# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:06:11 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: [(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl] 4-azanylbenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)C(=O)O[C@H]2C[C@H]3CC[C@@H]2C3
#
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
 XD5  XD5  '[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl] 4-azanylbenzoate'  ligand  34  17  .  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_XD5
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
 XD5  O1   O  O     0  -0.466   0.0043  -2.2316   0.2550
 XD5  C6   C  C     0   0.587   0.2344  -1.0763  -0.0303
 XD5  C4   C  CR6   0  -0.125   1.5767  -0.4734  -0.0167
 XD5  C3   C  CR16  0  -0.267   1.8153   0.8611  -0.3597
 XD5  C2   C  CR16  0  -0.317   3.0901   1.3851  -0.3388
 XD5  C1   C  CR6   0   0.339   4.1884   0.5904   0.0316
 XD5  N    N  NH2   0  -0.854   5.4408   1.1157   0.0969
 XD5  C5   C  CR16  0  -0.252   2.6697  -1.2636   0.3490
 XD5  C    C  CR16  0  -0.319   3.9481  -0.7511   0.3754
 XD5  O    O  O2    0  -0.480  -0.7094  -0.2173  -0.3941
 XD5  C7   C  CH1   0   0.067  -2.0616  -0.6753  -0.4559
 XD5  C12  C  CH2   0  -0.471  -2.7181  -0.9222   0.9249
 XD5  C11  C  CH1   0  -0.255  -3.9374   0.0082   0.8965
 XD5  C10  C  CH2   0  -0.439  -3.4459   1.4553   1.0398
 XD5  C9   C  CH2   0  -0.447  -2.7716   1.7335  -0.3288
 XD5  C13  C  CH2   0  -0.448  -4.3197  -0.0480  -0.5882
 XD5  C8   C  CH1   0  -0.297  -2.9418   0.4075  -1.0836
 XD5  H1   H  HCR6  0   0.261   0.9981   1.5081  -0.6498
 XD5  H2   H  HCR6  0   0.263   3.2488   2.4224  -0.6077
 XD5  H3   H  HNH2  0   0.391   5.6228   1.9739  -0.3954
 XD5  H4   H  HNH2  0   0.391   6.2219   0.4821   0.1230
 XD5  H5   H  HCR6  0   0.256   2.5160  -2.3016   0.6141
 XD5  H6   H  HCR6  0   0.262   4.7779  -1.3868   0.6603
 XD5  H7   H  HCH1  0   0.254  -2.0921  -1.5808  -1.0674
 XD5  H8   H  HCH2  0   0.245  -3.0179  -1.9665   1.0230
 XD5  H9   H  HCH2  0   0.241  -2.0419  -0.7019   1.7536
 XD5  H10  H  HCH1  0   0.228  -4.7172  -0.2671   1.6069
 XD5  H11  H  HCH2  0   0.233  -4.2805   2.1370   1.2142
 XD5  H12  H  HCH2  0   0.227  -2.7559   1.5675   1.8785
 XD5  H13  H  HCH2  0   0.236  -3.2922   2.5275  -0.8671
 XD5  H14  H  HCH2  0   0.240  -1.7316   2.0462  -0.2384
 XD5  H15  H  HCH2  0   0.239  -4.5961  -1.0492  -0.9281
 XD5  H16  H  HCH2  0   0.241  -5.1177   0.6445  -0.8642
 XD5  H17  H  HCH1  0   0.236  -2.8196   0.4898  -2.1643

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
 XD5  N    C1   single    1.360  0.020  1.360
 XD5  C2   C1   aromatic  1.405  0.020  1.405
 XD5  C2   C3   aromatic  1.378  0.020  1.378
 XD5  C1   C    aromatic  1.406  0.020  1.406
 XD5  C3   C4   aromatic  1.398  0.020  1.398
 XD5  C    C5   aromatic  1.378  0.020  1.378
 XD5  C4   C5   aromatic  1.397  0.020  1.397
 XD5  C4   C6   single    1.471  0.020  1.471
 XD5  C9   C10  single    1.551  0.020  1.551
 XD5  C9   C8   single    1.535  0.020  1.535
 XD5  O    C6   single    1.327  0.020  1.327
 XD5  O    C7   single    1.429  0.020  1.429
 XD5  C6   O1   double    1.212  0.020  1.212
 XD5  C10  C11  single    1.535  0.020  1.535
 XD5  C8   C7   single    1.530  0.020  1.530
 XD5  C8   C13  single    1.533  0.020  1.533
 XD5  C7   C12  single    1.549  0.020  1.549
 XD5  C12  C11  single    1.534  0.020  1.534
 XD5  C11  C13  single    1.534  0.020  1.534
 XD5  C3   H1   single    0.930  0.020  1.080
 XD5  C2   H2   single    0.930  0.020  1.080
 XD5  N    H3   single    0.890  0.020  1.040
 XD5  N    H4   single    0.890  0.020  1.040
 XD5  C5   H5   single    0.930  0.020  1.080
 XD5  C    H6   single    0.930  0.020  1.080
 XD5  C7   H7   single    0.970  0.020  1.090
 XD5  C12  H8   single    0.970  0.020  1.090
 XD5  C12  H9   single    0.970  0.020  1.090
 XD5  C11  H10  single    0.970  0.020  1.090
 XD5  C10  H11  single    0.970  0.020  1.090
 XD5  C10  H12  single    0.970  0.020  1.090
 XD5  C9   H13  single    0.970  0.020  1.090
 XD5  C9   H14  single    0.970  0.020  1.090
 XD5  C13  H15  single    0.970  0.020  1.090
 XD5  C13  H16  single    0.970  0.020  1.090
 XD5  C8   H17  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
 XD5  O    C6   C4   112.71  3.000
 XD5  O    C6   O1   123.13  3.000
 XD5  C4   C6   O1   124.16  3.000
 XD5  C5   C4   C3   118.06  3.000
 XD5  C5   C4   C6   118.96  3.000
 XD5  C3   C4   C6   122.98  3.000
 XD5  H1   C3   C2   118.37  3.000
 XD5  H1   C3   C4   120.51  3.000
 XD5  C2   C3   C4   121.12  3.000
 XD5  H2   C2   C1   119.50  3.000
 XD5  H2   C2   C3   119.72  3.000
 XD5  C1   C2   C3   120.78  3.000
 XD5  C    C1   N    120.97  3.000
 XD5  C    C1   C2   118.07  3.000
 XD5  N    C1   C2   120.93  3.000
 XD5  H4   N    H3   114.17  3.000
 XD5  H4   N    C1   118.23  3.000
 XD5  H3   N    C1   118.21  3.000
 XD5  H5   C5   C    118.94  3.000
 XD5  H5   C5   C4   119.69  3.000
 XD5  C    C5   C4   121.36  3.000
 XD5  H6   C    C5   119.83  3.000
 XD5  H6   C    C1   119.56  3.000
 XD5  C5   C    C1   120.60  3.000
 XD5  C7   O    C6   118.52  3.000
 XD5  H7   C7   C8   109.92  3.000
 XD5  H7   C7   C12  110.78  3.000
 XD5  C8   C7   C12  103.57  3.000
 XD5  H7   C7   O    108.43  3.000
 XD5  C12  C7   O    114.43  3.000
 XD5  C8   C7   O    109.59  3.000
 XD5  H9   C12  H8   107.16  3.000
 XD5  H9   C12  C11  112.57  3.000
 XD5  H8   C12  C11  111.34  3.000
 XD5  H9   C12  C7   112.45  3.000
 XD5  H8   C12  C7   110.44  3.000
 XD5  C11  C12  C7   102.93  3.000
 XD5  H10  C11  C13  116.30  3.000
 XD5  H10  C11  C10  113.97  3.000
 XD5  C13  C11  C10  101.81  3.000
 XD5  H10  C11  C12  113.79  3.000
 XD5  C13  C11  C12  101.17  3.000
 XD5  C10  C11  C12  108.40  3.000
 XD5  H12  C10  H11  107.23  3.000
 XD5  H12  C10  C9   112.63  3.000
 XD5  H11  C10  C9   111.19  3.000
 XD5  H12  C10  C11  111.77  3.000
 XD5  H11  C10  C11  111.02  3.000
 XD5  C9   C10  C11  103.06  3.000
 XD5  H14  C9   H13  106.70  3.000
 XD5  H14  C9   C8   113.23  3.000
 XD5  H13  C9   C8   109.45  3.000
 XD5  H14  C9   C10  113.15  3.000
 XD5  H13  C9   C10  111.00  3.000
 XD5  C8   C9   C10  103.34  3.000
 XD5  H16  C13  H15  108.51  3.000
 XD5  H16  C13  C8   112.74  3.000
 XD5  H15  C13  C8   113.51  3.000
 XD5  H16  C13  C11  113.80  3.000
 XD5  H15  C13  C11  113.43  3.000
 XD5  C8   C13  C11   94.47  3.000
 XD5  H17  C8   C13  116.31  3.000
 XD5  H17  C8   C9   114.18  3.000
 XD5  C13  C8   C9   101.38  3.000
 XD5  H17  C8   C7   113.29  3.000
 XD5  C13  C8   C7   100.03  3.000
 XD5  C9   C8   C7   110.23  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
 XD5  CONST_01  C1  C2  C3   C4     0.00   0.0  0
 XD5  CONST_02  C1  C   C5   C4     0.00   0.0  0
 XD5  CONST_03  C   C1  C2   C3     0.00   0.0  0
 XD5  CONST_04  C   C5  C4   C3     0.00   0.0  0
 XD5  CONST_05  C5  C   C1   C2     0.00   0.0  0
 XD5  CONST_06  C5  C4  C3   C2     0.00   0.0  0
 XD5  CONST_07  C2  C3  C4   C6   180.00   0.0  0
 XD5  CONST_08  C   C5  C4   C6   180.00   0.0  0
 XD5  CONST_09  N   C1  C2   C3   180.00   0.0  0
 XD5  CONST_10  C5  C   C1   N    180.00   0.0  0
 XD5  CONST_11  H2  C2  C3   C4   180.00   0.0  0
 XD5  CONST_12  H6  C   C5   C4   180.00   0.0  0
 XD5  CONST_13  H5  C5  C4   C3   180.00   0.0  0
 XD5  CONST_14  H1  C3  C2   C1   180.00   0.0  0
 XD5  Var_01    C8  C9  C10  C11   -0.71  30.0  1
 XD5  Var_02    C3  C4  C6   O1   179.54  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
 XD5  chir_01  C7   O    C8   C12  positiv
 XD5  chir_02  C11  C13  C12  C10  negativ
 XD5  chir_03  C8   C13  C7   C9   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
 XD5  plan-1  C6  0.020
 XD5  plan-1  C4  0.020
 XD5  plan-1  C3  0.020
 XD5  plan-1  C2  0.020
 XD5  plan-1  C1  0.020
 XD5  plan-1  N   0.020
 XD5  plan-1  C5  0.020
 XD5  plan-1  C   0.020
 XD5  plan-1  H1  0.020
 XD5  plan-1  H2  0.020
 XD5  plan-1  H5  0.020
 XD5  plan-1  H6  0.020
 XD5  plan-2  C1  0.020
 XD5  plan-2  N   0.020
 XD5  plan-2  H3  0.020
 XD5  plan-2  H4  0.020
 XD5  plan-3  O1  0.020
 XD5  plan-3  C6  0.020
 XD5  plan-3  C4  0.020
 XD5  plan-3  O   0.020

