# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 01:32:31 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCc1cccnc1
#
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
 0JR  0JR  (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide  ligand  45  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0JR
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
 0JR  OAE  O  O     0  -0.500   3.3588  -1.5914   1.0828
 0JR  CAU  C  C     0   0.519   3.1105  -0.9216   0.0858
 0JR  CAV  C  CH1   0  -0.034   4.2485  -0.3459  -0.7584
 0JR  OAG  O  OH1   0  -0.663   5.3071  -1.2664  -0.7524
 0JR  CAW  C  CT    0  -0.145   4.6892   1.0786  -0.3197
 0JR  CAB  C  CH3   0  -0.645   5.7957   1.5286  -1.2785
 0JR  CAC  C  CH3   0  -0.666   3.5111   2.0490  -0.4391
 0JR  CAP  C  CH2   0  -0.131   5.2058   1.0537   1.1209
 0JR  OAS  O  OH1   0  -0.671   5.6627   2.3406   1.4741
 0JR  NAR  N  NH1   0  -0.637   1.8685  -0.6641  -0.3285
 0JR  CAN  C  CH2   0  -0.236   0.6927  -1.1176   0.3867
 0JR  CAO  C  CH2   0  -0.631  -0.5478  -0.4771  -0.2143
 0JR  CAT  C  C     0   0.569  -1.7986  -0.8601   0.5486
 0JR  OAD  O  O     0  -0.496  -1.8117  -0.9263   1.7692
 0JR  NAQ  N  NH1   0  -0.630  -2.8770  -1.0925  -0.2198
 0JR  CAM  C  CH2   0  -0.365  -4.1925  -1.3953   0.2901
 0JR  CAL  C  CR6   0   0.019  -5.1886  -0.3052  -0.0039
 0JR  C2   C  CR16  0  -0.108  -6.4264  -0.6075  -0.5585
 0JR  N1   N  N     0  -0.399  -7.3605   0.2957  -0.8332
 0JR  C6   C  CR16  0  -0.071  -7.0901   1.5663  -0.5648
 0JR  C5   C  CR16  0  -0.316  -5.8857   1.9839  -0.0148
 0JR  C4   C  CR16  0  -0.178  -4.9214   1.0321   0.2690
 0JR  H13  H  HCH1  0   0.251   3.9059  -0.2589  -1.7963
 0JR  H14  H  HOH1  0   0.444   5.3308  -1.6797   0.1201
 0JR  H15  H  HCH3  0   0.222   5.4251   1.5509  -2.3062
 0JR  H16  H  HCH3  0   0.235   6.1418   2.5322  -1.0339
 0JR  H17  H  HCH3  0   0.230   6.6563   0.8603  -1.2497
 0JR  H18  H  HCH3  0   0.229   2.7291   1.8502   0.2951
 0JR  H19  H  HCH3  0   0.244   3.8472   3.0741  -0.2880
 0JR  H20  H  HCH3  0   0.226   3.0608   2.0029  -1.4339
 0JR  H21  H  HCH2  0   0.202   4.4018   0.7320   1.7955
 0JR  H22  H  HCH2  0   0.198   6.0153   0.3171   1.2097
 0JR  H23  H  HOH1  0   0.454   6.0160   2.2926   2.3665
 0JR  H12  H  HNH1  0   0.407   1.7412  -0.1844  -1.2053
 0JR  H11  H  HCH2  0   0.249   0.6154  -2.2071   0.3336
 0JR  H10  H  HCH2  0   0.251   0.7819  -0.8489   1.4390
 0JR  H8   H  HCH2  0   0.286  -0.4577   0.6130  -0.1670
 0JR  H9   H  HCH2  0   0.270  -0.6370  -0.7410  -1.2705
 0JR  H7   H  HNH1  0   0.406  -2.7794  -1.0187  -1.2198
 0JR  H5   H  HCH2  0   0.271  -4.5428  -2.3364  -0.1387
 0JR  H6   H  HCH2  0   0.275  -4.1120  -1.5508   1.3657
 0JR  H4   H  HCR6  0   0.260  -6.6699  -1.6393  -0.7946
 0JR  H3   H  HCR6  0   0.265  -7.8630   2.2893  -0.8009
 0JR  H2   H  HCR6  0   0.273  -5.7111   3.0326   0.1829
 0JR  H1   H  HCR6  0   0.269  -3.9720   1.3314   0.6967

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
 0JR  OAD  CAT  double    1.223  0.020  1.223
 0JR  CAT  CAO  single    1.514  0.020  1.514
 0JR  CAT  NAQ  single    1.344  0.020  1.344
 0JR  CAO  CAN  single    1.520  0.020  1.520
 0JR  CAM  NAQ  single    1.443  0.020  1.443
 0JR  CAM  CAL  single    1.506  0.020  1.506
 0JR  OAG  CAV  single    1.403  0.020  1.403
 0JR  CAL  C2   aromatic  1.390  0.020  1.390
 0JR  CAL  C4   aromatic  1.391  0.020  1.391
 0JR  NAR  CAN  single    1.449  0.020  1.449
 0JR  NAR  CAU  single    1.334  0.020  1.334
 0JR  CAV  CAU  single    1.529  0.020  1.529
 0JR  CAV  CAW  single    1.554  0.020  1.554
 0JR  C2   N1   aromatic  1.328  0.020  1.328
 0JR  C4   C5   aromatic  1.384  0.020  1.384
 0JR  OAS  CAP  single    1.411  0.020  1.411
 0JR  CAP  CAW  single    1.531  0.020  1.531
 0JR  CAU  OAE  double    1.226  0.020  1.226
 0JR  N1   C6   aromatic  1.326  0.020  1.326
 0JR  C5   C6   aromatic  1.388  0.020  1.388
 0JR  CAW  CAB  single    1.532  0.020  1.532
 0JR  CAW  CAC  single    1.531  0.020  1.531
 0JR  C4   H1   single    0.930  0.020  1.080
 0JR  C5   H2   single    0.930  0.020  1.080
 0JR  C6   H3   single    0.930  0.020  1.080
 0JR  C2   H4   single    0.930  0.020  1.080
 0JR  CAM  H5   single    0.970  0.020  1.090
 0JR  CAM  H6   single    0.970  0.020  1.090
 0JR  NAQ  H7   single    0.860  0.020  1.020
 0JR  CAO  H8   single    0.970  0.020  1.090
 0JR  CAO  H9   single    0.970  0.020  1.090
 0JR  CAN  H10  single    0.970  0.020  1.090
 0JR  CAN  H11  single    0.970  0.020  1.090
 0JR  NAR  H12  single    0.860  0.020  1.020
 0JR  CAV  H13  single    0.970  0.020  1.090
 0JR  OAG  H14  single    0.850  0.020  0.980
 0JR  CAB  H15  single    0.970  0.020  1.090
 0JR  CAB  H16  single    0.970  0.020  1.090
 0JR  CAB  H17  single    0.970  0.020  1.090
 0JR  CAC  H18  single    0.970  0.020  1.090
 0JR  CAC  H19  single    0.970  0.020  1.090
 0JR  CAC  H20  single    0.970  0.020  1.090
 0JR  CAP  H21  single    0.970  0.020  1.090
 0JR  CAP  H22  single    0.970  0.020  1.090
 0JR  OAS  H23  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
 0JR  NAR  CAU  CAV  116.65  3.000
 0JR  CAV  CAU  OAE  120.24  3.000
 0JR  NAR  CAU  OAE  123.11  3.000
 0JR  H13  CAV  CAW  106.44  3.000
 0JR  H13  CAV  OAG  106.97  3.000
 0JR  CAW  CAV  OAG  112.72  3.000
 0JR  H13  CAV  CAU  108.65  3.000
 0JR  CAW  CAV  CAU  113.58  3.000
 0JR  OAG  CAV  CAU  108.19  3.000
 0JR  H14  OAG  CAV  107.65  3.000
 0JR  CAP  CAW  CAC  110.09  3.000
 0JR  CAC  CAW  CAB  108.72  3.000
 0JR  CAP  CAW  CAB  110.49  3.000
 0JR  CAC  CAW  CAV  109.92  3.000
 0JR  CAB  CAW  CAV  107.30  3.000
 0JR  CAP  CAW  CAV  110.27  3.000
 0JR  H17  CAB  H16  107.94  3.000
 0JR  H17  CAB  H15  107.77  3.000
 0JR  H16  CAB  H15  107.47  3.000
 0JR  H17  CAB  CAW  111.94  3.000
 0JR  H16  CAB  CAW  111.07  3.000
 0JR  H15  CAB  CAW  110.47  3.000
 0JR  H20  CAC  H19  107.04  3.000
 0JR  H20  CAC  H18  108.03  3.000
 0JR  H19  CAC  H18  107.41  3.000
 0JR  H20  CAC  CAW  111.18  3.000
 0JR  H19  CAC  CAW  110.38  3.000
 0JR  H18  CAC  CAW  112.56  3.000
 0JR  H22  CAP  H21  107.08  3.000
 0JR  H22  CAP  OAS  110.67  3.000
 0JR  H21  CAP  OAS  110.53  3.000
 0JR  H22  CAP  CAW  109.63  3.000
 0JR  H21  CAP  CAW  109.63  3.000
 0JR  OAS  CAP  CAW  109.28  3.000
 0JR  H23  OAS  CAP  107.82  3.000
 0JR  H12  NAR  CAN  118.42  3.000
 0JR  H12  NAR  CAU  118.67  3.000
 0JR  CAN  NAR  CAU  122.80  3.000
 0JR  H10  CAN  H11  107.35  3.000
 0JR  H11  CAN  CAO  110.06  3.000
 0JR  H10  CAN  CAO  110.16  3.000
 0JR  H11  CAN  NAR  110.20  3.000
 0JR  H10  CAN  NAR  109.45  3.000
 0JR  CAO  CAN  NAR  109.59  3.000
 0JR  H9   CAO  H8   106.80  3.000
 0JR  H9   CAO  CAT  111.01  3.000
 0JR  H8   CAO  CAT  107.34  3.000
 0JR  H9   CAO  CAN  110.32  3.000
 0JR  H8   CAO  CAN  109.60  3.000
 0JR  CAT  CAO  CAN  111.61  3.000
 0JR  NAQ  CAT  OAD  123.55  3.000
 0JR  NAQ  CAT  CAO  114.73  3.000
 0JR  OAD  CAT  CAO  121.71  3.000
 0JR  H7   NAQ  CAM  117.03  3.000
 0JR  H7   NAQ  CAT  118.49  3.000
 0JR  CAM  NAQ  CAT  124.45  3.000
 0JR  H6   CAM  H5   106.76  3.000
 0JR  H6   CAM  CAL  110.18  3.000
 0JR  H5   CAM  CAL  109.58  3.000
 0JR  H6   CAM  NAQ  108.14  3.000
 0JR  H5   CAM  NAQ  109.54  3.000
 0JR  CAL  CAM  NAQ  112.47  3.000
 0JR  C4   CAL  C2   117.30  3.000
 0JR  C4   CAL  CAM  122.05  3.000
 0JR  C2   CAL  CAM  120.65  3.000
 0JR  H4   C2   N1   116.32  3.000
 0JR  H4   C2   CAL  119.55  3.000
 0JR  N1   C2   CAL  124.13  3.000
 0JR  C6   N1   C2   117.78  3.000
 0JR  H3   C6   C5   120.26  3.000
 0JR  H3   C6   N1   116.70  3.000
 0JR  C5   C6   N1   123.04  3.000
 0JR  H2   C5   C4   121.12  3.000
 0JR  H2   C5   C6   120.28  3.000
 0JR  C4   C5   C6   118.60  3.000
 0JR  H1   C4   C5   120.09  3.000
 0JR  H1   C4   CAL  120.76  3.000
 0JR  C5   C4   CAL  119.14  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
 0JR  CONST_01  C6   N1   C2   CAL     0.00   0.0  0
 0JR  CONST_02  C6   C5   C4   CAL     0.00   0.0  0
 0JR  CONST_03  C5   C4   CAL  C2      0.00   0.0  0
 0JR  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 0JR  CONST_05  C4   CAL  C2   N1      0.00   0.0  0
 0JR  CONST_06  C4   C5   C6   N1      0.00   0.0  0
 0JR  CONST_07  N1   C2   CAL  CAM   180.00   0.0  0
 0JR  CONST_08  C5   C4   CAL  CAM   180.00   0.0  0
 0JR  CONST_09  H2   C5   C4   CAL   180.00   0.0  0
 0JR  CONST_10  H1   C4   CAL  C2    180.00   0.0  0
 0JR  CONST_11  H3   C6   N1   C2    180.00   0.0  0
 0JR  CONST_12  H4   C2   N1   C6    180.00   0.0  0
 0JR  CONST_13  CAN  NAR  CAU  OAE     0.00   0.0  0
 0JR  CONST_14  CAN  NAR  CAU  CAV   180.00   0.0  0
 0JR  CONST_15  CAM  NAQ  CAT  CAO   180.00   0.0  0
 0JR  CONST_16  CAM  NAQ  CAT  OAD     0.00   0.0  0
 0JR  CONST_17  H12  NAR  CAU  OAE   180.00   0.0  0
 0JR  CONST_18  H7   NAQ  CAT  CAO     0.00   0.0  0
 0JR  Var_01    C2   CAL  CAM  NAQ   131.03  30.0  2
 0JR  Var_02    CAL  CAM  NAQ  CAT   113.26  30.0  1
 0JR  Var_03    CAO  CAN  NAR  CAU   170.97  30.0  3
 0JR  Var_04    OAS  CAP  CAW  CAV   177.04  30.0  3
 0JR  Var_05    CAT  CAO  CAN  NAR  -176.83  30.0  1
 0JR  Var_06    OAD  CAT  CAO  CAN    40.38  30.0  1
 0JR  Var_07    H15  CAB  CAW  CAV    60.03  30.0  3
 0JR  Var_08    H18  CAC  CAW  CAV    69.01  30.0  3

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
 0JR  chir_01  CAV  OAG  CAU  CAW  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
 0JR  plan-1  CAM  0.020
 0JR  plan-1  CAL  0.020
 0JR  plan-1  C2   0.020
 0JR  plan-1  N1   0.020
 0JR  plan-1  C6   0.020
 0JR  plan-1  C5   0.020
 0JR  plan-1  C4   0.020
 0JR  plan-1  H4   0.020
 0JR  plan-1  H3   0.020
 0JR  plan-1  H2   0.020
 0JR  plan-1  H1   0.020
 0JR  plan-2  OAE  0.020
 0JR  plan-2  CAU  0.020
 0JR  plan-2  CAV  0.020
 0JR  plan-2  NAR  0.020
 0JR  plan-2  CAN  0.020
 0JR  plan-2  H12  0.020
 0JR  plan-3  CAO  0.020
 0JR  plan-3  CAT  0.020
 0JR  plan-3  OAD  0.020
 0JR  plan-3  NAQ  0.020
 0JR  plan-3  CAM  0.020
 0JR  plan-3  H7   0.020

