# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:19:41 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: {1-[(3S)-4-(benzylamino)-3-hydroxy-4-oxobutanoyl]hydrazinyl}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)NCc1ccccc1
#
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
 MY3  MY3  '{1-[(3S)-4-(benzylamino)-3-hydroxy-4-oxobutanoyl]hydrazinyl}acetic acid'  ligand  38  21  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY3
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
 MY3  C1    C  CR6   0  -0.134  -4.0468   0.2485   0.0098
 MY3  C2    C  CR16  0  -0.151  -3.5187  -0.7653   0.8072
 MY3  N20   N  NH2   0  -0.618   1.9729  -2.0095   1.1083
 MY3  C3    C  CR16  0  -0.267  -4.0669  -2.0380   0.7853
 MY3  C4    C  CR16  0  -0.222  -5.1534  -2.3163  -0.0360
 MY3  C5    C  CR16  0  -0.213  -5.6853  -1.3138  -0.8319
 MY3  C6    C  CR16  0  -0.223  -5.1311  -0.0396  -0.8094
 MY3  C7    C  CH2   0  -0.309  -3.4410   1.6283   0.0263
 MY3  C9    C  CH1   0  -0.088   0.3692   1.6674  -0.0971
 MY3  C10   C  CH2   0  -0.578   0.6646   0.1827   0.1167
 MY3  C11   C  C     0   0.560   2.0270  -0.1981  -0.4133
 MY3  C15   C  C     0   0.514  -1.0323   1.9338   0.4497
 MY3  C12   C  CH2   0  -0.429   3.8998  -1.7062  -0.3828
 MY3  C13   C  C     0   0.530   5.0047  -0.7973   0.1007
 MY3  N2    N  NT    0  -0.393   2.6140  -1.2939   0.1187
 MY3  N3    N  NH1   0  -0.544  -2.0459   1.5962  -0.3509
 MY3  O4    O  O     0  -0.613  -1.1561   2.4015   1.5739
 MY3  O6    O  O     0  -0.481   2.5765   0.4226  -1.3140
 MY3  O7    O  O     0  -0.366   4.8935   0.0274   0.9698
 MY3  O8    O  OH1   0  -0.625   6.1386  -1.0425  -0.5440
 MY3  O57   O  OH1   0  -0.672   1.2918   2.4697   0.5788
 MY3  H2    H  HCR6  0   0.252  -2.6734  -0.5652   1.4557
 MY3  H201  H  HNH2  0   0.364   1.7366  -2.9355   0.7805
 MY3  H202  H  HNH2  0   0.374   2.5566  -2.0893   1.9300
 MY3  H3    H  HCR6  0   0.188  -3.6475  -2.8142   1.4114
 MY3  H4    H  HCR6  0   0.260  -5.5799  -3.3101  -0.0540
 MY3  H5    H  HCR6  0   0.225  -6.5297  -1.5201  -1.4761
 MY3  H6    H  HCR6  0   0.263  -5.5507   0.7358  -1.4390
 MY3  H7C1  H  HCH2  0   0.295  -3.9818   2.2875  -0.6543
 MY3  H7C2  H  HCH2  0   0.290  -3.5105   2.0688   1.0199
 MY3  H9    H  HCH1  0   0.263   0.4144   1.9108  -1.1633
 MY3  H101  H  HCH2  0   0.268   0.5731  -0.0757   1.1715
 MY3  H102  H  HCH2  0   0.294  -0.0715  -0.4350  -0.4085
 MY3  H121  H  HCH2  0   0.337   3.9171  -1.7420  -1.4727
 MY3  H122  H  HCH2  0   0.310   4.1096  -2.7229  -0.0468
 MY3  HA    H  HNH1  0   0.439  -1.8416   1.2974  -1.2903
 MY3  H8    H  HOH1  0   0.469   6.8363  -0.4741  -0.2004
 MY3  H57   H  HOH1  0   0.432   0.8947   2.6696   1.4376

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
 MY3  C1   C2    aromatic  1.394  0.020  1.394
 MY3  C1   C6    aromatic  1.389  0.020  1.389
 MY3  C1   C7    single    1.507  0.020  1.507
 MY3  C2   C3    aromatic  1.386  0.020  1.386
 MY3  C2   H2    single    0.930  0.020  1.080
 MY3  N20  N2    single    1.379  0.020  1.379
 MY3  N20  H201  single    0.890  0.020  1.040
 MY3  N20  H202  single    0.890  0.020  1.040
 MY3  C3   C4    aromatic  1.390  0.020  1.390
 MY3  C3   H3    single    0.930  0.020  1.080
 MY3  C4   C5    aromatic  1.386  0.020  1.386
 MY3  C4   H4    single    0.930  0.020  1.080
 MY3  C5   C6    aromatic  1.390  0.020  1.390
 MY3  C5   H5    single    0.930  0.020  1.080
 MY3  C6   H6    single    0.930  0.020  1.080
 MY3  C7   N3    single    1.446  0.020  1.446
 MY3  C7   H7C1  single    0.970  0.020  1.090
 MY3  C7   H7C2  single    0.970  0.020  1.090
 MY3  C9   C10   single    1.529  0.020  1.529
 MY3  C9   C15   single    1.528  0.020  1.528
 MY3  C9   O57   single    1.397  0.020  1.397
 MY3  C9   H9    single    0.970  0.020  1.090
 MY3  C10  C11   single    1.511  0.020  1.511
 MY3  C10  H101  single    0.970  0.020  1.090
 MY3  C10  H102  single    0.970  0.020  1.090
 MY3  C11  N2    single    1.352  0.020  1.352
 MY3  C11  O6    double    1.224  0.020  1.224
 MY3  C15  N3    single    1.335  0.020  1.335
 MY3  C15  O4    double    1.224  0.020  1.224
 MY3  C12  C13   single    1.510  0.020  1.510
 MY3  C12  N2    single    1.440  0.020  1.440
 MY3  C12  H121  single    0.970  0.020  1.090
 MY3  C12  H122  single    0.970  0.020  1.090
 MY3  C13  O7    double    1.203  0.020  1.203
 MY3  C13  O8    single    1.327  0.020  1.327
 MY3  N3   HA    single    0.860  0.020  1.020
 MY3  O8   H8    single    0.850  0.020  0.980
 MY3  O57  H57   single    0.850  0.020  0.980

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
 MY3  C7    C1   C6    120.67  3.000
 MY3  C7    C1   C2    120.49  3.000
 MY3  C6    C1   C2    118.84  3.000
 MY3  H2    C2   C3    119.17  3.000
 MY3  H2    C2   C1    120.23  3.000
 MY3  C3    C2   C1    120.60  3.000
 MY3  H202  N20  H201  109.05  3.000
 MY3  H202  N20  N2    110.84  3.000
 MY3  H201  N20  N2    110.58  3.000
 MY3  H3    C3   C4    120.09  3.000
 MY3  H3    C3   C2    119.76  3.000
 MY3  C4    C3   C2    120.15  3.000
 MY3  H4    C4   C5    120.24  3.000
 MY3  H4    C4   C3    120.13  3.000
 MY3  C5    C4   C3    119.63  3.000
 MY3  H5    C5   C6    119.72  3.000
 MY3  H5    C5   C4    120.23  3.000
 MY3  C6    C5   C4    120.05  3.000
 MY3  H6    C6   C5    119.49  3.000
 MY3  H6    C6   C1    119.77  3.000
 MY3  C5    C6   C1    120.73  3.000
 MY3  H7C2  C7   H7C1  107.05  3.000
 MY3  H7C2  C7   N3    107.98  3.000
 MY3  H7C1  C7   N3    109.21  3.000
 MY3  H7C2  C7   C1    110.77  3.000
 MY3  H7C1  C7   C1    110.31  3.000
 MY3  N3    C7   C1    111.39  3.000
 MY3  H9    C9   O57   108.44  3.000
 MY3  H9    C9   C15   110.35  3.000
 MY3  O57   C9   C15   109.43  3.000
 MY3  H9    C9   C10   110.13  3.000
 MY3  O57   C9   C10   111.25  3.000
 MY3  C15   C9   C10   107.25  3.000
 MY3  H102  C10  H101  105.91  3.000
 MY3  H102  C10  C11   107.20  3.000
 MY3  H101  C10  C11   110.83  3.000
 MY3  H102  C10  C9    110.54  3.000
 MY3  H101  C10  C9    110.45  3.000
 MY3  C11   C10  C9    111.72  3.000
 MY3  O6    C11  N2    120.37  3.000
 MY3  O6    C11  C10   122.36  3.000
 MY3  N2    C11  C10   117.24  3.000
 MY3  O4    C15  N3    124.80  3.000
 MY3  O4    C15  C9    119.22  3.000
 MY3  N3    C15  C9    115.96  3.000
 MY3  H122  C12  H121  105.90  3.000
 MY3  H122  C12  N2    109.34  3.000
 MY3  H121  C12  N2    111.81  3.000
 MY3  H122  C12  C13   108.75  3.000
 MY3  H121  C12  C13   109.15  3.000
 MY3  N2    C12  C13   111.68  3.000
 MY3  O8    C13  O7    123.82  3.000
 MY3  O8    C13  C12   111.00  3.000
 MY3  O7    C13  C12   125.17  3.000
 MY3  C12   N2   C11   118.85  3.000
 MY3  C12   N2   N20   121.08  3.000
 MY3  C11   N2   N20   120.07  3.000
 MY3  HA    N3   C15   118.72  3.000
 MY3  HA    N3   C7    116.48  3.000
 MY3  C15   N3   C7    124.79  3.000
 MY3  H8    O8   C13   109.66  3.000
 MY3  H57   O57  C9    106.09  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
 MY3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MY3  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MY3  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MY3  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MY3  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MY3  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 MY3  CONST_07  C7    C1   C2   C3    180.00   0.0  0
 MY3  CONST_08  C7    C1   C6   C5    180.00   0.0  0
 MY3  CONST_09  H3    C3   C2   C1    180.00   0.0  0
 MY3  CONST_10  H5    C5   C6   C1    180.00   0.0  0
 MY3  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 MY3  CONST_12  H4    C4   C3   C2    180.00   0.0  0
 MY3  CONST_13  H2    C2   C3   C4    180.00   0.0  0
 MY3  CONST_14  C10   C11  N2   N20     0.00   0.0  0
 MY3  CONST_15  O6    C11  N2   N20   180.00   0.0  0
 MY3  CONST_16  C9    C15  N3   C7    180.00   0.0  0
 MY3  CONST_17  O4    C15  N3   C7      0.00   0.0  0
 MY3  CONST_18  C12   N2   C11  C10   180.00   0.0  0
 MY3  CONST_19  O6    C11  N2   C12     0.00   0.0  0
 MY3  CONST_20  HA    N3   C15  C9      0.00   0.0  0
 MY3  CONST_21  H8    O8   C13  C12   180.00   0.0  0
 MY3  Var_01    N3    C7   C1   C2     58.63  30.0  2
 MY3  Var_02    C15   N3   C7   C1   -116.00  30.0  3
 MY3  Var_03    C13   C12  N2   N20  -106.94  30.0  2
 MY3  Var_04    N2    C11  C10  C9    156.34  30.0  3
 MY3  Var_05    O7    C13  C12  N2     12.00  30.0  3
 MY3  Var_06    H201  N20  N2   C11   114.61  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
 MY3  chir_01  C9  C10  C15  O57  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
 MY3  plan-1  C1   0.020
 MY3  plan-1  C2   0.020
 MY3  plan-1  C3   0.020
 MY3  plan-1  C4   0.020
 MY3  plan-1  C5   0.020
 MY3  plan-1  C6   0.020
 MY3  plan-1  C7   0.020
 MY3  plan-1  H2   0.020
 MY3  plan-1  H3   0.020
 MY3  plan-1  H4   0.020
 MY3  plan-1  H5   0.020
 MY3  plan-1  H6   0.020
 MY3  plan-2  N20  0.020
 MY3  plan-2  C10  0.020
 MY3  plan-2  C11  0.020
 MY3  plan-2  C12  0.020
 MY3  plan-2  N2   0.020
 MY3  plan-2  O6   0.020
 MY3  plan-3  C7   0.020
 MY3  plan-3  C9   0.020
 MY3  plan-3  C15  0.020
 MY3  plan-3  N3   0.020
 MY3  plan-3  O4   0.020
 MY3  plan-3  HA   0.020
 MY3  plan-4  C12  0.020
 MY3  plan-4  C13  0.020
 MY3  plan-4  O7   0.020
 MY3  plan-4  O8   0.020
 MY3  plan-4  H8   0.020

