# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:46:35 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  38  17  .  2022-03-10  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.781  -2.6633  -1.1435   1.6879
 24O  C41   C  CH1   0  -0.134  -1.7782  -0.6602   0.6383
 24O  C43   C  CH1   0   0.052  -0.3314  -0.4686   1.1366
 24O  O45   O  OH1   0  -0.664   0.1605  -1.6714   1.7035
 24O  C47   C  CH1   0  -0.290   0.6410   0.0883   0.0920
 24O  C49   C  CH1   0  -0.386   2.0469   0.3202   0.7103
 24O  C51   C  CH2   0  -0.568   2.8404  -0.9615   0.4181
 24O  C54   C  C     0   0.411   2.1913  -1.5638  -0.8068
 24O  C55   C  CH2   0  -0.595   0.8838  -0.8583  -1.0868
 24O  O58   O  O     0  -0.401   2.6463  -2.4743  -1.4548
 24O  C59   C  C     0   0.563   2.7488   1.4701   0.0350
 24O  O60   O  O     0  -0.442   2.7464   1.6587  -1.1577
 24O  C92   C  CH2   0  -0.429  -2.3498   0.6214   0.0347
 24O  C95   C  CH1   0  -0.217  -3.8185   0.5485  -0.3880
 24O  C97   C  CH3   0  -0.651  -4.2730   1.9096  -0.9063
 24O  C98   C  CH3   0  -0.661  -4.0496  -0.5292  -1.4420
 24O  H39   H  HNH2  0   0.343  -2.2501  -1.9459   2.1467
 24O  H41   H  HCH1  0   0.219  -1.7604  -1.4315  -0.1435
 24O  H43   H  HCH1  0   0.230  -0.3640   0.2502   1.9645
 24O  H45   H  HOH1  0   0.447   0.0082  -2.3952   1.0853
 24O  H47   H  HCH1  0   0.280   0.2390   1.0414  -0.2539
 24O  H49   H  HCH1  0   0.290   1.9825   0.5124   1.7816
 24O  H511  H  HCH2  0   0.290   3.9126  -0.8193   0.2721
 24O  H512  H  HCH2  0   0.305   2.7264  -1.6691   1.2416
 24O  H551  H  HCH2  0   0.279   0.0893  -1.5872  -1.2627
 24O  H552  H  HCH2  0   0.304   0.9937  -0.3037  -2.0216
 24O  H921  H  HCH2  0   0.219  -2.2248   1.4356   0.7601
 24O  H922  H  HCH2  0   0.224  -1.7627   0.9054  -0.8442
 24O  H95   H  HCH1  0   0.217  -4.4194   0.2994   0.4909
 24O  H971  H  HCH3  0   0.210  -3.6972   2.2062  -1.7869
 24O  H972  H  HCH3  0   0.223  -5.3262   1.8938  -1.1922
 24O  H973  H  HCH3  0   0.222  -4.1461   2.6881  -0.1518
 24O  H981  H  HCH3  0   0.228  -3.7997  -1.5237  -1.0708
 24O  H982  H  HCH3  0   0.224  -5.0941  -0.5518  -1.7578
 24O  H983  H  HCH3  0   0.209  -3.4411  -0.3405  -2.3308
 24O  H2    H  HNH2  0   0.334  -2.7541  -0.4323   2.4062
 24O  OXT   O  OH1   0  -0.586   3.4175   2.2345   0.8881
 24O  HXT   H  HOH1  0   0.481   3.8899   2.9321   0.4081

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  1.456  0.020  1.456
 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  1.418  0.020  1.418
 24O  C43  C47   single  1.532  0.020  1.532
 24O  C43  H43   single  0.970  0.020  1.090
 24O  O45  H45   single  0.850  0.020  0.980
 24O  C47  C49   single  1.553  0.020  1.553
 24O  C47  C55   single  1.531  0.020  1.531
 24O  C47  H47   single  0.970  0.020  1.090
 24O  C49  C51   single  1.536  0.020  1.536
 24O  C49  C59   single  1.507  0.020  1.507
 24O  C49  H49   single  0.970  0.020  1.090
 24O  C51  C54   single  1.511  0.020  1.511
 24O  C51  H511  single  0.970  0.020  1.090
 24O  C51  H512  single  0.970  0.020  1.090
 24O  C54  C55   single  1.512  0.020  1.512
 24O  C54  O58   double  1.207  0.020  1.207
 24O  C55  H551  single  0.970  0.020  1.090
 24O  C55  H552  single  0.970  0.020  1.090
 24O  C59  O60   double  1.208  0.020  1.208
 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   single  1.326  0.020  1.326
 24O  OXT  HXT   single  0.850  0.020  0.980

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   105.73  3.000
 24O  H2    N    C41   109.40  3.000
 24O  H39   N    C41   109.98  3.000
 24O  H41   C41  C92   108.30  3.000
 24O  H41   C41  C43   107.58  3.000
 24O  C92   C41  C43   111.99  3.000
 24O  H41   C41  N     106.86  3.000
 24O  C92   C41  N     109.63  3.000
 24O  C43   C41  N     112.25  3.000
 24O  H43   C43  C47   107.18  3.000
 24O  H43   C43  O45   105.33  3.000
 24O  C47   C43  O45   111.15  3.000
 24O  H43   C43  C41   107.31  3.000
 24O  C47   C43  C41   114.85  3.000
 24O  O45   C43  C41   110.44  3.000
 24O  H45   O45  C43   109.01  3.000
 24O  H47   C47  C55   110.77  3.000
 24O  H47   C47  C49   109.23  3.000
 24O  C55   C47  C49   104.79  3.000
 24O  H47   C47  C43   107.45  3.000
 24O  C55   C47  C43   113.64  3.000
 24O  C49   C47  C43   110.94  3.000
 24O  H49   C49  C59   109.47  3.000
 24O  H49   C49  C51   111.38  3.000
 24O  C59   C49  C51   108.12  3.000
 24O  H49   C49  C47   111.34  3.000
 24O  C59   C49  C47   110.92  3.000
 24O  C51   C49  C47   105.50  3.000
 24O  H512  C51  H511  106.74  3.000
 24O  H512  C51  C54   107.95  3.000
 24O  H511  C51  C54   111.43  3.000
 24O  H512  C51  C49   110.09  3.000
 24O  H511  C51  C49   115.11  3.000
 24O  C54   C51  C49   105.36  3.000
 24O  O58   C54  C55   125.37  3.000
 24O  O58   C54  C51   125.03  3.000
 24O  C55   C54  C51   109.61  3.000
 24O  H552  C55  H551  105.91  3.000
 24O  H552  C55  C54   107.96  3.000
 24O  H551  C55  C54   110.33  3.000
 24O  H552  C55  C47   111.15  3.000
 24O  H551  C55  C47   114.90  3.000
 24O  C54   C55  C47   106.44  3.000
 24O  OXT   C59  O60   123.11  3.000
 24O  OXT   C59  C49   112.73  3.000
 24O  O60   C59  C49   124.12  3.000
 24O  H922  C92  H921  106.09  3.000
 24O  H922  C92  C95   107.78  3.000
 24O  H921  C92  C95   109.10  3.000
 24O  H922  C92  C41   109.53  3.000
 24O  H921  C92  C41   108.58  3.000
 24O  C95   C92  C41   115.36  3.000
 24O  H95   C95  C98   108.14  3.000
 24O  H95   C95  C97   108.22  3.000
 24O  C98   C95  C97   110.52  3.000
 24O  H95   C95  C92   108.44  3.000
 24O  C98   C95  C92   111.72  3.000
 24O  C97   C95  C92   109.71  3.000
 24O  H973  C97  H972  107.67  3.000
 24O  H973  C97  H971  107.58  3.000
 24O  H972  C97  H971  107.53  3.000
 24O  H973  C97  C95   111.52  3.000
 24O  H972  C97  C95   111.31  3.000
 24O  H971  C97  C95   111.03  3.000
 24O  H983  C98  H982  107.51  3.000
 24O  H983  C98  H981  107.85  3.000
 24O  H982  C98  H981  107.39  3.000
 24O  H983  C98  C95   110.82  3.000
 24O  H982  C98  C95   111.07  3.000
 24O  H981  C98  C95   111.99  3.000
 24O  HXT   OXT  C59   109.99  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  CONST_01  HXT   OXT  C59  C49  180.00   0.0  0
 24O  Var_01    C51   C54  C55  C47   -6.81  30.0  1
 24O  Var_02    C55   C54  C51  C49  -11.52  30.0  1
 24O  Var_03    C97   C95  C92  C41  177.23  30.0  3
 24O  Var_04    H971  C97  C95  C92   61.67  30.0  3
 24O  Var_05    H981  C98  C95  C92   61.65  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
 24O  plan-2  HXT  0.020

