# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:53:44 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (1-{4-[benzyl(methyl)amino]-4-oxobutanoyl}hydrazino)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccccc1)C(=O)CCC(=O)N(N)CC(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
 MX3  MX3  '(1-{4-[benzyl(methyl)amino]-4-oxobutanoyl}hydrazino)acetic acid'  ligand  39  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MX3
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
 MX3  C1    C  CR6    0   0.133  -4.3304   0.2471   0.4105
 MX3  C2    C  CR16   0  -0.309  -5.4663   0.8876  -0.0717
 MX3  N20   N  NH2    0  -0.652   3.6153  -1.9346   0.7479
 MX3  C3    C  CR16   0  -0.242  -6.3866   0.2062  -0.8601
 MX3  C4    C  CR16   0  -0.268  -6.1764  -1.1281  -1.1758
 MX3  C5    C  CR16   0  -0.241  -5.0437  -1.7776  -0.6971
 MX3  C6    C  CR16   0  -0.296  -4.1289  -1.0949   0.0902
 MX3  C7    C  CH2    0  -0.414  -3.3214   0.9933   1.2477
 MX3  C9    C  CH2    0  -0.595   0.2448   0.6107  -0.0114
 MX3  C10   C  CH2    0  -0.594   1.3626  -0.3430   0.3677
 MX3  C11   C  C      0   0.579   2.5749  -0.1800  -0.5266
 MX3  C15   C  C      0   0.595  -0.9931   0.4088   0.8410
 MX3  C12   C  CH2    0  -0.435   4.8602  -0.8405  -0.9633
 MX3  C13   C  C      0   0.404   5.7256   0.1852  -0.1983
 MX3  C14   C  CH3    0  -0.530  -2.1048   2.0934  -0.5803
 MX3  N2    N  NT     0  -0.335   3.5774  -1.0727  -0.3458
 MX3  N3    N  NT     0  -0.450  -2.0607   1.1891   0.5514
 MX3  O4    O  O      0  -0.509  -1.0158  -0.4181   1.7448
 MX3  O6    O  O      0  -0.504   2.6338   0.6846  -1.3908
 MX3  O7    O  O      0  -0.600   5.2350   0.6963   0.8238
 MX3  O8    O  OC    -1  -0.622   6.8503   0.3968  -0.6915
 MX3  H2    H  HCR6   0   0.251  -5.6370   1.9298   0.1726
 MX3  H201  H  HNH2   0   0.360   3.5981  -1.4077   1.6133
 MX3  H202  H  HNH2   0   0.370   2.8178  -2.5554   0.7303
 MX3  H3    H  HCR6   0   0.255  -7.2653   0.7197  -1.2288
 MX3  H4    H  HCR6   0   0.256  -6.8901  -1.6615  -1.7902
 MX3  H5    H  HCR6   0   0.255  -4.8751  -2.8198  -0.9366
 MX3  H6    H  HCR6   0   0.251  -3.2535  -1.6109   0.4657
 MX3  H7C1  H  HCH2   0   0.276  -3.1284   0.4613   2.1767
 MX3  H7C2  H  HCH2   0   0.266  -3.7206   1.9742   1.5151
 MX3  H9C1  H  HCH2   0   0.274  -0.0230   0.4837  -1.0636
 MX3  H9C2  H  HCH2   0   0.277   0.5850   1.6452   0.0828
 MX3  H101  H  HCH2   0   0.270   1.6668  -0.1757   1.4049
 MX3  H102  H  HCH2   0   0.269   1.0083  -1.3760   0.3286
 MX3  H121  H  HCH2   0   0.248   5.3840  -1.7967  -1.0112
 MX3  H122  H  HCH2   0   0.245   4.7244  -0.5061  -1.9923
 MX3  H141  H  HCH3   0   0.264  -1.1416   2.5649  -0.7540
 MX3  H142  H  HCH3   0   0.243  -2.4196   1.5950  -1.5001
 MX3  H143  H  HCH3   0   0.253  -2.8185   2.8879  -0.3675

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
 MX3  C1   C2    aromatic  1.390  0.020  1.390
 MX3  C1   C6    aromatic  1.394  0.020  1.394
 MX3  C1   C7    single    1.509  0.020  1.509
 MX3  C2   C3    aromatic  1.390  0.020  1.390
 MX3  C2   H2    single    0.930  0.020  1.080
 MX3  N20  N2    single    1.393  0.020  1.393
 MX3  N20  H201  single    0.890  0.020  1.040
 MX3  N20  H202  single    0.890  0.020  1.040
 MX3  C3   C4    aromatic  1.387  0.020  1.387
 MX3  C3   H3    single    0.930  0.020  1.080
 MX3  C4   C5    aromatic  1.391  0.020  1.391
 MX3  C4   H4    single    0.930  0.020  1.080
 MX3  C5   C6    aromatic  1.387  0.020  1.387
 MX3  C5   H5    single    0.930  0.020  1.080
 MX3  C6   H6    single    0.930  0.020  1.080
 MX3  C7   N3    single    1.453  0.020  1.453
 MX3  C7   H7C1  single    0.970  0.020  1.090
 MX3  C7   H7C2  single    0.970  0.020  1.090
 MX3  C9   C10   single    1.517  0.020  1.517
 MX3  C9   C15   single    1.516  0.020  1.516
 MX3  C9   H9C1  single    0.970  0.020  1.090
 MX3  C9   H9C2  single    0.970  0.020  1.090
 MX3  C10  C11   single    1.515  0.020  1.515
 MX3  C10  H101  single    0.970  0.020  1.090
 MX3  C10  H102  single    0.970  0.020  1.090
 MX3  C11  N2    single    1.355  0.020  1.355
 MX3  C11  O6    double    1.224  0.020  1.224
 MX3  C15  N3    single    1.354  0.020  1.354
 MX3  C15  O4    double    1.225  0.020  1.225
 MX3  C12  C13   single    1.545  0.020  1.545
 MX3  C12  N2    single    1.442  0.020  1.442
 MX3  C12  H121  single    0.970  0.020  1.090
 MX3  C12  H122  single    0.970  0.020  1.090
 MX3  C13  O7    deloc     1.244  0.020  1.244
 MX3  C13  O8    deloc     1.246  0.020  1.246
 MX3  C14  N3    single    1.449  0.020  1.449
 MX3  C14  H141  single    0.970  0.020  1.090
 MX3  C14  H142  single    0.970  0.020  1.090
 MX3  C14  H143  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
 MX3  C7    C1   C6    120.45  3.000
 MX3  C7    C1   C2    120.74  3.000
 MX3  C6    C1   C2    118.80  3.000
 MX3  H2    C2   C3    119.66  3.000
 MX3  H2    C2   C1    119.57  3.000
 MX3  C3    C2   C1    120.78  3.000
 MX3  H202  N20  H201  108.71  3.000
 MX3  H202  N20  N2    110.17  3.000
 MX3  H201  N20  N2    110.38  3.000
 MX3  H3    C3   C4    120.13  3.000
 MX3  H3    C3   C2    119.86  3.000
 MX3  C4    C3   C2    120.01  3.000
 MX3  H4    C4   C5    120.15  3.000
 MX3  H4    C4   C3    120.22  3.000
 MX3  C5    C4   C3    119.63  3.000
 MX3  H5    C5   C6    119.79  3.000
 MX3  H5    C5   C4    120.03  3.000
 MX3  C6    C5   C4    120.18  3.000
 MX3  H6    C6   C5    119.69  3.000
 MX3  H6    C6   C1    119.71  3.000
 MX3  C5    C6   C1    120.59  3.000
 MX3  H7C2  C7   H7C1  107.16  3.000
 MX3  H7C2  C7   N3    108.26  3.000
 MX3  H7C1  C7   N3    108.73  3.000
 MX3  H7C2  C7   C1    109.60  3.000
 MX3  H7C1  C7   C1    110.52  3.000
 MX3  N3    C7   C1    112.39  3.000
 MX3  H9C2  C9   H9C1  105.61  3.000
 MX3  H9C2  C9   C15   109.37  3.000
 MX3  H9C1  C9   C15   109.00  3.000
 MX3  H9C2  C9   C10   110.13  3.000
 MX3  H9C1  C9   C10   110.36  3.000
 MX3  C15   C9   C10   112.16  3.000
 MX3  H102  C10  H101  105.58  3.000
 MX3  H102  C10  C11   109.88  3.000
 MX3  H101  C10  C11   108.71  3.000
 MX3  H102  C10  C9    110.27  3.000
 MX3  H101  C10  C9    110.22  3.000
 MX3  C11   C10  C9    111.98  3.000
 MX3  O6    C11  N2    121.61  3.000
 MX3  O6    C11  C10   122.09  3.000
 MX3  N2    C11  C10   116.26  3.000
 MX3  O4    C15  N3    122.15  3.000
 MX3  O4    C15  C9    121.31  3.000
 MX3  N3    C15  C9    116.54  3.000
 MX3  H122  C12  H121  106.68  3.000
 MX3  H122  C12  N2    110.03  3.000
 MX3  H121  C12  N2    107.73  3.000
 MX3  H122  C12  C13   109.48  3.000
 MX3  H121  C12  C13   109.55  3.000
 MX3  N2    C12  C13   113.15  3.000
 MX3  O8    C13  O7    127.70  3.000
 MX3  O8    C13  C12   114.98  3.000
 MX3  O7    C13  C12   117.31  3.000
 MX3  H143  C14  H142  107.97  3.000
 MX3  H143  C14  H141  107.20  3.000
 MX3  H142  C14  H141  108.59  3.000
 MX3  H143  C14  N3    108.82  3.000
 MX3  H142  C14  N3    112.43  3.000
 MX3  H141  C14  N3    111.64  3.000
 MX3  C12   N2   C11   119.67  3.000
 MX3  C12   N2   N20   114.30  3.000
 MX3  C11   N2   N20   122.19  3.000
 MX3  C14   N3   C15   123.41  3.000
 MX3  C14   N3   C7    115.58  3.000
 MX3  C15   N3   C7    120.26  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
 MX3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MX3  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MX3  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MX3  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MX3  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MX3  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 MX3  CONST_07  C7    C1   C2   C3    180.00   0.0  0
 MX3  CONST_08  C7    C1   C6   C5    180.00   0.0  0
 MX3  CONST_09  H3    C3   C2   C1    180.00   0.0  0
 MX3  CONST_10  H5    C5   C6   C1    180.00   0.0  0
 MX3  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 MX3  CONST_12  H4    C4   C3   C2    180.00   0.0  0
 MX3  CONST_13  H2    C2   C3   C4    180.00   0.0  0
 MX3  CONST_14  C10   C11  N2   N20     0.00   0.0  0
 MX3  CONST_15  O6    C11  N2   N20   180.00   0.0  0
 MX3  CONST_16  C9    C15  N3   C7    180.00   0.0  0
 MX3  CONST_17  O4    C15  N3   C7      0.00   0.0  0
 MX3  CONST_18  C14   N3   C15  C9      0.00   0.0  0
 MX3  CONST_19  C12   N2   C11  C10   180.00   0.0  0
 MX3  CONST_20  O6    C11  N2   C12     0.00   0.0  0
 MX3  CONST_21  O4    C15  N3   C14   180.00   0.0  0
 MX3  Var_01    N3    C7   C1   C2   -111.07  30.0  2
 MX3  Var_02    C15   N3   C7   C1   -102.23  30.0  3
 MX3  Var_03    C13   C12  N2   N20   -79.34  30.0  2
 MX3  Var_04    N2    C11  C10  C9   -174.07  30.0  3
 MX3  Var_05    N3    C15  C9   C10  -178.14  30.0  3
 MX3  Var_06    C15   C9   C10  C11   177.45  30.0  1
 MX3  Var_07    O7    C13  C12  N2     -0.84  30.0  3
 MX3  Var_08    H141  C14  N3   C7    152.68  30.0  3
 MX3  Var_09    H201  N20  N2   C11   -57.45  30.0  2

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
 MX3  plan-1  C1   0.020
 MX3  plan-1  C2   0.020
 MX3  plan-1  C3   0.020
 MX3  plan-1  C4   0.020
 MX3  plan-1  C5   0.020
 MX3  plan-1  C6   0.020
 MX3  plan-1  C7   0.020
 MX3  plan-1  H2   0.020
 MX3  plan-1  H3   0.020
 MX3  plan-1  H4   0.020
 MX3  plan-1  H5   0.020
 MX3  plan-1  H6   0.020
 MX3  plan-2  N20  0.020
 MX3  plan-2  C10  0.020
 MX3  plan-2  C11  0.020
 MX3  plan-2  C12  0.020
 MX3  plan-2  N2   0.020
 MX3  plan-2  O6   0.020
 MX3  plan-3  C7   0.020
 MX3  plan-3  C9   0.020
 MX3  plan-3  C15  0.020
 MX3  plan-3  C14  0.020
 MX3  plan-3  N3   0.020
 MX3  plan-3  O4   0.020
 MX3  plan-4  C12  0.020
 MX3  plan-4  C13  0.020
 MX3  plan-4  O7   0.020
 MX3  plan-4  O8   0.020

