# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:46:19 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  31  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 PERFECT
;

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   0.584   3.5991  -0.5420  -0.3284
 9DK  C69  C  CT    0  -0.327   2.7176   0.6309   0.0746
 9DK  C70  C  CH3   0  -0.639   3.2301   1.3989   1.2966
 9DK  C71  C  CH3   0  -0.701   2.6648   1.5758  -1.1336
 9DK  C72  C  C     0   0.592   1.3751  -0.0006   0.4622
 9DK  C75  C  CH2   0  -0.232  -1.0504  -0.0269   0.1949
 9DK  C76  C  CH2   0  -0.572  -2.1080   0.7546  -0.5762
 9DK  C77  C  CR5   0   0.143  -3.4810   0.2550  -0.2821
 9DK  C78  C  CR15  0  -0.129  -4.4655   0.8623   0.4472
 9DK  C80  C  CR15  0   0.085  -5.1407  -1.0898  -0.2699
 9DK  N74  N  NH1   0  -0.653   0.2751   0.4571  -0.1379
 9DK  N79  N  NR15  0  -0.561  -5.5146  -0.0108   0.4419
 9DK  N81  N  N     0  -0.460  -3.9187  -0.9654  -0.7226
 9DK  O68  O  O     0  -0.443   3.2297  -1.4001  -1.0914
 9DK  O73  O  O     0  -0.502   1.3470  -0.8684   1.3252
 9DK  H2   H  HCH3  0   0.248   4.1887   1.8715   1.0876
 9DK  H3   H  HCH3  0   0.243   2.5246   2.1921   1.5482
 9DK  H4   H  HCH3  0   0.248   3.3426   0.7582   2.1691
 9DK  H5   H  HCH3  0   0.257   2.2400   1.1031  -2.0193
 9DK  H6   H  HCH3  0   0.257   2.0848   2.4688  -0.8956
 9DK  H7   H  HCH3  0   0.269   3.6695   1.9129  -1.3893
 9DK  H8   H  HCH2  0   0.240  -1.2222   0.0805   1.2684
 9DK  H9   H  HCH2  0   0.240  -1.1328  -1.0909  -0.0399
 9DK  H10  H  HCH2  0   0.255  -2.0402   1.8142  -0.3190
 9DK  H11  H  HCH2  0   0.251  -1.9086   0.6728  -1.6492
 9DK  H12  H  HCR5  0   0.283  -4.5043   1.8129   0.9520
 9DK  H13  H  HCR5  0   0.276  -5.7956  -1.9322  -0.4316
 9DK  H14  H  HNH1  0   0.419   0.3533   1.1592  -0.8545
 9DK  H15  H  HNR5  0   0.420  -6.4068   0.1269   0.8892
 9DK  O1   O  OH1   0  -0.576   4.8157  -0.5006   0.1867
 9DK  H1   H  HOH1  0   0.484   5.3417  -1.2416  -0.1513

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    1.224  0.020  1.224
 9DK  C76  C77  single    1.490  0.020  1.490
 9DK  C76  C75  single    1.525  0.020  1.525
 9DK  C78  C77  aromatic  1.367  0.020  1.367
 9DK  C78  N79  aromatic  1.365  0.020  1.365
 9DK  O68  C67  double    1.206  0.020  1.206
 9DK  C77  N81  aromatic  1.369  0.020  1.369
 9DK  N79  C80  aromatic  1.346  0.020  1.346
 9DK  C67  C69  single    1.522  0.020  1.522
 9DK  C72  N74  single    1.334  0.020  1.334
 9DK  C72  C69  single    1.533  0.020  1.533
 9DK  N81  C80  aromatic  1.309  0.020  1.309
 9DK  C75  N74  single    1.450  0.020  1.450
 9DK  C69  C70  single    1.532  0.020  1.532
 9DK  C69  C71  single    1.535  0.020  1.535
 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   single    1.322  0.020  1.322
 9DK  O1   H1   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
 9DK  O1   C67  O68  123.42  3.000
 9DK  O1   C67  C69  113.95  3.000
 9DK  O68  C67  C69  122.58  3.000
 9DK  C72  C69  C71  114.99  3.000
 9DK  C71  C69  C70  109.32  3.000
 9DK  C72  C69  C70  107.33  3.000
 9DK  C71  C69  C67  106.62  3.000
 9DK  C70  C69  C67  113.83  3.000
 9DK  C72  C69  C67  104.87  3.000
 9DK  H4   C70  H3   108.06  3.000
 9DK  H4   C70  H2   108.56  3.000
 9DK  H3   C70  H2   107.34  3.000
 9DK  H4   C70  C69  112.27  3.000
 9DK  H3   C70  C69  109.40  3.000
 9DK  H2   C70  C69  111.04  3.000
 9DK  H7   C71  H6   106.74  3.000
 9DK  H7   C71  H5   107.61  3.000
 9DK  H6   C71  H5   108.97  3.000
 9DK  H7   C71  C69  110.08  3.000
 9DK  H6   C71  C69  110.52  3.000
 9DK  H5   C71  C69  112.71  3.000
 9DK  O73  C72  N74  122.78  3.000
 9DK  N74  C72  C69  117.83  3.000
 9DK  O73  C72  C69  119.36  3.000
 9DK  H9   C75  H8   107.16  3.000
 9DK  H9   C75  N74  110.17  3.000
 9DK  H8   C75  N74  109.66  3.000
 9DK  H9   C75  C76  109.76  3.000
 9DK  H8   C75  C76  109.73  3.000
 9DK  N74  C75  C76  110.30  3.000
 9DK  H11  C76  H10  106.98  3.000
 9DK  H11  C76  C77  109.65  3.000
 9DK  H10  C76  C77  109.63  3.000
 9DK  H11  C76  C75  109.34  3.000
 9DK  H10  C76  C75  109.58  3.000
 9DK  C77  C76  C75  111.55  3.000
 9DK  N81  C77  C78  109.71  3.000
 9DK  N81  C77  C76  121.99  3.000
 9DK  C78  C77  C76  128.29  3.000
 9DK  H12  C78  N79  122.59  3.000
 9DK  H12  C78  C77  131.91  3.000
 9DK  N79  C78  C77  105.50  3.000
 9DK  H13  C80  N81  126.07  3.000
 9DK  H13  C80  N79  122.45  3.000
 9DK  N81  C80  N79  111.47  3.000
 9DK  H14  N74  C75  117.87  3.000
 9DK  H14  N74  C72  119.71  3.000
 9DK  C75  N74  C72  122.41  3.000
 9DK  H15  N79  C80  126.19  3.000
 9DK  H15  N79  C78  126.27  3.000
 9DK  C80  N79  C78  107.54  3.000
 9DK  C80  N81  C77  105.78  3.000
 9DK  H1   O1   C67  109.84  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  CONST_14  H1   O1   C67  C69  180.00   0.0  0
 9DK  Var_01    C78  C77  C76  C75  108.35  30.0  2
 9DK  Var_02    N74  C75  C76  C77  178.49  30.0  3
 9DK  Var_03    O73  C72  C69  C67   55.90  30.0  2
 9DK  Var_04    O68  C67  C69  C70  165.53  30.0  1
 9DK  Var_05    C76  C75  N74  C72  175.69  30.0  1
 9DK  Var_06    H2   C70  C69  C67   64.21  30.0  3
 9DK  Var_07    H5   C71  C69  C67   60.58  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
 9DK  plan-3  H1   0.020

