# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 16:33:00 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[2,2-bis(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)CCC2(CO)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
 RA2  RA2  '4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(1-ethylpropyl)amino]benzoic acid'  ligand  51  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RA2
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
 RA2  C1    C  CR16  0  -0.241  -2.1537  -0.0635  -0.6667
 RA2  C2    C  CR6   0   0.249  -0.9548  -0.1152   0.0219
 RA2  C3    C  CR6   0   0.427   0.2757   0.0478  -0.6564
 RA2  C4    C  CR16  0  -0.390   0.2122   0.2749  -2.0394
 RA2  C5    C  CR6   0  -0.068  -1.0002   0.3384  -2.7120
 RA2  C6    C  CR16  0  -0.331  -2.2030   0.1691  -2.0304
 RA2  C10   C  C     0   0.534  -0.9572   0.5860  -4.1763
 RA2  N11   N  NT    0  -0.592  -0.9667  -0.4140   1.4079
 RA2  N12   N  NH1   0  -0.718   1.4451  -0.0063   0.0284
 RA2  C13   C  CH1   0  -0.097   2.7844  -0.0776  -0.5161
 RA2  C14   C  CH2   0  -0.420   3.7118   0.8368   0.2843
 RA2  C15   C  CH3   0  -0.669   3.3539   2.3106   0.1719
 RA2  C21   C  CH2   0  -0.396   3.3091  -1.5158  -0.5471
 RA2  C23   C  CH3   0  -0.680   2.4300  -2.4741  -1.3368
 RA2  C29   C  CT    0   0.061  -1.1578   0.5634   2.4905
 RA2  C30   C  CH2   0  -0.477  -1.4095  -0.3547   3.7057
 RA2  C31   C  CH2   0  -0.569  -0.8098  -1.7031   3.3398
 RA2  C32   C  C     0   0.520  -0.7626  -1.6896   1.8338
 RA2  O37   O  O     0  -0.474  -0.5684  -2.6427   1.1035
 RA2  C38   C  CH2   0  -0.161   0.0833   1.4287   2.6824
 RA2  O39   O  OH1   0  -0.661   1.1734   0.5900   3.0004
 RA2  C42   C  CH2   0  -0.151  -2.3818   1.4501   2.2948
 RA2  O43   O  OH1   0  -0.660  -2.1496   2.4211   1.3078
 RA2  O49   O  OH1   0  -0.594  -2.1605   0.6104  -4.7336
 RA2  O50   O  O     0  -0.441   0.0606   0.7500  -4.8071
 RA2  H1    H  HCR6  0   0.256  -3.0722  -0.2238  -0.1172
 RA2  H4    H  HCR6  0   0.264   1.1225   0.4010  -2.6073
 RA2  H6    H  HCR6  0   0.254  -3.1563   0.2038  -2.5366
 RA2  H12   H  HNH1  0   0.390   1.3815  -0.1386   1.0282
 RA2  H13   H  HCH1  0   0.232   2.7639   0.2953  -1.5429
 RA2  H141  H  HCH2  0   0.230   4.7349   0.6802  -0.0663
 RA2  H142  H  HCH2  0   0.211   3.7045   0.5236   1.3339
 RA2  H151  H  HCH3  0   0.231   4.0208   2.9262   0.7757
 RA2  H152  H  HCH3  0   0.221   3.4312   2.6532  -0.8616
 RA2  H153  H  HCH3  0   0.225   2.3331   2.5024   0.5041
 RA2  H211  H  HCH2  0   0.218   4.3152  -1.4972  -0.9757
 RA2  H212  H  HCH2  0   0.211   3.4202  -1.8768   0.4810
 RA2  H231  H  HCH3  0   0.229   2.8861  -3.4635  -1.3905
 RA2  H232  H  HCH3  0   0.234   1.4494  -2.5891  -0.8745
 RA2  H233  H  HCH3  0   0.214   2.2810  -2.1265  -2.3612
 RA2  H301  H  HCH2  0   0.258  -2.4865  -0.4619   3.8550
 RA2  H302  H  HCH2  0   0.264  -0.9985   0.0687   4.6204
 RA2  H311  H  HCH2  0   0.274  -1.3944  -2.5510   3.6954
 RA2  H312  H  HCH2  0   0.277   0.2071  -1.8276   3.7162
 RA2  H381  H  HCH2  0   0.229   0.2830   2.0149   1.7786
 RA2  H282  H  HCH2  0   0.229  -0.1186   2.1404   3.4925
 RA2  H39   H  HOH1  0   0.466   1.9456   1.1426   3.1545
 RA2  H421  H  HCH2  0   0.217  -3.2387   0.8084   2.0528
 RA2  H422  H  HCH2  0   0.219  -2.6011   1.9143   3.2672
 RA2  H43   H  HOH1  0   0.459  -2.9640   2.9149   1.1768
 RA2  H49   H  HOH1  0   0.486  -2.0767   0.7724  -5.6849

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
 RA2  C1   C2    aromatic  1.384  0.020  1.384
 RA2  C1   C6    aromatic  1.384  0.020  1.384
 RA2  C1   H1    single    0.930  0.020  1.080
 RA2  C2   C3    aromatic  1.415  0.020  1.415
 RA2  C2   N11   single    1.418  0.020  1.418
 RA2  C3   C4    aromatic  1.403  0.020  1.403
 RA2  C3   N12   single    1.356  0.020  1.356
 RA2  C4   C5    aromatic  1.388  0.020  1.388
 RA2  C4   H4    single    0.930  0.020  1.080
 RA2  C5   C6    aromatic  1.393  0.020  1.393
 RA2  C5   C10   single    1.486  0.020  1.486
 RA2  C6   H6    single    0.930  0.020  1.080
 RA2  C10  O49   single    1.326  0.020  1.326
 RA2  C10  O50   double    1.209  0.020  1.209
 RA2  N11  C29   single    1.471  0.020  1.471
 RA2  N11  C32   single    1.360  0.020  1.360
 RA2  N12  C13   single    1.448  0.020  1.448
 RA2  N12  H12   single    0.860  0.020  1.020
 RA2  C13  C14   single    1.529  0.020  1.529
 RA2  C13  C21   single    1.531  0.020  1.531
 RA2  C13  H13   single    0.970  0.020  1.090
 RA2  C14  C15   single    1.521  0.020  1.521
 RA2  C14  H141  single    0.970  0.020  1.090
 RA2  C14  H142  single    0.970  0.020  1.090
 RA2  C15  H151  single    0.970  0.020  1.090
 RA2  C15  H152  single    0.970  0.020  1.090
 RA2  C15  H153  single    0.970  0.020  1.090
 RA2  C21  C23   single    1.521  0.020  1.521
 RA2  C21  H211  single    0.970  0.020  1.090
 RA2  C21  H212  single    0.970  0.020  1.090
 RA2  C23  H231  single    0.970  0.020  1.090
 RA2  C23  H232  single    0.970  0.020  1.090
 RA2  C23  H233  single    0.970  0.020  1.090
 RA2  C29  C30   single    1.544  0.020  1.544
 RA2  C29  C38   single    1.525  0.020  1.525
 RA2  C29  C42   single    1.524  0.020  1.524
 RA2  C30  C31   single    1.520  0.020  1.520
 RA2  C30  H301  single    0.970  0.020  1.090
 RA2  C30  H302  single    0.970  0.020  1.090
 RA2  C31  C32   single    1.507  0.020  1.507
 RA2  C31  H311  single    0.970  0.020  1.090
 RA2  C31  H312  single    0.970  0.020  1.090
 RA2  C32  O37   double    1.216  0.020  1.216
 RA2  C38  O39   single    1.412  0.020  1.412
 RA2  C38  H381  single    0.970  0.020  1.090
 RA2  C38  H282  single    0.970  0.020  1.090
 RA2  O39  H39   single    0.850  0.020  0.980
 RA2  C42  O43   single    1.404  0.020  1.404
 RA2  C42  H421  single    0.970  0.020  1.090
 RA2  C42  H422  single    0.970  0.020  1.090
 RA2  O43  H43   single    0.850  0.020  0.980
 RA2  O49  H49   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
 RA2  H1    C1   C6    119.66  3.000
 RA2  H1    C1   C2    118.50  3.000
 RA2  C6    C1   C2    121.83  3.000
 RA2  N11   C2   C3    120.02  3.000
 RA2  N11   C2   C1    119.15  3.000
 RA2  C3    C2   C1    120.72  3.000
 RA2  N12   C3   C4    122.90  3.000
 RA2  N12   C3   C2    120.22  3.000
 RA2  C4    C3   C2    116.87  3.000
 RA2  H4    C4   C5    118.42  3.000
 RA2  H4    C4   C3    119.93  3.000
 RA2  C5    C4   C3    121.65  3.000
 RA2  C10   C5   C6    121.84  3.000
 RA2  C10   C5   C4    117.39  3.000
 RA2  C6    C5   C4    120.77  3.000
 RA2  H6    C6   C5    121.94  3.000
 RA2  H6    C6   C1    119.90  3.000
 RA2  C5    C6   C1    118.15  3.000
 RA2  O50   C10  O49   122.84  3.000
 RA2  O50   C10  C5    124.14  3.000
 RA2  O49   C10  C5    113.02  3.000
 RA2  C32   N11  C29   114.34  3.000
 RA2  C32   N11  C2    120.16  3.000
 RA2  C29   N11  C2    125.48  3.000
 RA2  H12   N12  C13   115.09  3.000
 RA2  H12   N12  C3    116.77  3.000
 RA2  C13   N12  C3    127.58  3.000
 RA2  H13   C13  C21   107.93  3.000
 RA2  H13   C13  C14   107.42  3.000
 RA2  C21   C13  C14   111.38  3.000
 RA2  H13   C13  N12   108.62  3.000
 RA2  C21   C13  N12   111.77  3.000
 RA2  C14   C13  N12   109.57  3.000
 RA2  H142  C14  H141  105.83  3.000
 RA2  H142  C14  C15   110.27  3.000
 RA2  H141  C14  C15   109.60  3.000
 RA2  H142  C14  C13   109.06  3.000
 RA2  H141  C14  C13   108.32  3.000
 RA2  C15   C14  C13   113.46  3.000
 RA2  H153  C15  H152  107.43  3.000
 RA2  H153  C15  H151  107.73  3.000
 RA2  H152  C15  H151  107.69  3.000
 RA2  H153  C15  C14   111.61  3.000
 RA2  H152  C15  C14   110.95  3.000
 RA2  H151  C15  C14   111.24  3.000
 RA2  H212  C21  H211  106.27  3.000
 RA2  H212  C21  C23   109.77  3.000
 RA2  H211  C21  C23   109.81  3.000
 RA2  H212  C21  C13   108.98  3.000
 RA2  H211  C21  C13   107.89  3.000
 RA2  C23   C21  C13   113.84  3.000
 RA2  H233  C23  H232  107.98  3.000
 RA2  H233  C23  H231  107.44  3.000
 RA2  H232  C23  H231  107.54  3.000
 RA2  H233  C23  C21   111.42  3.000
 RA2  H232  C23  C21   111.47  3.000
 RA2  H231  C23  C21   110.81  3.000
 RA2  C42   C29  C38   109.85  3.000
 RA2  C42   C29  C30   108.43  3.000
 RA2  C38   C29  C30   111.78  3.000
 RA2  C42   C29  N11   113.36  3.000
 RA2  C38   C29  N11   111.34  3.000
 RA2  C30   C29  N11   101.85  3.000
 RA2  H302  C30  H301  107.19  3.000
 RA2  H302  C30  C31   113.47  3.000
 RA2  H301  C30  C31   109.56  3.000
 RA2  H302  C30  C29   111.63  3.000
 RA2  H301  C30  C29   109.07  3.000
 RA2  C31   C30  C29   105.89  3.000
 RA2  H312  C31  H311  107.38  3.000
 RA2  H312  C31  C32   108.45  3.000
 RA2  H311  C31  C32   110.48  3.000
 RA2  H312  C31  C30   112.69  3.000
 RA2  H311  C31  C30   113.58  3.000
 RA2  C32   C31  C30   104.18  3.000
 RA2  O37   C32  C31   126.74  3.000
 RA2  O37   C32  N11   124.80  3.000
 RA2  C31   C32  N11   108.46  3.000
 RA2  H282  C38  H381  107.19  3.000
 RA2  H282  C38  O39   111.17  3.000
 RA2  H381  C38  O39   111.29  3.000
 RA2  H282  C38  C29   108.13  3.000
 RA2  H381  C38  C29   110.37  3.000
 RA2  O39   C38  C29   108.64  3.000
 RA2  H39   O39  C38   108.34  3.000
 RA2  H422  C42  H421  106.63  3.000
 RA2  H422  C42  O43   111.26  3.000
 RA2  H421  C42  O43   112.24  3.000
 RA2  H422  C42  C29   106.99  3.000
 RA2  H421  C42  C29   108.37  3.000
 RA2  O43   C42  C29   111.09  3.000
 RA2  H43   O43  C42   108.12  3.000
 RA2  H49   O49  C10   109.71  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
 RA2  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 RA2  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 RA2  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 RA2  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 RA2  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 RA2  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 RA2  CONST_07  N11   C2   C3   C4   180.00   0.0  0
 RA2  CONST_08  N11   C2   C1   C6   180.00   0.0  0
 RA2  CONST_09  C31   C32  N11  C2   180.00   0.0  0
 RA2  CONST_10  C31   C32  N11  C29    0.00   0.0  0
 RA2  CONST_11  N12   C3   C2   C1   180.00   0.0  0
 RA2  CONST_12  C10   C5   C6   C1   180.00   0.0  0
 RA2  CONST_13  C10   C5   C4   C3   180.00   0.0  0
 RA2  CONST_14  N12   C3   C4   C5   180.00   0.0  0
 RA2  CONST_15  N12   C3   C2   N11    0.00   0.0  0
 RA2  CONST_16  O37   C32  N11  C2     0.00   0.0  0
 RA2  CONST_17  O37   C32  N11  C29  180.00   0.0  0
 RA2  CONST_18  H6    C6   C1   C2   180.00   0.0  0
 RA2  CONST_19  H4    C4   C3   C2   180.00   0.0  0
 RA2  CONST_20  H1    C1   C2   C3   180.00   0.0  0
 RA2  CONST_21  C13   N12  C3   C2   180.00   0.0  0
 RA2  CONST_22  C13   N12  C3   C4     0.00   0.0  0
 RA2  CONST_23  H12   N12  C3   C2     0.00   0.0  0
 RA2  CONST_24  H49   O49  C10  C5   180.00   0.0  0
 RA2  Var_01    C29   N11  C2   C1   -85.66  30.0  2
 RA2  Var_02    C30   C29  N11  C2   167.16  30.0  1
 RA2  Var_03    C31   C30  C29  N11   21.83  30.0  1
 RA2  Var_04    C30   C31  C32  N11   13.81  30.0  1
 RA2  Var_05    C32   C31  C30  C29  -22.06  30.0  1
 RA2  Var_06    O49   C10  C5   C4   179.07  30.0  2
 RA2  Var_07    O39   C38  C29  N11  -59.68  30.0  3
 RA2  Var_08    O43   C42  C29  N11  -74.98  30.0  3
 RA2  Var_09    C14   C13  N12  C3   138.51  30.0  3
 RA2  Var_10    C15   C14  C13  N12  -64.58  30.0  3
 RA2  Var_11    C23   C21  C13  N12   57.35  30.0  3
 RA2  Var_12    H151  C15  C14  C13  178.54  30.0  3
 RA2  Var_13    H231  C23  C21  C13  175.71  30.0  3

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
 RA2  plan-1  C1   0.020
 RA2  plan-1  C2   0.020
 RA2  plan-1  C3   0.020
 RA2  plan-1  C4   0.020
 RA2  plan-1  C5   0.020
 RA2  plan-1  C6   0.020
 RA2  plan-1  C10  0.020
 RA2  plan-1  N11  0.020
 RA2  plan-1  N12  0.020
 RA2  plan-1  H1   0.020
 RA2  plan-1  H4   0.020
 RA2  plan-1  H6   0.020
 RA2  plan-2  C3   0.020
 RA2  plan-2  N12  0.020
 RA2  plan-2  C13  0.020
 RA2  plan-2  H12  0.020
 RA2  plan-3  C2   0.020
 RA2  plan-3  N11  0.020
 RA2  plan-3  C29  0.020
 RA2  plan-3  C31  0.020
 RA2  plan-3  C32  0.020
 RA2  plan-3  O37  0.020
 RA2  plan-4  C5   0.020
 RA2  plan-4  C10  0.020
 RA2  plan-4  O49  0.020
 RA2  plan-4  O50  0.020
 RA2  plan-4  H49  0.020

