# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:06:32 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: ethyl (3S,4S)-4,8-diamino-3-hydroxyoctanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C[C@H](O)[C@@H](N)CCCCN
#
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
 LTA  LTA  'ethyl (3S,4S)-4,8-diamino-3-hydroxyoctanoate'  L-peptide  37  15  .  2019-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LTA
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
 LTA  N     N  NH2   0  -0.820  21.8852  10.4041  20.1126
 LTA  CA    C  CH1   0  -0.105  23.3143  10.6101  20.3163
 LTA  CB    C  CH2   0  -0.419  24.1172   9.9643  19.1867
 LTA  CG    C  CH2   0  -0.454  23.9575   8.4503  19.0523
 LTA  CD    C  CH2   0  -0.431  24.2612   7.6605  20.3195
 LTA  CE    C  CH2   0  -0.266  24.2392   6.1584  20.0826
 LTA  NZ    N  NH2   0  -0.798  24.5093   5.4288  21.3134
 LTA  C     C  CH1   0   0.095  23.6430  12.1036  20.4159
 LTA  O     O  OH1   0  -0.671  23.2955  12.7328  19.1997
 LTA  C2    C  CH2   0  -0.643  22.9317  12.8101  21.5735
 LTA  C1    C  C     0   0.595  23.3722  12.3731  22.9451
 LTA  O1    O  O     0  -0.448  24.4073  11.8049  23.1939
 LTA  O2    O  O2    0  -0.454  22.4939  12.7296  23.8730
 LTA  C9    C  CH2   0  -0.180  22.8094  12.4479  25.2454
 LTA  C10   C  CH3   0  -0.686  21.6802  12.9755  26.0972
 LTA  H     H  HNH2  0   0.344  21.3809  10.5920  20.9698
 LTA  H2    H  HNH2  0   0.351  21.7092   9.4265  19.9187
 LTA  HA    H  HCH1  0   0.217  23.6651  10.1645  21.2579
 LTA  HB2   H  HCH2  0   0.227  23.8520  10.4322  18.2361
 LTA  HB3   H  HCH2  0   0.213  25.1746  10.1881  19.3592
 LTA  HG2   H  HCH2  0   0.213  22.9508   8.2012  18.7000
 LTA  HG3   H  HCH2  0   0.228  24.6284   8.1151  18.2551
 LTA  HD2   H  HCH2  0   0.212  25.2408   7.9477  20.7149
 LTA  HD3   H  HCH2  0   0.215  23.5303   7.9050  21.0981
 LTA  HE2   H  HCH2  0   0.185  23.2807   5.8881  19.6147
 LTA  HE3   H  HCH2  0   0.210  25.0146   5.9018  19.3551
 LTA  HZ1   H  HNH2  0   0.343  24.5139   4.4348  21.1230
 LTA  HZ2   H  HNH2  0   0.335  23.7444   5.5769  21.9608
 LTA  HC    H  HCH1  0   0.209  24.7253  12.1742  20.5877
 LTA  HO    H  HOH1  0   0.447  23.7313  13.5900  19.1712
 LTA  H21   H  HCH2  0   0.292  23.1470  13.8843  21.5121
 LTA  H22   H  HCH2  0   0.270  21.8462  12.7281  21.4821
 LTA  H91   H  HCH2  0   0.233  22.9299  11.3712  25.3808
 LTA  H92   H  HCH2  0   0.233  23.7540  12.9263  25.5125
 LTA  H101  H  HCH3  0   0.238  21.8964  12.7698  27.1451
 LTA  H102  H  HCH3  0   0.235  21.5633  14.0534  25.9862
 LTA  H103  H  HCH3  0   0.235  20.7331  12.4952  25.8517

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
 LTA  N    CA    single  1.458  0.019  1.458
 LTA  N    H     single  0.860  0.020  0.860
 LTA  N    H2    single  0.890  0.020  1.040
 LTA  CA   CB    single  1.521  0.033  1.521
 LTA  CA   C     single  1.525  0.021  1.525
 LTA  CA   HA    single  0.970  0.020  0.970
 LTA  CB   CG    single  1.528  0.020  1.528
 LTA  CB   HB2   single  0.970  0.020  1.090
 LTA  CB   HB3   single  0.970  0.020  1.090
 LTA  CG   CD    single  1.524  0.020  1.524
 LTA  CG   HG2   single  0.970  0.020  1.090
 LTA  CG   HG3   single  0.970  0.020  1.090
 LTA  CD   CE    single  1.521  0.020  1.521
 LTA  CD   HD2   single  0.970  0.020  1.090
 LTA  CD   HD3   single  0.970  0.020  1.090
 LTA  CE   NZ    single  1.456  0.020  1.456
 LTA  CE   HE2   single  0.970  0.020  1.090
 LTA  CE   HE3   single  0.970  0.020  1.090
 LTA  NZ   HZ1   single  0.890  0.020  1.040
 LTA  NZ   HZ2   single  0.890  0.020  1.040
 LTA  C    O     single  1.231  0.020  1.231
 LTA  C    C2    single  1.531  0.020  1.531
 LTA  C    HC    single  0.970  0.020  1.090
 LTA  O    HO    single  0.850  0.020  0.980
 LTA  C2   C1    single  1.505  0.020  1.505
 LTA  C2   H21   single  0.970  0.020  1.090
 LTA  C2   H22   single  0.970  0.020  1.090
 LTA  C1   O1    double  1.207  0.020  1.207
 LTA  C1   O2    single  1.326  0.020  1.326
 LTA  O2   C9    single  1.436  0.020  1.436
 LTA  C9   C10   single  1.510  0.020  1.510
 LTA  C9   H91   single  0.970  0.020  1.090
 LTA  C9   H92   single  0.970  0.020  1.090
 LTA  C10  H101  single  0.970  0.020  1.090
 LTA  C10  H102  single  0.970  0.020  1.090
 LTA  C10  H103  single  0.970  0.020  1.090

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
 LTA  H2    N    H     104.77  3.000
 LTA  H2    N    CA    109.50  3.000
 LTA  H     N    CA    114.00  3.000
 LTA  HA    CA   C     110.00  3.000
 LTA  HA    CA   CB    109.00  3.000
 LTA  C     CA   CB    110.50  1.500
 LTA  HA    CA   N     110.00  3.000
 LTA  C     CA   N     111.00  2.800
 LTA  CB    CA   N     110.40  1.500
 LTA  HB3   CB   HB2   106.50  3.000
 LTA  HB3   CB   CG    108.50  3.000
 LTA  HB2   CB   CG    108.81  3.000
 LTA  HB3   CB   CA    107.73  3.000
 LTA  HB2   CB   CA    109.55  3.000
 LTA  CG    CB   CA    115.38  3.000
 LTA  HG3   CG   HG2   105.03  3.000
 LTA  HG3   CG   CD    108.95  3.000
 LTA  HG2   CG   CD    109.44  3.000
 LTA  HG3   CG   CB    107.67  3.000
 LTA  HG2   CG   CB    110.46  3.000
 LTA  CD    CG   CB    114.81  3.000
 LTA  HD3   CD   HD2   106.36  3.000
 LTA  HD3   CD   CE    108.76  3.000
 LTA  HD2   CD   CE    109.17  3.000
 LTA  HD3   CD   CG    110.02  3.000
 LTA  HD2   CD   CG    110.04  3.000
 LTA  CE    CD   CG    112.30  3.000
 LTA  HE3   CE   HE2   106.09  3.000
 LTA  HE3   CE   NZ    108.25  3.000
 LTA  HE2   CE   NZ    113.45  3.000
 LTA  HE3   CE   CD    108.97  3.000
 LTA  HE2   CE   CD    108.75  3.000
 LTA  NZ    CE   CD    111.13  3.000
 LTA  HZ2   NZ   HZ1   105.50  3.000
 LTA  HZ2   NZ   CE    109.08  3.000
 LTA  HZ1   NZ   CE    109.50  3.000
 LTA  HC    C    C2    108.05  3.000
 LTA  HC    C    O     110.39  3.000
 LTA  C2    C    O     109.33  3.000
 LTA  HC    C    CA    106.52  3.000
 LTA  C2    C    CA    113.53  3.000
 LTA  O     C    CA    120.80  1.700
 LTA  HO    O    C     108.12  3.000
 LTA  H22   C2   H21   105.30  3.000
 LTA  H22   C2   C1    110.19  3.000
 LTA  H21   C2   C1    106.12  3.000
 LTA  H22   C2   C     111.33  3.000
 LTA  H21   C2   C     108.56  3.000
 LTA  C1    C2   C     114.76  3.000
 LTA  O2    C1   O1    123.38  3.000
 LTA  O2    C1   C2    111.44  3.000
 LTA  O1    C1   C2    125.14  3.000
 LTA  C9    O2   C1    118.06  3.000
 LTA  H92   C9   H91   107.83  3.000
 LTA  H92   C9   C10   110.85  3.000
 LTA  H91   C9   C10   110.93  3.000
 LTA  H92   C9   O2    109.75  3.000
 LTA  H91   C9   O2    109.64  3.000
 LTA  C10   C9   O2    107.84  3.000
 LTA  H103  C10  H102  108.64  3.000
 LTA  H103  C10  H101  107.81  3.000
 LTA  H102  C10  H101  107.81  3.000
 LTA  H103  C10  C9    111.65  3.000
 LTA  H102  C10  C9    111.62  3.000
 LTA  H101  C10  C9    109.16  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
 LTA  Var_01  CD    CG   CB  CA   -54.98  30.0  3
 LTA  Var_02  CE    CD   CG  CB  -173.50  30.0  3
 LTA  Var_03  NZ    CE   CD  CG  -179.01  30.0  3
 LTA  Var_04  O1    C1   C2  C     19.29  30.0  3
 LTA  Var_05  C10   C9   O2  C1   178.63  30.0  3
 LTA  Var_06  HZ1   NZ   CE  CD  -178.46  30.0  3
 LTA  Var_07  H101  C10  C9  O2   179.82  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
 LTA  chir_01  CA  N  CB  C   negativ
 LTA  chir_02  C   O  CA  C2  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
 LTA  plan-1  C2  0.020
 LTA  plan-1  C1  0.020
 LTA  plan-1  O1  0.020
 LTA  plan-1  O2  0.020

