# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:55:08 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1(CCN(CC1)c2ncnc3[nH]ccc23)C(=O)NCc4ccc(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
 X39  X39  4-amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide  ligand  48  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X39
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
 X39  N1    N   NT    0  -0.460  -2.7703   0.5277   1.1460
 X39  C2    C   CH2   0  -0.350  -1.6526   0.2677   2.0381
 X39  C3    C   CH2   0  -0.439  -0.3583   0.1504   1.2349
 X39  C4    C   CT    0  -0.047  -0.1051   1.3765   0.3327
 X39  N5    N   NH2   0  -0.814   0.3125   2.4912   1.1723
 X39  C9    C   CH2   0  -0.431  -1.3710   1.6774  -0.4922
 X39  C10   C   CH2   0  -0.355  -2.5852   1.7691   0.4227
 X39  C11   C   C     0   0.583   1.0466   0.9868  -0.6067
 X39  O12   O   O     0  -0.490   0.8666   0.3041  -1.6056
 X39  N13   N   NH1   0  -0.633   2.2560   1.4031  -0.2134
 X39  C14   C   CH2   0  -0.333   3.4637   1.0177  -0.8916
 X39  C15   C   CR6   0   0.108   3.8495  -0.4286  -0.6871
 X39  C16   C   CR16  0  -0.298   3.5273  -1.1154   0.4785
 X39  C17   C   CR16  0  -0.198   3.9190  -2.4332   0.6656
 X39  C18   C   CR6   0  -0.056   4.6492  -3.0684  -0.3261
 X39  CL1   CL  CL    0  -0.135   5.1423  -4.7169  -0.1025
 X39  C20   C   CR16  0  -0.199   4.9880  -2.4068  -1.4956
 X39  C21   C   CR16  0  -0.308   4.5823  -1.0915  -1.6661
 X39  C22   C   CR6   0   0.498  -3.5392  -0.4918   0.6903
 X39  N23   N   N     0  -0.494  -3.5362  -1.6129   1.4206
 X39  C24   C   CR16  0   0.038  -4.3059  -2.6359   1.0741
 X39  N25   N   N     0  -0.453  -5.1229  -2.7199   0.0465
 X39  C26   C   CR56  0   0.470  -5.1104  -1.6142  -0.7011
 X39  N27   N   NR15  0  -0.655  -5.8175  -1.4428  -1.8397
 X39  C29   C   CR15  0  -0.013  -5.5358  -0.2129  -2.3692
 X39  C30   C   CR15  0  -0.449  -4.6425   0.4330  -1.5695
 X39  C31   C   CR56  0  -0.079  -4.3527  -0.4478  -0.4727
 X39  H21C  H   HCH2  0   0.246  -1.5969   1.0824   2.7655
 X39  H22C  H   HCH2  0   0.284  -1.8254  -0.6443   2.6000
 X39  H101  H   HCH2  0   0.273  -3.4856   2.0414  -0.1154
 X39  H102  H   HCH2  0   0.254  -2.4408   2.5605   1.1633
 X39  H31C  H   HCH2  0   0.256   0.4838   0.0243   1.9212
 X39  H32C  H   HCH2  0   0.253  -0.4112  -0.7503   0.6185
 X39  H51N  H   HNH2  0   0.359   0.1963   3.3734   0.6881
 X39  H52N  H   HNH2  0   0.363  -0.2424   2.5502   2.0155
 X39  H91C  H   HCH2  0   0.249  -1.2436   2.6152  -1.0403
 X39  H92C  H   HCH2  0   0.245  -1.5364   0.8919  -1.2320
 X39  H13   H   HNH1  0   0.406   2.2879   1.9660   0.6244
 X39  H141  H   HCH2  0   0.255   3.3730   1.2183  -1.9611
 X39  H142  H   HCH2  0   0.277   4.2631   1.6617  -0.5211
 X39  H16   H   HCR6  0   0.256   2.9574  -0.6257   1.2585
 X39  H21   H   HCR6  0   0.260   4.8418  -0.5796  -2.5852
 X39  H17   H   HCR6  0   0.278   3.6562  -2.9551   1.5759
 X39  H20   H   HCR6  0   0.278   5.5534  -2.9086  -2.2690
 X39  H24   H   HCR6  0   0.243  -4.2494  -3.5055   1.7214
 X39  H27   H   HNR5  0   0.413  -6.4422  -2.1244  -2.2394
 X39  H29   H   HCR5  0   0.288  -5.9954   0.1106  -3.2882
 X39  H30   H   HCR5  0   0.257  -4.2529   1.4141  -1.7774

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
 X39  N1   C2    single    1.453  0.020  1.453
 X39  N1   C10   single    1.449  0.020  1.449
 X39  N1   C22   single    1.356  0.020  1.356
 X39  C2   C3    single    1.528  0.020  1.528
 X39  C3   C4    single    1.543  0.020  1.543
 X39  C4   N5    single    1.457  0.020  1.457
 X39  C4   C9    single    1.541  0.020  1.541
 X39  C4   C11   single    1.536  0.020  1.536
 X39  C9   C10   single    1.523  0.020  1.523
 X39  C11  O12   double    1.223  0.020  1.223
 X39  C11  N13   single    1.338  0.020  1.338
 X39  N13  C14   single    1.438  0.020  1.438
 X39  C14  C15   single    1.511  0.020  1.511
 X39  C15  C16   aromatic  1.391  0.020  1.391
 X39  C15  C21   aromatic  1.391  0.020  1.391
 X39  C16  C17   aromatic  1.387  0.020  1.387
 X39  C17  C18   aromatic  1.386  0.020  1.386
 X39  C18  CL1   single    1.735  0.020  1.735
 X39  C18  C20   aromatic  1.386  0.020  1.386
 X39  C20  C21   aromatic  1.387  0.020  1.387
 X39  C22  N23   aromatic  1.338  0.020  1.338
 X39  C22  C31   aromatic  1.420  0.020  1.420
 X39  N23  C24   aromatic  1.326  0.020  1.326
 X39  C24  N25   aromatic  1.315  0.020  1.315
 X39  N25  C26   aromatic  1.335  0.020  1.335
 X39  C26  N27   aromatic  1.351  0.020  1.351
 X39  C26  C31   aromatic  1.409  0.020  1.409
 X39  N27  C29   aromatic  1.368  0.020  1.368
 X39  C29  C30   aromatic  1.362  0.020  1.362
 X39  C30  C31   aromatic  1.436  0.020  1.436
 X39  C2   H21C  single    0.970  0.020  1.090
 X39  C2   H22C  single    0.970  0.020  1.090
 X39  C10  H101  single    0.970  0.020  1.090
 X39  C10  H102  single    0.970  0.020  1.090
 X39  C3   H31C  single    0.970  0.020  1.090
 X39  C3   H32C  single    0.970  0.020  1.090
 X39  N5   H51N  single    0.890  0.020  1.040
 X39  N5   H52N  single    0.890  0.020  1.040
 X39  C9   H91C  single    0.970  0.020  1.090
 X39  C9   H92C  single    0.970  0.020  1.090
 X39  N13  H13   single    0.860  0.020  1.020
 X39  C14  H141  single    0.970  0.020  1.090
 X39  C14  H142  single    0.970  0.020  1.090
 X39  C16  H16   single    0.930  0.020  1.080
 X39  C21  H21   single    0.930  0.020  1.080
 X39  C17  H17   single    0.930  0.020  1.080
 X39  C20  H20   single    0.930  0.020  1.080
 X39  C24  H24   single    0.930  0.020  1.080
 X39  N27  H27   single    0.860  0.020  1.020
 X39  C29  H29   single    0.930  0.020  1.080
 X39  C30  H30   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
 X39  C22   N1   C10   123.30  3.000
 X39  C22   N1   C2    120.52  3.000
 X39  C10   N1   C2    111.19  3.000
 X39  H22C  C2   H21C  106.85  3.000
 X39  H22C  C2   C3    110.03  3.000
 X39  H21C  C2   C3    111.33  3.000
 X39  H22C  C2   N1    110.23  3.000
 X39  H21C  C2   N1    108.31  3.000
 X39  C3    C2   N1    110.03  3.000
 X39  H32C  C3   H31C  107.23  3.000
 X39  H32C  C3   C4    109.46  3.000
 X39  H31C  C3   C4    109.40  3.000
 X39  H32C  C3   C2    108.60  3.000
 X39  H31C  C3   C2    109.35  3.000
 X39  C4    C3   C2    112.66  3.000
 X39  C11   C4   C9    109.76  3.000
 X39  C11   C4   N5    109.37  3.000
 X39  C9    C4   N5    113.25  3.000
 X39  C11   C4   C3    106.20  3.000
 X39  C9    C4   C3    109.47  3.000
 X39  N5    C4   C3    108.55  3.000
 X39  H52N  N5   H51N  106.55  3.000
 X39  H52N  N5   C4    111.59  3.000
 X39  H51N  N5   C4    110.98  3.000
 X39  H92C  C9   H91C  107.15  3.000
 X39  H92C  C9   C10   109.25  3.000
 X39  H91C  C9   C10   110.02  3.000
 X39  H92C  C9   C4    110.29  3.000
 X39  H91C  C9   C4    109.88  3.000
 X39  C10   C9   C4    110.19  3.000
 X39  H102  C10  H101  105.31  3.000
 X39  H102  C10  C9    110.19  3.000
 X39  H101  C10  C9    112.29  3.000
 X39  H102  C10  N1    107.39  3.000
 X39  H101  C10  N1    110.92  3.000
 X39  C9    C10  N1    110.50  3.000
 X39  N13   C11  O12   123.14  3.000
 X39  N13   C11  C4    114.76  3.000
 X39  O12   C11  C4    122.04  3.000
 X39  H13   N13  C14   120.94  3.000
 X39  H13   N13  C11   116.48  3.000
 X39  C14   N13  C11   122.49  3.000
 X39  H142  C14  H141  106.56  3.000
 X39  H142  C14  C15   109.38  3.000
 X39  H141  C14  C15   109.24  3.000
 X39  H142  C14  N13   107.28  3.000
 X39  H141  C14  N13   110.06  3.000
 X39  C15   C14  N13   114.03  3.000
 X39  C21   C15  C16   118.47  3.000
 X39  C21   C15  C14   119.70  3.000
 X39  C16   C15  C14   121.80  3.000
 X39  H16   C16  C17   118.74  3.000
 X39  H16   C16  C15   120.15  3.000
 X39  C17   C16  C15   121.11  3.000
 X39  H17   C17  C18   120.61  3.000
 X39  H17   C17  C16   120.21  3.000
 X39  C18   C17  C16   119.18  3.000
 X39  C20   C18  CL1   119.53  3.000
 X39  C20   C18  C17   120.93  3.000
 X39  CL1   C18  C17   119.54  3.000
 X39  H20   C20  C21   120.34  3.000
 X39  H20   C20  C18   120.65  3.000
 X39  C21   C20  C18   119.01  3.000
 X39  H21   C21  C20   118.83  3.000
 X39  H21   C21  C15   119.87  3.000
 X39  C20   C21  C15   121.30  3.000
 X39  C31   C22  N23   118.31  3.000
 X39  C31   C22  N1    125.23  3.000
 X39  N23   C22  N1    116.45  3.000
 X39  C24   N23  C22   120.16  3.000
 X39  H24   C24  N25   116.55  3.000
 X39  H24   C24  N23   115.58  3.000
 X39  N25   C24  N23   127.86  3.000
 X39  C26   N25  C24   112.26  3.000
 X39  C31   C26  N27   108.24  3.000
 X39  C31   C26  N25   126.85  3.000
 X39  N27   C26  N25   124.90  3.000
 X39  H27   N27  C29   125.61  3.000
 X39  H27   N27  C26   124.97  3.000
 X39  C29   N27  C26   109.41  3.000
 X39  H29   C29  C30   129.67  3.000
 X39  H29   C29  N27   120.81  3.000
 X39  C30   C29  N27   109.52  3.000
 X39  H30   C30  C31   129.33  3.000
 X39  H30   C30  C29   123.82  3.000
 X39  C31   C30  C29   106.85  3.000
 X39  C30   C31  C26   105.98  3.000
 X39  C30   C31  C22   139.46  3.000
 X39  C26   C31  C22   114.53  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
 X39  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 X39  CONST_02  C18  C20  C21  C15    0.00   0.0  0
 X39  CONST_03  C20  C21  C15  C16    0.00   0.0  0
 X39  CONST_04  C20  C18  C17  C16    0.00   0.0  0
 X39  CONST_05  C21  C15  C16  C17    0.00   0.0  0
 X39  CONST_06  C21  C20  C18  C17    0.00   0.0  0
 X39  CONST_07  N25  C24  N23  C22    0.00   0.0  0
 X39  CONST_08  N25  C26  C31  C22    0.00   0.0  0
 X39  CONST_09  N27  C26  C31  C22  180.00   0.0  0
 X39  CONST_10  C29  C30  C31  C22  180.00   0.0  0
 X39  CONST_11  C26  C31  C22  N23    0.00   0.0  0
 X39  CONST_12  C30  C31  C22  N23  180.00   0.0  0
 X39  CONST_13  C26  N25  C24  N23    0.00   0.0  0
 X39  CONST_14  C31  C22  N23  C24    0.00   0.0  0
 X39  CONST_15  N27  C26  N25  C24  180.00   0.0  0
 X39  CONST_16  C31  C26  N25  C24    0.00   0.0  0
 X39  CONST_17  C29  N27  C26  N25  180.00   0.0  0
 X39  CONST_18  C30  C31  C26  N25  180.00   0.0  0
 X39  CONST_19  C30  C29  N27  C26    0.00   0.0  0
 X39  CONST_20  C29  C30  C31  C26    0.00   0.0  0
 X39  CONST_21  C30  C31  C26  N27    0.00   0.0  0
 X39  CONST_22  C31  C30  C29  N27    0.00   0.0  0
 X39  CONST_23  C31  C26  N27  C29    0.00   0.0  0
 X39  CONST_24  C24  N23  C22  N1   180.00   0.0  0
 X39  CONST_25  C26  C31  C22  N1   180.00   0.0  0
 X39  CONST_26  C30  C31  C22  N1     0.00   0.0  0
 X39  CONST_27  C17  C16  C15  C14  180.00   0.0  0
 X39  CONST_28  C20  C21  C15  C14  180.00   0.0  0
 X39  CONST_29  CL1  C18  C17  C16  180.00   0.0  0
 X39  CONST_30  C21  C20  C18  CL1  180.00   0.0  0
 X39  CONST_31  H17  C17  C16  C15  180.00   0.0  0
 X39  CONST_32  H20  C20  C21  C15  180.00   0.0  0
 X39  CONST_33  H21  C21  C15  C16  180.00   0.0  0
 X39  CONST_34  H16  C16  C17  C18  180.00   0.0  0
 X39  CONST_35  H24  C24  N23  C22  180.00   0.0  0
 X39  CONST_36  H30  C30  C31  C22    0.00   0.0  0
 X39  CONST_37  H27  N27  C26  N25    0.00   0.0  0
 X39  CONST_38  H29  C29  N27  C26  180.00   0.0  0
 X39  CONST_39  C14  N13  C11  C4   180.00   0.0  0
 X39  CONST_40  H13  N13  C11  C4     0.00   0.0  0
 X39  CONST_41  C14  N13  C11  O12    0.00   0.0  0
 X39  Var_01    C4   C3   C2   N1    54.24  30.0  1
 X39  Var_02    C4   C9   C10  N1   -59.17  30.0  1
 X39  Var_03    C9   C10  N1   C2    64.08  30.0  1
 X39  Var_04    N23  C22  N1   C2    22.46  30.0  2
 X39  Var_05    C10  N1   C2   C3   -60.70  30.0  1
 X39  Var_06    C16  C15  C14  N13  -29.99  30.0  2
 X39  Var_07    C15  C14  N13  C11  -71.38  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
 X39  chir_01  C4  C3  C9  C11  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
 X39  plan-1  C14  0.020
 X39  plan-1  C15  0.020
 X39  plan-1  C16  0.020
 X39  plan-1  C17  0.020
 X39  plan-1  C18  0.020
 X39  plan-1  CL1  0.020
 X39  plan-1  C20  0.020
 X39  plan-1  C21  0.020
 X39  plan-1  H16  0.020
 X39  plan-1  H21  0.020
 X39  plan-1  H17  0.020
 X39  plan-1  H20  0.020
 X39  plan-2  N1   0.020
 X39  plan-2  C22  0.020
 X39  plan-2  N23  0.020
 X39  plan-2  C24  0.020
 X39  plan-2  N25  0.020
 X39  plan-2  C26  0.020
 X39  plan-2  N27  0.020
 X39  plan-2  C29  0.020
 X39  plan-2  C30  0.020
 X39  plan-2  C31  0.020
 X39  plan-2  H24  0.020
 X39  plan-2  H27  0.020
 X39  plan-2  H29  0.020
 X39  plan-2  H30  0.020
 X39  plan-3  C4   0.020
 X39  plan-3  C11  0.020
 X39  plan-3  O12  0.020
 X39  plan-3  N13  0.020
 X39  plan-3  C14  0.020
 X39  plan-3  H13  0.020

