# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 18:18:19 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 4-{(6R,7R)-7-amino-3-[3-(4-methylpiperazin-1-yl)phenyl]-6,7-dihydropyrazolo[1,5-a]pyrimidin-6-yl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2cccc(c2)c3cnn4[C@@H](N)[C@@H](C=Nc34)c5ccc(O)cc5
#
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
 5LK  5LK  4-{(6R,7R)-7-amino-3-[3-(4-methylpiperazin-1-yl)phenyl]-6,7-dihydropyrazolo[1,5-a]pyrimidin-6-yl}phenol  ligand  56  30  .  2022-07-23  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_5LK
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
 5LK  N1    N  NR5   0  -0.328   1.9931   1.5504  -0.1505
 5LK  N2    N  N     0  -0.274   1.2867   1.8614  -1.2290
 5LK  C3    C  CR15  0  -0.097   0.1232   1.2630  -1.0636
 5LK  C5    C  CR5   0  -0.176   0.0547   0.5568   0.1573
 5LK  C6    C  CR5   0   0.524   1.3009   0.7858   0.7220
 5LK  N7    N  N     0  -0.382   1.8404   0.3729   1.9224
 5LK  C8    C  C1    0  -0.056   3.0914   0.5524   2.0876
 5LK  C10   C  CH1   0  -0.455   4.0200   1.1504   1.0662
 5LK  C11   C  CH1   0   0.050   3.2824   2.1541   0.1635
 5LK  N12   N  NH2   0  -0.772   3.1932   3.4422   0.7845
 5LK  C15   C  CR6   0   0.151   4.7133   0.0580   0.2766
 5LK  C16   C  CR16  0  -0.290   6.0569   0.2058  -0.0542
 5LK  C18   C  CR16  0  -0.370   6.7239  -0.7399  -0.8169
 5LK  C20   C  CR6   0   0.346   6.0477  -1.8704  -1.2678
 5LK  C21   C  CR16  0  -0.321   4.7042  -2.0361  -0.9402
 5LK  C23   C  CR16  0  -0.288   4.0527  -1.0823  -0.1761
 5LK  O25   O  OH1   0  -0.629   6.6383  -2.8268  -2.0088
 5LK  C27   C  CR6   0   0.122  -1.0638  -0.2362   0.6636
 5LK  C28   C  CR16  0  -0.424  -2.3508   0.0315   0.2052
 5LK  C30   C  CR6   0   0.395  -3.4593  -0.7171   0.6206
 5LK  C31   C  CR16  0  -0.373  -3.2405  -1.7596   1.5278
 5LK  C33   C  CR16  0  -0.224  -1.9570  -2.0326   1.9828
 5LK  C35   C  CR16  0  -0.362  -0.8689  -1.2871   1.5667
 5LK  N37   N  NT    0  -0.521  -4.7216  -0.4295   0.1006
 5LK  C38   C  CH2   0  -0.313  -5.8010  -1.3524   0.3848
 5LK  C41   C  CH2   0  -0.278  -6.9683  -1.0985  -0.5514
 5LK  N44   N  NT    0  -0.412  -7.4286   0.2700  -0.4506
 5LK  C45   C  CH2   0  -0.283  -6.3458   1.1740  -0.7765
 5LK  C48   C  CH2   0  -0.306  -5.1695   0.9554   0.1541
 5LK  C51   C  CH3   0  -0.517  -8.5928   0.5055  -1.2730
 5LK  H3    H  HCR5  0   0.265  -0.6333   1.3315  -1.8311
 5LK  H8    H  H     0   0.282   3.5274   0.2186   3.0245
 5LK  H10   H  HCH1  0   0.306   4.7879   1.7133   1.6017
 5LK  HN12  H  HNH2  0   0.365   2.7320   4.1022   0.1717
 5LK  H16   H  HCR6  0   0.261   6.6001   1.0782   0.2890
 5LK  H18   H  HCR6  0   0.272   7.7713  -0.5949  -1.0563
 5LK  H21   H  HCR6  0   0.266   4.1715  -2.9141  -1.2834
 5LK  H23   H  HCR6  0   0.252   3.0115  -1.2540   0.0660
 5LK  HO25  H  HOH1  0   0.474   7.5581  -2.5989  -2.1836
 5LK  H28   H  HCR6  0   0.252  -2.4941   0.8357  -0.5058
 5LK  H31   H  HCR6  0   0.266  -4.0610  -2.3600   1.8950
 5LK  H33   H  HCR6  0   0.251  -1.8115  -2.8465   2.6820
 5LK  H35   H  HCR6  0   0.243   0.1217  -1.5219   1.9294
 5LK  H38   H  HCH2  0   0.251  -5.4549  -2.3749   0.2274
 5LK  H38A  H  HCH2  0   0.211  -6.1461  -1.2759   1.4275
 5LK  H41   H  HCH2  0   0.193  -6.6626  -1.3474  -1.5828
 5LK  H41A  H  HCH2  0   0.240  -7.7834  -1.7754  -0.2836
 5LK  H45   H  HCH2  0   0.193  -6.0084   1.0491  -1.8208
 5LK  H45A  H  HCH2  0   0.239  -6.6916   2.2047  -0.6679
 5LK  H48   H  HCH2  0   0.215  -5.4614   1.2266   1.1794
 5LK  H48A  H  HCH2  0   0.254  -4.3642   1.6248  -0.1419
 5LK  H51   H  HCH3  0   0.233  -9.4062  -0.1544  -0.9672
 5LK  H51A  H  HCH3  0   0.233  -8.9351   1.5344  -1.1518
 5LK  H51B  H  HCH3  0   0.192  -8.4096   0.3359  -2.3458
 5LK  H25   H  HCH1  0   0.293   3.8175   2.2639  -0.7798
 5LK  H26   H  HNH2  0   0.364   2.6610   3.4112   1.6461

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
 5LK  N1   C6    aromatic  1.351  0.020  1.351
 5LK  N1   C11   single    1.458  0.020  1.458
 5LK  N2   N1    aromatic  1.326  0.020  1.326
 5LK  C3   N2    aromatic  1.319  0.020  1.319
 5LK  C3   C5    aromatic  1.412  0.020  1.412
 5LK  C3   H3    single    0.930  0.020  1.080
 5LK  C5   C6    aromatic  1.387  0.020  1.387
 5LK  C5   C27   single    1.462  0.020  1.462
 5LK  C6   N7    single    1.379  0.020  1.379
 5LK  N7   C8    double    1.275  0.020  1.275
 5LK  C8   H8    single    0.930  0.020  1.080
 5LK  C10  C8    single    1.504  0.020  1.504
 5LK  C10  C15   single    1.516  0.020  1.516
 5LK  C10  H10   single    0.970  0.020  1.090
 5LK  C11  C10   single    1.538  0.020  1.538
 5LK  N12  C11   single    1.433  0.020  1.433
 5LK  N12  HN12  single    0.890  0.020  1.040
 5LK  C15  C16   aromatic  1.392  0.020  1.392
 5LK  C16  C18   aromatic  1.386  0.020  1.386
 5LK  C16  H16   single    0.930  0.020  1.080
 5LK  C18  H18   single    0.930  0.020  1.080
 5LK  C20  C18   aromatic  1.392  0.020  1.392
 5LK  C20  O25   single    1.346  0.020  1.346
 5LK  C21  C20   aromatic  1.393  0.020  1.393
 5LK  C21  H21   single    0.930  0.020  1.080
 5LK  C23  C15   aromatic  1.393  0.020  1.393
 5LK  C23  C21   aromatic  1.385  0.020  1.385
 5LK  C23  H23   single    0.930  0.020  1.080
 5LK  O25  HO25  single    0.850  0.020  0.980
 5LK  C27  C35   aromatic  1.399  0.020  1.399
 5LK  C28  C27   aromatic  1.392  0.020  1.392
 5LK  C28  C30   aromatic  1.401  0.020  1.401
 5LK  C28  H28   single    0.930  0.020  1.080
 5LK  C30  C31   aromatic  1.399  0.020  1.399
 5LK  C31  C33   aromatic  1.389  0.020  1.389
 5LK  C31  H31   single    0.930  0.020  1.080
 5LK  C33  H33   single    0.930  0.020  1.080
 5LK  C35  C33   aromatic  1.383  0.020  1.383
 5LK  C35  H35   single    0.930  0.020  1.080
 5LK  N37  C30   single    1.395  0.020  1.395
 5LK  C38  N37   single    1.448  0.020  1.448
 5LK  C38  H38   single    0.970  0.020  1.090
 5LK  C38  H38A  single    0.970  0.020  1.090
 5LK  C41  C38   single    1.518  0.020  1.518
 5LK  C41  H41   single    0.970  0.020  1.090
 5LK  C41  H41A  single    0.970  0.020  1.090
 5LK  N44  C41   single    1.447  0.020  1.447
 5LK  N44  C45   single    1.448  0.020  1.448
 5LK  C45  C48   single    1.516  0.020  1.516
 5LK  C45  H45   single    0.970  0.020  1.090
 5LK  C45  H45A  single    0.970  0.020  1.090
 5LK  C48  N37   single    1.456  0.020  1.456
 5LK  C48  H48   single    0.970  0.020  1.090
 5LK  C48  H48A  single    0.970  0.020  1.090
 5LK  C51  N44   single    1.445  0.020  1.445
 5LK  C51  H51   single    0.970  0.020  1.090
 5LK  C51  H51A  single    0.970  0.020  1.090
 5LK  C51  H51B  single    0.970  0.020  1.090
 5LK  C11  H25   single    0.970  0.020  1.090
 5LK  N12  H26   single    0.890  0.020  1.040

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
 5LK  C11   N1   C6    123.26  3.000
 5LK  C11   N1   N2    123.30  3.000
 5LK  C6    N1   N2    112.65  3.000
 5LK  C3    N2   N1    105.16  3.000
 5LK  H3    C3   C5    127.75  3.000
 5LK  H3    C3   N2    120.02  3.000
 5LK  C5    C3   N2    112.22  3.000
 5LK  C27   C5   C6    129.49  3.000
 5LK  C27   C5   C3    127.44  3.000
 5LK  C6    C5   C3    103.05  3.000
 5LK  N7    C6   C5    131.02  3.000
 5LK  N7    C6   N1    122.08  3.000
 5LK  C5    C6   N1    106.90  3.000
 5LK  C8    N7   C6    117.03  3.000
 5LK  H8    C8   C10   117.40  3.000
 5LK  C10   C8   N7    125.02  3.000
 5LK  H8    C8   N7    117.55  3.000
 5LK  H10   C10  C15   107.77  3.000
 5LK  H10   C10  C11   106.77  3.000
 5LK  C15   C10  C11   112.57  3.000
 5LK  C11   C10  C8    111.22  3.000
 5LK  H10   C10  C8    107.81  3.000
 5LK  C15   C10  C8    110.46  3.000
 5LK  H25   C11  N12   108.37  3.000
 5LK  H25   C11  C10   109.77  3.000
 5LK  N12   C11  C10   111.23  3.000
 5LK  H25   C11  N1    106.83  3.000
 5LK  N12   C11  N1    114.24  3.000
 5LK  C10   C11  N1    106.27  3.000
 5LK  H26   N12  HN12  107.19  3.000
 5LK  H26   N12  C11   111.95  3.000
 5LK  HN12  N12  C11   110.63  3.000
 5LK  C23   C15  C16   117.86  3.000
 5LK  C23   C15  C10   122.84  3.000
 5LK  C16   C15  C10   119.27  3.000
 5LK  H16   C16  C18   118.84  3.000
 5LK  H16   C16  C15   119.62  3.000
 5LK  C18   C16  C15   121.54  3.000
 5LK  H18   C18  C20   120.42  3.000
 5LK  C20   C18  C16   119.90  3.000
 5LK  H18   C18  C16   119.69  3.000
 5LK  O25   C20  C21   117.91  3.000
 5LK  C21   C20  C18   119.27  3.000
 5LK  O25   C20  C18   122.82  3.000
 5LK  H21   C21  C23   120.13  3.000
 5LK  C23   C21  C20   120.11  3.000
 5LK  H21   C21  C20   119.77  3.000
 5LK  H23   C23  C21   117.81  3.000
 5LK  H23   C23  C15   120.86  3.000
 5LK  C21   C23  C15   121.32  3.000
 5LK  HO25  O25  C20   110.52  3.000
 5LK  C35   C27  C28   119.06  3.000
 5LK  C28   C27  C5    119.28  3.000
 5LK  C35   C27  C5    121.63  3.000
 5LK  H28   C28  C30   119.13  3.000
 5LK  H28   C28  C27   118.78  3.000
 5LK  C30   C28  C27   122.09  3.000
 5LK  N37   C30  C31   122.46  3.000
 5LK  N37   C30  C28   119.69  3.000
 5LK  C31   C30  C28   117.83  3.000
 5LK  H31   C31  C33   118.75  3.000
 5LK  H31   C31  C30   121.02  3.000
 5LK  C33   C31  C30   120.22  3.000
 5LK  H33   C33  C35   119.59  3.000
 5LK  C35   C33  C31   121.50  3.000
 5LK  H33   C33  C31   118.91  3.000
 5LK  H35   C35  C33   120.20  3.000
 5LK  H35   C35  C27   120.50  3.000
 5LK  C33   C35  C27   119.30  3.000
 5LK  C48   N37  C38   111.69  3.000
 5LK  C48   N37  C30   117.43  3.000
 5LK  C38   N37  C30   118.02  3.000
 5LK  H38A  C38  H38   107.54  3.000
 5LK  H38A  C38  C41   109.35  3.000
 5LK  H38   C38  C41   108.17  3.000
 5LK  C41   C38  N37   110.22  3.000
 5LK  H38A  C38  N37   112.03  3.000
 5LK  H38   C38  N37   109.42  3.000
 5LK  H41A  C41  H41   107.20  3.000
 5LK  H41A  C41  N44   109.36  3.000
 5LK  H41   C41  N44   111.48  3.000
 5LK  N44   C41  C38   111.09  3.000
 5LK  H41A  C41  C38   108.60  3.000
 5LK  H41   C41  C38   109.00  3.000
 5LK  C51   N44  C45   111.89  3.000
 5LK  C51   N44  C41   111.76  3.000
 5LK  C45   N44  C41   109.69  3.000
 5LK  H45A  C45  H45   107.31  3.000
 5LK  H45A  C45  C48   108.70  3.000
 5LK  H45   C45  C48   109.09  3.000
 5LK  H45A  C45  N44   109.26  3.000
 5LK  H45   C45  N44   111.76  3.000
 5LK  C48   C45  N44   110.62  3.000
 5LK  H48A  C48  H48   107.35  3.000
 5LK  H48A  C48  C45   108.58  3.000
 5LK  H48   C48  C45   109.31  3.000
 5LK  H48A  C48  N37   110.33  3.000
 5LK  H48   C48  N37   110.50  3.000
 5LK  C45   C48  N37   110.69  3.000
 5LK  H51B  C51  H51A  107.79  3.000
 5LK  H51B  C51  H51   107.69  3.000
 5LK  H51A  C51  H51   107.77  3.000
 5LK  H51B  C51  N44   113.29  3.000
 5LK  H51A  C51  N44   110.08  3.000
 5LK  H51   C51  N44   110.04  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
 5LK  CONST_01  C3   C5   C6   N1      0.00   0.0  0
 5LK  CONST_02  C27  C5   C6   N1    180.00   0.0  0
 5LK  CONST_03  C5   C3   N2   N1      0.00   0.0  0
 5LK  CONST_04  C5   C6   N1   N2      0.00   0.0  0
 5LK  CONST_05  C6   C5   C3   N2      0.00   0.0  0
 5LK  CONST_06  C27  C5   C3   N2    180.00   0.0  0
 5LK  CONST_07  C6   N1   N2   C3      0.00   0.0  0
 5LK  CONST_10  C33  C35  C27  C5    180.00   0.0  0
 5LK  CONST_11  C30  C28  C27  C5    180.00   0.0  0
 5LK  CONST_14  C20  C18  C16  C15     0.00   0.0  0
 5LK  CONST_15  C20  C21  C23  C15     0.00   0.0  0
 5LK  CONST_16  C21  C23  C15  C16     0.00   0.0  0
 5LK  CONST_17  C21  C20  C18  C16     0.00   0.0  0
 5LK  CONST_18  C23  C15  C16  C18     0.00   0.0  0
 5LK  CONST_19  C23  C21  C20  C18     0.00   0.0  0
 5LK  CONST_20  C31  C33  C35  C27     0.00   0.0  0
 5LK  CONST_21  C31  C30  C28  C27     0.00   0.0  0
 5LK  CONST_22  C33  C35  C27  C28     0.00   0.0  0
 5LK  CONST_23  C33  C31  C30  C28     0.00   0.0  0
 5LK  CONST_24  C35  C27  C28  C30     0.00   0.0  0
 5LK  CONST_25  C35  C33  C31  C30     0.00   0.0  0
 5LK  CONST_26  C27  C5   C6   N7      0.00   0.0  0
 5LK  CONST_27  C18  C16  C15  C10   180.00   0.0  0
 5LK  CONST_28  C21  C23  C15  C10   180.00   0.0  0
 5LK  CONST_29  N37  C30  C28  C27   180.00   0.0  0
 5LK  CONST_30  N37  C30  C31  C33   180.00   0.0  0
 5LK  CONST_31  O25  C20  C18  C16   180.00   0.0  0
 5LK  CONST_32  O25  C20  C21  C23   180.00   0.0  0
 5LK  CONST_33  H3   C3   N2   N1    180.00   0.0  0
 5LK  CONST_34  H35  C35  C27  C5      0.00   0.0  0
 5LK  CONST_35  H28  C28  C27  C5      0.00   0.0  0
 5LK  CONST_36  H16  C16  C15  C10     0.00   0.0  0
 5LK  CONST_37  H23  C23  C15  C10     0.00   0.0  0
 5LK  CONST_38  H18  C18  C16  C15   180.00   0.0  0
 5LK  CONST_39  H21  C21  C23  C15   180.00   0.0  0
 5LK  CONST_40  H33  C33  C35  C27   180.00   0.0  0
 5LK  CONST_41  H31  C31  C30  C28   180.00   0.0  0
 5LK  Var_01    C10  C8   N7   C6     -1.34  30.0  1
 5LK  Var_02    C38  N37  C30  C28   170.31  30.0  2
 5LK  Var_03    C41  C38  N37  C30  -164.40  30.0  1
 5LK  Var_04    C45  C48  N37  C30   163.94  30.0  1
 5LK  Var_05    N44  C41  C38  N37   -57.05  30.0  1
 5LK  Var_06    N44  C45  C48  N37    56.77  30.0  1
 5LK  Var_07    C45  N44  C41  C38    58.94  30.0  1
 5LK  Var_08    C48  C45  N44  C41   -58.60  30.0  1
 5LK  Var_09    H51  C51  N44  C41    59.54  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
 5LK  chir_01  C10  C8  C15  C11  negativ
 5LK  chir_02  C11  N1  N12  C10  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
 5LK  plan-1  C10  0.020
 5LK  plan-1  C15  0.020
 5LK  plan-1  C16  0.020
 5LK  plan-1  C18  0.020
 5LK  plan-1  C20  0.020
 5LK  plan-1  C21  0.020
 5LK  plan-1  C23  0.020
 5LK  plan-1  O25  0.020
 5LK  plan-1  H16  0.020
 5LK  plan-1  H18  0.020
 5LK  plan-1  H21  0.020
 5LK  plan-1  H23  0.020
 5LK  plan-2  C5   0.020
 5LK  plan-2  C27  0.020
 5LK  plan-2  C28  0.020
 5LK  plan-2  C30  0.020
 5LK  plan-2  C31  0.020
 5LK  plan-2  C33  0.020
 5LK  plan-2  C35  0.020
 5LK  plan-2  N37  0.020
 5LK  plan-2  H28  0.020
 5LK  plan-2  H31  0.020
 5LK  plan-2  H33  0.020
 5LK  plan-2  H35  0.020
 5LK  plan-3  N1   0.020
 5LK  plan-3  N2   0.020
 5LK  plan-3  C3   0.020
 5LK  plan-3  C5   0.020
 5LK  plan-3  C6   0.020
 5LK  plan-3  N7   0.020
 5LK  plan-3  C11  0.020
 5LK  plan-3  C27  0.020
 5LK  plan-3  H3   0.020

