# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:06:25 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-[2-(1~{H}-imidazol-4-yl)ethylamino]-2,2-dimethyl-3-oxidanylidene-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C(O)=O)C(=O)NCCc1c[nH]cn1
#
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
 9DK  9DK  '3-[2-(1~{H}-imidazol-4-yl)ethylamino]-2,2-dimethyl-3-oxidanylidene-propanoic acid'  ligand  30  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9DK
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
 9DK  C67  C  C      0   0.444   3.4719  -0.3057   0.8482
 9DK  C69  C  CT     0  -0.300   2.7259   0.5436  -0.2248
 9DK  C70  C  CH3    0  -0.702   2.6424   1.9782   0.3049
 9DK  C71  C  CH3    0  -0.635   3.4428   0.5472  -1.5726
 9DK  C72  C  C      0   0.580   1.3743  -0.1330  -0.4063
 9DK  C75  C  CH2    0  -0.226  -1.0569  -0.0206  -0.1768
 9DK  C76  C  CH2    0  -0.570  -2.0927   0.9425   0.3932
 9DK  C77  C  CR5    0   0.145  -3.4783   0.4125   0.2484
 9DK  C78  C  CR15   0  -0.131  -4.3294  -0.0107   1.2317
 9DK  C80  C  CR15   0   0.084  -5.2571  -0.2475  -0.7338
 9DK  N74  N  NH1    0  -0.658   0.2699   0.5463  -0.0663
 9DK  N79  N  NR15   0  -0.561  -5.4571  -0.4265   0.5846
 9DK  N81  N  N      0  -0.460  -4.0736   0.2570  -0.9752
 9DK  O68  O  O      0  -0.610   2.8088  -0.5614   1.8730
 9DK  O73  O  O      0  -0.526   1.3054  -1.2700  -0.8649
 9DK  H2   H  HCH3   0   0.245   3.6481   2.3812   0.4333
 9DK  H3   H  HCH3   0   0.232   2.1197   2.6415  -0.3890
 9DK  H4   H  HCH3   0   0.234   2.1487   2.0307   1.2761
 9DK  H5   H  HCH3   0   0.225   3.5794  -0.4595  -1.9635
 9DK  H6   H  HCH3   0   0.211   2.8819   1.1230  -2.3129
 9DK  H7   H  HCH3   0   0.223   4.4272   1.0044  -1.4771
 9DK  H8   H  HCH2   0   0.231  -1.1036  -0.9686   0.3651
 9DK  H9   H  HCH2   0   0.230  -1.2935  -0.2381  -1.2219
 9DK  H10  H  HCH2   0   0.251  -1.8817   1.1240   1.4498
 9DK  H11  H  HCH2   0   0.246  -2.0089   1.9069  -0.1181
 9DK  H12  H  HCR5   0   0.282  -4.2281  -0.0487   2.3032
 9DK  H13  H  HCR5   0   0.275  -6.0038  -0.4981  -1.4714
 9DK  H14  H  HNH1   0   0.410   0.3519   1.4827   0.2921
 9DK  H15  H  HNR5   0   0.419  -6.2898  -0.7951   1.0149
 9DK  O1   O  OC    -1  -0.587   4.6505  -0.6258   0.6211

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
 9DK  O73  C72  double    1.228  0.020  1.228
 9DK  C76  C77  single    1.491  0.020  1.491
 9DK  C76  C75  single    1.525  0.020  1.525
 9DK  C78  C77  aromatic  1.368  0.020  1.368
 9DK  C78  N79  aromatic  1.365  0.020  1.365
 9DK  O68  C67  deloc     1.247  0.020  1.247
 9DK  C77  N81  aromatic  1.370  0.020  1.370
 9DK  N79  C80  aromatic  1.345  0.020  1.345
 9DK  C67  C69  single    1.559  0.020  1.559
 9DK  C72  N74  single    1.340  0.020  1.340
 9DK  C72  C69  single    1.522  0.020  1.522
 9DK  N81  C80  aromatic  1.309  0.020  1.309
 9DK  C75  N74  single    1.447  0.020  1.447
 9DK  C69  C70  single    1.532  0.020  1.532
 9DK  C69  C71  single    1.527  0.020  1.527
 9DK  C70  H2   single    0.970  0.020  1.090
 9DK  C70  H3   single    0.970  0.020  1.090
 9DK  C70  H4   single    0.970  0.020  1.090
 9DK  C71  H5   single    0.970  0.020  1.090
 9DK  C71  H6   single    0.970  0.020  1.090
 9DK  C71  H7   single    0.970  0.020  1.090
 9DK  C75  H8   single    0.970  0.020  1.090
 9DK  C75  H9   single    0.970  0.020  1.090
 9DK  C76  H10  single    0.970  0.020  1.090
 9DK  C76  H11  single    0.970  0.020  1.090
 9DK  C78  H12  single    0.930  0.020  1.080
 9DK  C80  H13  single    0.930  0.020  1.080
 9DK  N74  H14  single    0.860  0.020  1.020
 9DK  N79  H15  single    0.860  0.020  1.020
 9DK  C67  O1   deloc     1.242  0.020  1.242

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
 9DK  O1   C67  O68  126.99  3.000
 9DK  O1   C67  C69  117.95  3.000
 9DK  O68  C67  C69  115.03  3.000
 9DK  C72  C69  C71  108.22  3.000
 9DK  C71  C69  C70  109.19  3.000
 9DK  C72  C69  C70  114.15  3.000
 9DK  C71  C69  C67  112.60  3.000
 9DK  C70  C69  C67  107.36  3.000
 9DK  C72  C69  C67  105.36  3.000
 9DK  H4   C70  H3   108.64  3.000
 9DK  H4   C70  H2   107.13  3.000
 9DK  H3   C70  H2   106.94  3.000
 9DK  H4   C70  C69  112.19  3.000
 9DK  H3   C70  C69  112.02  3.000
 9DK  H2   C70  C69  109.66  3.000
 9DK  H7   C71  H6   107.58  3.000
 9DK  H7   C71  H5   107.82  3.000
 9DK  H6   C71  H5   107.97  3.000
 9DK  H7   C71  C69  110.36  3.000
 9DK  H6   C71  C69  111.00  3.000
 9DK  H5   C71  C69  111.95  3.000
 9DK  O73  C72  N74  121.18  3.000
 9DK  N74  C72  C69  118.42  3.000
 9DK  O73  C72  C69  120.39  3.000
 9DK  H9   C75  H8   106.98  3.000
 9DK  H9   C75  N74  110.44  3.000
 9DK  H8   C75  N74  109.94  3.000
 9DK  H9   C75  C76  109.63  3.000
 9DK  H8   C75  C76  109.48  3.000
 9DK  N74  C75  C76  110.30  3.000
 9DK  H11  C76  H10  106.89  3.000
 9DK  H11  C76  C77  109.82  3.000
 9DK  H10  C76  C77  109.42  3.000
 9DK  H11  C76  C75  109.25  3.000
 9DK  H10  C76  C75  109.58  3.000
 9DK  C77  C76  C75  111.75  3.000
 9DK  N81  C77  C78  109.67  3.000
 9DK  N81  C77  C76  122.08  3.000
 9DK  C78  C77  C76  128.23  3.000
 9DK  H12  C78  N79  122.59  3.000
 9DK  H12  C78  C77  131.89  3.000
 9DK  N79  C78  C77  105.52  3.000
 9DK  H13  C80  N81  126.09  3.000
 9DK  H13  C80  N79  122.42  3.000
 9DK  N81  C80  N79  111.49  3.000
 9DK  H14  N74  C75  117.81  3.000
 9DK  H14  N74  C72  119.66  3.000
 9DK  C75  N74  C72  122.52  3.000
 9DK  H15  N79  C80  126.17  3.000
 9DK  H15  N79  C78  126.30  3.000
 9DK  C80  N79  C78  107.53  3.000
 9DK  C80  N81  C77  105.78  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
 9DK  CONST_01  C80  N79  C78  C77    0.00   0.0  0
 9DK  CONST_02  N79  C80  N81  C77    0.00   0.0  0
 9DK  CONST_03  C80  N81  C77  C78    0.00   0.0  0
 9DK  CONST_04  N81  C80  N79  C78    0.00   0.0  0
 9DK  CONST_05  N81  C77  C78  N79    0.00   0.0  0
 9DK  CONST_06  N79  C78  C77  C76  180.00   0.0  0
 9DK  CONST_07  C80  N81  C77  C76  180.00   0.0  0
 9DK  CONST_08  H15  N79  C78  C77  180.00   0.0  0
 9DK  CONST_09  H13  C80  N81  C77  180.00   0.0  0
 9DK  CONST_10  H12  C78  N79  C80  180.00   0.0  0
 9DK  CONST_11  C75  N74  C72  C69  180.00   0.0  0
 9DK  CONST_12  O73  C72  N74  C75    0.00   0.0  0
 9DK  CONST_13  H14  N74  C72  C69    0.00   0.0  0
 9DK  Var_01    C78  C77  C76  C75  111.45  30.0  2
 9DK  Var_02    N74  C75  C76  C77  177.83  30.0  3
 9DK  Var_03    O73  C72  C69  C67  -64.77  30.0  2
 9DK  Var_04    O68  C67  C69  C70   73.38  30.0  3
 9DK  Var_05    C76  C75  N74  C72  175.18  30.0  1
 9DK  Var_06    H2   C70  C69  C67   62.04  30.0  3
 9DK  Var_07    H5   C71  C69  C67   57.46  30.0  3

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
 9DK  plan-1  C76  0.020
 9DK  plan-1  C77  0.020
 9DK  plan-1  C78  0.020
 9DK  plan-1  C80  0.020
 9DK  plan-1  N79  0.020
 9DK  plan-1  N81  0.020
 9DK  plan-1  H12  0.020
 9DK  plan-1  H13  0.020
 9DK  plan-1  H15  0.020
 9DK  plan-2  C69  0.020
 9DK  plan-2  C72  0.020
 9DK  plan-2  C75  0.020
 9DK  plan-2  N74  0.020
 9DK  plan-2  O73  0.020
 9DK  plan-2  H14  0.020
 9DK  plan-3  C67  0.020
 9DK  plan-3  C69  0.020
 9DK  plan-3  O68  0.020
 9DK  plan-3  O1   0.020

