0  -0.233   0.2837   2.5504   0.6565
 4YR  C18  C  CR16  0  -0.289   1.0343   1.4462   1.0546
 4YR  C14  C  CR6   0   0.532   0.7146   3.8065   1.0531
 4YR  F20  F  F     0  -0.297   0.0026   4.8859   0.7108
 4YR  C15  C  CR16  0  -0.395   1.8488   3.9798   1.8211
 4YR  C16  C  CR16  0  -0.275   2.5836   2.8660   2.1926
 4YR  C17  C  CR6   0   0.087   2.1850   1.5875   1.8160
 4YR  C13  C  CH2   0  -0.393   2.9913   0.3990   2.2785
 4YR  N7   N  NR6   0  -0.619   2.8189  -0.7831   1.4523
 4YR  C1   C  CR66  0   0.440   3.4269  -0.8505   0.2026
 4YR  C6   C  CR16  0  -0.317   4.1728   0.2195  -0.3004
 4YR  C5   C  CR16  0  -0.233   4.7746   0.1198  -1.5409
 4YR  C4   C  CR16  0  -0.261   4.6507  -1.0310  -2.3142
 4YR  C3   C  CR16  0  -0.275   3.9090  -2.0861  -1.8275
 4YR  C2   C  CR66  0  -0.142   3.2961  -2.0043  -0.5781
 4YR  C8   C  CR6   0   0.568   2.5060  -3.1293  -0.0844
 4YR  O11  O  O     0  -0.436   2.3347  -4.1727  -0.6813
 4YR  N9   N  NR16  0  -0.732   1.9387  -2.9160   1.1472
 4YR  C10  C  CR6   0   0.708   2.0426  -1.8026   1.9462
 4YR  O12  O  O     0  -0.471   1.4728  -1.7481   3.0162
 4YR  H1   H  HCH2  0   0.247  -8.4994  -1.4919  -0.2859
 4YR  H2   H  HCH2  0   0.240  -7.2708  -1.7272   1.0345
 4YR  H3   H  HCH2  0   0.241  -6.7350  -4.0137   0.1445
 4YR  H4   H  HCH2  0   0.249  -7.9597  -3.7953  -1.1801
 4YR  H5   H  HCH1  0   0.250  -6.7324  -1.7953  -2.0120
 4YR  H6   H  HCH2  0   0.186  -4.8933  -2.3511   0.3979
 4YR  H7   H  HCH2  0   0.236  -4.4382  -2.6153  -1.2830
 4YR  H9   H  HCH2  0   0.195  -2.8242  -0.9101   0.4075
 4YR  H10  H  HCH2  0   0.248  -2.5694  -0.9812  -1.3450
 4YR  H11  H  HCH2  0   0.241  -6.2059   0.5581  -0.1539
 4YR  H12  H  HCH2  0   0.192  -5.1944  -0.0360   1.1652
 4YR  H13  H  HCH2  0   0.248  -4.6837   2.3442  -0.6088
 4YR  H14  H  HCH2  0   0.245  -4.1025   2.0223   1.0158
 4YR  H15  H  HCR5  0   0.271  -2.8256   1.3820  -1.5803
 4YR  H16  H  HNH1  0   0.403  -1.6130   0.9990   1.0750
 4YR  H17  H  HCR6  0   0.262   0.7181   0.4636   0.7269
 4YR  H18  H  HCR6  0   0.289   2.1553   4.9731   2.1209
 4YR  H19  H  HCR6  0   0.274   3.4806   3.0016   2.7843
 4YR  H20  H  HCH2  0   0.290   4.0523   0.6485   2.3219
 4YR  H21  H  HCH2  0   0.316   2.7038   0.1389   3.2949
 4YR  H22  H  HCR6  0   0.287   4.2882   1.1376   0.2557
 4YR  H23  H  HCR6  0   0.277   5.3489   0.9592  -1.9097
 4YR  H24  H  HCR6  0   0.269   5.1269  -1.0954  -3.2824
 4YR  H25  H  HCR6  0   0.273   3.7951  -2.9898  -2.4108
 4YR  H26  H  HNR6  0   0.430   1.3664  -3.6615   1.5242

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
 4YR  O11  C8   double    1.214  0.020  1.214
 4YR  N9   C8   single    1.373  0.020  1.373
 4YR  N9   C10  single    1.374  0.020  1.374
 4YR  C8   C2   single    1.461  0.020  1.461
 4YR  O12  C10  double    1.214  0.020  1.214
 4YR  C10  N7   single    1.373  0.020  1.373
 4YR  C2   C3   aromatic  1.394  0.020  1.394
 4YR  C2   C1   aromatic  1.399  0.020  1.399
 4YR  C3   C4   aromatic  1.378  0.020  1.378
 4YR  N7   C1   single    1.391  0.020  1.391
 4YR  N7   C13  single    1.453  0.020  1.453
 4YR  C1   C6   aromatic  1.398  0.020  1.398
 4YR  C4   C5   aromatic  1.392  0.020  1.392
 4YR  C13  C17  single    1.509  0.020  1.509
 4YR  C6   C5   aromatic  1.382  0.020  1.382
 4YR  C17  C18  aromatic  1.387  0.020  1.387
 4YR  C17  C16  aromatic  1.391  0.020  1.391
 4YR  C18  C19  aromatic  1.393  0.020  1.393
 4YR  C28  C24  single    1.527  0.020  1.527
 4YR  C28  N27  single    1.445  0.020  1.445
 4YR  C24  N22  single    1.443  0.020  1.443
 4YR  C24  C25  single    1.546  0.020  1.546
 4YR  C45  N27  single    1.445  0.020  1.445
 4YR  C45  C48  single    1.505  0.020  1.505
 4YR  N22  C21  single    1.343  0.020  1.343
 4YR  C16  C15  aromatic  1.385  0.020  1.385
 4YR  N27  C26  single    1.455  0.020  1.455
 4YR  C19  C21  single    1.497  0.020  1.497
 4YR  C19  C14  aromatic  1.386  0.020  1.386
 4YR  C21  O23  double    1.221  0.020  1.221
 4YR  C50  C48  single    1.498  0.020  1.498
 4YR  C50  C49  single    1.498  0.020  1.498
 4YR  C48  C49  single    1.499  0.020  1.499
 4YR  C15  C14  aromatic  1.381  0.020  1.381
 4YR  C25  C26  single    1.532  0.020  1.532
 4YR  C14  F20  single    1.338  0.020  1.338
 4YR  C49  H1   single    0.970  0.020  1.090
 4YR  C49  H2   single    0.970  0.020  1.090
 4YR  C50  H3   single    0.970  0.020  1.090
 4YR  C50  H4   single    0.970  0.020  1.090
 4YR  C48  H5   single    0.970  0.020  1.090
 4YR  C45  H6   single    0.970  0.020  1.090
 4YR  C45  H7   single    0.970  0.020  1.090
 4YR  C28  H9   single    0.970  0.020  1.090
 4YR  C28  H10  single    0.970  0.020  1.090
 4YR  C26  H11  single    0.970  0.020  1.090
 4YR  C26  H12  single    0.970  0.020  1.090
 4YR  C25  H13  single    0.970  0.020  1.090
 4YR  C25  H14  single    0.970  0.020  1.090
 4YR  C24  H15  single    0.970  0.020  1.090
 4YR  N22  H16  single    0.860  0.020  1.020
 4YR  C18  H17  single    0.930  0.020  1.080
 4YR  C15  H18  single    0.930  0.020  1.080
 4YR  C16  H19  single    0.930  0.020  1.080
 4YR  C13  H20  single    0.970  0.020  1.090
 4YR  C13  H21  single    0.970  0.020  1.090
 4YR  C6   H22  single    0.930  0.020  1.080
 4YR  C5   H23  single    0.930  0.020  1.080
 4YR  C4   H24  single    0.930  0.020  1.080
 4YR  C3   H25  single    0.930  0.020  1.080
 4YR  N9   H26  single    0.860  0.020  1.020

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
 4YR  H2   C49  H1   114.21  3.000
 4YR  H2   C49  C48  117.77  3.000
 4YR  H1   C49  C48  118.15  3.000
 4YR  H2   C49  C50  117.90  3.000
 4YR  H1   C49  C50  118.43  3.000
 4YR  C48  C49  C50   59.96  3.000
 4YR  H4   C50  H3   114.03  3.000
 4YR  H4   C50  C48  118.33  3.000
 4YR  H3   C50  C48  117.83  3.000
 4YR  H4   C50  C49  118.46  3.000
 4YR  H3   C50  C49  117.86  3.000
 4YR  C48  C50  C49   60.05  3.000
 4YR  H5   C48  C45  114.29  3.000
 4YR  H5   C48  C50  116.13  3.000
 4YR  C45  C48  C50  119.04  3.000
 4YR  H5   C48  C49  116.17  3.000
 4YR  C50  C48  C49   59.98  3.000
 4YR  C45  C48  C49  120.71  3.000
 4YR  H7   C45  H6   106.35  3.000
 4YR  H7   C45  N27  107.84  3.000
 4YR  H6   C45  N27  111.31  3.000
 4YR  H7   C45  C48  109.03  3.000
 4YR  H6   C45  C48  109.23  3.000
 4YR  N27  C45  C48  112.84  3.000
 4YR  C26  N27  C28  104.91  3.000
 4YR  C26  N27  C45  115.07  3.000
 4YR  C28  N27  C45  113.55  3.000
 4YR  H10  C28  H9   107.46  3.000
 4YR  H10  C28  C24  112.66  3.000
 4YR  H9   C28  C24  109.99  3.000
 4YR  H10  C28  N27  111.70  3.000
 4YR  H9   C28  N27  112.14  3.000
 4YR  C24  C28  N27  102.93  3.000
 4YR  H12  C26  H11  107.21  3.000
 4YR  H12  C26  C25  110.12  3.000
 4YR  H11  C26  C25  112.88  3.000
 4YR  H12  C26  N27  111.20  3.000
 4YR  H11  C26  N27  111.31  3.000
 4YR  C25  C26  N27  104.18  3.000
 4YR  H14  C25  H13  107.26  3.000
 4YR  H14  C25  C24  111.25  3.000
 4YR  H13  C25  C24  110.47  3.000
 4YR  H14  C25  C26  111.36  3.000
 4YR  H13  C25  C26  112.05  3.000
 4YR  C24  C25  C26  104.51  3.000
 4YR  H15  C24  N22  107.19  3.000
 4YR  H15  C24  C25  109.93  3.000
 4YR  N22  C24  C25  114.88  3.000
 4YR  H15  C24  C28  109.35  3.000
 4YR  C25  C24  C28  103.68  3.000
 4YR  N22  C24  C28  111.75  3.000
 4YR  H16  N22  C21  118.09  3.000
 4YR  H16  N22  C24  117.31  3.000
 4YR  C21  N22  C24  124.11  3.000
 4YR  C19  C21  O23  121.51  3.000
 4YR  O23  C21  N22  124.29  3.000
 4YR  C19  C21  N22  114.18  3.000
 4YR  C14  C19  C18  117.97  3.000
 4YR  C14  C19  C21  121.20  3.000
 4YR  C18  C19  C21  120.77  3.000
 4YR  H17  C18  C17  120.05  3.000
 4YR  H17  C18  C19  118.38  3.000
 4YR  C17  C18  C19  121.54  3.000
 4YR  C15  C14  F20  118.58  3.000
 4YR  F20  C14  C19  119.51  3.000
 4YR  C15  C14  C19  121.90  3.000
 4YR  H18  C15  C16  120.91  3.000
 4YR  H18  C15  C14  120.14  3.000
 4YR  C16  C15  C14  118.95  3.000
 4YR  H19  C16  C17  120.01  3.000
 4YR  H19  C16  C15  119.03  3.000
 4YR  C17  C16  C15  120.96  3.000
 4YR  C13  C17  C16  119.20  3.000
 4YR  C16  C17  C18  118.68  3.000
 4YR  C13  C17  C18  122.10  3.000
 4YR  H21  C13  H20  105.94  3.000
 4YR  H21  C13  N7   107.79  3.000
 4YR  H20  C13  N7   108.92  3.000
 4YR  H21  C13  C17  109.48  3.000
 4YR  H20  C13  C17  110.60  3.000
 4YR  N7   C13  C17  113.78  3.000
 4YR  C10  N7   C1   122.28  3.000
 4YR  C1   N7   C13  119.90  3.000
 4YR  C10  N7   C13  117.82  3.000
 4YR  C2   C1   C6   118.70  3.000
 4YR  C6   C1   N7   121.28  3.000
 4YR  C2   C1   N7   120.01  3.000
 4YR  H22  C6   C5   118.49  3.000
 4YR  H22  C6   C1   121.51  3.000
 4YR  C5   C6   C1   120.00  3.000
 4YR  H23  C5   C4   119.96  3.000
 4YR  H23  C5   C6   118.75  3.000
 4YR  C4   C5   C6   121.29  3.000
 4YR  H24  C4   C3   120.51  3.000
 4YR  H24  C4   C5   120.51  3.000
 4YR  C3   C4   C5   118.98  3.000
 4YR  H25  C3   C2   119.08  3.000
 4YR  H25  C3   C4   120.38  3.000
 4YR  C2   C3   C4   120.54  3.000
 4YR  C8   C2   C3   119.71  3.000
 4YR  C3   C2   C1   120.48  3.000
 4YR  C8   C2   C1   119.81  3.000
 4YR  N9   C8   O11  121.09  3.000
 4YR  N9   C8   C2   114.02  3.000
 4YR  O11  C8   C2   124.89  3.000
 4YR  H26  N9   C10  115.01  3.000
 4YR  H26  N9   C8   116.95  3.000
 4YR  C10  N9   C8   128.04  3.000
 4YR  O12  C10  N9   120.89  3.000
 4YR  O12  C10  N7   123.32  3.000
 4YR  N9   C10  N7   115.79  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
 4YR  CONST_01  C16  C17  C18  C19     0.00   0.0  0
 4YR  CONST_02  C16  C15  C14  C19     0.00   0.0  0
 4YR  CONST_03  C15  C16  C17  C18     0.00   0.0  0
 4YR  CONST_04  C15  C14  C19  C18     0.00   0.0  0
 4YR  CONST_05  C17  C18  C19  C14     0.00   0.0  0
 4YR  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 4YR  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 4YR  CONST_08  C4   C5   C6   C1      0.00   0.0  0
 4YR  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 4YR  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 4YR  CONST_11  C2   C3   C4   C5      0.00   0.0  0
 4YR  CONST_12  C2   C1   C6   C5      0.00   0.0  0
 4YR  CONST_13  C8   N9   C10  N7      0.00   0.0  0
 4YR  CONST_14  N9   C10  N7   C1      0.00   0.0  0
 4YR  CONST_15  C10  N9   C8   C2      0.00   0.0  0
 4YR  CONST_16  C17  C18  C19  C21   180.00   0.0  0
 4YR  CONST_17  C15  C14  C19  C21   180.00   0.0  0
 4YR  CONST_18  C13  C17  C18  C19   180.00   0.0  0
 4YR  CONST_19  F20  C14  C19  C18   180.00   0.0  0
 4YR  CONST_20  C16  C15  C14  F20   180.00   0.0  0
 4YR  CONST_21  C13  C17  C16  C15   180.00   0.0  0
 4YR  CONST_22  N9   C10  N7   C13   180.00   0.0  0
 4YR  CONST_23  O12  C10  N7   C1    180.00   0.0  0
 4YR  CONST_24  O12  C10  N9   C8    180.00   0.0  0
 4YR  CONST_25  C10  N9   C8   O11   180.00   0.0  0
 4YR  CONST_26  H18  C15  C14  C19   180.00   0.0  0
 4YR  CONST_27  H19  C16  C17  C18   180.00   0.0  0
 4YR  CONST_28  H17  C18  C19  C14   180.00   0.0  0
 4YR  CONST_29  H22  C6   C1   N7      0.00   0.0  0
 4YR  CONST_30  H25  C3   C2   C1    180.00   0.0  0
 4YR  CONST_31  H23  C5   C6   C1    180.00   0.0  0
 4YR  CONST_32  H24  C4   C5   C6    180.00   0.0  0
 4YR  CONST_33  H26  N9   C10  N7    180.00   0.0  0
 4YR  CONST_34  C19  C21  N22  C24   180.00   0.0  0
 4YR  CONST_35  O12  C10  N7   C13     0.00   0.0  0
 4YR  CONST_36  O23  C21  N22  C24     0.00   0.0  0
 4YR  CONST_37  H16  N22  C21  C19     0.00   0.0  0
 4YR  Var_01    C24  C25  C26  N27   -18.69  30.0  1
 4YR  Var_02    C25  C26  N27  C28    40.20  30.0  1
 4YR  Var_03    C24  C28  N27  C26   -45.35  30.0  1
 4YR  Var_04    C45  C48  C50  C49   110.72  30.0  1
 4YR  Var_05    N27  C45  C48  C49   -89.97  30.0  3
 4YR  Var_06    C28  N27  C45  C48  -173.51  30.0  3
 4YR  Var_07    N7   C13  C17  C18    24.05  30.0  2
 4YR  Var_08    C10  N7   C13  C17  -104.66  30.0  2
 4YR  Var_09    C18  C19  C21  N22    47.39  30.0  1

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
 4YR  chir_02  C24  C28  N22  C25  positiv
 4YR  chir_03  C48  C45  C50  C49  both

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
 4YR  plan-1  C24  0.020
 4YR  plan-1  N22  0.020
 4YR  plan-1  C21  0.020
 4YR  plan-1  O23  0.020
 4YR  plan-1  C19  0.020
 4YR  plan-1  H16  0.020
 4YR  plan-2  C21  0.020
 4YR  plan-2  C19  0.020
 4YR  plan-2  C18  0.020
 4YR  plan-2  C14  0.020
 4YR  plan-2  F20  0.020
 4YR  plan-2  C15  0.020
 4YR  plan-2  C16  0.020
 4YR  plan-2  C17  0.020
 4YR  plan-2  C13  0.020
 4YR  plan-2  H17  0.020
 4YR  plan-2  H18  0.020
 4YR  plan-2  H19  0.020
 4YR  plan-3  C13  0.020
 4YR  plan-3  N7   0.020
 4YR  plan-3  C1   0.020
 4YR  plan-3  C6   0.020
 4YR  plan-3  C5   0.020
 4YR  plan-3  C4   0.020
 4YR  plan-3  C3   0.020
 4YR  plan-3  C2   0.020
 4YR  plan-3  C8   0.020
 4YR  plan-3  O11  0.020
 4YR  plan-3  N9   0.020
 4YR  plan-3  C10  0.020
 4YR  plan-3  O12  0.020
 4YR  plan-3  H22  0.020
 4YR  plan-3  H23  0.020
 4YR  plan-3  H24  0.020
 4YR  plan-3  H25  0.020
 4YR  plan-3  H26  0.020

