# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 14:44:59 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 5-{2-[1-(tert-butoxycarbonyl)-2,3-dihydro-1H-indol-5-yl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N1CCc2cc(CCC3=C(NC(=O)NC3=O)C(O)=O)ccc12
#
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
 W7Q  W7Q  '5-{2-[1-(tert-butoxycarbonyl)-2,3-dihydro-1H-indol-5-yl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  52  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W7Q
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
 W7Q  OAD  O  OH1   0  -0.592  -5.4291  -2.8461   1.0038
 W7Q  CAS  C  C     0   0.524  -4.4555  -2.0790   0.5474
 W7Q  OAH  O  O     0  -0.395  -3.3395  -2.4575   0.3172
 W7Q  CAX  C  CR6   0   0.279  -4.9271  -0.6724   0.3334
 W7Q  NAP  N  NR16  0  -0.733  -6.2857  -0.5320   0.1943
 W7Q  CAZ  C  CR6   0   0.670  -6.9156   0.6551  -0.0361
 W7Q  OAF  O  O     0  -0.473  -8.1170   0.7579  -0.1668
 W7Q  NAQ  N  NR16  0  -0.716  -6.0594   1.7224  -0.1098
 W7Q  CBA  C  CR6   0   0.586  -4.6875   1.7017   0.0177
 W7Q  OAG  O  O     0  -0.440  -4.0464   2.7290  -0.0876
 W7Q  CAY  C  CR6   0  -0.119  -4.0898   0.3868   0.2742
 W7Q  CAN  C  CH2   0  -0.498  -2.5994   0.3536   0.4171
 W7Q  CAL  C  CH2   0  -0.502  -1.8879   0.2125  -0.9375
 W7Q  CAU  C  CR6   0   0.119  -0.3980   0.1291  -0.7659
 W7Q  CAK  C  CR16  0  -0.376   0.2358  -1.1097  -0.6510
 W7Q  CAI  C  CR16  0  -0.315   0.3794   1.2785  -0.6708
 W7Q  CAJ  C  CR16  0  -0.288   1.7560   1.2327  -0.4673
 W7Q  CAW  C  CR56  0   0.388   2.3617  -0.0132  -0.3619
 W7Q  CAV  C  CR56  0  -0.004   1.6000  -1.1758  -0.4563
 W7Q  CAM  C  CH2   0  -0.508   2.4725  -2.3864  -0.3117
 W7Q  CAO  C  CH2   0  -0.273   3.8945  -1.8095  -0.2183
 W7Q  NBB  N  NR5   0  -0.631   3.7078  -0.3511  -0.1767
 W7Q  CAT  C  C     0   0.764   4.7244   0.5332  -0.0031
 W7Q  OAE  O  O     0  -0.507   4.5758   1.7366   0.0526
 W7Q  OAR  O  O2    0  -0.495   5.8797  -0.1115   0.0935
 W7Q  CBC  C  CT    0   0.189   7.1443   0.5683   0.3264
 W7Q  CAB  C  CH3   0  -0.656   8.1489  -0.5763   0.3507
 W7Q  CAC  C  CH3   0  -0.672   7.4766   1.5173  -0.8186
 W7Q  CAA  C  CH3   0  -0.672   7.1353   1.2761   1.6757
 W7Q  H1   H  HOH1  0   0.504  -5.1279  -3.7637   1.0974
 W7Q  H2   H  HNR6  0   0.431  -6.4862   2.6230  -0.2908
 W7Q  H4   H  HCH2  0   0.260  -2.2779   1.2851   0.8861
 W7Q  H5   H  HCH2  0   0.264  -2.2861  -0.4507   1.0781
 W7Q  H6   H  HCH2  0   0.252  -2.2552  -0.6814  -1.4431
 W7Q  H7   H  HCH2  0   0.248  -2.1446   1.0649  -1.5701
 W7Q  H8   H  HCR6  0   0.242  -0.3479  -2.0211  -0.7201
 W7Q  H9   H  HCR6  0   0.244  -0.0962   2.2486  -0.7623
 W7Q  H10  H  HCR6  0   0.269   2.3201   2.1487  -0.4012
 W7Q  H11  H  HCH2  0   0.266   2.2136  -2.9565   0.5822
 W7Q  H12  H  HCH2  0   0.267   2.3722  -3.0639  -1.1601
 W7Q  H13  H  HCH2  0   0.259   4.4127  -2.1518   0.6756
 W7Q  H14  H  HCH2  0   0.257   4.4976  -2.0880  -1.0830
 W7Q  H15  H  HCH3  0   0.238   8.1501  -1.1236  -0.5931
 W7Q  H16  H  HCH3  0   0.230   9.1517  -0.1808   0.5097
 W7Q  H17  H  HCH3  0   0.238   7.9344  -1.2790   1.1571
 W7Q  H18  H  HCH3  0   0.247   6.8080   2.3736  -0.8628
 W7Q  H19  H  HCH3  0   0.235   8.4914   1.8938  -0.6847
 W7Q  H20  H  HCH3  0   0.236   7.4461   0.9966  -1.7772
 W7Q  H21  H  HCH3  0   0.236   6.8534   0.5871   2.4740
 W7Q  H22  H  HCH3  0   0.236   8.1399   1.6386   1.8960
 W7Q  H23  H  HCH3  0   0.246   6.4616   2.1299   1.6970
 W7Q  H24  H  HNR6  0   0.439  -6.8801  -1.3473   0.2461

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
 W7Q  CAB  CBC  single    1.523  0.020  1.523
 W7Q  CAC  CBC  single    1.524  0.020  1.524
 W7Q  CBC  OAR  single    1.454  0.020  1.454
 W7Q  CBC  CAA  single    1.524  0.020  1.524
 W7Q  OAR  CAT  single    1.327  0.020  1.327
 W7Q  CAJ  CAI  aromatic  1.392  0.020  1.392
 W7Q  CAJ  CAW  aromatic  1.389  0.020  1.389
 W7Q  CAI  CAU  aromatic  1.391  0.020  1.391
 W7Q  CAT  OAE  double    1.214  0.020  1.214
 W7Q  CAT  NBB  single    1.358  0.020  1.358
 W7Q  CAW  NBB  single    1.400  0.020  1.400
 W7Q  CAW  CAV  aromatic  1.393  0.020  1.393
 W7Q  NBB  CAO  single    1.471  0.020  1.471
 W7Q  CAU  CAL  single    1.502  0.020  1.502
 W7Q  CAU  CAK  aromatic  1.396  0.020  1.396
 W7Q  CAL  CAN  single    1.537  0.020  1.537
 W7Q  CAV  CAK  aromatic  1.380  0.020  1.380
 W7Q  CAV  CAM  single    1.499  0.020  1.499
 W7Q  CAO  CAM  single    1.537  0.020  1.537
 W7Q  CAN  CAY  single    1.498  0.020  1.498
 W7Q  OAG  CBA  double    1.215  0.020  1.215
 W7Q  CAY  CBA  single    1.467  0.020  1.467
 W7Q  CAY  CAX  double    1.351  0.020  1.351
 W7Q  CBA  NAQ  single    1.378  0.020  1.378
 W7Q  OAH  CAS  double    1.201  0.020  1.201
 W7Q  CAX  CAS  single    1.499  0.020  1.499
 W7Q  CAX  NAP  single    1.373  0.020  1.373
 W7Q  CAS  OAD  single    1.321  0.020  1.321
 W7Q  NAQ  CAZ  single    1.370  0.020  1.370
 W7Q  NAP  CAZ  single    1.364  0.020  1.364
 W7Q  CAZ  OAF  double    1.213  0.020  1.213
 W7Q  OAD  H1   single    0.850  0.020  0.980
 W7Q  NAQ  H2   single    0.860  0.020  1.020
 W7Q  CAN  H4   single    0.970  0.020  1.090
 W7Q  CAN  H5   single    0.970  0.020  1.090
 W7Q  CAL  H6   single    0.970  0.020  1.090
 W7Q  CAL  H7   single    0.970  0.020  1.090
 W7Q  CAK  H8   single    0.930  0.020  1.080
 W7Q  CAI  H9   single    0.930  0.020  1.080
 W7Q  CAJ  H10  single    0.930  0.020  1.080
 W7Q  CAM  H11  single    0.970  0.020  1.090
 W7Q  CAM  H12  single    0.970  0.020  1.090
 W7Q  CAO  H13  single    0.970  0.020  1.090
 W7Q  CAO  H14  single    0.970  0.020  1.090
 W7Q  CAB  H15  single    0.970  0.020  1.090
 W7Q  CAB  H16  single    0.970  0.020  1.090
 W7Q  CAB  H17  single    0.970  0.020  1.090
 W7Q  CAC  H18  single    0.970  0.020  1.090
 W7Q  CAC  H19  single    0.970  0.020  1.090
 W7Q  CAC  H20  single    0.970  0.020  1.090
 W7Q  CAA  H21  single    0.970  0.020  1.090
 W7Q  CAA  H22  single    0.970  0.020  1.090
 W7Q  CAA  H23  single    0.970  0.020  1.090
 W7Q  NAP  H24  single    0.860  0.020  1.020

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
 W7Q  H1   OAD  CAS  110.72  3.000
 W7Q  CAX  CAS  OAH  124.12  3.000
 W7Q  CAX  CAS  OAD  111.25  3.000
 W7Q  OAH  CAS  OAD  124.63  3.000
 W7Q  CAY  CAX  NAP  121.91  3.000
 W7Q  NAP  CAX  CAS  114.95  3.000
 W7Q  CAY  CAX  CAS  123.15  3.000
 W7Q  H24  NAP  CAZ  116.07  3.000
 W7Q  H24  NAP  CAX  119.64  3.000
 W7Q  CAZ  NAP  CAX  124.29  3.000
 W7Q  NAQ  CAZ  OAF  123.17  3.000
 W7Q  OAF  CAZ  NAP  123.34  3.000
 W7Q  NAQ  CAZ  NAP  113.49  3.000
 W7Q  H2   NAQ  CBA  116.70  3.000
 W7Q  H2   NAQ  CAZ  116.03  3.000
 W7Q  CBA  NAQ  CAZ  127.26  3.000
 W7Q  CAY  CBA  OAG  123.91  3.000
 W7Q  CAY  CBA  NAQ  115.80  3.000
 W7Q  OAG  CBA  NAQ  120.29  3.000
 W7Q  CAN  CAY  CBA  116.23  3.000
 W7Q  CBA  CAY  CAX  117.24  3.000
 W7Q  CAN  CAY  CAX  126.51  3.000
 W7Q  H5   CAN  H4   106.58  3.000
 W7Q  H5   CAN  CAL  109.55  3.000
 W7Q  H4   CAN  CAL  108.71  3.000
 W7Q  H5   CAN  CAY  111.17  3.000
 W7Q  H4   CAN  CAY  108.37  3.000
 W7Q  CAL  CAN  CAY  112.25  3.000
 W7Q  H7   CAL  H6   106.98  3.000
 W7Q  H7   CAL  CAU  110.04  3.000
 W7Q  H6   CAL  CAU  109.97  3.000
 W7Q  H7   CAL  CAN  109.28  3.000
 W7Q  H6   CAL  CAN  109.15  3.000
 W7Q  CAU  CAL  CAN  111.32  3.000
 W7Q  CAI  CAU  CAK  118.28  3.000
 W7Q  CAK  CAU  CAL  120.59  3.000
 W7Q  CAI  CAU  CAL  121.09  3.000
 W7Q  H8   CAK  CAV  120.06  3.000
 W7Q  H8   CAK  CAU  119.74  3.000
 W7Q  CAV  CAK  CAU  120.20  3.000
 W7Q  H9   CAI  CAJ  118.39  3.000
 W7Q  H9   CAI  CAU  119.23  3.000
 W7Q  CAJ  CAI  CAU  122.38  3.000
 W7Q  H10  CAJ  CAW  121.95  3.000
 W7Q  H10  CAJ  CAI  119.91  3.000
 W7Q  CAW  CAJ  CAI  118.14  3.000
 W7Q  NBB  CAW  CAV  109.47  3.000
 W7Q  CAV  CAW  CAJ  120.32  3.000
 W7Q  NBB  CAW  CAJ  130.21  3.000
 W7Q  CAM  CAV  CAW  110.43  3.000
 W7Q  CAM  CAV  CAK  128.89  3.000
 W7Q  CAW  CAV  CAK  120.68  3.000
 W7Q  H12  CAM  H11  106.90  3.000
 W7Q  H12  CAM  CAO  111.44  3.000
 W7Q  H11  CAM  CAO  111.45  3.000
 W7Q  H12  CAM  CAV  111.91  3.000
 W7Q  H11  CAM  CAV  111.27  3.000
 W7Q  CAO  CAM  CAV  103.96  3.000
 W7Q  H14  CAO  H13  107.92  3.000
 W7Q  H14  CAO  NBB  110.24  3.000
 W7Q  H13  CAO  NBB  110.43  3.000
 W7Q  H14  CAO  CAM  111.57  3.000
 W7Q  H13  CAO  CAM  111.85  3.000
 W7Q  NBB  CAO  CAM  104.85  3.000
 W7Q  CAT  NBB  CAO  123.65  3.000
 W7Q  CAO  NBB  CAW  110.95  3.000
 W7Q  CAT  NBB  CAW  125.39  3.000
 W7Q  OAR  CAT  OAE  125.81  3.000
 W7Q  OAE  CAT  NBB  124.03  3.000
 W7Q  OAR  CAT  NBB  110.16  3.000
 W7Q  CBC  OAR  CAT  122.80  3.000
 W7Q  CAA  CBC  CAC  112.17  3.000
 W7Q  CAA  CBC  CAB  109.81  3.000
 W7Q  CAC  CBC  CAB  109.64  3.000
 W7Q  CAA  CBC  OAR  110.72  3.000
 W7Q  CAC  CBC  OAR  111.12  3.000
 W7Q  CAB  CBC  OAR  102.99  3.000
 W7Q  H17  CAB  H16  107.88  3.000
 W7Q  H17  CAB  H15  108.46  3.000
 W7Q  H16  CAB  H15  107.90  3.000
 W7Q  H17  CAB  CBC  111.48  3.000
 W7Q  H16  CAB  CBC  109.66  3.000
 W7Q  H15  CAB  CBC  111.34  3.000
 W7Q  H20  CAC  H19  107.37  3.000
 W7Q  H20  CAC  H18  108.83  3.000
 W7Q  H19  CAC  H18  107.77  3.000
 W7Q  H20  CAC  CBC  110.91  3.000
 W7Q  H19  CAC  CBC  109.01  3.000
 W7Q  H18  CAC  CBC  112.76  3.000
 W7Q  H23  CAA  H22  107.80  3.000
 W7Q  H23  CAA  H21  108.74  3.000
 W7Q  H22  CAA  H21  107.45  3.000
 W7Q  H23  CAA  CBC  112.68  3.000
 W7Q  H22  CAA  CBC  109.14  3.000
 W7Q  H21  CAA  CBC  110.85  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
 W7Q  CONST_01  CAW  CAJ  CAI  CAU     0.00   0.0  0
 W7Q  CONST_02  CAW  CAV  CAK  CAU     0.00   0.0  0
 W7Q  CONST_03  CAJ  CAI  CAU  CAK     0.00   0.0  0
 W7Q  CONST_04  CAJ  CAW  CAV  CAK     0.00   0.0  0
 W7Q  CONST_05  CAV  CAW  CAJ  CAI     0.00   0.0  0
 W7Q  CONST_06  CAV  CAK  CAU  CAI     0.00   0.0  0
 W7Q  CONST_07  NAQ  CAZ  NAP  CAX     0.00   0.0  0
 W7Q  CONST_08  CBA  NAQ  CAZ  NAP     0.00   0.0  0
 W7Q  CONST_09  CAY  CBA  NAQ  CAZ     0.00   0.0  0
 W7Q  CONST_10  CAJ  CAI  CAU  CAL   180.00   0.0  0
 W7Q  CONST_11  CAV  CAK  CAU  CAL   180.00   0.0  0
 W7Q  CONST_12  OAF  CAZ  NAP  CAX   180.00   0.0  0
 W7Q  CONST_13  OAG  CBA  NAQ  CAZ   180.00   0.0  0
 W7Q  CONST_14  CBA  NAQ  CAZ  OAF   180.00   0.0  0
 W7Q  CONST_15  H10  CAJ  CAI  CAU   180.00   0.0  0
 W7Q  CONST_16  H9   CAI  CAU  CAK   180.00   0.0  0
 W7Q  CONST_17  H8   CAK  CAU  CAI   180.00   0.0  0
 W7Q  CONST_18  H2   NAQ  CAZ  NAP   180.00   0.0  0
 W7Q  CONST_19  H24  NAP  CAZ  NAQ   180.00   0.0  0
 W7Q  CONST_20  H1   OAD  CAS  CAX   180.00   0.0  0
 W7Q  Var_01    CAO  CAM  CAV  CAK   176.25  30.0  1
 W7Q  Var_02    CAO  NBB  CAW  CAJ  -176.03  30.0  1
 W7Q  Var_03    CAM  CAO  NBB  CAW    -5.60  30.0  1
 W7Q  Var_04    NBB  CAO  CAM  CAV     5.60  30.0  1
 W7Q  Var_05    CAY  CAX  CAS  OAD   159.06  30.0  2
 W7Q  Var_06    CAL  CAN  CAY  CAX    92.17  30.0  1
 W7Q  Var_07    CAU  CAL  CAN  CAY  -177.85  30.0  1
 W7Q  Var_08    CAI  CAU  CAL  CAN   -85.31  30.0  2
 W7Q  Var_09    OAR  CAT  NBB  CAW  -177.64  30.0  2
 W7Q  Var_10    CAB  CBC  OAR  CAT  -179.77  30.0  3
 W7Q  Var_11    H15  CAB  CBC  OAR    60.00  30.0  3
 W7Q  Var_12    H18  CAC  CBC  OAR    68.70  30.0  3
 W7Q  Var_13    H21  CAA  CBC  OAR    52.81  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
 W7Q  plan-1  CAS  0.020
 W7Q  plan-1  CAX  0.020
 W7Q  plan-1  NAP  0.020
 W7Q  plan-1  CAZ  0.020
 W7Q  plan-1  OAF  0.020
 W7Q  plan-1  NAQ  0.020
 W7Q  plan-1  CBA  0.020
 W7Q  plan-1  OAG  0.020
 W7Q  plan-1  CAY  0.020
 W7Q  plan-1  CAN  0.020
 W7Q  plan-1  H2   0.020
 W7Q  plan-1  H24  0.020
 W7Q  plan-2  CAL  0.020
 W7Q  plan-2  CAU  0.020
 W7Q  plan-2  CAK  0.020
 W7Q  plan-2  CAI  0.020
 W7Q  plan-2  CAJ  0.020
 W7Q  plan-2  CAW  0.020
 W7Q  plan-2  CAV  0.020
 W7Q  plan-2  CAM  0.020
 W7Q  plan-2  NBB  0.020
 W7Q  plan-2  H8   0.020
 W7Q  plan-2  H9   0.020
 W7Q  plan-2  H10  0.020
 W7Q  plan-3  OAD  0.020
 W7Q  plan-3  CAS  0.020
 W7Q  plan-3  OAH  0.020
 W7Q  plan-3  CAX  0.020
 W7Q  plan-3  H1   0.020
 W7Q  plan-4  NBB  0.020
 W7Q  plan-4  CAT  0.020
 W7Q  plan-4  OAE  0.020
 W7Q  plan-4  OAR  0.020

