# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:43:22 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-2-cyclopropylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](NC(=O)CC1CC1)C(=O)N2CC[C@](O)(c3ccc(Cl)cc3)C(C)(C)C2
#
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
 40U  40U  N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-2-cyclopropylacetamide  ligand  62  29  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_40U
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
 40U  C13  C   C     0   0.575   5.1325  -0.5949   0.3421
 40U  C18  C   CH1   0  -0.229   2.4595  -2.1676  -0.5916
 40U  C17  C   CH2   0  -0.499   8.6948   0.8394   0.6777
 40U  C16  C   CH2   0  -0.482   7.6561   1.0914   1.7306
 40U  C15  C   CH1   0  -0.219   7.5505  -0.1120   0.8487
 40U  C19  C   CH3   0  -0.682   1.1078  -2.6743  -0.1059
 40U  C20  C   CH3   0  -0.658   2.6234  -2.4085  -2.0871
 40U  C21  C   CH3   0  -0.651  -2.4270   2.3863  -1.6542
 40U  C22  C   CH3   0  -0.670  -1.7778   0.0114  -1.8801
 40U  C11  C   C     0   0.571   1.8192   0.2980  -0.8752
 40U  C12  C   CH1   0  -0.183   2.7318  -0.7038  -0.1637
 40U  C    C   CR6   0  -0.057  -6.2279  -0.3975   0.5478
 40U  C5   C   CR16  0  -0.196  -5.2064  -1.3256   0.4416
 40U  C4   C   CR16  0  -0.318  -3.8909  -0.8857   0.4185
 40U  C3   C   CR6   0   0.116  -3.5697   0.4687   0.4986
 40U  C2   C   CR16  0  -0.304  -4.6240   1.3750   0.6117
 40U  C1   C   CR16  0  -0.197  -5.9456   0.9553   0.6342
 40U  C6   C   CT    0   0.201  -2.1318   0.9774   0.4641
 40U  O2   O   OH1   0  -0.666  -2.0527   2.2207   1.1324
 40U  C10  C   CH2   0  -0.468  -1.1717  -0.0068   1.1478
 40U  C9   C   CH2   0  -0.309   0.2748   0.4567   1.0903
 40U  N    N   NT    0  -0.468   0.6816   0.7096  -0.2816
 40U  C8   C   CH2   0  -0.272  -0.1699   1.6830  -0.9473
 40U  C7   C   CT    0  -0.103  -1.6441   1.2502  -0.9930
 40U  O    O   O     0  -0.502   2.1531   0.6879  -1.9895
 40U  N1   N   NH1   0  -0.649   4.0906  -0.3097  -0.4591
 40U  O1   O   O     0  -0.501   5.0095  -1.1659   1.4166
 40U  C14  C   CH2   0  -0.610   6.4806  -0.1688  -0.2058
 40U  H1   H   HCH1  0   0.244   3.2288  -2.7478  -0.0732
 40U  H2   H   HCH2  0   0.242   8.6984   1.4795  -0.1965
 40U  H3   H   HCH2  0   0.250   9.6789   0.5188   0.9945
 40U  H4   H   HCH2  0   0.248   7.9298   0.9476   2.7680
 40U  H5   H   HCH2  0   0.242   6.9535   1.8999   1.5661
 40U  H6   H   HCH1  0   0.254   7.7927  -1.0633   1.3088
 40U  H7   H   HCH3  0   0.223   0.2801  -2.1819  -0.6192
 40U  H8   H   HCH3  0   0.247   1.0138  -3.7429  -0.3012
 40U  H9   H   HCH3  0   0.234   0.9776  -2.5275   0.9677
 40U  H10  H   HCH3  0   0.221   1.8281  -1.9383  -2.6669
 40U  H11  H   HCH3  0   0.227   3.5790  -2.0395  -2.4613
 40U  H12  H   HCH3  0   0.230   2.5864  -3.4794  -2.2912
 40U  H13  H   HCH3  0   0.237  -3.4731   2.1160  -1.8015
 40U  H14  H   HCH3  0   0.237  -2.3944   3.3106  -1.0788
 40U  H15  H   HCH3  0   0.232  -2.0062   2.5929  -2.6404
 40U  H16  H   HCH3  0   0.241  -1.3458   0.2178  -2.8610
 40U  H17  H   HCH3  0   0.236  -1.2693  -0.8671  -1.4822
 40U  H18  H   HCH3  0   0.243  -2.8225  -0.2573  -2.0365
 40U  H19  H   HCH1  0   0.274   2.6192  -0.6521   0.9186
 40U  H21  H   HCR6  0   0.257  -3.1183  -1.6378   0.3402
 40U  H22  H   HCR6  0   0.264  -4.4249   2.4350   0.6877
 40U  H23  H   HCR6  0   0.277  -6.7434   1.6805   0.7200
 40U  H24  H   HOH1  0   0.450  -2.2638   2.0838   2.0628
 40U  H25  H   HCH2  0   0.263  -1.4600  -0.1277   2.1963
 40U  H26  H   HCH2  0   0.237  -1.2367  -0.9979   0.7019
 40U  H27  H   HCH2  0   0.255   0.4037   1.3733   1.6727
 40U  H28  H   HCH2  0   0.266   0.9014  -0.2986   1.5515
 40U  H29  H   HCH2  0   0.253  -0.0729   2.6443  -0.4333
 40U  H30  H   HCH2  0   0.264   0.1851   1.8257  -1.9650
 40U  H31  H   HNH1  0   0.397   4.2605   0.1372  -1.3469
 40U  H32  H   HCH2  0   0.279   6.7612  -0.8794  -0.9912
 40U  H33  H   HCH2  0   0.260   6.3879   0.8005  -0.7047
 40U  H20  H   HCR6  0   0.278  -5.4236  -2.3834   0.3809
 40U  CL   CL  CL    0  -0.133  -7.8763  -0.9353   0.5791

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
 40U  C17  C15  single    1.498  0.020  1.498
 40U  C17  C16  single    1.500  0.020  1.500
 40U  C14  C15  single    1.503  0.020  1.503
 40U  C14  C13  single    1.516  0.020  1.516
 40U  C15  C16  single    1.496  0.020  1.496
 40U  O1   C13  double    1.223  0.020  1.223
 40U  C13  N1   single    1.345  0.020  1.345
 40U  N1   C12  single    1.445  0.020  1.445
 40U  C22  C7   single    1.530  0.020  1.530
 40U  C12  C18  single    1.549  0.020  1.549
 40U  C12  C11  single    1.531  0.020  1.531
 40U  C19  C18  single    1.523  0.020  1.523
 40U  CL   C    single    1.734  0.020  1.734
 40U  C1   C2   aromatic  1.387  0.020  1.387
 40U  C1   C    aromatic  1.385  0.020  1.385
 40U  C2   C3   aromatic  1.395  0.020  1.395
 40U  C    C5   aromatic  1.384  0.020  1.384
 40U  C18  C20  single    1.524  0.020  1.524
 40U  C11  O    double    1.227  0.020  1.227
 40U  C11  N    single    1.348  0.020  1.348
 40U  C7   C21  single    1.530  0.020  1.530
 40U  C7   C8   single    1.537  0.020  1.537
 40U  C7   C6   single    1.561  0.020  1.561
 40U  C8   N    single    1.455  0.020  1.455
 40U  N    C9   single    1.453  0.020  1.453
 40U  C3   C6   single    1.526  0.020  1.526
 40U  C3   C4   aromatic  1.394  0.020  1.394
 40U  C5   C4   aromatic  1.387  0.020  1.387
 40U  C6   C10  single    1.536  0.020  1.536
 40U  C6   O2   single    1.414  0.020  1.414
 40U  C10  C9   single    1.520  0.020  1.520
 40U  C18  H1   single    0.970  0.020  1.090
 40U  C17  H2   single    0.970  0.020  1.090
 40U  C17  H3   single    0.970  0.020  1.090
 40U  C16  H4   single    0.970  0.020  1.090
 40U  C16  H5   single    0.970  0.020  1.090
 40U  C15  H6   single    0.970  0.020  1.090
 40U  C19  H7   single    0.970  0.020  1.090
 40U  C19  H8   single    0.970  0.020  1.090
 40U  C19  H9   single    0.970  0.020  1.090
 40U  C20  H10  single    0.970  0.020  1.090
 40U  C20  H11  single    0.970  0.020  1.090
 40U  C20  H12  single    0.970  0.020  1.090
 40U  C21  H13  single    0.970  0.020  1.090
 40U  C21  H14  single    0.970  0.020  1.090
 40U  C21  H15  single    0.970  0.020  1.090
 40U  C22  H16  single    0.970  0.020  1.090
 40U  C22  H17  single    0.970  0.020  1.090
 40U  C22  H18  single    0.970  0.020  1.090
 40U  C12  H19  single    0.970  0.020  1.090
 40U  C5   H20  single    0.930  0.020  1.080
 40U  C4   H21  single    0.930  0.020  1.080
 40U  C2   H22  single    0.930  0.020  1.080
 40U  C1   H23  single    0.930  0.020  1.080
 40U  O2   H24  single    0.850  0.020  0.980
 40U  C10  H25  single    0.970  0.020  1.090
 40U  C10  H26  single    0.970  0.020  1.090
 40U  C9   H27  single    0.970  0.020  1.090
 40U  C9   H28  single    0.970  0.020  1.090
 40U  C8   H29  single    0.970  0.020  1.090
 40U  C8   H30  single    0.970  0.020  1.090
 40U  N1   H31  single    0.860  0.020  1.020
 40U  C14  H32  single    0.970  0.020  1.090
 40U  C14  H33  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
 40U  C14  C13  O1   122.56  3.000
 40U  O1   C13  N1   122.99  3.000
 40U  C14  C13  N1   114.45  3.000
 40U  H1   C18  C12  104.28  3.000
 40U  H1   C18  C20  107.80  3.000
 40U  C12  C18  C20  113.68  3.000
 40U  H1   C18  C19  107.25  3.000
 40U  C20  C18  C19  110.85  3.000
 40U  C12  C18  C19  112.47  3.000
 40U  H3   C17  H2   114.09  3.000
 40U  H3   C17  C15  118.23  3.000
 40U  H2   C17  C15  118.03  3.000
 40U  H3   C17  C16  118.28  3.000
 40U  H2   C17  C16  117.99  3.000
 40U  C15  C17  C16   59.85  3.000
 40U  H5   C16  H4   114.11  3.000
 40U  H5   C16  C15  117.71  3.000
 40U  H4   C16  C15  118.43  3.000
 40U  H5   C16  C17  117.88  3.000
 40U  H4   C16  C17  118.37  3.000
 40U  C15  C16  C17   60.00  3.000
 40U  H6   C15  C14  115.06  3.000
 40U  H6   C15  C16  116.11  3.000
 40U  C14  C15  C16  119.62  3.000
 40U  H6   C15  C17  115.79  3.000
 40U  C16  C15  C17   60.16  3.000
 40U  C14  C15  C17  119.18  3.000
 40U  H9   C19  H8   107.32  3.000
 40U  H9   C19  H7   108.15  3.000
 40U  H8   C19  H7   107.01  3.000
 40U  H9   C19  C18  112.02  3.000
 40U  H8   C19  C18  110.21  3.000
 40U  H7   C19  C18  111.90  3.000
 40U  H12  C20  H11  107.32  3.000
 40U  H12  C20  H10  107.40  3.000
 40U  H11  C20  H10  108.10  3.000
 40U  H12  C20  C18  109.58  3.000
 40U  H11  C20  C18  112.18  3.000
 40U  H10  C20  C18  112.03  3.000
 40U  H15  C21  H14  107.76  3.000
 40U  H15  C21  H13  107.13  3.000
 40U  H14  C21  H13  108.08  3.000
 40U  H15  C21  C7   109.49  3.000
 40U  H14  C21  C7   112.74  3.000
 40U  H13  C21  C7   111.42  3.000
 40U  H18  C22  H17  107.50  3.000
 40U  H18  C22  H16  107.28  3.000
 40U  H17  C22  H16  107.20  3.000
 40U  H18  C22  C7   111.51  3.000
 40U  H17  C22  C7   113.58  3.000
 40U  H16  C22  C7   109.48  3.000
 40U  O    C11  N    122.19  3.000
 40U  N    C11  C12  119.90  3.000
 40U  O    C11  C12  117.90  3.000
 40U  H19  C12  N1   106.70  3.000
 40U  H19  C12  C11  111.66  3.000
 40U  N1   C12  C11  106.68  3.000
 40U  H19  C12  C18  107.52  3.000
 40U  C11  C12  C18  112.66  3.000
 40U  N1   C12  C18  111.50  3.000
 40U  C1   C    C5   120.62  3.000
 40U  C5   C    CL   119.67  3.000
 40U  C1   C    CL   119.71  3.000
 40U  H20  C5   C4   119.98  3.000
 40U  H20  C5   C    120.78  3.000
 40U  C4   C5   C    119.24  3.000
 40U  H21  C4   C3   121.02  3.000
 40U  H21  C4   C5   117.28  3.000
 40U  C3   C4   C5   121.70  3.000
 40U  C6   C3   C2   119.84  3.000
 40U  C6   C3   C4   122.66  3.000
 40U  C2   C3   C4   117.50  3.000
 40U  H22  C2   C1   118.10  3.000
 40U  H22  C2   C3   120.24  3.000
 40U  C1   C2   C3   121.67  3.000
 40U  H23  C1   C2   120.09  3.000
 40U  H23  C1   C    120.64  3.000
 40U  C2   C1   C    119.27  3.000
 40U  C7   C6   C10  109.41  3.000
 40U  C10  C6   O2   108.55  3.000
 40U  C7   C6   O2   105.67  3.000
 40U  O2   C6   C3   109.59  3.000
 40U  C10  C6   C3   111.44  3.000
 40U  C7   C6   C3   111.96  3.000
 40U  H24  O2   C6   108.61  3.000
 40U  H26  C10  H25  106.03  3.000
 40U  H26  C10  C9   108.60  3.000
 40U  H25  C10  C9   108.71  3.000
 40U  H26  C10  C6   111.33  3.000
 40U  H25  C10  C6   109.43  3.000
 40U  C9   C10  C6   112.50  3.000
 40U  H28  C9   H27  106.80  3.000
 40U  H28  C9   N    111.16  3.000
 40U  H27  C9   N    108.90  3.000
 40U  H28  C9   C10  108.75  3.000
 40U  H27  C9   C10  110.34  3.000
 40U  N    C9   C10  110.81  3.000
 40U  C8   N    C9   112.62  3.000
 40U  C9   N    C11  126.80  3.000
 40U  C8   N    C11  119.80  3.000
 40U  H30  C8   H29  107.18  3.000
 40U  H30  C8   C7   108.80  3.000
 40U  H29  C8   C7   110.26  3.000
 40U  H30  C8   N    108.97  3.000
 40U  H29  C8   N    108.72  3.000
 40U  C7   C8   N    112.74  3.000
 40U  C8   C7   C6   108.74  3.000
 40U  C6   C7   C22  111.88  3.000
 40U  C8   C7   C22  109.21  3.000
 40U  C6   C7   C21  111.93  3.000
 40U  C8   C7   C21  107.12  3.000
 40U  C22  C7   C21  107.82  3.000
 40U  H31  N1   C12  117.33  3.000
 40U  H31  N1   C13  119.21  3.000
 40U  C12  N1   C13  123.28  3.000
 40U  H33  C14  H32  105.62  3.000
 40U  H33  C14  C15  110.28  3.000
 40U  H32  C14  C15  110.19  3.000
 40U  H33  C14  C13  109.78  3.000
 40U  H32  C14  C13  107.73  3.000
 40U  C15  C14  C13  112.95  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
 40U  CONST_01  C3   C2   C1   C       0.00   0.0  0
 40U  CONST_02  C3   C4   C5   C       0.00   0.0  0
 40U  CONST_03  C2   C1   C    C5      0.00   0.0  0
 40U  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 40U  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 40U  CONST_06  C1   C    C5   C4      0.00   0.0  0
 40U  CONST_07  C6   C3   C4   C5    180.00   0.0  0
 40U  CONST_08  C6   C3   C2   C1    180.00   0.0  0
 40U  CONST_09  C2   C1   C    CL    180.00   0.0  0
 40U  CONST_10  C4   C5   C    CL    180.00   0.0  0
 40U  CONST_11  H22  C2   C1   C     180.00   0.0  0
 40U  CONST_12  H21  C4   C5   C     180.00   0.0  0
 40U  CONST_13  H23  C1   C    C5    180.00   0.0  0
 40U  CONST_14  H20  C5   C4   C3    180.00   0.0  0
 40U  CONST_15  C8   N    C11  C12   180.00   0.0  0
 40U  CONST_16  C9   N    C11  C12     0.00   0.0  0
 40U  CONST_17  O    C11  N    C9    180.00   0.0  0
 40U  CONST_18  O    C11  N    C8      0.00   0.0  0
 40U  CONST_19  C14  C13  N1   C12   180.00   0.0  0
 40U  CONST_20  O1   C13  N1   C12     0.00   0.0  0
 40U  CONST_21  H31  N1   C13  O1    180.00   0.0  0
 40U  Var_01    N    C8   C7   C6     56.22  30.0  1
 40U  Var_02    N    C9   C10  C6    -55.21  30.0  1
 40U  Var_03    C8   N    C9   C10    56.81  30.0  1
 40U  Var_04    C7   C8   N    C9    -59.02  30.0  1
 40U  Var_05    C14  C15  C16  C17  -108.69  30.0  1
 40U  Var_06    C17  C15  C14  C13  -151.84  30.0  3
 40U  Var_07    H16  C22  C7   C6   -175.01  30.0  3
 40U  Var_08    H13  C21  C7   C6    -65.85  30.0  3
 40U  Var_09    O1   C13  C14  C15   -18.31  30.0  3
 40U  Var_10    H10  C20  C18  C19    57.32  30.0  3
 40U  Var_11    H7   C19  C18  C20   -59.38  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
 40U  chir_02  C12  N1   C18  C11  positiv
 40U  chir_03  C6   C7   C3   C10  negativ
 40U  chir_04  C15  C17  C14  C16  both

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
 40U  plan-1  C    0.020
 40U  plan-1  C5   0.020
 40U  plan-1  C4   0.020
 40U  plan-1  C3   0.020
 40U  plan-1  C2   0.020
 40U  plan-1  C1   0.020
 40U  plan-1  C6   0.020
 40U  plan-1  H21  0.020
 40U  plan-1  H22  0.020
 40U  plan-1  H23  0.020
 40U  plan-1  H20  0.020
 40U  plan-1  CL   0.020
 40U  plan-2  C11  0.020
 40U  plan-2  C12  0.020
 40U  plan-2  C9   0.020
 40U  plan-2  N    0.020
 40U  plan-2  C8   0.020
 40U  plan-2  O    0.020
 40U  plan-3  C13  0.020
 40U  plan-3  C12  0.020
 40U  plan-3  N1   0.020
 40U  plan-3  O1   0.020
 40U  plan-3  C14  0.020
 40U  plan-3  H31  0.020

