# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 19:45:32 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  47  24  .  2021-08-23  2023-02-16
;
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  -0.446  -6.7444  -1.3471   1.2567
 TNA  C12   C  C     0   0.550  -5.6728  -1.4772   1.7949
 TNA  O7    O  OH1   0  -0.598  -5.5376  -1.9377   3.0353
 TNA  C10   C  CH2   0  -0.574  -4.3442  -1.1466   1.1779
 TNA  C9    C  CH2   0  -0.434  -4.4509  -0.6739  -0.2614
 TNA  C8    C  CH1   0  -0.200  -3.0632  -0.3647  -0.8417
 TNA  C11   C  C     0   0.533  -3.2152  -0.0283  -2.3213
 TNA  O6    O  O     0  -0.439  -3.1837   1.0903  -2.7702
 TNA  O5    O  OH1   0  -0.591  -3.4227  -1.1088  -3.0634
 TNA  N3    N  NH1   0  -0.586  -2.4067   0.6701  -0.0885
 TNA  C7    C  CH2   0  -0.244  -0.9805   0.7832  -0.3269
 TNA  C6    C  CH2   0  -0.460  -0.3626   1.7856   0.6361
 TNA  C4    C  CH1   0  -0.201   1.1403   1.9687   0.3807
 TNA  C5    C  C     0   0.532   1.6733   3.0234   1.3429
 TNA  O3    O  OH1   0  -0.593   1.3269   4.2536   0.9834
 TNA  O4    O  O     0  -0.440   2.3087   2.7773   2.3379
 TNA  N2    N  NH1   0  -0.585   1.8290   0.7095   0.4690
 TNA  C3    C  CH2   0  -0.243   3.1905   0.7020  -0.0308
 TNA  C2    C  CH2   0  -0.454   3.6890  -0.7314  -0.1381
 TNA  C1    C  CH1   0  -0.211   5.1512  -0.8133  -0.5923
 TNA  N1    N  NH2   0  -0.777   5.3314  -0.1462  -1.8586
 TNA  C     C  C     0   0.522   5.5881  -2.2727  -0.6051
 TNA  O2    O  OH1   0  -0.594   5.6790  -2.7788   0.6196
 TNA  O1    O  O     0  -0.440   5.8170  -2.9111  -1.6022
 TNA  HO7   H  HOH1  0   0.479  -6.4076  -2.1405   3.4099
 TNA  H10   H  HCH2  0   0.287  -3.8551  -0.3873   1.7929
 TNA  H10A  H  HCH2  0   0.277  -3.7042  -2.0321   1.2427
 TNA  H9    H  HCH2  0   0.255  -4.9348  -1.4396  -0.8697
 TNA  H9A   H  HCH2  0   0.245  -5.0769   0.2203  -0.3219
 TNA  H8    H  HCH1  0   0.268  -2.4561  -1.2738  -0.7698
 TNA  HO5   H  HOH1  0   0.481  -3.5636  -0.8576  -3.9890
 TNA  HN3   H  HNH1  0   0.343  -2.8628   1.5598  -0.2546
 TNA  H7    H  HCH2  0   0.229  -0.5293  -0.1964  -0.1635
 TNA  H7A   H  HCH2  0   0.195  -0.7272   1.0749  -1.3574
 TNA  H6    H  HCH2  0   0.245  -0.8661   2.7498   0.5291
 TNA  H6A   H  HCH2  0   0.236  -0.5305   1.4535   1.6652
 TNA  H4    H  HCH1  0   0.265   1.2648   2.3506  -0.6388
 TNA  HO3   H  HOH1  0   0.480   1.6317   4.8941   1.6440
 TNA  HN2   H  HNH1  0   0.342   1.8002   0.3601   1.4198
 TNA  H3    H  HCH2  0   0.227   3.1920   1.1646  -1.0192
 TNA  H3A   H  HCH2  0   0.196   3.8895   1.2842   0.5877
 TNA  H2    H  HCH2  0   0.243   3.5853  -1.2206   0.8334
 TNA  H2A   H  HCH2  0   0.234   3.0526  -1.2823  -0.8377
 TNA  H1    H  HCH1  0   0.268   5.7663  -0.2999   0.1549
 TNA  HN1   H  HNH2  0   0.354   6.3042  -0.1712  -2.1360
 TNA  HN1A  H  HNH2  0   0.344   4.8163  -0.6288  -2.5850
 TNA  HO2   H  HOH1  0   0.481   5.9293  -3.7139   0.5758

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   double  1.206  0.020  1.206
 TNA  C10  C12   single  1.502  0.020  1.502
 TNA  C12  O7    single  1.330  0.020  1.330
 TNA  O7   HO7   single  0.850  0.020  0.980
 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  1.536  0.020  1.536
 TNA  C9   H9    single  0.970  0.020  1.090
 TNA  C9   H9A   single  0.970  0.020  1.090
 TNA  N3   C8    single  1.438  0.020  1.438
 TNA  C8   C11   single  1.525  0.020  1.525
 TNA  C8   H8    single  0.970  0.020  1.090
 TNA  C11  O6    double  1.206  0.020  1.206
 TNA  C11  O5    single  1.327  0.020  1.327
 TNA  O5   HO5   single  0.850  0.020  0.980
 TNA  C7   N3    single  1.450  0.020  1.450
 TNA  N3   HN3   single  0.890  0.020  1.040
 TNA  C6   C7    single  1.521  0.020  1.521
 TNA  C7   H7    single  0.970  0.020  1.090
 TNA  C7   H7A   single  0.970  0.020  1.090
 TNA  C4   C6    single  1.535  0.020  1.535
 TNA  C6   H6    single  0.970  0.020  1.090
 TNA  C6   H6A   single  0.970  0.020  1.090
 TNA  N2   C4    single  1.438  0.020  1.438
 TNA  C4   C5    single  1.524  0.020  1.524
 TNA  C4   H4    single  0.970  0.020  1.090
 TNA  O4   C5    double  1.206  0.020  1.206
 TNA  C5   O3    single  1.328  0.020  1.328
 TNA  O3   HO3   single  0.850  0.020  0.980
 TNA  C3   N2    single  1.450  0.020  1.450
 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  1.533  0.020  1.533
 TNA  C2   H2    single  0.970  0.020  1.090
 TNA  C2   H2A   single  0.970  0.020  1.090
 TNA  N1   C1    single  1.442  0.020  1.442
 TNA  C    C1    single  1.523  0.020  1.523
 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     double  1.206  0.020  1.206
 TNA  C    O2    single  1.328  0.020  1.328
 TNA  O2   HO2   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
 TNA  C10   C12  O7   111.68  3.000
 TNA  O7    C12  O8   122.94  3.000
 TNA  C10   C12  O8   125.37  3.000
 TNA  HO7   O7   C12  109.99  3.000
 TNA  H10A  C10  H10  105.50  3.000
 TNA  H10A  C10  C9   110.43  3.000
 TNA  H10   C10  C9   110.40  3.000
 TNA  H10A  C10  C12  108.35  3.000
 TNA  H10   C10  C12  108.53  3.000
 TNA  C9    C10  C12  113.31  3.000
 TNA  H9A   C9   H9   106.82  3.000
 TNA  H9A   C9   C8   109.38  3.000
 TNA  H9    C9   C8   109.35  3.000
 TNA  H9A   C9   C10  110.32  3.000
 TNA  H9    C9   C10  109.95  3.000
 TNA  C8    C9   C10  110.93  3.000
 TNA  H8    C8   N3   108.04  3.000
 TNA  H8    C8   C11  107.58  3.000
 TNA  N3    C8   C11  113.26  3.000
 TNA  H8    C8   C9   107.99  3.000
 TNA  C11   C8   C9   108.72  3.000
 TNA  N3    C8   C9   111.06  3.000
 TNA  O5    C11  O6   123.45  3.000
 TNA  O5    C11  C8   112.24  3.000
 TNA  O6    C11  C8   124.28  3.000
 TNA  HO5   O5   C11  110.23  3.000
 TNA  HN3   N3   C7   110.31  3.000
 TNA  HN3   N3   C8   109.89  3.000
 TNA  C7    N3   C8   114.76  3.000
 TNA  H7A   C7   H7   106.44  3.000
 TNA  H7A   C7   C6   108.95  3.000
 TNA  H7    C7   C6   109.21  3.000
 TNA  H7A   C7   N3   113.63  3.000
 TNA  H7    C7   N3   108.18  3.000
 TNA  C6    C7   N3   110.29  3.000
 TNA  H6A   C6   H6   106.80  3.000
 TNA  H6A   C6   C4   110.05  3.000
 TNA  H6    C6   C4   109.23  3.000
 TNA  H6A   C6   C7   109.45  3.000
 TNA  H6    C6   C7   109.40  3.000
 TNA  C4    C6   C7   111.77  3.000
 TNA  H4    C4   N2   107.94  3.000
 TNA  H4    C4   C5   107.85  3.000
 TNA  N2    C4   C5   113.56  3.000
 TNA  H4    C4   C6   107.91  3.000
 TNA  C5    C4   C6   108.65  3.000
 TNA  N2    C4   C6   110.74  3.000
 TNA  O4    C5   O3   123.36  3.000
 TNA  O3    C5   C4   112.28  3.000
 TNA  O4    C5   C4   124.33  3.000
 TNA  HO3   O3   C5   110.23  3.000
 TNA  HN2   N2   C3   110.38  3.000
 TNA  HN2   N2   C4   110.24  3.000
 TNA  C3    N2   C4   115.65  3.000
 TNA  H3A   C3   H3   106.50  3.000
 TNA  H3A   C3   C2   109.27  3.000
 TNA  H3    C3   C2   109.58  3.000
 TNA  H3A   C3   N2   113.58  3.000
 TNA  H3    C3   N2   108.13  3.000
 TNA  C2    C3   N2   109.68  3.000
 TNA  H2A   C2   H2   106.72  3.000
 TNA  H2A   C2   C1   109.77  3.000
 TNA  H2    C2   C1   109.27  3.000
 TNA  H2A   C2   C3   109.20  3.000
 TNA  H2    C2   C3   109.15  3.000
 TNA  C1    C2   C3   112.56  3.000
 TNA  H1    C1   C    107.07  3.000
 TNA  H1    C1   N1   108.17  3.000
 TNA  C     C1   N1   113.56  3.000
 TNA  H1    C1   C2   107.96  3.000
 TNA  C     C1   C2   109.10  3.000
 TNA  N1    C1   C2   110.76  3.000
 TNA  HN1A  N1   HN1  106.29  3.000
 TNA  HN1A  N1   C1   110.23  3.000
 TNA  HN1   N1   C1   110.45  3.000
 TNA  O1    C    O2   123.21  3.000
 TNA  O2    C    C1   112.14  3.000
 TNA  O1    C    C1   124.65  3.000
 TNA  HO2   O2   C    110.10  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  CONST_01  HO7  O7   C12  O8      0.00   0.0  0
 TNA  CONST_02  HO5  O5   C11  C8    180.00   0.0  0
 TNA  CONST_03  HO3  O3   C5   C4    180.00   0.0  0
 TNA  CONST_04  HO2  O2   C    C1    180.00   0.0  0
 TNA  Var_01    C9   C10  C12  O8     -2.72  30.0  2
 TNA  Var_02    C8   C9   C10  C12  -179.45  30.0  1
 TNA  Var_03    C6   C7   N3   C8   -173.18  30.0  1
 TNA  Var_04    C4   C6   C7   N3   -178.00  30.0  1
 TNA  Var_05    C2   C3   N2   C4   -168.54  30.0  1
 TNA  Var_06    C1   C2   C3   N2   -177.01  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-1  HO7  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-2  HO5  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-3  HO3  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
 TNA  plan-4  HO2  0.020

