# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:54:26 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (3R)-4-[4-(2-methoxyethyl)piperazin-1-yl]-N-methyl-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]([C@H](C)CN1CCN(CCOC)CC1)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
 34E  34E  (3R)-4-[4-(2-methoxyethyl)piperazin-1-yl]-N-methyl-L-valine  L-peptide  45  19  .  2016-04-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_34E
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
 34E  CM    C  CH3    0  -0.522  -16.3048  -30.9275   -5.6790
 34E  CA    C  CH1    0  -0.160  -15.9414  -30.8780   -8.1291
 34E  CB    C  CH1    0  -0.280  -16.8323  -32.0897   -8.4578
 34E  CG1   C  CH2    0  -0.238  -17.1958  -32.0510   -9.9431
 34E  N     N  NH1    0  -0.606  -15.3667  -30.8669   -6.7830
 34E  C     C  C      0   0.408  -16.6402  -29.5080   -8.3594
 34E  O     O  O      0  -0.605  -17.8512  -29.4217   -8.0651
 34E  CG2   C  CH3    0  -0.667  -16.1506  -33.4082   -8.1082
 34E  NH    N  NT     0  -0.420  -20.2612  -34.3713  -11.7135
 34E  CQ    C  CH2    0  -0.309  -21.0901  -35.4643  -12.1885
 34E  CI    C  CH2    0  -0.169  -21.7946  -35.1941  -13.5103
 34E  OK    O  O2     0  -0.478  -20.9779  -35.1115  -14.6548
 34E  CL    C  CH3    0  -0.400  -20.4643  -36.3480  -15.0788
 34E  CZ2   C  CH2    0  -0.282  -20.0945  -34.4174  -10.2727
 34E  CE2   C  CH2    0  -0.290  -19.3044  -33.2219   -9.7761
 34E  ND    N  NT     0  -0.421  -17.9993  -33.1710  -10.4030
 34E  CE1   C  CH2    0  -0.277  -18.1554  -33.1364  -11.8430
 34E  CZ1   C  CH2    0  -0.295  -18.9533  -34.3261  -12.3431
 34E  HM1   H  HCH3   0   0.219  -15.7442  -30.9724   -4.7446
 34E  HM2   H  HCH3   0   0.221  -16.9185  -30.0284   -5.6472
 34E  HM3   H  HCH3   0   0.188  -16.9861  -31.7886   -5.6912
 34E  HA    H  HCH1   0   0.192  -15.0781  -30.9197   -8.8052
 34E  HB    H  HCH1   0   0.212  -17.7487  -32.0063   -7.8670
 34E  HG11  H  HCH2   0   0.210  -16.2659  -32.0586  -10.5245
 34E  HG12  H  HCH2   0   0.197  -17.6983  -31.0974  -10.1740
 34E  HG21  H  HCH3   0   0.220  -15.9469  -33.4941   -7.0400
 34E  HG22  H  HCH3   0   0.230  -16.7732  -34.2589   -8.3844
 34E  HG23  H  HCH3   0   0.206  -15.1996  -33.5145   -8.6379
 34E  HQ1   H  HCH2   0   0.237  -21.8921  -35.6140  -11.4604
 34E  HQ2   H  HCH2   0   0.204  -20.5362  -36.4176  -12.2200
 34E  HI1   H  HCH2   0   0.223  -22.3140  -34.2358  -13.4344
 34E  HI2   H  HCH2   0   0.199  -22.5602  -35.9715  -13.6493
 34E  HL1   H  HCH3   0   0.231  -19.9417  -36.1858  -16.0211
 34E  HL2   H  HCH3   0   0.205  -19.7526  -36.7835  -14.3689
 34E  HL3   H  HCH3   0   0.205  -21.2607  -37.0832  -15.2488
 34E  HZ21  H  HCH2   0   0.232  -21.0781  -34.4098   -9.7974
 34E  HZ22  H  HCH2   0   0.185  -19.5831  -35.3411   -9.9495
 34E  HE21  H  HCH2   0   0.237  -19.1921  -33.3126   -8.6945
 34E  HE22  H  HCH2   0   0.186  -19.8827  -32.2995   -9.9651
 34E  HE11  H  HCH2   0   0.230  -17.1678  -33.1531  -12.3109
 34E  HE12  H  HCH2   0   0.181  -18.6540  -32.2076  -12.1731
 34E  HZ11  H  HCH2   0   0.244  -19.0655  -34.2403  -13.4226
 34E  HZ12  H  HCH2   0   0.182  -18.3829  -35.2516  -12.1463
 34E  OXT   O  OC    -1  -0.606  -15.9150  -28.5887   -8.7885
 34E  H     H  HNH1   0   0.341  -14.7131  -31.6342   -6.6980

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
 34E  CL   OK    single  1.404  0.020  1.404
 34E  OK   CI    single  1.408  0.020  1.408
 34E  CI   CQ    single  1.522  0.020  1.522
 34E  CQ   NH    single  1.452  0.020  1.452
 34E  CZ1  CE1   single  1.517  0.020  1.517
 34E  CZ1  NH    single  1.452  0.020  1.452
 34E  CE1  ND    single  1.449  0.020  1.449
 34E  NH   CZ2   single  1.451  0.020  1.451
 34E  ND   CG1   single  1.453  0.020  1.453
 34E  ND   CE2   single  1.449  0.020  1.449
 34E  CZ2  CE2   single  1.517  0.020  1.517
 34E  CG1  CB    single  1.530  0.020  1.530
 34E  C    O     deloc   1.231  0.020  1.231
 34E  C    CA    single  1.525  0.021  1.525
 34E  CB   CA    single  1.540  0.027  1.540
 34E  CB   CG2   single  1.525  0.020  1.525
 34E  CA   N     single  1.458  0.019  1.458
 34E  N    CM    single  1.450  0.020  1.450
 34E  CM   HM1   single  0.970  0.020  1.090
 34E  CM   HM2   single  0.970  0.020  1.090
 34E  CM   HM3   single  0.970  0.020  1.090
 34E  CA   HA    single  0.970  0.020  0.970
 34E  CB   HB    single  0.970  0.020  1.090
 34E  CG1  HG11  single  0.970  0.020  1.090
 34E  CG1  HG12  single  0.970  0.020  1.090
 34E  CG2  HG21  single  0.970  0.020  1.090
 34E  CG2  HG22  single  0.970  0.020  1.090
 34E  CG2  HG23  single  0.970  0.020  1.090
 34E  CQ   HQ1   single  0.970  0.020  1.090
 34E  CQ   HQ2   single  0.970  0.020  1.090
 34E  CI   HI1   single  0.970  0.020  1.090
 34E  CI   HI2   single  0.970  0.020  1.090
 34E  CL   HL1   single  0.970  0.020  1.090
 34E  CL   HL2   single  0.970  0.020  1.090
 34E  CL   HL3   single  0.970  0.020  1.090
 34E  CZ2  HZ21  single  0.970  0.020  1.090
 34E  CZ2  HZ22  single  0.970  0.020  1.090
 34E  CE2  HE21  single  0.970  0.020  1.090
 34E  CE2  HE22  single  0.970  0.020  1.090
 34E  CE1  HE11  single  0.970  0.020  1.090
 34E  CE1  HE12  single  0.970  0.020  1.090
 34E  CZ1  HZ11  single  0.970  0.020  1.090
 34E  CZ1  HZ12  single  0.970  0.020  1.090
 34E  C    OXT   deloc   1.247  0.020  1.247
 34E  N    H     single  0.860  0.020  0.860

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
 34E  HM3   CM   HM2   107.34  3.000
 34E  HM3   CM   HM1   107.23  3.000
 34E  HM2   CM   HM1   107.37  3.000
 34E  HM3   CM   N     115.20  3.000
 34E  HM2   CM   N     110.63  3.000
 34E  HM1   CM   N     108.75  3.000
 34E  HA    CA   C     109.00  3.000
 34E  HA    CA   N     110.00  3.000
 34E  C     CA   N     111.00  2.800
 34E  HA    CA   CB    109.00  3.000
 34E  N     CA   CB    111.50  1.700
 34E  C     CA   CB    111.40  1.900
 34E  HB    CB   CG2   108.47  3.000
 34E  HB    CB   CG1   108.88  3.000
 34E  CG2   CB   CG1   110.53  3.000
 34E  HB    CB   CA    108.03  3.000
 34E  CG2   CB   CA    111.89  3.000
 34E  CG1   CB   CA    108.96  3.000
 34E  HG12  CG1  HG11  106.36  3.000
 34E  HG12  CG1  ND    110.39  3.000
 34E  HG11  CG1  ND    107.20  3.000
 34E  HG12  CG1  CB    109.48  3.000
 34E  HG11  CG1  CB    108.25  3.000
 34E  ND    CG1  CB    114.78  3.000
 34E  H     N    CA    114.00  3.000
 34E  H     N    CM    108.81  3.000
 34E  CA    N    CM    116.48  3.000
 34E  OXT   C    O     126.43  3.000
 34E  OXT   C    CA    116.05  3.000
 34E  O     C    CA    120.80  1.700
 34E  HG23  CG2  HG22  107.35  3.000
 34E  HG23  CG2  HG21  107.71  3.000
 34E  HG22  CG2  HG21  107.07  3.000
 34E  HG23  CG2  CB    111.20  3.000
 34E  HG22  CG2  CB    111.19  3.000
 34E  HG21  CG2  CB    112.09  3.000
 34E  CZ1   NH   CZ2   109.14  3.000
 34E  CZ2   NH   CQ    111.50  3.000
 34E  CZ1   NH   CQ    113.32  3.000
 34E  HQ2   CQ   HQ1   105.60  3.000
 34E  HQ2   CQ   CI    111.17  3.000
 34E  HQ1   CQ   CI    105.25  3.000
 34E  HQ2   CQ   NH    111.93  3.000
 34E  HQ1   CQ   NH    107.70  3.000
 34E  CI    CQ   NH    114.51  3.000
 34E  HI2   CI   HI1   107.33  3.000
 34E  HI2   CI   OK    110.02  3.000
 34E  HI1   CI   OK    106.30  3.000
 34E  HI2   CI   CQ    107.84  3.000
 34E  HI1   CI   CQ    108.38  3.000
 34E  OK    CI   CQ    116.60  3.000
 34E  CL    OK   CI    113.94  3.000
 34E  HL3   CL   HL2   107.80  3.000
 34E  HL3   CL   HL1   108.30  3.000
 34E  HL2   CL   HL1   107.94  3.000
 34E  HL3   CL   OK    111.79  3.000
 34E  HL2   CL   OK    113.08  3.000
 34E  HL1   CL   OK    107.78  3.000
 34E  HZ22  CZ2  HZ21  107.19  3.000
 34E  HZ22  CZ2  CE2   108.80  3.000
 34E  HZ21  CZ2  CE2   108.73  3.000
 34E  HZ22  CZ2  NH    111.74  3.000
 34E  HZ21  CZ2  NH    109.17  3.000
 34E  CE2   CZ2  NH    111.10  3.000
 34E  HE22  CE2  HE21  107.02  3.000
 34E  HE22  CE2  ND    111.60  3.000
 34E  HE21  CE2  ND    109.83  3.000
 34E  HE22  CE2  CZ2   109.23  3.000
 34E  HE21  CE2  CZ2   108.22  3.000
 34E  ND    CE2  CZ2   110.82  3.000
 34E  CE1   ND   CE2   109.50  3.000
 34E  CE2   ND   CG1   112.85  3.000
 34E  CE1   ND   CG1   110.84  3.000
 34E  HE12  CE1  HE11  107.02  3.000
 34E  HE12  CE1  CZ1   108.87  3.000
 34E  HE11  CE1  CZ1   108.80  3.000
 34E  HE12  CE1  ND    111.45  3.000
 34E  HE11  CE1  ND    109.13  3.000
 34E  CZ1   CE1  ND    111.44  3.000
 34E  HZ12  CZ1  HZ11  107.20  3.000
 34E  HZ12  CZ1  CE1   109.06  3.000
 34E  HZ11  CZ1  CE1   108.62  3.000
 34E  HZ12  CZ1  NH    111.20  3.000
 34E  HZ11  CZ1  NH    109.84  3.000
 34E  CE1   CZ1  NH    110.81  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
 34E  Var_01  ND   CE1  CZ1  NH    57.74  30.0  1
 34E  Var_02  ND   CE2  CZ2  NH   -58.53  30.0  1
 34E  Var_03  CE1  CZ1  NH   CZ2  -57.13  30.0  1
 34E  Var_04  CE1  ND   CE2  CZ2   56.88  30.0  1
 34E  Var_05  CZ1  CE1  ND   CE2  -56.77  30.0  1
 34E  Var_06  CZ1  NH   CZ2  CE2   57.78  30.0  1
 34E  Var_07  OK   CI   CQ   NH    68.74  30.0  2
 34E  Var_08  HM1  CM   N    CA   176.64  30.0  3
 34E  Var_09  HL1  CL   OK   CI   174.05  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
 34E  chir_01  CA  C    CB  N    positiv
 34E  chir_02  CB  CG1  CA  CG2  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
 34E  plan-1  CA   0.020
 34E  plan-1  C    0.020
 34E  plan-1  O    0.020
 34E  plan-1  OXT  0.020

