# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:20:24 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  37  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.467  -4.4892   0.7469  -1.7462
 CWL  CAN  C  C     0   0.556  -4.4281   0.8513  -0.5433
 CWL  OAF  O  OH1   0  -0.598  -5.5111   0.8655   0.2293
 CWL  CAL  C  CH2   0  -0.552  -3.1596   1.0952   0.2246
 CWL  CAP  C  CH1   0  -0.240  -1.9959   0.1832  -0.1745
 CWL  CAO  C  CH1   0  -0.064  -2.1973  -1.2554   0.3276
 CWL  CAA  C  CH3   0  -0.681  -2.1182  -1.3878   1.8423
 CWL  NAB  N  NH2   0  -0.797  -3.4972  -1.7372  -0.1253
 CWL  CAK  C  CH2   0  -0.422  -0.6752   0.8048   0.2843
 CWL  CAI  C  CH2   0  -0.426   0.5715  -0.0131  -0.0376
 CWL  CAG  C  CH2   0  -0.413   1.8537   0.7803   0.1812
 CWL  CAH  C  CH2   0  -0.417   3.1109  -0.0502  -0.0409
 CWL  CAJ  C  CH2   0  -0.580   4.3733   0.7760   0.1404
 CWL  CAM  C  C     0   0.550   5.6439  -0.0035  -0.0520
 CWL  OAE  O  O     0  -0.446   5.7077  -1.1719  -0.3443
 CWL  OAC  O  OH1   0  -0.599   6.7230   0.7520   0.1378
 CWL  H1   H  HOH1  0   0.472  -6.3019   0.7611  -0.3203
 CWL  H2   H  HCH2  0   0.276  -2.8795   2.1332   0.0113
 CWL  H3   H  HCH2  0   0.253  -3.3471   1.0448   1.2974
 CWL  H4   H  HCH1  0   0.231  -1.9654   0.1406  -1.2702
 CWL  H5   H  HCH1  0   0.212  -1.3784  -1.8576  -0.0914
 CWL  H6   H  HCH3  0   0.224  -2.8558  -0.7645   2.3494
 CWL  H7   H  HCH3  0   0.232  -2.3025  -2.4218   2.1412
 CWL  H8   H  HCH3  0   0.230  -1.1306  -1.1202   2.2182
 CWL  H9   H  HNH2  0   0.344  -3.5033  -1.8047  -1.1360
 CWL  H10  H  HNH2  0   0.347  -3.6452  -2.6807   0.2128
 CWL  H12  H  HCH2  0   0.225  -0.5832   1.7873  -0.1908
 CWL  H13  H  HCH2  0   0.216  -0.7078   1.0005   1.3613
 CWL  H14  H  HCH2  0   0.216   0.5982  -0.9146   0.5821
 CWL  H15  H  HCH2  0   0.214   0.5313  -0.3580  -1.0766
 CWL  H16  H  HCH2  0   0.214   1.8612   1.6440  -0.4926
 CWL  H17  H  HCH2  0   0.214   1.8611   1.1886   1.1977
 CWL  H18  H  HCH2  0   0.225   3.1165  -0.8926   0.6561
 CWL  H19  H  HCH2  0   0.225   3.0914  -0.4805  -1.0458
 CWL  H20  H  HCH2  0   0.275   4.3855   1.6178  -0.5598
 CWL  H21  H  HCH2  0   0.274   4.3980   1.2286   1.1371
 CWL  H22  H  HOH1  0   0.478   7.5231   0.2226   0.0037

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  double  1.209  0.020  1.209
 CWL  NAB  CAO  single  1.458  0.020  1.458
 CWL  OAF  CAN  single  1.330  0.020  1.330
 CWL  CAN  CAL  single  1.503  0.020  1.503
 CWL  CAO  CAA  single  1.523  0.020  1.523
 CWL  CAO  CAP  single  1.537  0.020  1.537
 CWL  CAL  CAP  single  1.531  0.020  1.531
 CWL  CAP  CAK  single  1.530  0.020  1.530
 CWL  CAK  CAI  single  1.525  0.020  1.525
 CWL  CAI  CAG  single  1.524  0.020  1.524
 CWL  CAG  CAH  single  1.523  0.020  1.523
 CWL  CAH  CAJ  single  1.520  0.020  1.520
 CWL  CAJ  CAM  single  1.503  0.020  1.503
 CWL  CAM  OAE  double  1.206  0.020  1.206
 CWL  CAM  OAC  single  1.331  0.020  1.331
 CWL  OAF  H1   single  0.850  0.020  0.980
 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
 CWL  OAC  H22  single  0.850  0.020  0.980

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  112.87  3.000
 CWL  CAL  CAN  OAD  124.41  3.000
 CWL  OAF  CAN  OAD  122.52  3.000
 CWL  H1   OAF  CAN  109.51  3.000
 CWL  H3   CAL  H2   106.22  3.000
 CWL  H3   CAL  CAP  111.07  3.000
 CWL  H2   CAL  CAP  108.60  3.000
 CWL  H3   CAL  CAN  110.50  3.000
 CWL  H2   CAL  CAN  105.66  3.000
 CWL  CAP  CAL  CAN  114.31  3.000
 CWL  H4   CAP  CAK  106.94  3.000
 CWL  H4   CAP  CAO  107.07  3.000
 CWL  CAK  CAP  CAO  113.29  3.000
 CWL  H4   CAP  CAL  107.73  3.000
 CWL  CAK  CAP  CAL  109.62  3.000
 CWL  CAO  CAP  CAL  111.88  3.000
 CWL  H5   CAO  NAB  111.38  3.000
 CWL  H5   CAO  CAA  107.02  3.000
 CWL  NAB  CAO  CAA  109.06  3.000
 CWL  H5   CAO  CAP  106.89  3.000
 CWL  CAA  CAO  CAP  113.55  3.000
 CWL  NAB  CAO  CAP  108.94  3.000
 CWL  H8   CAA  H7   106.92  3.000
 CWL  H8   CAA  H6   108.18  3.000
 CWL  H7   CAA  H6   107.44  3.000
 CWL  H8   CAA  CAO  111.64  3.000
 CWL  H7   CAA  CAO  110.23  3.000
 CWL  H6   CAA  CAO  112.19  3.000
 CWL  H10  NAB  H9   105.67  3.000
 CWL  H10  NAB  CAO  109.52  3.000
 CWL  H9   NAB  CAO  109.71  3.000
 CWL  H13  CAK  H12  105.60  3.000
 CWL  H13  CAK  CAI  109.12  3.000
 CWL  H12  CAK  CAI  108.71  3.000
 CWL  H13  CAK  CAP  109.99  3.000
 CWL  H12  CAK  CAP  107.87  3.000
 CWL  CAI  CAK  CAP  115.11  3.000
 CWL  H15  CAI  H14  106.17  3.000
 CWL  H15  CAI  CAG  109.33  3.000
 CWL  H14  CAI  CAG  109.09  3.000
 CWL  H15  CAI  CAK  109.81  3.000
 CWL  H14  CAI  CAK  110.01  3.000
 CWL  CAG  CAI  CAK  112.23  3.000
 CWL  H17  CAG  H16  106.07  3.000
 CWL  H17  CAG  CAH  109.45  3.000
 CWL  H16  CAG  CAH  109.55  3.000
 CWL  H17  CAG  CAI  109.45  3.000
 CWL  H16  CAG  CAI  109.15  3.000
 CWL  CAH  CAG  CAI  112.94  3.000
 CWL  H19  CAH  H18  106.43  3.000
 CWL  H19  CAH  CAJ  109.78  3.000
 CWL  H18  CAH  CAJ  109.79  3.000
 CWL  H19  CAH  CAG  109.51  3.000
 CWL  H18  CAH  CAG  109.35  3.000
 CWL  CAJ  CAH  CAG  111.83  3.000
 CWL  H21  CAJ  H20  105.30  3.000
 CWL  H21  CAJ  CAM  108.18  3.000
 CWL  H20  CAJ  CAM  107.91  3.000
 CWL  H21  CAJ  CAH  110.61  3.000
 CWL  H20  CAJ  CAH  110.54  3.000
 CWL  CAM  CAJ  CAH  113.90  3.000
 CWL  OAC  CAM  OAE  122.80  3.000
 CWL  OAC  CAM  CAJ  111.89  3.000
 CWL  OAE  CAM  CAJ  125.32  3.000
 CWL  H22  OAC  CAM  109.86  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  CONST_01  H1   OAF  CAN  OAD    0.00   0.0  0
 CWL  CONST_02  H22  OAC  CAM  CAJ  180.00   0.0  0
 CWL  Var_01    CAP  CAL  CAN  OAD  -47.81  30.0  3
 CWL  Var_02    CAG  CAI  CAK  CAP  168.20  30.0  3
 CWL  Var_03    CAH  CAG  CAI  CAK  175.96  30.0  3
 CWL  Var_04    CAJ  CAH  CAG  CAI  178.18  30.0  3
 CWL  Var_05    CAM  CAJ  CAH  CAG  179.29  30.0  3
 CWL  Var_06    OAE  CAM  CAJ  CAH    1.12  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-1  H1   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
 CWL  plan-2  H22  0.020

