# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:34:36 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 9-cyclopentyl-N-[5-(piperazin-1-yl)pyridin-2-yl]-9H-pyrido[4',3':4,5]pyrrolo[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(C1)n2c3cnccc3c4cnc(Nc5ccc(cn5)N6CCNCC6)nc24
#
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
 24V  24V  9-cyclopentyl-N-[5-(piperazin-1-yl)pyridin-2-yl]-9H-pyrido[4',3':4,5]pyrrolo[2,3-d]pyrimidin-2-amine  ligand  57  31  .  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_24V
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
 24V  N1   N  N     0  -0.410  -6.7747  -2.4085  -0.3896
 24V  C10  C  CH1   0  -0.097  -4.6752   1.4698   0.2942
 24V  C13  C  CH2   0  -0.451  -4.2587   3.8181  -0.0828
 24V  C17  C  CR16  0  -0.168   3.5742  -0.6310   0.5754
 24V  C20  C  CR16  0  -0.361   2.6466   1.5952  -0.6387
 24V  C21  C  CH2   0  -0.305   6.3104  -1.3593   0.4707
 24V  C22  C  CH2   0  -0.299   7.7403  -1.6486   0.0498
 24V  C24  C  CH2   0  -0.298   6.7906   1.0066   0.3007
 24V  C02  C  CR16  0  -0.107  -6.2566  -1.2074  -0.1740
 24V  C03  C  CR56  0   0.269  -4.8832  -1.0106  -0.1645
 24V  C04  C  CR56  0   0.120  -4.0201  -2.1014  -0.3902
 24V  C05  C  CR16  0  -0.435  -4.5781  -3.3525  -0.6146
 24V  C06  C  CR56  0  -0.050  -2.6930  -1.5674  -0.3243
 24V  C07  C  CR16  0  -0.079  -1.3937  -2.0214  -0.4593
 24V  N01  N  N     0  -0.450  -0.3577  -1.2078  -0.3402
 24V  C08  C  CR6   0   0.570  -0.6109   0.0806  -0.0765
 24V  N02  N  N     0  -0.497  -1.8117   0.6433   0.0725
 24V  C09  C  CR56  0   0.540  -2.8257  -0.1876  -0.0603
 24V  N03  N  NR5   0  -0.629  -4.1410   0.1421   0.0351
 24V  C11  C  CH2   0  -0.454  -4.1743   2.1100   1.6148
 24V  C12  C  CH2   0  -0.441  -3.5397   3.4430   1.2120
 24V  C14  C  CH2   0  -0.449  -4.3583   2.4853  -0.8186
 24V  N04  N  NH1   0  -0.743   0.4311   0.9478   0.0304
 24V  C16  C  CR6   0   0.456   1.8002   0.6785  -0.0121
 24V  N05  N  N     0  -0.404   2.2662  -0.3976   0.5866
 24V  C18  C  CR6   0   0.283   4.5184   0.2076  -0.0239
 24V  C19  C  CR16  0  -0.221   4.0027   1.3598  -0.6360
 24V  N06  N  NT    0  -0.519   5.8793  -0.0767  -0.0538
 24V  N07  N  NH1   0  -0.598   8.6108  -0.5782   0.4918
 24V  C23  C  CH2   0  -0.301   8.2079   0.6719  -0.1210
 24V  C2   C  CR16  0  -0.093  -5.9602  -3.4437  -0.6019
 24V  H1   H  HCH1  0   0.276  -5.7545   1.3420   0.3573
 24V  H2   H  HCH2  0   0.222  -5.2560   4.2107   0.1368
 24V  H3   H  HCH2  0   0.236  -3.7306   4.5766  -0.6622
 24V  H5   H  HCR6  0   0.276   2.2450   2.4702  -1.1330
 24V  H6   H  HCH2  0   0.249   5.6704  -2.1478   0.0715
 24V  H7   H  HCH2  0   0.213   6.2369  -1.3965   1.5685
 24V  H8   H  HCH2  0   0.240   8.0542  -2.5884   0.5068
 24V  H9   H  HCH2  0   0.196   7.7614  -1.7898  -1.0426
 24V  H10  H  HCH2  0   0.252   6.4865   1.9275  -0.1930
 24V  H11  H  HCH2  0   0.216   6.7663   1.1913   1.3844
 24V  H12  H  HCR6  0   0.272  -6.9540  -0.3933  -0.0103
 24V  H13  H  HCR6  0   0.263  -3.9700  -4.2285  -0.7959
 24V  H14  H  HCR6  0   0.269  -1.1735  -3.0617  -0.6766
 24V  H15  H  HCH2  0   0.243  -5.0266   2.2759   2.2753
 24V  H16  H  HCH2  0   0.247  -3.4836   1.4609   2.1516
 24V  H17  H  HCH2  0   0.228  -2.4766   3.2995   1.0080
 24V  H18  H  HCH2  0   0.232  -3.6292   4.2029   1.9888
 24V  H19  H  HCH2  0   0.242  -3.3952   2.2510  -1.2743
 24V  H20  H  HCH2  0   0.244  -5.1111   2.4721  -1.6071
 24V  H21  H  HNH1  0   0.409   0.1619   1.9197   0.0511
 24V  H22  H  HCR6  0   0.278   4.6552   2.0604  -1.1403
 24V  H23  H  HNH1  0   0.357   9.5686  -0.7893   0.2451
 24V  H25  H  HCH2  0   0.197   8.2527   0.6403  -1.2212
 24V  H26  H  HCH2  0   0.239   8.8707   1.4730   0.2108
 24V  H27  H  HCR6  0   0.260  -6.4380  -4.4013  -0.7740
 24V  H4   H  HCR6  0   0.267   3.8813  -1.5340   1.0883

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
 24V  C13  C12  single    1.528  0.020  1.528
 24V  C13  C14  single    1.526  0.020  1.526
 24V  C12  C11  single    1.530  0.020  1.530
 24V  C14  C10  single    1.539  0.020  1.539
 24V  N07  C23  single    1.449  0.020  1.449
 24V  N07  C22  single    1.449  0.020  1.449
 24V  C23  C24  single    1.516  0.020  1.516
 24V  C11  C10  single    1.551  0.020  1.551
 24V  C10  N03  single    1.454  0.020  1.454
 24V  C24  N06  single    1.459  0.020  1.459
 24V  C02  N1   aromatic  1.326  0.020  1.326
 24V  C02  C03  aromatic  1.387  0.020  1.387
 24V  C22  C21  single    1.518  0.020  1.518
 24V  N1   C2   aromatic  1.334  0.020  1.334
 24V  C21  N06  single    1.451  0.020  1.451
 24V  N03  C03  aromatic  1.385  0.020  1.385
 24V  N03  C09  aromatic  1.359  0.020  1.359
 24V  C03  C04  aromatic  1.409  0.020  1.409
 24V  N06  C18  single    1.391  0.020  1.391
 24V  C2   C05  aromatic  1.385  0.020  1.385
 24V  C19  C18  aromatic  1.403  0.020  1.403
 24V  C19  C20  aromatic  1.376  0.020  1.376
 24V  C18  C17  aromatic  1.398  0.020  1.398
 24V  C09  N02  aromatic  1.318  0.020  1.318
 24V  C09  C06  aromatic  1.411  0.020  1.411
 24V  C04  C05  aromatic  1.388  0.020  1.388
 24V  C04  C06  aromatic  1.432  0.020  1.432
 24V  C20  C16  aromatic  1.396  0.020  1.396
 24V  N02  C08  aromatic  1.334  0.020  1.334
 24V  C17  N05  aromatic  1.329  0.020  1.329
 24V  C06  C07  aromatic  1.383  0.020  1.383
 24V  C16  N05  aromatic  1.317  0.020  1.317
 24V  C16  N04  single    1.396  0.020  1.396
 24V  C08  N04  single    1.360  0.020  1.360
 24V  C08  N01  aromatic  1.339  0.020  1.339
 24V  C07  N01  aromatic  1.323  0.020  1.323
 24V  C10  H1   single    0.970  0.020  1.090
 24V  C13  H2   single    0.970  0.020  1.090
 24V  C13  H3   single    0.970  0.020  1.090
 24V  C17  H4   single    0.930  0.020  1.080
 24V  C20  H5   single    0.930  0.020  1.080
 24V  C21  H6   single    0.970  0.020  1.090
 24V  C21  H7   single    0.970  0.020  1.090
 24V  C22  H8   single    0.970  0.020  1.090
 24V  C22  H9   single    0.970  0.020  1.090
 24V  C24  H10  single    0.970  0.020  1.090
 24V  C24  H11  single    0.970  0.020  1.090
 24V  C02  H12  single    0.930  0.020  1.080
 24V  C05  H13  single    0.930  0.020  1.080
 24V  C07  H14  single    0.930  0.020  1.080
 24V  C11  H15  single    0.970  0.020  1.090
 24V  C11  H16  single    0.970  0.020  1.090
 24V  C12  H17  single    0.970  0.020  1.090
 24V  C12  H18  single    0.970  0.020  1.090
 24V  C14  H19  single    0.970  0.020  1.090
 24V  C14  H20  single    0.970  0.020  1.090
 24V  N04  H21  single    0.860  0.020  1.020
 24V  C19  H22  single    0.930  0.020  1.080
 24V  N07  H23  single    0.890  0.020  1.040
 24V  C23  H25  single    0.970  0.020  1.090
 24V  C23  H26  single    0.970  0.020  1.090
 24V  C2   H27  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
 24V  C2   N1   C02  119.36  3.000
 24V  H1   C10  C14  108.87  3.000
 24V  H1   C10  C11  108.63  3.000
 24V  C14  C10  C11  106.07  3.000
 24V  H1   C10  N03  105.50  3.000
 24V  C11  C10  N03  114.20  3.000
 24V  C14  C10  N03  113.44  3.000
 24V  H3   C13  H2   107.36  3.000
 24V  H3   C13  C14  112.51  3.000
 24V  H2   C13  C14  110.54  3.000
 24V  H3   C13  C12  113.14  3.000
 24V  H2   C13  C12  110.31  3.000
 24V  C14  C13  C12  103.00  3.000
 24V  H4   C17  C18  120.78  3.000
 24V  H4   C17  N05  114.94  3.000
 24V  C18  C17  N05  124.28  3.000
 24V  H5   C20  C19  120.32  3.000
 24V  H5   C20  C16  120.73  3.000
 24V  C19  C20  C16  118.95  3.000
 24V  H7   C21  H6   107.53  3.000
 24V  H7   C21  N06  111.74  3.000
 24V  H6   C21  N06  109.40  3.000
 24V  H7   C21  C22  109.45  3.000
 24V  H6   C21  C22  108.25  3.000
 24V  N06  C21  C22  110.36  3.000
 24V  H9   C22  H8   107.42  3.000
 24V  H9   C22  N07  112.69  3.000
 24V  H8   C22  N07  109.61  3.000
 24V  H9   C22  C21  108.51  3.000
 24V  H8   C22  C21  108.59  3.000
 24V  N07  C22  C21  109.91  3.000
 24V  H11  C24  H10  107.39  3.000
 24V  H11  C24  C23  109.38  3.000
 24V  H10  C24  C23  108.78  3.000
 24V  H11  C24  N06  110.50  3.000
 24V  H10  C24  N06  110.09  3.000
 24V  C23  C24  N06  110.63  3.000
 24V  H12  C02  C03  121.95  3.000
 24V  H12  C02  N1   116.96  3.000
 24V  C03  C02  N1   121.09  3.000
 24V  N03  C03  C04  109.82  3.000
 24V  C04  C03  C02  119.70  3.000
 24V  N03  C03  C02  130.49  3.000
 24V  C06  C04  C05  135.73  3.000
 24V  C06  C04  C03  105.76  3.000
 24V  C05  C04  C03  118.51  3.000
 24V  H13  C05  C2   120.60  3.000
 24V  H13  C05  C04  122.07  3.000
 24V  C2   C05  C04  117.32  3.000
 24V  C09  C06  C07  115.31  3.000
 24V  C07  C06  C04  138.05  3.000
 24V  C09  C06  C04  106.63  3.000
 24V  H14  C07  N01  116.66  3.000
 24V  H14  C07  C06  121.66  3.000
 24V  N01  C07  C06  121.68  3.000
 24V  C08  N01  C07  117.48  3.000
 24V  N04  C08  N02  114.31  3.000
 24V  N04  C08  N01  118.96  3.000
 24V  N02  C08  N01  126.71  3.000
 24V  C09  N02  C08  114.53  3.000
 24V  N03  C09  N02  125.77  3.000
 24V  N02  C09  C06  124.27  3.000
 24V  N03  C09  C06  109.95  3.000
 24V  C09  N03  C03  107.84  3.000
 24V  C09  N03  C10  126.10  3.000
 24V  C03  N03  C10  126.05  3.000
 24V  H16  C11  H15  106.71  3.000
 24V  H16  C11  C12  112.70  3.000
 24V  H15  C11  C12  110.54  3.000
 24V  H16  C11  C10  112.24  3.000
 24V  H15  C11  C10  109.03  3.000
 24V  C12  C11  C10  105.63  3.000
 24V  H18  C12  H17  107.74  3.000
 24V  H18  C12  C11  112.68  3.000
 24V  H17  C12  C11  109.78  3.000
 24V  H18  C12  C13  113.20  3.000
 24V  H17  C12  C13  109.40  3.000
 24V  C11  C12  C13  103.99  3.000
 24V  H20  C14  H19  107.74  3.000
 24V  H20  C14  C13  113.86  3.000
 24V  H19  C14  C13  109.36  3.000
 24V  H20  C14  C10  111.88  3.000
 24V  H19  C14  C10  110.00  3.000
 24V  C13  C14  C10  103.95  3.000
 24V  H21  N04  C16  116.63  3.000
 24V  H21  N04  C08  114.31  3.000
 24V  C16  N04  C08  128.76  3.000
 24V  N05  C16  N04  119.40  3.000
 24V  N04  C16  C20  118.78  3.000
 24V  N05  C16  C20  121.75  3.000
 24V  C16  N05  C17  119.22  3.000
 24V  N06  C18  C19  121.22  3.000
 24V  C19  C18  C17  115.56  3.000
 24V  N06  C18  C17  123.20  3.000
 24V  H22  C19  C18  120.89  3.000
 24V  H22  C19  C20  118.84  3.000
 24V  C18  C19  C20  120.23  3.000
 24V  C18  N06  C24  117.01  3.000
 24V  C18  N06  C21  117.62  3.000
 24V  C24  N06  C21  112.50  3.000
 24V  H23  N07  C23  109.89  3.000
 24V  H23  N07  C22  109.90  3.000
 24V  C23  N07  C22  109.95  3.000
 24V  H26  C23  H25  107.46  3.000
 24V  H26  C23  N07  109.62  3.000
 24V  H25  C23  N07  112.72  3.000
 24V  H26  C23  C24  108.73  3.000
 24V  H25  C23  C24  108.79  3.000
 24V  N07  C23  C24  109.43  3.000
 24V  H27  C2   C05  119.77  3.000
 24V  H27  C2   N1   116.21  3.000
 24V  C05  C2   N1   124.02  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
 24V  CONST_01  N03  C03  C02  N1    180.00   0.0  0
 24V  CONST_02  C04  C03  C02  N1      0.00   0.0  0
 24V  CONST_03  C04  C05  C2   N1      0.00   0.0  0
 24V  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 24V  CONST_05  C20  C16  N05  C17     0.00   0.0  0
 24V  CONST_06  C05  C2   N1   C02     0.00   0.0  0
 24V  CONST_07  C09  N03  C03  C02   180.00   0.0  0
 24V  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 24V  CONST_09  C06  C04  C03  C02   180.00   0.0  0
 24V  CONST_10  C2   N1   C02  C03     0.00   0.0  0
 24V  CONST_11  N02  C09  N03  C03   180.00   0.0  0
 24V  CONST_12  C06  C09  N03  C03     0.00   0.0  0
 24V  CONST_13  C2   C05  C04  C03     0.00   0.0  0
 24V  CONST_14  C09  C06  C04  C03     0.00   0.0  0
 24V  CONST_15  C07  C06  C04  C03   180.00   0.0  0
 24V  CONST_16  C09  N03  C03  C04     0.00   0.0  0
 24V  CONST_17  N03  C09  C06  C04     0.00   0.0  0
 24V  CONST_18  N02  C09  C06  C04   180.00   0.0  0
 24V  CONST_19  N01  C07  C06  C04   180.00   0.0  0
 24V  CONST_20  N03  C03  C04  C05   180.00   0.0  0
 24V  CONST_21  C09  C06  C04  C05   180.00   0.0  0
 24V  CONST_22  C07  C06  C04  C05     0.00   0.0  0
 24V  CONST_23  C08  N02  C09  C06     0.00   0.0  0
 24V  CONST_24  N03  C03  C04  C06     0.00   0.0  0
 24V  CONST_25  C2   C05  C04  C06   180.00   0.0  0
 24V  CONST_26  C08  N01  C07  C06     0.00   0.0  0
 24V  CONST_27  N03  C09  C06  C07   180.00   0.0  0
 24V  CONST_28  N02  C09  C06  C07     0.00   0.0  0
 24V  CONST_29  N02  C08  N01  C07     0.00   0.0  0
 24V  CONST_30  C09  N02  C08  N01     0.00   0.0  0
 24V  CONST_31  C09  C06  C07  N01     0.00   0.0  0
 24V  CONST_32  N03  C09  N02  C08   180.00   0.0  0
 24V  CONST_33  C18  C19  C20  C16     0.00   0.0  0
 24V  CONST_34  C18  C17  N05  C16     0.00   0.0  0
 24V  CONST_35  C19  C18  C17  N05     0.00   0.0  0
 24V  CONST_36  C19  C20  C16  N05     0.00   0.0  0
 24V  CONST_37  C02  C03  N03  C10     0.00   0.0  0
 24V  CONST_38  C04  C03  N03  C10   180.00   0.0  0
 24V  CONST_39  N02  C09  N03  C10     0.00   0.0  0
 24V  CONST_40  C06  C09  N03  C10   180.00   0.0  0
 24V  CONST_41  N06  C18  C19  C20   180.00   0.0  0
 24V  CONST_42  N06  C18  C17  N05   180.00   0.0  0
 24V  CONST_43  N04  C16  N05  C17   180.00   0.0  0
 24V  CONST_44  N04  C08  N01  C07   180.00   0.0  0
 24V  CONST_45  N04  C08  N02  C09   180.00   0.0  0
 24V  CONST_46  C19  C20  C16  N04   180.00   0.0  0
 24V  CONST_47  H13  C05  C2   N1    180.00   0.0  0
 24V  CONST_48  H22  C19  C18  C17   180.00   0.0  0
 24V  CONST_49  H27  C2   N1   C02   180.00   0.0  0
 24V  CONST_50  H12  C02  C03  C04   180.00   0.0  0
 24V  CONST_51  H14  C07  C06  C04     0.00   0.0  0
 24V  CONST_52  H4   C17  N05  C16   180.00   0.0  0
 24V  CONST_53  H5   C20  C16  N05   180.00   0.0  0
 24V  Var_01    C12  C13  C14  C10    39.29  30.0  1
 24V  Var_02    C13  C12  C11  C10    26.33  30.0  1
 24V  Var_03    C24  N06  C18  C17  -133.62  30.0  2
 24V  Var_04    C23  N07  C22  C21   -61.25  30.0  1
 24V  Var_05    C23  C24  N06  C21    54.08  30.0  1
 24V  Var_06    C24  C23  N07  C22    61.18  30.0  1
 24V  Var_07    C14  C13  C12  C11   -40.83  30.0  1
 24V  Var_08    N07  C23  C24  N06   -56.96  30.0  1
 24V  Var_09    N07  C22  C21  N06    56.80  30.0  1
 24V  Var_10    C08  N04  C16  C20   143.10  30.0  2
 24V  Var_11    C16  N04  C08  N01    -4.62  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
 24V  chir_01  C10  C14  C11  N03  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
 24V  plan-1  C17  0.020
 24V  plan-1  C20  0.020
 24V  plan-1  N04  0.020
 24V  plan-1  C16  0.020
 24V  plan-1  N05  0.020
 24V  plan-1  C18  0.020
 24V  plan-1  C19  0.020
 24V  plan-1  N06  0.020
 24V  plan-1  H5   0.020
 24V  plan-1  H22  0.020
 24V  plan-1  H4   0.020
 24V  plan-2  N1   0.020
 24V  plan-2  C10  0.020
 24V  plan-2  C02  0.020
 24V  plan-2  C03  0.020
 24V  plan-2  C04  0.020
 24V  plan-2  C05  0.020
 24V  plan-2  C06  0.020
 24V  plan-2  C07  0.020
 24V  plan-2  N01  0.020
 24V  plan-2  C08  0.020
 24V  plan-2  N02  0.020
 24V  plan-2  C09  0.020
 24V  plan-2  N03  0.020
 24V  plan-2  N04  0.020
 24V  plan-2  C2   0.020
 24V  plan-2  H12  0.020
 24V  plan-2  H13  0.020
 24V  plan-2  H14  0.020
 24V  plan-2  H27  0.020

