# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:29:47 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-[4-(4-chlorophenyl)-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)c4ccc(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
 M03  M03  1-[4-(4-chlorophenyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine  ligand  44  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_M03
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
 M03  N1    N   NT    0  -0.483   6.8167   9.2534   3.1806
 M03  C2    C   CH2   0  -0.300   7.4763   8.9088   1.9378
 M03  C3    C   CH2   0  -0.453   8.6395   7.9488   2.1700
 M03  C4    C   CT    0  -0.202   9.6476   8.4200   3.2204
 M03  C5    C   CH2   0  -0.259  10.6487   7.2791   3.5293
 M03  N6    N   NH2   0  -0.791  11.4999   6.8322   2.4479
 M03  C7    C   CH2   0  -0.434   8.8281   8.7011   4.4861
 M03  C8    C   CH2   0  -0.300   7.7088   9.6979   4.2405
 M03  C9    C   CR6   0   0.178  10.4464   9.6414   2.7830
 M03  C10   C   CR16  0  -0.310  11.1637  10.3880   3.7212
 M03  C11   C   CR16  0  -0.196  11.9580  11.4619   3.3536
 M03  C12   C   CR6   0  -0.061  12.0522  11.8067   2.0146
 M03  CL1   CL  CL    0  -0.134  13.0401  13.1518   1.5424
 M03  C14   C   CR16  0  -0.195  11.3686  11.0850   1.0538
 M03  C15   C   CR16  0  -0.331  10.5796  10.0109   1.4457
 M03  C16   C   CR6   0   0.516   5.4750   9.3656   3.3034
 M03  N17   N   N     0  -0.498   4.9911   9.5354   4.5407
 M03  C18   C   CR16  0   0.037   3.6819   9.6026   4.7412
 M03  N19   N   N     0  -0.455   2.7210   9.5300   3.8453
 M03  C20   C   CR56  0   0.468   3.1974   9.3995   2.6048
 M03  N21   N   NR15  0  -0.655   2.4411   9.3662   1.4851
 M03  C22   C   CR15  0  -0.016   3.2557   9.2882   0.3880
 M03  C23   C   CR15  0  -0.445   4.5567   9.2587   0.7896
 M03  C24   C   CR56  0  -0.098   4.5509   9.3176   2.2245
 M03  H2C1  H   HCH2  0   0.266   6.7762   8.4007   1.2844
 M03  HA2   H   HCH2  0   0.234   7.8134   9.8144   1.4200
 M03  H8C1  H   HCH2  0   0.232   8.1313  10.6722   3.9632
 M03  H8C2  H   HCH2  0   0.274   7.1308   9.8407   5.1475
 M03  HA1   H   HCH2  0   0.251   8.2290   6.9927   2.5096
 M03  HB2   H   HCH2  0   0.249   9.1082   7.7444   1.2051
 M03  HB1   H   HCH2  0   0.226  11.2824   7.5943   4.3643
 M03  HC2   H   HCH2  0   0.229  10.0764   6.4199   3.8919
 M03  H7C1  H   HCH2  0   0.242   8.3976   7.7577   4.8360
 M03  H7C2  H   HCH2  0   0.246   9.4500   9.0737   5.3019
 M03  HC1   H   HNH2  0   0.348  10.9499   6.4084   1.7122
 M03  HD2   H   HNH2  0   0.345  11.9842   7.6163   2.0277
 M03  H10   H   HCR6  0   0.260  11.1210  10.1368   4.7728
 M03  H15   H   HCR6  0   0.262  10.0617   9.4677   0.6679
 M03  H11   H   HCR6  0   0.278  12.4994  12.0191   4.1061
 M03  H14   H   HCR6  0   0.278  11.4442  11.3473   0.0071
 M03  H18   H   HCR6  0   0.242   3.3728   9.7296   5.7741
 M03  H21   H   HNR5  0   0.412   1.4353   9.4147   1.4673
 M03  H22   H   HCR5  0   0.286   2.8419   9.2636  -0.6065
 M03  H23   H   HCR5  0   0.258   5.3946   9.2175   0.1158

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
 M03  N1   C2    single    1.449  0.020  1.449
 M03  N1   C8    single    1.455  0.020  1.455
 M03  N1   C16   single    1.352  0.020  1.352
 M03  C2   C3    single    1.526  0.020  1.526
 M03  C3   C4    single    1.530  0.020  1.530
 M03  C4   C5    single    1.549  0.020  1.549
 M03  C4   C7    single    1.534  0.020  1.534
 M03  C4   C9    single    1.523  0.020  1.523
 M03  C5   N6    single    1.447  0.020  1.447
 M03  C7   C8    single    1.519  0.020  1.519
 M03  C9   C10   aromatic  1.397  0.020  1.397
 M03  C9   C15   aromatic  1.394  0.020  1.394
 M03  C10  C11   aromatic  1.385  0.020  1.385
 M03  C11  C12   aromatic  1.386  0.020  1.386
 M03  C12  CL1   single    1.734  0.020  1.734
 M03  C12  C14   aromatic  1.383  0.020  1.383
 M03  C14  C15   aromatic  1.389  0.020  1.389
 M03  C16  N17   aromatic  1.339  0.020  1.339
 M03  C16  C24   aromatic  1.421  0.020  1.421
 M03  N17  C18   aromatic  1.326  0.020  1.326
 M03  C18  N19   aromatic  1.316  0.020  1.316
 M03  N19  C20   aromatic  1.335  0.020  1.335
 M03  C20  N21   aromatic  1.352  0.020  1.352
 M03  C20  C24   aromatic  1.408  0.020  1.408
 M03  N21  C22   aromatic  1.369  0.020  1.369
 M03  C22  C23   aromatic  1.362  0.020  1.362
 M03  C23  C24   aromatic  1.436  0.020  1.436
 M03  C2   H2C1  single    0.970  0.020  1.090
 M03  C2   HA2   single    0.970  0.020  1.090
 M03  C8   H8C1  single    0.970  0.020  1.090
 M03  C8   H8C2  single    0.970  0.020  1.090
 M03  C3   HA1   single    0.970  0.020  1.090
 M03  C3   HB2   single    0.970  0.020  1.090
 M03  C5   HB1   single    0.970  0.020  1.090
 M03  C5   HC2   single    0.970  0.020  1.090
 M03  C7   H7C1  single    0.970  0.020  1.090
 M03  C7   H7C2  single    0.970  0.020  1.090
 M03  N6   HC1   single    0.890  0.020  1.040
 M03  N6   HD2   single    0.890  0.020  1.040
 M03  C10  H10   single    0.930  0.020  1.080
 M03  C15  H15   single    0.930  0.020  1.080
 M03  C11  H11   single    0.930  0.020  1.080
 M03  C14  H14   single    0.930  0.020  1.080
 M03  C18  H18   single    0.930  0.020  1.080
 M03  N21  H21   single    0.860  0.020  1.020
 M03  C22  H22   single    0.930  0.020  1.080
 M03  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
 M03  C16   N1   C8    121.13  3.000
 M03  C16   N1   C2    123.34  3.000
 M03  C8    N1   C2    114.74  3.000
 M03  HA2   C2   H2C1  107.52  3.000
 M03  HA2   C2   C3    110.93  3.000
 M03  H2C1  C2   C3    106.80  3.000
 M03  HA2   C2   N1    110.41  3.000
 M03  H2C1  C2   N1    109.54  3.000
 M03  C3    C2   N1    111.48  3.000
 M03  HB2   C3   HA1   105.76  3.000
 M03  HB2   C3   C4    112.42  3.000
 M03  HA1   C3   C4    107.65  3.000
 M03  HB2   C3   C2    108.09  3.000
 M03  HA1   C3   C2    108.11  3.000
 M03  C4    C3   C2    114.39  3.000
 M03  C9    C4   C7    111.72  3.000
 M03  C9    C4   C5    108.00  3.000
 M03  C7    C4   C5    108.40  3.000
 M03  C9    C4   C3    113.28  3.000
 M03  C7    C4   C3    105.72  3.000
 M03  C5    C4   C3    109.62  3.000
 M03  HC2   C5   HB1   106.03  3.000
 M03  HC2   C5   N6    108.23  3.000
 M03  HB1   C5   N6    108.57  3.000
 M03  HC2   C5   C4    107.85  3.000
 M03  HB1   C5   C4    108.31  3.000
 M03  N6    C5   C4    117.30  3.000
 M03  HD2   N6   HC1   106.42  3.000
 M03  HD2   N6   C5    110.63  3.000
 M03  HC1   N6   C5    110.67  3.000
 M03  H7C2  C7   H7C1  106.23  3.000
 M03  H7C2  C7   C8    108.47  3.000
 M03  H7C1  C7   C8    109.12  3.000
 M03  H7C2  C7   C4    112.02  3.000
 M03  H7C1  C7   C4    108.42  3.000
 M03  C8    C7   C4    112.37  3.000
 M03  H8C2  C8   H8C1  107.42  3.000
 M03  H8C2  C8   C7    110.11  3.000
 M03  H8C1  C8   C7    109.86  3.000
 M03  H8C2  C8   N1    108.82  3.000
 M03  H8C1  C8   N1    108.85  3.000
 M03  C7    C8   N1    111.67  3.000
 M03  C15   C9   C10   116.97  3.000
 M03  C15   C9   C4    122.56  3.000
 M03  C10   C9   C4    120.31  3.000
 M03  H10   C10  C11   117.41  3.000
 M03  H10   C10  C9    120.55  3.000
 M03  C11   C10  C9    122.03  3.000
 M03  H11   C11  C12   120.66  3.000
 M03  H11   C11  C10   120.11  3.000
 M03  C12   C11  C10   119.22  3.000
 M03  C14   C12  CL1   119.82  3.000
 M03  C14   C12  C11   120.53  3.000
 M03  CL1   C12  C11   119.66  3.000
 M03  H14   C14  C15   120.02  3.000
 M03  H14   C14  C12   120.75  3.000
 M03  C15   C14  C12   119.24  3.000
 M03  H15   C15  C14   117.24  3.000
 M03  H15   C15  C9    120.76  3.000
 M03  C14   C15  C9    122.00  3.000
 M03  C24   C16  N17   118.07  3.000
 M03  C24   C16  N1    124.99  3.000
 M03  N17   C16  N1    116.94  3.000
 M03  C18   N17  C16   120.18  3.000
 M03  H18   C18  N19   116.51  3.000
 M03  H18   C18  N17   115.52  3.000
 M03  N19   C18  N17   127.97  3.000
 M03  C20   N19  C18   112.17  3.000
 M03  C24   C20  N21   108.22  3.000
 M03  C24   C20  N19   126.83  3.000
 M03  N21   C20  N19   124.92  3.000
 M03  H21   N21  C22   125.66  3.000
 M03  H21   N21  C20   124.91  3.000
 M03  C22   N21  C20   109.41  3.000
 M03  H22   C22  C23   129.69  3.000
 M03  H22   C22  N21   120.83  3.000
 M03  C23   C22  N21   109.48  3.000
 M03  H23   C23  C24   129.08  3.000
 M03  H23   C23  C22   124.06  3.000
 M03  C24   C23  C22   106.85  3.000
 M03  C23   C24  C20   106.03  3.000
 M03  C23   C24  C16   139.22  3.000
 M03  C20   C24  C16   114.70  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
 M03  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 M03  CONST_02  C12  C14  C15  C9     0.00   0.0  0
 M03  CONST_03  C14  C15  C9   C10    0.00   0.0  0
 M03  CONST_04  C14  C12  C11  C10    0.00   0.0  0
 M03  CONST_05  C15  C9   C10  C11    0.00   0.0  0
 M03  CONST_06  C15  C14  C12  C11    0.00   0.0  0
 M03  CONST_07  N19  C18  N17  C16    0.00   0.0  0
 M03  CONST_08  N19  C20  C24  C16    0.00   0.0  0
 M03  CONST_09  N21  C20  C24  C16  180.00   0.0  0
 M03  CONST_10  C22  C23  C24  C16  180.00   0.0  0
 M03  CONST_11  C20  C24  C16  N17    0.00   0.0  0
 M03  CONST_12  C23  C24  C16  N17  180.00   0.0  0
 M03  CONST_13  C20  N19  C18  N17    0.00   0.0  0
 M03  CONST_14  C24  C16  N17  C18    0.00   0.0  0
 M03  CONST_15  N21  C20  N19  C18  180.00   0.0  0
 M03  CONST_16  C24  C20  N19  C18    0.00   0.0  0
 M03  CONST_17  C22  N21  C20  N19  180.00   0.0  0
 M03  CONST_18  C23  C24  C20  N19  180.00   0.0  0
 M03  CONST_19  C23  C22  N21  C20    0.00   0.0  0
 M03  CONST_20  C22  C23  C24  C20    0.00   0.0  0
 M03  CONST_21  C23  C24  C20  N21    0.00   0.0  0
 M03  CONST_22  C24  C23  C22  N21    0.00   0.0  0
 M03  CONST_23  C24  C20  N21  C22    0.00   0.0  0
 M03  CONST_24  C18  N17  C16  N1   180.00   0.0  0
 M03  CONST_25  C20  C24  C16  N1   180.00   0.0  0
 M03  CONST_26  C23  C24  C16  N1     0.00   0.0  0
 M03  CONST_27  C11  C10  C9   C4   180.00   0.0  0
 M03  CONST_28  C14  C15  C9   C4   180.00   0.0  0
 M03  CONST_29  CL1  C12  C11  C10  180.00   0.0  0
 M03  CONST_30  C15  C14  C12  CL1  180.00   0.0  0
 M03  CONST_31  H10  C10  C9   C4     0.00   0.0  0
 M03  CONST_32  H15  C15  C9   C4     0.00   0.0  0
 M03  CONST_33  H11  C11  C10  C9   180.00   0.0  0
 M03  CONST_34  H14  C14  C15  C9   180.00   0.0  0
 M03  CONST_35  H18  C18  N17  C16  180.00   0.0  0
 M03  CONST_36  H23  C23  C24  C16    0.00   0.0  0
 M03  CONST_37  H21  N21  C20  N19    0.00   0.0  0
 M03  CONST_38  H22  C22  N21  C20  180.00   0.0  0
 M03  Var_01    C4   C3   C2   N1   -52.72  30.0  1
 M03  Var_02    C4   C7   C8   N1    56.84  30.0  1
 M03  Var_03    C7   C8   N1   C2   -53.04  30.0  1
 M03  Var_04    N17  C16  N1   C2   172.41  30.0  2
 M03  Var_05    C8   N1   C2   C3    50.35  30.0  1
 M03  Var_06    HC1  N6   C5   C4   -65.13  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
 M03  chir_01  C4  C3  C7  C9  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
 M03  plan-1  C4   0.020
 M03  plan-1  C9   0.020
 M03  plan-1  C10  0.020
 M03  plan-1  C11  0.020
 M03  plan-1  C12  0.020
 M03  plan-1  CL1  0.020
 M03  plan-1  C14  0.020
 M03  plan-1  C15  0.020
 M03  plan-1  H10  0.020
 M03  plan-1  H15  0.020
 M03  plan-1  H11  0.020
 M03  plan-1  H14  0.020
 M03  plan-2  N1   0.020
 M03  plan-2  C16  0.020
 M03  plan-2  N17  0.020
 M03  plan-2  C18  0.020
 M03  plan-2  N19  0.020
 M03  plan-2  C20  0.020
 M03  plan-2  N21  0.020
 M03  plan-2  C22  0.020
 M03  plan-2  C23  0.020
 M03  plan-2  C24  0.020
 M03  plan-2  H18  0.020
 M03  plan-2  H21  0.020
 M03  plan-2  H22  0.020
 M03  plan-2  H23  0.020

