# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:42:04 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: [(1~{R},2~{R},4~{R})-1,7,7-trimethyl-2-bicyclo[2.2.1]heptanyl] 4-azanyl-3-methyl-benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1N)C(=O)O[C@@H]2C[C@H]3CC[C@]2(C)C3(C)C
#
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
 XD4  XD4  '[(1~{R},2~{R},4~{R})-1,7,7-trimethyl-2-bicyclo[2.2.1]heptanyl] 4-azanyl-3-methyl-benzoate'  ligand  46  21  .  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_XD4
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
 XD4  O1   O  O     0  -0.468   0.5247   2.3170   0.1629
 XD4  C3   C  C     0   0.592   0.6334   1.1339  -0.0791
 XD4  C4   C  CR6   0  -0.112   1.9174   0.4158  -0.1349
 XD4  C10  C  CR16  0  -0.286   2.0105  -0.9487  -0.4131
 XD4  C9   C  CR16  0  -0.313   3.2388  -1.5745  -0.4381
 XD4  C8   C  CR6   0   0.289   4.4205  -0.8608  -0.1876
 XD4  N    N  NH2   0  -0.852   5.6309  -1.4859  -0.2575
 XD4  C6   C  CR6   0   0.070   4.3409   0.5223   0.0882
 XD4  C7   C  CH3   0  -0.750   5.5904   1.3095   0.3487
 XD4  C5   C  CR16  0  -0.321   3.0976   1.1235   0.1087
 XD4  O    O  O2    0  -0.479  -0.4035   0.3438  -0.3214
 XD4  C2   C  CH1   0   0.095  -1.7194   0.9050  -0.2774
 XD4  C11  C  CH2   0  -0.476  -2.2152   1.2024   1.1562
 XD4  C12  C  CH1   0  -0.231  -3.5108   0.3841   1.2545
 XD4  C13  C  CT    0  -0.029  -3.1606  -0.8996   0.4720
 XD4  C15  C  CH3   0  -0.666  -4.3484  -1.8410   0.2609
 XD4  C14  C  CH3   0  -0.656  -2.0662  -1.7407   1.1309
 XD4  C16  C  CH2   0  -0.439  -4.5377   1.0695   0.3446
 XD4  C17  C  CH2   0  -0.450  -4.0009   0.7421  -1.0693
 XD4  C1   C  CT    0  -0.087  -2.7424  -0.1167  -0.8074
 XD4  C    C  CH3   0  -0.677  -2.2971  -0.9110  -2.0152
 XD4  H1   H  HCR6  0   0.259   1.1222  -1.5352  -0.6055
 XD4  H2   H  HCR6  0   0.260   3.2968  -2.6357  -0.6491
 XD4  H3   H  HNH2  0   0.390   5.6324  -2.4921  -0.2297
 XD4  H4   H  HNH2  0   0.394   6.4108  -1.0756   0.2281
 XD4  H5   H  HCH3  0   0.246   6.3005   1.2217  -0.4766
 XD4  H6   H  HCH3  0   0.258   5.3674   2.3665   0.4831
 XD4  H7   H  HCH3  0   0.245   6.1062   0.9696   1.2511
 XD4  H8   H  HCR6  0   0.247   3.0412   2.1845   0.3208
 XD4  H9   H  HCH1  0   0.243  -1.7197   1.7993  -0.9060
 XD4  H10  H  HCH2  0   0.249  -1.4804   0.8863   1.8984
 XD4  H11  H  HCH2  0   0.243  -2.3857   2.2674   1.3187
 XD4  H12  H  HCH1  0   0.222  -3.8519   0.2276   2.2801
 XD4  H13  H  HCH3  0   0.234  -5.1986  -1.3925  -0.2495
 XD4  H14  H  HCH3  0   0.227  -4.0443  -2.7120  -0.3240
 XD4  H15  H  HCH3  0   0.227  -4.7061  -2.2108   1.2245
 XD4  H16  H  HCH3  0   0.221  -2.4496  -2.1731   2.0584
 XD4  H17  H  HCH3  0   0.222  -1.7787  -2.5756   0.4879
 XD4  H18  H  HCH3  0   0.235  -1.1574  -1.2000   1.3793
 XD4  H19  H  HCH2  0   0.236  -5.5433   0.6742   0.4951
 XD4  H20  H  HCH2  0   0.231  -4.5938   2.1426   0.5365
 XD4  H21  H  HCH2  0   0.240  -4.7290   0.1821  -1.6585
 XD4  H22  H  HCH2  0   0.236  -3.7582   1.6358  -1.6485
 XD4  H23  H  HCH3  0   0.226  -1.9569  -0.2528  -2.8179
 XD4  H24  H  HCH3  0   0.232  -1.4821  -1.5990  -1.7879
 XD4  H25  H  HCH3  0   0.226  -3.1272  -1.4980  -2.4118

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
 XD4  C16  C17  single    1.547  0.020  1.547
 XD4  C16  C12  single    1.534  0.020  1.534
 XD4  C17  C1   single    1.546  0.020  1.546
 XD4  C9   C10  aromatic  1.379  0.020  1.379
 XD4  C9   C8   aromatic  1.403  0.020  1.403
 XD4  N    C8   single    1.364  0.020  1.364
 XD4  C10  C4   aromatic  1.396  0.020  1.396
 XD4  C12  C11  single    1.536  0.020  1.536
 XD4  C12  C13  single    1.544  0.020  1.544
 XD4  C1   C2   single    1.540  0.020  1.540
 XD4  C1   C    single    1.513  0.020  1.513
 XD4  C1   C13  single    1.557  0.020  1.557
 XD4  C11  C2   single    1.546  0.020  1.546
 XD4  C2   O    single    1.431  0.020  1.431
 XD4  C8   C6   aromatic  1.413  0.020  1.413
 XD4  C15  C13  single    1.530  0.020  1.530
 XD4  C13  C14  single    1.529  0.020  1.529
 XD4  C4   C3   single    1.472  0.020  1.472
 XD4  C4   C5   aromatic  1.398  0.020  1.398
 XD4  C3   O    single    1.326  0.020  1.326
 XD4  C3   O1   double    1.213  0.020  1.213
 XD4  C6   C5   aromatic  1.381  0.020  1.381
 XD4  C6   C7   single    1.500  0.020  1.500
 XD4  C10  H1   single    0.930  0.020  1.080
 XD4  C9   H2   single    0.930  0.020  1.080
 XD4  N    H3   single    0.890  0.020  1.040
 XD4  N    H4   single    0.890  0.020  1.040
 XD4  C7   H5   single    0.970  0.020  1.090
 XD4  C7   H6   single    0.970  0.020  1.090
 XD4  C7   H7   single    0.970  0.020  1.090
 XD4  C5   H8   single    0.930  0.020  1.080
 XD4  C2   H9   single    0.970  0.020  1.090
 XD4  C11  H10  single    0.970  0.020  1.090
 XD4  C11  H11  single    0.970  0.020  1.090
 XD4  C12  H12  single    0.970  0.020  1.090
 XD4  C15  H13  single    0.970  0.020  1.090
 XD4  C15  H14  single    0.970  0.020  1.090
 XD4  C15  H15  single    0.970  0.020  1.090
 XD4  C14  H16  single    0.970  0.020  1.090
 XD4  C14  H17  single    0.970  0.020  1.090
 XD4  C14  H18  single    0.970  0.020  1.090
 XD4  C16  H19  single    0.970  0.020  1.090
 XD4  C16  H20  single    0.970  0.020  1.090
 XD4  C17  H21  single    0.970  0.020  1.090
 XD4  C17  H22  single    0.970  0.020  1.090
 XD4  C    H23  single    0.970  0.020  1.090
 XD4  C    H24  single    0.970  0.020  1.090
 XD4  C    H25  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
 XD4  O    C3   C4   112.61  3.000
 XD4  O    C3   O1   123.21  3.000
 XD4  C4   C3   O1   124.18  3.000
 XD4  C5   C4   C10  118.26  3.000
 XD4  C5   C4   C3   118.88  3.000
 XD4  C10  C4   C3   122.86  3.000
 XD4  H1   C10  C9   118.84  3.000
 XD4  H1   C10  C4   120.71  3.000
 XD4  C9   C10  C4   120.45  3.000
 XD4  H2   C9   C8   119.20  3.000
 XD4  H2   C9   C10  119.72  3.000
 XD4  C8   C9   C10  121.08  3.000
 XD4  C6   C8   N    120.58  3.000
 XD4  C6   C8   C9   119.04  3.000
 XD4  N    C8   C9   120.34  3.000
 XD4  H4   N    H3   113.15  3.000
 XD4  H4   N    C8   118.44  3.000
 XD4  H3   N    C8   117.25  3.000
 XD4  C5   C6   C7   121.27  3.000
 XD4  C7   C6   C8   120.06  3.000
 XD4  C5   C6   C8   118.67  3.000
 XD4  H7   C7   H6   107.25  3.000
 XD4  H7   C7   H5   106.97  3.000
 XD4  H6   C7   H5   107.73  3.000
 XD4  H7   C7   C6   111.92  3.000
 XD4  H6   C7   C6   111.13  3.000
 XD4  H5   C7   C6   111.60  3.000
 XD4  H8   C5   C6   118.43  3.000
 XD4  H8   C5   C4   119.08  3.000
 XD4  C6   C5   C4   122.49  3.000
 XD4  C2   O    C3   118.67  3.000
 XD4  H9   C2   C1   110.16  3.000
 XD4  H9   C2   C11  112.08  3.000
 XD4  C1   C2   C11  103.52  3.000
 XD4  H9   C2   O    107.67  3.000
 XD4  C11  C2   O    113.50  3.000
 XD4  C1   C2   O    109.88  3.000
 XD4  H11  C11  H10  106.66  3.000
 XD4  H11  C11  C12  112.27  3.000
 XD4  H10  C11  C12  111.73  3.000
 XD4  H11  C11  C2   112.09  3.000
 XD4  H10  C11  C2   111.04  3.000
 XD4  C12  C11  C2   103.15  3.000
 XD4  H12  C12  C16  114.34  3.000
 XD4  H12  C12  C13  115.33  3.000
 XD4  C16  C12  C13  102.88  3.000
 XD4  H12  C12  C11  113.58  3.000
 XD4  C13  C12  C11  102.67  3.000
 XD4  C16  C12  C11  106.78  3.000
 XD4  C1   C13  C14  115.99  3.000
 XD4  C14  C13  C15  106.05  3.000
 XD4  C1   C13  C15  113.85  3.000
 XD4  C14  C13  C12  113.66  3.000
 XD4  C15  C13  C12  113.92  3.000
 XD4  C1   C13  C12   93.40  3.000
 XD4  H15  C15  H14  107.08  3.000
 XD4  H15  C15  H13  107.31  3.000
 XD4  H14  C15  H13  107.15  3.000
 XD4  H15  C15  C13  109.92  3.000
 XD4  H14  C15  C13  110.38  3.000
 XD4  H13  C15  C13  114.68  3.000
 XD4  H18  C14  H17  107.14  3.000
 XD4  H18  C14  H16  107.25  3.000
 XD4  H17  C14  H16  106.83  3.000
 XD4  H18  C14  C13  115.05  3.000
 XD4  H17  C14  C13  110.80  3.000
 XD4  H16  C14  C13  109.40  3.000
 XD4  H20  C16  H19  106.53  3.000
 XD4  H20  C16  C17  112.74  3.000
 XD4  H19  C16  C17  111.67  3.000
 XD4  H20  C16  C12  111.68  3.000
 XD4  H19  C16  C12  111.92  3.000
 XD4  C17  C16  C12  102.43  3.000
 XD4  H22  C17  H21  106.37  3.000
 XD4  H22  C17  C1   111.32  3.000
 XD4  H21  C17  C1   110.46  3.000
 XD4  H22  C17  C16  112.86  3.000
 XD4  H21  C17  C16  111.74  3.000
 XD4  C1   C17  C16  104.19  3.000
 XD4  C    C1   C17  113.34  3.000
 XD4  C    C1   C13  118.11  3.000
 XD4  C17  C1   C13  101.53  3.000
 XD4  C13  C1   C2   103.25  3.000
 XD4  C    C1   C2   115.32  3.000
 XD4  C17  C1   C2   103.33  3.000
 XD4  H25  C    H24  107.76  3.000
 XD4  H25  C    H23  107.09  3.000
 XD4  H24  C    H23  107.49  3.000
 XD4  H25  C    C1   110.40  3.000
 XD4  H24  C    C1   112.64  3.000
 XD4  H23  C    C1   111.22  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
 XD4  CONST_01  C8   C9   C10  C4     0.00   0.0  0
 XD4  CONST_02  C8   C6   C5   C4     0.00   0.0  0
 XD4  CONST_03  C6   C8   C9   C10    0.00   0.0  0
 XD4  CONST_04  C6   C5   C4   C10    0.00   0.0  0
 XD4  CONST_05  C5   C4   C10  C9     0.00   0.0  0
 XD4  CONST_06  C5   C6   C8   C9     0.00   0.0  0
 XD4  CONST_07  C9   C10  C4   C3   180.00   0.0  0
 XD4  CONST_08  C6   C5   C4   C3   180.00   0.0  0
 XD4  CONST_09  C7   C6   C5   C4   180.00   0.0  0
 XD4  CONST_10  N    C8   C9   C10  180.00   0.0  0
 XD4  CONST_11  C7   C6   C8   C9   180.00   0.0  0
 XD4  CONST_12  C5   C6   C8   N    180.00   0.0  0
 XD4  CONST_13  H2   C9   C10  C4   180.00   0.0  0
 XD4  CONST_14  H8   C5   C4   C10  180.00   0.0  0
 XD4  CONST_15  H1   C10  C9   C8   180.00   0.0  0
 XD4  Var_01    C1   C17  C16  C12    1.05  30.0  1
 XD4  Var_02    C10  C4   C3   O1   179.84  30.0  3
 XD4  Var_03    H5   C7   C6   C8    56.23  30.0  2
 XD4  Var_04    H13  C15  C13  C12   57.08  30.0  3
 XD4  Var_05    H16  C14  C13  C12   68.68  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
 XD4  chir_01  C2   C1   C11  O    negativ
 XD4  chir_02  C12  C16  C11  C13  positiv
 XD4  chir_03  C1   C2   C17  C13  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
 XD4  plan-1  C3   0.020
 XD4  plan-1  C4   0.020
 XD4  plan-1  C10  0.020
 XD4  plan-1  C9   0.020
 XD4  plan-1  C8   0.020
 XD4  plan-1  N    0.020
 XD4  plan-1  C6   0.020
 XD4  plan-1  C7   0.020
 XD4  plan-1  C5   0.020
 XD4  plan-1  H1   0.020
 XD4  plan-1  H2   0.020
 XD4  plan-1  H8   0.020
 XD4  plan-2  C8   0.020
 XD4  plan-2  N    0.020
 XD4  plan-2  H3   0.020
 XD4  plan-2  H4   0.020
 XD4  plan-3  O1   0.020
 XD4  plan-3  C3   0.020
 XD4  plan-3  C4   0.020
 XD4  plan-3  O    0.020

