# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:36:31 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (4S)-4-amino-5-hydroxypentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)CCC(N)=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
 ECC  ECC  (4S)-4-amino-5-hydroxypentanamide  L-peptide  21  9  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_ECC
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
 ECC  C     C  CH2   0  -0.140  15.1412  -3.6146  23.7330
 ECC  N     N  NH2   0  -0.812  16.3235  -1.5424  23.4771
 ECC  O     O  OH1   0  -0.668  14.2721  -4.3445  24.5681
 ECC  CA    C  CH1   0  -0.111  15.3053  -2.2045  24.2844
 ECC  CB    C  CH2   0  -0.406  13.9895  -1.4343  24.2186
 ECC  CD    C  C     0   0.526  12.7280   0.6534  24.9131
 ECC  CG    C  CH2   0  -0.588  14.0602  -0.0687  24.8927
 ECC  OE1   O  O     0  -0.488  11.9025   0.5281  24.0203
 ECC  NE2   N  NH2   0  -0.805  12.5344   1.4581  25.9716
 ECC  H     H  HCH2  0   0.188  14.7621  -3.5453  22.7045
 ECC  HA    H  HCH2  0   0.196  16.1303  -4.0918  23.6774
 ECC  HN    H  HNH2  0   0.350  16.4937  -0.6085  23.8271
 ECC  HNA   H  HNH2  0   0.344  17.2063  -2.0277  23.5848
 ECC  HO    H  HOH1  0   0.452  14.1057  -5.1979  24.1592
 ECC  HAA   H  HCH1  0   0.197  15.5994  -2.2934  25.3433
 ECC  HB    H  HCH2  0   0.219  13.7021  -1.3231  23.1700
 ECC  HBA   H  HCH2  0   0.232  13.2119  -2.0296  24.7010
 ECC  HG    H  HCH2  0   0.250  14.4513  -0.1720  25.9086
 ECC  HGA   H  HCH2  0   0.266  14.7596   0.5896  24.3654
 ECC  HNE2  H  HNH2  0   0.394  11.7072   2.0294  26.0335
 ECC  HNEA  H  HNH2  0   0.403  13.2253   1.5648  26.6941

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
 ECC  C    CA    single  1.525  0.021  1.525
 ECC  C    O     single  1.231  0.020  1.231
 ECC  C    H     single  0.970  0.020  1.090
 ECC  C    HA    single  0.970  0.020  1.090
 ECC  N    CA    single  1.458  0.019  1.458
 ECC  N    HN    single  0.890  0.020  1.040
 ECC  N    HNA   single  0.890  0.020  1.040
 ECC  O    HO    single  0.850  0.020  0.980
 ECC  CB   CA    single  1.530  0.020  1.530
 ECC  CA   HAA   single  0.970  0.020  1.090
 ECC  CB   CG    single  1.525  0.020  1.525
 ECC  CB   HB    single  0.970  0.020  1.090
 ECC  CB   HBA   single  0.970  0.020  1.090
 ECC  OE1  CD    double  1.222  0.020  1.222
 ECC  CG   CD    single  1.515  0.020  1.515
 ECC  CD   NE2   single  1.344  0.020  1.344
 ECC  CG   HG    single  0.970  0.020  1.090
 ECC  CG   HGA   single  0.970  0.020  1.090
 ECC  NE2  HNE2  single  0.860  0.020  1.020
 ECC  NE2  HNEA  single  0.860  0.020  1.020

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
 ECC  HA    C    H     106.89  3.000
 ECC  HA    C    CA    109.00  3.000
 ECC  H     C    CA    108.53  3.000
 ECC  HA    C    O     111.10  3.000
 ECC  H     C    O     112.01  3.000
 ECC  CA    C    O     120.80  1.700
 ECC  HNA   N    HN    105.00  3.000
 ECC  HNA   N    CA    109.39  3.000
 ECC  HN    N    CA    110.18  3.000
 ECC  HO    O    C     108.34  3.000
 ECC  HAA   CA   CB    108.19  3.000
 ECC  HAA   CA   N     112.46  3.000
 ECC  CB    CA   N     110.50  1.700
 ECC  HAA   CA   C     107.57  3.000
 ECC  CB    CA   C     110.10  1.900
 ECC  N     CA   C     111.00  2.800
 ECC  HBA   CB   HB    106.98  3.000
 ECC  HBA   CB   CG    109.03  3.000
 ECC  HB    CB   CG    110.19  3.000
 ECC  HBA   CB   CA    108.66  3.000
 ECC  HB    CB   CA    108.63  3.000
 ECC  CG    CB   CA    113.14  3.000
 ECC  NE2   CD   OE1   122.65  3.000
 ECC  NE2   CD   CG    115.00  3.000
 ECC  OE1   CD   CG    122.34  3.000
 ECC  HGA   CG   HG    105.99  3.000
 ECC  HGA   CG   CD    106.34  3.000
 ECC  HG    CG   CD    110.30  3.000
 ECC  HGA   CG   CB    110.79  3.000
 ECC  HG    CG   CB    110.04  3.000
 ECC  CD    CG   CB    113.08  3.000
 ECC  HNEA  NE2  HNE2  117.39  3.000
 ECC  HNEA  NE2  CD    122.06  3.000
 ECC  HNE2  NE2  CD    120.42  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
 ECC  CONST_01  HNE2  NE2  CD  CG   180.00   0.0  0
 ECC  CONST_02  HNEA  NE2  CD  CG     0.00   0.0  0
 ECC  Var_01    CD    CG   CB  CA  -175.92  30.0  3
 ECC  Var_02    OE1   CD   CG  CB   -32.46  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
 ECC  chir_01  CA  C  N  CB  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
 ECC  plan-1  CD    0.020
 ECC  plan-1  CG    0.020
 ECC  plan-1  OE1   0.020
 ECC  plan-1  NE2   0.020
 ECC  plan-1  HNE2  0.020
 ECC  plan-1  HNEA  0.020

