# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 16:23:01 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 5-{[(2S)-2-aminopropyl]amino}-3-(1H-indol-2-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CNc1cnc(C(N)=O)c(n1)c2[nH]c3ccccc3c2
#
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
 7CU  7CU  5-{[(2S)-2-aminopropyl]amino}-3-(1H-indol-2-yl)pyrazine-2-carboxamide  ligand  41  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7CU
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
 7CU  C    C  CR6   0   0.040  -0.1399  -2.2062  -0.1177
 7CU  N    N  N     0  -0.372  -1.4091  -2.5621  -0.3309
 7CU  O    O  O     0  -0.474   1.8559  -3.2192   0.7033
 7CU  C1   C  CR6   0   0.192   0.1730  -0.8421   0.0006
 7CU  N2   N  N     0  -0.470  -0.8065   0.0585   0.0540
 7CU  C3   C  CR6   0   0.478  -2.0732  -0.3187  -0.0584
 7CU  C4   C  CR16  0  -0.175  -2.3676  -1.6764  -0.3315
 7CU  C5   C  C     0   0.446   0.8095  -3.3438   0.0833
 7CU  N6   N  NH1   0  -0.666  -3.0248   0.6180   0.0754
 7CU  C7   C  CH2   0  -0.248  -4.4399   0.3244   0.1498
 7CU  C8   C  CH1   0  -0.158  -5.2539   1.6074   0.3343
 7CU  N9   N  NH2   0  -0.779  -5.1428   2.5580  -0.7606
 7CU  C10  C  CR5   0   0.366   1.5049  -0.2351   0.0006
 7CU  C11  C  CH3   0  -0.654  -6.7172   1.2546   0.5546
 7CU  N12  N  NR15  0  -0.728   1.6083   1.0782   0.3928
 7CU  C13  C  CR56  0   0.351   2.8807   1.5149   0.2185
 7CU  C14  C  CR56  0   0.072   3.6270   0.4385  -0.3141
 7CU  C15  C  CR15  0  -0.439   2.7340  -0.6603  -0.4415
 7CU  C16  C  CR16  0  -0.312   3.4562   2.7606   0.4768
 7CU  C17  C  CR16  0  -0.280   4.7967   2.9113   0.1874
 7CU  C18  C  CR16  0  -0.272   5.5576   1.8534  -0.3463
 7CU  C19  C  CR16  0  -0.343   4.9872   0.6243  -0.5990
 7CU  N20  N  NH2   0  -0.800   0.4003  -4.5078  -0.4430
 7CU  H1   H  HCR6  0   0.284  -3.3756  -2.0203  -0.5251
 7CU  H2   H  HNH1  0   0.390  -2.7043   1.5128   0.4147
 7CU  H3   H  HCH2  0   0.235  -4.7675  -0.1702  -0.7706
 7CU  H4   H  HCH2  0   0.235  -4.6433  -0.3646   0.9778
 7CU  H5   H  HCH1  0   0.236  -4.8836   2.1057   1.2375
 7CU  H6   H  HNH2  0   0.344  -4.1780   2.8214  -0.9175
 7CU  H7   H  HNH2  0   0.339  -5.4585   2.1251  -1.6213
 7CU  H9   H  HCH3  0   0.230  -6.8397   0.5833   1.4046
 7CU  H10  H  HCH3  0   0.239  -7.3020   2.1540   0.7445
 7CU  H11  H  HCH3  0   0.222  -7.1364   0.7599  -0.3246
 7CU  H12  H  HNR5  0   0.406   0.8220   1.6292   0.6979
 7CU  H13  H  HCR5  0   0.249   2.9804  -1.6334  -0.8275
 7CU  H14  H  HCR6  0   0.260   2.8749   3.5776   0.8847
 7CU  H15  H  HCR6  0   0.252   5.2744   3.8646   0.3737
 7CU  H16  H  HCR6  0   0.248   6.6063   2.0141  -0.5601
 7CU  H17  H  HCR6  0   0.248   5.5784  -0.1852  -1.0092
 7CU  H18  H  HNH2  0   0.401   0.9094  -5.3516  -0.2383
 7CU  H19  H  HNH2  0   0.406  -0.5206  -4.5941  -0.8382

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
 7CU  O    C5   double    1.223  0.020  1.223
 7CU  N20  C5   single    1.341  0.020  1.341
 7CU  C16  C17  aromatic  1.380  0.020  1.380
 7CU  C16  C13  aromatic  1.396  0.020  1.396
 7CU  C5   C    single    1.495  0.020  1.495
 7CU  C17  C18  aromatic  1.408  0.020  1.408
 7CU  N12  C13  aromatic  1.357  0.020  1.357
 7CU  N12  C10  aromatic  1.375  0.020  1.375
 7CU  C13  C14  aromatic  1.414  0.020  1.414
 7CU  C18  C19  aromatic  1.378  0.020  1.378
 7CU  C    N    aromatic  1.335  0.020  1.335
 7CU  C    C1   aromatic  1.405  0.020  1.405
 7CU  C10  C1   single    1.464  0.020  1.464
 7CU  C10  C15  aromatic  1.374  0.020  1.374
 7CU  N    C4   aromatic  1.305  0.020  1.305
 7CU  C14  C19  aromatic  1.402  0.020  1.402
 7CU  C14  C15  aromatic  1.422  0.020  1.422
 7CU  C1   N2   aromatic  1.332  0.020  1.332
 7CU  N9   C8   single    1.454  0.020  1.454
 7CU  C4   C3   aromatic  1.416  0.020  1.416
 7CU  N2   C3   aromatic  1.326  0.020  1.326
 7CU  C8   C11  single    1.521  0.020  1.521
 7CU  C8   C7   single    1.531  0.020  1.531
 7CU  C3   N6   single    1.342  0.020  1.342
 7CU  N6   C7   single    1.447  0.020  1.447
 7CU  C4   H1   single    0.930  0.020  1.080
 7CU  N6   H2   single    0.860  0.020  1.020
 7CU  C7   H3   single    0.970  0.020  1.090
 7CU  C7   H4   single    0.970  0.020  1.090
 7CU  C8   H5   single    0.970  0.020  1.090
 7CU  N9   H6   single    0.890  0.020  1.040
 7CU  N9   H7   single    0.890  0.020  1.040
 7CU  C11  H9   single    0.970  0.020  1.090
 7CU  C11  H10  single    0.970  0.020  1.090
 7CU  C11  H11  single    0.970  0.020  1.090
 7CU  N12  H12  single    0.860  0.020  1.020
 7CU  C15  H13  single    0.930  0.020  1.080
 7CU  C16  H14  single    0.930  0.020  1.080
 7CU  C17  H15  single    0.930  0.020  1.080
 7CU  C18  H16  single    0.930  0.020  1.080
 7CU  C19  H17  single    0.930  0.020  1.080
 7CU  N20  H18  single    0.860  0.020  1.020
 7CU  N20  H19  single    0.860  0.020  1.020

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
 7CU  C5   C    C1   125.88  3.000
 7CU  C1   C    N    118.95  3.000
 7CU  C5   C    N    114.97  3.000
 7CU  C4   N    C    121.15  3.000
 7CU  C10  C1   N2   112.89  3.000
 7CU  N2   C1   C    119.76  3.000
 7CU  C10  C1   C    127.26  3.000
 7CU  C3   N2   C1   120.45  3.000
 7CU  N6   C3   C4   122.76  3.000
 7CU  N6   C3   N2   118.05  3.000
 7CU  C4   C3   N2   119.18  3.000
 7CU  H1   C4   C3   122.19  3.000
 7CU  H1   C4   N    117.93  3.000
 7CU  C3   C4   N    119.87  3.000
 7CU  N20  C5   O    123.26  3.000
 7CU  N20  C5   C    114.44  3.000
 7CU  O    C5   C    122.28  3.000
 7CU  H2   N6   C7   118.24  3.000
 7CU  H2   N6   C3   115.29  3.000
 7CU  C7   N6   C3   123.84  3.000
 7CU  H4   C7   H3   107.19  3.000
 7CU  H4   C7   C8   109.70  3.000
 7CU  H3   C7   C8   108.71  3.000
 7CU  H4   C7   N6   110.35  3.000
 7CU  H3   C7   N6   109.94  3.000
 7CU  C8   C7   N6   110.86  3.000
 7CU  H5   C8   C11  108.12  3.000
 7CU  H5   C8   N9   107.30  3.000
 7CU  C11  C8   N9   109.52  3.000
 7CU  H5   C8   C7   107.50  3.000
 7CU  C11  C8   C7   109.55  3.000
 7CU  N9   C8   C7   114.62  3.000
 7CU  H7   N9   H6   106.04  3.000
 7CU  H7   N9   C8   109.65  3.000
 7CU  H6   N9   C8   111.07  3.000
 7CU  C15  C10  N12  108.68  3.000
 7CU  C15  C10  C1   133.30  3.000
 7CU  N12  C10  C1   117.69  3.000
 7CU  H11  C11  H10  107.95  3.000
 7CU  H11  C11  H9   107.78  3.000
 7CU  H10  C11  H9   108.19  3.000
 7CU  H11  C11  C8   110.95  3.000
 7CU  H10  C11  C8   110.50  3.000
 7CU  H9   C11  C8   111.34  3.000
 7CU  H12  N12  C13  126.51  3.000
 7CU  H12  N12  C10  123.39  3.000
 7CU  C13  N12  C10  109.96  3.000
 7CU  C16  C13  C14  122.09  3.000
 7CU  C14  C13  N12  107.36  3.000
 7CU  C16  C13  N12  130.54  3.000
 7CU  C19  C14  C15  133.91  3.000
 7CU  C15  C14  C13  106.89  3.000
 7CU  C19  C14  C13  119.19  3.000
 7CU  H13  C15  C14  125.98  3.000
 7CU  H13  C15  C10  126.92  3.000
 7CU  C14  C15  C10  107.09  3.000
 7CU  H14  C16  C17  121.23  3.000
 7CU  H14  C16  C13  121.45  3.000
 7CU  C17  C16  C13  117.33  3.000
 7CU  H15  C17  C18  119.23  3.000
 7CU  H15  C17  C16  119.27  3.000
 7CU  C18  C17  C16  121.50  3.000
 7CU  H16  C18  C19  119.81  3.000
 7CU  H16  C18  C17  119.14  3.000
 7CU  C19  C18  C17  121.05  3.000
 7CU  H17  C19  C18  120.67  3.000
 7CU  H17  C19  C14  120.50  3.000
 7CU  C18  C19  C14  118.84  3.000
 7CU  H19  N20  H18  118.10  3.000
 7CU  H19  N20  C5   120.52  3.000
 7CU  H18  N20  C5   119.56  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
 7CU  CONST_01  C3   C4   N    C       0.00   0.0  0
 7CU  CONST_02  N12  C10  C1   C     180.00   0.0  0
 7CU  CONST_04  C3   N2   C1   C       0.00   0.0  0
 7CU  CONST_05  C10  C1   C    N     180.00   0.0  0
 7CU  CONST_06  N2   C1   C    N       0.00   0.0  0
 7CU  CONST_07  N2   C3   C4   N       0.00   0.0  0
 7CU  CONST_08  C4   N    C    C1      0.00   0.0  0
 7CU  CONST_09  C13  N12  C10  C1    180.00   0.0  0
 7CU  CONST_10  C14  C15  C10  C1    180.00   0.0  0
 7CU  CONST_11  C4   C3   N2   C1      0.00   0.0  0
 7CU  CONST_14  C10  C1   N2   C3    180.00   0.0  0
 7CU  CONST_15  C16  C13  N12  C10   180.00   0.0  0
 7CU  CONST_16  C14  C13  N12  C10     0.00   0.0  0
 7CU  CONST_17  C13  C14  C15  C10     0.00   0.0  0
 7CU  CONST_18  C19  C14  C15  C10   180.00   0.0  0
 7CU  CONST_19  C17  C16  C13  N12   180.00   0.0  0
 7CU  CONST_20  C19  C14  C13  N12   180.00   0.0  0
 7CU  CONST_21  C15  C14  C13  N12     0.00   0.0  0
 7CU  CONST_22  C14  C15  C10  N12     0.00   0.0  0
 7CU  CONST_23  C18  C17  C16  C13     0.00   0.0  0
 7CU  CONST_24  C15  C10  N12  C13     0.00   0.0  0
 7CU  CONST_25  C18  C19  C14  C13     0.00   0.0  0
 7CU  CONST_26  C17  C16  C13  C14     0.00   0.0  0
 7CU  CONST_27  C17  C18  C19  C14     0.00   0.0  0
 7CU  CONST_28  C16  C13  C14  C15   180.00   0.0  0
 7CU  CONST_29  C18  C19  C14  C15   180.00   0.0  0
 7CU  CONST_30  C19  C18  C17  C16     0.00   0.0  0
 7CU  CONST_31  C19  C14  C13  C16     0.00   0.0  0
 7CU  CONST_32  N6   C3   C4   N     180.00   0.0  0
 7CU  CONST_33  N6   C3   N2   C1    180.00   0.0  0
 7CU  CONST_34  C5   C    C1   N2    180.00   0.0  0
 7CU  CONST_35  C5   C    N    C4    180.00   0.0  0
 7CU  CONST_37  H1   C4   N    C     180.00   0.0  0
 7CU  CONST_38  H12  N12  C10  C1      0.00   0.0  0
 7CU  CONST_39  H13  C15  C10  C1      0.00   0.0  0
 7CU  CONST_40  H14  C16  C13  N12     0.00   0.0  0
 7CU  CONST_41  H15  C17  C16  C13   180.00   0.0  0
 7CU  CONST_42  H17  C19  C14  C13   180.00   0.0  0
 7CU  CONST_43  H16  C18  C19  C14   180.00   0.0  0
 7CU  CONST_44  C7   N6   C3   N2    180.00   0.0  0
 7CU  CONST_45  C7   N6   C3   C4      0.00   0.0  0
 7CU  CONST_46  H2   N6   C3   N2      0.00   0.0  0
 7CU  CONST_47  H18  N20  C5   C     180.00   0.0  0
 7CU  CONST_48  H19  N20  C5   C       0.00   0.0  0
 7CU  Var_01    O    C5   C    N    -155.27  30.0  2
 7CU  Var_02    C8   C7   N6   C3    178.62  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
 7CU  chir_01  C8  N9  C11  C7  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
 7CU  plan-1  C    0.020
 7CU  plan-1  N    0.020
 7CU  plan-1  C1   0.020
 7CU  plan-1  N2   0.020
 7CU  plan-1  C3   0.020
 7CU  plan-1  C4   0.020
 7CU  plan-1  C5   0.020
 7CU  plan-1  N6   0.020
 7CU  plan-1  C10  0.020
 7CU  plan-1  H1   0.020
 7CU  plan-2  C1   0.020
 7CU  plan-2  C10  0.020
 7CU  plan-2  N12  0.020
 7CU  plan-2  C13  0.020
 7CU  plan-2  C14  0.020
 7CU  plan-2  C15  0.020
 7CU  plan-2  C16  0.020
 7CU  plan-2  C17  0.020
 7CU  plan-2  C18  0.020
 7CU  plan-2  C19  0.020
 7CU  plan-2  H12  0.020
 7CU  plan-2  H13  0.020
 7CU  plan-2  H14  0.020
 7CU  plan-2  H15  0.020
 7CU  plan-2  H16  0.020
 7CU  plan-2  H17  0.020
 7CU  plan-3  C    0.020
 7CU  plan-3  O    0.020
 7CU  plan-3  C5   0.020
 7CU  plan-3  N20  0.020
 7CU  plan-3  H18  0.020
 7CU  plan-3  H19  0.020
 7CU  plan-4  C3   0.020
 7CU  plan-4  N6   0.020
 7CU  plan-4  C7   0.020
 7CU  plan-4  H2   0.020

