# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:02:38 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: N~2~-acetyl-N-prop-2-en-1-yl-D-allothreoninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](NC(C)=O)C(=O)NCC=C
#
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
 T9M  T9M  N~2~-acetyl-N-prop-2-en-1-yl-D-allothreoninamide  ligand  30  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T9M
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
 T9M  N1   N  NH1   0  -0.628   2.0549  -5.8259  23.1354
 T9M  C4   C  C     0   0.536   1.5178  -5.6047  21.9212
 T9M  C5   C  CH3   0  -0.776   0.2858  -4.7379  21.9025
 T9M  C6   C  C     0   0.541   4.4814  -5.7223  22.9598
 T9M  C7   C  CH2   0  -0.330   6.5955  -5.6712  21.7245
 T9M  C8   C  C1    0  -0.186   6.4493  -4.9122  20.4387
 T9M  C1   C  CH3   0  -0.673   2.2871  -8.0435  25.1279
 T9M  C2   C  CH1   0   0.028   3.3716  -7.0391  24.7867
 T9M  C3   C  CH1   0  -0.215   3.2672  -6.5795  23.3191
 T9M  C9   C  C2    0  -0.537   5.3382  -4.7966  19.7236
 T9M  N2   N  NH1   0  -0.619   5.3917  -6.3181  22.1791
 T9M  O1   O  OH1   0  -0.666   4.6207  -7.6511  25.0122
 T9M  O2   O  O     0  -0.497   1.9984  -6.0750  20.8990
 T9M  O3   O  O     0  -0.487   4.5993  -4.5906  23.4040
 T9M  H7   H  HNH1  0   0.403   1.6786  -5.3305  23.9280
 T9M  H9   H  HCH3  0   0.267  -0.4971  -5.2304  21.3276
 T9M  H10  H  HCH3  0   0.251  -0.1019  -4.5100  22.8935
 T9M  H8   H  HCH3  0   0.270   0.5174  -3.7989  21.3987
 T9M  H13  H  HCH2  0   0.259   6.9601  -4.9998  22.5043
 T9M  H12  H  HCH2  0   0.267   7.3672  -6.4348  21.6047
 T9M  H14  H  H     0   0.248   7.3618  -4.4336  20.0963
 T9M  H3   H  HCH3  0   0.234   1.2939  -7.6304  24.9573
 T9M  H1   H  HCH3  0   0.231   2.3849  -8.9441  24.5186
 T9M  H2   H  HCH3  0   0.244   2.3514  -8.3301  26.1775
 T9M  H4   H  HCH1  0   0.225   3.2553  -6.1529  25.4258
 T9M  H6   H  HCH1  0   0.269   3.2297  -7.4666  22.6809
 T9M  H16  H  H     0   0.239   5.3272  -4.2283  18.8029
 T9M  H15  H  H     0   0.239   4.4045  -5.2552  20.0261
 T9M  H11  H  HNH1  0   0.405   5.1852  -7.2321  21.8108
 T9M  H5   H  HOH1  0   0.458   5.2763  -6.9764  25.2112

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
 T9M  C1  C2   single  1.517  0.020  1.517
 T9M  C2  O1   single  1.409  0.020  1.409
 T9M  C2  C3   single  1.541  0.020  1.541
 T9M  C3  N1   single  1.439  0.020  1.439
 T9M  N1  C4   single  1.346  0.020  1.346
 T9M  C4  C5   single  1.507  0.020  1.507
 T9M  C4  O2   double  1.223  0.020  1.223
 T9M  C3  C6   single  1.529  0.020  1.529
 T9M  C6  O3   double  1.222  0.020  1.222
 T9M  C6  N2   single  1.339  0.020  1.339
 T9M  N2  C7   single  1.440  0.020  1.440
 T9M  C7  C8   single  1.500  0.020  1.500
 T9M  C8  C9   double  1.326  0.020  1.326
 T9M  N1  H7   single  0.860  0.020  1.020
 T9M  C5  H9   single  0.970  0.020  1.090
 T9M  C5  H10  single  0.970  0.020  1.090
 T9M  C5  H8   single  0.970  0.020  1.090
 T9M  C7  H13  single  0.970  0.020  1.090
 T9M  C7  H12  single  0.970  0.020  1.090
 T9M  C8  H14  single  0.930  0.020  1.080
 T9M  C1  H3   single  0.970  0.020  1.090
 T9M  C1  H1   single  0.970  0.020  1.090
 T9M  C1  H2   single  0.970  0.020  1.090
 T9M  C2  H4   single  0.970  0.020  1.090
 T9M  C3  H6   single  0.970  0.020  1.090
 T9M  C9  H16  single  0.930  0.020  1.080
 T9M  C9  H15  single  0.930  0.020  1.080
 T9M  N2  H11  single  0.860  0.020  1.020
 T9M  O1  H5   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
 T9M  H7   N1  C3   118.14  3.000
 T9M  H7   N1  C4   118.67  3.000
 T9M  C3   N1  C4   122.50  3.000
 T9M  O2   C4  C5   122.14  3.000
 T9M  O2   C4  N1   122.26  3.000
 T9M  C5   C4  N1   115.60  3.000
 T9M  H8   C5  H10  108.43  3.000
 T9M  H8   C5  H9   107.35  3.000
 T9M  H10  C5  H9   108.62  3.000
 T9M  H8   C5  C4   109.12  3.000
 T9M  H10  C5  C4   113.61  3.000
 T9M  H9   C5  C4   109.53  3.000
 T9M  O3   C6  N2   123.97  3.000
 T9M  N2   C6  C3   115.30  3.000
 T9M  O3   C6  C3   120.70  3.000
 T9M  H12  C7  H13  105.81  3.000
 T9M  H12  C7  N2   108.13  3.000
 T9M  H13  C7  N2   109.26  3.000
 T9M  H12  C7  C8   109.18  3.000
 T9M  H13  C7  C8   109.49  3.000
 T9M  N2   C7  C8   114.60  3.000
 T9M  H14  C8  C9   119.71  3.000
 T9M  H14  C8  C7   114.29  3.000
 T9M  C9   C8  C7   126.00  3.000
 T9M  H2   C1  H1   108.37  3.000
 T9M  H2   C1  H3   107.71  3.000
 T9M  H1   C1  H3   107.89  3.000
 T9M  H2   C1  C2   110.40  3.000
 T9M  H1   C1  C2   110.90  3.000
 T9M  H3   C1  C2   111.45  3.000
 T9M  H4   C2  O1   110.55  3.000
 T9M  H4   C2  C3   107.83  3.000
 T9M  O1   C2  C3   109.99  3.000
 T9M  H4   C2  C1   109.12  3.000
 T9M  C3   C2  C1   111.29  3.000
 T9M  O1   C2  C1   108.07  3.000
 T9M  H6   C3  C2   108.43  3.000
 T9M  H6   C3  C6   110.17  3.000
 T9M  C2   C3  C6   109.70  3.000
 T9M  H6   C3  N1   108.75  3.000
 T9M  C6   C3  N1   110.20  3.000
 T9M  C2   C3  N1   109.56  3.000
 T9M  H15  C9  H16  116.82  3.000
 T9M  H15  C9  C8   122.32  3.000
 T9M  H16  C9  C8   120.86  3.000
 T9M  H11  N2  C7   117.63  3.000
 T9M  H11  N2  C6   118.54  3.000
 T9M  C7   N2  C6   123.53  3.000
 T9M  H5   O1  C2   109.43  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
 T9M  CONST_01  C3   N1  C4  C5   180.00   0.0  0
 T9M  CONST_02  C3   C6  N2  C7   180.00   0.0  0
 T9M  CONST_03  O3   C6  N2  C7     0.00   0.0  0
 T9M  CONST_04  O2   C4  N1  C3     0.00   0.0  0
 T9M  CONST_05  H7   N1  C4  C5     0.00   0.0  0
 T9M  CONST_06  H11  N2  C6  C3     0.00   0.0  0
 T9M  Var_01    C8   C7  N2  C6   -88.37  30.0  3
 T9M  Var_02    N2   C7  C8  C9     0.18  30.0  2
 T9M  Var_03    H16  C9  C8  C7  -179.84   0.0  2
 T9M  Var_04    H9   C5  C4  N1  -129.83  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
 T9M  chir_01  C2  C1  O1  C3  negativ
 T9M  chir_02  C3  N1  C2  C6  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
 T9M  plan-1  N1   0.020
 T9M  plan-1  C4   0.020
 T9M  plan-1  C5   0.020
 T9M  plan-1  C3   0.020
 T9M  plan-1  O2   0.020
 T9M  plan-1  H7   0.020
 T9M  plan-2  C6   0.020
 T9M  plan-2  C7   0.020
 T9M  plan-2  C3   0.020
 T9M  plan-2  N2   0.020
 T9M  plan-2  O3   0.020
 T9M  plan-2  H11  0.020
 T9M  plan-3  C7   0.020
 T9M  plan-3  C8   0.020
 T9M  plan-3  C9   0.020
 T9M  plan-3  H14  0.020
 T9M  plan-3  H16  0.020
 T9M  plan-3  H15  0.020

