# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:29:26 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: (2~{S})-3-(1-adamantyl)-2-azanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC12CC3CC(CC(C3)C1)C2)C(O)=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
 BW5  BW5  '(2~{S})-3-(1-adamantyl)-2-azanyl-propanoic acid'  L-peptide  36  16  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_BW5
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
 BW5  C1   C  CT     0  -0.090  15.4814  -30.5039  21.2609
 BW5  C2   C  CH2    0  -0.384  16.8519  -30.9530  20.7353
 BW5  C3   C  CH1    0  -0.243  17.6290  -29.7632  20.1665
 BW5  C4   C  CH2    0  -0.416  17.8389  -28.7209  21.2673
 BW5  C5   C  CH1    0  -0.241  16.4796  -28.2435  21.7818
 BW5  C6   C  CH2    0  -0.403  15.7008  -29.4352  22.3431
 BW5  N    N  NH2    0  -0.785  16.0208  -33.6174  22.3167
 BW5  CA   C  CH1    0  -0.214  15.2226  -32.5469  22.9034
 BW5  C    C  C      0   0.375  14.0756  -33.0304  23.8300
 BW5  CB   C  CH2    0  -0.386  14.6275  -31.6612  21.7955
 BW5  C9   C  CH2    0  -0.397  14.7163  -29.8475  20.1001
 BW5  C8   C  CH1    0  -0.244  15.4847  -28.6551  19.5299
 BW5  C7   C  CH2    0  -0.414  15.6939  -27.6137  20.6310
 BW5  C10  C  CH2    0  -0.414  16.8433  -29.1342  19.0150
 BW5  H3   H  HCH2   0   0.203  16.7147  -31.7181  19.9637
 BW5  H4   H  HCH2   0   0.219  17.4269  -31.4221  21.5380
 BW5  H9   H  HCH2   0   0.216  18.4233  -29.1509  22.0877
 BW5  H8   H  HCH2   0   0.215  18.4150  -27.8730  20.8816
 BW5  H1   H  HCH1   0   0.215  16.6270  -27.5019  22.5734
 BW5  H11  H  HCH2   0   0.210  14.7311  -29.1009  22.7309
 BW5  H10  H  HCH2   0   0.218  16.2484  -29.8592  23.1915
 BW5  H6   H  HCH1   0   0.213  18.6011  -30.1089  19.8006
 BW5  HA   H  HCH1   0   0.208  15.8949  -31.9371  23.5163
 BW5  OXT  O  OC    -1  -0.606  13.6642  -34.1977  23.6679
 BW5  HB2  H  HCH2   0   0.210  13.6910  -31.2173  22.1493
 BW5  HB3  H  HCH2   0   0.203  14.3499  -32.3100  20.9551
 BW5  H14  H  HCH2   0   0.212  13.7281  -29.5258  20.4490
 BW5  H15  H  HCH2   0   0.213  14.5462  -30.5909  19.3127
 BW5  H2   H  HCH1   0   0.215  14.9125  -28.2138  18.7079
 BW5  H12  H  HCH2   0   0.216  16.2347  -26.7467  20.2369
 BW5  H13  H  HCH2   0   0.216  14.7266  -27.2475  20.9910
 BW5  H16  H  HCH2   0   0.215  16.7025  -29.8668  18.2136
 BW5  H17  H  HCH2   0   0.215  17.4039  -28.2967  18.5867
 BW5  H    H  HNH2   0   0.327  16.5084  -34.1016  23.0620
 BW5  O    O  O      0  -0.618  13.6378  -32.1913  24.6458
 BW5  HN2  H  HNH2   0   0.319  15.3732  -34.3089  21.9539

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
 BW5  C10  C8   single  1.530  0.020  1.530
 BW5  C10  C3   single  1.529  0.020  1.529
 BW5  C8   C9   single  1.529  0.020  1.529
 BW5  C8   C7   single  1.530  0.020  1.530
 BW5  C3   C2   single  1.531  0.020  1.531
 BW5  C3   C4   single  1.530  0.020  1.530
 BW5  C9   C1   single  1.537  0.020  1.537
 BW5  C7   C5   single  1.529  0.020  1.529
 BW5  C2   C1   single  1.535  0.020  1.535
 BW5  C4   C5   single  1.530  0.020  1.530
 BW5  C1   CB   single  1.534  0.020  1.534
 BW5  C1   C6   single  1.537  0.020  1.537
 BW5  CB   CA   single  1.521  0.033  1.521
 BW5  C5   C6   single  1.530  0.020  1.530
 BW5  N    CA   single  1.458  0.019  1.458
 BW5  CA   C    single  1.525  0.021  1.525
 BW5  C    O    deloc   1.231  0.020  1.231
 BW5  C2   H3   single  0.970  0.020  1.090
 BW5  C2   H4   single  0.970  0.020  1.090
 BW5  C3   H6   single  0.970  0.020  1.090
 BW5  C4   H9   single  0.970  0.020  1.090
 BW5  C4   H8   single  0.970  0.020  1.090
 BW5  C5   H1   single  0.970  0.020  1.090
 BW5  C6   H11  single  0.970  0.020  1.090
 BW5  C6   H10  single  0.970  0.020  1.090
 BW5  N    H    single  0.860  0.020  0.860
 BW5  CA   HA   single  0.970  0.020  0.970
 BW5  C    OXT  deloc   1.248  0.020  1.248
 BW5  CB   HB2  single  0.970  0.020  1.090
 BW5  CB   HB3  single  0.970  0.020  1.090
 BW5  C9   H14  single  0.970  0.020  1.090
 BW5  C9   H15  single  0.970  0.020  1.090
 BW5  C8   H2   single  0.970  0.020  1.090
 BW5  C7   H12  single  0.970  0.020  1.090
 BW5  C7   H13  single  0.970  0.020  1.090
 BW5  C10  H16  single  0.970  0.020  1.090
 BW5  C10  H17  single  0.970  0.020  1.090
 BW5  N    HN2  single  0.890  0.020  1.040

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
 BW5  C9   C1   CB   107.95  3.000
 BW5  CB   C1   C6   111.02  3.000
 BW5  C9   C1   C6   107.81  3.000
 BW5  C6   C1   C2   108.49  3.000
 BW5  CB   C1   C2   113.29  3.000
 BW5  C9   C1   C2   108.10  3.000
 BW5  H4   C2   H3   106.47  3.000
 BW5  H4   C2   C3   109.84  3.000
 BW5  H3   C2   C3   110.17  3.000
 BW5  H4   C2   C1   110.11  3.000
 BW5  H3   C2   C1   109.50  3.000
 BW5  C3   C2   C1   110.68  3.000
 BW5  H6   C3   C10  109.53  3.000
 BW5  H6   C3   C4   109.50  3.000
 BW5  C10  C3   C4   109.39  3.000
 BW5  H6   C3   C2   109.24  3.000
 BW5  C4   C3   C2   109.37  3.000
 BW5  C10  C3   C2   109.79  3.000
 BW5  H8   C4   H9   106.69  3.000
 BW5  H8   C4   C5   110.14  3.000
 BW5  H9   C4   C5   110.17  3.000
 BW5  H8   C4   C3   110.24  3.000
 BW5  H9   C4   C3   110.16  3.000
 BW5  C5   C4   C3   109.42  3.000
 BW5  H1   C5   C7   109.53  3.000
 BW5  H1   C5   C6   109.32  3.000
 BW5  C7   C5   C6   109.60  3.000
 BW5  H1   C5   C4   109.57  3.000
 BW5  C6   C5   C4   109.43  3.000
 BW5  C7   C5   C4   109.39  3.000
 BW5  H10  C6   H11  106.63  3.000
 BW5  H10  C6   C5   109.34  3.000
 BW5  H11  C6   C5   110.02  3.000
 BW5  H10  C6   C1   110.34  3.000
 BW5  H11  C6   C1   109.56  3.000
 BW5  C5   C6   C1   110.85  3.000
 BW5  HN2  N    H    104.14  3.000
 BW5  HN2  N    CA   107.14  3.000
 BW5  H    N    CA   114.00  3.000
 BW5  HA   CA   CB   109.00  3.000
 BW5  HA   CA   C    110.00  3.000
 BW5  CB   CA   C    110.50  1.500
 BW5  HA   CA   N    110.00  3.000
 BW5  C    CA   N    111.00  2.800
 BW5  CB   CA   N    110.40  1.500
 BW5  OXT  C    CA   120.80  1.700
 BW5  OXT  C    O    126.68  3.000
 BW5  CA   C    O    120.80  1.700
 BW5  HB3  CB   HB2  105.71  3.000
 BW5  HB3  CB   CA   108.00  3.000
 BW5  HB2  CB   CA   109.36  3.000
 BW5  HB3  CB   C1   108.66  3.000
 BW5  HB2  CB   C1   106.42  3.000
 BW5  CA   CB   C1   118.04  3.000
 BW5  H15  C9   H14  106.72  3.000
 BW5  H15  C9   C8   109.82  3.000
 BW5  H14  C9   C8   110.06  3.000
 BW5  H15  C9   C1   109.27  3.000
 BW5  H14  C9   C1   109.48  3.000
 BW5  C8   C9   C1   111.38  3.000
 BW5  H2   C8   C10  109.74  3.000
 BW5  H2   C8   C7   109.73  3.000
 BW5  C10  C8   C7   109.51  3.000
 BW5  H2   C8   C9   109.38  3.000
 BW5  C7   C8   C9   109.34  3.000
 BW5  C10  C8   C9   109.12  3.000
 BW5  H13  C7   H12  106.84  3.000
 BW5  H13  C7   C8   110.08  3.000
 BW5  H12  C7   C8   110.33  3.000
 BW5  H13  C7   C5   110.13  3.000
 BW5  H12  C7   C5   110.08  3.000
 BW5  C8   C7   C5   109.36  3.000
 BW5  H17  C10  H16  106.94  3.000
 BW5  H17  C10  C8   110.29  3.000
 BW5  H16  C10  C8   109.98  3.000
 BW5  H17  C10  C3   110.24  3.000
 BW5  H16  C10  C3   110.00  3.000
 BW5  C8   C10  C3   109.37  3.000

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
 BW5  chir_01  C1  C2   CB  C6   negativ
 BW5  chir_02  C3  C4   C2  C10  negativ
 BW5  chir_03  C5  C7   C4  C6   positiv
 BW5  chir_04  CA  N    CB  C    negativ
 BW5  chir_05  C8  C10  C9  C7   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
 BW5  plan-1  CA   0.020
 BW5  plan-1  C    0.020
 BW5  plan-1  OXT  0.020
 BW5  plan-1  O    0.020

