# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:21:14 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (1-{(3S)-3-hydroxy-4-oxo-4-[(2-phenylethyl)amino]butanoyl}hydrazino)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NN(CC(O)=O)C(=O)C[C@H](O)C(=O)NCCc1ccccc1
#
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
 MY4  MY4  '(1-{(3S)-3-hydroxy-4-oxo-4-[(2-phenylethyl)amino]butanoyl}hydrazino)acetic acid'  ligand  40  22  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY4
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
 MY4  C1    C  CR16   0  -0.270   7.5960   0.8255   0.4412
 MY4  C2    C  CR16   0  -0.240   7.2816  -0.2786  -0.3405
 MY4  N20   N  NH2    0  -0.654  -3.4175   2.0077   0.8178
 MY4  C3    C  CR16   0  -0.306   5.9881  -0.4497  -0.8161
 MY4  C4    C  CR6    0   0.124   4.9914   0.4774  -0.5215
 MY4  C5    C  CR16   0  -0.304   5.3180   1.5813   0.2632
 MY4  C6    C  CR16   0  -0.240   6.6097   1.7565   0.7414
 MY4  C9    C  CH1    0  -0.060  -0.9410  -1.3080  -0.3156
 MY4  C10   C  CH2    0  -0.626  -1.6162   0.0189   0.0285
 MY4  C11   C  C      0   0.586  -2.9455   0.1845  -0.6853
 MY4  C15   C  C      0   0.508   0.4669  -1.3000   0.2792
 MY4  C12   C  CH2    0  -0.434  -5.0566   1.3711  -0.7842
 MY4  C13   C  C      0   0.404  -6.0713   0.5658   0.0567
 MY4  C14   C  CH2    0  -0.231   2.7595  -0.4812   0.0384
 MY4  N2    N  NT     0  -0.333  -3.7001   1.2426  -0.3105
 MY4  N3    N  NH1    0  -0.639   1.3993  -0.6603  -0.4293
 MY4  O4    O  O      0  -0.497   0.6828  -1.8265   1.3638
 MY4  O6    O  O      0  -0.501  -3.2763  -0.5535  -1.6024
 MY4  O7    O  OC    -1  -0.622  -7.2626   0.7052  -0.2825
 MY4  O8    O  O      0  -0.598  -5.6199  -0.1355   0.9783
 MY4  O14   O  OH1    0  -0.658  -1.6574  -2.4038   0.1736
 MY4  C16   C  CH2    0  -0.564   3.5831   0.2687  -1.0032
 MY4  H1    H  HCR6   0   0.255   8.6040   0.9610   0.8116
 MY4  H2    H  HCR6   0   0.254   8.0453  -1.0061  -0.5844
 MY4  H201  H  HNH2   0   0.363  -3.4601   1.4351   1.6522
 MY4  H202  H  HNH2   0   0.373  -2.4983   2.4210   0.7450
 MY4  H3    H  HCR6   0   0.248   5.7505  -1.3114  -1.4293
 MY4  H5    H  HCR6   0   0.249   4.5542   2.3136   0.4995
 MY4  H6    H  HCR6   0   0.254   6.8470   2.6226   1.3461
 MY4  H9    H  HCH1   0   0.256  -0.8756  -1.4105  -1.4020
 MY4  H101  H  HCH2   0   0.284  -0.9687   0.8566  -0.2527
 MY4  H102  H  HCH2   0   0.271  -1.7376   0.0866   1.1129
 MY4  H121  H  HCH2   0   0.247  -5.3194   2.4300  -0.7602
 MY4  H122  H  HCH2   0   0.248  -5.1185   1.0566  -1.8266
 MY4  H141  H  HCH2   0   0.244   2.7585   0.0760   0.9789
 MY4  H142  H  HCH2   0   0.245   3.2170  -1.4528   0.2418
 MY4  HA    H  HNH1   0   0.408   1.1530  -0.2864  -1.3324
 MY4  H14   H  HOH1   0   0.441  -1.3735  -2.5481   1.0859
 MY4  H161  H  HCH2   0   0.260   3.5883  -0.2979  -1.9379
 MY4  H162  H  HCH2   0   0.260   3.1122   1.2327  -1.2132

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
 MY4  C1   C2    aromatic  1.389  0.020  1.389
 MY4  C1   C6    aromatic  1.389  0.020  1.389
 MY4  C1   H1    single    0.930  0.020  1.080
 MY4  C2   C3    aromatic  1.389  0.020  1.389
 MY4  C2   H2    single    0.930  0.020  1.080
 MY4  N20  N2    single    1.392  0.020  1.392
 MY4  N20  H201  single    0.890  0.020  1.040
 MY4  N20  H202  single    0.890  0.020  1.040
 MY4  C3   C4    aromatic  1.393  0.020  1.393
 MY4  C3   H3    single    0.930  0.020  1.080
 MY4  C4   C5    aromatic  1.393  0.020  1.393
 MY4  C4   C16   single    1.503  0.020  1.503
 MY4  C5   C6    aromatic  1.388  0.020  1.388
 MY4  C5   H5    single    0.930  0.020  1.080
 MY4  C6   H6    single    0.930  0.020  1.080
 MY4  C9   C10   single    1.528  0.020  1.528
 MY4  C9   C15   single    1.528  0.020  1.528
 MY4  C9   O14   single    1.398  0.020  1.398
 MY4  C9   H9    single    0.970  0.020  1.090
 MY4  C10  C11   single    1.518  0.020  1.518
 MY4  C10  H101  single    0.970  0.020  1.090
 MY4  C10  H102  single    0.970  0.020  1.090
 MY4  C11  N2    single    1.353  0.020  1.353
 MY4  C11  O6    double    1.223  0.020  1.223
 MY4  C15  N3    single    1.334  0.020  1.334
 MY4  C15  O4    double    1.225  0.020  1.225
 MY4  C12  C13   single    1.544  0.020  1.544
 MY4  C12  N2    single    1.443  0.020  1.443
 MY4  C12  H121  single    0.970  0.020  1.090
 MY4  C12  H122  single    0.970  0.020  1.090
 MY4  C13  O7    deloc     1.246  0.020  1.246
 MY4  C13  O8    deloc     1.243  0.020  1.243
 MY4  C14  N3    single    1.449  0.020  1.449
 MY4  C14  C16   single    1.525  0.020  1.525
 MY4  C14  H141  single    0.970  0.020  1.090
 MY4  C14  H142  single    0.970  0.020  1.090
 MY4  N3   HA    single    0.860  0.020  1.020
 MY4  O14  H14   single    0.850  0.020  0.980
 MY4  C16  H161  single    0.970  0.020  1.090
 MY4  C16  H162  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
 MY4  H1    C1   C6    120.22  3.000
 MY4  H1    C1   C2    120.20  3.000
 MY4  C6    C1   C2    119.59  3.000
 MY4  H2    C2   C3    119.81  3.000
 MY4  H2    C2   C1    120.09  3.000
 MY4  C3    C2   C1    120.10  3.000
 MY4  H202  N20  H201  109.19  3.000
 MY4  H202  N20  N2    110.55  3.000
 MY4  H201  N20  N2    110.39  3.000
 MY4  H3    C3   C4    119.47  3.000
 MY4  H3    C3   C2    119.73  3.000
 MY4  C4    C3   C2    120.80  3.000
 MY4  C16   C4   C5    120.67  3.000
 MY4  C16   C4   C3    120.69  3.000
 MY4  C5    C4   C3    118.61  3.000
 MY4  H5    C5   C6    119.68  3.000
 MY4  H5    C5   C4    119.52  3.000
 MY4  C6    C5   C4    120.80  3.000
 MY4  H6    C6   C5    119.81  3.000
 MY4  H6    C6   C1    120.09  3.000
 MY4  C5    C6   C1    120.10  3.000
 MY4  H9    C9   O14   107.76  3.000
 MY4  H9    C9   C15   109.40  3.000
 MY4  O14   C9   C15   109.88  3.000
 MY4  H9    C9   C10   109.37  3.000
 MY4  O14   C9   C10   112.05  3.000
 MY4  C15   C9   C10   108.35  3.000
 MY4  H102  C10  H101  105.83  3.000
 MY4  H102  C10  C11   111.25  3.000
 MY4  H101  C10  C11   108.27  3.000
 MY4  H102  C10  C9    109.04  3.000
 MY4  H101  C10  C9    110.18  3.000
 MY4  C11   C10  C9    112.07  3.000
 MY4  O6    C11  N2    121.94  3.000
 MY4  O6    C11  C10   121.59  3.000
 MY4  N2    C11  C10   116.34  3.000
 MY4  O4    C15  N3    123.58  3.000
 MY4  O4    C15  C9    120.32  3.000
 MY4  N3    C15  C9    116.07  3.000
 MY4  H122  C12  H121  106.69  3.000
 MY4  H122  C12  N2    109.97  3.000
 MY4  H121  C12  N2    107.79  3.000
 MY4  H122  C12  C13   109.44  3.000
 MY4  H121  C12  C13   109.62  3.000
 MY4  N2    C12  C13   113.11  3.000
 MY4  O8    C13  O7    127.74  3.000
 MY4  O8    C13  C12   117.34  3.000
 MY4  O7    C13  C12   114.92  3.000
 MY4  H142  C14  H141  107.06  3.000
 MY4  H142  C14  C16   109.76  3.000
 MY4  H141  C14  C16   109.72  3.000
 MY4  H142  C14  N3    110.06  3.000
 MY4  H141  C14  N3    109.86  3.000
 MY4  C16   C14  N3    110.31  3.000
 MY4  C12   N2   C11   120.22  3.000
 MY4  C12   N2   N20   114.08  3.000
 MY4  C11   N2   N20   122.77  3.000
 MY4  HA    N3   C14   118.21  3.000
 MY4  HA    N3   C15   118.87  3.000
 MY4  C14   N3   C15   122.93  3.000
 MY4  H14   O14  C9    107.28  3.000
 MY4  H162  C16  H161  107.15  3.000
 MY4  H162  C16  C14   109.41  3.000
 MY4  H161  C16  C14   109.37  3.000
 MY4  H162  C16  C4    110.04  3.000
 MY4  H161  C16  C4    109.97  3.000
 MY4  C14   C16  C4    110.82  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
 MY4  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 MY4  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 MY4  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 MY4  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 MY4  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 MY4  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 MY4  CONST_07  C16   C4   C3   C2   180.00   0.0  0
 MY4  CONST_08  C16   C4   C5   C6   180.00   0.0  0
 MY4  CONST_09  H3    C3   C2   C1   180.00   0.0  0
 MY4  CONST_10  H5    C5   C6   C1   180.00   0.0  0
 MY4  CONST_11  H6    C6   C1   C2   180.00   0.0  0
 MY4  CONST_12  H1    C1   C2   C3   180.00   0.0  0
 MY4  CONST_13  H2    C2   C3   C4   180.00   0.0  0
 MY4  CONST_14  C10   C11  N2   N20    0.00   0.0  0
 MY4  CONST_15  O6    C11  N2   N20  180.00   0.0  0
 MY4  CONST_16  C14   N3   C15  C9   180.00   0.0  0
 MY4  CONST_17  C12   N2   C11  C10  180.00   0.0  0
 MY4  CONST_18  O6    C11  N2   C12    0.00   0.0  0
 MY4  CONST_19  O4    C15  N3   C14    0.00   0.0  0
 MY4  CONST_20  HA    N3   C15  C9     0.00   0.0  0
 MY4  Var_01    C14   C16  C4   C3    91.58  30.0  2
 MY4  Var_02    N3    C14  C16  C4   179.22  30.0  2
 MY4  Var_03    C13   C12  N2   N20  -77.51  30.0  2
 MY4  Var_04    N2    C11  C10  C9   171.55  30.0  3
 MY4  Var_05    C16   C14  N3   C15  179.18  30.0  2
 MY4  Var_06    O7    C13  C12  N2   176.61  30.0  3
 MY4  Var_07    H201  N20  N2   C11  -61.25  30.0  2

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
 MY4  chir_01  C9  C10  C15  O14  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
 MY4  plan-1  C1   0.020
 MY4  plan-1  C2   0.020
 MY4  plan-1  C3   0.020
 MY4  plan-1  C4   0.020
 MY4  plan-1  C5   0.020
 MY4  plan-1  C6   0.020
 MY4  plan-1  C16  0.020
 MY4  plan-1  H1   0.020
 MY4  plan-1  H2   0.020
 MY4  plan-1  H3   0.020
 MY4  plan-1  H5   0.020
 MY4  plan-1  H6   0.020
 MY4  plan-2  N20  0.020
 MY4  plan-2  C10  0.020
 MY4  plan-2  C11  0.020
 MY4  plan-2  C12  0.020
 MY4  plan-2  N2   0.020
 MY4  plan-2  O6   0.020
 MY4  plan-3  C9   0.020
 MY4  plan-3  C15  0.020
 MY4  plan-3  C14  0.020
 MY4  plan-3  N3   0.020
 MY4  plan-3  O4   0.020
 MY4  plan-3  HA   0.020
 MY4  plan-4  C12  0.020
 MY4  plan-4  C13  0.020
 MY4  plan-4  O7   0.020
 MY4  plan-4  O8   0.020

