# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 21:08:35 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCN[C@@H]1CC(=O)CN2C=Nc3ccccc3C2=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
 9SF  9SF  3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one  ligand  41  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 PERFECT
;

data_comp_9SF
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
 9SF  N1   N  N     0  -0.462  -3.3986   1.8354   0.1490
 9SF  C2   C  CR16  0   0.153  -2.1840   1.9535  -0.2326
 9SF  C5   C  CR16  0  -0.275  -3.6991  -1.8476  -0.0033
 9SF  C6   C  CR16  0  -0.257  -5.0096  -2.0020   0.3919
 9SF  C7   C  CR16  0  -0.237  -5.7813  -0.8778   0.7068
 9SF  C8   C  CR16  0  -0.310  -5.2440   0.3884   0.6255
 9SF  C10  C  CR66  0  -0.100  -3.1428  -0.5677  -0.0921
 9SF  C2'  C  CH1   0  -0.108   3.2430   0.2652   0.3874
 9SF  C21  C  C     0   0.439   0.9320   1.1848   0.2818
 9SF  C3'  C  CH2   0  -0.576   2.3856   1.4664  -0.0020
 9SF  C39  C  CH1   0   0.090   4.7328   0.5035   0.1339
 9SF  C4   C  CR6   0   0.586  -1.7542  -0.3959  -0.5031
 9SF  C4'  C  CH2   0  -0.483   5.5256  -0.7513   0.4883
 9SF  C5'  C  CH2   0  -0.451   4.9862  -1.9688  -0.2558
 9SF  C6'  C  CH2   0  -0.311   3.4878  -2.1124  -0.0094
 9SF  C9   C  CR66  0   0.244  -3.9133   0.5607   0.2234
 9SF  N1'  N  NH1   0  -0.574   2.7399  -0.9040  -0.3138
 9SF  N3   N  NR6   0  -0.509  -1.3549   0.9296  -0.5829
 9SF  O11  O  O     0  -0.445  -0.9881  -1.3006  -0.7717
 9SF  O4'  O  O     0  -0.390   0.5074   0.9700   1.3900
 9SF  O7'  O  OH1   0  -0.677   5.1343   1.6210   0.8958
 9SF  H1   H  HCR6  0   0.295  -1.7458   2.9427  -0.3076
 9SF  H2   H  HCR6  0   0.267  -3.0963  -2.7122  -0.2475
 9SF  H3   H  HCR6  0   0.267  -5.4424  -2.9907   0.4610
 9SF  H4   H  HCR6  0   0.270  -6.8105  -1.0049   1.0160
 9SF  H5   H  HCR6  0   0.267  -5.8340   1.2631   0.8664
 9SF  H6   H  HCH2  0   0.320   0.0735   2.2168  -1.3755
 9SF  H7   H  HCH2  0   0.314   0.3835   0.5227  -1.6727
 9SF  H8   H  HCH1  0   0.235   3.1110   0.0825   1.4618
 9SF  H9   H  HCH2  0   0.293   2.6848   2.3505   0.5642
 9SF  H10  H  HCH2  0   0.252   2.5298   1.7000  -1.0616
 9SF  H11  H  HCH1  0   0.186   4.8596   0.7015  -0.9437
 9SF  H12  H  HCH2  0   0.238   6.5843  -0.5997   0.2571
 9SF  H13  H  HCH2  0   0.220   5.4566  -0.9184   1.5691
 9SF  H14  H  HCH2  0   0.219   5.1661  -1.8574  -1.3303
 9SF  H15  H  HCH2  0   0.232   5.5134  -2.8724   0.0596
 9SF  H16  H  HCH2  0   0.239   3.0744  -2.9323  -0.5996
 9SF  H17  H  HCH2  0   0.218   3.3146  -2.3644   1.0422
 9SF  H18  H  HNH1  0   0.337   2.7724  -0.7381  -1.3145
 9SF  H20  H  HOH1  0   0.450   6.0724   1.7714   0.7424
 9SF  C1'  C  CH2   0  -0.463   0.0168   1.2238  -0.9222

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
 9SF  C4'  C5'  single    1.525  0.020  1.525
 9SF  C4'  C39  single    1.526  0.020  1.526
 9SF  C5'  C6'  single    1.525  0.020  1.525
 9SF  O7'  C39  single    1.411  0.020  1.411
 9SF  C39  C2'  single    1.530  0.020  1.530
 9SF  C6'  N1'  single    1.453  0.020  1.453
 9SF  C2'  N1'  single    1.453  0.020  1.453
 9SF  C2'  C3'  single    1.526  0.020  1.526
 9SF  C3'  C21  single    1.508  0.020  1.508
 9SF  C21  O4'  double    1.206  0.020  1.206
 9SF  C21  C1'  single    1.513  0.020  1.513
 9SF  C1'  N3   single    1.443  0.020  1.443
 9SF  N3   C2   single    1.363  0.020  1.363
 9SF  N3   C4   single    1.387  0.020  1.387
 9SF  O11  C4   double    1.216  0.020  1.216
 9SF  C2   N1   double    1.279  0.020  1.279
 9SF  C4   C10  single    1.458  0.020  1.458
 9SF  N1   C9   single    1.377  0.020  1.377
 9SF  C10  C9   aromatic  1.402  0.020  1.402
 9SF  C10  C5   aromatic  1.398  0.020  1.398
 9SF  C9   C8   aromatic  1.401  0.020  1.401
 9SF  C5   C6   aromatic  1.377  0.020  1.377
 9SF  C8   C7   aromatic  1.378  0.020  1.378
 9SF  C6   C7   aromatic  1.399  0.020  1.399
 9SF  C2   H1   single    0.930  0.020  1.080
 9SF  C5   H2   single    0.930  0.020  1.080
 9SF  C6   H3   single    0.930  0.020  1.080
 9SF  C7   H4   single    0.930  0.020  1.080
 9SF  C8   H5   single    0.930  0.020  1.080
 9SF  C1'  H6   single    0.970  0.020  1.090
 9SF  C1'  H7   single    0.970  0.020  1.090
 9SF  C2'  H8   single    0.970  0.020  1.090
 9SF  C3'  H9   single    0.970  0.020  1.090
 9SF  C3'  H10  single    0.970  0.020  1.090
 9SF  C39  H11  single    0.970  0.020  1.090
 9SF  C4'  H12  single    0.970  0.020  1.090
 9SF  C4'  H13  single    0.970  0.020  1.090
 9SF  C5'  H14  single    0.970  0.020  1.090
 9SF  C5'  H15  single    0.970  0.020  1.090
 9SF  C6'  H16  single    0.970  0.020  1.090
 9SF  C6'  H17  single    0.970  0.020  1.090
 9SF  N1'  H18  single    0.890  0.020  1.040
 9SF  O7'  H20  single    0.850  0.020  0.980

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
 9SF  C9   N1   C2   117.18  3.000
 9SF  H1   C2   N3   114.94  3.000
 9SF  H1   C2   N1   119.25  3.000
 9SF  N3   C2   N1   125.80  3.000
 9SF  H2   C5   C10  119.71  3.000
 9SF  H2   C5   C6   120.35  3.000
 9SF  C10  C5   C6   119.95  3.000
 9SF  H3   C6   C7   119.95  3.000
 9SF  H3   C6   C5   120.10  3.000
 9SF  C7   C6   C5   119.95  3.000
 9SF  H4   C7   C8   119.72  3.000
 9SF  H4   C7   C6   119.63  3.000
 9SF  C8   C7   C6   120.65  3.000
 9SF  H5   C8   C9   118.84  3.000
 9SF  H5   C8   C7   121.13  3.000
 9SF  C9   C8   C7   120.03  3.000
 9SF  C9   C10  C4   119.46  3.000
 9SF  C9   C10  C5   120.24  3.000
 9SF  C4   C10  C5   120.30  3.000
 9SF  H8   C2'  N1'  107.26  3.000
 9SF  H8   C2'  C39  107.77  3.000
 9SF  N1'  C2'  C39  112.49  3.000
 9SF  H8   C2'  C3'  108.25  3.000
 9SF  N1'  C2'  C3'  108.40  3.000
 9SF  C39  C2'  C3'  112.47  3.000
 9SF  O4'  C21  C3'  123.08  3.000
 9SF  O4'  C21  C1'  121.53  3.000
 9SF  C3'  C21  C1'  115.38  3.000
 9SF  H10  C3'  H9   107.05  3.000
 9SF  H10  C3'  C21  110.44  3.000
 9SF  H9   C3'  C21  108.54  3.000
 9SF  H10  C3'  C2'  109.93  3.000
 9SF  H9   C3'  C2'  110.55  3.000
 9SF  C21  C3'  C2'  110.28  3.000
 9SF  H11  C39  O7'  110.65  3.000
 9SF  H11  C39  C4'  108.34  3.000
 9SF  O7'  C39  C4'  112.21  3.000
 9SF  H11  C39  C2'  107.57  3.000
 9SF  O7'  C39  C2'  108.12  3.000
 9SF  C4'  C39  C2'  109.84  3.000
 9SF  O11  C4   N3   121.14  3.000
 9SF  O11  C4   C10  125.08  3.000
 9SF  N3   C4   C10  113.77  3.000
 9SF  H13  C4'  H12  106.88  3.000
 9SF  H13  C4'  C5'  109.71  3.000
 9SF  H12  C4'  C5'  110.47  3.000
 9SF  H13  C4'  C39  108.76  3.000
 9SF  H12  C4'  C39  109.85  3.000
 9SF  C5'  C4'  C39  111.06  3.000
 9SF  H15  C5'  H14  106.74  3.000
 9SF  H15  C5'  C6'  110.46  3.000
 9SF  H14  C5'  C6'  109.24  3.000
 9SF  H15  C5'  C4'  110.40  3.000
 9SF  H14  C5'  C4'  109.84  3.000
 9SF  C6'  C5'  C4'  110.10  3.000
 9SF  H17  C6'  H16  106.65  3.000
 9SF  H17  C6'  N1'  108.12  3.000
 9SF  H16  C6'  N1'  108.44  3.000
 9SF  H17  C6'  C5'  109.40  3.000
 9SF  H16  C6'  C5'  110.82  3.000
 9SF  N1'  C6'  C5'  113.17  3.000
 9SF  C10  C9   C8   119.18  3.000
 9SF  C8   C9   N1   118.99  3.000
 9SF  C10  C9   N1   121.83  3.000
 9SF  H18  N1'  C6'  109.02  3.000
 9SF  H18  N1'  C2'  109.46  3.000
 9SF  C6'  N1'  C2'  112.94  3.000
 9SF  C4   N3   C1'  118.82  3.000
 9SF  C4   N3   C2   121.87  3.000
 9SF  C1'  N3   C2   119.03  3.000
 9SF  H20  O7'  C39  108.36  3.000
 9SF  H7   C1'  H6   106.33  3.000
 9SF  H7   C1'  N3   110.50  3.000
 9SF  H6   C1'  N3   109.39  3.000
 9SF  H7   C1'  C21  109.13  3.000
 9SF  H6   C1'  C21  108.79  3.000
 9SF  N3   C1'  C21  112.49  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
 9SF  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 9SF  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 9SF  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 9SF  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 9SF  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 9SF  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 9SF  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 9SF  CONST_08  C10  C4   N3   C2      0.00   0.0  0
 9SF  CONST_09  N3   C2   N1   C9      0.00   0.0  0
 9SF  CONST_10  C1'  N3   C2   N1    180.00   0.0  0
 9SF  CONST_11  O11  C4   N3   C2    180.00   0.0  0
 9SF  CONST_12  C1'  N3   C4   C10   180.00   0.0  0
 9SF  CONST_13  H5   C8   C9   N1      0.00   0.0  0
 9SF  CONST_14  H4   C7   C6   C5    180.00   0.0  0
 9SF  CONST_15  H2   C5   C6   C7    180.00   0.0  0
 9SF  CONST_16  H3   C6   C7   C8    180.00   0.0  0
 9SF  CONST_17  H1   C2   N3   C4    180.00   0.0  0
 9SF  CONST_18  O11  C4   N3   C1'     0.00   0.0  0
 9SF  Var_01    C5'  C6'  N1'  C2'   -54.54  30.0  1
 9SF  Var_02    C6'  C5'  C4'  C39   -53.69  30.0  1
 9SF  Var_03    N1'  C6'  C5'  C4'    53.41  30.0  1
 9SF  Var_04    C21  C1'  N3   C2     89.80  30.0  2
 9SF  Var_05    C2'  C3'  C21  C1'  -119.29  30.0  1
 9SF  Var_06    N3   C1'  C21  C3'   179.28  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
 9SF  chir_01  C2'  C39  N1'  C3'  positiv
 9SF  chir_02  C39  O7'  C2'  C4'  positiv

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
 9SF  plan-1  N1   0.020
 9SF  plan-1  C2   0.020
 9SF  plan-1  C5   0.020
 9SF  plan-1  C6   0.020
 9SF  plan-1  C7   0.020
 9SF  plan-1  C8   0.020
 9SF  plan-1  C10  0.020
 9SF  plan-1  C4   0.020
 9SF  plan-1  C9   0.020
 9SF  plan-1  N3   0.020
 9SF  plan-1  O11  0.020
 9SF  plan-1  H1   0.020
 9SF  plan-1  H2   0.020
 9SF  plan-1  H3   0.020
 9SF  plan-1  H4   0.020
 9SF  plan-1  H5   0.020
 9SF  plan-1  C1'  0.020
 9SF  plan-2  C21  0.020
 9SF  plan-2  C3'  0.020
 9SF  plan-2  O4'  0.020
 9SF  plan-2  C1'  0.020

