# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:46:28 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-[(1~{R},2~{R},6~{S},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C(=O)[C@H]2[C@H]3CC[C@H](C3)[C@H]2C1=O
#
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
 JWB  JWB  '2-[(1~{R},2~{R},6~{S},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]ethanoic acid'  ligand  28  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JWB
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
 JWB  C2   C  C      0   0.418   3.1749   0.0232   0.2244
 JWB  C4   C  CH2    0  -0.473   2.0504   0.0108  -0.8371
 JWB  C6   C  CR5    0   0.561   0.1033   1.1543   0.1685
 JWB  C8   C  CR15   0  -0.386  -1.1809   0.7689   0.8501
 JWB  C11  C  CH2    0  -0.462  -2.3437  -0.7907  -1.3835
 JWB  C12  C  CH1    0  -0.237  -2.4698  -1.1389   0.1064
 JWB  C15  C  CR5    0   0.561   0.1149  -1.1455   0.1763
 JWB  O1   O  O      0  -0.592   2.8290   0.0249   1.4161
 JWB  O3   O  OC    -1  -0.613   4.3268   0.0290  -0.2456
 JWB  N5   N  NR5    0  -0.488   0.7365   0.0062  -0.2493
 JWB  C9   C  CH1    0  -0.237  -2.4811   1.1198   0.0962
 JWB  C10  C  CH2    0  -0.462  -2.3513   0.7597  -1.3905
 JWB  C13  C  CH2    0  -0.445  -3.3883  -0.0118   0.6006
 JWB  C14  C  CR15   0  -0.386  -1.1728  -0.7681   0.8561
 JWB  H1   H  HCH2   0   0.268   2.1402   0.8827  -1.4856
 JWB  H2   H  HCH2   0   0.268   2.1503  -0.8692  -1.4733
 JWB  H3   H  HCR5   0   0.307  -1.1964   1.1967   1.8545
 JWB  H4   H  HCH2   0   0.241  -1.4586  -1.2182  -1.8577
 JWB  H5   H  HCH2   0   0.251  -3.2030  -1.1876  -1.9259
 JWB  H6   H  HCH1   0   0.246  -2.8023  -2.1576   0.3006
 JWB  H8   H  HCH1   0   0.246  -2.8230   2.1371   0.2813
 JWB  H9   H  HCH2   0   0.241  -1.4707   1.1921  -1.8683
 JWB  H10  H  HCH2   0   0.250  -3.2144   1.1433  -1.9366
 JWB  H11  H  HCH2   0   0.249  -4.3721  -0.0190   0.1262
 JWB  H12  H  HCH2   0   0.246  -3.5216  -0.0072   1.6846
 JWB  H13  H  HCR5   0   0.306  -1.1813  -1.1884   1.8638
 JWB  O7   O  O      0  -0.439   0.5280   2.2708  -0.0189
 JWB  O16  O  O      0  -0.439   0.5514  -2.2588  -0.0024

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
 JWB  O7   C6   double  1.209  0.020  1.209
 JWB  O1   C2   deloc   1.241  0.020  1.241
 JWB  O3   C2   deloc   1.244  0.020  1.244
 JWB  C2   C4   single  1.546  0.020  1.546
 JWB  C6   C8   single  1.504  0.020  1.504
 JWB  C6   N5   single  1.376  0.020  1.376
 JWB  C4   N5   single  1.439  0.020  1.439
 JWB  C8   C9   single  1.543  0.020  1.543
 JWB  C8   C14  single  1.537  0.020  1.537
 JWB  N5   C15  single  1.376  0.020  1.376
 JWB  C9   C10  single  1.535  0.020  1.535
 JWB  C9   C13  single  1.536  0.020  1.536
 JWB  C10  C11  single  1.550  0.020  1.550
 JWB  C15  C14  single  1.504  0.020  1.504
 JWB  C15  O16  double  1.209  0.020  1.209
 JWB  C14  C12  single  1.543  0.020  1.543
 JWB  C13  C12  single  1.536  0.020  1.536
 JWB  C11  C12  single  1.535  0.020  1.535
 JWB  C4   H1   single  0.970  0.020  1.090
 JWB  C4   H2   single  0.970  0.020  1.090
 JWB  C8   H3   single  0.970  0.020  1.090
 JWB  C11  H4   single  0.970  0.020  1.090
 JWB  C11  H5   single  0.970  0.020  1.090
 JWB  C12  H6   single  0.970  0.020  1.090
 JWB  C9   H8   single  0.970  0.020  1.090
 JWB  C10  H9   single  0.970  0.020  1.090
 JWB  C10  H10  single  0.970  0.020  1.090
 JWB  C13  H11  single  0.970  0.020  1.090
 JWB  C13  H12  single  0.970  0.020  1.090
 JWB  C14  H13  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
 JWB  O3   C2   O1   128.38  3.000
 JWB  O3   C2   C4   114.45  3.000
 JWB  O1   C2   C4   117.17  3.000
 JWB  H2   C4   H1   106.90  3.000
 JWB  H2   C4   N5   108.62  3.000
 JWB  H1   C4   N5   108.70  3.000
 JWB  H2   C4   C2   109.90  3.000
 JWB  H1   C4   C2   110.00  3.000
 JWB  N5   C4   C2   112.55  3.000
 JWB  O7   C6   N5   124.18  3.000
 JWB  N5   C6   C8   108.46  3.000
 JWB  O7   C6   C8   127.35  3.000
 JWB  H3   C8   C14  112.85  3.000
 JWB  H3   C8   C9   110.38  3.000
 JWB  C14  C8   C9   103.51  3.000
 JWB  H3   C8   C6   109.19  3.000
 JWB  C14  C8   C6   104.68  3.000
 JWB  C9   C8   C6   116.08  3.000
 JWB  H5   C11  H4   106.28  3.000
 JWB  H5   C11  C10  110.95  3.000
 JWB  H4   C11  C10  113.19  3.000
 JWB  H5   C11  C12  109.59  3.000
 JWB  H4   C11  C12  113.54  3.000
 JWB  C10  C11  C12  103.34  3.000
 JWB  H6   C12  C14  113.25  3.000
 JWB  H6   C12  C13  116.52  3.000
 JWB  C14  C12  C13   99.79  3.000
 JWB  H6   C12  C11  114.22  3.000
 JWB  C13  C12  C11  101.24  3.000
 JWB  C14  C12  C11  110.36  3.000
 JWB  O16  C15  C14  127.36  3.000
 JWB  O16  C15  N5   124.18  3.000
 JWB  C14  C15  N5   108.45  3.000
 JWB  C15  N5   C6   113.36  3.000
 JWB  C15  N5   C4   122.77  3.000
 JWB  C6   N5   C4   122.77  3.000
 JWB  H8   C9   C13  116.55  3.000
 JWB  H8   C9   C10  114.22  3.000
 JWB  C13  C9   C10  101.25  3.000
 JWB  H8   C9   C8   113.19  3.000
 JWB  C13  C9   C8    99.77  3.000
 JWB  C10  C9   C8   110.40  3.000
 JWB  H10  C10  H9   106.26  3.000
 JWB  H10  C10  C9   109.59  3.000
 JWB  H9   C10  C9   113.53  3.000
 JWB  H10  C10  C11  110.97  3.000
 JWB  H9   C10  C11  113.22  3.000
 JWB  C9   C10  C11  103.33  3.000
 JWB  H12  C13  H11  108.74  3.000
 JWB  H12  C13  C9   113.27  3.000
 JWB  H11  C13  C9   113.23  3.000
 JWB  H12  C13  C12  113.29  3.000
 JWB  H11  C13  C12  113.21  3.000
 JWB  C9   C13  C12   94.69  3.000
 JWB  H13  C14  C15  109.10  3.000
 JWB  H13  C14  C12  110.44  3.000
 JWB  C15  C14  C12  116.08  3.000
 JWB  H13  C14  C8   112.86  3.000
 JWB  C12  C14  C8   103.53  3.000
 JWB  C15  C14  C8   104.69  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
 JWB  CONST_01  C15  N5   C6   C8     0.00   0.0  0
 JWB  CONST_02  C8   C6   N5   C4   180.00   0.0  0
 JWB  CONST_03  O7   C6   N5   C15  180.00   0.0  0
 JWB  CONST_04  O7   C6   N5   C4     0.00   0.0  0
 JWB  Var_01    C14  C15  N5   C6     6.12  30.0  1
 JWB  Var_02    C9   C10  C11  C12   -0.01  30.0  1
 JWB  Var_03    C6   N5   C4   C2    83.48  30.0  3
 JWB  Var_04    N5   C4   C2   O1     0.14  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
 JWB  chir_01  C8   C6   C9   C14  negativ
 JWB  chir_02  C12  C11  C13  C14  positiv
 JWB  chir_03  C9   C13  C10  C8   positiv
 JWB  chir_04  C14  C12  C15  C8   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
 JWB  plan-1  C15  0.020
 JWB  plan-1  N5   0.020
 JWB  plan-1  C14  0.020
 JWB  plan-1  O16  0.020
 JWB  plan-2  C4   0.020
 JWB  plan-2  C6   0.020
 JWB  plan-2  C8   0.020
 JWB  plan-2  C15  0.020
 JWB  plan-2  N5   0.020
 JWB  plan-2  O7   0.020
 JWB  plan-3  C2   0.020
 JWB  plan-3  C4   0.020
 JWB  plan-3  O1   0.020
 JWB  plan-3  O3   0.020

