# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:19:35 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[(2R)-2-(aminomethyl)-2-(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(1-ethylpropyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)Nc1cc(ccc1N2C(=O)CC[C@@]2(CN)CO)C(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
 IBA  IBA  '4-[(2R)-2-(aminomethyl)-2-(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(1-ethylpropyl)amino]benzoic acid'  ligand  51  25  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IBA
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
 IBA  C6    C  CR16   0  -0.232   4.7112   0.7404   0.3038
 IBA  C5    C  CR6    0   0.221   4.0568   0.0603   1.3176
 IBA  C4    C  CR6    0   0.408   4.6609  -0.0685   2.5881
 IBA  C3    C  CR16   0  -0.421   5.9499   0.4616   2.7498
 IBA  C2    C  CR6    0  -0.086   6.6072   1.1244   1.7228
 IBA  C7    C  CR16   0  -0.356   5.9773   1.2709   0.4897
 IBA  C1    C  C      0   0.395   8.0074   1.6855   1.9522
 IBA  O21   O  OC    -1  -0.594   8.4972   1.5362   3.0888
 IBA  O20   O  O      0  -0.595   8.5474   2.2473   0.9795
 IBA  N4    N  NH1    0  -0.699   3.9957  -0.6793   3.6079
 IBA  C8    C  CH1    0  -0.073   4.4304  -0.7536   4.9853
 IBA  C11   C  CH2    0  -0.418   5.2884  -1.9942   5.2615
 IBA  C9    C  CH2    0  -0.449   3.2154  -0.6515   5.9061
 IBA  C12   C  CH3    0  -0.685   4.5715  -3.3218   5.0608
 IBA  C10   C  CH3    0  -0.663   2.5180   0.6998   5.8290
 IBA  N5    N  NT     0  -0.589   2.7500  -0.4582   1.1182
 IBA  C13   C  CT     0   0.069   2.4290  -1.7228   0.4275
 IBA  C14   C  CH2    0  -0.482   0.9748  -1.9464   0.8827
 IBA  C15   C  CH2    0  -0.582   0.4272  -0.5475   1.1289
 IBA  C16   C  C      0   0.511   1.6531   0.2624   1.4735
 IBA  O13   O  O      0  -0.475   1.6760   1.3688   1.9791
 IBA  C18   C  CH2    0  -0.129   2.4450  -1.5768  -1.0959
 IBA  O18   O  OH1    0  -0.659   3.7652  -1.5190  -1.5732
 IBA  C17   C  CH2    0  -0.312   3.3685  -2.8435   0.8973
 IBA  N17   N  NH2    0  -0.792   3.1442  -4.1463   0.3099
 IBA  H7    H  HCR6   0   0.231   6.4710   1.7964  -0.3154
 IBA  H6    H  HCR6   0   0.237   4.2153   0.8519  -0.6502
 IBA  H151  H  HCH2   0   0.280  -0.3096  -0.4969   1.9296
 IBA  H152  H  HCH2   0   0.278  -0.0359  -0.1197   0.2353
 IBA  H141  H  HCH2   0   0.258   0.9682  -2.5202   1.8128
 IBA  H142  H  HCH2   0   0.260   0.3925  -2.5094   0.1545
 IBA  H181  H  HCH2   0   0.217   1.8721  -0.6822  -1.3745
 IBA  H182  H  HCH2   0   0.202   1.9104  -2.4347  -1.5239
 IBA  H18   H  HOH1   0   0.458   3.7345  -1.3711  -2.5226
 IBA  H171  H  HCH2   0   0.227   3.2667  -2.9324   1.9823
 IBA  H172  H  HCH2   0   0.244   4.4055  -2.5583   0.7121
 IBA  H11   H  HNH2   0   0.349   2.1836  -4.4430   0.4275
 IBA  H12   H  HNH2   0   0.351   3.3275  -4.1285  -0.6843
 IBA  HN4   H  HNH1   0   0.362   3.0785  -1.0346   3.4038
 IBA  H8    H  HCH1   0   0.234   5.0546   0.1231   5.1892
 IBA  H111  H  HCH2   0   0.226   6.1679  -1.9601   4.6120
 IBA  H112  H  HCH2   0   0.218   5.6656  -1.9292   6.2865
 IBA  H121  H  HCH3   0   0.224   3.7351  -3.4479   5.7489
 IBA  H122  H  HCH3   0   0.224   4.1846  -3.4162   4.0453
 IBA  H123  H  HCH3   0   0.233   5.2540  -4.1564   5.2238
 IBA  H91   H  HCH2   0   0.233   3.5491  -0.8352   6.9307
 IBA  H92   H  HCH2   0   0.222   2.5010  -1.4490   5.6768
 IBA  H101  H  HCH3   0   0.218   3.1976   1.5066   6.1100
 IBA  H102  H  HCH3   0   0.225   2.1532   0.9115   4.8233
 IBA  H103  H  HCH3   0   0.229   1.6633   0.7378   6.5051
 IBA  H3    H  HCR6   0   0.246   6.4600   0.3637   3.6977

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
 IBA  C6   C7    aromatic  1.385  0.020  1.385
 IBA  C6   H6    single    0.930  0.020  1.080
 IBA  C6   C5    aromatic  1.385  0.020  1.385
 IBA  C5   N5    single    1.420  0.020  1.420
 IBA  C5   C4    aromatic  1.413  0.020  1.413
 IBA  C4   N4    single    1.362  0.020  1.362
 IBA  C4   C3    aromatic  1.403  0.020  1.403
 IBA  C3   C2    aromatic  1.388  0.020  1.388
 IBA  C3   H3    single    0.930  0.020  1.080
 IBA  C2   C1    single    1.526  0.020  1.526
 IBA  C2   C7    aromatic  1.392  0.020  1.392
 IBA  C7   H7    single    0.930  0.020  1.080
 IBA  C1   O21   deloc     1.247  0.020  1.247
 IBA  C1   O20   deloc     1.246  0.020  1.246
 IBA  N4   HN4   single    0.860  0.020  1.020
 IBA  N4   C8    single    1.446  0.020  1.446
 IBA  C8   H8    single    0.970  0.020  1.090
 IBA  C8   C11   single    1.534  0.020  1.534
 IBA  C8   C9    single    1.528  0.020  1.528
 IBA  C11  H111  single    0.970  0.020  1.090
 IBA  C11  H112  single    0.970  0.020  1.090
 IBA  C11  C12   single    1.522  0.020  1.522
 IBA  C9   H91   single    0.970  0.020  1.090
 IBA  C9   H92   single    0.970  0.020  1.090
 IBA  C9   C10   single    1.523  0.020  1.523
 IBA  C12  H121  single    0.970  0.020  1.090
 IBA  C12  H122  single    0.970  0.020  1.090
 IBA  C12  H123  single    0.970  0.020  1.090
 IBA  C10  H101  single    0.970  0.020  1.090
 IBA  C10  H102  single    0.970  0.020  1.090
 IBA  C10  H103  single    0.970  0.020  1.090
 IBA  N5   C16   single    1.360  0.020  1.360
 IBA  N5   C13   single    1.476  0.020  1.476
 IBA  C13  C14   single    1.540  0.020  1.540
 IBA  C13  C18   single    1.530  0.020  1.530
 IBA  C13  C17   single    1.536  0.020  1.536
 IBA  C14  C15   single    1.522  0.020  1.522
 IBA  C14  H141  single    0.970  0.020  1.090
 IBA  C14  H142  single    0.970  0.020  1.090
 IBA  C15  C16   single    1.509  0.020  1.509
 IBA  C15  H151  single    0.970  0.020  1.090
 IBA  C15  H152  single    0.970  0.020  1.090
 IBA  C16  O13   double    1.217  0.020  1.217
 IBA  C18  H181  single    0.970  0.020  1.090
 IBA  C18  H182  single    0.970  0.020  1.090
 IBA  C18  O18   single    1.405  0.020  1.405
 IBA  O18  H18   single    0.850  0.020  0.980
 IBA  C17  H171  single    0.970  0.020  1.090
 IBA  C17  H172  single    0.970  0.020  1.090
 IBA  C17  N17   single    1.447  0.020  1.447
 IBA  N17  H11   single    0.890  0.020  1.040
 IBA  N17  H12   single    0.890  0.020  1.040

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
 IBA  H6    C6   C7    119.88  3.000
 IBA  H6    C6   C5    118.67  3.000
 IBA  C7    C6   C5    121.44  3.000
 IBA  N5    C5   C4    119.11  3.000
 IBA  C4    C5   C6    120.07  3.000
 IBA  N5    C5   C6    120.75  3.000
 IBA  N4    C4   C3    122.12  3.000
 IBA  C3    C4   C5    117.52  3.000
 IBA  N4    C4   C5    120.36  3.000
 IBA  H3    C3   C2    117.95  3.000
 IBA  H3    C3   C4    120.03  3.000
 IBA  C2    C3   C4    122.02  3.000
 IBA  C1    C2   C7    120.64  3.000
 IBA  C7    C2   C3    119.43  3.000
 IBA  C1    C2   C3    119.93  3.000
 IBA  H7    C7   C2    120.28  3.000
 IBA  H7    C7   C6    120.25  3.000
 IBA  C2    C7   C6    119.47  3.000
 IBA  O20   C1   O21   126.54  3.000
 IBA  O20   C1   C2    116.49  3.000
 IBA  O21   C1   C2    116.97  3.000
 IBA  HN4   N4   C8    116.72  3.000
 IBA  C8    N4   C4    126.11  3.000
 IBA  HN4   N4   C4    116.90  3.000
 IBA  H8    C8   C9    106.71  3.000
 IBA  C9    C8   C11   112.98  3.000
 IBA  H8    C8   C11   107.17  3.000
 IBA  C9    C8   N4    109.36  3.000
 IBA  C11   C8   N4    112.42  3.000
 IBA  H8    C8   N4    107.90  3.000
 IBA  H112  C11  H111  106.09  3.000
 IBA  H112  C11  C12   109.74  3.000
 IBA  H111  C11  C12   109.12  3.000
 IBA  C12   C11  C8    114.73  3.000
 IBA  H112  C11  C8    108.27  3.000
 IBA  H111  C11  C8    108.52  3.000
 IBA  H92   C9   H91   105.85  3.000
 IBA  H92   C9   C10   109.69  3.000
 IBA  H91   C9   C10   109.66  3.000
 IBA  C10   C9   C8    113.14  3.000
 IBA  H92   C9   C8    110.11  3.000
 IBA  H91   C9   C8    108.12  3.000
 IBA  H123  C12  H122  107.16  3.000
 IBA  H123  C12  H121  107.29  3.000
 IBA  H122  C12  H121  107.78  3.000
 IBA  H123  C12  C11   110.68  3.000
 IBA  H122  C12  C11   111.43  3.000
 IBA  H121  C12  C11   112.27  3.000
 IBA  H103  C10  H102  107.63  3.000
 IBA  H103  C10  H101  107.61  3.000
 IBA  H102  C10  H101  107.59  3.000
 IBA  H103  C10  C9    111.01  3.000
 IBA  H102  C10  C9    111.85  3.000
 IBA  H101  C10  C9    110.96  3.000
 IBA  C16   N5   C13   113.63  3.000
 IBA  C13   N5   C5    125.36  3.000
 IBA  C16   N5   C5    120.81  3.000
 IBA  C17   C13  C18   111.57  3.000
 IBA  C17   C13  C14   112.40  3.000
 IBA  C18   C13  C14   108.54  3.000
 IBA  C17   C13  N5    110.42  3.000
 IBA  C18   C13  N5    112.44  3.000
 IBA  C14   C13  N5    101.04  3.000
 IBA  H142  C14  H141  107.12  3.000
 IBA  H142  C14  C15   113.01  3.000
 IBA  H141  C14  C15   110.04  3.000
 IBA  H142  C14  C13   112.47  3.000
 IBA  H141  C14  C13   109.48  3.000
 IBA  C15   C14  C13   104.71  3.000
 IBA  H152  C15  H151  107.22  3.000
 IBA  H152  C15  C16   108.70  3.000
 IBA  H151  C15  C16   110.90  3.000
 IBA  H152  C15  C14   112.31  3.000
 IBA  H151  C15  C14   113.88  3.000
 IBA  C16   C15  C14   103.76  3.000
 IBA  O13   C16  C15   126.74  3.000
 IBA  O13   C16  N5    125.12  3.000
 IBA  C15   C16  N5    108.13  3.000
 IBA  H182  C18  H181  106.49  3.000
 IBA  H182  C18  O18   110.94  3.000
 IBA  H181  C18  O18   111.74  3.000
 IBA  O18   C18  C13   110.60  3.000
 IBA  H182  C18  C13   107.96  3.000
 IBA  H181  C18  C13   108.95  3.000
 IBA  H18   O18  C18   108.16  3.000
 IBA  H172  C17  H171  106.14  3.000
 IBA  H172  C17  N17   108.29  3.000
 IBA  H171  C17  N17   108.38  3.000
 IBA  N17   C17  C13   115.98  3.000
 IBA  H172  C17  C13   109.79  3.000
 IBA  H171  C17  C13   107.81  3.000
 IBA  H12   N17  H11   106.95  3.000
 IBA  H12   N17  C17   110.81  3.000
 IBA  H11   N17  C17   111.34  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
 IBA  CONST_01  C3    C2   C7   C6     0.00   0.0  0
 IBA  CONST_02  C3    C4   C5   C6     0.00   0.0  0
 IBA  CONST_03  C2    C7   C6   C5     0.00   0.0  0
 IBA  CONST_04  C2    C3   C4   C5     0.00   0.0  0
 IBA  CONST_05  C7    C6   C5   C4     0.00   0.0  0
 IBA  CONST_06  C7    C2   C3   C4     0.00   0.0  0
 IBA  CONST_07  N5    C5   C4   C3   180.00   0.0  0
 IBA  CONST_08  N5    C5   C6   C7   180.00   0.0  0
 IBA  CONST_09  C15   C16  N5   C5   180.00   0.0  0
 IBA  CONST_10  C15   C16  N5   C13    0.00   0.0  0
 IBA  CONST_11  C1    C2   C7   C6   180.00   0.0  0
 IBA  CONST_12  N4    C4   C5   C6   180.00   0.0  0
 IBA  CONST_13  C1    C2   C3   C4   180.00   0.0  0
 IBA  CONST_14  N4    C4   C3   C2   180.00   0.0  0
 IBA  CONST_15  N5    C5   C4   N4     0.00   0.0  0
 IBA  CONST_16  O13   C16  N5   C5     0.00   0.0  0
 IBA  CONST_17  O13   C16  N5   C13  180.00   0.0  0
 IBA  CONST_18  H7    C7   C6   C5   180.00   0.0  0
 IBA  CONST_19  H3    C3   C4   C5   180.00   0.0  0
 IBA  CONST_20  H6    C6   C5   C4   180.00   0.0  0
 IBA  CONST_21  C8    N4   C4   C5   180.00   0.0  0
 IBA  CONST_22  C8    N4   C4   C3     0.00   0.0  0
 IBA  CONST_23  HN4   N4   C4   C5     0.00   0.0  0
 IBA  Var_01    C16   N5   C5   C6   -93.90  30.0  2
 IBA  Var_02    C14   C15  C16  N5    14.53  30.0  1
 IBA  Var_03    C16   C15  C14  C13  -26.89  30.0  1
 IBA  Var_04    O21   C1   C2   C3    -1.17  30.0  2
 IBA  Var_05    C11   C8   N4   C4   -89.97  30.0  3
 IBA  Var_06    H11   N17  C17  C13  -54.15  30.0  3
 IBA  Var_07    C12   C11  C8   N4   -62.95  30.0  3
 IBA  Var_08    C10   C9   C8   N4   -65.35  30.0  3
 IBA  Var_09    H121  C12  C11  C8   -63.09  30.0  3
 IBA  Var_10    H101  C10  C9   C8   -59.87  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
 IBA  chir_01  C13  C14  N5  C17  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
 IBA  plan-1  C6   0.020
 IBA  plan-1  C5   0.020
 IBA  plan-1  C4   0.020
 IBA  plan-1  C3   0.020
 IBA  plan-1  C2   0.020
 IBA  plan-1  C7   0.020
 IBA  plan-1  C1   0.020
 IBA  plan-1  N4   0.020
 IBA  plan-1  N5   0.020
 IBA  plan-1  H7   0.020
 IBA  plan-1  H6   0.020
 IBA  plan-1  H3   0.020
 IBA  plan-2  C4   0.020
 IBA  plan-2  N4   0.020
 IBA  plan-2  C8   0.020
 IBA  plan-2  HN4  0.020
 IBA  plan-3  C5   0.020
 IBA  plan-3  N5   0.020
 IBA  plan-3  C13  0.020
 IBA  plan-3  C15  0.020
 IBA  plan-3  C16  0.020
 IBA  plan-3  O13  0.020
 IBA  plan-4  C2   0.020
 IBA  plan-4  C1   0.020
 IBA  plan-4  O21  0.020
 IBA  plan-4  O20  0.020

