# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:14:37 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]cyclopentanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)[C@@H]1CCC[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
 24M  24M  '(1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]cyclopentanecarboxylic acid'  peptide  38  16  .  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_24M
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
 24M  N1    N  NH2    0  -0.831  -1.9461   1.7882   0.3412
 24M  C3    C  CH1    0  -0.132  -1.6019   0.3857   0.1115
 24M  C5    C  CH1    0   0.059  -0.2911   0.3466  -0.7138
 24M  O7    O  OH1    0  -0.693  -0.3220   1.3747  -1.6774
 24M  C9    C  CH1    0  -0.215   0.9622   0.3896   0.1587
 24M  C11   C  CH1    0  -0.345   2.2743   0.2504  -0.6092
 24M  C13   C  CH2    0  -0.441   3.3123   0.5819   0.4696
 24M  C16   C  CH2    0  -0.436   2.6871   1.7343   1.2728
 24M  C19   C  CH2    0  -0.459   1.1686   1.6592   0.9972
 24M  C22   C  C      0   0.412   2.5463  -1.1113  -1.2624
 24M  O23   O  O      0  -0.612   2.0187  -2.1186  -0.7449
 24M  C36   C  CH2    0  -0.408  -2.7293  -0.3202  -0.6378
 24M  C39   C  CH1    0  -0.252  -4.0694  -0.4404   0.0941
 24M  C41   C  CH3    0  -0.648  -5.0745  -1.1622  -0.7986
 24M  C45   C  CH3    0  -0.658  -3.9342  -1.1600   1.4321
 24M  HN1   H  HNH2   0   0.364  -2.9332   1.9034   0.5242
 24M  H3    H  HCH1   0   0.219  -1.4157  -0.1499   1.0512
 24M  H5    H  HCH1   0   0.208  -0.2642  -0.6131  -1.2446
 24M  HO7   H  HOH1   0   0.433  -0.9064   2.0431  -1.2726
 24M  H9    H  HCH1   0   0.204   0.8942  -0.4696   0.8368
 24M  H11   H  HCH1   0   0.198   2.3206   1.0296  -1.3800
 24M  H131  H  HCH2   0   0.210   3.4479  -0.2935   1.1125
 24M  H132  H  HCH2   0   0.223   4.2913   0.8341   0.0588
 24M  H161  H  HCH2   0   0.221   2.9146   1.6520   2.3367
 24M  H162  H  HCH2   0   0.220   3.0885   2.6944   0.9434
 24M  H191  H  HCH2   0   0.215   0.8482   2.5419   0.4390
 24M  H192  H  HCH2   0   0.220   0.5851   1.6400   1.9208
 24M  H361  H  HCH2   0   0.221  -2.8903   0.1876  -1.5957
 24M  H362  H  HCH2   0   0.219  -2.3853  -1.3306  -0.8844
 24M  H39   H  HCH1   0   0.211  -4.4703   0.5626   0.2865
 24M  H411  H  HCH3   0   0.213  -4.7290  -2.1725  -1.0313
 24M  H412  H  HCH3   0   0.225  -6.0472  -1.2493  -0.3117
 24M  H413  H  HCH3   0   0.224  -5.2213  -0.6369  -1.7440
 24M  H451  H  HCH3   0   0.228  -3.2872  -0.6258   2.1290
 24M  H452  H  HCH3   0   0.227  -4.9071  -1.2729   1.9138
 24M  H453  H  HCH3   0   0.213  -3.5176  -2.1614   1.2939
 24M  H2    H  HNH2   0   0.365  -1.4603   2.1559   1.1481
 24M  OXT   O  OC    -1  -0.625   3.3182  -1.1135  -2.2452

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
 24M  N1   C3    single  1.462  0.020  1.462
 24M  N1   HN1   single  0.890  0.020  1.040
 24M  C3   C5    single  1.549  0.020  1.549
 24M  C3   C36   single  1.527  0.020  1.527
 24M  C3   H3    single  0.970  0.020  1.090
 24M  C5   O7    single  1.409  0.020  1.409
 24M  C5   C9    single  1.528  0.020  1.528
 24M  C5   H5    single  0.970  0.020  1.090
 24M  O7   HO7   single  0.850  0.020  0.980
 24M  C9   C11   single  1.527  0.020  1.527
 24M  C9   C19   single  1.535  0.020  1.535
 24M  C9   H9    single  0.970  0.020  1.090
 24M  C11  C13   single  1.533  0.020  1.533
 24M  C11  C22   single  1.535  0.020  1.535
 24M  C11  H11   single  0.970  0.020  1.090
 24M  C13  C16   single  1.538  0.020  1.538
 24M  C13  H131  single  0.970  0.020  1.090
 24M  C13  H132  single  0.970  0.020  1.090
 24M  C16  C19   single  1.545  0.020  1.545
 24M  C16  H161  single  0.970  0.020  1.090
 24M  C16  H162  single  0.970  0.020  1.090
 24M  C19  H191  single  0.970  0.020  1.090
 24M  C19  H192  single  0.970  0.020  1.090
 24M  C22  O23   deloc   1.249  0.020  1.249
 24M  C36  C39   single  1.532  0.020  1.532
 24M  C36  H361  single  0.970  0.020  1.090
 24M  C36  H362  single  0.970  0.020  1.090
 24M  C39  C41   single  1.526  0.020  1.526
 24M  C39  C45   single  1.525  0.020  1.525
 24M  C39  H39   single  0.970  0.020  1.090
 24M  C41  H411  single  0.970  0.020  1.090
 24M  C41  H412  single  0.970  0.020  1.090
 24M  C41  H413  single  0.970  0.020  1.090
 24M  C45  H451  single  0.970  0.020  1.090
 24M  C45  H452  single  0.970  0.020  1.090
 24M  C45  H453  single  0.970  0.020  1.090
 24M  N1   H2    single  0.890  0.020  1.040
 24M  C22  OXT   deloc   1.250  0.020  1.250

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
 24M  H2    N1   HN1   106.46  3.000
 24M  H2    N1   C3    111.17  3.000
 24M  HN1   N1   C3    111.58  3.000
 24M  H3    C3   C36   108.65  3.000
 24M  H3    C3   C5    107.47  3.000
 24M  C36   C3   C5    110.59  3.000
 24M  H3    C3   N1    111.93  3.000
 24M  C36   C3   N1    110.29  3.000
 24M  C5    C3   N1    107.88  3.000
 24M  H5    C5   C9    106.31  3.000
 24M  H5    C5   O7    107.93  3.000
 24M  C9    C5   O7    112.83  3.000
 24M  H5    C5   C3    107.49  3.000
 24M  C9    C5   C3    112.90  3.000
 24M  O7    C5   C3    109.10  3.000
 24M  HO7   O7   C5    103.25  3.000
 24M  H9    C9   C19   108.57  3.000
 24M  H9    C9   C11   107.03  3.000
 24M  C19   C9   C11   103.56  3.000
 24M  H9    C9   C5    106.28  3.000
 24M  C19   C9   C5    116.45  3.000
 24M  C11   C9   C5    114.54  3.000
 24M  H11   C11  C22   108.89  3.000
 24M  H11   C11  C13   108.19  3.000
 24M  C22   C11  C13   111.79  3.000
 24M  H11   C11  C9    108.96  3.000
 24M  C22   C11  C9    116.57  3.000
 24M  C13   C11  C9    102.02  3.000
 24M  H132  C13  H131  107.15  3.000
 24M  H132  C13  C16   112.84  3.000
 24M  H131  C13  C16   110.06  3.000
 24M  H132  C13  C11   113.10  3.000
 24M  H131  C13  C11   108.92  3.000
 24M  C16   C13  C11   104.73  3.000
 24M  H162  C16  H161  106.50  3.000
 24M  H162  C16  C19   110.51  3.000
 24M  H161  C16  C19   112.04  3.000
 24M  H162  C16  C13   110.61  3.000
 24M  H161  C16  C13   111.59  3.000
 24M  C19   C16  C13   105.66  3.000
 24M  H192  C19  H191  106.82  3.000
 24M  H192  C19  C16   112.02  3.000
 24M  H191  C19  C16   109.88  3.000
 24M  H192  C19  C9    112.04  3.000
 24M  H191  C19  C9    110.47  3.000
 24M  C16   C19  C9    105.65  3.000
 24M  OXT   C22  O23   125.82  3.000
 24M  OXT   C22  C11   116.47  3.000
 24M  O23   C22  C11   117.67  3.000
 24M  H362  C36  H361  106.06  3.000
 24M  H362  C36  C39   108.06  3.000
 24M  H361  C36  C39   109.00  3.000
 24M  H362  C36  C3    107.76  3.000
 24M  H361  C36  C3    108.86  3.000
 24M  C39   C36  C3    116.61  3.000
 24M  H39   C39  C45   108.06  3.000
 24M  H39   C39  C41   107.12  3.000
 24M  C45   C39  C41   110.39  3.000
 24M  H39   C39  C36   109.37  3.000
 24M  C45   C39  C36   112.25  3.000
 24M  C41   C39  C36   109.50  3.000
 24M  H413  C41  H412  107.76  3.000
 24M  H413  C41  H411  107.63  3.000
 24M  H412  C41  H411  107.63  3.000
 24M  H413  C41  C39   111.58  3.000
 24M  H412  C41  C39   111.34  3.000
 24M  H411  C41  C39   110.71  3.000
 24M  H453  C45  H452  107.50  3.000
 24M  H453  C45  H451  107.65  3.000
 24M  H452  C45  H451  107.30  3.000
 24M  H453  C45  C39   110.80  3.000
 24M  H452  C45  C39   110.91  3.000
 24M  H451  C45  C39   112.46  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
 24M  Var_01  C13   C16  C19  C9     5.32  30.0  1
 24M  Var_02  C19   C16  C13  C11   20.90  30.0  1
 24M  Var_03  C41   C39  C36  C3   179.75  30.0  3
 24M  Var_04  H411  C41  C39  C36   61.26  30.0  3
 24M  Var_05  H451  C45  C39  C36   62.37  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
 24M  chir_01  C3   N1  C5   C36  positiv
 24M  chir_02  C5   O7  C3   C9   positiv
 24M  chir_03  C9   C5  C11  C19  negativ
 24M  chir_04  C11  C9  C13  C22  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
 24M  plan-1  C11  0.020
 24M  plan-1  C22  0.020
 24M  plan-1  O23  0.020
 24M  plan-1  OXT  0.020

