# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:57:08 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: O-tert-butyl-D-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC[C@@H](N)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
 3PM  3PM  'O-tert-butyl-D-serine    '  L-peptide  25  11  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_3PM
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
 3PM  N     N  NH2    0  -0.814  16.1294  21.6075  38.1630
 3PM  CA    C  CH1    0  -0.208  16.2164  22.7908  37.3099
 3PM  C11   C  CH2    0  -0.133  15.4518  23.9075  38.0049
 3PM  O12   O  O2     0  -0.503  15.5876  25.0828  37.2426
 3PM  C13   C  CT     0   0.211  14.6358  26.1226  37.4440
 3PM  C15   C  CH3    0  -0.681  14.4609  26.4584  38.9252
 3PM  C16   C  CH3    0  -0.663  13.2896  25.7443  36.8251
 3PM  C14   C  CH3    0  -0.656  15.2157  27.3281  36.7122
 3PM  C     C  C      0   0.391  15.5940  22.5009  35.9193
 3PM  O     O  O      0  -0.609  14.4073  22.1175  35.9129
 3PM  HN9   H  HNH2   0   0.340  16.5889  20.8271  37.7105
 3PM  H10   H  HCH1   0   0.174  17.2542  23.1240  37.1613
 3PM  H11   H  HCH2   0   0.190  14.4080  23.5924  38.1143
 3PM  H11A  H  HCH2   0   0.192  15.8499  24.0528  39.0207
 3PM  H15   H  HCH3   0   0.233  13.8080  27.3249  39.0359
 3PM  H15A  H  HCH3   0   0.231  14.0073  25.6379  39.4836
 3PM  H15B  H  HCH3   0   0.229  15.4183  26.6996  39.3912
 3PM  H16   H  HCH3   0   0.223  12.5822  26.5682  36.9255
 3PM  H16A  H  HCH3   0   0.226  13.3990  25.5221  35.7623
 3PM  H16B  H  HCH3   0   0.227  12.8445  24.8736  37.3098
 3PM  H14   H  HCH3   0   0.219  14.5326  28.1759  36.7694
 3PM  H14A  H  HCH3   0   0.226  16.1672  27.6320  37.1519
 3PM  H14B  H  HCH3   0   0.227  15.3826  27.1038  35.6570
 3PM  H2    H  HNH2   0   0.334  16.6577  21.7714  39.0120
 3PM  OXT   O  OC    -1  -0.606  16.3275  22.6761  34.9267

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
 3PM  N    HN9   single  0.890  0.020  1.040
 3PM  CA   N     single  1.458  0.019  1.458
 3PM  CA   C11   single  1.521  0.020  1.521
 3PM  CA   H10   single  0.970  0.020  1.090
 3PM  C11  H11   single  0.970  0.020  1.090
 3PM  C11  H11A  single  0.970  0.020  1.090
 3PM  O12  C11   single  1.407  0.020  1.407
 3PM  O12  C13   single  1.424  0.020  1.424
 3PM  C13  C15   single  1.529  0.020  1.529
 3PM  C15  H15   single  0.970  0.020  1.090
 3PM  C15  H15A  single  0.970  0.020  1.090
 3PM  C15  H15B  single  0.970  0.020  1.090
 3PM  C16  C13   single  1.529  0.020  1.529
 3PM  C16  H16   single  0.970  0.020  1.090
 3PM  C16  H16A  single  0.970  0.020  1.090
 3PM  C16  H16B  single  0.970  0.020  1.090
 3PM  C14  C13   single  1.525  0.020  1.525
 3PM  C14  H14   single  0.970  0.020  1.090
 3PM  C14  H14A  single  0.970  0.020  1.090
 3PM  C14  H14B  single  0.970  0.020  1.090
 3PM  C    CA    single  1.525  0.021  1.525
 3PM  C    O     deloc   1.231  0.020  1.231
 3PM  N    H2    single  0.890  0.020  1.040
 3PM  C    OXT   deloc   1.247  0.020  1.247

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
 3PM  H2    N    HN9   105.22  3.000
 3PM  H2    N    CA    109.09  3.000
 3PM  HN9   N    CA    109.64  3.000
 3PM  H10   CA   C     108.31  3.000
 3PM  C     CA   C11   110.19  3.000
 3PM  H10   CA   C11   108.27  3.000
 3PM  C     CA   N     111.00  2.800
 3PM  H10   CA   N     112.35  3.000
 3PM  C11   CA   N     107.32  3.000
 3PM  H11A  C11  H11   106.88  3.000
 3PM  H11A  C11  O12   110.77  3.000
 3PM  H11   C11  O12   112.72  3.000
 3PM  O12   C11  CA    108.48  3.000
 3PM  H11A  C11  CA    109.68  3.000
 3PM  H11   C11  CA    108.26  3.000
 3PM  C13   O12  C11   117.95  3.000
 3PM  C14   C13  C16   109.64  3.000
 3PM  C14   C13  C15   109.57  3.000
 3PM  C16   C13  C15   110.23  3.000
 3PM  C14   C13  O12   104.79  3.000
 3PM  C16   C13  O12   110.52  3.000
 3PM  C15   C13  O12   111.95  3.000
 3PM  H15B  C15  H15A  108.20  3.000
 3PM  H15B  C15  H15   107.82  3.000
 3PM  H15A  C15  H15   107.25  3.000
 3PM  H15B  C15  C13   111.20  3.000
 3PM  H15A  C15  C13   112.22  3.000
 3PM  H15   C15  C13   109.96  3.000
 3PM  H16B  C16  H16A  108.12  3.000
 3PM  H16B  C16  H16   107.30  3.000
 3PM  H16A  C16  H16   107.97  3.000
 3PM  H16B  C16  C13   112.13  3.000
 3PM  H16A  C16  C13   110.87  3.000
 3PM  H16   C16  C13   110.29  3.000
 3PM  H14B  C14  H14A  108.26  3.000
 3PM  H14B  C14  H14   107.84  3.000
 3PM  H14A  C14  H14   107.97  3.000
 3PM  H14B  C14  C13   111.08  3.000
 3PM  H14A  C14  C13   111.00  3.000
 3PM  H14   C14  C13   110.56  3.000
 3PM  OXT   C    O     126.80  3.000
 3PM  OXT   C    CA    120.80  1.700
 3PM  O     C    CA    120.80  1.700

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
 3PM  Var_01  C15  C13  O12  C11    49.91  30.0  3
 3PM  Var_02  H15  C15  C13  O12   174.05  30.0  3
 3PM  Var_03  H16  C16  C13  O12  -176.41  30.0  3
 3PM  Var_04  H14  C14  C13  O12   177.49  30.0  3
 3PM  Var_05  H11  C11  O12  C13    40.26  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
 3PM  chir_01  CA  N  C11  C  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
 3PM  plan-1  CA   0.020
 3PM  plan-1  C    0.020
 3PM  plan-1  O    0.020
 3PM  plan-1  OXT  0.020

