# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:15:29 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]C1(CCN(CC1)c2ncnc3[nH]ccc23)Cc4ccc(Cl)cc4
#
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
 M05  M05  4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium  ligand  45  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M05
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
 M05  N1    N   NT    0  -0.469   -6.7650   -8.0705   -8.1541
 M05  C8    C   CH2   0  -0.345   -7.9590   -8.4784   -7.4363
 M05  C4    C   CH2   0  -0.539  -10.2396   -7.1381   -9.2059
 M05  C5    C   CT    0   0.020   -9.3076   -8.3157   -9.5513
 M05  N6    N   NT3   1  -0.797  -10.0370   -9.1864  -10.5339
 M05  C2    C   CH2   0  -0.360   -7.0785   -7.1603   -9.2393
 M05  C9    C   CR6   0   0.135  -11.5337   -7.5201   -8.5415
 M05  C10   C   CR16  0  -0.338  -12.6756   -7.7756   -9.2974
 M05  C11   C   CR16  0  -0.190  -13.8695   -8.1506   -8.6972
 M05  C12   C   CR6   0  -0.052  -13.9219   -8.2619   -7.3180
 M05  CL1   CL  CL    0  -0.124  -15.4053   -8.7279   -6.5546
 M05  C14   C   CR16  0  -0.191  -12.8074   -7.9961   -6.5367
 M05  C15   C   CR16  0  -0.307  -11.6239   -7.6263   -7.1547
 M05  C16   C   CR6   0   0.492   -5.7003   -8.9224   -8.2224
 M05  N17   N   N     0  -0.489   -5.8272  -10.1086   -7.6286
 M05  C18   C   CR16  0   0.037   -4.8167  -10.9733   -7.6525
 M05  N19   N   N     0  -0.445   -3.6416  -10.8201   -8.2220
 M05  C20   C   CR56  0   0.474   -3.5028   -9.6229   -8.7935
 M05  N21   N   NR15  0  -0.656   -2.3810   -9.1688   -9.3962
 M05  C22   C   CR15  0  -0.007   -2.5788   -7.8788   -9.8079
 M05  C23   C   CR15  0  -0.451   -3.8425   -7.4841   -9.4855
 M05  C3    C   CH2   0  -0.441   -8.9382   -9.1955   -8.3584
 M05  C17   C   CH2   0  -0.428   -8.0373   -7.8103  -10.2375
 M05  C24   C   CR56  0  -0.061   -4.4681   -8.5991   -8.8386
 M05  H8C1  H   HCH2  0   0.286   -7.6902   -9.1285   -6.6097
 M05  H8C2  H   HCH2  0   0.262   -8.4121   -7.5818   -7.0049
 M05  H2C1  H   HCH2  0   0.266   -7.5083   -6.2475   -8.8206
 M05  H2C2  H   HCH2  0   0.289   -6.1854   -6.8555   -9.7706
 M05  H3C1  H   HCH2  0   0.273   -8.4604  -10.1124   -8.7164
 M05  H3C2  H   HCH2  0   0.274   -9.8277   -9.5031   -7.8049
 M05  H4C1  H   HCH2  0   0.294   -9.6918   -6.4482   -8.5627
 M05  H4C2  H   HCH2  0   0.291  -10.4473   -6.5873  -10.1277
 M05  H6N1  H   HNT3  0   0.471  -10.2634   -8.6918  -11.3988
 M05  H6N2  H   HNT3  0   0.477   -9.4841  -10.0028  -10.8012
 M05  H171  H   HCH2  0   0.270   -7.5223   -8.6474  -10.7192
 M05  H172  H   HCH2  0   0.276   -8.2846   -7.0897  -11.0211
 M05  H10   H   HCR6  0   0.273  -12.6517   -7.6641  -10.3753
 M05  H15   H   HCR6  0   0.272  -10.7609   -7.4062   -6.5376
 M05  H11   H   HCR6  0   0.285  -14.7450   -8.3439   -9.3018
 M05  H14   H   HCR6  0   0.285  -12.8586   -8.0717   -5.4592
 M05  H18   H   HCR6  0   0.247   -4.9944  -11.9176   -7.1486
 M05  H21   H   HNR5  0   0.415   -1.5266   -9.6925   -9.4997
 M05  H22   H   HCR5  0   0.290   -1.7921   -7.3323  -10.3007
 M05  H23   H   HCR5  0   0.259   -4.2399   -6.5022   -9.6787
 M05  H4    H   HNT3  0   0.473  -10.9155   -9.5439  -10.1513

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
 M05  N1   C8    single    1.452  0.020  1.452
 M05  N1   C2    single    1.451  0.020  1.451
 M05  N1   C16   single    1.365  0.020  1.365
 M05  C8   C3    single    1.524  0.020  1.524
 M05  C4   C5    single    1.541  0.020  1.541
 M05  C4   C9    single    1.504  0.020  1.504
 M05  C5   N6    single    1.502  0.020  1.502
 M05  C5   C3    single    1.528  0.020  1.528
 M05  C5   C17   single    1.530  0.020  1.530
 M05  C2   C17   single    1.529  0.020  1.529
 M05  C9   C10   aromatic  1.393  0.020  1.393
 M05  C9   C15   aromatic  1.394  0.020  1.394
 M05  C10  C11   aromatic  1.388  0.020  1.388
 M05  C11  C12   aromatic  1.385  0.020  1.385
 M05  C12  CL1   single    1.732  0.020  1.732
 M05  C12  C14   aromatic  1.387  0.020  1.387
 M05  C14  C15   aromatic  1.385  0.020  1.385
 M05  C16  N17   aromatic  1.333  0.020  1.333
 M05  C16  C24   aromatic  1.415  0.020  1.415
 M05  N17  C18   aromatic  1.330  0.020  1.330
 M05  C18  N19   aromatic  1.315  0.020  1.315
 M05  N19  C20   aromatic  1.334  0.020  1.334
 M05  C20  N21   aromatic  1.352  0.020  1.352
 M05  C20  C24   aromatic  1.408  0.020  1.408
 M05  N21  C22   aromatic  1.368  0.020  1.368
 M05  C22  C23   aromatic  1.363  0.020  1.363
 M05  C23  C24   aromatic  1.433  0.020  1.433
 M05  C8   H8C1  single    0.970  0.020  1.090
 M05  C8   H8C2  single    0.970  0.020  1.090
 M05  C2   H2C1  single    0.970  0.020  1.090
 M05  C2   H2C2  single    0.970  0.020  1.090
 M05  C3   H3C1  single    0.970  0.020  1.090
 M05  C3   H3C2  single    0.970  0.020  1.090
 M05  C4   H4C1  single    0.970  0.020  1.090
 M05  C4   H4C2  single    0.970  0.020  1.090
 M05  N6   H6N1  single    0.890  0.020  1.040
 M05  N6   H6N2  single    0.890  0.020  1.040
 M05  C17  H171  single    0.970  0.020  1.090
 M05  C17  H172  single    0.970  0.020  1.090
 M05  C10  H10   single    0.930  0.020  1.080
 M05  C15  H15   single    0.930  0.020  1.080
 M05  C11  H11   single    0.930  0.020  1.080
 M05  C14  H14   single    0.930  0.020  1.080
 M05  C18  H18   single    0.930  0.020  1.080
 M05  N21  H21   single    0.860  0.020  1.020
 M05  C22  H22   single    0.930  0.020  1.080
 M05  C23  H23   single    0.930  0.020  1.080
 M05  N6   H4    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
 M05  C16   N1   C2    121.51  3.000
 M05  C16   N1   C8    119.40  3.000
 M05  C2    N1   C8    111.62  3.000
 M05  H8C2  C8   H8C1  107.05  3.000
 M05  H8C2  C8   C3    111.00  3.000
 M05  H8C1  C8   C3    109.76  3.000
 M05  H8C2  C8   N1    107.79  3.000
 M05  H8C1  C8   N1    109.95  3.000
 M05  C3    C8   N1    111.19  3.000
 M05  H4C2  C4   H4C1  105.89  3.000
 M05  H4C2  C4   C9    109.68  3.000
 M05  H4C1  C4   C9    109.41  3.000
 M05  H4C2  C4   C5    108.11  3.000
 M05  H4C1  C4   C5    108.17  3.000
 M05  C9    C4   C5    115.17  3.000
 M05  C17   C5   C3    109.87  3.000
 M05  C17   C5   N6    107.54  3.000
 M05  C3    C5   N6    107.13  3.000
 M05  C17   C5   C4    110.50  3.000
 M05  C3    C5   C4    114.29  3.000
 M05  N6    C5   C4    107.21  3.000
 M05  H4    N6   H6N2  106.46  3.000
 M05  H4    N6   H6N1  107.19  3.000
 M05  H6N2  N6   H6N1  106.58  3.000
 M05  H4    N6   C5    112.03  3.000
 M05  H6N2  N6   C5    111.81  3.000
 M05  H6N1  N6   C5    112.39  3.000
 M05  H2C2  C2   H2C1  106.10  3.000
 M05  H2C2  C2   C17   108.45  3.000
 M05  H2C1  C2   C17   111.02  3.000
 M05  H2C2  C2   N1    111.43  3.000
 M05  H2C1  C2   N1    108.82  3.000
 M05  C17   C2   N1    110.92  3.000
 M05  C15   C9   C10   118.22  3.000
 M05  C15   C9   C4    120.97  3.000
 M05  C10   C9   C4    120.81  3.000
 M05  H10   C10  C11   118.47  3.000
 M05  H10   C10  C9    120.18  3.000
 M05  C11   C10  C9    121.34  3.000
 M05  H11   C11  C12   120.79  3.000
 M05  H11   C11  C10   120.20  3.000
 M05  C12   C11  C10   119.01  3.000
 M05  C14   C12  CL1   119.44  3.000
 M05  C14   C12  C11   121.02  3.000
 M05  CL1   C12  C11   119.54  3.000
 M05  H14   C14  C15   120.24  3.000
 M05  H14   C14  C12   120.66  3.000
 M05  C15   C14  C12   119.10  3.000
 M05  H15   C15  C14   118.72  3.000
 M05  H15   C15  C9    119.98  3.000
 M05  C14   C15  C9    121.30  3.000
 M05  C24   C16  N17   118.71  3.000
 M05  C24   C16  N1    123.93  3.000
 M05  N17   C16  N1    117.32  3.000
 M05  C18   N17  C16   119.88  3.000
 M05  H18   C18  N19   116.68  3.000
 M05  H18   C18  N17   115.66  3.000
 M05  N19   C18  N17   127.67  3.000
 M05  C20   N19  C18   112.53  3.000
 M05  C24   C20  N21   108.08  3.000
 M05  C24   C20  N19   126.52  3.000
 M05  N21   C20  N19   125.36  3.000
 M05  H21   N21  C22   125.57  3.000
 M05  H21   N21  C20   125.09  3.000
 M05  C22   N21  C20   109.31  3.000
 M05  H22   C22  C23   129.68  3.000
 M05  H22   C22  N21   120.68  3.000
 M05  C23   C22  N21   109.63  3.000
 M05  H23   C23  C24   129.01  3.000
 M05  H23   C23  C22   124.34  3.000
 M05  C24   C23  C22   106.64  3.000
 M05  H3C2  C3   H3C1  106.59  3.000
 M05  H3C2  C3   C5    111.17  3.000
 M05  H3C1  C3   C5    109.43  3.000
 M05  H3C2  C3   C8    110.44  3.000
 M05  H3C1  C3   C8    108.16  3.000
 M05  C5    C3   C8    110.90  3.000
 M05  H172  C17  H171  107.17  3.000
 M05  H172  C17  C2    109.25  3.000
 M05  H171  C17  C2    108.50  3.000
 M05  H172  C17  C5    110.58  3.000
 M05  H171  C17  C5    109.60  3.000
 M05  C2    C17  C5    111.61  3.000
 M05  C23   C24  C20   106.32  3.000
 M05  C23   C24  C16   138.99  3.000
 M05  C20   C24  C16   114.64  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
 M05  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 M05  CONST_02  C12  C14  C15  C9     0.00   0.0  0
 M05  CONST_03  C14  C15  C9   C10    0.00   0.0  0
 M05  CONST_04  C14  C12  C11  C10    0.00   0.0  0
 M05  CONST_05  C15  C9   C10  C11    0.00   0.0  0
 M05  CONST_06  C15  C14  C12  C11    0.00   0.0  0
 M05  CONST_07  N19  C18  N17  C16    0.00   0.0  0
 M05  CONST_08  N19  C20  C24  C16    0.00   0.0  0
 M05  CONST_09  N21  C20  C24  C16  180.00   0.0  0
 M05  CONST_10  C22  C23  C24  C16  180.00   0.0  0
 M05  CONST_11  C20  C24  C16  N17    0.00   0.0  0
 M05  CONST_12  C23  C24  C16  N17  180.00   0.0  0
 M05  CONST_13  C20  N19  C18  N17    0.00   0.0  0
 M05  CONST_14  C24  C16  N17  C18    0.00   0.0  0
 M05  CONST_15  N21  C20  N19  C18  180.00   0.0  0
 M05  CONST_16  C24  C20  N19  C18    0.00   0.0  0
 M05  CONST_17  C22  N21  C20  N19  180.00   0.0  0
 M05  CONST_18  C23  C24  C20  N19  180.00   0.0  0
 M05  CONST_19  C23  C22  N21  C20    0.00   0.0  0
 M05  CONST_20  C22  C23  C24  C20    0.00   0.0  0
 M05  CONST_21  C23  C24  C20  N21    0.00   0.0  0
 M05  CONST_22  C24  C23  C22  N21    0.00   0.0  0
 M05  CONST_23  C24  C20  N21  C22    0.00   0.0  0
 M05  CONST_24  C18  N17  C16  N1   180.00   0.0  0
 M05  CONST_25  C20  C24  C16  N1   180.00   0.0  0
 M05  CONST_26  C23  C24  C16  N1     0.00   0.0  0
 M05  CONST_27  C11  C10  C9   C4   180.00   0.0  0
 M05  CONST_28  C14  C15  C9   C4   180.00   0.0  0
 M05  CONST_29  CL1  C12  C11  C10  180.00   0.0  0
 M05  CONST_30  C15  C14  C12  CL1  180.00   0.0  0
 M05  CONST_31  H11  C11  C10  C9   180.00   0.0  0
 M05  CONST_32  H14  C14  C15  C9   180.00   0.0  0
 M05  CONST_33  H15  C15  C9   C10  180.00   0.0  0
 M05  CONST_34  H10  C10  C11  C12  180.00   0.0  0
 M05  CONST_35  H18  C18  N17  C16  180.00   0.0  0
 M05  CONST_36  H23  C23  C24  C16    0.00   0.0  0
 M05  CONST_37  H21  N21  C20  N19    0.00   0.0  0
 M05  CONST_38  H22  C22  N21  C20  180.00   0.0  0
 M05  Var_01    C5   C3   C8   N1   -56.71  30.0  1
 M05  Var_02    C5   C17  C2   N1    55.25  30.0  1
 M05  Var_03    C17  C2   N1   C8   -59.25  30.0  1
 M05  Var_04    N17  C16  N1   C8     0.82  30.0  2
 M05  Var_05    C3   C8   N1   C2    60.31  30.0  1
 M05  Var_06    C10  C9   C4   C5   -91.19  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
 M05  chir_01  C5  N6  C3  C17  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
 M05  plan-1  C4   0.020
 M05  plan-1  C9   0.020
 M05  plan-1  C10  0.020
 M05  plan-1  C11  0.020
 M05  plan-1  C12  0.020
 M05  plan-1  CL1  0.020
 M05  plan-1  C14  0.020
 M05  plan-1  C15  0.020
 M05  plan-1  H10  0.020
 M05  plan-1  H15  0.020
 M05  plan-1  H11  0.020
 M05  plan-1  H14  0.020
 M05  plan-2  N1   0.020
 M05  plan-2  C16  0.020
 M05  plan-2  N17  0.020
 M05  plan-2  C18  0.020
 M05  plan-2  N19  0.020
 M05  plan-2  C20  0.020
 M05  plan-2  N21  0.020
 M05  plan-2  C22  0.020
 M05  plan-2  C23  0.020
 M05  plan-2  C24  0.020
 M05  plan-2  H18  0.020
 M05  plan-2  H21  0.020
 M05  plan-2  H22  0.020
 M05  plan-2  H23  0.020

