# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:51:16 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-[4-(2-{[4-(morpholin-4-yl)phenyl]amino}pyrimidin-4-yl)phenyl]-D-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(cc1)c2ccnc(Nc3ccc(cc3)N4CCOCC4)n2)[C@H]5CCCN5
#
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
 O19  O19  N-[4-(2-{[4-(morpholin-4-yl)phenyl]amino}pyrimidin-4-yl)phenyl]-D-prolinamide  ligand  61  33  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O19
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
 O19  O10   O  O     0  -0.454    6.5613  -1.8263  -0.3019
 O19  C9    C  C     0   0.520    7.0927  -0.7424  -0.4545
 O19  C11   C  CH1   0  -0.203    8.6040  -0.5663  -0.4951
 O19  C15   C  CH2   0  -0.487    9.1265  -0.0991   0.8970
 O19  C14   C  CH2   0  -0.450    9.7533  -1.3592   1.4808
 O19  C13   C  CH2   0  -0.312   10.2934  -2.0373   0.2266
 O19  N12   N  NH1   0  -0.603    9.2799  -1.8189  -0.8052
 O19  N8    N  NH1   0  -0.740    6.4172   0.4304  -0.5704
 O19  C6    C  CR6   0   0.381    5.0538   0.6876  -0.4491
 O19  C1    C  CR16  0  -0.334    4.6618   2.0289  -0.4945
 O19  C5    C  CR16  0  -0.297    4.0714  -0.2929  -0.2910
 O19  C4    C  CR16  0  -0.270    2.7431   0.0788  -0.1728
 O19  C3    C  CR6   0   0.040    2.3450   1.4142  -0.1974
 O19  C2    C  CR16  0  -0.305    3.3345   2.3837  -0.3677
 O19  C7    C  CR6   0   0.297    0.9252   1.7757  -0.0389
 O19  N20   N  N     0  -0.500    0.0345   0.8096  -0.2044
 O19  C19   C  CR6   0   0.598   -1.2578   1.1101  -0.0451
 O19  N18   N  N     0  -0.470   -1.7420   2.3105   0.2628
 O19  C17   C  CR16  0   0.004   -0.8408   3.2702   0.4279
 O19  C16   C  CR16  0  -0.410    0.5169   3.0717   0.2936
 O19  N21   N  NH1   0  -0.771   -2.1006   0.0621  -0.2321
 O19  C22   C  CR6   0   0.333   -3.4865  -0.0447  -0.1116
 O19  C27   C  CR16  0  -0.341   -4.0586  -1.2681  -0.4795
 O19  C26   C  CR16  0  -0.316   -5.4144  -1.4950  -0.3680
 O19  C25   C  CR6   0   0.349   -6.2846  -0.5039   0.1082
 O19  C24   C  CR16  0  -0.345   -5.7088   0.7187   0.4555
 O19  C23   C  CR16  0  -0.302   -4.3403   0.9474   0.3606
 O19  N28   N  NT    0  -0.521   -7.6488  -0.7715   0.2594
 O19  C33   C  CH2   0  -0.328   -8.4683   0.2513   0.8779
 O19  C32   C  CH2   0  -0.184   -9.8209  -0.3266   1.2517
 O19  O31   O  O2    0  -0.482  -10.4778  -0.8946   0.1425
 O19  C30   C  CH2   0  -0.188   -9.6888  -1.9167  -0.4225
 O19  C29   C  CH2   0  -0.322   -8.3333  -1.3994  -0.8627
 O19  H11   H  HCH1  0   0.268    8.8376   0.1982  -1.2439
 O19  H8    H  HNH1  0   0.421    6.9884   1.2503  -0.7148
 O19  H151  H  HCH2  0   0.251    9.8868   0.6704   0.7551
 O19  H152  H  HCH2  0   0.255    8.3457   0.3335   1.5237
 O19  H12   H  HNH1  0   0.352    8.6025  -2.5707  -0.7556
 O19  H141  H  HCH2  0   0.239   10.5242  -1.1437   2.2213
 O19  H142  H  HCH2  0   0.230    8.9980  -1.9891   1.9570
 O19  H131  H  HCH2  0   0.218   11.2369  -1.5698  -0.0711
 O19  H132  H  HCH2  0   0.241   10.4835  -3.1038   0.3477
 O19  H1    H  HCR6  0   0.277    5.4072   2.8040  -0.6267
 O19  H5    H  HCR6  0   0.283    4.3269  -1.3387  -0.2582
 O19  H2    H  HCR6  0   0.260    3.0806   3.4343  -0.4162
 O19  H4    H  HCR6  0   0.261    1.9972  -0.6946  -0.0504
 O19  H16   H  HCR6  0   0.271    1.2103   3.8808   0.4627
 O19  H21   H  HNH1  0   0.405   -1.6235  -0.7888  -0.4890
 O19  H17   H  HCR6  0   0.273   -1.2266   4.2498   0.6872
 O19  H27   H  HCR6  0   0.264   -3.4259  -2.0681  -0.8472
 O19  H23   H  HCR6  0   0.280   -3.9533   1.9103   0.6499
 O19  H26   H  HCR6  0   0.263   -5.7904  -2.4719  -0.6419
 O19  H24   H  HCR6  0   0.265   -6.3189   1.5361   0.8146
 O19  H331  H  HCH2  0   0.254   -7.9921   0.6019   1.7950
 O19  H332  H  HCH2  0   0.216   -8.6028   1.1249   0.2210
 O19  H291  H  HCH2  0   0.220   -8.4552  -0.6893  -1.6946
 O19  H292  H  HCH2  0   0.256   -7.7579  -2.2439  -1.2381
 O19  H321  H  HCH2  0   0.204   -9.6822  -1.0794   2.0404
 O19  H322  H  HCH2  0   0.241  -10.4611   0.4632   1.6473
 O19  H301  H  HCH2  0   0.205   -9.5471  -2.7339   0.2989
 O19  H302  H  HCH2  0   0.241  -10.2287  -2.3141  -1.2829

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
 O19  O10  C9    double    1.217  0.020  1.217
 O19  C9   C11   single    1.522  0.020  1.522
 O19  C9   N8    single    1.358  0.020  1.358
 O19  C11  C15   single    1.559  0.020  1.559
 O19  C11  N12   single    1.457  0.020  1.457
 O19  C15  C14   single    1.524  0.020  1.524
 O19  C14  C13   single    1.525  0.020  1.525
 O19  C13  N12   single    1.463  0.020  1.463
 O19  N8   C6    single    1.393  0.020  1.393
 O19  C6   C1    aromatic  1.398  0.020  1.398
 O19  C6   C5    aromatic  1.397  0.020  1.397
 O19  C1   C2    aromatic  1.380  0.020  1.380
 O19  C5   C4    aromatic  1.384  0.020  1.384
 O19  C4   C3    aromatic  1.394  0.020  1.394
 O19  C3   C2    aromatic  1.396  0.020  1.396
 O19  C3   C7    single    1.474  0.020  1.474
 O19  C7   N20   aromatic  1.324  0.020  1.324
 O19  C7   C16   aromatic  1.399  0.020  1.399
 O19  N20  C19   aromatic  1.336  0.020  1.336
 O19  C19  N18   aromatic  1.330  0.020  1.330
 O19  C19  N21   single    1.358  0.020  1.358
 O19  N18  C17   aromatic  1.327  0.020  1.327
 O19  C17  C16   aromatic  1.379  0.020  1.379
 O19  N21  C22   single    1.395  0.020  1.395
 O19  C22  C27   aromatic  1.400  0.020  1.400
 O19  C22  C23   aromatic  1.391  0.020  1.391
 O19  C27  C26   aromatic  1.379  0.020  1.379
 O19  C26  C25   aromatic  1.402  0.020  1.402
 O19  C25  C24   aromatic  1.395  0.020  1.395
 O19  C25  N28   single    1.398  0.020  1.398
 O19  C24  C23   aromatic  1.391  0.020  1.391
 O19  N28  C33   single    1.449  0.020  1.449
 O19  N28  C29   single    1.457  0.020  1.457
 O19  C33  C32   single    1.518  0.020  1.518
 O19  C32  O31   single    1.409  0.020  1.409
 O19  O31  C30   single    1.409  0.020  1.409
 O19  C30  C29   single    1.516  0.020  1.516
 O19  C11  H11   single    0.970  0.020  1.090
 O19  N8   H8    single    0.860  0.020  1.020
 O19  C15  H151  single    0.970  0.020  1.090
 O19  C15  H152  single    0.970  0.020  1.090
 O19  N12  H12   single    0.890  0.020  1.040
 O19  C14  H141  single    0.970  0.020  1.090
 O19  C14  H142  single    0.970  0.020  1.090
 O19  C13  H131  single    0.970  0.020  1.090
 O19  C13  H132  single    0.970  0.020  1.090
 O19  C1   H1    single    0.930  0.020  1.080
 O19  C5   H5    single    0.930  0.020  1.080
 O19  C2   H2    single    0.930  0.020  1.080
 O19  C4   H4    single    0.930  0.020  1.080
 O19  C16  H16   single    0.930  0.020  1.080
 O19  N21  H21   single    0.860  0.020  1.020
 O19  C17  H17   single    0.930  0.020  1.080
 O19  C27  H27   single    0.930  0.020  1.080
 O19  C23  H23   single    0.930  0.020  1.080
 O19  C26  H26   single    0.930  0.020  1.080
 O19  C24  H24   single    0.930  0.020  1.080
 O19  C33  H331  single    0.970  0.020  1.090
 O19  C33  H332  single    0.970  0.020  1.090
 O19  C29  H291  single    0.970  0.020  1.090
 O19  C29  H292  single    0.970  0.020  1.090
 O19  C32  H321  single    0.970  0.020  1.090
 O19  C32  H322  single    0.970  0.020  1.090
 O19  C30  H301  single    0.970  0.020  1.090
 O19  C30  H302  single    0.970  0.020  1.090

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
 O19  N8    C9   C11   113.05  3.000
 O19  N8    C9   O10   124.24  3.000
 O19  C11   C9   O10   122.69  3.000
 O19  H11   C11  N12   110.84  3.000
 O19  H11   C11  C15   109.26  3.000
 O19  N12   C11  C15   107.00  3.000
 O19  H11   C11  C9    108.11  3.000
 O19  N12   C11  C9    111.52  3.000
 O19  C15   C11  C9    110.10  3.000
 O19  H152  C15  H151  107.09  3.000
 O19  H152  C15  C14   113.73  3.000
 O19  H151  C15  C14   110.27  3.000
 O19  H152  C15  C11   113.09  3.000
 O19  H151  C15  C11   109.20  3.000
 O19  C14   C15  C11   103.43  3.000
 O19  H142  C14  H141  107.85  3.000
 O19  H142  C14  C13   110.30  3.000
 O19  H141  C14  C13   113.34  3.000
 O19  H142  C14  C15   111.06  3.000
 O19  H141  C14  C15   112.80  3.000
 O19  C13   C14  C15   101.44  3.000
 O19  H132  C13  H131  107.33  3.000
 O19  H132  C13  N12   110.20  3.000
 O19  H131  C13  N12   109.98  3.000
 O19  H132  C13  C14   113.93  3.000
 O19  H131  C13  C14   109.83  3.000
 O19  N12   C13  C14   105.57  3.000
 O19  H12   N12  C13   108.54  3.000
 O19  H12   N12  C11   108.51  3.000
 O19  C13   N12  C11   107.44  3.000
 O19  H8    N8   C6    114.60  3.000
 O19  H8    N8   C9    115.59  3.000
 O19  C6    N8   C9    129.71  3.000
 O19  C5    C6   C1    118.68  3.000
 O19  C5    C6   N8    124.65  3.000
 O19  C1    C6   N8    116.67  3.000
 O19  H1    C1   C2    119.28  3.000
 O19  H1    C1   C6    119.82  3.000
 O19  C2    C1   C6    120.89  3.000
 O19  H5    C5   C4    119.06  3.000
 O19  H5    C5   C6    121.21  3.000
 O19  C4    C5   C6    119.73  3.000
 O19  H4    C4   C3    119.36  3.000
 O19  H4    C4   C5    118.65  3.000
 O19  C3    C4   C5    121.99  3.000
 O19  C7    C3   C2    121.72  3.000
 O19  C7    C3   C4    120.55  3.000
 O19  C2    C3   C4    117.73  3.000
 O19  H2    C2   C3    120.91  3.000
 O19  H2    C2   C1    118.12  3.000
 O19  C3    C2   C1    120.97  3.000
 O19  C16   C7   N20   120.61  3.000
 O19  C16   C7   C3    122.28  3.000
 O19  N20   C7   C3    117.10  3.000
 O19  C19   N20  C7    118.13  3.000
 O19  N21   C19  N18   120.16  3.000
 O19  N21   C19  N20   114.22  3.000
 O19  N18   C19  N20   125.62  3.000
 O19  C17   N18  C19   115.74  3.000
 O19  H17   C17  C16   120.25  3.000
 O19  H17   C17  N18   116.20  3.000
 O19  C16   C17  N18   123.55  3.000
 O19  H16   C16  C17   120.64  3.000
 O19  H16   C16  C7    122.99  3.000
 O19  C17   C16  C7    116.36  3.000
 O19  H21   N21  C22   115.29  3.000
 O19  H21   N21  C19   113.12  3.000
 O19  C22   N21  C19   131.58  3.000
 O19  C23   C22  C27   117.49  3.000
 O19  C23   C22  N21   125.75  3.000
 O19  C27   C22  N21   116.76  3.000
 O19  H27   C27  C26   118.67  3.000
 O19  H27   C27  C22   119.70  3.000
 O19  C26   C27  C22   121.62  3.000
 O19  H26   C26  C25   120.56  3.000
 O19  H26   C26  C27   118.01  3.000
 O19  C25   C26  C27   121.42  3.000
 O19  N28   C25  C24   122.91  3.000
 O19  N28   C25  C26   120.46  3.000
 O19  C24   C25  C26   116.60  3.000
 O19  H24   C24  C23   116.97  3.000
 O19  H24   C24  C25   120.81  3.000
 O19  C23   C24  C25   122.22  3.000
 O19  H23   C23  C24   118.83  3.000
 O19  H23   C23  C22   120.52  3.000
 O19  C24   C23  C22   120.65  3.000
 O19  C29   N28  C33   111.54  3.000
 O19  C29   N28  C25   117.24  3.000
 O19  C33   N28  C25   117.56  3.000
 O19  H332  C33  H331  107.44  3.000
 O19  H332  C33  C32   109.89  3.000
 O19  H331  C33  C32   107.71  3.000
 O19  H332  C33  N28   111.98  3.000
 O19  H331  C33  N28   109.80  3.000
 O19  C32   C33  N28   109.90  3.000
 O19  H322  C32  H321  108.04  3.000
 O19  H322  C32  O31   107.68  3.000
 O19  H321  C32  O31   110.35  3.000
 O19  H322  C32  C33   109.67  3.000
 O19  H321  C32  C33   108.97  3.000
 O19  O31   C32  C33   112.03  3.000
 O19  C30   O31  C32   110.30  3.000
 O19  H302  C30  H301  108.09  3.000
 O19  H302  C30  C29   109.75  3.000
 O19  H301  C30  C29   109.21  3.000
 O19  H302  C30  O31   107.65  3.000
 O19  H301  C30  O31   110.38  3.000
 O19  C29   C30  O31   111.68  3.000
 O19  H292  C29  H291  107.37  3.000
 O19  H292  C29  C30   107.94  3.000
 O19  H291  C29  C30   109.92  3.000
 O19  H292  C29  N28   110.58  3.000
 O19  H291  C29  N28   110.87  3.000
 O19  C30   C29  N28   110.09  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
 O19  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 O19  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 O19  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 O19  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 O19  CONST_05  C7   C3   C2   C1    180.00   0.0  0
 O19  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 O19  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 O19  CONST_08  C7   C3   C4   C5    180.00   0.0  0
 O19  CONST_11  C19  N20  C7   C3    180.00   0.0  0
 O19  CONST_12  C17  C16  C7   C3    180.00   0.0  0
 O19  CONST_15  N18  C19  N20  C7      0.00   0.0  0
 O19  CONST_16  N18  C17  C16  C7      0.00   0.0  0
 O19  CONST_17  C17  C16  C7   N20     0.00   0.0  0
 O19  CONST_18  C17  N18  C19  N20     0.00   0.0  0
 O19  CONST_19  C16  C7   N20  C19     0.00   0.0  0
 O19  CONST_20  C16  C17  N18  C19     0.00   0.0  0
 O19  CONST_21  C25  C26  C27  C22     0.00   0.0  0
 O19  CONST_22  C25  C24  C23  C22     0.00   0.0  0
 O19  CONST_23  C24  C23  C22  C27     0.00   0.0  0
 O19  CONST_24  C24  C25  C26  C27     0.00   0.0  0
 O19  CONST_25  C23  C22  C27  C26     0.00   0.0  0
 O19  CONST_26  C23  C24  C25  C26     0.00   0.0  0
 O19  CONST_27  N28  C25  C26  C27   180.00   0.0  0
 O19  CONST_28  N28  C25  C24  C23   180.00   0.0  0
 O19  CONST_29  C2   C1   C6   N8    180.00   0.0  0
 O19  CONST_30  C4   C5   C6   N8    180.00   0.0  0
 O19  CONST_31  N21  C19  N20  C7    180.00   0.0  0
 O19  CONST_32  N21  C19  N18  C17   180.00   0.0  0
 O19  CONST_33  C26  C27  C22  N21   180.00   0.0  0
 O19  CONST_34  C24  C23  C22  N21   180.00   0.0  0
 O19  CONST_35  H2   C2   C1   C6    180.00   0.0  0
 O19  CONST_36  H4   C4   C5   C6    180.00   0.0  0
 O19  CONST_37  H5   C5   C6   C1    180.00   0.0  0
 O19  CONST_38  H1   C1   C6   C5    180.00   0.0  0
 O19  CONST_39  H16  C16  C7   C3      0.00   0.0  0
 O19  CONST_40  H17  C17  C16  C7    180.00   0.0  0
 O19  CONST_41  H26  C26  C27  C22   180.00   0.0  0
 O19  CONST_42  H24  C24  C23  C22   180.00   0.0  0
 O19  CONST_43  H23  C23  C22  C27   180.00   0.0  0
 O19  CONST_44  H27  C27  C26  C25   180.00   0.0  0
 O19  CONST_45  C6   N8   C9   C11   180.00   0.0  0
 O19  CONST_46  C1   C6   N8   C9    180.00   0.0  0
 O19  CONST_47  C5   C6   N8   C9      0.00   0.0  0
 O19  CONST_48  H8   N8   C6   C1      0.00   0.0  0
 O19  CONST_49  C6   N8   C9   O10     0.00   0.0  0
 O19  Var_01    C13  C14  C15  C11    33.45  30.0  1
 O19  Var_02    C14  C13  N12  C11    29.18  30.0  1
 O19  Var_03    N12  C13  C14  C15   -39.16  30.0  1
 O19  Var_04    C33  N28  C25  C26   174.10  30.0  2
 O19  Var_05    C32  C33  N28  C25  -166.77  30.0  1
 O19  Var_06    C30  C29  N28  C25   166.40  30.0  1
 O19  Var_07    O31  C32  C33  N28   -56.22  30.0  1
 O19  Var_08    O31  C30  C29  N28    56.22  30.0  1
 O19  Var_09    C29  C30  O31  C32   -58.61  30.0  1
 O19  Var_10    C22  N21  C19  N20   177.34  30.0  2
 O19  Var_11    C27  C22  N21  C19   175.35  30.0  2

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
 O19  chir_01  C11  C9  C15  N12  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
 O19  plan-1  N8   0.020
 O19  plan-1  C6   0.020
 O19  plan-1  C1   0.020
 O19  plan-1  C5   0.020
 O19  plan-1  C4   0.020
 O19  plan-1  C3   0.020
 O19  plan-1  C2   0.020
 O19  plan-1  C7   0.020
 O19  plan-1  H1   0.020
 O19  plan-1  H5   0.020
 O19  plan-1  H2   0.020
 O19  plan-1  H4   0.020
 O19  plan-2  C3   0.020
 O19  plan-2  C7   0.020
 O19  plan-2  N20  0.020
 O19  plan-2  C19  0.020
 O19  plan-2  N18  0.020
 O19  plan-2  C17  0.020
 O19  plan-2  C16  0.020
 O19  plan-2  N21  0.020
 O19  plan-2  H16  0.020
 O19  plan-2  H17  0.020
 O19  plan-3  N21  0.020
 O19  plan-3  C22  0.020
 O19  plan-3  C27  0.020
 O19  plan-3  C26  0.020
 O19  plan-3  C25  0.020
 O19  plan-3  C24  0.020
 O19  plan-3  C23  0.020
 O19  plan-3  N28  0.020
 O19  plan-3  H27  0.020
 O19  plan-3  H23  0.020
 O19  plan-3  H26  0.020
 O19  plan-3  H24  0.020
 O19  plan-4  O10  0.020
 O19  plan-4  C9   0.020
 O19  plan-4  C11  0.020
 O19  plan-4  N8   0.020
 O19  plan-4  C6   0.020
 O19  plan-4  H8   0.020

