# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:03:10 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: {1-[4-(benzyloxy)-4-oxobutanoyl]hydrazino}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NN(CC(O)=O)C(=O)CCC(=O)OCc1ccccc1
#
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
 MX4  MX4  '{1-[4-(benzyloxy)-4-oxobutanoyl]hydrazino}acetic acid'  ligand  35  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MX4
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
 MX4  C2    C  CH2    0  -0.603  -1.4396   0.9773  -0.1169
 MX4  C3    C  CH2    0  -0.573  -0.0883   0.4480  -0.5590
 MX4  C4    C  C      0   0.612   1.0545   1.2256   0.0363
 MX4  O5    O  O      0  -0.454   0.9653   2.3094   0.5577
 MX4  O6    O  O2     0  -0.456   2.2033   0.5736  -0.1015
 MX4  C7    C  C      0   0.582  -2.5816   0.2167  -0.7589
 MX4  O8    O  O      0  -0.503  -2.3858  -0.7452  -1.4889
 MX4  N9    N  NT     0  -0.334  -3.8293   0.6831  -0.5143
 MX4  C10   C  CH2    0  -0.435  -4.9705  -0.1327  -0.8518
 MX4  C12   C  CR16   0  -0.294   4.8990  -0.5992   1.2506
 MX4  C13   C  CR16   0  -0.241   5.9217  -1.5228   1.0801
 MX4  C14   C  CR16   0  -0.261   6.5716  -1.6212  -0.1430
 MX4  C15   C  CR16   0  -0.242   6.1972  -0.7921  -1.1933
 MX4  C16   C  CR16   0  -0.286   5.1760   0.1310  -1.0188
 MX4  C17   C  CR6    0   0.078   4.5184   0.2353   0.2041
 MX4  C18   C  C      0   0.404  -5.2399  -1.2506   0.1804
 MX4  C9    C  CH2    0  -0.253   3.3971   1.2121   0.3817
 MX4  O19   O  O      0  -0.599  -4.4500  -1.3464   1.1358
 MX4  N16   N  NH2    0  -0.652  -4.0851   1.6462   0.4587
 MX4  O20   O  OC    -1  -0.622  -6.2427  -1.9529  -0.0533
 MX4  H2C1  H  HCH2   0   0.275  -1.5253   2.0414  -0.3472
 MX4  H2C2  H  HCH2   0   0.273  -1.5306   0.9032   0.9710
 MX4  H3C1  H  HCH2   0   0.278   0.0266  -0.6064  -0.3043
 MX4  H3C2  H  HCH2   0   0.287   0.0124   0.5042  -1.6473
 MX4  H101  H  HCH2   0   0.248  -5.8403   0.5227  -0.9168
 MX4  H102  H  HCH2   0   0.246  -4.8352  -0.5742  -1.8398
 MX4  H14   H  HCR6   0   0.260   7.3710  -2.3386  -0.2754
 MX4  H15   H  HCR6   0   0.258   6.7040  -0.8619  -2.1471
 MX4  H16   H  HCR6   0   0.255   4.8917   0.7805  -1.8384
 MX4  H9C1  H  HCH2   0   0.253   3.5790   2.1275  -0.1858
 MX4  H9C2  H  HCH2   0   0.253   3.2769   1.4815   1.4326
 MX4  H161  H  HNH2   0   0.360  -3.7396   1.3409   1.3607
 MX4  H162  H  HNH2   0   0.371  -3.6382   2.5198   0.2151
 MX4  H12   H  HCR6   0   0.256   4.3971  -0.5239   2.2080
 MX4  H13   H  HCR6   0   0.259   6.2120  -2.1639   1.9023

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
 MX4  C2   C3    single    1.517  0.020  1.517
 MX4  C2   C7    single    1.515  0.020  1.515
 MX4  C2   H2C1  single    0.970  0.020  1.090
 MX4  C2   H2C2  single    0.970  0.020  1.090
 MX4  C3   C4    single    1.505  0.020  1.505
 MX4  C3   H3C1  single    0.970  0.020  1.090
 MX4  C3   H3C2  single    0.970  0.020  1.090
 MX4  C4   O5    double    1.206  0.020  1.206
 MX4  C4   O6    single    1.328  0.020  1.328
 MX4  O6   C9    single    1.437  0.020  1.437
 MX4  C7   O8    double    1.223  0.020  1.223
 MX4  C7   N9    single    1.354  0.020  1.354
 MX4  N9   C10   single    1.443  0.020  1.443
 MX4  N9   N16   single    1.393  0.020  1.393
 MX4  C10  C18   single    1.545  0.020  1.545
 MX4  C10  H101  single    0.970  0.020  1.090
 MX4  C10  H102  single    0.970  0.020  1.090
 MX4  C12  C13   aromatic  1.388  0.020  1.388
 MX4  C12  C17   aromatic  1.392  0.020  1.392
 MX4  C12  H12   single    0.930  0.020  1.080
 MX4  C13  C14   aromatic  1.389  0.020  1.389
 MX4  C13  H13   single    0.930  0.020  1.080
 MX4  C14  C15   aromatic  1.389  0.020  1.389
 MX4  C14  H14   single    0.930  0.020  1.080
 MX4  C15  C16   aromatic  1.388  0.020  1.388
 MX4  C15  H15   single    0.930  0.020  1.080
 MX4  C16  C17   aromatic  1.392  0.020  1.392
 MX4  C16  H16   single    0.930  0.020  1.080
 MX4  C17  C9    single    1.498  0.020  1.498
 MX4  C18  O19   deloc     1.243  0.020  1.243
 MX4  C18  O20   deloc     1.246  0.020  1.246
 MX4  C9   H9C1  single    0.970  0.020  1.090
 MX4  C9   H9C2  single    0.970  0.020  1.090
 MX4  N16  H161  single    0.890  0.020  1.040
 MX4  N16  H162  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
 MX4  H2C2  C2   H2C1  105.61  3.000
 MX4  H2C2  C2   C7    108.95  3.000
 MX4  H2C1  C2   C7    109.91  3.000
 MX4  H2C2  C2   C3    109.89  3.000
 MX4  H2C1  C2   C3    110.39  3.000
 MX4  C7    C2   C3    111.89  3.000
 MX4  H3C2  C3   H3C1  105.79  3.000
 MX4  H3C2  C3   C4    107.27  3.000
 MX4  H3C1  C3   C4    109.09  3.000
 MX4  H3C2  C3   C2    110.73  3.000
 MX4  H3C1  C3   C2    111.28  3.000
 MX4  C4    C3   C2    112.38  3.000
 MX4  O6    C4   O5    123.37  3.000
 MX4  O6    C4   C3    111.23  3.000
 MX4  O5    C4   C3    125.39  3.000
 MX4  C9    O6   C4    117.74  3.000
 MX4  N9    C7   O8    121.74  3.000
 MX4  N9    C7   C2    116.43  3.000
 MX4  O8    C7   C2    121.80  3.000
 MX4  N16   N9   C10   114.16  3.000
 MX4  N16   N9   C7    122.25  3.000
 MX4  C10   N9   C7    119.45  3.000
 MX4  H102  C10  H101  106.74  3.000
 MX4  H102  C10  C18   109.51  3.000
 MX4  H101  C10  C18   109.60  3.000
 MX4  H102  C10  N9    110.04  3.000
 MX4  H101  C10  N9    107.75  3.000
 MX4  C18   C10  N9    113.00  3.000
 MX4  H12   C12  C17   119.74  3.000
 MX4  H12   C12  C13   119.73  3.000
 MX4  C17   C12  C13   120.53  3.000
 MX4  H13   C13  C14   120.11  3.000
 MX4  H13   C13  C12   119.89  3.000
 MX4  C14   C13  C12   120.00  3.000
 MX4  H14   C14  C15   120.14  3.000
 MX4  H14   C14  C13   120.03  3.000
 MX4  C15   C14  C13   119.83  3.000
 MX4  H15   C15  C16   119.89  3.000
 MX4  H15   C15  C14   120.10  3.000
 MX4  C16   C15  C14   120.01  3.000
 MX4  H16   C16  C17   119.71  3.000
 MX4  H16   C16  C15   119.77  3.000
 MX4  C17   C16  C15   120.52  3.000
 MX4  C9    C17  C16   120.44  3.000
 MX4  C9    C17  C12   120.45  3.000
 MX4  C16   C17  C12   119.10  3.000
 MX4  O20   C18  O19   127.72  3.000
 MX4  O20   C18  C10   115.00  3.000
 MX4  O19   C18  C10   117.27  3.000
 MX4  H9C2  C9   H9C1  108.16  3.000
 MX4  H9C2  C9   C17   110.95  3.000
 MX4  H9C1  C9   C17   111.12  3.000
 MX4  H9C2  C9   O6    109.99  3.000
 MX4  H9C1  C9   O6    109.63  3.000
 MX4  C17   C9   O6    106.99  3.000
 MX4  H162  N16  H161  108.92  3.000
 MX4  H162  N16  N9    110.37  3.000
 MX4  H161  N16  N9    110.55  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
 MX4  CONST_01  C15   C14  C13  C12    0.00   0.0  0
 MX4  CONST_02  C15   C16  C17  C12    0.00   0.0  0
 MX4  CONST_03  C16   C17  C12  C13    0.00   0.0  0
 MX4  CONST_04  C16   C15  C14  C13    0.00   0.0  0
 MX4  CONST_05  C17   C12  C13  C14    0.00   0.0  0
 MX4  CONST_06  C17   C16  C15  C14    0.00   0.0  0
 MX4  CONST_07  C9    C17  C12  C13  180.00   0.0  0
 MX4  CONST_08  C9    C17  C16  C15  180.00   0.0  0
 MX4  CONST_09  H14   C14  C13  C12  180.00   0.0  0
 MX4  CONST_10  H16   C16  C17  C12  180.00   0.0  0
 MX4  CONST_11  H15   C15  C14  C13  180.00   0.0  0
 MX4  CONST_12  H12   C12  C13  C14  180.00   0.0  0
 MX4  CONST_13  H13   C13  C14  C15  180.00   0.0  0
 MX4  CONST_14  C10   N9   C7   C2   180.00   0.0  0
 MX4  CONST_15  N16   N9   C7   C2     0.00   0.0  0
 MX4  CONST_16  C10   N9   C7   O8     0.00   0.0  0
 MX4  CONST_17  N16   N9   C7   O8   180.00   0.0  0
 MX4  Var_01    C12   C17  C9   O6   -94.56  30.0  1
 MX4  Var_02    C17   C9   O6   C4   175.74  30.0  3
 MX4  Var_03    O5    C4   C3   C2   -15.62  30.0  3
 MX4  Var_04    O8    C7   C2   C3     3.31  30.0  3
 MX4  Var_05    C7    C2   C3   C4   178.08  30.0  2
 MX4  Var_06    C18   C10  N9   C7    78.49  30.0  3
 MX4  Var_07    O19   C18  C10  N9    -1.92  30.0  3
 MX4  Var_08    H161  N16  N9   C7   -55.87  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
 MX4  plan-1  C12  0.020
 MX4  plan-1  C13  0.020
 MX4  plan-1  C14  0.020
 MX4  plan-1  C15  0.020
 MX4  plan-1  C16  0.020
 MX4  plan-1  C17  0.020
 MX4  plan-1  C9   0.020
 MX4  plan-1  H14  0.020
 MX4  plan-1  H15  0.020
 MX4  plan-1  H16  0.020
 MX4  plan-1  H12  0.020
 MX4  plan-1  H13  0.020
 MX4  plan-2  C2   0.020
 MX4  plan-2  C7   0.020
 MX4  plan-2  O8   0.020
 MX4  plan-2  N9   0.020
 MX4  plan-2  C10  0.020
 MX4  plan-2  N16  0.020
 MX4  plan-3  C10  0.020
 MX4  plan-3  C18  0.020
 MX4  plan-3  O19  0.020
 MX4  plan-3  O20  0.020
 MX4  plan-4  C3   0.020
 MX4  plan-4  C4   0.020
 MX4  plan-4  O5   0.020
 MX4  plan-4  O6   0.020

