# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:55:47 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-adamantyl-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Cl)cc1N2CCN(CC2)C(=O)C34CC5CC(CC(C5)C3)C4
#
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
 AWL  AWL  1-adamantyl-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]methanone  ligand  55  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AWL
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
 AWL  C    C   CH2   0  -0.319  -0.1900   2.0891   1.0154
 AWL  C10  C   CR6   0   0.079  -4.2982   1.4608  -0.2273
 AWL  C6   C   C     0  -0.387   4.2922   0.0903   1.2658
 AWL  C19  C   CR16  0  -0.253   5.4457  -0.6981   0.6421
 AWL  C17  C   CH2   0  -0.416   5.9304   0.0046  -0.6253
 AWL  C21  C   C     0  -0.417   4.9752  -2.1085   0.2895
 AWL  C20  C   C     0  -0.244   3.8076  -2.0098  -0.6897
 AWL  C7   C   C     0  -0.422   2.6571  -1.2348  -0.0428
 AWL  C18  C   C     0  -0.420   4.2569  -1.2853  -1.9613
 AWL  C16  C   CR16  0  -0.243   4.7656   0.1144  -1.6064
 AWL  C8   C   C     0  -0.426   3.6305   0.9238  -0.9724
 AWL  C5   C   C     0  -0.265   3.1033   0.2061   0.2892
 AWL  C4   C   C     0   0.620   1.9893   1.0088   0.9810
 AWL  O    O   O     0  -0.495   2.1563   1.3926   2.1332
 AWL  N    N   NT    0  -0.471   0.8333   1.3118   0.3336
 AWL  C1   C   CH2   0  -0.332   0.3895   0.9273  -0.9934
 AWL  C2   C   CH2   0  -0.297  -0.9169   0.1506  -0.9216
 AWL  C3   C   CH2   0  -0.307  -1.4918   1.3151   1.0900
 AWL  N1   N   NT    0  -0.513  -1.9276   0.9387  -0.2473
 AWL  C9   C   CR6   0   0.285  -3.2618   0.5167  -0.3574
 AWL  C14  C   CR16  0  -0.267  -3.5773  -0.8165  -0.6264
 AWL  C13  C   CR6   0  -0.053  -4.8992  -1.2060  -0.7583
 AWL  CL   CL  CL    0  -0.140  -5.2558  -2.8717  -1.1011
 AWL  C12  C   CR16  0  -0.227  -5.9345  -0.3020  -0.6130
 AWL  C11  C   CR16  0  -0.312  -5.6113   1.0217  -0.3493
 AWL  H1   H   HCH2  0   0.271   0.1449   2.3460   2.0147
 AWL  H2   H   HCH2  0   0.242  -0.3562   3.0208   0.4640
 AWL  H3   H   H     0   0.226   3.9742  -0.4029   2.1874
 AWL  H4   H   H     0   0.226   4.6430   1.0863   1.5466
 AWL  H5   H   HCR6  0   0.225   6.2615  -0.7528   1.3692
 AWL  H6   H   HCH2  0   0.222   6.3184   0.9999  -0.3848
 AWL  H7   H   HCH2  0   0.222   6.7556  -0.5566  -1.0755
 AWL  H8   H   H     0   0.222   5.7957  -2.6844  -0.1513
 AWL  H9   H   H     0   0.222   4.6622  -2.6421   1.1930
 AWL  H10  H   H     0   0.229   3.4512  -3.0118  -0.9462
 AWL  H11  H   H     0   0.239   1.7988  -1.2621  -0.7149
 AWL  H12  H   H     0   0.236   2.3404  -1.7357   0.8779
 AWL  H13  H   H     0   0.227   5.0446  -1.8575  -2.4613
 AWL  H14  H   H     0   0.223   3.4221  -1.2137  -2.6667
 AWL  H15  H   HCR6  0   0.228   5.0926   0.6271  -2.5160
 AWL  H16  H   H     0   0.236   3.9904   1.9197  -0.6941
 AWL  H17  H   H     0   0.245   2.8526   1.0786  -1.7209
 AWL  H18  H   HCH2  0   0.255   0.2454   1.8306  -1.5951
 AWL  H19  H   HCH2  0   0.261   1.1206   0.3185  -1.5081
 AWL  H20  H   HCH2  0   0.262  -1.2464  -0.0673  -1.9387
 AWL  H21  H   HCH2  0   0.216  -0.7227  -0.8121  -0.4230
 AWL  H22  H   HCH2  0   0.228  -1.3603   0.4274   1.7274
 AWL  H23  H   HCH2  0   0.261  -2.2416   1.9416   1.5699
 AWL  H24  H   HCR6  0   0.280  -2.7944  -1.5564  -0.7232
 AWL  H25  H   HCR6  0   0.273  -6.9658  -0.6087  -0.7196
 AWL  H26  H   HCR6  0   0.257  -6.4142   1.7437  -0.2615
 AWL  H27  H   HCH3  0   0.248  -3.9489   3.1715   1.0490
 AWL  H28  H   HCH3  0   0.248  -3.0811   3.2168  -0.4786
 AWL  H29  H   HCH3  0   0.255  -4.8207   3.5286  -0.4280
 AWL  C15  C   CH3   0  -0.744  -4.0196   2.9189  -0.0114

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
 AWL  C21  C19  single    1.528  0.020  1.528
 AWL  C21  C20  single    1.527  0.020  1.527
 AWL  C19  C17  single    1.528  0.020  1.528
 AWL  C19  C6   single    1.530  0.020  1.530
 AWL  C17  C16  single    1.527  0.020  1.527
 AWL  C6   C5   single    1.543  0.020  1.543
 AWL  C20  C18  single    1.531  0.020  1.531
 AWL  C20  C7   single    1.531  0.020  1.531
 AWL  C18  C16  single    1.531  0.020  1.531
 AWL  C16  C8   single    1.532  0.020  1.532
 AWL  C7   C5   single    1.545  0.020  1.545
 AWL  C5   C8   single    1.544  0.020  1.544
 AWL  C5   C4   single    1.537  0.020  1.537
 AWL  O    C4   double    1.226  0.020  1.226
 AWL  C4   N    single    1.359  0.020  1.359
 AWL  N    C    single    1.455  0.020  1.455
 AWL  N    C1   single    1.451  0.020  1.451
 AWL  C    C3   single    1.516  0.020  1.516
 AWL  C1   C2   single    1.522  0.020  1.522
 AWL  C3   N1   single    1.456  0.020  1.456
 AWL  C2   N1   single    1.448  0.020  1.448
 AWL  N1   C9   single    1.404  0.020  1.404
 AWL  C14  C9   aromatic  1.396  0.020  1.396
 AWL  C14  C13  aromatic  1.384  0.020  1.384
 AWL  C9   C10  aromatic  1.408  0.020  1.408
 AWL  CL   C13  single    1.738  0.020  1.738
 AWL  C13  C12  aromatic  1.382  0.020  1.382
 AWL  C10  C15  single    1.500  0.020  1.500
 AWL  C10  C11  aromatic  1.390  0.020  1.390
 AWL  C12  C11  aromatic  1.388  0.020  1.388
 AWL  C    H1   single    0.970  0.020  1.090
 AWL  C    H2   single    0.970  0.020  1.090
 AWL  C6   H3   single    0.970  0.020  1.090
 AWL  C6   H4   single    0.970  0.020  1.090
 AWL  C19  H5   single    0.970  0.020  1.090
 AWL  C17  H6   single    0.970  0.020  1.090
 AWL  C17  H7   single    0.970  0.020  1.090
 AWL  C21  H8   single    0.970  0.020  1.090
 AWL  C21  H9   single    0.970  0.020  1.090
 AWL  C20  H10  single    0.970  0.020  1.090
 AWL  C7   H11  single    0.970  0.020  1.090
 AWL  C7   H12  single    0.970  0.020  1.090
 AWL  C18  H13  single    0.970  0.020  1.090
 AWL  C18  H14  single    0.970  0.020  1.090
 AWL  C16  H15  single    0.970  0.020  1.090
 AWL  C8   H16  single    0.970  0.020  1.090
 AWL  C8   H17  single    0.970  0.020  1.090
 AWL  C1   H18  single    0.970  0.020  1.090
 AWL  C1   H19  single    0.970  0.020  1.090
 AWL  C2   H20  single    0.970  0.020  1.090
 AWL  C2   H21  single    0.970  0.020  1.090
 AWL  C3   H22  single    0.970  0.020  1.090
 AWL  C3   H23  single    0.970  0.020  1.090
 AWL  C14  H24  single    0.930  0.020  1.080
 AWL  C12  H25  single    0.930  0.020  1.080
 AWL  C11  H26  single    0.930  0.020  1.080
 AWL  C15  H27  single    0.970  0.020  1.090
 AWL  C15  H28  single    0.970  0.020  1.090
 AWL  C15  H29  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
 AWL  H2   C    H1   108.01  3.000
 AWL  H2   C    C3   109.19  3.000
 AWL  H1   C    C3   109.91  3.000
 AWL  H2   C    N    108.98  3.000
 AWL  H1   C    N    109.95  3.000
 AWL  C3   C    N    110.74  3.000
 AWL  C15  C10  C11  119.68  3.000
 AWL  C11  C10  C9   118.39  3.000
 AWL  C15  C10  C9   121.90  3.000
 AWL  H4   C6   H3   106.75  3.000
 AWL  H4   C6   C5   109.97  3.000
 AWL  H3   C6   C5   110.09  3.000
 AWL  H4   C6   C19  109.41  3.000
 AWL  H3   C6   C19  109.31  3.000
 AWL  C5   C6   C19  111.20  3.000
 AWL  H5   C19  C21  109.68  3.000
 AWL  H5   C19  C17  109.73  3.000
 AWL  C21  C19  C17  109.31  3.000
 AWL  H5   C19  C6   108.48  3.000
 AWL  C17  C19  C6   109.89  3.000
 AWL  C21  C19  C6   109.73  3.000
 AWL  H7   C17  H6   106.80  3.000
 AWL  H7   C17  C16  110.35  3.000
 AWL  H6   C17  C16  110.25  3.000
 AWL  H7   C17  C19  110.15  3.000
 AWL  H6   C17  C19  110.38  3.000
 AWL  C16  C17  C19  108.91  3.000
 AWL  H9   C21  H8   106.86  3.000
 AWL  H9   C21  C20  110.00  3.000
 AWL  H8   C21  C20  110.41  3.000
 AWL  H9   C21  C19  110.33  3.000
 AWL  H8   C21  C19  110.34  3.000
 AWL  C20  C21  C19  108.89  3.000
 AWL  H10  C20  C18  109.54  3.000
 AWL  H10  C20  C7   108.54  3.000
 AWL  C18  C20  C7   109.39  3.000
 AWL  H10  C20  C21  109.89  3.000
 AWL  C7   C20  C21  109.66  3.000
 AWL  C18  C20  C21  109.81  3.000
 AWL  H12  C7   H11  106.21  3.000
 AWL  H12  C7   C5   109.24  3.000
 AWL  H11  C7   C5   112.53  3.000
 AWL  H12  C7   C20  109.95  3.000
 AWL  H11  C7   C20  108.57  3.000
 AWL  C5   C7   C20  110.25  3.000
 AWL  H14  C18  H13  106.77  3.000
 AWL  H14  C18  C16  110.05  3.000
 AWL  H13  C18  C16  110.17  3.000
 AWL  H14  C18  C20  110.01  3.000
 AWL  H13  C18  C20  110.07  3.000
 AWL  C16  C18  C20  109.73  3.000
 AWL  H15  C16  C8   108.54  3.000
 AWL  H15  C16  C18  109.57  3.000
 AWL  C8   C16  C18  109.44  3.000
 AWL  H15  C16  C17  109.87  3.000
 AWL  C8   C16  C17  109.72  3.000
 AWL  C18  C16  C17  109.67  3.000
 AWL  H17  C8   H16  106.25  3.000
 AWL  H17  C8   C5   112.53  3.000
 AWL  H16  C8   C5   109.11  3.000
 AWL  H17  C8   C16  108.64  3.000
 AWL  H16  C8   C16  110.02  3.000
 AWL  C5   C8   C16  110.22  3.000
 AWL  C4   C5   C8   111.86  3.000
 AWL  C4   C5   C7   111.99  3.000
 AWL  C8   C5   C7   110.89  3.000
 AWL  C4   C5   C6   108.22  3.000
 AWL  C8   C5   C6   106.79  3.000
 AWL  C7   C5   C6   106.77  3.000
 AWL  N    C4   O    119.58  3.000
 AWL  N    C4   C5   121.22  3.000
 AWL  O    C4   C5   119.19  3.000
 AWL  C1   N    C4   129.54  3.000
 AWL  C1   N    C    110.80  3.000
 AWL  C4   N    C    119.62  3.000
 AWL  H19  C1   H18  106.97  3.000
 AWL  H19  C1   C2   108.39  3.000
 AWL  H18  C1   C2   109.52  3.000
 AWL  H19  C1   N    112.18  3.000
 AWL  H18  C1   N    108.92  3.000
 AWL  C2   C1   N    110.77  3.000
 AWL  H21  C2   H20  107.50  3.000
 AWL  H21  C2   N1   112.83  3.000
 AWL  H20  C2   N1   109.39  3.000
 AWL  H21  C2   C1   108.43  3.000
 AWL  H20  C2   C1   108.49  3.000
 AWL  N1   C2   C1   110.09  3.000
 AWL  H23  C3   H22  106.93  3.000
 AWL  H23  C3   N1   110.34  3.000
 AWL  H22  C3   N1   111.04  3.000
 AWL  H23  C3   C    108.62  3.000
 AWL  H22  C3   C    109.73  3.000
 AWL  N1   C3   C    110.11  3.000
 AWL  C9   N1   C3   115.74  3.000
 AWL  C9   N1   C2   117.60  3.000
 AWL  C3   N1   C2   111.06  3.000
 AWL  C14  C9   N1   121.13  3.000
 AWL  C14  C9   C10  119.46  3.000
 AWL  N1   C9   C10  119.40  3.000
 AWL  H24  C14  C13  119.35  3.000
 AWL  H24  C14  C9   120.46  3.000
 AWL  C13  C14  C9   120.19  3.000
 AWL  C12  C13  CL   119.61  3.000
 AWL  C12  C13  C14  121.41  3.000
 AWL  CL   C13  C14  118.98  3.000
 AWL  H25  C12  C11  120.75  3.000
 AWL  H25  C12  C13  121.23  3.000
 AWL  C11  C12  C13  118.00  3.000
 AWL  H26  C11  C12  118.59  3.000
 AWL  H26  C11  C10  118.85  3.000
 AWL  C12  C11  C10  122.54  3.000
 AWL  H29  C15  H28  108.44  3.000
 AWL  H29  C15  H27  106.82  3.000
 AWL  H28  C15  H27  107.29  3.000
 AWL  H29  C15  C10  110.63  3.000
 AWL  H28  C15  C10  111.34  3.000
 AWL  H27  C15  C10  112.12  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
 AWL  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 AWL  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 AWL  CONST_03  C12  C13  C14  C9     0.00   0.0  0
 AWL  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 AWL  CONST_05  C11  C10  C9   C14    0.00   0.0  0
 AWL  CONST_06  C11  C12  C13  C14    0.00   0.0  0
 AWL  CONST_07  C13  C14  C9   N1   180.00   0.0  0
 AWL  CONST_08  C11  C10  C9   N1   180.00   0.0  0
 AWL  CONST_09  C15  C10  C9   N1     0.00   0.0  0
 AWL  CONST_10  CL   C13  C14  C9   180.00   0.0  0
 AWL  CONST_11  C15  C10  C9   C14  180.00   0.0  0
 AWL  CONST_12  C11  C12  C13  CL   180.00   0.0  0
 AWL  CONST_13  C15  C10  C11  C12  180.00   0.0  0
 AWL  CONST_14  C5   C4   N    C    180.00   0.0  0
 AWL  CONST_15  C1   N    C4   C5     0.00   0.0  0
 AWL  CONST_16  H24  C14  C9   C10  180.00   0.0  0
 AWL  CONST_17  H25  C12  C11  C10  180.00   0.0  0
 AWL  CONST_18  H26  C11  C10  C9   180.00   0.0  0
 AWL  CONST_19  O    C4   N    C      0.00   0.0  0
 AWL  CONST_20  C1   N    C4   O    180.00   0.0  0
 AWL  Var_01    C2   C1   N    C    -56.75  30.0  1
 AWL  Var_02    C2   N1   C3   C     57.73  30.0  1
 AWL  Var_03    C3   N1   C9   C10   71.34  30.0  2
 AWL  Var_04    N1   C3   C    N    -56.88  30.0  1
 AWL  Var_05    N1   C2   C1   N     57.00  30.0  1
 AWL  Var_06    C3   C    N    C1    56.81  30.0  1
 AWL  Var_07    H27  C15  C10  C9   -89.86  30.0  2

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
 AWL  chir_01  C19  C21  C17  C6  negativ
 AWL  chir_02  C20  C21  C18  C7  positiv
 AWL  chir_03  C16  C17  C18  C8  negativ
 AWL  chir_04  C5   C8   C7   C6  negativ

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
 AWL  plan-1  C10  0.020
 AWL  plan-1  N1   0.020
 AWL  plan-1  C9   0.020
 AWL  plan-1  C14  0.020
 AWL  plan-1  C13  0.020
 AWL  plan-1  CL   0.020
 AWL  plan-1  C12  0.020
 AWL  plan-1  C11  0.020
 AWL  plan-1  H24  0.020
 AWL  plan-1  H25  0.020
 AWL  plan-1  H26  0.020
 AWL  plan-1  C15  0.020
 AWL  plan-2  C    0.020
 AWL  plan-2  C5   0.020
 AWL  plan-2  C4   0.020
 AWL  plan-2  O    0.020
 AWL  plan-2  N    0.020
 AWL  plan-2  C1   0.020

