# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 13:29:28 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-[(2S)-2-amino-4-methylpentyl]-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)CN[C@@H](Cc1ccccc1)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
 DC0  DC0  N-[(2S)-2-amino-4-methylpentyl]-L-phenylalanine  peptide  42  19  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DC0
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
 DC0  N    N  NH2    0  -0.786  -1.6471   1.5835   0.0293
 DC0  C1   C  CH1    0  -0.136  -2.1595   0.2168   0.0269
 DC0  C2   C  CH2    0  -0.229  -1.0933  -0.7068  -0.5532
 DC0  C3   C  CH2    0  -0.398  -3.4823   0.0414  -0.7236
 DC0  C4   C  CH1    0  -0.236  -4.6507   0.8832  -0.2071
 DC0  C5   C  CH3    0  -0.648  -5.8580   0.7287  -1.1270
 DC0  C6   C  CH3    0  -0.659  -5.0269   0.5301   1.2283
 DC0  N2   N  NH1    0  -0.606   0.1303  -0.6255   0.2124
 DC0  C7   C  CH1    0  -0.153   1.2443  -1.3218  -0.3876
 DC0  C    C  C      0   0.394   1.0767  -2.8609  -0.3914
 DC0  O    O  O      0  -0.600   0.3266  -3.3711   0.4598
 DC0  C9   C  CH2    0  -0.519   2.5339  -0.9956   0.3855
 DC0  C10  C  CR6    0   0.113   2.8739   0.4686   0.3695
 DC0  C11  C  CR16   0  -0.308   2.5776   1.2932   1.4526
 DC0  C12  C  CR16   0  -0.304   3.4653   1.0436  -0.7554
 DC0  C13  C  CR16   0  -0.241   2.8610   2.6531   1.4157
 DC0  C14  C  CR16   0  -0.241   3.7523   2.4003  -0.7973
 DC0  C15  C  CR16   0  -0.274   3.4497   3.2118   0.2900
 DC0  OXT  O  OC    -1  -0.623   1.7599  -3.4682  -1.2429
 DC0  H    H  HNH2   0   0.333  -1.6702   1.9518  -0.9157
 DC0  H1   H  HCH1   0   0.218  -2.3004  -0.0719   1.0740
 DC0  H3   H  HCH2   0   0.213  -1.4638  -1.7338  -0.5373
 DC0  H4   H  HCH2   0   0.164  -0.9432  -0.4460  -1.6187
 DC0  H5   H  HCH2   0   0.210  -3.3130   0.2849  -1.7803
 DC0  H6   H  HCH2   0   0.205  -3.7725  -1.0160  -0.6968
 DC0  H7   H  HCH1   0   0.203  -4.3511   1.9372  -0.2318
 DC0  H8   H  HCH3   0   0.211  -6.2020  -0.3084  -1.1514
 DC0  H9   H  HCH3   0   0.223  -6.6953   1.3435  -0.7911
 DC0  H10  H  HCH3   0   0.222  -5.6195   1.0224  -2.1509
 DC0  H11  H  HCH3   0   0.227  -4.2145   0.7206   1.9309
 DC0  H12  H  HCH3   0   0.225  -5.8852   1.1157   1.5628
 DC0  H13  H  HCH3   0   0.213  -5.2941  -0.5264   1.3133
 DC0  H14  H  HNH1   0   0.345   0.3527   0.3610   0.2970
 DC0  H15  H  HCH1   0   0.175   1.4022  -1.0109  -1.4364
 DC0  H16  H  HCH2   0   0.235   2.4184  -1.3395   1.4169
 DC0  H17  H  HCH2   0   0.243   3.3523  -1.5668  -0.0573
 DC0  H18  H  HCR6   0   0.247   2.1205   0.8647   2.3370
 DC0  H19  H  HCR6   0   0.243   3.7078   0.4189  -1.6080
 DC0  H20  H  HCR6   0   0.251   2.6218   3.2757   2.2686
 DC0  H21  H  HCR6   0   0.251   4.2157   2.8254  -1.6785
 DC0  H22  H  HCR6   0   0.251   3.6745   4.2702   0.2599
 DC0  H2   H  HNH2   0   0.347  -2.2457   2.1861   0.5792

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
 DC0  N    C1   single    1.460  0.020  1.460
 DC0  N    H    single    0.860  0.020  0.860
 DC0  C1   C2   single    1.525  0.020  1.525
 DC0  C1   C3   single    1.531  0.020  1.531
 DC0  C1   H1   single    0.970  0.020  1.090
 DC0  C2   H3   single    0.970  0.020  1.090
 DC0  C2   H4   single    0.970  0.020  1.090
 DC0  C2   N2   single    1.446  0.020  1.446
 DC0  C3   C4   single    1.530  0.020  1.530
 DC0  C3   H5   single    0.970  0.020  1.090
 DC0  C3   H6   single    0.970  0.020  1.090
 DC0  C4   C5   single    1.526  0.020  1.526
 DC0  C4   C6   single    1.525  0.020  1.525
 DC0  C4   H7   single    0.970  0.020  1.090
 DC0  C5   H8   single    0.970  0.020  1.090
 DC0  C5   H9   single    0.970  0.020  1.090
 DC0  C5   H10  single    0.970  0.020  1.090
 DC0  C6   H11  single    0.970  0.020  1.090
 DC0  C6   H12  single    0.970  0.020  1.090
 DC0  C6   H13  single    0.970  0.020  1.090
 DC0  N2   C7   single    1.444  0.020  1.444
 DC0  N2   H14  single    0.890  0.020  1.040
 DC0  C7   C    single    1.548  0.020  1.548
 DC0  C7   C9   single    1.539  0.020  1.539
 DC0  C7   H15  single    0.970  0.020  1.090
 DC0  C    O    deloc     1.231  0.020  1.231
 DC0  C    OXT  deloc     1.249  0.020  1.249
 DC0  C9   C10  single    1.503  0.020  1.503
 DC0  C9   H16  single    0.970  0.020  1.090
 DC0  C9   H17  single    0.970  0.020  1.090
 DC0  C10  C11  aromatic  1.393  0.020  1.393
 DC0  C10  C12  aromatic  1.395  0.020  1.395
 DC0  C11  C13  aromatic  1.390  0.020  1.390
 DC0  C11  H18  single    0.930  0.020  1.080
 DC0  C12  C14  aromatic  1.387  0.020  1.387
 DC0  C12  H19  single    0.930  0.020  1.080
 DC0  C13  C15  aromatic  1.388  0.020  1.388
 DC0  C13  H20  single    0.930  0.020  1.080
 DC0  C14  C15  aromatic  1.390  0.020  1.390
 DC0  C14  H21  single    0.930  0.020  1.080
 DC0  C15  H22  single    0.930  0.020  1.080
 DC0  N    H2   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
 DC0  H2   N    H    106.06  3.000
 DC0  H2   N    C1   110.54  3.000
 DC0  H    N    C1   109.30  3.000
 DC0  H1   C1   C3   109.11  3.000
 DC0  H1   C1   C2   107.09  3.000
 DC0  C3   C1   C2   110.37  3.000
 DC0  H1   C1   N    106.88  3.000
 DC0  C3   C1   N    114.29  3.000
 DC0  C2   C1   N    108.80  3.000
 DC0  H4   C2   H3   106.35  3.000
 DC0  H4   C2   N2   112.44  3.000
 DC0  H3   C2   N2   109.41  3.000
 DC0  N2   C2   C1   110.87  3.000
 DC0  H4   C2   C1   108.55  3.000
 DC0  H3   C2   C1   109.07  3.000
 DC0  H6   C3   H5   106.16  3.000
 DC0  H6   C3   C4   108.67  3.000
 DC0  H5   C3   C4   108.71  3.000
 DC0  H6   C3   C1   109.09  3.000
 DC0  H5   C3   C1   108.25  3.000
 DC0  C4   C3   C1   115.55  3.000
 DC0  H7   C4   C6   108.13  3.000
 DC0  H7   C4   C5   107.46  3.000
 DC0  C6   C4   C5   110.42  3.000
 DC0  H7   C4   C3   108.23  3.000
 DC0  C6   C4   C3   112.25  3.000
 DC0  C5   C4   C3   110.18  3.000
 DC0  H10  C5   H9   107.73  3.000
 DC0  H10  C5   H8   107.65  3.000
 DC0  H9   C5   H8   107.45  3.000
 DC0  H10  C5   C4   111.44  3.000
 DC0  H9   C5   C4   111.37  3.000
 DC0  H8   C5   C4   111.01  3.000
 DC0  H13  C6   H12  107.61  3.000
 DC0  H13  C6   H11  107.51  3.000
 DC0  H12  C6   H11  107.13  3.000
 DC0  H13  C6   C4   110.93  3.000
 DC0  H12  C6   C4   110.98  3.000
 DC0  H11  C6   C4   112.45  3.000
 DC0  H14  N2   C7   109.53  3.000
 DC0  H14  N2   C2   106.52  3.000
 DC0  C7   N2   C2   113.93  3.000
 DC0  H15  C7   C9   107.30  3.000
 DC0  H15  C7   C    107.02  3.000
 DC0  C9   C7   C    107.63  3.000
 DC0  H15  C7   N2   111.64  3.000
 DC0  C9   C7   N2   109.60  3.000
 DC0  C    C7   N2   113.38  3.000
 DC0  OXT  C    O    126.64  3.000
 DC0  OXT  C    C7   115.20  3.000
 DC0  O    C    C7   118.12  3.000
 DC0  H17  C9   H16  107.28  3.000
 DC0  H17  C9   C10  109.62  3.000
 DC0  H16  C9   C10  109.89  3.000
 DC0  H17  C9   C7   108.28  3.000
 DC0  H16  C9   C7   108.59  3.000
 DC0  C10  C9   C7   113.00  3.000
 DC0  C12  C10  C11  118.24  3.000
 DC0  C12  C10  C9   120.39  3.000
 DC0  C11  C10  C9   121.34  3.000
 DC0  H18  C11  C13  119.64  3.000
 DC0  H18  C11  C10  119.34  3.000
 DC0  C13  C11  C10  121.01  3.000
 DC0  H19  C12  C14  119.56  3.000
 DC0  H19  C12  C10  119.43  3.000
 DC0  C14  C12  C10  121.01  3.000
 DC0  H20  C13  C15  120.07  3.000
 DC0  H20  C13  C11  119.79  3.000
 DC0  C15  C13  C11  120.14  3.000
 DC0  H21  C14  C15  120.04  3.000
 DC0  H21  C14  C12  119.81  3.000
 DC0  C15  C14  C12  120.15  3.000
 DC0  H22  C15  C14  120.26  3.000
 DC0  H22  C15  C13  120.29  3.000
 DC0  C14  C15  C13  119.46  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
 DC0  CONST_01  C15  C13  C11  C10     0.00   0.0  0
 DC0  CONST_02  C15  C14  C12  C10     0.00   0.0  0
 DC0  CONST_03  C14  C12  C10  C11     0.00   0.0  0
 DC0  CONST_04  C14  C15  C13  C11     0.00   0.0  0
 DC0  CONST_05  C13  C11  C10  C12     0.00   0.0  0
 DC0  CONST_06  C13  C15  C14  C12     0.00   0.0  0
 DC0  CONST_07  C13  C11  C10  C9    180.00   0.0  0
 DC0  CONST_08  C14  C12  C10  C9    180.00   0.0  0
 DC0  CONST_09  H20  C13  C11  C10   180.00   0.0  0
 DC0  CONST_10  H21  C14  C12  C10   180.00   0.0  0
 DC0  CONST_11  H19  C12  C10  C11   180.00   0.0  0
 DC0  CONST_12  H22  C15  C13  C11   180.00   0.0  0
 DC0  CONST_13  H18  C11  C10  C12   180.00   0.0  0
 DC0  Var_01    C11  C10  C9   C7     99.86  30.0  2
 DC0  Var_02    C7   N2   C2   C1   -171.49  30.0  3
 DC0  Var_03    C5   C4   C3   C1    173.96  30.0  3
 DC0  Var_04    H8   C5   C4   C3     61.88  30.0  3
 DC0  Var_05    H11  C6   C4   C3     62.13  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
 DC0  chir_01  C1  N   C2  C3  positiv
 DC0  chir_02  C7  N2  C9  C   negativ

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
 DC0  plan-1  C9   0.020
 DC0  plan-1  C10  0.020
 DC0  plan-1  C11  0.020
 DC0  plan-1  C12  0.020
 DC0  plan-1  C13  0.020
 DC0  plan-1  C14  0.020
 DC0  plan-1  C15  0.020
 DC0  plan-1  H18  0.020
 DC0  plan-1  H19  0.020
 DC0  plan-1  H20  0.020
 DC0  plan-1  H21  0.020
 DC0  plan-1  H22  0.020
 DC0  plan-2  C7   0.020
 DC0  plan-2  C    0.020
 DC0  plan-2  O    0.020
 DC0  plan-2  OXT  0.020

