# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 05:14:53 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-[4-[(2~{R})-3-(~{tert}-butylamino)-2-oxidanyl-propoxy]phenyl]-3-cyclohexyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC[C@@H](O)COc1ccc(NC(=O)NC2CCCCC2)cc1
#
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
 G3Q  G3Q  1-[4-[(2~{R})-3-(~{tert}-butylamino)-2-oxidanyl-propoxy]phenyl]-3-cyclohexyl-urea  ligand  59  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G3Q
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
 G3Q  C10  C  CH1   0  -0.030   4.6972   0.5719  -0.1690
 G3Q  N12  N  NH1   0  -0.600   7.0149  -0.1530   0.0627
 G3Q  C13  C  CT    0   0.075   8.0477  -1.1780   0.2531
 G3Q  C15  C  CH3   0  -0.651   7.9813  -2.2949  -0.7963
 G3Q  C21  C  CR16  0  -0.049  -6.3380  -0.6764   0.1811
 G3Q  C22  C  C     0  -0.442  -7.4810  -0.4583   1.1691
 G3Q  C24  C  C     0  -0.431  -9.1353  -1.2550  -0.5576
 G3Q  C26  C  C     0  -0.425  -6.8277  -0.5303  -1.2598
 G3Q  C02  C  C     0   0.723  -3.9540  -0.0605   0.2290
 G3Q  C04  C  CR6   0   0.339  -1.7053   0.9647   0.2957
 G3Q  C05  C  CR16  0  -0.319  -1.0786   2.1514  -0.0915
 G3Q  C06  C  CR16  0  -0.341   0.2938   2.2239  -0.2310
 G3Q  C07  C  CR6   0   0.371   1.0873   1.1000  -0.0035
 G3Q  C09  C  CH2   0  -0.188   3.2579   0.1424   0.0551
 G3Q  C11  C  CH2   0  -0.283   5.6366  -0.5900   0.1377
 G3Q  C14  C  CH3   0  -0.645   9.3928  -0.4626   0.1286
 G3Q  C16  C  CH3   0  -0.652   7.9260  -1.7780   1.6529
 G3Q  C18  C  CR16  0  -0.377   0.4707  -0.0883   0.3739
 G3Q  C19  C  CR16  0  -0.288  -0.9095  -0.1511   0.5321
 G3Q  C23  C  C     0  -0.437  -8.6482  -1.3974   0.8804
 G3Q  C25  C  C     0  -0.439  -7.9938  -1.4721  -1.5453
 G3Q  N20  N  NH1   0  -0.689  -5.2507   0.2308   0.4876
 G3Q  O01  O  O     0  -0.529  -3.5775  -1.1558  -0.1671
 G3Q  O08  O  O2    0  -0.476   2.4193   1.2571  -0.1638
 G3Q  O17  O  OH1   0  -0.658   4.9013   1.0940  -1.4637
 G3Q  H1   H  HCH1  0   0.234   4.9304   1.3904   0.5191
 G3Q  H2   H  HNH1  0   0.332   7.1638   0.2726  -0.8457
 G3Q  H4   H  HCH3  0   0.220   8.0488  -1.8821  -1.8058
 G3Q  H5   H  HCH3  0   0.223   8.8083  -2.9953  -0.6690
 G3Q  H6   H  HCH3  0   0.226   7.0559  -2.8695  -0.7305
 G3Q  H7   H  HCR6  0   0.233  -5.9632  -1.6946   0.3170
 G3Q  H8   H  H     0   0.238  -7.1168  -0.6037   2.1891
 G3Q  H9   H  H     0   0.215  -7.8285   0.5796   1.0988
 G3Q  H10  H  H     0   0.229  -9.9470  -1.9595  -0.7539
 G3Q  H11  H  H     0   0.210  -9.5492  -0.2508  -0.6998
 G3Q  H12  H  H     0   0.210  -7.1415   0.5067  -1.4253
 G3Q  H13  H  H     0   0.233  -6.0024  -0.7248  -1.9494
 G3Q  H14  H  HCR6  0   0.266  -1.6756   3.0347  -0.2863
 G3Q  H15  H  HCR6  0   0.262   0.7567   3.1568  -0.5276
 G3Q  H16  H  HCH2  0   0.222   2.9953  -0.6791  -0.6254
 G3Q  H17  H  HCH2  0   0.228   3.1484  -0.2319   1.0798
 G3Q  H18  H  HCH2  0   0.230   5.4224  -0.9417   1.1497
 G3Q  H19  H  HCH2  0   0.196   5.3936  -1.4265  -0.5382
 G3Q  H20  H  HCH3  0   0.226   9.4909   0.3220   0.8808
 G3Q  H21  H  HCH3  0   0.222  10.2210  -1.1615   0.2541
 G3Q  H22  H  HCH3  0   0.222   9.5008  -0.0001  -0.8560
 G3Q  H23  H  HCH3  0   0.227   7.0053  -2.3511   1.7763
 G3Q  H24  H  HCH3  0   0.227   8.7553  -2.4600   1.8475
 G3Q  H25  H  HCH3  0   0.225   7.9435  -0.9963   2.4143
 G3Q  H26  H  HCR6  0   0.279   1.0444  -0.9842   0.5691
 G3Q  H27  H  HCR6  0   0.267  -1.3478  -1.0825   0.8548
 G3Q  H28  H  H     0   0.214  -8.3326  -2.4314   1.0571
 G3Q  H29  H  H     0   0.232  -9.4624  -1.1992   1.5810
 G3Q  H30  H  H     0   0.213  -7.6458  -2.5087  -1.4758
 G3Q  H31  H  H     0   0.231  -8.3441  -1.3313  -2.5704
 G3Q  H32  H  HNH1  0   0.401  -3.4947   1.8867   0.6571
 G3Q  H33  H  HNH1  0   0.388  -5.5036   1.1761   0.7300
 G3Q  H34  H  HOH1  0   0.445   4.7111   0.4023  -2.1082
 G3Q  N03  N  NH1   0  -0.787  -3.0927   0.9788   0.4826

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
 G3Q  C25  C24  single    1.525  0.020  1.525
 G3Q  C25  C26  single    1.526  0.020  1.526
 G3Q  C24  C23  single    1.525  0.020  1.525
 G3Q  C26  C21  single    1.529  0.020  1.529
 G3Q  C23  C22  single    1.526  0.020  1.526
 G3Q  C21  C22  single    1.526  0.020  1.526
 G3Q  C21  N20  single    1.449  0.020  1.449
 G3Q  O01  C02  double    1.224  0.020  1.224
 G3Q  N20  C02  single    1.354  0.020  1.354
 G3Q  C02  N03  single    1.373  0.020  1.373
 G3Q  C19  C18  aromatic  1.391  0.020  1.391
 G3Q  C19  C04  aromatic  1.391  0.020  1.391
 G3Q  C18  C07  aromatic  1.391  0.020  1.391
 G3Q  N03  C04  single    1.400  0.020  1.400
 G3Q  C09  O08  single    1.412  0.020  1.412
 G3Q  C09  C10  single    1.519  0.020  1.519
 G3Q  C04  C05  aromatic  1.397  0.020  1.397
 G3Q  C11  C10  single    1.525  0.020  1.525
 G3Q  C11  N12  single    1.448  0.020  1.448
 G3Q  C16  C13  single    1.528  0.020  1.528
 G3Q  C07  O08  single    1.351  0.020  1.351
 G3Q  C07  C06  aromatic  1.395  0.020  1.395
 G3Q  C10  O17  single    1.411  0.020  1.411
 G3Q  N12  C13  single    1.467  0.020  1.467
 G3Q  C05  C06  aromatic  1.381  0.020  1.381
 G3Q  C14  C13  single    1.529  0.020  1.529
 G3Q  C13  C15  single    1.534  0.020  1.534
 G3Q  C10  H1   single    0.970  0.020  1.090
 G3Q  N12  H2   single    0.890  0.020  1.040
 G3Q  C15  H4   single    0.970  0.020  1.090
 G3Q  C15  H5   single    0.970  0.020  1.090
 G3Q  C15  H6   single    0.970  0.020  1.090
 G3Q  C21  H7   single    0.970  0.020  1.090
 G3Q  C22  H8   single    0.970  0.020  1.090
 G3Q  C22  H9   single    0.970  0.020  1.090
 G3Q  C24  H10  single    0.970  0.020  1.090
 G3Q  C24  H11  single    0.970  0.020  1.090
 G3Q  C26  H12  single    0.970  0.020  1.090
 G3Q  C26  H13  single    0.970  0.020  1.090
 G3Q  C05  H14  single    0.930  0.020  1.080
 G3Q  C06  H15  single    0.930  0.020  1.080
 G3Q  C09  H16  single    0.970  0.020  1.090
 G3Q  C09  H17  single    0.970  0.020  1.090
 G3Q  C11  H18  single    0.970  0.020  1.090
 G3Q  C11  H19  single    0.970  0.020  1.090
 G3Q  C14  H20  single    0.970  0.020  1.090
 G3Q  C14  H21  single    0.970  0.020  1.090
 G3Q  C14  H22  single    0.970  0.020  1.090
 G3Q  C16  H23  single    0.970  0.020  1.090
 G3Q  C16  H24  single    0.970  0.020  1.090
 G3Q  C16  H25  single    0.970  0.020  1.090
 G3Q  C18  H26  single    0.930  0.020  1.080
 G3Q  C19  H27  single    0.930  0.020  1.080
 G3Q  C23  H28  single    0.970  0.020  1.090
 G3Q  C23  H29  single    0.970  0.020  1.090
 G3Q  C25  H30  single    0.970  0.020  1.090
 G3Q  C25  H31  single    0.970  0.020  1.090
 G3Q  N03  H32  single    0.860  0.020  1.020
 G3Q  N20  H33  single    0.860  0.020  1.020
 G3Q  O17  H34  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
 G3Q  H1   C10  O17  105.63  3.000
 G3Q  H1   C10  C11  108.18  3.000
 G3Q  O17  C10  C11  112.16  3.000
 G3Q  H1   C10  C09  108.71  3.000
 G3Q  O17  C10  C09  112.16  3.000
 G3Q  C11  C10  C09  109.79  3.000
 G3Q  H2   N12  C11  108.23  3.000
 G3Q  H2   N12  C13  107.82  3.000
 G3Q  C11  N12  C13  116.90  3.000
 G3Q  C16  C13  C14  109.18  3.000
 G3Q  C14  C13  C15  108.85  3.000
 G3Q  C16  C13  C15  109.72  3.000
 G3Q  C15  C13  N12  112.91  3.000
 G3Q  C14  C13  N12  106.37  3.000
 G3Q  C16  C13  N12  109.70  3.000
 G3Q  H6   C15  H5   107.32  3.000
 G3Q  H6   C15  H4   107.88  3.000
 G3Q  H5   C15  H4   107.66  3.000
 G3Q  H6   C15  C13  112.26  3.000
 G3Q  H5   C15  C13  110.78  3.000
 G3Q  H4   C15  C13  110.75  3.000
 G3Q  H7   C21  N20  107.43  3.000
 G3Q  H7   C21  C26  108.41  3.000
 G3Q  N20  C21  C26  112.33  3.000
 G3Q  H7   C21  C22  108.02  3.000
 G3Q  N20  C21  C22  109.61  3.000
 G3Q  C26  C21  C22  110.89  3.000
 G3Q  H9   C22  H8   106.93  3.000
 G3Q  H9   C22  C23  109.15  3.000
 G3Q  H8   C22  C23  110.47  3.000
 G3Q  H9   C22  C21  109.33  3.000
 G3Q  H8   C22  C21  109.61  3.000
 G3Q  C23  C22  C21  111.25  3.000
 G3Q  H11  C24  H10  106.68  3.000
 G3Q  H11  C24  C25  109.22  3.000
 G3Q  H10  C24  C25  110.36  3.000
 G3Q  H11  C24  C23  109.19  3.000
 G3Q  H10  C24  C23  110.28  3.000
 G3Q  C25  C24  C23  111.00  3.000
 G3Q  H13  C26  H12  106.82  3.000
 G3Q  H13  C26  C25  110.44  3.000
 G3Q  H12  C26  C25  109.69  3.000
 G3Q  H13  C26  C21  109.62  3.000
 G3Q  H12  C26  C21  108.93  3.000
 G3Q  C25  C26  C21  111.23  3.000
 G3Q  O01  C02  N20  123.29  3.000
 G3Q  N20  C02  N03  113.74  3.000
 G3Q  O01  C02  N03  122.96  3.000
 G3Q  N03  C04  C19  123.54  3.000
 G3Q  N03  C04  C05  118.24  3.000
 G3Q  C19  C04  C05  118.16  3.000
 G3Q  H14  C05  C06  119.09  3.000
 G3Q  H14  C05  C04  119.68  3.000
 G3Q  C06  C05  C04  121.23  3.000
 G3Q  H15  C06  C07  119.72  3.000
 G3Q  H15  C06  C05  119.85  3.000
 G3Q  C07  C06  C05  120.43  3.000
 G3Q  O08  C07  C18  124.66  3.000
 G3Q  O08  C07  C06  116.61  3.000
 G3Q  C18  C07  C06  118.72  3.000
 G3Q  H17  C09  H16  107.45  3.000
 G3Q  H17  C09  O08  110.80  3.000
 G3Q  H16  C09  O08  110.63  3.000
 G3Q  H17  C09  C10  109.21  3.000
 G3Q  H16  C09  C10  110.28  3.000
 G3Q  O08  C09  C10  108.46  3.000
 G3Q  H19  C11  H18  106.28  3.000
 G3Q  H19  C11  N12  114.02  3.000
 G3Q  H18  C11  N12  109.37  3.000
 G3Q  H19  C11  C10  108.60  3.000
 G3Q  H18  C11  C10  108.10  3.000
 G3Q  N12  C11  C10  110.25  3.000
 G3Q  H22  C14  H21  107.44  3.000
 G3Q  H22  C14  H20  107.93  3.000
 G3Q  H21  C14  H20  108.24  3.000
 G3Q  H22  C14  C13  111.00  3.000
 G3Q  H21  C14  C13  111.02  3.000
 G3Q  H20  C14  C13  111.06  3.000
 G3Q  H25  C16  H24  108.13  3.000
 G3Q  H25  C16  H23  108.10  3.000
 G3Q  H24  C16  H23  107.02  3.000
 G3Q  H25  C16  C13  110.89  3.000
 G3Q  H24  C16  C13  110.39  3.000
 G3Q  H23  C16  C13  112.15  3.000
 G3Q  H26  C18  C19  117.94  3.000
 G3Q  H26  C18  C07  121.43  3.000
 G3Q  C19  C18  C07  120.63  3.000
 G3Q  H27  C19  C18  118.44  3.000
 G3Q  H27  C19  C04  120.73  3.000
 G3Q  C18  C19  C04  120.82  3.000
 G3Q  H29  C23  H28  106.41  3.000
 G3Q  H29  C23  C24  110.47  3.000
 G3Q  H28  C23  C24  109.41  3.000
 G3Q  H29  C23  C22  109.70  3.000
 G3Q  H28  C23  C22  109.28  3.000
 G3Q  C24  C23  C22  111.43  3.000
 G3Q  H31  C25  H30  106.45  3.000
 G3Q  H31  C25  C26  109.94  3.000
 G3Q  H30  C25  C26  109.23  3.000
 G3Q  H31  C25  C24  110.45  3.000
 G3Q  H30  C25  C24  109.35  3.000
 G3Q  C26  C25  C24  111.28  3.000
 G3Q  H33  N20  C02  119.20  3.000
 G3Q  H33  N20  C21  116.73  3.000
 G3Q  C02  N20  C21  122.93  3.000
 G3Q  C09  O08  C07  118.38  3.000
 G3Q  H34  O17  C10  108.62  3.000
 G3Q  H32  N03  C04  115.30  3.000
 G3Q  H32  N03  C02  117.60  3.000
 G3Q  C04  N03  C02  126.10  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
 G3Q  CONST_01  C07  C18  C19  C04     0.00   0.0  0
 G3Q  CONST_02  C07  C06  C05  C04     0.00   0.0  0
 G3Q  CONST_03  C18  C19  C04  C05     0.00   0.0  0
 G3Q  CONST_04  C18  C07  C06  C05     0.00   0.0  0
 G3Q  CONST_05  C19  C18  C07  C06     0.00   0.0  0
 G3Q  CONST_06  C19  C04  C05  C06     0.00   0.0  0
 G3Q  CONST_07  O08  C07  C06  C05   180.00   0.0  0
 G3Q  CONST_08  N03  C04  C05  C06   180.00   0.0  0
 G3Q  CONST_09  N03  C04  C19  C18   180.00   0.0  0
 G3Q  CONST_10  O08  C07  C18  C19   180.00   0.0  0
 G3Q  CONST_11  H26  C18  C19  C04   180.00   0.0  0
 G3Q  CONST_12  H15  C06  C05  C04   180.00   0.0  0
 G3Q  CONST_13  H27  C19  C04  C05   180.00   0.0  0
 G3Q  CONST_14  H14  C05  C06  C07   180.00   0.0  0
 G3Q  CONST_18  O01  C02  N20  C21     0.00   0.0  0
 G3Q  CONST_19  O01  C02  N03  C04     0.00   0.0  0
 G3Q  CONST_20  N20  C02  N03  C04   180.00   0.0  0
 G3Q  CONST_21  N03  C02  N20  C21   180.00   0.0  0
 G3Q  CONST_22  H33  N20  C02  O01   180.00   0.0  0
 G3Q  Var_01    C24  C25  C26  C21    55.77  30.0  1
 G3Q  Var_02    C24  C23  C22  C21   -55.60  30.0  1
 G3Q  Var_03    C25  C24  C23  C22    55.41  30.0  1
 G3Q  Var_04    C23  C24  C25  C26   -55.48  30.0  1
 G3Q  Var_05    C18  C07  O08  C09     0.44  30.0  2
 G3Q  Var_06    H16  C09  O08  C07    59.60  30.0  1
 G3Q  Var_07    C13  N12  C11  C10  -176.39  30.0  3
 G3Q  Var_08    C11  N12  C13  C15    60.72  30.0  2
 G3Q  Var_09    H23  C16  C13  N12    67.10  30.0  3
 G3Q  Var_10    H20  C14  C13  N12    59.77  30.0  3
 G3Q  Var_11    H4   C15  C13  N12    56.28  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
 G3Q  chir_01  C10  C09  C11  O17  negativ
 G3Q  chir_02  C21  C26  C22  N20  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
 G3Q  plan-1  C04  0.020
 G3Q  plan-1  C05  0.020
 G3Q  plan-1  C06  0.020
 G3Q  plan-1  C07  0.020
 G3Q  plan-1  C18  0.020
 G3Q  plan-1  C19  0.020
 G3Q  plan-1  O08  0.020
 G3Q  plan-1  H14  0.020
 G3Q  plan-1  H15  0.020
 G3Q  plan-1  H26  0.020
 G3Q  plan-1  H27  0.020
 G3Q  plan-1  N03  0.020
 G3Q  plan-2  C21  0.020
 G3Q  plan-2  C02  0.020
 G3Q  plan-2  C04  0.020
 G3Q  plan-2  N20  0.020
 G3Q  plan-2  O01  0.020
 G3Q  plan-2  H32  0.020
 G3Q  plan-2  H33  0.020
 G3Q  plan-2  N03  0.020

