# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:57:42 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2S)-3-methyl-1-oxo-1-pyrrolidin-1-ylbutan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N1CCCC1
#
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
 A3M  A3M  (2S)-3-methyl-1-oxo-1-pyrrolidin-1-ylbutan-2-amine  ligand  30  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3M
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
 A3M  C1    C  CH2   0  -0.483  -0.0397  -0.0142  -3.5011
 A3M  C2    C  CH2   0  -0.260   0.8937   0.4188  -2.3772
 A3M  N3    N  NT    0  -0.472   0.2136  -0.0444  -1.1708
 A3M  C4    C  CH2   0  -0.282  -1.1596  -0.4677  -1.4394
 A3M  C5    C  CH2   0  -0.476  -1.4177   0.0457  -2.8512
 A3M  C14   C  C     0   0.568   0.8574  -0.1243   0.0025
 A3M  C15   C  CH1   0  -0.212   0.0679  -0.6368   1.2003
 A3M  C16   C  CH1   0  -0.253  -0.6948   0.5319   1.8803
 A3M  C17   C  CH3   0  -0.661  -1.6964  -0.0160   2.8939
 A3M  O18   O  O     0  -0.513   2.0288   0.2232   0.1208
 A3M  N19   N  NH2   0  -0.792   0.9763  -1.3776   2.0538
 A3M  C26   C  CH3   0  -0.658   0.2313   1.5477   2.5396
 A3M  HC11  H  HCH2  0   0.251   0.0499   0.6270  -4.3771
 A3M  HC12  H  HCH2  0   0.239   0.1898  -1.0366  -3.8092
 A3M  HC21  H  HCH2  0   0.235   1.0149   1.5058  -2.3554
 A3M  HC22  H  HCH2  0   0.246   1.8874  -0.0210  -2.4603
 A3M  HC41  H  HCH2  0   0.245  -1.2460  -1.5576  -1.3966
 A3M  HC42  H  HCH2  0   0.253  -1.8614  -0.0478  -0.7184
 A3M  HC51  H  HCH2  0   0.241  -1.7747   1.0773  -2.8159
 A3M  HC52  H  HCH2  0   0.253  -2.1679  -0.5503  -3.3690
 A3M  H15   H  HCH1  0   0.254  -0.6904  -1.3444   0.8510
 A3M  H16   H  HCH1  0   0.228  -1.2675   1.0516   1.1032
 A3M  H171  H  HCH3  0   0.236  -2.2761   0.7928   3.3405
 A3M  H172  H  HCH3  0   0.229  -2.3974  -0.7116   2.4285
 A3M  H173  H  HCH3  0   0.214  -1.1970  -0.5421   3.7112
 A3M  H191  H  HNH2  0   0.346   1.7358  -0.7810   2.3561
 A3M  H192  H  HNH2  0   0.348   0.4932  -1.6799   2.8898
 A3M  H261  H  HCH3  0   0.212   0.8435   1.0819   3.3150
 A3M  H262  H  HCH3  0   0.234   0.9007   2.0310   1.8286
 A3M  H263  H  HCH3  0   0.230  -0.3553   2.3316   3.0207

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
 A3M  C1   C2    single  1.524  0.020  1.524
 A3M  C1   C5    single  1.525  0.020  1.525
 A3M  C1   HC11  single  0.970  0.020  1.090
 A3M  C1   HC12  single  0.970  0.020  1.090
 A3M  C2   N3    single  1.460  0.020  1.460
 A3M  C2   HC21  single  0.970  0.020  1.090
 A3M  C2   HC22  single  0.970  0.020  1.090
 A3M  N3   C4    single  1.462  0.020  1.462
 A3M  N3   C14   single  1.341  0.020  1.341
 A3M  C4   C5    single  1.524  0.020  1.524
 A3M  C4   HC41  single  0.970  0.020  1.090
 A3M  C4   HC42  single  0.970  0.020  1.090
 A3M  C5   HC51  single  0.970  0.020  1.090
 A3M  C5   HC52  single  0.970  0.020  1.090
 A3M  C14  C15   single  1.523  0.020  1.523
 A3M  C14  O18   double  1.228  0.020  1.228
 A3M  C15  C16   single  1.552  0.020  1.552
 A3M  C15  N19   single  1.450  0.020  1.450
 A3M  C15  H15   single  0.970  0.020  1.090
 A3M  C16  C17   single  1.527  0.020  1.527
 A3M  C16  C26   single  1.525  0.020  1.525
 A3M  C16  H16   single  0.970  0.020  1.090
 A3M  C17  H171  single  0.970  0.020  1.090
 A3M  C17  H172  single  0.970  0.020  1.090
 A3M  C17  H173  single  0.970  0.020  1.090
 A3M  N19  H191  single  0.890  0.020  1.040
 A3M  N19  H192  single  0.890  0.020  1.040
 A3M  C26  H261  single  0.970  0.020  1.090
 A3M  C26  H262  single  0.970  0.020  1.090
 A3M  C26  H263  single  0.970  0.020  1.090

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
 A3M  HC12  C1   HC11  107.87  3.000
 A3M  HC12  C1   C5    110.29  3.000
 A3M  HC11  C1   C5    113.20  3.000
 A3M  HC12  C1   C2    110.20  3.000
 A3M  HC11  C1   C2    112.07  3.000
 A3M  C5    C1   C2    103.18  3.000
 A3M  HC22  C2   HC21  107.54  3.000
 A3M  HC22  C2   N3    111.08  3.000
 A3M  HC21  C2   N3    110.51  3.000
 A3M  HC22  C2   C1    112.80  3.000
 A3M  HC21  C2   C1    111.40  3.000
 A3M  N3    C2   C1    103.53  3.000
 A3M  C14   N3   C4    126.48  3.000
 A3M  C14   N3   C2    121.21  3.000
 A3M  C4    N3   C2    112.18  3.000
 A3M  HC42  C4   HC41  107.88  3.000
 A3M  HC42  C4   C5    111.95  3.000
 A3M  HC41  C4   C5    111.00  3.000
 A3M  HC42  C4   N3    111.82  3.000
 A3M  HC41  C4   N3    110.82  3.000
 A3M  C5    C4   N3    103.39  3.000
 A3M  HC52  C5   HC51  107.88  3.000
 A3M  HC52  C5   C4    111.88  3.000
 A3M  HC51  C5   C4    110.09  3.000
 A3M  HC52  C5   C1    113.48  3.000
 A3M  HC51  C5   C1    110.26  3.000
 A3M  C4    C5   C1    103.21  3.000
 A3M  O18   C14  C15   120.93  3.000
 A3M  O18   C14  N3    121.72  3.000
 A3M  C15   C14  N3    117.34  3.000
 A3M  H15   C15  N19   106.96  3.000
 A3M  H15   C15  C16   106.63  3.000
 A3M  N19   C15  C16   115.76  3.000
 A3M  H15   C15  C14   109.00  3.000
 A3M  N19   C15  C14   108.06  3.000
 A3M  C16   C15  C14   110.23  3.000
 A3M  H16   C16  C26   107.93  3.000
 A3M  H16   C16  C17   107.33  3.000
 A3M  C26   C16  C17   110.52  3.000
 A3M  H16   C16  C15   107.65  3.000
 A3M  C26   C16  C15   113.12  3.000
 A3M  C17   C16  C15   110.06  3.000
 A3M  H173  C17  H172  107.79  3.000
 A3M  H173  C17  H171  107.08  3.000
 A3M  H172  C17  H171  107.80  3.000
 A3M  H173  C17  C16   111.69  3.000
 A3M  H172  C17  C16   111.53  3.000
 A3M  H171  C17  C16   110.76  3.000
 A3M  H192  N19  H191  106.72  3.000
 A3M  H192  N19  C15   109.87  3.000
 A3M  H191  N19  C15   110.17  3.000
 A3M  H263  C26  H262  107.43  3.000
 A3M  H263  C26  H261  107.14  3.000
 A3M  H262  C26  H261  107.95  3.000
 A3M  H263  C26  C16   110.05  3.000
 A3M  H262  C26  C16   112.74  3.000
 A3M  H261  C26  C16   111.30  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
 A3M  CONST_01  C15   C14  N3   C2    180.00   0.0  0
 A3M  CONST_02  O18   C14  N3   C2      0.00   0.0  0
 A3M  CONST_03  C15   C14  N3   C4      0.00   0.0  0
 A3M  CONST_04  O18   C14  N3   C4    180.00   0.0  0
 A3M  Var_01    C4    N3   C2   C1    -11.72  30.0  1
 A3M  Var_02    C4    C5   C1   C2    -38.35  30.0  1
 A3M  Var_03    C5    C4   N3   C2    -12.14  30.0  1
 A3M  Var_04    C5    C1   C2   N3     30.70  30.0  1
 A3M  Var_05    H171  C17  C16  C15  -177.00  30.0  3
 A3M  Var_06    H261  C26  C16  C15   -60.03  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
 A3M  chir_01  C15  C14  C16  N19  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
 A3M  plan-1  C2   0.020
 A3M  plan-1  N3   0.020
 A3M  plan-1  C4   0.020
 A3M  plan-1  C14  0.020
 A3M  plan-1  C15  0.020
 A3M  plan-1  O18  0.020

