# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:49:28 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 1-[4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(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
 M04  M04  1-[4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine  ligand  47  25  .  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_M04
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
 M04  N1    N   NT    0  -0.460   7.4227   8.8965   3.8301
 M04  C2    C   CH2   0  -0.350   8.0135   7.9051   2.9554
 M04  C3    C   CH2   0  -0.431   9.3061   8.4329   2.3461
 M04  C5    C   CH2   0  -0.282  10.9008   7.6455   4.1621
 M04  N6    N   NH2   0  -0.797  11.6224   6.6498   3.3941
 M04  C7    C   CH2   0  -0.424   9.6133   9.7673   4.4492
 M04  C8    C   CH2   0  -0.339   8.2940   9.1879   4.9583
 M04  C9    C   CR6   0   0.157  11.1826  10.8804   2.0220
 M04  C10   C   CR16  0  -0.318  10.8618  10.8527   0.6657
 M04  C11   C   CR16  0  -0.197  10.5518  12.0105  -0.0320
 M04  C12   C   CR6   0  -0.059  10.5712  13.2243   0.6357
 M04  CL1   CL  CL    0  -0.138  10.1909  14.6814  -0.2276
 M04  C14   C   CR16  0  -0.199  10.9018  13.2916   1.9794
 M04  C15   C   CR16  0  -0.319  11.2059  12.1202   2.6578
 M04  C16   C   CR6   0   0.496   6.4938   9.7936   3.4235
 M04  N17   N   N     0  -0.494   6.0893  10.6887   4.3337
 M04  C13   C   CH2   0  -0.505  11.5075   9.6192   2.7689
 M04  C18   C   CR16  0   0.036   5.1326  11.5570   4.0351
 M04  N19   N   N     0  -0.454   4.4821  11.6842   2.8984
 M04  C20   C   CR56  0   0.467   4.9040  10.8163   1.9761
 M04  N21   N   NR15  0  -0.656   4.4482  10.7566   0.7052
 M04  C22   C   CR15  0  -0.015   5.1303   9.7861   0.0226
 M04  C23   C   CR15  0  -0.446   6.0360   9.1981   0.8523
 M04  C24   C   CR56  0  -0.079   5.9062   9.8383   2.1311
 M04  C4    C   CT    0  -0.108  10.3170   8.8722   3.4165
 M04  H2C1  H   HCH2  0   0.261   8.2070   7.0138   3.5583
 M04  H2C2  H   HCH2  0   0.268   7.3078   7.5911   2.1938
 M04  H8C1  H   HCH2  0   0.274   7.8045   9.8862   5.6296
 M04  H8C2  H   HCH2  0   0.244   8.4510   8.2601   5.5140
 M04  H3C1  H   HCH2  0   0.229   9.7495   7.6740   1.6946
 M04  H3C2  H   HCH2  0   0.249   9.0581   9.2791   1.6993
 M04  H5C1  H   HCH2  0   0.229  10.0993   7.1261   4.6933
 M04  H5C2  H   HCH2  0   0.229  11.5713   8.0239   4.9402
 M04  H6N1  H   HNH2  0   0.345  11.0392   6.2543   2.6682
 M04  H6N2  H   HNH2  0   0.348  12.4249   7.0555   2.9317
 M04  H7C1  H   HCH2  0   0.244   9.3945  10.7442   4.0091
 M04  H7C2  H   HCH2  0   0.235  10.2818   9.9508   5.2969
 M04  H10   H   HCR6  0   0.261  10.8572   9.9099   0.1318
 M04  H15   H   HCR6  0   0.260  11.4740  12.1807   3.7058
 M04  H131  H   HCH2  0   0.241  12.0092   8.9322   2.0817
 M04  H132  H   HCH2  0   0.247  12.2304   9.8463   3.5591
 M04  H11   H   HCR6  0   0.276  10.3072  11.9635  -1.0846
 M04  H14   H   HCR6  0   0.276  10.9320  14.2427   2.4937
 M04  H18   H   HCR6  0   0.242   4.8565  12.2421   4.8309
 M04  H21   H   HNR5  0   0.412   3.7278  11.3471   0.3220
 M04  H22   H   HCR5  0   0.287   4.9193   9.5900  -1.0154
 M04  H23   H   HCR5  0   0.255   6.7104   8.4163   0.5492

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
 M04  N1   C2    single    1.448  0.020  1.448
 M04  N1   C8    single    1.455  0.020  1.455
 M04  N1   C16   single    1.354  0.020  1.354
 M04  C2   C3    single    1.523  0.020  1.523
 M04  C3   C4    single    1.536  0.020  1.536
 M04  C5   N6    single    1.450  0.020  1.450
 M04  C5   C4    single    1.550  0.020  1.550
 M04  C7   C8    single    1.528  0.020  1.528
 M04  C7   C4    single    1.537  0.020  1.537
 M04  C9   C10   aromatic  1.394  0.020  1.394
 M04  C9   C15   aromatic  1.394  0.020  1.394
 M04  C9   C13   single    1.501  0.020  1.501
 M04  C10  C11   aromatic  1.387  0.020  1.387
 M04  C11  C12   aromatic  1.385  0.020  1.385
 M04  C12  CL1   single    1.736  0.020  1.736
 M04  C12  C14   aromatic  1.385  0.020  1.385
 M04  C14  C15   aromatic  1.387  0.020  1.387
 M04  C16  N17   aromatic  1.339  0.020  1.339
 M04  C16  C24   aromatic  1.420  0.020  1.420
 M04  N17  C18   aromatic  1.326  0.020  1.326
 M04  C18  N19   aromatic  1.316  0.020  1.316
 M04  C13  C4    single    1.548  0.020  1.548
 M04  N19  C20   aromatic  1.335  0.020  1.335
 M04  C20  N21   aromatic  1.352  0.020  1.352
 M04  C20  C24   aromatic  1.409  0.020  1.409
 M04  N21  C22   aromatic  1.369  0.020  1.369
 M04  C22  C23   aromatic  1.362  0.020  1.362
 M04  C23  C24   aromatic  1.436  0.020  1.436
 M04  C2   H2C1  single    0.970  0.020  1.090
 M04  C2   H2C2  single    0.970  0.020  1.090
 M04  C8   H8C1  single    0.970  0.020  1.090
 M04  C8   H8C2  single    0.970  0.020  1.090
 M04  C3   H3C1  single    0.970  0.020  1.090
 M04  C3   H3C2  single    0.970  0.020  1.090
 M04  C5   H5C1  single    0.970  0.020  1.090
 M04  C5   H5C2  single    0.970  0.020  1.090
 M04  N6   H6N1  single    0.890  0.020  1.040
 M04  N6   H6N2  single    0.890  0.020  1.040
 M04  C7   H7C1  single    0.970  0.020  1.090
 M04  C7   H7C2  single    0.970  0.020  1.090
 M04  C10  H10   single    0.930  0.020  1.080
 M04  C15  H15   single    0.930  0.020  1.080
 M04  C13  H131  single    0.970  0.020  1.090
 M04  C13  H132  single    0.970  0.020  1.090
 M04  C11  H11   single    0.930  0.020  1.080
 M04  C14  H14   single    0.930  0.020  1.080
 M04  C18  H18   single    0.930  0.020  1.080
 M04  N21  H21   single    0.860  0.020  1.020
 M04  C22  H22   single    0.930  0.020  1.080
 M04  C23  H23   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
 M04  C16   N1   C8    120.73  3.000
 M04  C16   N1   C2    123.52  3.000
 M04  C8    N1   C2    111.17  3.000
 M04  H2C2  C2   H2C1  105.44  3.000
 M04  H2C2  C2   C3    111.80  3.000
 M04  H2C1  C2   C3    110.66  3.000
 M04  H2C2  C2   N1    110.90  3.000
 M04  H2C1  C2   N1    107.29  3.000
 M04  C3    C2   N1    110.53  3.000
 M04  H3C2  C3   H3C1  106.05  3.000
 M04  H3C2  C3   C4    109.88  3.000
 M04  H3C1  C3   C4    110.28  3.000
 M04  H3C2  C3   C2    108.19  3.000
 M04  H3C1  C3   C2    109.98  3.000
 M04  C4    C3   C2    112.25  3.000
 M04  H5C2  C5   H5C1  105.54  3.000
 M04  H5C2  C5   C4    107.40  3.000
 M04  H5C1  C5   C4    109.50  3.000
 M04  H5C2  C5   N6    108.01  3.000
 M04  H5C1  C5   N6    107.22  3.000
 M04  C4    C5   N6    118.44  3.000
 M04  H6N2  N6   H6N1  106.63  3.000
 M04  H6N2  N6   C5    111.21  3.000
 M04  H6N1  N6   C5    111.21  3.000
 M04  H7C2  C7   H7C1  106.50  3.000
 M04  H7C2  C7   C4    109.77  3.000
 M04  H7C1  C7   C4    109.96  3.000
 M04  H7C2  C7   C8    109.43  3.000
 M04  H7C1  C7   C8    107.46  3.000
 M04  C4    C7   C8    113.47  3.000
 M04  H8C2  C8   H8C1  107.25  3.000
 M04  H8C2  C8   C7    111.55  3.000
 M04  H8C1  C8   C7    110.58  3.000
 M04  H8C2  C8   N1    108.07  3.000
 M04  H8C1  C8   N1    109.77  3.000
 M04  C7    C8   N1    109.55  3.000
 M04  C13   C9   C15   121.12  3.000
 M04  C13   C9   C10   121.14  3.000
 M04  C15   C9   C10   117.74  3.000
 M04  H10   C10  C11   118.53  3.000
 M04  H10   C10  C9    119.84  3.000
 M04  C11   C10  C9    121.63  3.000
 M04  H11   C11  C12   120.68  3.000
 M04  H11   C11  C10   120.25  3.000
 M04  C12   C11  C10   119.06  3.000
 M04  C14   C12  CL1   119.59  3.000
 M04  C14   C12  C11   120.89  3.000
 M04  CL1   C12  C11   119.52  3.000
 M04  H14   C14  C15   120.24  3.000
 M04  H14   C14  C12   120.70  3.000
 M04  C15   C14  C12   119.05  3.000
 M04  H15   C15  C14   118.69  3.000
 M04  H15   C15  C9    119.68  3.000
 M04  C14   C15  C9    121.63  3.000
 M04  C24   C16  N17   118.19  3.000
 M04  C24   C16  N1    125.31  3.000
 M04  N17   C16  N1    116.49  3.000
 M04  C18   N17  C16   120.17  3.000
 M04  H132  C13  H131  106.32  3.000
 M04  H132  C13  C4    107.82  3.000
 M04  H131  C13  C4    108.22  3.000
 M04  H132  C13  C9    109.13  3.000
 M04  H131  C13  C9    108.33  3.000
 M04  C4    C13  C9    116.57  3.000
 M04  H18   C18  N19   116.52  3.000
 M04  H18   C18  N17   115.57  3.000
 M04  N19   C18  N17   127.91  3.000
 M04  C20   N19  C18   112.20  3.000
 M04  C24   C20  N21   108.22  3.000
 M04  C24   C20  N19   126.88  3.000
 M04  N21   C20  N19   124.88  3.000
 M04  H21   N21  C22   125.62  3.000
 M04  H21   N21  C20   124.97  3.000
 M04  C22   N21  C20   109.41  3.000
 M04  H22   C22  C23   129.70  3.000
 M04  H22   C22  N21   120.80  3.000
 M04  C23   C22  N21   109.50  3.000
 M04  H23   C23  C24   129.16  3.000
 M04  H23   C23  C22   123.98  3.000
 M04  C24   C23  C22   106.86  3.000
 M04  C23   C24  C20   106.01  3.000
 M04  C23   C24  C16   139.36  3.000
 M04  C20   C24  C16   114.59  3.000
 M04  C13   C4   C7    110.62  3.000
 M04  C13   C4   C5    107.08  3.000
 M04  C7    C4   C5    108.07  3.000
 M04  C13   C4   C3    110.65  3.000
 M04  C7    C4   C3    109.47  3.000
 M04  C5    C4   C3    110.90  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
 M04  CONST_01  C12   C11  C10  C9      0.00   0.0  0
 M04  CONST_02  C12   C14  C15  C9      0.00   0.0  0
 M04  CONST_03  C14   C15  C9   C10     0.00   0.0  0
 M04  CONST_04  C14   C12  C11  C10     0.00   0.0  0
 M04  CONST_05  C15   C9   C10  C11     0.00   0.0  0
 M04  CONST_06  C15   C14  C12  C11     0.00   0.0  0
 M04  CONST_07  N19   C18  N17  C16     0.00   0.0  0
 M04  CONST_08  N19   C20  C24  C16     0.00   0.0  0
 M04  CONST_09  N21   C20  C24  C16   180.00   0.0  0
 M04  CONST_10  C22   C23  C24  C16   180.00   0.0  0
 M04  CONST_11  C20   C24  C16  N17     0.00   0.0  0
 M04  CONST_12  C23   C24  C16  N17   180.00   0.0  0
 M04  CONST_13  C20   N19  C18  N17     0.00   0.0  0
 M04  CONST_14  C24   C16  N17  C18     0.00   0.0  0
 M04  CONST_15  N21   C20  N19  C18   180.00   0.0  0
 M04  CONST_16  C24   C20  N19  C18     0.00   0.0  0
 M04  CONST_17  C22   N21  C20  N19   180.00   0.0  0
 M04  CONST_18  C23   C24  C20  N19   180.00   0.0  0
 M04  CONST_19  C23   C22  N21  C20     0.00   0.0  0
 M04  CONST_20  C22   C23  C24  C20     0.00   0.0  0
 M04  CONST_21  C23   C24  C20  N21     0.00   0.0  0
 M04  CONST_22  C24   C23  C22  N21     0.00   0.0  0
 M04  CONST_23  C24   C20  N21  C22     0.00   0.0  0
 M04  CONST_24  C18   N17  C16  N1    180.00   0.0  0
 M04  CONST_25  C20   C24  C16  N1    180.00   0.0  0
 M04  CONST_26  C23   C24  C16  N1      0.00   0.0  0
 M04  CONST_27  CL1   C12  C11  C10   180.00   0.0  0
 M04  CONST_28  C13   C9   C10  C11   180.00   0.0  0
 M04  CONST_29  C15   C14  C12  CL1   180.00   0.0  0
 M04  CONST_30  C13   C9   C15  C14   180.00   0.0  0
 M04  CONST_31  H11   C11  C10  C9    180.00   0.0  0
 M04  CONST_32  H14   C14  C15  C9    180.00   0.0  0
 M04  CONST_33  H15   C15  C9   C10   180.00   0.0  0
 M04  CONST_34  H10   C10  C11  C12   180.00   0.0  0
 M04  CONST_35  H18   C18  N17  C16   180.00   0.0  0
 M04  CONST_36  H23   C23  C24  C16     0.00   0.0  0
 M04  CONST_37  H21   N21  C20  N19     0.00   0.0  0
 M04  CONST_38  H22   C22  N21  C20   180.00   0.0  0
 M04  Var_01    C4    C3   C2   N1     56.30  30.0  1
 M04  Var_02    C4    C7   C8   N1    -54.93  30.0  1
 M04  Var_03    C7    C8   N1   C2     61.84  30.0  1
 M04  Var_04    N17   C16  N1   C2   -176.89  30.0  2
 M04  Var_05    C8    N1   C2   C3    -63.18  30.0  1
 M04  Var_06    C4    C13  C9   C10   -89.20  30.0  2
 M04  Var_07    H6N1  N6   C5   C4    -58.76  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
 M04  chir_01  C4  C3  C7  C13  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
 M04  plan-1  C9   0.020
 M04  plan-1  C10  0.020
 M04  plan-1  C11  0.020
 M04  plan-1  C12  0.020
 M04  plan-1  CL1  0.020
 M04  plan-1  C14  0.020
 M04  plan-1  C15  0.020
 M04  plan-1  C13  0.020
 M04  plan-1  H10  0.020
 M04  plan-1  H15  0.020
 M04  plan-1  H11  0.020
 M04  plan-1  H14  0.020
 M04  plan-2  N1   0.020
 M04  plan-2  C16  0.020
 M04  plan-2  N17  0.020
 M04  plan-2  C18  0.020
 M04  plan-2  N19  0.020
 M04  plan-2  C20  0.020
 M04  plan-2  N21  0.020
 M04  plan-2  C22  0.020
 M04  plan-2  C23  0.020
 M04  plan-2  C24  0.020
 M04  plan-2  H18  0.020
 M04  plan-2  H21  0.020
 M04  plan-2  H22  0.020
 M04  plan-2  H23  0.020

