# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 23:46:15 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[(2S)-2-amino-3-phenylpropyl]-L-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC[C@@H](N)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
 13E  13E  N-[(2S)-2-amino-3-phenylpropyl]-L-methionine  L-peptide  40  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13E
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
 13E  N    N  NH2    0  -0.776   1.3010   1.3506   0.1326
 13E  C1   C  CH1    0  -0.117   1.4375  -0.0947   0.1581
 13E  C2   C  CH2    0  -0.515   2.6683  -0.6052   0.9367
 13E  C3   C  CR6    0   0.128   3.9572  -0.0556   0.3987
 13E  C4   C  CR16   0  -0.321   4.5539   1.0715   0.9614
 13E  C5   C  CR16   0  -0.304   4.5583  -0.6305  -0.7212
 13E  C6   C  CR16   0  -0.242   5.7184   1.6079   0.4250
 13E  C7   C  CR16   0  -0.240   5.7217  -0.0997  -1.2603
 13E  C8   C  CR16   0  -0.273   6.3059   1.0248  -0.6892
 13E  C9   C  CH2    0  -0.240   0.1842  -0.7458   0.7324
 13E  N2   N  NH1    0  -0.571  -1.0041  -0.4485  -0.0356
 13E  C10  C  CH1    0  -0.191  -2.2058  -1.0378   0.5203
 13E  C11  C  CH2    0  -0.432  -3.4435  -0.3982  -0.1203
 13E  C12  C  CH2    0  -0.535  -3.4981   1.1032   0.1112
 13E  SD   S  S2     0  -0.058  -4.9401   1.8111  -0.7358
 13E  C13  C  CH3    0  -0.762  -4.7224   3.5553  -0.3208
 13E  C    C  C      0   0.395  -2.3138  -2.5771   0.3685
 13E  O    O  O      0  -0.606  -1.6600  -3.1022  -0.5545
 13E  O1   O  OC    -1  -0.619  -3.0845  -3.1581   1.1597
 13E  H1   H  HNH2   0   0.330   1.1227   1.6914   1.0710
 13E  H2   H  HNH2   0   0.343   2.1769   1.7735  -0.1517
 13E  H4   H  HCH1   0   0.219   1.5522  -0.4311  -0.8806
 13E  H5   H  HCH2   0   0.236   2.5562  -0.3338   1.9912
 13E  H6   H  HCH2   0   0.237   2.6856  -1.6977   0.8905
 13E  H7   H  HCR6   0   0.248   4.1069   1.5315   1.8354
 13E  H8   H  HCR6   0   0.245   4.1110  -1.5079  -1.1752
 13E  H9   H  HCR6   0   0.252   6.1670   2.4820   0.8802
 13E  H10  H  HCR6   0   0.252   6.1754  -0.5659  -2.1258
 13E  H11  H  HCR6   0   0.252   7.2136   1.4401  -1.1080
 13E  H12  H  HCH2   0   0.190   0.3750  -1.8261   0.8252
 13E  H13  H  HCH2   0   0.205   0.0370  -0.3750   1.7545
 13E  H14  H  HNH1   0   0.319  -0.8799  -0.8309  -0.9674
 13E  H16  H  HCH1   0   0.206  -2.2276  -0.7995   1.5910
 13E  H17  H  HCH2   0   0.221  -3.4403  -0.6062  -1.1961
 13E  H18  H  HCH2   0   0.232  -4.3397  -0.8702   0.2888
 13E  H19  H  HCH2   0   0.247  -3.5727   1.3198   1.1800
 13E  H20  H  HCH2   0   0.261  -2.5878   1.5722  -0.2629
 13E  H21  H  HCH3   0   0.270  -5.5355   4.1125  -0.7827
 13E  H22  H  HCH3   0   0.258  -4.7626   3.7114   0.7565
 13E  H23  H  HCH3   0   0.258  -3.7768   3.9365  -0.7045

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
 13E  C11  C12  single    1.520  0.020  1.520
 13E  C11  C10  single    1.533  0.020  1.533
 13E  C12  SD   single    1.816  0.020  1.816
 13E  SD   C13  single    1.806  0.020  1.806
 13E  C10  C    single    1.550  0.020  1.550
 13E  C10  N2   single    1.449  0.020  1.449
 13E  C    O    deloc     1.231  0.020  1.231
 13E  N2   C9   single    1.446  0.020  1.446
 13E  C9   C1   single    1.525  0.020  1.525
 13E  C1   C2   single    1.543  0.020  1.543
 13E  C1   N    single    1.452  0.020  1.452
 13E  C2   C3   single    1.501  0.020  1.501
 13E  C3   C4   aromatic  1.394  0.020  1.394
 13E  C3   C5   aromatic  1.395  0.020  1.395
 13E  C4   C6   aromatic  1.390  0.020  1.390
 13E  C5   C7   aromatic  1.388  0.020  1.388
 13E  C6   C8   aromatic  1.388  0.020  1.388
 13E  C7   C8   aromatic  1.390  0.020  1.390
 13E  C    O1   deloc     1.248  0.020  1.248
 13E  N    H1   single    0.890  0.020  1.040
 13E  N    H2   single    0.890  0.020  1.040
 13E  C1   H4   single    0.970  0.020  1.090
 13E  C2   H5   single    0.970  0.020  1.090
 13E  C2   H6   single    0.970  0.020  1.090
 13E  C4   H7   single    0.930  0.020  1.080
 13E  C5   H8   single    0.930  0.020  1.080
 13E  C6   H9   single    0.930  0.020  1.080
 13E  C7   H10  single    0.930  0.020  1.080
 13E  C8   H11  single    0.930  0.020  1.080
 13E  C9   H12  single    0.970  0.020  1.090
 13E  C9   H13  single    0.970  0.020  1.090
 13E  N2   H14  single    0.890  0.020  1.040
 13E  C10  H16  single    0.970  0.020  1.090
 13E  C11  H17  single    0.970  0.020  1.090
 13E  C11  H18  single    0.970  0.020  1.090
 13E  C12  H19  single    0.970  0.020  1.090
 13E  C12  H20  single    0.970  0.020  1.090
 13E  C13  H21  single    0.970  0.020  1.090
 13E  C13  H22  single    0.970  0.020  1.090
 13E  C13  H23  single    0.970  0.020  1.090

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
 13E  H2   N    H1   105.74  3.000
 13E  H2   N    C1   109.82  3.000
 13E  H1   N    C1   109.56  3.000
 13E  H4   C1   C9   108.14  3.000
 13E  H4   C1   C2   107.02  3.000
 13E  C9   C1   C2   108.93  3.000
 13E  H4   C1   N    107.35  3.000
 13E  C2   C1   N    114.40  3.000
 13E  C9   C1   N    110.76  3.000
 13E  H6   C2   H5   106.86  3.000
 13E  H6   C2   C3   109.70  3.000
 13E  H5   C2   C3   110.03  3.000
 13E  H6   C2   C1   108.76  3.000
 13E  H5   C2   C1   108.80  3.000
 13E  C3   C2   C1   112.51  3.000
 13E  C5   C3   C4   118.22  3.000
 13E  C5   C3   C2   120.46  3.000
 13E  C4   C3   C2   121.26  3.000
 13E  H7   C4   C6   119.53  3.000
 13E  H7   C4   C3   119.47  3.000
 13E  C6   C4   C3   121.00  3.000
 13E  H8   C5   C7   119.52  3.000
 13E  H8   C5   C3   119.45  3.000
 13E  C7   C5   C3   121.03  3.000
 13E  H9   C6   C8   120.08  3.000
 13E  H9   C6   C4   119.76  3.000
 13E  C8   C6   C4   120.15  3.000
 13E  H10  C7   C8   120.05  3.000
 13E  H10  C7   C5   119.81  3.000
 13E  C8   C7   C5   120.15  3.000
 13E  H11  C8   C7   120.25  3.000
 13E  H11  C8   C6   120.29  3.000
 13E  C7   C8   C6   119.46  3.000
 13E  H13  C9   H12  106.04  3.000
 13E  H13  C9   N2   108.37  3.000
 13E  H12  C9   N2   112.89  3.000
 13E  H13  C9   C1   108.47  3.000
 13E  H12  C9   C1   107.96  3.000
 13E  N2   C9   C1   112.82  3.000
 13E  H14  N2   C10  107.49  3.000
 13E  H14  N2   C9   108.04  3.000
 13E  C10  N2   C9   113.21  3.000
 13E  H16  C10  C    108.05  3.000
 13E  H16  C10  C11  107.52  3.000
 13E  C    C10  C11  108.48  3.000
 13E  H16  C10  N2   107.61  3.000
 13E  C    C10  N2   115.08  3.000
 13E  C11  C10  N2   109.84  3.000
 13E  H18  C11  H17  106.74  3.000
 13E  H18  C11  C12  109.89  3.000
 13E  H17  C11  C12  109.70  3.000
 13E  H18  C11  C10  109.00  3.000
 13E  H17  C11  C10  109.19  3.000
 13E  C12  C11  C10  112.17  3.000
 13E  H20  C12  H19  107.90  3.000
 13E  H20  C12  SD   109.59  3.000
 13E  H19  C12  SD   108.94  3.000
 13E  H20  C12  C11  110.04  3.000
 13E  H19  C12  C11  110.31  3.000
 13E  SD   C12  C11  110.03  3.000
 13E  C13  SD   C12   99.99  3.000
 13E  H23  C13  H22  109.29  3.000
 13E  H23  C13  H21  108.65  3.000
 13E  H22  C13  H21  108.58  3.000
 13E  H23  C13  SD   111.20  3.000
 13E  H22  C13  SD   111.17  3.000
 13E  H21  C13  SD   107.86  3.000
 13E  O1   C    O    126.65  3.000
 13E  O1   C    C10  116.30  3.000
 13E  O    C    C10  117.00  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
 13E  CONST_01  C8   C6   C4   C3      0.00   0.0  0
 13E  CONST_02  C8   C7   C5   C3      0.00   0.0  0
 13E  CONST_03  C7   C5   C3   C4      0.00   0.0  0
 13E  CONST_04  C7   C8   C6   C4      0.00   0.0  0
 13E  CONST_05  C6   C4   C3   C5      0.00   0.0  0
 13E  CONST_06  C6   C8   C7   C5      0.00   0.0  0
 13E  CONST_07  C6   C4   C3   C2    180.00   0.0  0
 13E  CONST_08  C7   C5   C3   C2    180.00   0.0  0
 13E  CONST_09  H9   C6   C4   C3    180.00   0.0  0
 13E  CONST_10  H10  C7   C5   C3    180.00   0.0  0
 13E  CONST_11  H8   C5   C3   C4    180.00   0.0  0
 13E  CONST_12  H11  C8   C6   C4    180.00   0.0  0
 13E  CONST_13  H7   C4   C3   C5    180.00   0.0  0
 13E  Var_01    C4   C3   C2   C1     95.73  30.0  2
 13E  Var_02    C10  N2   C9   C1   -178.65  30.0  1
 13E  Var_03    SD   C12  C11  C10   177.33  30.0  3
 13E  Var_04    H21  C13  SD   C12   179.60  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
 13E  chir_01  C1   C9  C2   N  positiv
 13E  chir_02  C10  N2  C11  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
 13E  plan-1  C2   0.020
 13E  plan-1  C3   0.020
 13E  plan-1  C4   0.020
 13E  plan-1  C5   0.020
 13E  plan-1  C6   0.020
 13E  plan-1  C7   0.020
 13E  plan-1  C8   0.020
 13E  plan-1  H7   0.020
 13E  plan-1  H8   0.020
 13E  plan-1  H9   0.020
 13E  plan-1  H10  0.020
 13E  plan-1  H11  0.020
 13E  plan-2  C10  0.020
 13E  plan-2  C    0.020
 13E  plan-2  O    0.020
 13E  plan-2  O1   0.020

