# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:48:02 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 1-(1-adamantyl)-3-(1-methylsulfonylpiperidin-4-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N1CCC(CC1)NC(=O)NC23CC4CC(CC(C4)C2)C3
#
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
 XQ9  XQ9  1-(1-adamantyl)-3-(1-methylsulfonylpiperidin-4-yl)urea  ligand  53  24  .  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_XQ9
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
 XQ9  C1    C  CH3   0  -0.807   4.8315   0.6632   2.1620
 XQ9  S2    S  S     0   1.348   5.6015  -0.0206   0.7076
 XQ9  O3    O  OS    0  -0.670   6.5843   0.9487   0.2434
 XQ9  O4    O  OS    0  -0.670   6.0437  -1.3675   1.0410
 XQ9  N5    N  N     0  -0.566   4.4623  -0.1593  -0.4666
 XQ9  C6    C  CH2   0  -0.332   3.9536   1.0412  -1.1272
 XQ9  C7    C  CH2   0  -0.450   2.6021   1.4852  -0.5810
 XQ9  C8    C  CH1   0  -0.059   1.5950   0.3413  -0.6162
 XQ9  C9    C  CH2   0  -0.443   2.1597  -0.8793   0.1106
 XQ9  C10   C  CH2   0  -0.328   3.5171  -1.2750  -0.4538
 XQ9  N11   N  NH1   0  -0.692   0.3310   0.7804  -0.0693
 XQ9  C12   C  C     0   0.746  -0.8411   0.1433  -0.3751
 XQ9  O13   O  O     0  -0.544  -0.9185  -0.6618  -1.2980
 XQ9  N14   N  NH1   0  -0.732  -1.8866   0.4894   0.4190
 XQ9  C15   C  CT    0   0.175  -3.2851   0.1383   0.1957
 XQ9  C16   C  CH2   0  -0.461  -4.0803   0.8034   1.3282
 XQ9  C17   C  CH1   0  -0.250  -5.5716   0.4996   1.1902
 XQ9  C18   C  CH2   0  -0.417  -6.0774   1.0299  -0.1525
 XQ9  C19   C  CH1   0  -0.254  -5.3037   0.3587  -1.2882
 XQ9  C20   C  CH2   0  -0.420  -3.8111   0.6692  -1.1467
 XQ9  C21   C  CH2   0  -0.418  -5.5096  -1.1565  -1.2246
 XQ9  C22   C  CH1   0  -0.253  -5.0116  -1.6842   0.1232
 XQ9  C23   C  CH2   0  -0.417  -5.7885  -1.0129   1.2564
 XQ9  C24   C  CH2   0  -0.421  -3.5189  -1.3774   0.2729
 XQ9  H11C  H  HCH3  0   0.287   4.4575   1.6618   1.9477
 XQ9  H12C  H  HCH3  0   0.288   4.0167   0.0184   2.4830
 XQ9  H13C  H  HCH3  0   0.308   5.5874   0.7170   2.9441
 XQ9  H61C  H  HCH2  0   0.280   4.6842   1.8441  -1.0546
 XQ9  H62C  H  HCH2  0   0.261   3.8598   0.8028  -2.1904
 XQ9  H101  H  HCH2  0   0.258   3.4049  -1.6048  -1.4910
 XQ9  H102  H  HCH2  0   0.279   3.9398  -2.1145   0.0931
 XQ9  H71C  H  HCH2  0   0.231   2.7140   1.8517   0.4448
 XQ9  H72C  H  HCH2  0   0.261   2.2397   2.3243  -1.1787
 XQ9  H8    H  HCH1  0   0.242   1.4252   0.0724  -1.6622
 XQ9  H91C  H  HCH2  0   0.226   2.2447  -0.6613   1.1800
 XQ9  H92C  H  HCH2  0   0.255   1.4745  -1.7236   0.0113
 XQ9  H11   H  HNH1  0   0.382   0.3812   1.2847   0.8033
 XQ9  H14   H  HNH1  0   0.384  -1.7357   1.2472   1.0667
 XQ9  H161  H  HCH2  0   0.236  -3.7093   0.4428   2.2944
 XQ9  H162  H  HCH2  0   0.233  -3.9160   1.8871   1.3068
 XQ9  H201  H  HCH2  0   0.220  -3.6395   1.7498  -1.2015
 XQ9  H202  H  HCH2  0   0.234  -3.2581   0.2125  -1.9707
 XQ9  H241  H  HCH2  0   0.238  -2.9520  -1.8830  -0.5101
 XQ9  H242  H  HCH2  0   0.220  -3.1511  -1.7512   1.2347
 XQ9  H17   H  HCH1  0   0.228  -6.1099   0.9865   2.0084
 XQ9  H181  H  HCH2  0   0.223  -7.1495   0.8333  -0.2541
 XQ9  H182  H  HCH2  0   0.222  -5.9508   2.1162  -0.2008
 XQ9  H231  H  HCH2  0   0.222  -5.4520  -1.4010   2.2236
 XQ9  H232  H  HCH2  0   0.223  -6.8554  -1.2447   1.1760
 XQ9  H19   H  HCH1  0   0.225  -5.6591   0.7396  -2.2502
 XQ9  H211  H  HCH2  0   0.223  -6.5683  -1.4006  -1.3589
 XQ9  H212  H  HCH2  0   0.222  -4.9669  -1.6416  -2.0424
 XQ9  H22   H  HCH1  0   0.225  -5.1569  -2.7676   0.1689

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
 XQ9  C1   S2    single  1.782  0.020  1.782
 XQ9  S2   O3    double  1.456  0.020  1.456
 XQ9  S2   O4    double  1.456  0.020  1.456
 XQ9  S2   N5    single  1.642  0.020  1.642
 XQ9  N5   C6    single  1.462  0.020  1.462
 XQ9  N5   C10   single  1.462  0.020  1.462
 XQ9  C6   C7    single  1.524  0.020  1.524
 XQ9  C7   C8    single  1.524  0.020  1.524
 XQ9  C8   C9    single  1.529  0.020  1.529
 XQ9  C8   N11   single  1.446  0.020  1.446
 XQ9  C9   C10   single  1.522  0.020  1.522
 XQ9  N11  C12   single  1.369  0.020  1.369
 XQ9  C12  O13   double  1.227  0.020  1.227
 XQ9  C12  N14   single  1.358  0.020  1.358
 XQ9  N14  C15   single  1.459  0.020  1.459
 XQ9  C15  C16   single  1.535  0.020  1.535
 XQ9  C15  C20   single  1.536  0.020  1.536
 XQ9  C15  C24   single  1.536  0.020  1.536
 XQ9  C16  C17   single  1.528  0.020  1.528
 XQ9  C17  C18   single  1.530  0.020  1.530
 XQ9  C17  C23   single  1.529  0.020  1.529
 XQ9  C18  C19   single  1.529  0.020  1.529
 XQ9  C19  C20   single  1.531  0.020  1.531
 XQ9  C19  C21   single  1.530  0.020  1.530
 XQ9  C21  C22   single  1.531  0.020  1.531
 XQ9  C22  C23   single  1.529  0.020  1.529
 XQ9  C22  C24   single  1.531  0.020  1.531
 XQ9  C1   H11C  single  0.970  0.020  1.090
 XQ9  C1   H12C  single  0.970  0.020  1.090
 XQ9  C1   H13C  single  0.970  0.020  1.090
 XQ9  C6   H61C  single  0.970  0.020  1.090
 XQ9  C6   H62C  single  0.970  0.020  1.090
 XQ9  C10  H101  single  0.970  0.020  1.090
 XQ9  C10  H102  single  0.970  0.020  1.090
 XQ9  C7   H71C  single  0.970  0.020  1.090
 XQ9  C7   H72C  single  0.970  0.020  1.090
 XQ9  C8   H8    single  0.970  0.020  1.090
 XQ9  C9   H91C  single  0.970  0.020  1.090
 XQ9  C9   H92C  single  0.970  0.020  1.090
 XQ9  N11  H11   single  0.890  0.020  1.040
 XQ9  N14  H14   single  0.860  0.020  1.020
 XQ9  C16  H161  single  0.970  0.020  1.090
 XQ9  C16  H162  single  0.970  0.020  1.090
 XQ9  C20  H201  single  0.970  0.020  1.090
 XQ9  C20  H202  single  0.970  0.020  1.090
 XQ9  C24  H241  single  0.970  0.020  1.090
 XQ9  C24  H242  single  0.970  0.020  1.090
 XQ9  C17  H17   single  0.970  0.020  1.090
 XQ9  C18  H181  single  0.970  0.020  1.090
 XQ9  C18  H182  single  0.970  0.020  1.090
 XQ9  C23  H231  single  0.970  0.020  1.090
 XQ9  C23  H232  single  0.970  0.020  1.090
 XQ9  C19  H19   single  0.970  0.020  1.090
 XQ9  C21  H211  single  0.970  0.020  1.090
 XQ9  C21  H212  single  0.970  0.020  1.090
 XQ9  C22  H22   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
 XQ9  H13C  C1   H12C  109.71  3.000
 XQ9  H13C  C1   H11C  109.56  3.000
 XQ9  H12C  C1   H11C  110.18  3.000
 XQ9  H13C  C1   S2    107.77  3.000
 XQ9  H12C  C1   S2    109.70  3.000
 XQ9  H11C  C1   S2    109.88  3.000
 XQ9  N5    S2   O4    107.23  3.000
 XQ9  N5    S2   O3    107.25  3.000
 XQ9  O4    S2   O3    118.92  3.000
 XQ9  N5    S2   C1    108.44  3.000
 XQ9  O4    S2   C1    107.41  3.000
 XQ9  O3    S2   C1    107.24  3.000
 XQ9  C10   N5   C6    113.93  3.000
 XQ9  C10   N5   S2    120.45  3.000
 XQ9  C6    N5   S2    119.69  3.000
 XQ9  H62C  C6   H61C  106.46  3.000
 XQ9  H62C  C6   C7    109.63  3.000
 XQ9  H61C  C6   C7    110.90  3.000
 XQ9  H62C  C6   N5    106.87  3.000
 XQ9  H61C  C6   N5    110.01  3.000
 XQ9  C7    C6   N5    112.70  3.000
 XQ9  H72C  C7   H71C  106.82  3.000
 XQ9  H72C  C7   C8    110.17  3.000
 XQ9  H71C  C7   C8    109.89  3.000
 XQ9  H72C  C7   C6    108.78  3.000
 XQ9  H71C  C7   C6    110.04  3.000
 XQ9  C8    C7   C6    111.04  3.000
 XQ9  H8    C8   N11   107.51  3.000
 XQ9  H8    C8   C9    108.42  3.000
 XQ9  N11   C8   C9    112.69  3.000
 XQ9  H8    C8   C7    108.01  3.000
 XQ9  N11   C8   C7    109.94  3.000
 XQ9  C9    C8   C7    110.13  3.000
 XQ9  H92C  C9   H91C  106.96  3.000
 XQ9  H92C  C9   C10   108.95  3.000
 XQ9  H91C  C9   C10   110.16  3.000
 XQ9  H92C  C9   C8    110.02  3.000
 XQ9  H91C  C9   C8    109.52  3.000
 XQ9  C10   C9   C8    111.14  3.000
 XQ9  H102  C10  H101  106.50  3.000
 XQ9  H102  C10  C9    111.15  3.000
 XQ9  H101  C10  C9    109.78  3.000
 XQ9  H102  C10  N5    110.00  3.000
 XQ9  H101  C10  N5    106.74  3.000
 XQ9  C9    C10  N5    112.41  3.000
 XQ9  H11   N11  C12   117.93  3.000
 XQ9  H11   N11  C8    115.82  3.000
 XQ9  C12   N11  C8    121.53  3.000
 XQ9  N14   C12  O13   123.96  3.000
 XQ9  N14   C12  N11   114.21  3.000
 XQ9  O13   C12  N11   121.83  3.000
 XQ9  H14   N14  C15   115.00  3.000
 XQ9  H14   N14  C12   116.88  3.000
 XQ9  C15   N14  C12   125.96  3.000
 XQ9  C24   C15  C20   109.44  3.000
 XQ9  C24   C15  C16   108.16  3.000
 XQ9  C20   C15  C16   108.51  3.000
 XQ9  C24   C15  N14   112.07  3.000
 XQ9  C20   C15  N14   112.26  3.000
 XQ9  C16   C15  N14   106.22  3.000
 XQ9  H162  C16  H161  106.96  3.000
 XQ9  H162  C16  C17   109.94  3.000
 XQ9  H161  C16  C17   110.16  3.000
 XQ9  H162  C16  C15   109.64  3.000
 XQ9  H161  C16  C15   109.42  3.000
 XQ9  C17   C16  C15   110.65  3.000
 XQ9  H17   C17  C23   109.76  3.000
 XQ9  H17   C17  C18   109.85  3.000
 XQ9  C23   C17  C18   109.50  3.000
 XQ9  H17   C17  C16   108.92  3.000
 XQ9  C23   C17  C16   109.33  3.000
 XQ9  C18   C17  C16   109.46  3.000
 XQ9  H182  C18  H181  106.70  3.000
 XQ9  H182  C18  C19   110.13  3.000
 XQ9  H181  C18  C19   110.35  3.000
 XQ9  H182  C18  C17   110.15  3.000
 XQ9  H181  C18  C17   110.06  3.000
 XQ9  C19   C18  C17   109.41  3.000
 XQ9  H19   C19  C21   109.73  3.000
 XQ9  H19   C19  C20   109.10  3.000
 XQ9  C21   C19  C20   109.15  3.000
 XQ9  H19   C19  C18   109.63  3.000
 XQ9  C21   C19  C18   109.61  3.000
 XQ9  C20   C19  C18   109.61  3.000
 XQ9  H202  C20  H201  107.18  3.000
 XQ9  H202  C20  C19   109.82  3.000
 XQ9  H201  C20  C19   110.38  3.000
 XQ9  H202  C20  C15   109.95  3.000
 XQ9  H201  C20  C15   109.32  3.000
 XQ9  C19   C20  C15   110.15  3.000
 XQ9  H212  C21  H211  106.80  3.000
 XQ9  H212  C21  C22   110.10  3.000
 XQ9  H211  C21  C22   110.23  3.000
 XQ9  H212  C21  C19   109.93  3.000
 XQ9  H211  C21  C19   110.22  3.000
 XQ9  C22   C21  C19   109.52  3.000
 XQ9  H22   C22  C24   108.89  3.000
 XQ9  H22   C22  C23   109.65  3.000
 XQ9  C24   C22  C23   109.56  3.000
 XQ9  H22   C22  C21   109.57  3.000
 XQ9  C24   C22  C21   109.53  3.000
 XQ9  C23   C22  C21   109.63  3.000
 XQ9  H232  C23  H231  106.82  3.000
 XQ9  H232  C23  C22   110.35  3.000
 XQ9  H231  C23  C22   110.05  3.000
 XQ9  H232  C23  C17   110.15  3.000
 XQ9  H231  C23  C17   110.18  3.000
 XQ9  C22   C23  C17   109.27  3.000
 XQ9  H242  C24  H241  107.31  3.000
 XQ9  H242  C24  C22   110.17  3.000
 XQ9  H241  C24  C22   110.09  3.000
 XQ9  H242  C24  C15   109.26  3.000
 XQ9  H241  C24  C15   110.02  3.000
 XQ9  C22   C24  C15   109.95  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
 XQ9  CONST_01  O13   C12  N11  C8     0.00   0.0  0
 XQ9  CONST_02  C15   N14  C12  O13    0.00   0.0  0
 XQ9  CONST_03  N14   C12  N11  C8   180.00   0.0  0
 XQ9  CONST_04  C15   N14  C12  N11  180.00   0.0  0
 XQ9  CONST_05  H11   N11  C12  O13  180.00   0.0  0
 XQ9  CONST_06  H14   N14  C12  O13  180.00   0.0  0
 XQ9  Var_01    C8    C7   C6   N5   -53.30  30.0  1
 XQ9  Var_02    C8    C9   C10  N5    53.57  30.0  1
 XQ9  Var_03    C9    C10  N5   C6   -52.80  30.0  1
 XQ9  Var_04    C10   N5   C6   C7    52.72  30.0  1
 XQ9  Var_05    C6    N5   S2   C1    72.10  30.0  3
 XQ9  Var_06    H11C  C1   S2   N5   -62.68  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
 XQ9  chir_01  C8   C7   C9   N11  negativ
 XQ9  chir_02  C15  C16  C20  C24  positiv
 XQ9  chir_03  C17  C16  C18  C23  negativ
 XQ9  chir_04  C19  C18  C20  C21  negativ
 XQ9  chir_05  C22  C21  C23  C24  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
 XQ9  plan-1  C8   0.020
 XQ9  plan-1  N11  0.020
 XQ9  plan-1  C12  0.020
 XQ9  plan-1  O13  0.020
 XQ9  plan-1  N14  0.020
 XQ9  plan-1  C15  0.020
 XQ9  plan-1  H11  0.020
 XQ9  plan-1  H14  0.020

