# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:52:45 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 12-aminododecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCCCCCCCC(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
 DOA  DOA  '12-aminododecanoic acid  '  L-peptide  39  15  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DOA
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
 DOA  N     N  NH2    0  -0.801  -0.4864  -0.0088   8.6279
 DOA  CA    C  CH2    0  -0.272   0.3792  -0.0212   7.4562
 DOA  C2    C  CH2    0  -0.425  -0.4371  -0.0263   6.1728
 DOA  C3    C  CH2    0  -0.418   0.4308  -0.0324   4.9208
 DOA  C4    C  CH2    0  -0.411  -0.3780  -0.0499   3.6298
 DOA  C5    C  CH2    0  -0.412   0.4900  -0.0442   2.3774
 DOA  C6    C  CH2    0  -0.412  -0.3173  -0.0574   1.0854
 DOA  C7    C  CH2    0  -0.411   0.5497  -0.0411  -0.1677
 DOA  C8    C  CH2    0  -0.410  -0.2585  -0.0476  -1.4592
 DOA  C9    C  CH2    0  -0.409   0.6053  -0.0159  -2.7142
 DOA  C10   C  CH2    0  -0.402  -0.2082  -0.0181  -4.0032
 DOA  CA2   C  CH2    0  -0.581   0.6594   0.0352  -5.2501
 DOA  C     C  C      0   0.409  -0.0887   0.0530  -6.5947
 DOA  O     O  O      0  -0.610  -1.3258  -0.1033  -6.5767
 DOA  OXT   O  OC    -1  -0.635   0.6178   0.2181  -7.6126
 DOA  H     H  HNH2   0   0.336  -0.9786   0.8759   8.6645
 DOA  H2    H  HNH2   0   0.344   0.0799  -0.0363   9.4663
 DOA  HA1   H  HCH2   0   0.185   1.0842   0.8226   7.4243
 DOA  HA2   H  HCH2   0   0.210   0.9906  -0.9276   7.4918
 DOA  H21   H  HCH2   0   0.211  -1.0973  -0.8996   6.1714
 DOA  H22   H  HCH2   0   0.209  -1.0899   0.8544   6.1559
 DOA  H31   H  HCH2   0   0.208   1.0841   0.8474   4.9258
 DOA  H32   H  HCH2   0   0.208   1.0959  -0.9031   4.9435
 DOA  H41   H  HCH2   0   0.207  -1.0259  -0.9337   3.6187
 DOA  H42   H  HCH2   0   0.207  -1.0484   0.8168   3.6099
 DOA  H51   H  HCH2   0   0.206   1.1388   0.8390   2.3905
 DOA  H52   H  HCH2   0   0.206   1.1599  -0.9114   2.3963
 DOA  H61   H  HCH2   0   0.206  -0.9621  -0.9436   1.0690
 DOA  H62   H  HCH2   0   0.206  -0.9913   0.8067   1.0703
 DOA  H71   H  HCH2   0   0.205   1.1961   0.8439  -0.1491
 DOA  H72   H  HCH2   0   0.205   1.2223  -0.9063  -0.1552
 DOA  H81   H  HCH2   0   0.204  -0.8998  -0.9363  -1.4820
 DOA  H82   H  HCH2   0   0.204  -0.9367   0.8134  -1.4658
 DOA  H91   H  HCH2   0   0.201   1.2466   0.8730  -2.6878
 DOA  H92   H  HCH2   0   0.202   1.2850  -0.8760  -2.7085
 DOA  H101  H  HCH2   0   0.200  -0.8404  -0.9108  -4.0288
 DOA  H102  H  HCH2   0   0.199  -0.8949   0.8342  -3.9945
 DOA  HA21  H  HCH2   0   0.212   1.3122   0.9149  -5.2078
 DOA  HA22  H  HCH2   0   0.217   1.3446  -0.8218  -5.2555

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
 DOA  N    CA    single  1.458  0.019  1.458
 DOA  N    H     single  0.860  0.020  0.860
 DOA  N    H2    single  0.890  0.020  1.040
 DOA  CA   C2    single  1.521  0.020  1.521
 DOA  CA   HA1   single  0.970  0.020  1.090
 DOA  CA   HA2   single  0.970  0.020  1.090
 DOA  C2   C3    single  1.523  0.020  1.523
 DOA  C2   H21   single  0.970  0.020  1.090
 DOA  C2   H22   single  0.970  0.020  1.090
 DOA  C3   C4    single  1.524  0.020  1.524
 DOA  C3   H31   single  0.970  0.020  1.090
 DOA  C3   H32   single  0.970  0.020  1.090
 DOA  C4   C5    single  1.524  0.020  1.524
 DOA  C4   H41   single  0.970  0.020  1.090
 DOA  C4   H42   single  0.970  0.020  1.090
 DOA  C5   C6    single  1.524  0.020  1.524
 DOA  C5   H51   single  0.970  0.020  1.090
 DOA  C5   H52   single  0.970  0.020  1.090
 DOA  C6   C7    single  1.524  0.020  1.524
 DOA  C6   H61   single  0.970  0.020  1.090
 DOA  C6   H62   single  0.970  0.020  1.090
 DOA  C7   C8    single  1.524  0.020  1.524
 DOA  C7   H71   single  0.970  0.020  1.090
 DOA  C7   H72   single  0.970  0.020  1.090
 DOA  C8   C9    single  1.524  0.020  1.524
 DOA  C8   H81   single  0.970  0.020  1.090
 DOA  C8   H82   single  0.970  0.020  1.090
 DOA  C9   C10   single  1.524  0.020  1.524
 DOA  C9   H91   single  0.970  0.020  1.090
 DOA  C9   H92   single  0.970  0.020  1.090
 DOA  C10  CA2   single  1.520  0.020  1.520
 DOA  C10  H101  single  0.970  0.020  1.090
 DOA  C10  H102  single  0.970  0.020  1.090
 DOA  CA2  C     single  1.539  0.020  1.539
 DOA  CA2  HA21  single  0.970  0.020  1.090
 DOA  CA2  HA22  single  0.970  0.020  1.090
 DOA  C    O     deloc   1.231  0.020  1.231
 DOA  C    OXT   deloc   1.250  0.020  1.250

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
 DOA  H2    N    H     105.41  3.000
 DOA  H2    N    CA    109.49  3.000
 DOA  H     N    CA    114.00  3.000
 DOA  HA2   CA   HA1   106.16  3.000
 DOA  HA2   CA   C2    108.95  3.000
 DOA  HA1   CA   C2    108.79  3.000
 DOA  HA2   CA   N     108.24  3.000
 DOA  HA1   CA   N     113.42  3.000
 DOA  C2    CA   N     111.09  3.000
 DOA  H22   C2   H21   106.36  3.000
 DOA  H22   C2   C3    109.25  3.000
 DOA  H21   C2   C3    109.84  3.000
 DOA  H22   C2   CA    109.26  3.000
 DOA  H21   C2   CA    109.11  3.000
 DOA  C3    C2   CA    112.81  3.000
 DOA  H32   C3   H31   106.02  3.000
 DOA  H32   C3   C4    109.30  3.000
 DOA  H31   C3   C4    109.24  3.000
 DOA  H32   C3   C2    109.39  3.000
 DOA  H31   C3   C2    109.43  3.000
 DOA  C4    C3   C2    113.20  3.000
 DOA  H42   C4   H41   106.02  3.000
 DOA  H42   C4   C5    109.31  3.000
 DOA  H41   C4   C5    109.36  3.000
 DOA  H42   C4   C3    109.33  3.000
 DOA  H41   C4   C3    109.37  3.000
 DOA  C5    C4   C3    113.20  3.000
 DOA  H52   C5   H51   106.00  3.000
 DOA  H52   C5   C6    109.37  3.000
 DOA  H51   C5   C6    109.32  3.000
 DOA  H52   C5   C4    109.33  3.000
 DOA  H51   C5   C4    109.29  3.000
 DOA  C6    C5   C4    113.27  3.000
 DOA  H62   C6   H61   105.99  3.000
 DOA  H62   C6   C7    109.27  3.000
 DOA  H61   C6   C7    109.34  3.000
 DOA  H62   C6   C5    109.31  3.000
 DOA  H61   C6   C5    109.36  3.000
 DOA  C7    C6   C5    113.31  3.000
 DOA  H72   C7   H71   105.98  3.000
 DOA  H72   C7   C8    109.38  3.000
 DOA  H71   C7   C8    109.31  3.000
 DOA  H72   C7   C6    109.35  3.000
 DOA  H71   C7   C6    109.28  3.000
 DOA  C8    C7   C6    113.27  3.000
 DOA  H82   C8   H81   105.95  3.000
 DOA  H82   C8   C9    109.23  3.000
 DOA  H81   C8   C9    109.35  3.000
 DOA  H82   C8   C7    109.27  3.000
 DOA  H81   C8   C7    109.36  3.000
 DOA  C9    C8   C7    113.41  3.000
 DOA  H92   C9   H91   105.86  3.000
 DOA  H92   C9   C10   109.52  3.000
 DOA  H91   C9   C10   109.49  3.000
 DOA  H92   C9   C8    109.32  3.000
 DOA  H91   C9   C8    109.19  3.000
 DOA  C10   C9   C8    113.20  3.000
 DOA  H102  C10  H101  105.85  3.000
 DOA  H102  C10  CA2   109.72  3.000
 DOA  H101  C10  CA2   109.83  3.000
 DOA  H102  C10  C9    109.08  3.000
 DOA  H101  C10  C9    109.23  3.000
 DOA  CA2   C10  C9    112.89  3.000
 DOA  HA22  CA2  HA21  104.78  3.000
 DOA  HA22  CA2  C     107.95  3.000
 DOA  HA21  CA2  C     108.30  3.000
 DOA  HA22  CA2  C10   109.46  3.000
 DOA  HA21  CA2  C10   109.66  3.000
 DOA  C     CA2  C10   116.09  3.000
 DOA  OXT   C    O     126.09  3.000
 DOA  OXT   C    CA2   116.00  3.000
 DOA  O     C    CA2   117.91  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
 DOA  Var_01  C3   C2   CA   N     179.72  30.0  3
 DOA  Var_02  C4   C3   C2   CA    179.49  30.0  3
 DOA  Var_03  C5   C4   C3   C2    179.52  30.0  3
 DOA  Var_04  C6   C5   C4   C3   -179.82  30.0  3
 DOA  Var_05  C7   C6   C5   C4    179.56  30.0  3
 DOA  Var_06  C8   C7   C6   C5   -179.73  30.0  3
 DOA  Var_07  C9   C8   C7   C6    179.37  30.0  3
 DOA  Var_08  C10  C9   C8   C7   -179.82  30.0  3
 DOA  Var_09  CA2  C10  C9   C8    179.11  30.0  3
 DOA  Var_10  C    CA2  C10  C9   -179.31  30.0  3
 DOA  Var_11  O    C    CA2  C10    -6.60  30.0  3
 DOA  Var_12  H    N    CA   C2    -67.02  30.0  3

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
 DOA  plan-1  CA2  0.020
 DOA  plan-1  C    0.020
 DOA  plan-1  O    0.020
 DOA  plan-1  OXT  0.020

