# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:02:58 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (4S)-4-amino-5-hydroxy-N,N-dimethylpentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)CC[C@H](N)CO
#
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
 1HB  1HB  (4S)-4-amino-5-hydroxy-N,N-dimethylpentanamide  peptide  27  11  .  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_1HB
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
 1HB  C    C  CH2   0  -0.134  16.9101  24.8858  33.7708
 1HB  CD   C  C     0   0.572  16.5500  20.1425  32.1399
 1HB  CG   C  CH2   0  -0.595  16.6835  21.0574  33.3420
 1HB  N    N  NH2   0  -0.787  15.7541  23.1770  35.1772
 1HB  OE1  O  O     0  -0.505  16.3850  20.5881  31.0099
 1HB  NE2  N  NT    0  -0.450  16.6320  18.8108  32.3535
 1HB  CH1  C  CH3   0  -0.528  16.7101  18.1818  33.6547
 1HB  CH2  C  CH3   0  -0.515  16.4778  17.9223  31.2180
 1HB  CA   C  CH1   0  -0.132  16.8116  23.4290  34.2084
 1HB  CB   C  CH2   0  -0.411  16.6291  22.5339  32.9851
 1HB  O    O  OH1   0  -0.669  17.1546  25.6885  34.9055
 1HB  H1   H  HCH2  0   0.268  15.9005  20.8285  34.0687
 1HB  H2   H  HCH2  0   0.258  17.6286  20.8423  33.8510
 1HB  H3   H  HNH2  0   0.344  15.8734  23.7863  35.9767
 1HB  H4   H  HNH2  0   0.332  14.8611  23.4323  34.7678
 1HB  H6   H  HCH3  0   0.264  16.9230  18.9013  34.4376
 1HB  H7   H  HCH3  0   0.238  15.7746  17.6773  33.9079
 1HB  H8   H  HCH3  0   0.244  17.5083  17.4387  33.6650
 1HB  H9   H  HCH3  0   0.242  16.7112  16.9082  31.5337
 1HB  H10  H  HCH3  0   0.234  15.4587  17.9288  30.8259
 1HB  H11  H  HCH3  0   0.241  17.1564  18.1881  30.4088
 1HB  H12  H  HCH1  0   0.218  17.7626  23.1605  34.6853
 1HB  H13  H  HCH2  0   0.229  17.4077  22.7691  32.2559
 1HB  H14  H  HCH2  0   0.220  15.6743  22.7743  32.5071
 1HB  H15  H  HOH1  0   0.452  17.0621  26.6104  34.6504
 1HB  H16  H  HCH2  0   0.185  17.7130  24.9902  33.0280
 1HB  H17  H  HCH2  0   0.184  15.9718  25.1681  33.2717

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
 1HB  OE1  CD   double  1.226  0.020  1.226
 1HB  CH2  NE2  single  1.450  0.020  1.450
 1HB  CD   NE2  single  1.351  0.020  1.351
 1HB  CD   CG   single  1.516  0.020  1.516
 1HB  NE2  CH1  single  1.447  0.020  1.447
 1HB  CB   CG   single  1.520  0.020  1.520
 1HB  CB   CA   single  1.521  0.033  1.521
 1HB  C    CA   single  1.525  0.021  1.525
 1HB  C    O    single  1.231  0.020  1.231
 1HB  CA   N    single  1.458  0.019  1.458
 1HB  CG   H1   single  0.970  0.020  1.090
 1HB  CG   H2   single  0.970  0.020  1.090
 1HB  N    H3   single  0.890  0.020  1.040
 1HB  N    H4   single  0.890  0.020  1.040
 1HB  CH1  H6   single  0.970  0.020  1.090
 1HB  CH1  H7   single  0.970  0.020  1.090
 1HB  CH1  H8   single  0.970  0.020  1.090
 1HB  CH2  H9   single  0.970  0.020  1.090
 1HB  CH2  H10  single  0.970  0.020  1.090
 1HB  CH2  H11  single  0.970  0.020  1.090
 1HB  CA   H12  single  0.970  0.020  1.090
 1HB  CB   H13  single  0.970  0.020  1.090
 1HB  CB   H14  single  0.970  0.020  1.090
 1HB  O    H15  single  0.850  0.020  0.980
 1HB  C    H16  single  0.970  0.020  1.090
 1HB  C    H17  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
 1HB  H17  C    H16  107.00  3.000
 1HB  H17  C    O    111.51  3.000
 1HB  H16  C    O    111.28  3.000
 1HB  H17  C    CA   108.69  3.000
 1HB  H16  C    CA   109.40  3.000
 1HB  O    C    CA   120.80  1.700
 1HB  NE2  CD   OE1  120.81  3.000
 1HB  NE2  CD   CG   117.65  3.000
 1HB  OE1  CD   CG   121.54  3.000
 1HB  H2   CG   H1   105.56  3.000
 1HB  H2   CG   CB   109.32  3.000
 1HB  H1   CG   CB   109.51  3.000
 1HB  H2   CG   CD   109.03  3.000
 1HB  H1   CG   CD   109.74  3.000
 1HB  CB   CG   CD   113.38  3.000
 1HB  H4   N    H3   105.72  3.000
 1HB  H4   N    CA   109.09  3.000
 1HB  H3   N    CA   109.61  3.000
 1HB  CH2  NE2  CH1  116.32  3.000
 1HB  CH1  NE2  CD   125.01  3.000
 1HB  CH2  NE2  CD   118.28  3.000
 1HB  H8   CH1  H7   108.05  3.000
 1HB  H8   CH1  H6   107.55  3.000
 1HB  H7   CH1  H6   107.88  3.000
 1HB  H8   CH1  NE2  110.13  3.000
 1HB  H7   CH1  NE2  111.27  3.000
 1HB  H6   CH1  NE2  111.80  3.000
 1HB  H11  CH2  H10  108.26  3.000
 1HB  H11  CH2  H9   108.03  3.000
 1HB  H10  CH2  H9   108.07  3.000
 1HB  H11  CH2  NE2  111.47  3.000
 1HB  H10  CH2  NE2  112.14  3.000
 1HB  H9   CH2  NE2  108.74  3.000
 1HB  H12  CA   CB   107.96  3.000
 1HB  H12  CA   N    107.34  3.000
 1HB  CB   CA   N    110.40  1.500
 1HB  H12  CA   C    107.62  3.000
 1HB  N    CA   C    111.00  2.800
 1HB  CB   CA   C    110.50  1.500
 1HB  H14  CB   H13  106.44  3.000
 1HB  H14  CB   CA   108.99  3.000
 1HB  H13  CB   CA   108.88  3.000
 1HB  H14  CB   CG   110.31  3.000
 1HB  H13  CB   CG   109.90  3.000
 1HB  CA   CB   CG   112.15  3.000
 1HB  H15  O    C    108.40  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
 1HB  CONST_01  CH2  NE2  CD   CG    180.00   0.0  0
 1HB  CONST_02  CH1  NE2  CD   CG      0.00   0.0  0
 1HB  CONST_03  CH2  NE2  CD   OE1     0.00   0.0  0
 1HB  CONST_04  CH1  NE2  CD   OE1   180.00   0.0  0
 1HB  Var_01    CA   CB   CG   CD   -178.14  30.0  1
 1HB  Var_02    CB   CG   CD   OE1    -1.56  30.0  3
 1HB  Var_03    H9   CH2  NE2  CD    171.96  30.0  3
 1HB  Var_04    H6   CH1  NE2  CD    -13.04  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
 1HB  chir_01  CA  CB  C  N  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
 1HB  plan-1  CD   0.020
 1HB  plan-1  CG   0.020
 1HB  plan-1  OE1  0.020
 1HB  plan-1  NE2  0.020
 1HB  plan-1  CH1  0.020
 1HB  plan-1  CH2  0.020

