# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 04:33:24 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3S)-3-amino-1-[4-(benzyloxy)phenyl]-4-(1H-imidazol-4-yl)butan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]cn1)C(=O)Cc2ccc(OCc3ccccc3)cc2
#
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
 0VD  0VD  (3S)-3-amino-1-[4-(benzyloxy)phenyl]-4-(1H-imidazol-4-yl)butan-2-one  ligand  46  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0VD
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
 0VD  C1   C  CR15  0  -0.137  -6.8407   0.4941  -1.6020
 0VD  N1   N  NR15  0  -0.563  -7.9853  -0.2359  -1.4526
 0VD  C2   C  CR15  0   0.081  -7.6940  -1.2884  -0.6665
 0VD  N2   N  N     0  -0.464  -6.4360  -1.2813  -0.3034
 0VD  C12  C  CR16  0  -0.371   1.8639   0.1196   1.4445
 0VD  C13  C  CR16  0  -0.293   0.5085   0.0038   1.7312
 0VD  C4   C  CH2   0  -0.539  -4.4556   0.1901  -0.6935
 0VD  C5   C  CH1   0  -0.197  -4.1265   0.5407   0.7696
 0VD  C6   C  C     0   0.397  -2.6130   0.6739   0.8839
 0VD  C8   C  CR6   0   0.143  -0.3900  -0.5245   0.8148
 0VD  C10  C  CR16  0  -0.333   1.4523  -0.8276  -0.7268
 0VD  C9   C  CR16  0  -0.285   0.1079  -0.9345  -0.4209
 0VD  C7   C  CH2   0  -0.692  -1.8520  -0.6129   1.1228
 0VD  C11  C  CR6   0   0.372   2.3446  -0.2971   0.2060
 0VD  C19  C  CR16  0  -0.241   7.8755   1.1957  -0.8870
 0VD  C18  C  CR16  0  -0.262   8.4394  -0.0487  -1.1284
 0VD  C17  C  CR16  0  -0.243   7.7585  -1.2005  -0.7498
 0VD  C20  C  CR16  0  -0.304   6.6315   1.2875  -0.2738
 0VD  C16  C  CR16  0  -0.285   6.5195  -1.1052  -0.1344
 0VD  C15  C  CR6   0   0.100   5.9454   0.1409   0.1095
 0VD  C14  C  CH2   0  -0.266   4.5985   0.2335   0.7610
 0VD  N3   N  NH2   0  -0.773  -4.8696   1.7067   1.1808
 0VD  C3   C  CR5   0   0.183  -5.8877  -0.1689  -0.8815
 0VD  O1   O  O     0  -0.387  -2.0614   1.7454   0.7963
 0VD  O2   O  O2    0  -0.470   3.6374  -0.2308  -0.1760
 0VD  H1   H  HCR5  0   0.280  -6.8017   1.3965  -2.1885
 0VD  H2   H  HNR5  0   0.418  -8.8807  -0.0328  -1.8669
 0VD  H3   H  HCR5  0   0.274  -8.4308  -2.0277  -0.3923
 0VD  H5   H  HCR6  0   0.279   2.5199   0.5375   2.1964
 0VD  H6   H  HCR6  0   0.252   0.1563   0.3302   2.7024
 0VD  H7   H  HCH2  0   0.255  -4.2016   1.0426  -1.3291
 0VD  H8   H  HCH2  0   0.252  -3.8246  -0.6402  -1.0242
 0VD  H9   H  HCH1  0   0.261  -4.4384  -0.3066   1.3896
 0VD  H10  H  HCR6  0   0.260   1.8214  -1.1593  -1.6893
 0VD  H11  H  HCR6  0   0.249  -0.5644  -1.3539  -1.1607
 0VD  H12  H  HCH2  0   0.305  -2.0178  -0.8586   2.1789
 0VD  H13  H  HCH2  0   0.284  -2.3289  -1.4264   0.5696
 0VD  H15  H  HCR6  0   0.258   9.4073  -0.1238  -1.6071
 0VD  H16  H  HCR6  0   0.258   8.1960  -2.1734  -0.9321
 0VD  H17  H  HCR6  0   0.255   6.1937   2.2614  -0.0901
 0VD  H18  H  HCR6  0   0.254   5.9984  -2.0075   0.1631
 0VD  H19  H  HCH2  0   0.240   4.5686  -0.3829   1.6667
 0VD  H20  H  HCH2  0   0.243   4.3853   1.2669   1.0537
 0VD  H21  H  HNH2  0   0.350  -4.6907   1.9073   2.1568
 0VD  H22  H  HNH2  0   0.341  -4.5535   2.5180   0.6630
 0VD  H14  H  HCR6  0   0.258   8.4006   2.0970  -1.1755

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
 0VD  C20  C19  aromatic  1.390  0.020  1.390
 0VD  C20  C15  aromatic  1.390  0.020  1.390
 0VD  C19  C18  aromatic  1.387  0.020  1.387
 0VD  O2   C14  single    1.420  0.020  1.420
 0VD  O2   C11  single    1.350  0.020  1.350
 0VD  C14  C15  single    1.499  0.020  1.499
 0VD  C15  C16  aromatic  1.394  0.020  1.394
 0VD  C18  C17  aromatic  1.391  0.020  1.391
 0VD  C10  C11  aromatic  1.396  0.020  1.396
 0VD  C10  C9   aromatic  1.383  0.020  1.383
 0VD  C11  C12  aromatic  1.392  0.020  1.392
 0VD  C1   N1   aromatic  1.366  0.020  1.366
 0VD  C1   C3   aromatic  1.366  0.020  1.366
 0VD  C16  C17  aromatic  1.387  0.020  1.387
 0VD  C9   C8   aromatic  1.394  0.020  1.394
 0VD  N1   C2   aromatic  1.345  0.020  1.345
 0VD  C12  C13  aromatic  1.390  0.020  1.390
 0VD  C3   C4   single    1.488  0.020  1.488
 0VD  C3   N2   aromatic  1.368  0.020  1.368
 0VD  C4   C5   single    1.540  0.020  1.540
 0VD  C2   N2   aromatic  1.309  0.020  1.309
 0VD  C8   C13  aromatic  1.388  0.020  1.388
 0VD  C8   C7   single    1.497  0.020  1.497
 0VD  C7   C6   single    1.514  0.020  1.514
 0VD  O1   C6   double    1.208  0.020  1.208
 0VD  C6   C5   single    1.524  0.020  1.524
 0VD  C5   N3   single    1.442  0.020  1.442
 0VD  C1   H1   single    0.930  0.020  1.080
 0VD  N1   H2   single    0.860  0.020  1.020
 0VD  C2   H3   single    0.930  0.020  1.080
 0VD  C12  H5   single    0.930  0.020  1.080
 0VD  C13  H6   single    0.930  0.020  1.080
 0VD  C4   H7   single    0.970  0.020  1.090
 0VD  C4   H8   single    0.970  0.020  1.090
 0VD  C5   H9   single    0.970  0.020  1.090
 0VD  C10  H10  single    0.930  0.020  1.080
 0VD  C9   H11  single    0.930  0.020  1.080
 0VD  C7   H12  single    0.970  0.020  1.090
 0VD  C7   H13  single    0.970  0.020  1.090
 0VD  C19  H14  single    0.930  0.020  1.080
 0VD  C18  H15  single    0.930  0.020  1.080
 0VD  C17  H16  single    0.930  0.020  1.080
 0VD  C20  H17  single    0.930  0.020  1.080
 0VD  C16  H18  single    0.930  0.020  1.080
 0VD  C14  H19  single    0.970  0.020  1.090
 0VD  C14  H20  single    0.970  0.020  1.090
 0VD  N3   H21  single    0.890  0.020  1.040
 0VD  N3   H22  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
 0VD  H1   C1   C3   131.95  3.000
 0VD  H1   C1   N1   122.54  3.000
 0VD  C3   C1   N1   105.51  3.000
 0VD  H2   N1   C2   126.19  3.000
 0VD  H2   N1   C1   126.31  3.000
 0VD  C2   N1   C1   107.50  3.000
 0VD  H3   C2   N2   126.10  3.000
 0VD  H3   C2   N1   122.45  3.000
 0VD  N2   C2   N1   111.45  3.000
 0VD  C3   N2   C2   105.80  3.000
 0VD  H5   C12  C11  121.63  3.000
 0VD  H5   C12  C13  118.69  3.000
 0VD  C11  C12  C13  119.68  3.000
 0VD  H6   C13  C8   119.75  3.000
 0VD  H6   C13  C12  118.47  3.000
 0VD  C8   C13  C12  121.78  3.000
 0VD  H8   C4   H7   106.38  3.000
 0VD  H8   C4   C3   109.50  3.000
 0VD  H7   C4   C3   109.76  3.000
 0VD  H8   C4   C5   109.68  3.000
 0VD  H7   C4   C5   108.97  3.000
 0VD  C3   C4   C5   112.36  3.000
 0VD  H9   C5   N3   108.50  3.000
 0VD  H9   C5   C6   107.94  3.000
 0VD  N3   C5   C6   114.81  3.000
 0VD  H9   C5   C4   107.50  3.000
 0VD  N3   C5   C4   110.17  3.000
 0VD  C6   C5   C4   107.66  3.000
 0VD  O1   C6   C7   122.39  3.000
 0VD  O1   C6   C5   121.71  3.000
 0VD  C7   C6   C5   115.90  3.000
 0VD  C7   C8   C9   120.93  3.000
 0VD  C7   C8   C13  121.26  3.000
 0VD  C9   C8   C13  117.78  3.000
 0VD  H10  C10  C11  119.51  3.000
 0VD  H10  C10  C9   120.28  3.000
 0VD  C11  C10  C9   120.21  3.000
 0VD  H11  C9   C10  118.81  3.000
 0VD  H11  C9   C8   119.82  3.000
 0VD  C10  C9   C8   121.37  3.000
 0VD  H13  C7   H12  104.75  3.000
 0VD  H13  C7   C8   111.46  3.000
 0VD  H12  C7   C8   111.04  3.000
 0VD  H13  C7   C6   109.47  3.000
 0VD  H12  C7   C6   105.45  3.000
 0VD  C8   C7   C6   114.10  3.000
 0VD  O2   C11  C10  116.22  3.000
 0VD  C10  C11  C12  119.18  3.000
 0VD  O2   C11  C12  124.60  3.000
 0VD  H14  C19  C20  119.80  3.000
 0VD  H14  C19  C18  120.22  3.000
 0VD  C20  C19  C18  119.98  3.000
 0VD  H15  C18  C17  120.06  3.000
 0VD  H15  C18  C19  120.17  3.000
 0VD  C17  C18  C19  119.77  3.000
 0VD  H16  C17  C16  119.85  3.000
 0VD  H16  C17  C18  120.05  3.000
 0VD  C16  C17  C18  120.10  3.000
 0VD  H17  C20  C15  119.68  3.000
 0VD  H17  C20  C19  119.72  3.000
 0VD  C15  C20  C19  120.60  3.000
 0VD  H18  C16  C15  119.89  3.000
 0VD  H18  C16  C17  119.63  3.000
 0VD  C15  C16  C17  120.48  3.000
 0VD  C14  C15  C16  120.10  3.000
 0VD  C16  C15  C20  119.07  3.000
 0VD  C14  C15  C20  120.82  3.000
 0VD  H20  C14  H19  107.73  3.000
 0VD  H20  C14  O2   110.68  3.000
 0VD  H19  C14  O2   110.06  3.000
 0VD  H20  C14  C15  110.45  3.000
 0VD  H19  C14  C15  110.42  3.000
 0VD  O2   C14  C15  107.52  3.000
 0VD  H22  N3   H21  106.20  3.000
 0VD  H22  N3   C5   109.93  3.000
 0VD  H21  N3   C5   110.12  3.000
 0VD  C4   C3   N2   121.89  3.000
 0VD  N2   C3   C1   109.75  3.000
 0VD  C4   C3   C1   128.37  3.000
 0VD  C14  O2   C11  118.52  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
 0VD  CONST_01  N2   C2   N1   C1     0.00   0.0  0
 0VD  CONST_02  C2   N2   C3   C1     0.00   0.0  0
 0VD  CONST_03  N2   C3   C1   N1     0.00   0.0  0
 0VD  CONST_04  C3   N2   C2   N1     0.00   0.0  0
 0VD  CONST_05  C3   C1   N1   C2     0.00   0.0  0
 0VD  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 0VD  CONST_07  C9   C8   C13  C12    0.00   0.0  0
 0VD  CONST_08  C10  C11  C12  C13    0.00   0.0  0
 0VD  CONST_09  C10  C9   C8   C13    0.00   0.0  0
 0VD  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 0VD  CONST_11  C11  C12  C13  C8     0.00   0.0  0
 0VD  CONST_12  C16  C15  C20  C19    0.00   0.0  0
 0VD  CONST_13  C16  C17  C18  C19    0.00   0.0  0
 0VD  CONST_14  C15  C20  C19  C18    0.00   0.0  0
 0VD  CONST_15  C15  C16  C17  C18    0.00   0.0  0
 0VD  CONST_16  C20  C19  C18  C17    0.00   0.0  0
 0VD  CONST_17  C20  C15  C16  C17    0.00   0.0  0
 0VD  CONST_18  C4   C3   C1   N1   180.00   0.0  0
 0VD  CONST_19  C4   C3   N2   C2   180.00   0.0  0
 0VD  CONST_20  C7   C8   C13  C12  180.00   0.0  0
 0VD  CONST_21  O2   C11  C12  C13  180.00   0.0  0
 0VD  CONST_22  C7   C8   C9   C10  180.00   0.0  0
 0VD  CONST_23  O2   C11  C10  C9   180.00   0.0  0
 0VD  CONST_24  C14  C15  C20  C19  180.00   0.0  0
 0VD  CONST_25  C14  C15  C16  C17  180.00   0.0  0
 0VD  CONST_26  H3   C2   N1   C1   180.00   0.0  0
 0VD  CONST_27  H1   C1   N1   C2   180.00   0.0  0
 0VD  CONST_28  H2   N1   C2   N2   180.00   0.0  0
 0VD  CONST_29  H10  C10  C11  C12  180.00   0.0  0
 0VD  CONST_30  H11  C9   C8   C13  180.00   0.0  0
 0VD  CONST_31  H5   C12  C13  C8   180.00   0.0  0
 0VD  CONST_32  H6   C13  C8   C9   180.00   0.0  0
 0VD  CONST_33  H16  C17  C18  C19  180.00   0.0  0
 0VD  CONST_34  H17  C20  C19  C18  180.00   0.0  0
 0VD  CONST_35  H18  C16  C17  C18  180.00   0.0  0
 0VD  CONST_36  H14  C19  C18  C17  180.00   0.0  0
 0VD  CONST_37  H15  C18  C19  C20  180.00   0.0  0
 0VD  Var_01    C5   C4   C3   C1   114.73  30.0  2
 0VD  Var_02    C6   C7   C8   C13   82.20  30.0  2
 0VD  Var_03    C15  C14  O2   C11  177.16  30.0  3
 0VD  Var_04    O2   C14  C15  C20  109.06  30.0  2
 0VD  Var_05    C8   C7   C6   C5   162.17  30.0  1

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
 0VD  chir_01  C5  C4  C6  N3  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
 0VD  plan-1  C1   0.020
 0VD  plan-1  N1   0.020
 0VD  plan-1  C2   0.020
 0VD  plan-1  N2   0.020
 0VD  plan-1  C4   0.020
 0VD  plan-1  C3   0.020
 0VD  plan-1  H1   0.020
 0VD  plan-1  H2   0.020
 0VD  plan-1  H3   0.020
 0VD  plan-2  C12  0.020
 0VD  plan-2  C13  0.020
 0VD  plan-2  C8   0.020
 0VD  plan-2  C10  0.020
 0VD  plan-2  C9   0.020
 0VD  plan-2  C7   0.020
 0VD  plan-2  C11  0.020
 0VD  plan-2  O2   0.020
 0VD  plan-2  H5   0.020
 0VD  plan-2  H6   0.020
 0VD  plan-2  H10  0.020
 0VD  plan-2  H11  0.020
 0VD  plan-3  C19  0.020
 0VD  plan-3  C18  0.020
 0VD  plan-3  C17  0.020
 0VD  plan-3  C20  0.020
 0VD  plan-3  C16  0.020
 0VD  plan-3  C15  0.020
 0VD  plan-3  C14  0.020
 0VD  plan-3  H15  0.020
 0VD  plan-3  H16  0.020
 0VD  plan-3  H17  0.020
 0VD  plan-3  H18  0.020
 0VD  plan-3  H14  0.020
 0VD  plan-4  C5   0.020
 0VD  plan-4  C6   0.020
 0VD  plan-4  C7   0.020
 0VD  plan-4  O1   0.020

