# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:37:04 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]-4-oxocyclopentanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)[C@@H]1CC(=O)C[C@H]1C(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
 24O  24O  '(1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]-4-oxocyclopentanecarboxylic acid'  peptide  37  17  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_24O
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
 24O  N     N  NH2    0  -0.782  -2.6488  -1.1687   1.6448
 24O  C41   C  CH1    0  -0.134  -1.7693  -0.6583   0.6012
 24O  C43   C  CH1    0   0.062  -0.3205  -0.4655   1.0925
 24O  O45   O  OH1    0  -0.667   0.1700  -1.6762   1.6540
 24O  C47   C  CH1    0  -0.294   0.6494   0.0977   0.0521
 24O  C49   C  CH1    0  -0.398   2.0497   0.3961   0.6330
 24O  C51   C  CH2    0  -0.546   2.8427  -0.9015   0.4811
 24O  C54   C  C      0   0.389   2.1262  -1.6954  -0.5844
 24O  C55   C  CH2    0  -0.593   0.9439  -0.8928  -1.0752
 24O  O58   O  O      0  -0.419   2.4501  -2.7905  -0.9848
 24O  C59   C  C      0   0.431   2.7339   1.6152  -0.0463
 24O  O60   O  O      0  -0.603   1.9910   2.5467  -0.4140
 24O  C92   C  CH2    0  -0.425  -2.3558   0.6307   0.0273
 24O  C95   C  CH1    0  -0.217  -3.8259   0.5549  -0.3896
 24O  C97   C  CH3    0  -0.652  -4.2950   1.9238  -0.8735
 24O  C98   C  CH3    0  -0.661  -4.0528  -0.4988  -1.4684
 24O  H39   H  HNH2   0   0.340  -2.2261  -1.9754   2.0870
 24O  H41   H  HCH1   0   0.215  -1.7508  -1.4123  -0.1977
 24O  H43   H  HCH1   0   0.217  -0.3527   0.2460   1.9277
 24O  H45   H  HOH1   0   0.444  -0.0151  -2.4008   1.0465
 24O  H47   H  HCH1   0   0.256   0.2333   1.0271  -0.3326
 24O  H49   H  HCH1   0   0.251   1.9606   0.6676   1.6915
 24O  H511  H  HCH2   0   0.266   3.8802  -0.7284   0.1903
 24O  H512  H  HCH2   0   0.267   2.8670  -1.4952   1.3969
 24O  H551  H  HCH2   0   0.267   0.1136  -1.5246  -1.3972
 24O  H552  H  HCH2   0   0.289   1.2805  -0.3500  -1.9668
 24O  H921  H  HCH2   0   0.216  -2.2332   1.4304   0.7691
 24O  H922  H  HCH2   0   0.222  -1.7741   0.9380  -0.8468
 24O  H95   H  HCH1   0   0.216  -4.4205   0.2790   0.4858
 24O  H971  H  HCH3   0   0.210  -3.7261   2.2445  -1.7500
 24O  H972  H  HCH3   0   0.222  -5.3497   1.9064  -1.1538
 24O  H973  H  HCH3   0   0.222  -4.1694   2.6857  -0.1019
 24O  H981  H  HCH3   0   0.229  -3.7855  -1.4987  -1.1248
 24O  H982  H  HCH3   0   0.223  -5.0999  -0.5274  -1.7757
 24O  H983  H  HCH3   0   0.208  -3.4557  -0.2788  -2.3578
 24O  H2    H  HNH2   0   0.332  -2.7375  -0.4716   2.3771
 24O  OXT   O  OC    -1  -0.604   3.9780   1.5949  -0.1249

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
 24O  N    C41   single  1.457  0.020  1.457
 24O  N    H39   single  0.890  0.020  1.040
 24O  C41  C43   single  1.542  0.020  1.542
 24O  C41  C92   single  1.528  0.020  1.528
 24O  C41  H41   single  0.970  0.020  1.090
 24O  C43  O45   single  1.422  0.020  1.422
 24O  C43  C47   single  1.530  0.020  1.530
 24O  C43  H43   single  0.970  0.020  1.090
 24O  O45  H45   single  0.850  0.020  0.980
 24O  C47  C49   single  1.545  0.020  1.545
 24O  C47  C55   single  1.529  0.020  1.529
 24O  C47  H47   single  0.970  0.020  1.090
 24O  C49  C51   single  1.528  0.020  1.528
 24O  C49  C59   single  1.554  0.020  1.554
 24O  C49  H49   single  0.970  0.020  1.090
 24O  C51  C54   single  1.510  0.020  1.510
 24O  C51  H511  single  0.970  0.020  1.090
 24O  C51  H512  single  0.970  0.020  1.090
 24O  C54  C55   single  1.511  0.020  1.511
 24O  C54  O58   double  1.210  0.020  1.210
 24O  C55  H551  single  0.970  0.020  1.090
 24O  C55  H552  single  0.970  0.020  1.090
 24O  C59  O60   deloc   1.247  0.020  1.247
 24O  C92  C95   single  1.530  0.020  1.530
 24O  C92  H921  single  0.970  0.020  1.090
 24O  C92  H922  single  0.970  0.020  1.090
 24O  C95  C97   single  1.526  0.020  1.526
 24O  C95  C98   single  1.525  0.020  1.525
 24O  C95  H95   single  0.970  0.020  1.090
 24O  C97  H971  single  0.970  0.020  1.090
 24O  C97  H972  single  0.970  0.020  1.090
 24O  C97  H973  single  0.970  0.020  1.090
 24O  C98  H981  single  0.970  0.020  1.090
 24O  C98  H982  single  0.970  0.020  1.090
 24O  C98  H983  single  0.970  0.020  1.090
 24O  N    H2    single  0.890  0.020  1.040
 24O  C59  OXT   deloc   1.247  0.020  1.247

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
 24O  H2    N    H39   105.58  3.000
 24O  H2    N    C41   109.20  3.000
 24O  H39   N    C41   109.87  3.000
 24O  H41   C41  C92   108.20  3.000
 24O  H41   C41  C43   107.56  3.000
 24O  C92   C41  C43   112.02  3.000
 24O  H41   C41  N     106.89  3.000
 24O  C92   C41  N     109.44  3.000
 24O  C43   C41  N     112.50  3.000
 24O  H43   C43  C47   107.30  3.000
 24O  H43   C43  O45   105.17  3.000
 24O  C47   C43  O45   111.30  3.000
 24O  H43   C43  C41   107.21  3.000
 24O  C47   C43  C41   115.15  3.000
 24O  O45   C43  C41   110.09  3.000
 24O  H45   O45  C43   108.97  3.000
 24O  H47   C47  C55   111.48  3.000
 24O  H47   C47  C49   108.33  3.000
 24O  C55   C47  C49   103.16  3.000
 24O  H47   C47  C43   108.20  3.000
 24O  C55   C47  C43   112.64  3.000
 24O  C49   C47  C43   112.96  3.000
 24O  H49   C49  C59   105.28  3.000
 24O  H49   C49  C51   110.39  3.000
 24O  C59   C49  C51   113.21  3.000
 24O  H49   C49  C47   109.70  3.000
 24O  C59   C49  C47   112.72  3.000
 24O  C51   C49  C47   105.60  3.000
 24O  H512  C51  H511  106.77  3.000
 24O  H512  C51  C54   108.46  3.000
 24O  H511  C51  C54   110.28  3.000
 24O  H512  C51  C49   112.95  3.000
 24O  H511  C51  C49   112.65  3.000
 24O  C54   C51  C49   105.69  3.000
 24O  O58   C54  C55   125.63  3.000
 24O  O58   C54  C51   125.62  3.000
 24O  C55   C54  C51   108.74  3.000
 24O  H552  C55  H551  106.26  3.000
 24O  H552  C55  C54   106.66  3.000
 24O  H551  C55  C54   112.55  3.000
 24O  H552  C55  C47   109.74  3.000
 24O  H551  C55  C47   116.47  3.000
 24O  C54   C55  C47   104.79  3.000
 24O  OXT   C59  O60   126.02  3.000
 24O  OXT   C59  C49   117.01  3.000
 24O  O60   C59  C49   116.91  3.000
 24O  H922  C92  H921  106.02  3.000
 24O  H922  C92  C95   107.89  3.000
 24O  H921  C92  C95   109.12  3.000
 24O  H922  C92  C41   109.45  3.000
 24O  H921  C92  C41   108.53  3.000
 24O  C95   C92  C41   115.43  3.000
 24O  H95   C95  C98   108.12  3.000
 24O  H95   C95  C97   108.24  3.000
 24O  C98   C95  C97   110.48  3.000
 24O  H95   C95  C92   108.47  3.000
 24O  C98   C95  C92   111.71  3.000
 24O  C97   C95  C92   109.71  3.000
 24O  H973  C97  H972  107.69  3.000
 24O  H973  C97  H971  107.59  3.000
 24O  H972  C97  H971  107.55  3.000
 24O  H973  C97  C95   111.51  3.000
 24O  H972  C97  C95   111.36  3.000
 24O  H971  C97  C95   110.95  3.000
 24O  H983  C98  H982  107.46  3.000
 24O  H983  C98  H981  107.87  3.000
 24O  H982  C98  H981  107.45  3.000
 24O  H983  C98  C95   110.80  3.000
 24O  H982  C98  C95   111.10  3.000
 24O  H981  C98  C95   111.97  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
 24O  Var_01  C51   C54  C55  C47  -21.56  30.0  1
 24O  Var_02  C55   C54  C51  C49    0.70  30.0  1
 24O  Var_03  C97   C95  C92  C41  177.08  30.0  3
 24O  Var_04  H971  C97  C95  C92   61.70  30.0  3
 24O  Var_05  H981  C98  C95  C92   61.26  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
 24O  chir_01  C41  N    C43  C92  positiv
 24O  chir_02  C43  O45  C41  C47  positiv
 24O  chir_03  C47  C43  C49  C55  negativ
 24O  chir_04  C49  C47  C51  C59  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
 24O  plan-1  C51  0.020
 24O  plan-1  C54  0.020
 24O  plan-1  C55  0.020
 24O  plan-1  O58  0.020
 24O  plan-2  C49  0.020
 24O  plan-2  C59  0.020
 24O  plan-2  O60  0.020
 24O  plan-2  OXT  0.020

