# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:01:43 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (3~{R})-3-[(1~{R})-1-azanylethyl]nonanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)[C@H](CCCCCC(O)=O)CC(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
 CWL  CWL  '(3~{R})-3-[(1~{R})-1-azanylethyl]nonanedioic acid'  ligand  35  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CWL
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
 CWL  OAD  O  O      0  -0.623  -4.3352   0.7026  -1.8107
 CWL  CAN  C  C      0   0.417  -4.4751   0.9307  -0.5892
 CWL  OAF  O  OC    -1  -0.631  -5.5614   1.1276  -0.0044
 CWL  CAL  C  CH2    0  -0.551  -3.1990   1.0681   0.2572
 CWL  CAP  C  CH1    0  -0.225  -2.0209   0.1715  -0.1259
 CWL  CAO  C  CH1    0  -0.060  -2.1772  -1.2732   0.3776
 CWL  CAA  C  CH3    0  -0.673  -2.0380  -1.4111   1.8886
 CWL  NAB  N  NH2    0  -0.799  -3.4786  -1.8000  -0.0210
 CWL  CAK  C  CH2    0  -0.418  -0.6976   0.8043   0.3163
 CWL  CAI  C  CH2    0  -0.420   0.5624   0.0144  -0.0252
 CWL  CAG  C  CH2    0  -0.407   1.8355   0.8266   0.1819
 CWL  CAH  C  CH2    0  -0.401   3.1109   0.0248  -0.0465
 CWL  CAJ  C  CH2    0  -0.581   4.3702   0.8603   0.1147
 CWL  CAM  C  C      0   0.410   5.7060   0.1185  -0.0691
 CWL  OAE  O  O      0  -0.610   5.6693  -1.1127  -0.2625
 CWL  OAC  O  OC    -1  -0.636   6.7366   0.8225  -0.0018
 CWL  H2   H  HCH2   0   0.218  -2.8766   2.1124   0.1476
 CWL  H3   H  HCH2   0   0.201  -3.4452   0.9508   1.3160
 CWL  H4   H  HCH1   0   0.206  -1.9976   0.1209  -1.2213
 CWL  H5   H  HCH1   0   0.195  -1.3576  -1.8531  -0.0739
 CWL  H6   H  HCH3   0   0.219  -2.7505  -0.7783   2.4194
 CWL  H7   H  HCH3   0   0.222  -2.2220  -2.4432   2.1961
 CWL  H8   H  HCH3   0   0.220  -1.0354  -1.1521   2.2301
 CWL  H9   H  HNH2   0   0.337  -3.6209  -1.6405  -1.0103
 CWL  H10  H  HNH2   0   0.334  -3.4879  -2.8044   0.1101
 CWL  H12  H  HCH2   0   0.212  -0.6278   1.7913  -0.1545
 CWL  H13  H  HCH2   0   0.205  -0.7164   0.9976   1.3948
 CWL  H14  H  HCH2   0   0.207   0.6135  -0.8919   0.5866
 CWL  H15  H  HCH2   0   0.204   0.5153  -0.3262  -1.0659
 CWL  H16  H  HCH2   0   0.201   1.8214   1.6922  -0.4905
 CWL  H17  H  HCH2   0   0.200   1.8421   1.2379   1.1982
 CWL  H18  H  HCH2   0   0.200   3.1344  -0.8177   0.6509
 CWL  H19  H  HCH2   0   0.198   3.0860  -0.4167  -1.0479
 CWL  H20  H  HCH2   0   0.214   4.3477   1.7010  -0.5887
 CWL  H21  H  HCH2   0   0.216   4.3762   1.3275   1.1075

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
 CWL  OAD  CAN  deloc   1.250  0.020  1.250
 CWL  NAB  CAO  single  1.460  0.020  1.460
 CWL  OAF  CAN  deloc   1.249  0.020  1.249
 CWL  CAN  CAL  single  1.537  0.020  1.537
 CWL  CAO  CAA  single  1.524  0.020  1.524
 CWL  CAO  CAP  single  1.538  0.020  1.538
 CWL  CAL  CAP  single  1.529  0.020  1.529
 CWL  CAP  CAK  single  1.532  0.020  1.532
 CWL  CAK  CAI  single  1.526  0.020  1.526
 CWL  CAI  CAG  single  1.524  0.020  1.524
 CWL  CAG  CAH  single  1.524  0.020  1.524
 CWL  CAH  CAJ  single  1.520  0.020  1.520
 CWL  CAJ  CAM  single  1.539  0.020  1.539
 CWL  CAM  OAE  deloc   1.247  0.020  1.247
 CWL  CAM  OAC  deloc   1.250  0.020  1.250
 CWL  CAL  H2   single  0.970  0.020  1.090
 CWL  CAL  H3   single  0.970  0.020  1.090
 CWL  CAP  H4   single  0.970  0.020  1.090
 CWL  CAO  H5   single  0.970  0.020  1.090
 CWL  CAA  H6   single  0.970  0.020  1.090
 CWL  CAA  H7   single  0.970  0.020  1.090
 CWL  CAA  H8   single  0.970  0.020  1.090
 CWL  NAB  H9   single  0.890  0.020  1.040
 CWL  NAB  H10  single  0.890  0.020  1.040
 CWL  CAK  H12  single  0.970  0.020  1.090
 CWL  CAK  H13  single  0.970  0.020  1.090
 CWL  CAI  H14  single  0.970  0.020  1.090
 CWL  CAI  H15  single  0.970  0.020  1.090
 CWL  CAG  H16  single  0.970  0.020  1.090
 CWL  CAG  H17  single  0.970  0.020  1.090
 CWL  CAH  H18  single  0.970  0.020  1.090
 CWL  CAH  H19  single  0.970  0.020  1.090
 CWL  CAJ  H20  single  0.970  0.020  1.090
 CWL  CAJ  H21  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
 CWL  CAL  CAN  OAF  116.74  3.000
 CWL  CAL  CAN  OAD  117.46  3.000
 CWL  OAF  CAN  OAD  125.69  3.000
 CWL  H3   CAL  H2   105.36  3.000
 CWL  H3   CAL  CAP  110.68  3.000
 CWL  H2   CAL  CAP  107.83  3.000
 CWL  H3   CAL  CAN  109.67  3.000
 CWL  H2   CAL  CAN  105.88  3.000
 CWL  CAP  CAL  CAN  116.69  3.000
 CWL  H4   CAP  CAK  106.80  3.000
 CWL  H4   CAP  CAO  106.61  3.000
 CWL  CAK  CAP  CAO  112.41  3.000
 CWL  H4   CAP  CAL  107.08  3.000
 CWL  CAK  CAP  CAL  110.54  3.000
 CWL  CAO  CAP  CAL  112.98  3.000
 CWL  H5   CAO  NAB  111.20  3.000
 CWL  H5   CAO  CAA  106.92  3.000
 CWL  NAB  CAO  CAA  108.64  3.000
 CWL  H5   CAO  CAP  106.56  3.000
 CWL  CAA  CAO  CAP  113.61  3.000
 CWL  NAB  CAO  CAP  109.89  3.000
 CWL  H8   CAA  H7   106.92  3.000
 CWL  H8   CAA  H6   108.08  3.000
 CWL  H7   CAA  H6   107.52  3.000
 CWL  H8   CAA  CAO  111.90  3.000
 CWL  H7   CAA  CAO  110.44  3.000
 CWL  H6   CAA  CAO  111.74  3.000
 CWL  H10  NAB  H9   106.35  3.000
 CWL  H10  NAB  CAO  109.31  3.000
 CWL  H9   NAB  CAO  109.60  3.000
 CWL  H13  CAK  H12  105.37  3.000
 CWL  H13  CAK  CAI  109.01  3.000
 CWL  H12  CAK  CAI  108.51  3.000
 CWL  H13  CAK  CAP  110.01  3.000
 CWL  H12  CAK  CAP  107.64  3.000
 CWL  CAI  CAK  CAP  115.78  3.000
 CWL  H15  CAI  H14  105.98  3.000
 CWL  H15  CAI  CAG  109.30  3.000
 CWL  H14  CAI  CAG  109.04  3.000
 CWL  H15  CAI  CAK  109.75  3.000
 CWL  H14  CAI  CAK  110.00  3.000
 CWL  CAG  CAI  CAK  112.55  3.000
 CWL  H17  CAG  H16  105.81  3.000
 CWL  H17  CAG  CAH  109.35  3.000
 CWL  H16  CAG  CAH  109.53  3.000
 CWL  H17  CAG  CAI  109.33  3.000
 CWL  H16  CAG  CAI  109.07  3.000
 CWL  CAH  CAG  CAI  113.47  3.000
 CWL  H19  CAH  H18  105.85  3.000
 CWL  H19  CAH  CAJ  109.73  3.000
 CWL  H18  CAH  CAJ  109.75  3.000
 CWL  H19  CAH  CAG  109.29  3.000
 CWL  H18  CAH  CAG  109.13  3.000
 CWL  CAJ  CAH  CAG  112.85  3.000
 CWL  H21  CAJ  H20  104.72  3.000
 CWL  H21  CAJ  CAM  107.97  3.000
 CWL  H20  CAJ  CAM  108.11  3.000
 CWL  H21  CAJ  CAH  109.55  3.000
 CWL  H20  CAJ  CAH  109.67  3.000
 CWL  CAM  CAJ  CAH  116.20  3.000
 CWL  OAC  CAM  OAE  126.07  3.000
 CWL  OAC  CAM  CAJ  115.96  3.000
 CWL  OAE  CAM  CAJ  117.97  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
 CWL  Var_01  CAP  CAL  CAN  OAD  -35.55  30.0  3
 CWL  Var_02  CAG  CAI  CAK  CAP  168.17  30.0  3
 CWL  Var_03  CAH  CAG  CAI  CAK  175.43  30.0  3
 CWL  Var_04  CAJ  CAH  CAG  CAI  177.93  30.0  3
 CWL  Var_05  CAM  CAJ  CAH  CAG  178.70  30.0  3
 CWL  Var_06  OAE  CAM  CAJ  CAH   -3.78  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
 CWL  chir_01  CAP  CAO  CAL  CAK  negativ
 CWL  chir_02  CAO  NAB  CAP  CAA  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
 CWL  plan-1  OAD  0.020
 CWL  plan-1  CAN  0.020
 CWL  plan-1  OAF  0.020
 CWL  plan-1  CAL  0.020
 CWL  plan-2  CAJ  0.020
 CWL  plan-2  CAM  0.020
 CWL  plan-2  OAE  0.020
 CWL  plan-2  OAC  0.020

