# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:21:06 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCN1C(=O)c2ccc(cc2N=C1SCc3ccccn3)C(=O)N4CCCC4
#
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
 WDS  WDS  3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one  ligand  59  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WDS
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
 WDS  C29  C  CR16  0  -0.147   4.1271   4.8880  -1.7776
 WDS  C31  C  CR16  0  -0.323   4.8371   5.1105  -0.6086
 WDS  C4   C  CR16  0  -0.272  -2.2642  -2.8230  -0.6455
 WDS  C9   C  CR16  0  -0.284  -3.5119  -2.2442  -0.6243
 WDS  C24  C  CR16  0  -0.323   3.0825   3.9765  -1.7595
 WDS  C6   C  CR16  0  -0.325  -2.5125  -0.0506  -0.5184
 WDS  C30  C  CR16  0  -0.074   4.4648   4.4081   0.5290
 WDS  C1   C  CR66  0  -0.109  -1.1200  -2.0206  -0.6201
 WDS  C11  C  CR6   0  -0.041  -3.6368  -0.8491  -0.5422
 WDS  C2   C  CR66  0   0.289  -1.2373  -0.6293  -0.5633
 WDS  C20  C  CR6   0   0.231   2.7832   3.3271  -0.5678
 WDS  C3   C  CR6   0   0.587   0.2088  -2.6159  -0.6488
 WDS  C10  C  CR6   0   0.348   1.0229  -0.3534  -0.5835
 WDS  C26  C  CH2   0  -0.470  -5.6523   1.4695   2.5135
 WDS  C27  C  CH2   0  -0.490  -6.5817   2.2144   1.5614
 WDS  C21  C  CH2   0  -0.272  -4.5780   0.9297   1.5783
 WDS  C22  C  CH2   0  -0.261  -6.6345   1.2970   0.3453
 WDS  C28  C  CH3   0  -0.663   6.5767  -3.8250   2.0599
 WDS  C16  C  CH2   0  -0.604   1.6672   2.3258  -0.5036
 WDS  C23  C  CH2   0  -0.420   5.1234  -3.3735   2.0950
 WDS  C19  C  CH2   0  -0.418   4.5897  -3.0059   0.7161
 WDS  C15  C  CH2   0  -0.423   3.1441  -2.5263   0.7514
 WDS  N25  N  N     0  -0.403   3.4651   3.5368   0.5548
 WDS  N5   N  N     0  -0.470  -0.1396   0.1871  -0.5446
 WDS  N7   N  NR6   0  -0.560   1.2602  -1.7034  -0.6484
 WDS  N17  N  NT    0  -0.466  -5.3214   0.6532   0.3470
 WDS  O8   O  O     0  -0.450   0.4208  -3.8132  -0.6736
 WDS  O18  O  O     0  -0.493  -5.7881  -0.5894  -1.4724
 WDS  S13  S  S2    0   0.065   2.4437   0.6810  -0.5530
 WDS  H1   H  HCR6  0   0.278   4.3794   5.4148  -2.6883
 WDS  H2   H  HCR6  0   0.275   5.6605   5.8099  -0.5731
 WDS  H3   H  HCR6  0   0.269  -2.1651  -3.8992  -0.6890
 WDS  H4   H  HCR6  0   0.268  -4.3959  -2.8664  -0.6577
 WDS  H5   H  HCR6  0   0.275   2.5048   3.7741  -2.6516
 WDS  H6   H  HCR6  0   0.274  -2.5864   1.0288  -0.4789
 WDS  H7   H  HCR6  0   0.267   4.9977   4.5582   1.4612
 WDS  H8   H  HCH2  0   0.254  -5.2311   2.1008   3.2947
 WDS  H9   H  HCH2  0   0.241  -6.1829   0.6450   2.9947
 WDS  H10  H  HCH2  0   0.255  -7.5715   2.3981   1.9771
 WDS  H11  H  HCH2  0   0.241  -6.1493   3.1798   1.2894
 WDS  H12  H  HCH2  0   0.244  -3.8063   1.6845   1.4096
 WDS  H13  H  HCH2  0   0.261  -4.0937   0.0315   1.9593
 WDS  H14  H  HCH2  0   0.240  -7.4238   0.5475   0.4483
 WDS  H15  H  HCH2  0   0.251  -6.8048   1.8343  -0.5881
 WDS  H16  H  HCH3  0   0.217   7.2252  -3.0313   1.6836
 WDS  H17  H  HCH3  0   0.228   6.9348  -4.1018   3.0519
 WDS  H18  H  HCH3  0   0.217   6.7060  -4.6906   1.4074
 WDS  H19  H  HCH2  0   0.308   1.1016   2.4214   0.4214
 WDS  H20  H  HCH2  0   0.305   0.9896   2.4229  -1.3486
 WDS  H21  H  HCH2  0   0.215   4.4996  -4.1642   2.5226
 WDS  H22  H  HCH2  0   0.215   5.0234  -2.5128   2.7627
 WDS  H23  H  HCH2  0   0.218   5.2224  -2.2270   0.2771
 WDS  H24  H  HCH2  0   0.218   4.6715  -3.8740   0.0535
 WDS  H25  H  HCH2  0   0.237   2.5136  -3.2830   1.2258
 WDS  H26  H  HCH2  0   0.230   3.0715  -1.6243   1.3658
 WDS  H27  H  HCH2  0   0.275   3.2725  -1.5470  -1.1797
 WDS  H28  H  HCH2  0   0.286   2.6132  -3.1550  -1.2444
 WDS  C14  C  C     0   0.519  -5.0091  -0.2500  -0.5885
 WDS  C12  C  CH2   0  -0.343   2.6218  -2.2439  -0.6501

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
 WDS  C30  N25  aromatic  1.326  0.020  1.326
 WDS  C30  C31  aromatic  1.388  0.020  1.388
 WDS  N25  C20  aromatic  1.330  0.020  1.330
 WDS  C31  C29  aromatic  1.386  0.020  1.386
 WDS  C20  C16  single    1.501  0.020  1.501
 WDS  C20  C24  aromatic  1.390  0.020  1.390
 WDS  C29  C24  aromatic  1.387  0.020  1.387
 WDS  C16  S13  single    1.820  0.020  1.820
 WDS  S13  C10  single    1.758  0.020  1.758
 WDS  N5   C10  double    1.283  0.020  1.283
 WDS  N5   C2   single    1.368  0.020  1.368
 WDS  C10  N7   single    1.372  0.020  1.372
 WDS  O18  C14  double    1.226  0.020  1.226
 WDS  C6   C2   aromatic  1.401  0.020  1.401
 WDS  C6   C11  aromatic  1.379  0.020  1.379
 WDS  C2   C1   aromatic  1.397  0.020  1.397
 WDS  C14  C11  single    1.498  0.020  1.498
 WDS  C14  N17  single    1.337  0.020  1.337
 WDS  N7   C12  single    1.465  0.020  1.465
 WDS  N7   C3   single    1.392  0.020  1.392
 WDS  C12  C15  single    1.522  0.020  1.522
 WDS  C11  C9   aromatic  1.403  0.020  1.403
 WDS  C23  C19  single    1.524  0.020  1.524
 WDS  C23  C28  single    1.522  0.020  1.522
 WDS  C19  C15  single    1.523  0.020  1.523
 WDS  C1   C3   single    1.456  0.020  1.456
 WDS  C1   C4   aromatic  1.398  0.020  1.398
 WDS  C22  N17  single    1.462  0.020  1.462
 WDS  C22  C27  single    1.524  0.020  1.524
 WDS  N17  C21  single    1.465  0.020  1.465
 WDS  C3   O8   double    1.216  0.020  1.216
 WDS  C27  C26  single    1.525  0.020  1.525
 WDS  C9   C4   aromatic  1.376  0.020  1.376
 WDS  C21  C26  single    1.523  0.020  1.523
 WDS  C29  H1   single    0.930  0.020  1.080
 WDS  C31  H2   single    0.930  0.020  1.080
 WDS  C4   H3   single    0.930  0.020  1.080
 WDS  C9   H4   single    0.930  0.020  1.080
 WDS  C24  H5   single    0.930  0.020  1.080
 WDS  C6   H6   single    0.930  0.020  1.080
 WDS  C30  H7   single    0.930  0.020  1.080
 WDS  C26  H8   single    0.970  0.020  1.090
 WDS  C26  H9   single    0.970  0.020  1.090
 WDS  C27  H10  single    0.970  0.020  1.090
 WDS  C27  H11  single    0.970  0.020  1.090
 WDS  C21  H12  single    0.970  0.020  1.090
 WDS  C21  H13  single    0.970  0.020  1.090
 WDS  C22  H14  single    0.970  0.020  1.090
 WDS  C22  H15  single    0.970  0.020  1.090
 WDS  C28  H16  single    0.970  0.020  1.090
 WDS  C28  H17  single    0.970  0.020  1.090
 WDS  C28  H18  single    0.970  0.020  1.090
 WDS  C16  H19  single    0.970  0.020  1.090
 WDS  C16  H20  single    0.970  0.020  1.090
 WDS  C23  H21  single    0.970  0.020  1.090
 WDS  C23  H22  single    0.970  0.020  1.090
 WDS  C19  H23  single    0.970  0.020  1.090
 WDS  C19  H24  single    0.970  0.020  1.090
 WDS  C15  H25  single    0.970  0.020  1.090
 WDS  C15  H26  single    0.970  0.020  1.090
 WDS  C12  H27  single    0.970  0.020  1.090
 WDS  C12  H28  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
 WDS  H1   C29  C24  120.45  3.000
 WDS  H1   C29  C31  120.83  3.000
 WDS  C24  C29  C31  118.72  3.000
 WDS  H2   C31  C30  120.33  3.000
 WDS  H2   C31  C29  121.46  3.000
 WDS  C30  C31  C29  118.22  3.000
 WDS  H3   C4   C1   119.80  3.000
 WDS  H3   C4   C9   120.16  3.000
 WDS  C1   C4   C9   120.04  3.000
 WDS  H4   C9   C11  120.07  3.000
 WDS  H4   C9   C4   119.92  3.000
 WDS  C11  C9   C4   120.01  3.000
 WDS  H5   C24  C20  120.31  3.000
 WDS  H5   C24  C29  120.96  3.000
 WDS  C20  C24  C29  118.73  3.000
 WDS  H6   C6   C2   118.37  3.000
 WDS  H6   C6   C11  121.48  3.000
 WDS  C2   C6   C11  120.15  3.000
 WDS  H7   C30  N25  116.41  3.000
 WDS  H7   C30  C31  120.19  3.000
 WDS  N25  C30  C31  123.41  3.000
 WDS  C3   C1   C2   118.98  3.000
 WDS  C3   C1   C4   120.79  3.000
 WDS  C2   C1   C4   120.24  3.000
 WDS  C14  C11  C6   121.05  3.000
 WDS  C14  C11  C9   118.51  3.000
 WDS  C6   C11  C9   120.27  3.000
 WDS  N5   C2   C1   121.82  3.000
 WDS  C1   C2   C6   119.27  3.000
 WDS  N5   C2   C6   118.91  3.000
 WDS  N25  C20  C16  116.76  3.000
 WDS  C16  C20  C24  120.57  3.000
 WDS  N25  C20  C24  122.66  3.000
 WDS  O8   C3   N7   120.91  3.000
 WDS  O8   C3   C1   124.19  3.000
 WDS  N7   C3   C1   114.90  3.000
 WDS  S13  C10  N7   116.11  3.000
 WDS  N7   C10  N5   124.94  3.000
 WDS  S13  C10  N5   118.96  3.000
 WDS  H9   C26  H8   108.02  3.000
 WDS  H9   C26  C21  110.22  3.000
 WDS  H8   C26  C21  111.91  3.000
 WDS  H9   C26  C27  110.35  3.000
 WDS  H8   C26  C27  113.60  3.000
 WDS  C21  C26  C27  102.69  3.000
 WDS  H11  C27  H10  107.81  3.000
 WDS  H11  C27  C22  110.30  3.000
 WDS  H10  C27  C22  112.00  3.000
 WDS  H11  C27  C26  110.24  3.000
 WDS  H10  C27  C26  113.45  3.000
 WDS  C22  C27  C26  103.02  3.000
 WDS  H13  C21  H12  108.04  3.000
 WDS  H13  C21  N17  111.35  3.000
 WDS  H12  C21  N17  111.05  3.000
 WDS  H13  C21  C26  113.02  3.000
 WDS  H12  C21  C26  110.37  3.000
 WDS  N17  C21  C26  103.00  3.000
 WDS  H15  C22  H14  107.80  3.000
 WDS  H15  C22  N17  110.99  3.000
 WDS  H14  C22  N17  110.26  3.000
 WDS  H15  C22  C27  113.06  3.000
 WDS  H14  C22  C27  111.25  3.000
 WDS  N17  C22  C27  103.47  3.000
 WDS  H18  C28  H17  107.67  3.000
 WDS  H18  C28  H16  107.46  3.000
 WDS  H17  C28  H16  107.64  3.000
 WDS  H18  C28  C23  111.23  3.000
 WDS  H17  C28  C23  111.58  3.000
 WDS  H16  C28  C23  111.07  3.000
 WDS  H20  C16  H19  109.20  3.000
 WDS  H20  C16  S13  108.99  3.000
 WDS  H19  C16  S13  108.92  3.000
 WDS  H20  C16  C20  111.75  3.000
 WDS  H19  C16  C20  111.36  3.000
 WDS  S13  C16  C20  106.53  3.000
 WDS  H22  C23  H21  106.15  3.000
 WDS  H22  C23  C19  109.30  3.000
 WDS  H21  C23  C19  109.17  3.000
 WDS  H22  C23  C28  109.55  3.000
 WDS  H21  C23  C28  109.82  3.000
 WDS  C19  C23  C28  112.65  3.000
 WDS  H24  C19  H23  106.15  3.000
 WDS  H24  C19  C15  109.54  3.000
 WDS  H23  C19  C15  109.48  3.000
 WDS  H24  C19  C23  109.28  3.000
 WDS  H23  C19  C23  109.39  3.000
 WDS  C15  C19  C23  112.79  3.000
 WDS  H26  C15  H25  106.78  3.000
 WDS  H26  C15  C12  109.97  3.000
 WDS  H25  C15  C12  109.27  3.000
 WDS  H26  C15  C19  109.61  3.000
 WDS  H25  C15  C19  109.84  3.000
 WDS  C12  C15  C19  111.27  3.000
 WDS  C20  N25  C30  118.27  3.000
 WDS  C10  N5   C2   118.39  3.000
 WDS  C12  N7   C10  121.58  3.000
 WDS  C12  N7   C3   117.39  3.000
 WDS  C10  N7   C3   120.96  3.000
 WDS  C22  N17  C21  111.94  3.000
 WDS  C21  N17  C14  126.65  3.000
 WDS  C22  N17  C14  120.41  3.000
 WDS  C16  S13  C10  100.81  3.000
 WDS  O18  C14  N17  122.87  3.000
 WDS  N17  C14  C11  117.54  3.000
 WDS  O18  C14  C11  119.58  3.000
 WDS  H28  C12  H27  105.94  3.000
 WDS  H28  C12  N7   107.60  3.000
 WDS  H27  C12  N7   108.62  3.000
 WDS  H28  C12  C15  110.51  3.000
 WDS  H27  C12  C15  111.15  3.000
 WDS  N7   C12  C15  112.73  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
 WDS  CONST_01  N25  C30  C31  C29     0.00   0.0  0
 WDS  CONST_02  N25  C20  C24  C29     0.00   0.0  0
 WDS  CONST_03  C20  N25  C30  C31     0.00   0.0  0
 WDS  CONST_04  C20  C24  C29  C31     0.00   0.0  0
 WDS  CONST_05  C6   C2   C1   C4      0.00   0.0  0
 WDS  CONST_06  C6   C11  C9   C4      0.00   0.0  0
 WDS  CONST_07  C2   C6   C11  C9      0.00   0.0  0
 WDS  CONST_08  C2   C1   C4   C9      0.00   0.0  0
 WDS  CONST_09  C30  N25  C20  C24     0.00   0.0  0
 WDS  CONST_10  C30  C31  C29  C24     0.00   0.0  0
 WDS  CONST_11  C11  C6   C2   C1      0.00   0.0  0
 WDS  CONST_12  C11  C9   C4   C1      0.00   0.0  0
 WDS  CONST_13  C10  N7   C3   C1      0.00   0.0  0
 WDS  CONST_14  N7   C10  N5   C2      0.00   0.0  0
 WDS  CONST_15  N5   C10  N7   C3      0.00   0.0  0
 WDS  CONST_16  C16  C20  C24  C29   180.00   0.0  0
 WDS  CONST_17  C14  C11  C9   C4    180.00   0.0  0
 WDS  CONST_18  C16  C20  N25  C30   180.00   0.0  0
 WDS  CONST_19  C14  C11  C6   C2    180.00   0.0  0
 WDS  CONST_20  C22  N17  C14  C11   180.00   0.0  0
 WDS  CONST_21  C21  N17  C14  C11     0.00   0.0  0
 WDS  CONST_22  C12  N7   C3   C1    180.00   0.0  0
 WDS  CONST_23  S13  C10  N5   C2    180.00   0.0  0
 WDS  CONST_24  S13  C10  N7   C3    180.00   0.0  0
 WDS  CONST_25  O8   C3   N7   C10   180.00   0.0  0
 WDS  CONST_26  N5   C10  N7   C12   180.00   0.0  0
 WDS  CONST_27  H7   C30  C31  C29   180.00   0.0  0
 WDS  CONST_28  H5   C24  C29  C31   180.00   0.0  0
 WDS  CONST_29  H6   C6   C11  C9    180.00   0.0  0
 WDS  CONST_30  H2   C31  C29  C24   180.00   0.0  0
 WDS  CONST_31  H4   C9   C11  C6    180.00   0.0  0
 WDS  CONST_32  H1   C29  C31  C30   180.00   0.0  0
 WDS  CONST_33  H3   C4   C9   C11   180.00   0.0  0
 WDS  CONST_34  O18  C14  N17  C21   180.00   0.0  0
 WDS  CONST_35  O18  C14  N17  C22     0.00   0.0  0
 WDS  CONST_36  S13  C10  N7   C12     0.00   0.0  0
 WDS  CONST_37  O8   C3   N7   C12     0.00   0.0  0
 WDS  Var_01    N17  C22  C27  C26   -30.60  30.0  1
 WDS  Var_02    C22  N17  C21  C26    15.08  30.0  1
 WDS  Var_03    C21  N17  C22  C27     9.78  30.0  1
 WDS  Var_04    N17  C21  C26  C27   -33.63  30.0  1
 WDS  Var_05    C22  C27  C26  C21    39.99  30.0  1
 WDS  Var_06    N17  C14  C11  C9    131.13  30.0  2
 WDS  Var_07    S13  C16  C20  C24   101.36  30.0  2
 WDS  Var_08    C15  C12  N7   C3    -87.21  30.0  3
 WDS  Var_09    N5   C10  S13  C16    -1.14  30.0  3
 WDS  Var_10    N7   C12  C15  C19  -176.54  30.0  1
 WDS  Var_11    C15  C19  C23  C28  -178.82  30.0  3
 WDS  Var_12    C12  C15  C19  C23  -176.79  30.0  3
 WDS  Var_13    H16  C28  C23  C19    60.99  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
 WDS  plan-1  C29  0.020
 WDS  plan-1  C31  0.020
 WDS  plan-1  C24  0.020
 WDS  plan-1  C30  0.020
 WDS  plan-1  C20  0.020
 WDS  plan-1  C16  0.020
 WDS  plan-1  N25  0.020
 WDS  plan-1  H1   0.020
 WDS  plan-1  H2   0.020
 WDS  plan-1  H5   0.020
 WDS  plan-1  H7   0.020
 WDS  plan-2  C4   0.020
 WDS  plan-2  C9   0.020
 WDS  plan-2  C6   0.020
 WDS  plan-2  C1   0.020
 WDS  plan-2  C11  0.020
 WDS  plan-2  C2   0.020
 WDS  plan-2  C3   0.020
 WDS  plan-2  C10  0.020
 WDS  plan-2  N5   0.020
 WDS  plan-2  N7   0.020
 WDS  plan-2  O8   0.020
 WDS  plan-2  S13  0.020
 WDS  plan-2  H3   0.020
 WDS  plan-2  H4   0.020
 WDS  plan-2  H6   0.020
 WDS  plan-2  C14  0.020
 WDS  plan-2  C12  0.020
 WDS  plan-3  C11  0.020
 WDS  plan-3  C21  0.020
 WDS  plan-3  C22  0.020
 WDS  plan-3  N17  0.020
 WDS  plan-3  O18  0.020
 WDS  plan-3  C14  0.020

