# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:19:15 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-[(3S)-3-{[(3S)-3-amino-3-carboxypropyl]amino}-3-carboxypropyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN[C@@H](CCN[C@@H](CCC(O)=O)C(O)=O)C(O)=O)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
 TNA  TNA  'N-[(3S)-3-{[(3S)-3-amino-3-carboxypropyl]amino}-3-carboxypropyl]-L-glutamic acid'  ligand  43  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TNA
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
 TNA  O8    O  O      0  -0.613  -6.6815  -1.4388   1.3787
 TNA  C12   C  C      0   0.406  -5.5729  -1.8533   1.7733
 TNA  O7    O  OC    -1  -0.639  -5.3779  -2.6078   2.7520
 TNA  C10   C  CH2    0  -0.575  -4.3161  -1.4026   1.0130
 TNA  C9    C  CH2    0  -0.409  -4.5438  -0.5556  -0.2275
 TNA  C8    C  CH1    0  -0.190  -3.2366  -0.1090  -0.8928
 TNA  C11   C  C      0   0.395  -3.5612   0.5541  -2.2541
 TNA  O6    O  O      0  -0.613  -3.5447   1.8021  -2.3005
 TNA  O5    O  OC    -1  -0.623  -3.8595  -0.2151  -3.1917
 TNA  N3    N  NH1    0  -0.587  -2.4699   0.7323   0.0093
 TNA  C7    C  CH2    0  -0.239  -1.0660   0.8206  -0.3456
 TNA  C6    C  CH2    0  -0.453  -0.3321   1.8059   0.5500
 TNA  C4    C  CH1    0  -0.190   1.1623   1.9150   0.2333
 TNA  C5    C  C      0   0.394   1.7597   3.0937   1.0416
 TNA  O3    O  OC    -1  -0.622   1.5212   4.2401   0.6071
 TNA  O4    O  O      0  -0.610   2.3906   2.8133   2.0809
 TNA  N2    N  NH1    0  -0.587   1.8178   0.6377   0.4453
 TNA  C3    C  CH2    0  -0.237   3.1296   0.5559  -0.1694
 TNA  C2    C  CH2    0  -0.450   3.7783  -0.7914   0.1068
 TNA  C1    C  CH1    0  -0.214   5.1653  -0.9421  -0.5174
 TNA  N1    N  NH2    0  -0.786   5.0756  -0.7944  -1.9629
 TNA  C     C  C      0   0.385   5.8422  -2.2448  -0.0190
 TNA  O2    O  OC    -1  -0.624   5.9933  -2.3424   1.2176
 TNA  O1    O  O      0  -0.609   6.1907  -3.0838  -0.8730
 TNA  H10   H  HCH2   0   0.221  -3.6717  -0.8534   1.7064
 TNA  H10A  H  HCH2   0   0.206  -3.7398  -2.2959   0.7421
 TNA  H9    H  HCH2   0   0.203  -5.1336  -1.1151  -0.9572
 TNA  H9A   H  HCH2   0   0.195  -5.1359   0.3296   0.0280
 TNA  H8    H  HCH1   0   0.194  -2.6434  -1.0102  -1.0923
 TNA  HN3   H  HNH1   0   0.315  -2.8646   1.6648  -0.0600
 TNA  H7    H  HCH2   0   0.204  -0.6133  -0.1675  -0.2331
 TNA  H7A   H  HCH2   0   0.166  -0.9047   1.1153  -1.3963
 TNA  H6    H  HCH2   0   0.212  -0.7840   2.7963   0.4400
 TNA  H6A   H  HCH2   0   0.205  -0.4677   1.5154   1.5982
 TNA  H4    H  HCH1   0   0.198   1.2538   2.1580  -0.8328
 TNA  HN2   H  HNH1   0   0.316   1.9350   0.5246   1.4471
 TNA  H3    H  HCH2   0   0.204   3.0132   0.6908  -1.2475
 TNA  H3A   H  HCH2   0   0.170   3.8138   1.3516   0.1683
 TNA  H2    H  HCH2   0   0.216   3.8665  -0.9357   1.1860
 TNA  H2A   H  HCH2   0   0.203   3.1214  -1.5891  -0.2611
 TNA  H1    H  HCH1   0   0.206   5.7800  -0.1115  -0.1442
 TNA  HN1   H  HNH2   0   0.331   5.9902  -0.9719  -2.3604
 TNA  HN1A  H  HNH2   0   0.322   4.5007  -1.5489  -2.3223

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
 TNA  O8   C12   deloc   1.248  0.020  1.248
 TNA  C10  C12   single  1.537  0.020  1.537
 TNA  C12  O7    deloc   1.251  0.020  1.251
 TNA  C9   C10   single  1.519  0.020  1.519
 TNA  C10  H10   single  0.970  0.020  1.090
 TNA  C10  H10A  single  0.970  0.020  1.090
 TNA  C8   C9    single  1.533  0.020  1.533
 TNA  C9   H9    single  0.970  0.020  1.090
 TNA  C9   H9A   single  0.970  0.020  1.090
 TNA  N3   C8    single  1.452  0.020  1.452
 TNA  C8   C11   single  1.549  0.020  1.549
 TNA  C8   H8    single  0.970  0.020  1.090
 TNA  C11  O6    deloc   1.249  0.020  1.249
 TNA  C11  O5    deloc   1.249  0.020  1.249
 TNA  C7   N3    single  1.451  0.020  1.451
 TNA  N3   HN3   single  0.890  0.020  1.040
 TNA  C6   C7    single  1.520  0.020  1.520
 TNA  C7   H7    single  0.970  0.020  1.090
 TNA  C7   H7A   single  0.970  0.020  1.090
 TNA  C4   C6    single  1.531  0.020  1.531
 TNA  C6   H6    single  0.970  0.020  1.090
 TNA  C6   H6A   single  0.970  0.020  1.090
 TNA  N2   C4    single  1.451  0.020  1.451
 TNA  C4   C5    single  1.549  0.020  1.549
 TNA  C4   H4    single  0.970  0.020  1.090
 TNA  O4   C5    deloc   1.248  0.020  1.248
 TNA  C5   O3    deloc   1.249  0.020  1.249
 TNA  C3   N2    single  1.451  0.020  1.451
 TNA  N2   HN2   single  0.890  0.020  1.040
 TNA  C2   C3    single  1.521  0.020  1.521
 TNA  C3   H3    single  0.970  0.020  1.090
 TNA  C3   H3A   single  0.970  0.020  1.090
 TNA  C1   C2    single  1.528  0.020  1.528
 TNA  C2   H2    single  0.970  0.020  1.090
 TNA  C2   H2A   single  0.970  0.020  1.090
 TNA  N1   C1    single  1.456  0.020  1.456
 TNA  C    C1    single  1.550  0.020  1.550
 TNA  C1   H1    single  0.970  0.020  1.090
 TNA  N1   HN1   single  0.890  0.020  1.040
 TNA  N1   HN1A  single  0.890  0.020  1.040
 TNA  O1   C     deloc   1.247  0.020  1.247
 TNA  C    O2    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
 TNA  C10   C12  O7   115.88  3.000
 TNA  O7    C12  O8   125.90  3.000
 TNA  C10   C12  O8   118.22  3.000
 TNA  H10A  C10  H10  104.82  3.000
 TNA  H10A  C10  C9   109.33  3.000
 TNA  H10   C10  C9   109.02  3.000
 TNA  H10A  C10  C12  108.24  3.000
 TNA  H10   C10  C12  108.38  3.000
 TNA  C9    C10  C12  116.42  3.000
 TNA  H9A   C9   H9   106.13  3.000
 TNA  H9A   C9   C8   109.07  3.000
 TNA  H9    C9   C8   108.64  3.000
 TNA  H9A   C9   C10  109.95  3.000
 TNA  H9    C9   C10  109.93  3.000
 TNA  C8    C9   C10  112.89  3.000
 TNA  H8    C8   N3   107.66  3.000
 TNA  H8    C8   C11  107.77  3.000
 TNA  N3    C8   C11  114.11  3.000
 TNA  H8    C8   C9   107.49  3.000
 TNA  C11   C8   C9   109.11  3.000
 TNA  N3    C8   C9   110.44  3.000
 TNA  O5    C11  O6   126.21  3.000
 TNA  O5    C11  C8   116.50  3.000
 TNA  O6    C11  C8   117.24  3.000
 TNA  HN3   N3   C7   107.68  3.000
 TNA  HN3   N3   C8   106.53  3.000
 TNA  C7    N3   C8   113.21  3.000
 TNA  H7A   C7   H7   106.21  3.000
 TNA  H7A   C7   C6   108.50  3.000
 TNA  H7    C7   C6   108.99  3.000
 TNA  H7A   C7   N3   113.01  3.000
 TNA  H7    C7   N3   108.70  3.000
 TNA  C6    C7   N3   111.25  3.000
 TNA  H6A   C6   H6   106.56  3.000
 TNA  H6A   C6   C4   109.72  3.000
 TNA  H6    C6   C4   108.53  3.000
 TNA  H6A   C6   C7   109.38  3.000
 TNA  H6    C6   C7   109.15  3.000
 TNA  C4    C6   C7   113.29  3.000
 TNA  H4    C4   N2   107.41  3.000
 TNA  H4    C4   C5   107.84  3.000
 TNA  N2    C4   C5   114.79  3.000
 TNA  H4    C4   C6   107.34  3.000
 TNA  C5    C4   C6   108.82  3.000
 TNA  N2    C4   C6   110.36  3.000
 TNA  O4    C5   O3   126.34  3.000
 TNA  O3    C5   C4   116.32  3.000
 TNA  O4    C5   C4   117.30  3.000
 TNA  HN2   N2   C3   107.91  3.000
 TNA  HN2   N2   C4   107.13  3.000
 TNA  C3    N2   C4   113.34  3.000
 TNA  H3A   C3   H3   106.21  3.000
 TNA  H3A   C3   C2   108.61  3.000
 TNA  H3    C3   C2   109.51  3.000
 TNA  H3A   C3   N2   112.99  3.000
 TNA  H3    C3   N2   108.34  3.000
 TNA  C2    C3   N2   111.02  3.000
 TNA  H2A   C2   H2   106.48  3.000
 TNA  H2A   C2   C1   109.56  3.000
 TNA  H2    C2   C1   108.50  3.000
 TNA  H2A   C2   C3   109.15  3.000
 TNA  H2    C2   C3   109.32  3.000
 TNA  C1    C2   C3   113.60  3.000
 TNA  H1    C1   C    106.36  3.000
 TNA  H1    C1   N1   107.17  3.000
 TNA  C     C1   N1   115.55  3.000
 TNA  H1    C1   C2   107.13  3.000
 TNA  C     C1   C2   110.35  3.000
 TNA  N1    C1   C2   109.86  3.000
 TNA  HN1A  N1   HN1  104.03  3.000
 TNA  HN1A  N1   C1   108.14  3.000
 TNA  HN1   N1   C1   108.44  3.000
 TNA  O1    C    O2   126.26  3.000
 TNA  O2    C    C1   115.88  3.000
 TNA  O1    C    C1   117.86  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
 TNA  Var_01  C9  C10  C12  O8    -4.08  30.0  2
 TNA  Var_02  C8  C9   C10  C12  177.91  30.0  1
 TNA  Var_03  C6  C7   N3   C8   174.96  30.0  1
 TNA  Var_04  C4  C6   C7   N3   178.86  30.0  1
 TNA  Var_05  C2  C3   N2   C4   178.94  30.0  1
 TNA  Var_06  C1  C2   C3   N2   179.91  30.0  1

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
 TNA  chir_01  C8  C9  N3  C11  positiv
 TNA  chir_02  C4  N2  C6  C5   negativ
 TNA  chir_03  C1  N1  C2  C    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
 TNA  plan-1  O8   0.020
 TNA  plan-1  C12  0.020
 TNA  plan-1  O7   0.020
 TNA  plan-1  C10  0.020
 TNA  plan-2  C8   0.020
 TNA  plan-2  C11  0.020
 TNA  plan-2  O6   0.020
 TNA  plan-2  O5   0.020
 TNA  plan-3  C4   0.020
 TNA  plan-3  C5   0.020
 TNA  plan-3  O3   0.020
 TNA  plan-3  O4   0.020
 TNA  plan-4  C1   0.020
 TNA  plan-4  C    0.020
 TNA  plan-4  O2   0.020
 TNA  plan-4  O1   0.020

