# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:26:50 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: (2S)-2-amino-3-methyl-1-(morpholin-4-yl)butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N1CCOCC1
#
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
 WKM  WKM  (2S)-2-amino-3-methyl-1-(morpholin-4-yl)butan-1-one  ligand  31  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WKM
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
 WKM  C10  C  CH2   0  -0.181  -13.0833  10.6150  4.5843
 WKM  C13  C  CH2   0  -0.345  -13.8966  13.0517  5.7224
 WKM  C02  C  CH1   0  -0.229  -16.9379  13.5064  4.4190
 WKM  C03  C  CH3   0  -0.671  -18.1082  14.3681  4.8830
 WKM  C04  C  CH1   0  -0.197  -15.7897  14.3925  3.8791
 WKM  C06  C  C     0   0.544  -14.6475  13.5190  3.3665
 WKM  C09  C  CH2   0  -0.329  -12.8598  11.9329  3.8628
 WKM  C12  C  CH2   0  -0.173  -14.0868  11.6998  6.3895
 WKM  N05  N  NH2   0  -0.797  -16.2693  15.2268  2.7926
 WKM  N08  N  NT    0  -0.469  -13.8747  12.8865  4.2793
 WKM  O07  O  O     0  -0.495  -14.4614  13.3811  2.1651
 WKM  O11  O  O2    0  -0.483  -13.0965  10.7819  5.9853
 WKM  H1   H  HCH2  0   0.207  -14.0279  10.1701  4.2392
 WKM  H2   H  HCH2  0   0.244  -12.2776   9.9189  4.3472
 WKM  H3   H  HCH2  0   0.260  -12.9428  13.4876  6.0404
 WKM  H4   H  HCH2  0   0.271  -14.6792  13.7317  6.0449
 WKM  H5   H  HCH3  0   0.226  -18.2834  11.9441  3.7733
 WKM  H6   H  HCH3  0   0.223  -17.6454  12.9254  2.4528
 WKM  H7   H  HCH3  0   0.224  -16.6331  11.7024  3.2293
 WKM  H8   H  HCH1  0   0.231  -16.5627  12.9762  5.2994
 WKM  H9   H  HCH3  0   0.228  -17.7872  15.1491  5.5753
 WKM  H10  H  HCH3  0   0.223  -18.6142  14.8469  4.0432
 WKM  H11  H  HCH3  0   0.236  -18.8477  13.7541  5.3984
 WKM  H12  H  HCH1  0   0.245  -15.4175  14.9957  4.7192
 WKM  H13  H  HCH2  0   0.269  -12.9079  11.7811  2.7881
 WKM  H14  H  HCH2  0   0.244  -11.8674  12.3295  4.1033
 WKM  H15  H  HCH2  0   0.245  -14.0117  11.8065  7.4724
 WKM  H16  H  HCH2  0   0.206  -15.0902  11.3162  6.1531
 WKM  H17  H  HNH2  0   0.350  -16.8094  15.9881  3.1820
 WKM  H18  H  HNH2  0   0.348  -15.4904  15.6592  2.3140
 WKM  C01  C  CH3   0  -0.657  -17.3958  12.4622  3.4070

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
 WKM  O07  C06  double  1.224  0.020  1.224
 WKM  N05  C04  single  1.451  0.020  1.451
 WKM  C06  C04  single  1.527  0.020  1.527
 WKM  C06  N08  single  1.353  0.020  1.353
 WKM  C01  C02  single  1.525  0.020  1.525
 WKM  C04  C02  single  1.548  0.020  1.548
 WKM  C09  N08  single  1.454  0.020  1.454
 WKM  C09  C10  single  1.519  0.020  1.519
 WKM  N08  C13  single  1.453  0.020  1.453
 WKM  C02  C03  single  1.526  0.020  1.526
 WKM  C10  O11  single  1.411  0.020  1.411
 WKM  C13  C12  single  1.520  0.020  1.520
 WKM  O11  C12  single  1.409  0.020  1.409
 WKM  C10  H1   single  0.970  0.020  1.090
 WKM  C10  H2   single  0.970  0.020  1.090
 WKM  C13  H3   single  0.970  0.020  1.090
 WKM  C13  H4   single  0.970  0.020  1.090
 WKM  C01  H5   single  0.970  0.020  1.090
 WKM  C01  H6   single  0.970  0.020  1.090
 WKM  C01  H7   single  0.970  0.020  1.090
 WKM  C02  H8   single  0.970  0.020  1.090
 WKM  C03  H9   single  0.970  0.020  1.090
 WKM  C03  H10  single  0.970  0.020  1.090
 WKM  C03  H11  single  0.970  0.020  1.090
 WKM  C04  H12  single  0.970  0.020  1.090
 WKM  C09  H13  single  0.970  0.020  1.090
 WKM  C09  H14  single  0.970  0.020  1.090
 WKM  C12  H15  single  0.970  0.020  1.090
 WKM  C12  H16  single  0.970  0.020  1.090
 WKM  N05  H17  single  0.890  0.020  1.040
 WKM  N05  H18  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
 WKM  H2   C10  H1   107.95  3.000
 WKM  H2   C10  O11  107.35  3.000
 WKM  H1   C10  O11  110.58  3.000
 WKM  H2   C10  C09  109.98  3.000
 WKM  H1   C10  C09  109.17  3.000
 WKM  O11  C10  C09  111.74  3.000
 WKM  H4   C13  H3   106.98  3.000
 WKM  H4   C13  N08  112.16  3.000
 WKM  H3   C13  N08  108.68  3.000
 WKM  H4   C13  C12  109.67  3.000
 WKM  H3   C13  C12  109.60  3.000
 WKM  N08  C13  C12  109.68  3.000
 WKM  H8   C02  C04  107.69  3.000
 WKM  H8   C02  C03  106.98  3.000
 WKM  C04  C02  C03  110.60  3.000
 WKM  H8   C02  C01  107.77  3.000
 WKM  C03  C02  C01  111.00  3.000
 WKM  C04  C02  C01  112.55  3.000
 WKM  H11  C03  H10  107.24  3.000
 WKM  H11  C03  H9   107.60  3.000
 WKM  H10  C03  H9   108.09  3.000
 WKM  H11  C03  C02  110.23  3.000
 WKM  H10  C03  C02  111.68  3.000
 WKM  H9   C03  C02  111.80  3.000
 WKM  H12  C04  N05  111.63  3.000
 WKM  H12  C04  C06  108.50  3.000
 WKM  N05  C04  C06  108.95  3.000
 WKM  H12  C04  C02  107.39  3.000
 WKM  C06  C04  C02  110.16  3.000
 WKM  N05  C04  C02  110.19  3.000
 WKM  O07  C06  N08  121.53  3.000
 WKM  N08  C06  C04  117.93  3.000
 WKM  O07  C06  C04  120.53  3.000
 WKM  H14  C09  H13  107.93  3.000
 WKM  H14  C09  N08  109.40  3.000
 WKM  H13  C09  N08  110.13  3.000
 WKM  H14  C09  C10  110.07  3.000
 WKM  H13  C09  C10  110.00  3.000
 WKM  N08  C09  C10  109.29  3.000
 WKM  H16  C12  H15  108.07  3.000
 WKM  H16  C12  O11  110.62  3.000
 WKM  H15  C12  O11  107.46  3.000
 WKM  H16  C12  C13  109.28  3.000
 WKM  H15  C12  C13  109.89  3.000
 WKM  O11  C12  C13  111.44  3.000
 WKM  H18  N05  H17  105.77  3.000
 WKM  H18  N05  C04  110.22  3.000
 WKM  H17  N05  C04  108.72  3.000
 WKM  C09  N08  C06  120.81  3.000
 WKM  C09  N08  C13  111.70  3.000
 WKM  C06  N08  C13  127.47  3.000
 WKM  C12  O11  C10  111.61  3.000
 WKM  H7   C01  H6   108.28  3.000
 WKM  H7   C01  H5   107.02  3.000
 WKM  H6   C01  H5   108.03  3.000
 WKM  H7   C01  C02  112.03  3.000
 WKM  H6   C01  C02  111.04  3.000
 WKM  H5   C01  C02  110.29  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
 WKM  CONST_01  O07  C06  N08  C13   180.00   0.0  0
 WKM  CONST_02  C04  C06  N08  C13     0.00   0.0  0
 WKM  CONST_03  C09  N08  C06  C04   180.00   0.0  0
 WKM  CONST_04  O07  C06  N08  C09     0.00   0.0  0
 WKM  Var_01    C13  N08  C09  C10    55.43  30.0  1
 WKM  Var_02    C13  C12  O11  C10   -57.38  30.0  1
 WKM  Var_03    O11  C10  C09  N08   -55.95  30.0  1
 WKM  Var_04    O11  C12  C13  N08    55.79  30.0  1
 WKM  Var_05    H1   C10  O11  C12   -64.15  30.0  1
 WKM  Var_06    H9   C03  C02  C01  -177.50  30.0  3
 WKM  Var_07    H5   C01  C02  C03   -48.33  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
 WKM  chir_01  C04  N05  C06  C02  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
 WKM  plan-1  C13  0.020
 WKM  plan-1  C04  0.020
 WKM  plan-1  C06  0.020
 WKM  plan-1  C09  0.020
 WKM  plan-1  N08  0.020
 WKM  plan-1  O07  0.020

