# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 05:00:30 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@@H](C)c2cc3OCOc3c(c2)c4ccc(cc4)C(O)=O
#
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
 UC9  UC9  '4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}benzoic acid'  ligand  54  32  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UC9
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
 UC9  C4   C  CR6   0   0.264  -5.6955   0.9620   0.4439
 UC9  C5   C  CR6   0  -0.339  -4.5533   0.2669   0.0522
 UC9  C6   C  CR6   0   0.453  -4.6575  -0.4787  -1.1522
 UC9  N1   N  N     0  -0.503  -5.7851  -0.5115  -1.8506
 UC9  N3   N  N     0  -0.498  -6.8220   0.9243  -0.2569
 UC9  CAK  C  CH3   0  -0.666  -5.1731   3.2381   1.3196
 UC9  CAI  C  CH2   0  -0.522  -5.6855   1.8381   1.6595
 UC9  C2   C  CR6   0   0.537  -6.8154   0.1837  -1.3707
 UC9  NAH  N  NH2   0  -0.820  -7.9687   0.1157  -2.0608
 UC9  NAG  N  NH2   0  -0.825  -3.6188  -1.1945  -1.6083
 UC9  CAJ  C  CSP   0   0.097  -3.3399   0.2779   0.7827
 UC9  CAL  C  CSP   0   0.139  -2.2807   0.2461   1.3620
 UC9  CAM  C  CH1   0  -0.510  -1.0072   0.1734   2.0751
 UC9  CBC  C  CH3   0  -0.640  -1.1776  -0.5001   3.4439
 UC9  CAN  C  CR6   0   0.158   0.0337  -0.5398   1.2350
 UC9  CAO  C  CR16  0  -0.413   1.2876   0.0181   1.0685
 UC9  CAS  C  CR16  0  -0.395  -0.2667  -1.7888   0.6663
 UC9  CAR  C  CR56  0   0.331   0.7308  -2.4066  -0.0401
 UC9  OAW  O  O     0  -0.485   0.6778  -3.5801  -0.7124
 UC9  CAV  C  CH2   0   0.066   2.0046  -3.8549  -1.1402
 UC9  OAU  O  O     0  -0.479   2.7450  -2.6520  -0.9781
 UC9  CAQ  C  CR56  0   0.241   1.9896  -1.8443  -0.1968
 UC9  CAP  C  CR6   0   0.013   2.3151  -0.6196   0.3437
 UC9  CAT  C  CR6   0   0.104   3.6309   0.0159   0.1608
 UC9  CAX  C  CR16  0  -0.290   4.8143  -0.7227   0.2304
 UC9  CAY  C  CR16  0  -0.239   6.0412  -0.1046   0.0739
 UC9  CAZ  C  CR6   0  -0.095   6.1194   1.2660  -0.1638
 UC9  CBD  C  C     0   0.531   7.4583   1.8799  -0.3316
 UC9  OBF  O  O     0  -0.439   8.4951   1.2659  -0.2426
 UC9  OBE  O  OH1   0  -0.593   7.4044   3.1778  -0.5958
 UC9  CBA  C  CR16  0  -0.243   4.9430   2.0097  -0.2344
 UC9  CBB  C  CR16  0  -0.295   3.7168   1.3894  -0.0727
 UC9  H1   H  HCH3  0   0.230  -5.7819   3.6974   0.5404
 UC9  H2   H  HCH3  0   0.239  -5.2087   3.8828   2.1974
 UC9  H3   H  HCH3  0   0.231  -4.1417   3.2069   0.9684
 UC9  H4   H  HCH2  0   0.249  -6.7020   1.9039   2.0495
 UC9  H5   H  HCH2  0   0.244  -5.0611   1.3980   2.4386
 UC9  H6   H  HNH2  0   0.395  -7.9670  -0.2880  -2.9809
 UC9  H7   H  HNH2  0   0.395  -8.7137   0.7499  -1.8317
 UC9  H8   H  HNH2  0   0.400  -2.7015  -1.0603  -1.2188
 UC9  H9   H  HNH2  0   0.397  -3.6746  -1.6064  -2.5241
 UC9  H10  H  HCH1  0   0.286  -0.6558   1.1958   2.2470
 UC9  H11  H  HCH3  0   0.233  -1.5164  -1.5302   3.3342
 UC9  H12  H  HCH3  0   0.242  -0.2280  -0.5055   3.9790
 UC9  H13  H  HCH3  0   0.242  -1.9076   0.0376   4.0486
 UC9  H14  H  HCR6  0   0.258   1.5009   0.9749   1.5297
 UC9  H15  H  HCR6  0   0.273  -1.2446  -2.2403   0.7782
 UC9  H16  H  HCH2  0   0.237   2.4400  -4.6453  -0.5201
 UC9  H17  H  HCH2  0   0.249   2.0025  -4.1476  -2.1897
 UC9  H18  H  HCR6  0   0.261   4.7846  -1.7848   0.4297
 UC9  H19  H  HCR6  0   0.268   6.9443  -0.6959   0.1414
 UC9  H20  H  HOH1  0   0.488   8.2999   3.5300  -0.7062
 UC9  H21  H  HCR6  0   0.270   4.9687   3.0745  -0.4191
 UC9  H22  H  HCR6  0   0.266   2.8142   1.9817  -0.1476

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
 UC9  OBF  CBD  double    1.208  0.020  1.208
 UC9  OBE  CBD  single    1.326  0.020  1.326
 UC9  CBD  CAZ  single    1.482  0.020  1.482
 UC9  CAY  CAZ  aromatic  1.393  0.020  1.393
 UC9  CAY  CAX  aromatic  1.383  0.020  1.383
 UC9  CAZ  CBA  aromatic  1.394  0.020  1.394
 UC9  NAG  C6   single    1.341  0.020  1.341
 UC9  N1   C6   aromatic  1.327  0.020  1.327
 UC9  N1   C2   aromatic  1.332  0.020  1.332
 UC9  CAX  CAT  aromatic  1.397  0.020  1.397
 UC9  CBA  CBB  aromatic  1.384  0.020  1.384
 UC9  NAH  C2   single    1.346  0.020  1.346
 UC9  C6   C5   aromatic  1.420  0.020  1.420
 UC9  C2   N3   aromatic  1.338  0.020  1.338
 UC9  CAT  CBB  aromatic  1.396  0.020  1.396
 UC9  CAT  CAP  single    1.473  0.020  1.473
 UC9  C5   CAJ  single    1.416  0.020  1.416
 UC9  C5   C4   aromatic  1.393  0.020  1.393
 UC9  N3   C4   aromatic  1.327  0.020  1.327
 UC9  CAJ  CAL  triple    1.208  0.020  1.208
 UC9  CAO  CAP  aromatic  1.410  0.020  1.410
 UC9  CAO  CAN  aromatic  1.382  0.020  1.382
 UC9  C4   CAI  single    1.498  0.020  1.498
 UC9  CAL  CAM  single    1.461  0.020  1.461
 UC9  CAP  CAQ  aromatic  1.378  0.020  1.378
 UC9  CAK  CAI  single    1.529  0.020  1.529
 UC9  CAM  CAN  single    1.516  0.020  1.516
 UC9  CAM  CBC  single    1.535  0.020  1.535
 UC9  CAN  CAS  aromatic  1.405  0.020  1.405
 UC9  CAQ  OAU  single    1.354  0.020  1.354
 UC9  CAQ  CAR  aromatic  1.388  0.020  1.388
 UC9  OAU  CAV  single    1.422  0.020  1.422
 UC9  CAS  CAR  aromatic  1.369  0.020  1.369
 UC9  CAR  OAW  single    1.354  0.020  1.354
 UC9  CAV  OAW  single    1.421  0.020  1.421
 UC9  CAK  H1   single    0.970  0.020  1.090
 UC9  CAK  H2   single    0.970  0.020  1.090
 UC9  CAK  H3   single    0.970  0.020  1.090
 UC9  CAI  H4   single    0.970  0.020  1.090
 UC9  CAI  H5   single    0.970  0.020  1.090
 UC9  NAH  H6   single    0.890  0.020  1.040
 UC9  NAH  H7   single    0.890  0.020  1.040
 UC9  NAG  H8   single    0.890  0.020  1.040
 UC9  NAG  H9   single    0.890  0.020  1.040
 UC9  CAM  H10  single    0.970  0.020  1.090
 UC9  CBC  H11  single    0.970  0.020  1.090
 UC9  CBC  H12  single    0.970  0.020  1.090
 UC9  CBC  H13  single    0.970  0.020  1.090
 UC9  CAO  H14  single    0.930  0.020  1.080
 UC9  CAS  H15  single    0.930  0.020  1.080
 UC9  CAV  H16  single    0.970  0.020  1.090
 UC9  CAV  H17  single    0.970  0.020  1.090
 UC9  CAX  H18  single    0.930  0.020  1.080
 UC9  CAY  H19  single    0.930  0.020  1.080
 UC9  OBE  H20  single    0.850  0.020  0.980
 UC9  CBA  H21  single    0.930  0.020  1.080
 UC9  CBB  H22  single    0.930  0.020  1.080

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
 UC9  CAI  C4   N3   116.78  3.000
 UC9  CAI  C4   C5   120.95  3.000
 UC9  N3   C4   C5   122.22  3.000
 UC9  CAJ  C5   C6   120.28  3.000
 UC9  CAJ  C5   C4   123.60  3.000
 UC9  C6   C5   C4   116.11  3.000
 UC9  NAG  C6   N1   117.78  3.000
 UC9  N1   C6   C5   121.44  3.000
 UC9  NAG  C6   C5   120.77  3.000
 UC9  C2   N1   C6   117.05  3.000
 UC9  C2   N3   C4   116.82  3.000
 UC9  H3   CAK  H2   107.90  3.000
 UC9  H3   CAK  H1   108.08  3.000
 UC9  H2   CAK  H1   107.95  3.000
 UC9  H3   CAK  CAI  111.25  3.000
 UC9  H2   CAK  CAI  110.59  3.000
 UC9  H1   CAK  CAI  110.94  3.000
 UC9  H5   CAI  H4   107.59  3.000
 UC9  H5   CAI  CAK  109.65  3.000
 UC9  H4   CAI  CAK  109.67  3.000
 UC9  H5   CAI  C4   110.32  3.000
 UC9  H4   CAI  C4   108.61  3.000
 UC9  CAK  CAI  C4   110.93  3.000
 UC9  NAH  C2   N3   116.79  3.000
 UC9  N3   C2   N1   126.34  3.000
 UC9  NAH  C2   N1   116.85  3.000
 UC9  H7   NAH  H6   117.62  3.000
 UC9  H7   NAH  C2   119.12  3.000
 UC9  H6   NAH  C2   119.24  3.000
 UC9  H9   NAG  H8   117.25  3.000
 UC9  H9   NAG  C6   119.03  3.000
 UC9  H8   NAG  C6   120.23  3.000
 UC9  CAL  CAJ  C5   180.00  3.000
 UC9  CAM  CAL  CAJ  180.00  3.000
 UC9  H10  CAM  CAN  107.82  3.000
 UC9  H10  CAM  CBC  107.78  3.000
 UC9  CAN  CAM  CBC  111.34  3.000
 UC9  H10  CAM  CAL  108.06  3.000
 UC9  CBC  CAM  CAL  111.11  3.000
 UC9  CAN  CAM  CAL  110.57  3.000
 UC9  H13  CBC  H12  108.28  3.000
 UC9  H13  CBC  H11  108.29  3.000
 UC9  H12  CBC  H11  108.39  3.000
 UC9  H13  CBC  CAM  110.65  3.000
 UC9  H12  CBC  CAM  110.08  3.000
 UC9  H11  CBC  CAM  111.07  3.000
 UC9  CAS  CAN  CAO  120.27  3.000
 UC9  CAS  CAN  CAM  119.72  3.000
 UC9  CAO  CAN  CAM  119.98  3.000
 UC9  H14  CAO  CAP  118.35  3.000
 UC9  H14  CAO  CAN  118.93  3.000
 UC9  CAP  CAO  CAN  122.71  3.000
 UC9  H15  CAS  CAR  121.53  3.000
 UC9  H15  CAS  CAN  121.46  3.000
 UC9  CAR  CAS  CAN  117.01  3.000
 UC9  CAQ  CAR  OAW  109.31  3.000
 UC9  OAW  CAR  CAS  128.23  3.000
 UC9  CAQ  CAR  CAS  122.43  3.000
 UC9  CAV  OAW  CAR  106.30  3.000
 UC9  H17  CAV  H16  110.63  3.000
 UC9  H17  CAV  OAU  109.76  3.000
 UC9  H16  CAV  OAU  109.83  3.000
 UC9  H17  CAV  OAW  109.88  3.000
 UC9  H16  CAV  OAW  109.90  3.000
 UC9  OAU  CAV  OAW  106.76  3.000
 UC9  CAQ  OAU  CAV  106.26  3.000
 UC9  CAP  CAQ  OAU  128.67  3.000
 UC9  OAU  CAQ  CAR  109.24  3.000
 UC9  CAP  CAQ  CAR  122.02  3.000
 UC9  CAT  CAP  CAQ  123.09  3.000
 UC9  CAQ  CAP  CAO  115.57  3.000
 UC9  CAT  CAP  CAO  121.32  3.000
 UC9  CBB  CAT  CAX  118.46  3.000
 UC9  CBB  CAT  CAP  120.02  3.000
 UC9  CAX  CAT  CAP  121.51  3.000
 UC9  H18  CAX  CAY  118.98  3.000
 UC9  H18  CAX  CAT  120.36  3.000
 UC9  CAY  CAX  CAT  120.64  3.000
 UC9  H19  CAY  CAZ  120.11  3.000
 UC9  H19  CAY  CAX  119.30  3.000
 UC9  CAZ  CAY  CAX  120.59  3.000
 UC9  CBA  CAZ  CBD  122.39  3.000
 UC9  CBA  CAZ  CAY  119.10  3.000
 UC9  CBD  CAZ  CAY  118.51  3.000
 UC9  OBE  CBD  OBF  123.17  3.000
 UC9  OBE  CBD  CAZ  113.03  3.000
 UC9  OBF  CBD  CAZ  123.80  3.000
 UC9  H20  OBE  CBD  109.94  3.000
 UC9  H21  CBA  CBB  118.86  3.000
 UC9  H21  CBA  CAZ  120.95  3.000
 UC9  CBB  CBA  CAZ  120.19  3.000
 UC9  H22  CBB  CBA  119.06  3.000
 UC9  H22  CBB  CAT  119.93  3.000
 UC9  CBA  CBB  CAT  121.01  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
 UC9  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 UC9  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 UC9  CONST_03  C2   N1   C6   C5     0.00   0.0  0
 UC9  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 UC9  CONST_05  N3   C2   N1   C6     0.00   0.0  0
 UC9  CONST_06  N3   C4   C5   C6     0.00   0.0  0
 UC9  CONST_07  CAT  CAP  CAO  CAN  180.00   0.0  0
 UC9  CONST_08  CAQ  CAP  CAO  CAN    0.00   0.0  0
 UC9  CONST_09  CAQ  CAR  CAS  CAN    0.00   0.0  0
 UC9  CONST_12  CAR  CAQ  CAP  CAO    0.00   0.0  0
 UC9  CONST_13  CAR  CAS  CAN  CAO    0.00   0.0  0
 UC9  CONST_14  CAP  CAO  CAN  CAS    0.00   0.0  0
 UC9  CONST_15  CAP  CAQ  CAR  CAS    0.00   0.0  0
 UC9  CONST_16  CAT  CAP  CAQ  CAR  180.00   0.0  0
 UC9  CONST_19  CAY  CAX  CAT  CAP  180.00   0.0  0
 UC9  CONST_20  CBA  CBB  CAT  CAP  180.00   0.0  0
 UC9  CONST_21  CAZ  CAY  CAX  CAT    0.00   0.0  0
 UC9  CONST_22  CAZ  CBA  CBB  CAT    0.00   0.0  0
 UC9  CONST_23  CBA  CAZ  CAY  CAX    0.00   0.0  0
 UC9  CONST_24  CBA  CBB  CAT  CAX    0.00   0.0  0
 UC9  CONST_25  CBB  CBA  CAZ  CAY    0.00   0.0  0
 UC9  CONST_26  CBB  CAT  CAX  CAY    0.00   0.0  0
 UC9  CONST_27  CAT  CAP  CAQ  OAU    0.00   0.0  0
 UC9  CONST_28  NAG  C6   C5   C4   180.00   0.0  0
 UC9  CONST_29  NAH  C2   N3   C4   180.00   0.0  0
 UC9  CONST_30  NAH  C2   N1   C6   180.00   0.0  0
 UC9  CONST_31  CAI  C4   C5   C6   180.00   0.0  0
 UC9  CONST_32  CAJ  C5   C6   N1   180.00   0.0  0
 UC9  CONST_33  CAJ  C5   C4   N3   180.00   0.0  0
 UC9  CONST_34  C2   N3   C4   CAI  180.00   0.0  0
 UC9  CONST_35  NAG  C6   N1   C2   180.00   0.0  0
 UC9  CONST_36  CAP  CAO  CAN  CAM  180.00   0.0  0
 UC9  CONST_37  CAR  CAS  CAN  CAM  180.00   0.0  0
 UC9  CONST_38  CBD  CAZ  CAY  CAX  180.00   0.0  0
 UC9  CONST_39  CBB  CBA  CAZ  CBD  180.00   0.0  0
 UC9  CONST_40  H15  CAS  CAN  CAO  180.00   0.0  0
 UC9  CONST_41  H14  CAO  CAN  CAS  180.00   0.0  0
 UC9  CONST_42  H18  CAX  CAT  CAP    0.00   0.0  0
 UC9  CONST_43  H22  CBB  CAT  CAP    0.00   0.0  0
 UC9  CONST_44  H19  CAY  CAX  CAT  180.00   0.0  0
 UC9  CONST_45  H21  CBA  CBB  CAT  180.00   0.0  0
 UC9  CONST_46  H8   NAG  C6   C5     0.00   0.0  0
 UC9  CONST_47  H9   NAG  C6   C5   180.00   0.0  0
 UC9  CONST_48  H6   NAH  C2   N1     0.00   0.0  0
 UC9  CONST_49  H7   NAH  C2   N1   180.00   0.0  0
 UC9  CONST_50  H20  OBE  CBD  CAZ  180.00   0.0  0
 UC9  Var_01    OAU  CAV  OAW  CAR  -14.07  30.0  1
 UC9  Var_02    CAP  CAQ  OAU  CAV  173.67  30.0  1
 UC9  Var_03    CAQ  CAR  OAW  CAV    8.59  30.0  1
 UC9  Var_04    CAK  CAI  C4   C5    85.40  30.0  2
 UC9  Var_05    OBF  CBD  CAZ  CAY   -1.85  30.0  2
 UC9  Var_06    H1   CAK  CAI  C4    57.80  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
 UC9  chir_01  CAM  CAL  CAN  CBC  positiv

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
 UC9  plan-1  C4   0.020
 UC9  plan-1  C5   0.020
 UC9  plan-1  C6   0.020
 UC9  plan-1  N1   0.020
 UC9  plan-1  N3   0.020
 UC9  plan-1  CAI  0.020
 UC9  plan-1  C2   0.020
 UC9  plan-1  NAH  0.020
 UC9  plan-1  NAG  0.020
 UC9  plan-1  CAJ  0.020
 UC9  plan-1  CAL  0.020
 UC9  plan-2  CAP  0.020
 UC9  plan-2  CAT  0.020
 UC9  plan-2  CAX  0.020
 UC9  plan-2  CAY  0.020
 UC9  plan-2  CAZ  0.020
 UC9  plan-2  CBD  0.020
 UC9  plan-2  CBA  0.020
 UC9  plan-2  CBB  0.020
 UC9  plan-2  H18  0.020
 UC9  plan-2  H19  0.020
 UC9  plan-2  H21  0.020
 UC9  plan-2  H22  0.020
 UC9  plan-3  CAM  0.020
 UC9  plan-3  CAN  0.020
 UC9  plan-3  CAO  0.020
 UC9  plan-3  CAS  0.020
 UC9  plan-3  CAR  0.020
 UC9  plan-3  OAW  0.020
 UC9  plan-3  OAU  0.020
 UC9  plan-3  CAQ  0.020
 UC9  plan-3  CAP  0.020
 UC9  plan-3  CAT  0.020
 UC9  plan-3  H14  0.020
 UC9  plan-3  H15  0.020
 UC9  plan-4  C2   0.020
 UC9  plan-4  NAH  0.020
 UC9  plan-4  H6   0.020
 UC9  plan-4  H7   0.020
 UC9  plan-5  C6   0.020
 UC9  plan-5  NAG  0.020
 UC9  plan-5  H8   0.020
 UC9  plan-5  H9   0.020
 UC9  plan-6  CAZ  0.020
 UC9  plan-6  CBD  0.020
 UC9  plan-6  OBF  0.020
 UC9  plan-6  OBE  0.020
 UC9  plan-6  H20  0.020

