# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 01:30:16 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 3-[2-oxidanylidene-3-[(2~{R},3~{R})-3-oxidanylpiperidin-2-yl]propyl]-5,6,7,8-tetrahydroquinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCN[C@@H]1CC(=O)CN2C=NC3=C(CCCC3)C2=O
#
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
 87C  87C  3-[2-oxidanylidene-3-[(2~{R},3~{R})-3-oxidanylpiperidin-2-yl]propyl]-5,6,7,8-tetrahydroquinazolin-4-one  ligand  45  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_87C
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
 87C  N10  N  N     0  -0.462  -3.4016   1.8108   0.7423
 87C  C11  C  CR6   0   0.245  -3.9392   0.5980   0.4083
 87C  C12  C  CR6   0  -0.143  -3.2528  -0.3414  -0.3022
 87C  C13  C  CH2   0  -0.480  -3.8210  -1.6894  -0.6401
 87C  C14  C  CH2   0  -0.449  -5.0639  -2.0107   0.1790
 87C  C15  C  CH2   0  -0.449  -6.0097  -0.8193   0.2108
 87C  C16  C  CH2   0  -0.503  -5.3394   0.3660   0.8900
 87C  C17  C  CR6   0   0.580  -1.9154  -0.0479  -0.7525
 87C  C09  C  CR16  0   0.159  -2.2029   2.0561   0.3476
 87C  N08  N  NR6   0  -0.492  -1.4485   1.2135  -0.3875
 87C  C07  C  CH2   0  -0.445  -0.0876   1.5593  -0.7221
 87C  C06  C  C     0   0.424   0.9087   0.9049   0.2180
 87C  O19  O  O     0  -0.385   0.5394   0.2333   1.1474
 87C  C05  C  CH2   0  -0.580   2.3504   1.2306  -0.0665
 87C  C04  C  CH1   0  -0.102   3.3241   0.1764   0.4365
 87C  C20  C  CH1   0   0.051   4.7690   0.6821   0.4501
 87C  O22  O  OH1   0  -0.678   5.0935   1.0927  -0.8637
 87C  C21  C  CH2   0  -0.483   5.6926  -0.4295   0.9458
 87C  C01  C  CH2   0  -0.436   5.5027  -1.7156   0.1477
 87C  C02  C  CH2   0  -0.313   4.0282  -2.1094   0.1281
 87C  N03  N  NH1   0  -0.576   3.1465  -1.0463  -0.3311
 87C  H1   H  HCH2  0   0.244  -4.0583  -1.7238  -1.7090
 87C  H2   H  HCH2  0   0.249  -3.0578  -2.4549  -0.4838
 87C  H3   H  HCH2  0   0.239  -5.5600  -2.8891  -0.2372
 87C  H4   H  HCH2  0   0.225  -4.7722  -2.2679   1.2019
 87C  H5   H  HCH2  0   0.227  -6.2914  -0.5472  -0.8109
 87C  H6   H  HCH2  0   0.241  -6.9339  -1.0704   0.7340
 87C  H7   H  HCH2  0   0.256  -5.3010   0.2070   1.9734
 87C  H8   H  HCH2  0   0.258  -5.9154   1.2828   0.7440
 87C  H9   H  HCR6  0   0.293  -1.7424   3.0055   0.5966
 87C  H10  H  HCH2  0   0.312   0.1328   1.2736  -1.7507
 87C  H11  H  HCH2  0   0.316   0.0355   2.6436  -0.6685
 87C  H12  H  HCH2  0   0.267   2.4830   1.4115  -1.1364
 87C  H13  H  HCH2  0   0.292   2.5489   2.1959   0.4161
 87C  H14  H  HCH1  0   0.238   3.0740  -0.0551   1.4781
 87C  H15  H  HCH1  0   0.208   4.8306   1.5311   1.1474
 87C  H16  H  HOH1  0   0.451   6.0182   1.3573  -0.8780
 87C  H17  H  HCH2  0   0.237   6.7342  -0.0951   0.9135
 87C  H18  H  HCH2  0   0.223   5.4639  -0.6167   2.0003
 87C  H19  H  HCH2  0   0.216   5.8586  -1.5790  -0.8777
 87C  H20  H  HCH2  0   0.227   6.1002  -2.5225   0.5797
 87C  H21  H  HCH2  0   0.234   3.8717  -2.9884  -0.5006
 87C  H22  H  HCH2  0   0.213   3.7176  -2.3866   1.1420
 87C  H23  H  HNH1  0   0.334   3.3465  -0.8545  -1.3070
 87C  O18  O  O     0  -0.482  -1.2071  -0.7982  -1.4086

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
 87C  C01  C21  single  1.525  0.020  1.525
 87C  C01  C02  single  1.526  0.020  1.526
 87C  C21  C20  single  1.528  0.020  1.528
 87C  C20  O22  single  1.414  0.020  1.414
 87C  C20  C04  single  1.531  0.020  1.531
 87C  C02  N03  single  1.455  0.020  1.455
 87C  C04  N03  single  1.455  0.020  1.455
 87C  C04  C05  single  1.521  0.020  1.521
 87C  C05  C06  single  1.505  0.020  1.505
 87C  C06  O19  double  1.205  0.020  1.205
 87C  C06  C07  single  1.518  0.020  1.518
 87C  C07  N08  single  1.443  0.020  1.443
 87C  N08  C09  single  1.349  0.020  1.349
 87C  N08  C17  single  1.394  0.020  1.394
 87C  O18  C17  double  1.223  0.020  1.223
 87C  C09  N10  double  1.286  0.020  1.286
 87C  C17  C12  single  1.441  0.020  1.441
 87C  N10  C11  single  1.368  0.020  1.368
 87C  C12  C11  double  1.363  0.020  1.363
 87C  C12  C13  single  1.501  0.020  1.501
 87C  C11  C16  single  1.499  0.020  1.499
 87C  C13  C14  single  1.523  0.020  1.523
 87C  C16  C15  single  1.522  0.020  1.522
 87C  C14  C15  single  1.521  0.020  1.521
 87C  C13  H1   single  0.970  0.020  1.090
 87C  C13  H2   single  0.970  0.020  1.090
 87C  C14  H3   single  0.970  0.020  1.090
 87C  C14  H4   single  0.970  0.020  1.090
 87C  C15  H5   single  0.970  0.020  1.090
 87C  C15  H6   single  0.970  0.020  1.090
 87C  C16  H7   single  0.970  0.020  1.090
 87C  C16  H8   single  0.970  0.020  1.090
 87C  C09  H9   single  0.930  0.020  1.080
 87C  C07  H10  single  0.970  0.020  1.090
 87C  C07  H11  single  0.970  0.020  1.090
 87C  C05  H12  single  0.970  0.020  1.090
 87C  C05  H13  single  0.970  0.020  1.090
 87C  C04  H14  single  0.970  0.020  1.090
 87C  C20  H15  single  0.970  0.020  1.090
 87C  O22  H16  single  0.850  0.020  0.980
 87C  C21  H17  single  0.970  0.020  1.090
 87C  C21  H18  single  0.970  0.020  1.090
 87C  C01  H19  single  0.970  0.020  1.090
 87C  C01  H20  single  0.970  0.020  1.090
 87C  C02  H21  single  0.970  0.020  1.090
 87C  C02  H22  single  0.970  0.020  1.090
 87C  N03  H23  single  0.890  0.020  1.040

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
 87C  C09  N10  C11  117.43  3.000
 87C  C16  C11  C12  122.08  3.000
 87C  C16  C11  N10  115.21  3.000
 87C  C12  C11  N10  122.70  3.000
 87C  C17  C12  C13  117.63  3.000
 87C  C13  C12  C11  123.05  3.000
 87C  C17  C12  C11  119.32  3.000
 87C  H2   C13  H1   105.60  3.000
 87C  H2   C13  C14  110.21  3.000
 87C  H1   C13  C14  109.96  3.000
 87C  H2   C13  C12  109.43  3.000
 87C  H1   C13  C12  109.26  3.000
 87C  C14  C13  C12  112.17  3.000
 87C  H4   C14  H3   106.76  3.000
 87C  H4   C14  C15  109.27  3.000
 87C  H3   C14  C15  110.83  3.000
 87C  H4   C14  C13  109.56  3.000
 87C  H3   C14  C13  109.62  3.000
 87C  C15  C14  C13  110.70  3.000
 87C  H6   C15  H5   106.67  3.000
 87C  H6   C15  C16  109.77  3.000
 87C  H5   C15  C16  109.66  3.000
 87C  H6   C15  C14  110.88  3.000
 87C  H5   C15  C14  109.58  3.000
 87C  C16  C15  C14  110.21  3.000
 87C  H8   C16  H7   105.81  3.000
 87C  H8   C16  C15  111.21  3.000
 87C  H7   C16  C15  110.10  3.000
 87C  H8   C16  C11  108.64  3.000
 87C  H7   C16  C11  107.90  3.000
 87C  C15  C16  C11  112.87  3.000
 87C  N08  C17  O18  120.12  3.000
 87C  O18  C17  C12  125.46  3.000
 87C  N08  C17  C12  114.41  3.000
 87C  H9   C09  N08  115.76  3.000
 87C  H9   C09  N10  119.51  3.000
 87C  N08  C09  N10  124.72  3.000
 87C  C07  N08  C09  120.26  3.000
 87C  C09  N08  C17  121.38  3.000
 87C  C07  N08  C17  118.17  3.000
 87C  H11  C07  H10  106.48  3.000
 87C  H11  C07  C06  108.87  3.000
 87C  H10  C07  C06  109.80  3.000
 87C  H11  C07  N08  109.43  3.000
 87C  H10  C07  N08  110.27  3.000
 87C  C06  C07  N08  111.83  3.000
 87C  C05  C06  O19  124.06  3.000
 87C  O19  C06  C07  121.13  3.000
 87C  C05  C06  C07  114.72  3.000
 87C  H13  C05  H12  105.24  3.000
 87C  H13  C05  C04  110.40  3.000
 87C  H12  C05  C04  111.15  3.000
 87C  H13  C05  C06  106.29  3.000
 87C  H12  C05  C06  109.69  3.000
 87C  C04  C05  C06  113.63  3.000
 87C  H14  C04  N03  107.22  3.000
 87C  H14  C04  C20  106.06  3.000
 87C  N03  C04  C20  113.43  3.000
 87C  H14  C04  C05  108.34  3.000
 87C  N03  C04  C05  109.27  3.000
 87C  C20  C04  C05  112.23  3.000
 87C  H15  C20  C21  108.78  3.000
 87C  H15  C20  O22  110.60  3.000
 87C  C21  C20  O22  111.96  3.000
 87C  H15  C20  C04  108.26  3.000
 87C  O22  C20  C04  107.71  3.000
 87C  C21  C20  C04  109.46  3.000
 87C  H16  O22  C20  108.31  3.000
 87C  H18  C21  H17  106.22  3.000
 87C  H18  C21  C01  109.49  3.000
 87C  H17  C21  C01  111.14  3.000
 87C  H18  C21  C20  108.09  3.000
 87C  H17  C21  C20  110.09  3.000
 87C  C01  C21  C20  111.62  3.000
 87C  H20  C01  H19  106.55  3.000
 87C  H20  C01  C02  110.04  3.000
 87C  H19  C01  C02  109.54  3.000
 87C  H20  C01  C21  110.35  3.000
 87C  H19  C01  C21  110.16  3.000
 87C  C02  C01  C21  110.15  3.000
 87C  H22  C02  H21  106.76  3.000
 87C  H22  C02  N03  107.75  3.000
 87C  H21  C02  N03  108.64  3.000
 87C  H22  C02  C01  109.09  3.000
 87C  H21  C02  C01  110.70  3.000
 87C  N03  C02  C01  113.63  3.000
 87C  H23  N03  C02  108.79  3.000
 87C  H23  N03  C04  108.95  3.000
 87C  C02  N03  C04  111.94  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
 87C  CONST_01  C17  N08  C09  N10     0.00   0.0  0
 87C  CONST_02  N08  C09  N10  C11     0.00   0.0  0
 87C  CONST_03  C09  N08  C17  C12     0.00   0.0  0
 87C  CONST_04  C07  N08  C09  N10   180.00   0.0  0
 87C  CONST_05  C07  N08  C17  C12   180.00   0.0  0
 87C  CONST_06  C09  N08  C17  O18   180.00   0.0  0
 87C  CONST_07  H9   C09  N10  C11   180.00   0.0  0
 87C  CONST_08  C07  N08  C17  O18     0.00   0.0  0
 87C  Var_01    C15  C16  C11  N10   165.51  30.0  1
 87C  Var_02    C14  C13  C12  C11   -14.44  30.0  1
 87C  Var_03    C14  C15  C16  C11    46.01  30.0  1
 87C  Var_04    C15  C14  C13  C12    45.63  30.0  1
 87C  Var_05    C16  C15  C14  C13   -62.46  30.0  1
 87C  Var_06    C01  C02  N03  C04   -54.68  30.0  1
 87C  Var_07    C02  C01  C21  C20   -52.82  30.0  1
 87C  Var_08    N03  C02  C01  C21    53.34  30.0  1
 87C  Var_09    C06  C07  N08  C17   -77.03  30.0  2
 87C  Var_10    C05  C06  C07  N08  -179.57  30.0  1
 87C  Var_11    C04  C05  C06  C07  -155.33  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
 87C  chir_01  C04  C20  N03  C05  positiv
 87C  chir_02  C20  O22  C04  C21  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
 87C  plan-1  C07  0.020
 87C  plan-1  C06  0.020
 87C  plan-1  O19  0.020
 87C  plan-1  C05  0.020
 87C  plan-2  N10  0.020
 87C  plan-2  C11  0.020
 87C  plan-2  C12  0.020
 87C  plan-2  C13  0.020
 87C  plan-2  C16  0.020
 87C  plan-2  C17  0.020
 87C  plan-2  C09  0.020
 87C  plan-2  N08  0.020
 87C  plan-2  C07  0.020
 87C  plan-2  H9   0.020
 87C  plan-2  O18  0.020

