# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:54:04 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (7R,8S)-7,8-diaminononanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H](N)CCCCCC(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
 DNN  DNN  '(7R,8S)-7,8-diaminononanoic acid'  ligand  32  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DNN
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
 DNN  C1    C  C      0   0.409   0.0955   0.1401  -4.7790
 DNN  O1    O  O      0  -0.610  -0.7872   1.0210  -4.7861
 DNN  O2    O  OC    -1  -0.635   0.6320  -0.3729  -5.7847
 DNN  C2    C  CH2    0  -0.582   0.5887  -0.3764  -3.4166
 DNN  C3    C  CH2    0  -0.401  -0.0884   0.2073  -2.1874
 DNN  C4    C  CH2    0  -0.411   0.4653  -0.3592  -0.8855
 DNN  C5    C  CH2    0  -0.409  -0.2344   0.1799   0.3557
 DNN  C6    C  CH2    0  -0.400   0.3553  -0.3530   1.6545
 DNN  C7    C  CH1    0  -0.076  -0.4318   0.0517   2.9002
 DNN  C8    C  CH1    0  -0.098   0.4049  -0.1411   4.1816
 DNN  C9    C  CH3    0  -0.680  -0.4271   0.0312   5.4519
 DNN  N7    N  NH2    0  -0.791  -1.7106  -0.6466   2.8945
 DNN  N8    N  NH2    0  -0.784   1.5489   0.7657   4.1338
 DNN  H21   H  HCH2   0   0.216   1.6697  -0.2011  -3.3572
 DNN  H22   H  HCH2   0   0.214   0.4836  -1.4679  -3.4072
 DNN  H31   H  HCH2   0   0.198  -1.1652   0.0176  -2.2331
 DNN  H32   H  HCH2   0   0.199   0.0221   1.2958  -2.1836
 DNN  H41   H  HCH2   0   0.199   1.5389  -0.1464  -0.8220
 DNN  H42   H  HCH2   0   0.199   0.3799  -1.4521  -0.8988
 DNN  H51   H  HCH2   0   0.207  -1.2986  -0.0683   0.3087
 DNN  H52   H  HCH2   0   0.199  -0.1771   1.2746   0.3571
 DNN  H61   H  HCH2   0   0.220   1.3875  -0.0128   1.7571
 DNN  H62   H  HCH2   0   0.197   0.3977  -1.4491   1.6143
 DNN  H7    H  HCH1   0   0.201  -0.6613   1.1249   2.8316
 DNN  H8    H  HCH1   0   0.206   0.8045  -1.1634   4.1687
 DNN  H91   H  HCH3   0   0.229   0.2141  -0.0240   6.3337
 DNN  H92   H  HCH3   0   0.213  -0.9227   1.0063   5.4635
 DNN  H93   H  HCH3   0   0.216  -1.1938  -0.7362   5.5658
 DNN  HN71  H  HNH2   0   0.332  -1.5628  -1.6295   3.0966
 DNN  HN72  H  HNH2   0   0.347  -2.3081  -0.2974   3.6325
 DNN  HN81  H  HNH2   0   0.331   1.2132   1.7196   4.2164
 DNN  HN82  H  HNH2   0   0.342   2.1304   0.6159   4.9496

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
 DNN  C1  O1    deloc   1.247  0.020  1.247
 DNN  C1  O2    deloc   1.250  0.020  1.250
 DNN  C1  C2    single  1.538  0.020  1.538
 DNN  C2  C3    single  1.520  0.020  1.520
 DNN  C2  H21   single  0.970  0.020  1.090
 DNN  C2  H22   single  0.970  0.020  1.090
 DNN  C3  C4    single  1.524  0.020  1.524
 DNN  C3  H31   single  0.970  0.020  1.090
 DNN  C3  H32   single  0.970  0.020  1.090
 DNN  C4  C5    single  1.523  0.020  1.523
 DNN  C4  H41   single  0.970  0.020  1.090
 DNN  C4  H42   single  0.970  0.020  1.090
 DNN  C5  C6    single  1.523  0.020  1.523
 DNN  C5  H51   single  0.970  0.020  1.090
 DNN  C5  H52   single  0.970  0.020  1.090
 DNN  C6  C7    single  1.528  0.020  1.528
 DNN  C6  H61   single  0.970  0.020  1.090
 DNN  C6  H62   single  0.970  0.020  1.090
 DNN  C7  C8    single  1.542  0.020  1.542
 DNN  C7  N7    single  1.457  0.020  1.457
 DNN  C7  H7    single  0.970  0.020  1.090
 DNN  C8  C9    single  1.528  0.020  1.528
 DNN  C8  N8    single  1.461  0.020  1.461
 DNN  C8  H8    single  0.970  0.020  1.090
 DNN  C9  H91   single  0.970  0.020  1.090
 DNN  C9  H92   single  0.970  0.020  1.090
 DNN  C9  H93   single  0.970  0.020  1.090
 DNN  N7  HN71  single  0.890  0.020  1.040
 DNN  N7  HN72  single  0.890  0.020  1.040
 DNN  N8  HN81  single  0.890  0.020  1.040
 DNN  N8  HN82  single  0.890  0.020  1.040

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
 DNN  C2    C1  O2    115.92  3.000
 DNN  C2    C1  O1    117.98  3.000
 DNN  O2    C1  O1    126.10  3.000
 DNN  H22   C2  H21   104.66  3.000
 DNN  H22   C2  C3    109.43  3.000
 DNN  H21   C2  C3    109.51  3.000
 DNN  H22   C2  C1    108.12  3.000
 DNN  H21   C2  C1    108.08  3.000
 DNN  C3    C2  C1    116.39  3.000
 DNN  H32   C3  H31   105.78  3.000
 DNN  H32   C3  C4    109.27  3.000
 DNN  H31   C3  C4    109.20  3.000
 DNN  H32   C3  C2    109.87  3.000
 DNN  H31   C3  C2    109.76  3.000
 DNN  C4    C3  C2    112.72  3.000
 DNN  H42   C4  H41   105.69  3.000
 DNN  H42   C4  C5    109.08  3.000
 DNN  H41   C4  C5    109.51  3.000
 DNN  H42   C4  C3    109.38  3.000
 DNN  H41   C4  C3    109.46  3.000
 DNN  C5    C4  C3    113.43  3.000
 DNN  H52   C5  H51   106.12  3.000
 DNN  H52   C5  C6    109.15  3.000
 DNN  H51   C5  C6    109.51  3.000
 DNN  H52   C5  C4    109.29  3.000
 DNN  H51   C5  C4    109.37  3.000
 DNN  C6    C5  C4    113.16  3.000
 DNN  H62   C6  H61   106.15  3.000
 DNN  H62   C6  C7    108.31  3.000
 DNN  H61   C6  C7    109.14  3.000
 DNN  H62   C6  C5    109.46  3.000
 DNN  H61   C6  C5    109.71  3.000
 DNN  C7    C6  C5    113.78  3.000
 DNN  H7    C7  N7    106.52  3.000
 DNN  H7    C7  C8    106.68  3.000
 DNN  N7    C7  C8    114.80  3.000
 DNN  H7    C7  C6    108.36  3.000
 DNN  N7    C7  C6    108.78  3.000
 DNN  C8    C7  C6    111.39  3.000
 DNN  H8    C8  N8    107.02  3.000
 DNN  H8    C8  C9    108.23  3.000
 DNN  N8    C8  C9    112.56  3.000
 DNN  H8    C8  C7    107.70  3.000
 DNN  N8    C8  C7    108.67  3.000
 DNN  C9    C8  C7    112.40  3.000
 DNN  H93   C9  H92   107.92  3.000
 DNN  H93   C9  H91   107.03  3.000
 DNN  H92   C9  H91   107.61  3.000
 DNN  H93   C9  C8    112.96  3.000
 DNN  H92   C9  C8    110.85  3.000
 DNN  H91   C9  C8    110.24  3.000
 DNN  HN72  N7  HN71  105.98  3.000
 DNN  HN72  N7  C7    110.49  3.000
 DNN  HN71  N7  C7    109.61  3.000
 DNN  HN82  N8  HN81  105.27  3.000
 DNN  HN82  N8  C8    109.36  3.000
 DNN  HN81  N8  C8    108.78  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
 DNN  Var_01  C4  C3  C2  C1  -179.87  30.0  3
 DNN  Var_02  C3  C2  C1  O1     2.08  30.0  3
 DNN  Var_03  C5  C4  C3  C2  -178.04  30.0  3
 DNN  Var_04  C6  C5  C4  C3  -178.00  30.0  3
 DNN  Var_05  C7  C6  C5  C4  -173.47  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
 DNN  chir_01  C7  C6  C8  N7  positiv
 DNN  chir_02  C8  N8  C7  C9  positiv

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
 DNN  plan-1  C1  0.020
 DNN  plan-1  O1  0.020
 DNN  plan-1  O2  0.020
 DNN  plan-1  C2  0.020

