# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:20:36 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: (2R)-N~4~-hydroxy-N~1~-[(1S)-1-{[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]carbonyl}-2-methylpropyl]-2-pentylbutanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](CC(=O)NO)C(=O)N[C@@H](C(C)C)C(=O)N1CCC[C@H]1CO
#
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
 BB2  BB2  (2R)-N~4~-hydroxy-N~1~-[(1S)-1-{[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]carbonyl}-2-methylpropyl]-2-pentylbutanediamide  ligand  62  27  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BB2
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
 BB2  C5    C  CH2   0  -0.570   2.1475   1.3823   3.2013
 BB2  C3    C  C     0   0.516   2.6195   0.6156   4.4165
 BB2  O4    O  O     0  -0.477   3.0704  -0.5153   4.3527
 BB2  N1    N  NH1   0  -0.371   2.5236   1.3127   5.5618
 BB2  O2    O  OH1   0  -0.543   2.8015   0.7190   6.7541
 BB2  C6    C  CH1   0  -0.386   1.1030   0.5855   2.4160
 BB2  C12   C  C     0   0.574   0.7857   1.3131   1.1217
 BB2  O13   O  O     0  -0.500   0.4304   2.4850   1.1151
 BB2  C7    C  CH2   0  -0.415  -0.1865   0.3964   3.2229
 BB2  C8    C  CH2   0  -0.424  -1.2665  -0.3951   2.4950
 BB2  C9    C  CH2   0  -0.407  -2.5042  -0.6189   3.3541
 BB2  C10   C  CH2   0  -0.420  -3.5950  -1.4061   2.6388
 BB2  C11   C  CH3   0  -0.663  -4.8322  -1.6148   3.5010
 BB2  N14   N  NH1   0  -0.637   0.8927   0.5708   0.0098
 BB2  C15   C  CH1   0  -0.174   0.5307   1.0465  -1.3050
 BB2  C16   C  CH1   0  -0.234   1.7196   1.7189  -2.0327
 BB2  C18   C  CH3   0  -0.660   2.9289   0.8078  -2.2047
 BB2  C17   C  CH3   0  -0.666   1.2947   2.3195  -3.3681
 BB2  C19   C  C     0   0.559   0.0014  -0.1516  -2.0872
 BB2  O20   O  O     0  -0.501   0.5563  -1.2383  -1.9560
 BB2  N21   N  NR5   0  -0.482  -1.0248   0.0257  -2.9334
 BB2  C22   C  CR15  0  -0.080  -1.5035  -1.0925  -3.7565
 BB2  C23   C  CH2   0  -0.298  -1.9638   1.1438  -2.9742
 BB2  C24   C  CH2   0  -0.451  -3.2921   0.4487  -3.2252
 BB2  C25   C  CH2   0  -0.482  -2.9066  -0.6561  -4.2024
 BB2  C26   C  CH2   0  -0.149  -0.5636  -1.3394  -4.9274
 BB2  O27   O  OH1   0  -0.670  -1.1008  -2.3990  -5.6849
 BB2  H51   H  HCH2  0   0.287   3.0280   1.5638   2.5784
 BB2  H52   H  HCH2  0   0.262   1.7433   2.3598   3.4709
 BB2  HN1   H  HNH1  0   0.417   2.0335   2.1930   5.6253
 BB2  HO2   H  HOH1  0   0.478   3.7166   0.9473   6.9638
 BB2  H6    H  HCH1  0   0.263   1.5207  -0.3999   2.1905
 BB2  H71   H  HCH2  0   0.226  -0.5765   1.3770   3.5129
 BB2  H72   H  HCH2  0   0.238   0.0590  -0.1215   4.1551
 BB2  H81   H  HCH2  0   0.216  -0.8603  -1.3622   2.1790
 BB2  H82   H  HCH2  0   0.218  -1.5615   0.1243   1.5773
 BB2  H91   H  HCH2  0   0.210  -2.9052   0.3501   3.6717
 BB2  H92   H  HCH2  0   0.210  -2.2209  -1.1443   4.2728
 BB2  H101  H  HCH2  0   0.212  -3.1949  -2.3763   2.3283
 BB2  H102  H  HCH2  0   0.211  -3.8712  -0.8842   1.7172
 BB2  H111  H  HCH3  0   0.226  -5.5991  -2.1837   2.9742
 BB2  H112  H  HCH3  0   0.216  -4.5865  -2.1591   4.4149
 BB2  H113  H  HCH3  0   0.216  -5.2722  -0.6602   3.7962
 BB2  H14   H  HNH1  0   0.399   1.2003  -0.3866   0.0854
 BB2  H15   H  HCH1  0   0.272  -0.2343   1.8117  -1.1742
 BB2  H16   H  HCH1  0   0.245   2.0122   2.5459  -1.3773
 BB2  H181  H  HCH3  0   0.231   3.7712   1.3868  -2.5857
 BB2  H182  H  HCH3  0   0.227   3.2451   0.3604  -1.2620
 BB2  H183  H  HCH3  0   0.223   2.7382   0.0040  -2.9166
 BB2  H171  H  HCH3  0   0.221   1.0227   1.5490  -4.0927
 BB2  H172  H  HCH3  0   0.232   0.4448   2.9948  -3.2582
 BB2  H173  H  HCH3  0   0.241   2.1147   2.8942  -3.8000
 BB2  H22   H  HCR5  0   0.255  -1.5552  -1.9925  -3.1375
 BB2  H231  H  HCH2  0   0.264  -1.9573   1.7150  -2.0492
 BB2  H232  H  HCH2  0   0.246  -1.7246   1.8269  -3.7938
 BB2  H241  H  HCH2  0   0.240  -3.6724   0.0292  -2.2915
 BB2  H242  H  HCH2  0   0.252  -4.0446   1.1278  -3.6241
 BB2  H251  H  HCH2  0   0.257  -3.6085  -1.4881  -4.2038
 BB2  H252  H  HCH2  0   0.238  -2.8723  -0.2545  -5.2184
 BB2  H261  H  HCH2  0   0.192  -0.4901  -0.4129  -5.5142
 BB2  H262  H  HCH2  0   0.214   0.4405  -1.5775  -4.5599
 BB2  H27   H  HOH1  0   0.458  -0.5097  -2.5687  -6.4237

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
 BB2  C5   C3    single  1.512  0.020  1.512
 BB2  C5   C6    single  1.530  0.020  1.530
 BB2  C5   H51   single  0.970  0.020  1.090
 BB2  C5   H52   single  0.970  0.020  1.090
 BB2  C3   O4    double  1.219  0.020  1.219
 BB2  C3   N1    single  1.344  0.020  1.344
 BB2  N1   O2    single  1.361  0.020  1.361
 BB2  N1   HN1   single  0.860  0.020  1.020
 BB2  O2   HO2   single  0.850  0.020  0.980
 BB2  C6   C12   single  1.518  0.020  1.518
 BB2  C6   C7    single  1.533  0.020  1.533
 BB2  C6   H6    single  0.970  0.020  1.090
 BB2  C12  O13   double  1.225  0.020  1.225
 BB2  C12  N14   single  1.341  0.020  1.341
 BB2  C7   C8    single  1.524  0.020  1.524
 BB2  C7   H71   single  0.970  0.020  1.090
 BB2  C7   H72   single  0.970  0.020  1.090
 BB2  C8   C9    single  1.523  0.020  1.523
 BB2  C8   H81   single  0.970  0.020  1.090
 BB2  C8   H82   single  0.970  0.020  1.090
 BB2  C9   C10   single  1.524  0.020  1.524
 BB2  C9   H91   single  0.970  0.020  1.090
 BB2  C9   H92   single  0.970  0.020  1.090
 BB2  C10  C11   single  1.522  0.020  1.522
 BB2  C10  H101  single  0.970  0.020  1.090
 BB2  C10  H102  single  0.970  0.020  1.090
 BB2  C11  H111  single  0.970  0.020  1.090
 BB2  C11  H112  single  0.970  0.020  1.090
 BB2  C11  H113  single  0.970  0.020  1.090
 BB2  N14  C15   single  1.444  0.020  1.444
 BB2  N14  H14   single  0.860  0.020  1.020
 BB2  C15  C16   single  1.548  0.020  1.548
 BB2  C15  C19   single  1.526  0.020  1.526
 BB2  C15  H15   single  0.970  0.020  1.090
 BB2  C16  C18   single  1.524  0.020  1.524
 BB2  C16  C17   single  1.525  0.020  1.525
 BB2  C16  H16   single  0.970  0.020  1.090
 BB2  C18  H181  single  0.970  0.020  1.090
 BB2  C18  H182  single  0.970  0.020  1.090
 BB2  C18  H183  single  0.970  0.020  1.090
 BB2  C17  H171  single  0.970  0.020  1.090
 BB2  C17  H172  single  0.970  0.020  1.090
 BB2  C17  H173  single  0.970  0.020  1.090
 BB2  C19  O20   double  1.227  0.020  1.227
 BB2  C19  N21   single  1.342  0.020  1.342
 BB2  N21  C22   single  1.469  0.020  1.469
 BB2  N21  C23   single  1.461  0.020  1.461
 BB2  C22  C25   single  1.536  0.020  1.536
 BB2  C22  C26   single  1.522  0.020  1.522
 BB2  C22  H22   single  0.970  0.020  1.090
 BB2  C23  C24   single  1.520  0.020  1.520
 BB2  C23  H231  single  0.970  0.020  1.090
 BB2  C23  H232  single  0.970  0.020  1.090
 BB2  C24  C25   single  1.525  0.020  1.525
 BB2  C24  H241  single  0.970  0.020  1.090
 BB2  C24  H242  single  0.970  0.020  1.090
 BB2  C25  H251  single  0.970  0.020  1.090
 BB2  C25  H252  single  0.970  0.020  1.090
 BB2  C26  O27   single  1.409  0.020  1.409
 BB2  C26  H261  single  0.970  0.020  1.090
 BB2  C26  H262  single  0.970  0.020  1.090
 BB2  O27  H27   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
 BB2  H52   C5   H51   106.87  3.000
 BB2  H52   C5   C6    109.89  3.000
 BB2  H51   C5   C6    110.10  3.000
 BB2  H52   C5   C3    111.78  3.000
 BB2  H51   C5   C3    106.88  3.000
 BB2  C6    C5   C3    111.18  3.000
 BB2  N1    C3   O4    123.51  3.000
 BB2  N1    C3   C5    113.54  3.000
 BB2  O4    C3   C5    122.93  3.000
 BB2  HN1   N1   O2    115.12  3.000
 BB2  HN1   N1   C3    122.71  3.000
 BB2  O2    N1   C3    120.38  3.000
 BB2  HO2   O2   N1    106.29  3.000
 BB2  H6    C6   C7    108.58  3.000
 BB2  H6    C6   C12   109.62  3.000
 BB2  C7    C6   C12   109.39  3.000
 BB2  H6    C6   C5    108.31  3.000
 BB2  C7    C6   C5    111.61  3.000
 BB2  C12   C6   C5    109.30  3.000
 BB2  N14   C12  O13   123.25  3.000
 BB2  N14   C12  C6    115.14  3.000
 BB2  O13   C12  C6    121.59  3.000
 BB2  H72   C7   H71   106.15  3.000
 BB2  H72   C7   C8    108.67  3.000
 BB2  H71   C7   C8    109.84  3.000
 BB2  H72   C7   C6    108.55  3.000
 BB2  H71   C7   C6    109.19  3.000
 BB2  C8    C7   C6    114.13  3.000
 BB2  H82   C8   H81   106.08  3.000
 BB2  H82   C8   C9    108.87  3.000
 BB2  H81   C8   C9    109.53  3.000
 BB2  H82   C8   C7    110.17  3.000
 BB2  H81   C8   C7    109.48  3.000
 BB2  C9    C8   C7    112.50  3.000
 BB2  H92   C9   H91   106.00  3.000
 BB2  H92   C9   C10   109.33  3.000
 BB2  H91   C9   C10   109.33  3.000
 BB2  H92   C9   C8    109.47  3.000
 BB2  H91   C9   C8    109.32  3.000
 BB2  C10   C9   C8    113.13  3.000
 BB2  H102  C10  H101  106.03  3.000
 BB2  H102  C10  C11   109.70  3.000
 BB2  H101  C10  C11   109.65  3.000
 BB2  H102  C10  C9    109.25  3.000
 BB2  H101  C10  C9    109.24  3.000
 BB2  C11   C10  C9    112.75  3.000
 BB2  H113  C11  H112  107.47  3.000
 BB2  H113  C11  H111  107.66  3.000
 BB2  H112  C11  H111  107.61  3.000
 BB2  H113  C11  C10   111.15  3.000
 BB2  H112  C11  C10   111.07  3.000
 BB2  H111  C11  C10   111.68  3.000
 BB2  H14   N14  C15   117.22  3.000
 BB2  H14   N14  C12   119.18  3.000
 BB2  C15   N14  C12   123.53  3.000
 BB2  H15   C15  C19   111.68  3.000
 BB2  H15   C15  C16   106.90  3.000
 BB2  C19   C15  C16   111.51  3.000
 BB2  H15   C15  N14   107.33  3.000
 BB2  C19   C15  N14   107.16  3.000
 BB2  C16   C15  N14   112.24  3.000
 BB2  H16   C16  C17   107.53  3.000
 BB2  H16   C16  C18   107.88  3.000
 BB2  C17   C16  C18   110.96  3.000
 BB2  H16   C16  C15   104.60  3.000
 BB2  C17   C16  C15   111.64  3.000
 BB2  C18   C16  C15   113.76  3.000
 BB2  H183  C18  H182  108.22  3.000
 BB2  H183  C18  H181  107.35  3.000
 BB2  H182  C18  H181  107.21  3.000
 BB2  H183  C18  C16   112.07  3.000
 BB2  H182  C18  C16   112.20  3.000
 BB2  H181  C18  C16   109.56  3.000
 BB2  H173  C17  H172  107.43  3.000
 BB2  H173  C17  H171  107.23  3.000
 BB2  H172  C17  H171  108.03  3.000
 BB2  H173  C17  C16   110.17  3.000
 BB2  H172  C17  C16   111.88  3.000
 BB2  H171  C17  C16   111.88  3.000
 BB2  N21   C19  O20   122.02  3.000
 BB2  N21   C19  C15   119.01  3.000
 BB2  O20   C19  C15   118.93  3.000
 BB2  C23   N21  C22   110.95  3.000
 BB2  C23   N21  C19   127.62  3.000
 BB2  C22   N21  C19   120.14  3.000
 BB2  H22   C22  C26   109.34  3.000
 BB2  H22   C22  C25   110.80  3.000
 BB2  C26   C22  C25   112.77  3.000
 BB2  H22   C22  N21   108.96  3.000
 BB2  C26   C22  N21   110.70  3.000
 BB2  C25   C22  N21   104.14  3.000
 BB2  H232  C23  H231  107.96  3.000
 BB2  H232  C23  C24   110.67  3.000
 BB2  H231  C23  C24   112.70  3.000
 BB2  H232  C23  N21   111.01  3.000
 BB2  H231  C23  N21   112.00  3.000
 BB2  C24   C23  N21   102.49  3.000
 BB2  H242  C24  H241  108.19  3.000
 BB2  H242  C24  C25   113.06  3.000
 BB2  H241  C24  C25   110.96  3.000
 BB2  H242  C24  C23   112.27  3.000
 BB2  H241  C24  C23   109.81  3.000
 BB2  C25   C24  C23   102.49  3.000
 BB2  H252  C25  H251  107.45  3.000
 BB2  H252  C25  C24   109.72  3.000
 BB2  H251  C25  C24   113.06  3.000
 BB2  H252  C25  C22   110.22  3.000
 BB2  H251  C25  C22   111.86  3.000
 BB2  C24   C25  C22   104.52  3.000
 BB2  H262  C26  H261  107.52  3.000
 BB2  H262  C26  O27   111.49  3.000
 BB2  H261  C26  O27   111.86  3.000
 BB2  H262  C26  C22   110.08  3.000
 BB2  H261  C26  C22   108.38  3.000
 BB2  O27   C26  C22   107.48  3.000
 BB2  H27   O27  C26   108.15  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
 BB2  CONST_01  C22   N21  C19  C15   180.00   0.0  0
 BB2  CONST_03  C22   N21  C19  O20     0.00   0.0  0
 BB2  CONST_05  O2    N1   C3   C5    180.00   0.0  0
 BB2  CONST_06  O2    N1   C3   O4      0.00   0.0  0
 BB2  CONST_07  C15   N14  C12  C6    180.00   0.0  0
 BB2  CONST_08  C15   N14  C12  O13     0.00   0.0  0
 BB2  CONST_09  HN1   N1   C3   C5      0.00   0.0  0
 BB2  CONST_10  H14   N14  C12  C6      0.00   0.0  0
 BB2  Var_01    C25   C24  C23  N21   -38.48  30.0  1
 BB2  Var_02    C24   C23  N21  C22    28.28  30.0  1
 BB2  Var_03    C6    C5   C3   O4     54.56  30.0  1
 BB2  Var_04    C9    C8   C7   C6    177.22  30.0  3
 BB2  Var_05    C10   C9   C8   C7    179.85  30.0  3
 BB2  Var_06    C11   C10  C9   C8   -179.52  30.0  3
 BB2  Var_07    H111  C11  C10  C9   -179.73  30.0  3
 BB2  Var_08    H181  C18  C16  C15  -171.59  30.0  3
 BB2  Var_09    H171  C17  C16  C15   -67.98  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
 BB2  chir_01  C6   C5   C12  C7   positiv
 BB2  chir_02  C15  N14  C16  C19  negativ
 BB2  chir_03  C22  N21  C26  C25  positiv

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
 BB2  plan-1  C5   0.020
 BB2  plan-1  C3   0.020
 BB2  plan-1  O4   0.020
 BB2  plan-1  N1   0.020
 BB2  plan-1  O2   0.020
 BB2  plan-1  HN1  0.020
 BB2  plan-2  C6   0.020
 BB2  plan-2  C12  0.020
 BB2  plan-2  O13  0.020
 BB2  plan-2  N14  0.020
 BB2  plan-2  C15  0.020
 BB2  plan-2  H14  0.020
 BB2  plan-3  C15  0.020
 BB2  plan-3  C19  0.020
 BB2  plan-3  O20  0.020
 BB2  plan-3  N21  0.020
 BB2  plan-3  C22  0.020
 BB2  plan-3  C23  0.020

