# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:16:51 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  52  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.233   4.8205   0.6761   0.2525
 IBA  C5    C  CR6   0   0.240   4.1081   0.0815   1.2791
 IBA  C4    C  CR6   0   0.415   4.6613   0.0017   2.5796
 IBA  C3    C  CR16  0  -0.397   5.9512   0.5180   2.7713
 IBA  C2    C  CR6   0  -0.068   6.6567   1.0964   1.7229
 IBA  C7    C  CR16  0  -0.319   6.0945   1.1790   0.4534
 IBA  C1    C  C     0   0.534   8.0247   1.6413   1.9185
 IBA  O21   O  OH1   0  -0.594   8.4651   1.5250   3.1641
 IBA  O20   O  O     0  -0.440   8.6788   2.1429   1.0353
 IBA  N4    N  NH1   0  -0.696   3.9451  -0.5351   3.6006
 IBA  C8    C  CH1   0  -0.078   4.3743  -0.6624   4.9773
 IBA  C11   C  CH2   0  -0.427   5.3537  -1.8230   5.1975
 IBA  C9    C  CH2   0  -0.456   3.1367  -0.7643   5.8671
 IBA  C12   C  CH3   0  -0.686   4.8149  -3.1954   4.8236
 IBA  C10   C  CH3   0  -0.660   2.2726   0.4896   5.8522
 IBA  N5    N  NT    0  -0.596   2.7848  -0.3834   1.0712
 IBA  C13   C  CT    0   0.081   2.3971  -1.6506   0.4178
 IBA  C14   C  CH2   0  -0.481   0.9508  -1.8052   0.9250
 IBA  C15   C  CH2   0  -0.584   0.4604  -0.3798   1.1330
 IBA  C16   C  C     0   0.514   1.7228   0.3908   1.4303
 IBA  O13   O  O     0  -0.469   1.8040   1.5050   1.9090
 IBA  C18   C  CH2   0  -0.100   2.3644  -1.5439  -1.1069
 IBA  O18   O  OH1   0  -0.661   3.6666  -1.4557  -1.6265
 IBA  C17   C  CH2   0  -0.309   3.2987  -2.7924   0.8844
 IBA  N17   N  NH2   0  -0.796   2.8434  -4.0581   0.3435
 IBA  H21   H  HOH1  0   0.487   9.3591   1.8915   3.2322
 IBA  H7    H  HCR6  0   0.255   6.6333   1.6356  -0.3644
 IBA  H6    H  HCR6  0   0.254   4.3664   0.7426  -0.7245
 IBA  H151  H  HCH2  0   0.284  -0.2574  -0.2742   1.9456
 IBA  H152  H  HCH2  0   0.281  -0.0043   0.0364   0.2352
 IBA  H141  H  HCH2  0   0.257   0.9534  -2.3412   1.8780
 IBA  H142  H  HCH2  0   0.266   0.3316  -2.3777   0.2360
 IBA  H181  H  HCH2  0   0.204   1.7583  -0.6722  -1.3887
 IBA  H182  H  HCH2  0   0.206   1.8489  -2.4329  -1.4860
 IBA  H18   H  HOH1  0   0.458   3.6008  -1.3282  -2.5771
 IBA  H171  H  HCH2  0   0.205   3.3247  -2.7743   1.9828
 IBA  H172  H  HCH2  0   0.246   4.3217  -2.6186   0.5474
 IBA  H11   H  HNH2  0   0.350   2.0366  -4.3849   0.8600
 IBA  H12   H  HNH2  0   0.357   3.5593  -4.7583   0.4814
 IBA  HN4   H  HNH1  0   0.365   3.0703  -0.9676   3.3598
 IBA  H8    H  HCH1  0   0.240   4.8913   0.2626   5.2576
 IBA  H111  H  HCH2  0   0.229   6.2677  -1.6305   4.6296
 IBA  H112  H  HCH2  0   0.225   5.6507  -1.8152   6.2500
 IBA  H121  H  HCH3  0   0.225   3.9339  -3.4681   5.4057
 IBA  H122  H  HCH3  0   0.227   4.5444  -3.2462   3.7683
 IBA  H123  H  HCH3  0   0.236   5.5686  -3.9635   4.9992
 IBA  H91   H  HCH2  0   0.239   3.4713  -0.9666   6.8871
 IBA  H92   H  HCH2  0   0.224   2.5367  -1.6309   5.5713
 IBA  H101  H  HCH3  0   0.221   2.8278   1.3523   6.2243
 IBA  H102  H  HCH3  0   0.222   1.9215   0.7316   4.8485
 IBA  H103  H  HCH3  0   0.231   1.3957   0.3632   6.4875
 IBA  H3    H  HCR6  0   0.273   6.3984   0.4675   3.7528

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  1.384  0.020  1.384
 IBA  C6   H6    single    0.930  0.020  1.080
 IBA  C6   C5    aromatic  1.384  0.020  1.384
 IBA  C5   N5    single    1.418  0.020  1.418
 IBA  C5   C4    aromatic  1.415  0.020  1.415
 IBA  C4   N4    single    1.358  0.020  1.358
 IBA  C4   C3    aromatic  1.403  0.020  1.403
 IBA  C3   C2    aromatic  1.390  0.020  1.390
 IBA  C3   H3    single    0.930  0.020  1.080
 IBA  C2   C1    single    1.486  0.020  1.486
 IBA  C2   C7    aromatic  1.391  0.020  1.391
 IBA  C7   H7    single    0.930  0.020  1.080
 IBA  C1   O21   single    1.326  0.020  1.326
 IBA  C1   O20   double    1.208  0.020  1.208
 IBA  O21  H21   single    0.850  0.020  0.980
 IBA  N4   HN4   single    0.860  0.020  1.020
 IBA  N4   C8    single    1.448  0.020  1.448
 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    1.521  0.020  1.521
 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    1.363  0.020  1.363
 IBA  N5   C13   single    1.477  0.020  1.477
 IBA  C13  C14   single    1.540  0.020  1.540
 IBA  C13  C18   single    1.529  0.020  1.529
 IBA  C13  C17   single    1.528  0.020  1.528
 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    1.215  0.020  1.215
 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    1.450  0.020  1.450
 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    119.75  3.000
 IBA  H6    C6   C5    118.77  3.000
 IBA  C7    C6   C5    121.48  3.000
 IBA  N5    C5   C4    118.75  3.000
 IBA  C4    C5   C6    120.31  3.000
 IBA  N5    C5   C6    120.83  3.000
 IBA  N4    C4   C3    121.86  3.000
 IBA  C3    C4   C5    117.66  3.000
 IBA  N4    C4   C5    120.46  3.000
 IBA  H3    C3   C2    119.67  3.000
 IBA  H3    C3   C4    119.20  3.000
 IBA  C2    C3   C4    121.13  3.000
 IBA  C1    C2   C7    118.07  3.000
 IBA  C7    C2   C3    120.54  3.000
 IBA  C1    C2   C3    121.39  3.000
 IBA  H7    C7   C2    120.96  3.000
 IBA  H7    C7   C6    120.17  3.000
 IBA  C2    C7   C6    118.87  3.000
 IBA  O20   C1   O21   122.91  3.000
 IBA  O20   C1   C2    123.68  3.000
 IBA  O21   C1   C2    113.41  3.000
 IBA  H21   O21  C1    109.83  3.000
 IBA  HN4   N4   C8    116.61  3.000
 IBA  C8    N4   C4    126.41  3.000
 IBA  HN4   N4   C4    116.69  3.000
 IBA  H8    C8   C9    106.83  3.000
 IBA  C9    C8   C11   112.52  3.000
 IBA  H8    C8   C11   107.49  3.000
 IBA  C9    C8   N4    108.64  3.000
 IBA  C11   C8   N4    113.09  3.000
 IBA  H8    C8   N4    107.98  3.000
 IBA  H112  C11  H111  105.76  3.000
 IBA  H112  C11  C12   109.83  3.000
 IBA  H111  C11  C12   109.11  3.000
 IBA  C12   C11  C8    114.90  3.000
 IBA  H112  C11  C8    107.82  3.000
 IBA  H111  C11  C8    109.02  3.000
 IBA  H92   C9   H91   105.87  3.000
 IBA  H92   C9   C10   109.76  3.000
 IBA  H91   C9   C10   109.59  3.000
 IBA  C10   C9   C8    113.52  3.000
 IBA  H92   C9   C8    109.85  3.000
 IBA  H91   C9   C8    107.94  3.000
 IBA  H123  C12  H122  107.13  3.000
 IBA  H123  C12  H121  107.24  3.000
 IBA  H122  C12  H121  107.73  3.000
 IBA  H123  C12  C11   110.56  3.000
 IBA  H122  C12  C11   111.57  3.000
 IBA  H121  C12  C11   112.37  3.000
 IBA  H103  C10  H102  107.65  3.000
 IBA  H103  C10  H101  107.59  3.000
 IBA  H102  C10  H101  107.58  3.000
 IBA  H103  C10  C9    110.81  3.000
 IBA  H102  C10  C9    111.99  3.000
 IBA  H101  C10  C9    111.03  3.000
 IBA  C16   N5   C13   113.54  3.000
 IBA  C13   N5   C5    126.23  3.000
 IBA  C16   N5   C5    120.16  3.000
 IBA  C17   C13  C18   111.68  3.000
 IBA  C17   C13  C14   112.24  3.000
 IBA  C18   C13  C14   108.38  3.000
 IBA  C17   C13  N5    110.55  3.000
 IBA  C18   C13  N5    112.76  3.000
 IBA  C14   C13  N5    100.77  3.000
 IBA  H142  C14  H141  107.16  3.000
 IBA  H142  C14  C15   113.31  3.000
 IBA  H141  C14  C15   109.93  3.000
 IBA  H142  C14  C13   112.23  3.000
 IBA  H141  C14  C13   109.51  3.000
 IBA  C15   C14  C13   104.69  3.000
 IBA  H152  C15  H151  107.19  3.000
 IBA  H152  C15  C16   108.85  3.000
 IBA  H151  C15  C16   110.79  3.000
 IBA  H152  C15  C14   112.42  3.000
 IBA  H151  C15  C14   113.89  3.000
 IBA  C16   C15  C14   103.64  3.000
 IBA  O13   C16  C15   127.00  3.000
 IBA  O13   C16  N5    124.94  3.000
 IBA  C15   C16  N5    108.06  3.000
 IBA  H182  C18  H181  107.20  3.000
 IBA  H182  C18  O18   111.05  3.000
 IBA  H181  C18  O18   111.51  3.000
 IBA  O18   C18  C13   110.70  3.000
 IBA  H182  C18  C13   107.37  3.000
 IBA  H181  C18  C13   108.85  3.000
 IBA  H18   O18  C18   108.09  3.000
 IBA  H172  C17  H171  106.49  3.000
 IBA  H172  C17  N17   108.56  3.000
 IBA  H171  C17  N17   113.25  3.000
 IBA  N17   C17  C13   110.68  3.000
 IBA  H172  C17  C13   109.88  3.000
 IBA  H171  C17  C13   107.87  3.000
 IBA  H12   N17  H11   105.74  3.000
 IBA  H12   N17  C17   109.36  3.000
 IBA  H11   N17  C17   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
 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  CONST_24  H21   O21  C1   C2   180.00   0.0  0
 IBA  Var_01    C16   N5   C5   C6   -97.36  30.0  2
 IBA  Var_02    C14   C15  C16  N5    14.95  30.0  1
 IBA  Var_03    C16   C15  C14  C13  -27.76  30.0  1
 IBA  Var_04    O21   C1   C2   C3    -0.60  30.0  2
 IBA  Var_05    C11   C8   N4   C4   -77.32  30.0  3
 IBA  Var_06    H11   N17  C17  C13  -77.25  30.0  3
 IBA  Var_07    C12   C11  C8   N4   -59.41  30.0  3
 IBA  Var_08    C10   C9   C8   N4   -64.25  30.0  3
 IBA  Var_09    H121  C12  C11  C8   -60.73  30.0  3
 IBA  Var_10    H101  C10  C9   C8   -61.41  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
 IBA  plan-4  H21  0.020

