# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:02:51 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: [4-[(4-tert-butylphenyl)methyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(CC2([NH3+])CCN(CC2)c3ncnc4[nH]ccc34)cc1
#
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
 X37  X37  '[4-[(4-tert-butylphenyl)methyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]azanium'  ligand  57  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_X37
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
 X37  N1    N  NT    0  -0.460  -2.6922  -0.8885   0.9767
 X37  C2    C  CH2   0  -0.362  -2.2980  -2.2854   1.0095
 X37  C3    C  CH2   0  -0.425  -1.1271  -2.5147   0.0552
 X37  C4    C  CT    0   0.008   0.0543  -1.5734   0.3019
 X37  N5    N  NT3   1  -0.800   0.7224  -2.0037   1.5837
 X37  C9    C  CH2   0  -0.513   1.0851  -1.7167  -0.8289
 X37  C10   C  CR6   0   0.091   2.3521  -0.9305  -0.6323
 X37  C11   C  CR16  0  -0.318   3.4600  -1.5002  -0.0058
 X37  C12   C  CR16  0  -0.291   4.6157  -0.7667   0.2099
 X37  C13   C  CR6   0   0.190   4.7228   0.5649  -0.1959
 X37  C14   C  CR16  0  -0.323   3.6186   1.1223  -0.8371
 X37  C15   C  CR16  0  -0.274   2.4576   0.3909  -1.0517
 X37  C16   C  CT    0  -0.175   6.0100   1.3391   0.0649
 X37  C17   C  CH3   0  -0.628   7.1772   0.6455  -0.6503
 X37  C18   C  CH3   0  -0.666   5.9321   2.7812  -0.4359
 X37  C19   C  CH3   0  -0.630   6.2812   1.3664   1.5753
 X37  C20   C  CH2   0  -0.429  -0.4184  -0.1292   0.4846
 X37  C21   C  CH2   0  -0.372  -1.6188  -0.0303   1.4210
 X37  C22   C  CR6   0   0.500  -3.6954  -0.4731   0.1578
 X37  N23   N  N     0  -0.490  -4.5815  -1.4027  -0.2082
 X37  C24   C  CR16  0   0.040  -5.6246  -1.0688  -0.9577
 X37  N25   N  N     0  -0.449  -5.9291   0.1208  -1.4288
 X37  C26   C  CR56  0   0.474  -5.0310   1.0465  -1.0895
 X37  N27   N  NR15  0  -0.655  -5.0674   2.3403  -1.4770
 X37  C29   C  CR15  0  -0.009  -3.9695   2.9928  -0.9870
 X37  C30   C  CR15  0  -0.452  -3.2084   2.1257  -0.2638
 X37  C31   C  CR56  0  -0.076  -3.8755   0.8547  -0.3046
 X37  HN5   H  HNT3  0   0.472   1.0567  -2.9675   1.5350
 X37  HN5A  H  HNT3  0   0.473   1.5272  -1.4168   1.8143
 X37  HN5B  H  HNT3  0   0.475   0.1001  -1.9641   2.3918
 X37  HN27  H  HNR5  0   0.414  -5.7842   2.7494  -2.0545
 X37  H2    H  HCH2  0   0.255  -2.0364  -2.5455   2.0397
 X37  H2A   H  HCH2  0   0.297  -3.1340  -2.9176   0.7291
 X37  H3    H  HCH2  0   0.274  -0.7945  -3.5550   0.1082
 X37  H3A   H  HCH2  0   0.273  -1.4695  -2.3488  -0.9688
 X37  H9    H  HCH2  0   0.281   1.3167  -2.7784  -0.9547
 X37  H9A   H  HCH2  0   0.287   0.5843  -1.4025  -1.7461
 X37  H11   H  HCR6  0   0.259   3.4318  -2.5389   0.3062
 X37  H12   H  HCR6  0   0.250   5.4472  -1.2561   0.7015
 X37  H14   H  HCR6  0   0.254   3.6460   2.1456  -1.1855
 X37  H15   H  HCR6  0   0.253   1.6267   0.8628  -1.5627
 X37  H17   H  HCH3  0   0.229   7.0114   0.6059  -1.7283
 X37  H17A  H  HCH3  0   0.228   8.1048   1.1939  -0.4743
 X37  H17B  H  HCH3  0   0.228   7.3282  -0.3754  -0.2972
 X37  H18   H  HCH3  0   0.231   5.1340   3.3435   0.0526
 X37  H18A  H  HCH3  0   0.239   6.8708   3.2934  -0.2192
 X37  H18B  H  HCH3  0   0.231   5.7734   2.8347  -1.5147
 X37  H19   H  HCH3  0   0.228   6.4046   0.3636   1.9869
 X37  H19A  H  HCH3  0   0.228   7.1974   1.9215   1.7866
 X37  H19B  H  HCH3  0   0.229   5.4648   1.8505   2.1143
 X37  H20   H  HCH2  0   0.277   0.3962   0.5022   0.8480
 X37  H20A  H  HCH2  0   0.274  -0.7007   0.2564  -0.4984
 X37  H21   H  HCH2  0   0.293  -1.9519   0.9960   1.5207
 X37  H21A  H  HCH2  0   0.271  -1.3529  -0.3336   2.4388
 X37  H24   H  HCR6  0   0.246  -6.3028  -1.8788  -1.2062
 X37  H29   H  HCR5  0   0.290  -3.8087   4.0370  -1.1974
 X37  H30   H  HCR5  0   0.258  -2.2824   2.3958   0.2133

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
 X37  N1   C2    single    1.452  0.020  1.452
 X37  N1   C21   single    1.444  0.020  1.444
 X37  N1   C22   single    1.360  0.020  1.360
 X37  C2   C3    single    1.528  0.020  1.528
 X37  C2   H2    single    0.970  0.020  1.090
 X37  C2   H2A   single    0.970  0.020  1.090
 X37  C3   C4    single    1.531  0.020  1.531
 X37  C3   H3    single    0.970  0.020  1.090
 X37  C3   H3A   single    0.970  0.020  1.090
 X37  C4   N5    single    1.508  0.020  1.508
 X37  C4   C9    single    1.537  0.020  1.537
 X37  C4   C20   single    1.531  0.020  1.531
 X37  N5   HN5   single    0.890  0.020  1.040
 X37  N5   HN5A  single    0.890  0.020  1.040
 X37  N5   HN5B  single    0.890  0.020  1.040
 X37  C9   C10   single    1.504  0.020  1.504
 X37  C9   H9    single    0.970  0.020  1.090
 X37  C9   H9A   single    0.970  0.020  1.090
 X37  C10  C11   aromatic  1.394  0.020  1.394
 X37  C10  C15   aromatic  1.390  0.020  1.390
 X37  C11  C12   aromatic  1.386  0.020  1.386
 X37  C11  H11   single    0.930  0.020  1.080
 X37  C12  C13   aromatic  1.396  0.020  1.396
 X37  C12  H12   single    0.930  0.020  1.080
 X37  C13  C14   aromatic  1.393  0.020  1.393
 X37  C13  C16   single    1.525  0.020  1.525
 X37  C14  C15   aromatic  1.389  0.020  1.389
 X37  C14  H14   single    0.930  0.020  1.080
 X37  C15  H15   single    0.930  0.020  1.080
 X37  C16  C17   single    1.535  0.020  1.535
 X37  C16  C18   single    1.529  0.020  1.529
 X37  C16  C19   single    1.535  0.020  1.535
 X37  C17  H17   single    0.970  0.020  1.090
 X37  C17  H17A  single    0.970  0.020  1.090
 X37  C17  H17B  single    0.970  0.020  1.090
 X37  C18  H18   single    0.970  0.020  1.090
 X37  C18  H18A  single    0.970  0.020  1.090
 X37  C18  H18B  single    0.970  0.020  1.090
 X37  C19  H19   single    0.970  0.020  1.090
 X37  C19  H19A  single    0.970  0.020  1.090
 X37  C19  H19B  single    0.970  0.020  1.090
 X37  C20  C21   single    1.526  0.020  1.526
 X37  C20  H20   single    0.970  0.020  1.090
 X37  C20  H20A  single    0.970  0.020  1.090
 X37  C21  H21   single    0.970  0.020  1.090
 X37  C21  H21A  single    0.970  0.020  1.090
 X37  C22  N23   aromatic  1.335  0.020  1.335
 X37  C22  C31   aromatic  1.417  0.020  1.417
 X37  N23  C24   aromatic  1.327  0.020  1.327
 X37  C24  N25   aromatic  1.315  0.020  1.315
 X37  C24  H24   single    0.930  0.020  1.080
 X37  N25  C26   aromatic  1.334  0.020  1.334
 X37  C26  N27   aromatic  1.351  0.020  1.351
 X37  C26  C31   aromatic  1.410  0.020  1.410
 X37  N27  C29   aromatic  1.368  0.020  1.368
 X37  N27  HN27  single    0.860  0.020  1.020
 X37  C29  C30   aromatic  1.362  0.020  1.362
 X37  C29  H29   single    0.930  0.020  1.080
 X37  C30  C31   aromatic  1.436  0.020  1.436
 X37  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
 X37  C22   N1   C21   123.50  3.000
 X37  C22   N1   C2    120.51  3.000
 X37  C21   N1   C2    111.29  3.000
 X37  H2A   C2   H2    106.79  3.000
 X37  H2A   C2   C3    109.98  3.000
 X37  H2    C2   C3    111.66  3.000
 X37  H2A   C2   N1    110.22  3.000
 X37  H2    C2   N1    108.35  3.000
 X37  C3    C2   N1    109.78  3.000
 X37  H3A   C3   H3    106.58  3.000
 X37  H3A   C3   C4    107.44  3.000
 X37  H3    C3   C4    110.03  3.000
 X37  H3A   C3   C2    108.81  3.000
 X37  H3    C3   C2    110.22  3.000
 X37  C4    C3   C2    113.49  3.000
 X37  C20   C4   C9    112.52  3.000
 X37  C20   C4   N5    107.73  3.000
 X37  C9    C4   N5    107.56  3.000
 X37  C20   C4   C3    111.17  3.000
 X37  C9    C4   C3    109.98  3.000
 X37  N5    C4   C3    107.67  3.000
 X37  HN5B  N5   HN5A  106.20  3.000
 X37  HN5B  N5   HN5   105.90  3.000
 X37  HN5A  N5   HN5   107.14  3.000
 X37  HN5B  N5   C4    113.07  3.000
 X37  HN5A  N5   C4    112.13  3.000
 X37  HN5   N5   C4    111.95  3.000
 X37  H9A   C9   H9    106.25  3.000
 X37  H9A   C9   C10   110.24  3.000
 X37  H9    C9   C10   110.12  3.000
 X37  H9A   C9   C4    106.49  3.000
 X37  H9    C9   C4    108.49  3.000
 X37  C10   C9   C4    114.84  3.000
 X37  C15   C10  C11   117.61  3.000
 X37  C15   C10  C9    121.42  3.000
 X37  C11   C10  C9    120.96  3.000
 X37  H11   C11  C12   118.92  3.000
 X37  H11   C11  C10   119.98  3.000
 X37  C12   C11  C10   121.09  3.000
 X37  H12   C12  C13   120.27  3.000
 X37  H12   C12  C11   118.16  3.000
 X37  C13   C12  C11   121.57  3.000
 X37  C16   C13  C14   123.00  3.000
 X37  C16   C13  C12   119.96  3.000
 X37  C14   C13  C12   117.04  3.000
 X37  H14   C14  C15   118.01  3.000
 X37  H14   C14  C13   120.46  3.000
 X37  C15   C14  C13   121.53  3.000
 X37  H15   C15  C14   118.98  3.000
 X37  H15   C15  C10   119.86  3.000
 X37  C14   C15  C10   121.15  3.000
 X37  C19   C16  C18   108.34  3.000
 X37  C19   C16  C17   109.41  3.000
 X37  C18   C16  C17   108.21  3.000
 X37  C19   C16  C13   109.06  3.000
 X37  C18   C16  C13   112.34  3.000
 X37  C17   C16  C13   109.44  3.000
 X37  H17B  C17  H17A  107.47  3.000
 X37  H17B  C17  H17   107.87  3.000
 X37  H17A  C17  H17   107.84  3.000
 X37  H17B  C17  C16   112.18  3.000
 X37  H17A  C17  C16   110.12  3.000
 X37  H17   C17  C16   111.17  3.000
 X37  H18B  C18  H18A  107.36  3.000
 X37  H18B  C18  H18   108.09  3.000
 X37  H18A  C18  H18   107.36  3.000
 X37  H18B  C18  C16   112.17  3.000
 X37  H18A  C18  C16   109.52  3.000
 X37  H18   C18  C16   112.12  3.000
 X37  H19B  C19  H19A  107.86  3.000
 X37  H19B  C19  H19   107.81  3.000
 X37  H19A  C19  H19   107.41  3.000
 X37  H19B  C19  C16   111.20  3.000
 X37  H19A  C19  C16   110.36  3.000
 X37  H19   C19  C16   112.02  3.000
 X37  H20A  C20  H20   106.72  3.000
 X37  H20A  C20  C21   109.02  3.000
 X37  H20   C20  C21   110.18  3.000
 X37  H20A  C20  C4    107.78  3.000
 X37  H20   C20  C4    110.77  3.000
 X37  C21   C20  C4    112.18  3.000
 X37  H21A  C21  H21   104.56  3.000
 X37  H21A  C21  C20   111.19  3.000
 X37  H21   C21  C20   111.09  3.000
 X37  H21A  C21  N1    107.57  3.000
 X37  H21   C21  N1    111.27  3.000
 X37  C20   C21  N1    110.94  3.000
 X37  C31   C22  N23   118.58  3.000
 X37  C31   C22  N1    125.19  3.000
 X37  N23   C22  N1    116.22  3.000
 X37  C24   N23  C22   120.08  3.000
 X37  H24   C24  N25   116.64  3.000
 X37  H24   C24  N23   115.64  3.000
 X37  N25   C24  N23   127.72  3.000
 X37  C26   N25  C24   112.39  3.000
 X37  C31   C26  N27   108.18  3.000
 X37  C31   C26  N25   126.80  3.000
 X37  N27   C26  N25   125.00  3.000
 X37  HN27  N27  C29   125.64  3.000
 X37  HN27  N27  C26   124.93  3.000
 X37  C29   N27  C26   109.42  3.000
 X37  H29   C29  C30   129.61  3.000
 X37  H29   C29  N27   120.81  3.000
 X37  C30   C29  N27   109.58  3.000
 X37  H30   C30  C31   129.38  3.000
 X37  H30   C30  C29   123.82  3.000
 X37  C31   C30  C29   106.79  3.000
 X37  C30   C31  C26   106.03  3.000
 X37  C30   C31  C22   139.54  3.000
 X37  C26   C31  C22   114.40  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
 X37  CONST_01  C13   C12  C11  C10    0.00   0.0  0
 X37  CONST_02  C13   C14  C15  C10    0.00   0.0  0
 X37  CONST_03  C14   C15  C10  C11    0.00   0.0  0
 X37  CONST_04  C14   C13  C12  C11    0.00   0.0  0
 X37  CONST_05  C15   C10  C11  C12    0.00   0.0  0
 X37  CONST_06  C15   C14  C13  C12    0.00   0.0  0
 X37  CONST_07  N25   C24  N23  C22    0.00   0.0  0
 X37  CONST_08  N25   C26  C31  C22    0.00   0.0  0
 X37  CONST_09  N27   C26  C31  C22  180.00   0.0  0
 X37  CONST_10  C29   C30  C31  C22  180.00   0.0  0
 X37  CONST_11  C26   C31  C22  N23    0.00   0.0  0
 X37  CONST_12  C30   C31  C22  N23  180.00   0.0  0
 X37  CONST_13  C26   N25  C24  N23    0.00   0.0  0
 X37  CONST_14  C31   C22  N23  C24    0.00   0.0  0
 X37  CONST_15  N27   C26  N25  C24  180.00   0.0  0
 X37  CONST_16  C31   C26  N25  C24    0.00   0.0  0
 X37  CONST_17  C29   N27  C26  N25  180.00   0.0  0
 X37  CONST_18  C30   C31  C26  N25  180.00   0.0  0
 X37  CONST_19  C30   C29  N27  C26    0.00   0.0  0
 X37  CONST_20  C29   C30  C31  C26    0.00   0.0  0
 X37  CONST_21  C30   C31  C26  N27    0.00   0.0  0
 X37  CONST_22  C31   C30  C29  N27    0.00   0.0  0
 X37  CONST_23  C31   C26  N27  C29    0.00   0.0  0
 X37  CONST_24  C24   N23  C22  N1   180.00   0.0  0
 X37  CONST_25  C26   C31  C22  N1   180.00   0.0  0
 X37  CONST_26  C30   C31  C22  N1     0.00   0.0  0
 X37  CONST_27  C12   C11  C10  C9   180.00   0.0  0
 X37  CONST_28  C14   C15  C10  C9   180.00   0.0  0
 X37  CONST_29  C16   C13  C12  C11  180.00   0.0  0
 X37  CONST_30  C16   C13  C14  C15  180.00   0.0  0
 X37  CONST_31  H12   C12  C11  C10  180.00   0.0  0
 X37  CONST_32  H14   C14  C15  C10  180.00   0.0  0
 X37  CONST_33  H15   C15  C10  C11  180.00   0.0  0
 X37  CONST_34  H11   C11  C12  C13  180.00   0.0  0
 X37  CONST_35  H24   C24  N23  C22  180.00   0.0  0
 X37  CONST_36  H30   C30  C31  C22    0.00   0.0  0
 X37  CONST_37  HN27  N27  C26  N25    0.00   0.0  0
 X37  CONST_38  H29   C29  N27  C26  180.00   0.0  0
 X37  Var_01    C4    C3   C2   N1    53.49  30.0  1
 X37  Var_02    C4    C20  C21  N1   -54.45  30.0  1
 X37  Var_03    C20   C21  N1   C2    63.23  30.0  1
 X37  Var_04    N23   C22  N1   C2    23.67  30.0  2
 X37  Var_05    C21   N1   C2   C3   -62.04  30.0  1
 X37  Var_06    C11   C10  C9   C4    91.79  30.0  2
 X37  Var_07    C17   C16  C13  C12   60.40  30.0  2
 X37  Var_08    H17   C17  C16  C13   60.29  30.0  3
 X37  Var_09    H18   C18  C16  C13   60.47  30.0  3
 X37  Var_10    H19   C19  C16  C13   60.67  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
 X37  chir_01  C4  C3  C9  C20  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
 X37  plan-1  C9    0.020
 X37  plan-1  C10   0.020
 X37  plan-1  C11   0.020
 X37  plan-1  C12   0.020
 X37  plan-1  C13   0.020
 X37  plan-1  C14   0.020
 X37  plan-1  C15   0.020
 X37  plan-1  C16   0.020
 X37  plan-1  H11   0.020
 X37  plan-1  H12   0.020
 X37  plan-1  H14   0.020
 X37  plan-1  H15   0.020
 X37  plan-2  N1    0.020
 X37  plan-2  C22   0.020
 X37  plan-2  N23   0.020
 X37  plan-2  C24   0.020
 X37  plan-2  N25   0.020
 X37  plan-2  C26   0.020
 X37  plan-2  N27   0.020
 X37  plan-2  C29   0.020
 X37  plan-2  C30   0.020
 X37  plan-2  C31   0.020
 X37  plan-2  HN27  0.020
 X37  plan-2  H24   0.020
 X37  plan-2  H29   0.020
 X37  plan-2  H30   0.020

