# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:55:22 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2c(CNCCC3(CCC#C)N=N3)c[nH]c2N1
#
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
 J0C  J0C  "2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one"
  ligand  39  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J0C
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
 J0C  C10  C  CH2   0  -0.355  -1.3930  -16.1993  -2.9548
 J0C  C13  C  CH2   0  -0.479   1.9601  -14.4956  -3.1059
 J0C  C17  C  CH2   0  -0.487   1.6100  -14.2862  -5.6915
 J0C  C20  C  CSP1  0  -0.537   4.1738  -16.7284  -5.1491
 J0C  C21  C  CR15  0  -0.082  -3.6413  -15.4667  -2.0265
 J0C  C2   C  CR6   0   0.406  -3.1096  -15.0468  -5.6409
 J0C  C4   C  CR6   0   0.655  -5.2028  -14.0326  -5.9776
 J0C  C7   C  CR56  0   0.642  -4.6634  -14.6823  -3.8156
 J0C  C8   C  CR56  0  -0.236  -3.4304  -15.1338  -4.2326
 J0C  C9   C  CR5   0  -0.022  -2.7733  -15.6439  -3.0642
 J0C  C12  C  CH2   0  -0.286   0.9606  -15.6361  -2.9761
 J0C  C14  C  CT    0   0.177   1.7509  -13.6458  -4.3345
 J0C  C18  C  CH2   0  -0.584   2.9483  -14.6844  -6.3304
 J0C  C19  C  CSP   0   0.268   3.6217  -15.7982  -5.6749
 J0C  N3   N  N     0  -0.535  -4.0598  -14.4527  -6.4435
 J0C  N6   N  NR16  0  -0.729  -5.5697  -14.1323  -4.6697
 J0C  N11  N  NH1   0  -0.585  -0.3981  -15.1455  -3.0627
 J0C  N15  N  N     0  -0.125   1.1192  -12.3447  -4.1551
 J0C  N16  N  N     0  -0.133   2.3236  -12.3027  -4.3111
 J0C  N22  N  NR15  0  -0.664  -4.7986  -14.8779  -2.4955
 J0C  O1   O  O     0  -0.491  -2.0651  -15.4674  -6.1326
 J0C  H1   H  HCH2  0   0.226  -1.2130  -16.9144  -3.7614
 J0C  H2   H  HCH2  0   0.203  -1.3090  -16.7658  -2.0148
 J0C  H3   H  HCH2  0   0.258   2.9705  -14.9119  -3.1104
 J0C  H4   H  HCH2  0   0.243   1.8969  -13.8568  -2.2200
 J0C  H5   H  HCH2  0   0.263   1.1239  -13.5802  -6.3682
 J0C  H6   H  HCH2  0   0.262   0.9516  -15.1536  -5.6346
 J0C  H7   H  H     0   0.277   4.6578  -17.5525  -4.6768
 J0C  H8   H  HCR5  0   0.281  -3.5362  -15.7086  -0.9814
 J0C  H9   H  HCH2  0   0.214   1.1701  -16.1776  -2.0405
 J0C  H10  H  HCH2  0   0.222   1.1171  -16.3603  -3.7810
 J0C  H11  H  HCH2  0   0.284   2.7686  -14.9571  -7.3731
 J0C  H12  H  HCH2  0   0.275   3.6183  -13.8210  -6.3554
 J0C  H13  H  HNH2  0   0.404  -5.7933  -13.2729  -7.7414
 J0C  H14  H  HNH2  0   0.407  -6.8686  -12.9358  -6.4609
 J0C  H15  H  HNR6  0   0.431  -6.4783  -13.8278  -4.3503
 J0C  H16  H  HNH1  0   0.338  -0.5586  -14.4700  -2.3239
 J0C  H20  H  HNR5  0   0.419  -5.6030  -14.6401  -1.9367
 J0C  N5   N  NH2   0  -0.825  -6.1133  -13.4999  -6.8152

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
 J0C  N5   C4   single    1.347  0.020  1.347
 J0C  C18  C17  single    1.536  0.020  1.536
 J0C  C18  C19  single    1.457  0.020  1.457
 J0C  N3   C4   double    1.304  0.020  1.304
 J0C  N3   C2   single    1.378  0.020  1.378
 J0C  C17  C14  single    1.507  0.020  1.507
 J0C  C4   N6   single    1.362  0.020  1.362
 J0C  O1   C2   double    1.229  0.020  1.229
 J0C  C2   C8   single    1.447  0.020  1.447
 J0C  C19  C20  triple    1.203  0.020  1.203
 J0C  N15  N16  double    1.215  0.020  1.215
 J0C  N15  C14  single    1.457  0.020  1.457
 J0C  N16  C14  single    1.460  0.020  1.460
 J0C  C14  C13  single    1.508  0.020  1.508
 J0C  N6   C7   single    1.361  0.020  1.361
 J0C  C8   C7   aromatic  1.378  0.020  1.378
 J0C  C8   C9   aromatic  1.434  0.020  1.434
 J0C  C7   N22  aromatic  1.341  0.020  1.341
 J0C  N11  C12  single    1.447  0.020  1.447
 J0C  N11  C10  single    1.453  0.020  1.453
 J0C  C13  C12  single    1.522  0.020  1.522
 J0C  C9   C10  single    1.492  0.020  1.492
 J0C  C9   C21  aromatic  1.364  0.020  1.364
 J0C  N22  C21  aromatic  1.381  0.020  1.381
 J0C  C10  H1   single    0.939  0.020  1.096
 J0C  C10  H2   single    0.939  0.020  1.096
 J0C  C13  H3   single    0.939  0.020  1.096
 J0C  C13  H4   single    0.939  0.020  1.096
 J0C  C17  H5   single    0.939  0.020  1.096
 J0C  C17  H6   single    0.939  0.020  1.096
 J0C  C20  H7   single    0.913  0.020  1.066
 J0C  C21  H8   single    0.929  0.020  1.085
 J0C  C12  H9   single    0.939  0.020  1.096
 J0C  C12  H10  single    0.939  0.020  1.096
 J0C  C18  H11  single    0.939  0.020  1.096
 J0C  C18  H12  single    0.939  0.020  1.096
 J0C  N5   H13  single    0.868  0.020  1.013
 J0C  N5   H14  single    0.868  0.020  1.013
 J0C  N6   H15  single    0.868  0.020  1.013
 J0C  N11  H16  single    0.868  0.020  1.013
 J0C  N22  H20  single    0.868  0.020  1.014

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
 J0C  H2   C10  H1   106.31  3.000
 J0C  H2   C10  N11  112.60  3.000
 J0C  H1   C10  N11  107.87  3.000
 J0C  H2   C10  C9   108.95  3.000
 J0C  H1   C10  C9   109.99  3.000
 J0C  N11  C10  C9   110.98  3.000
 J0C  H4   C13  H3   106.21  3.000
 J0C  H4   C13  C14  108.82  3.000
 J0C  H3   C13  C14  109.85  3.000
 J0C  H4   C13  C12  109.30  3.000
 J0C  H3   C13  C12  108.79  3.000
 J0C  C14  C13  C12  113.61  3.000
 J0C  H6   C17  H5   106.13  3.000
 J0C  H6   C17  C18  109.97  3.000
 J0C  H5   C17  C18  107.33  3.000
 J0C  H6   C17  C14  110.33  3.000
 J0C  H5   C17  C14  108.96  3.000
 J0C  C18  C17  C14  113.79  3.000
 J0C  H7   C20  C19  180.00  3.000
 J0C  H8   C21  N22  120.45  3.000
 J0C  H8   C21  C9   130.26  3.000
 J0C  N22  C21  C9   109.29  3.000
 J0C  O1   C2   N3   120.03  3.000
 J0C  O1   C2   C8   123.88  3.000
 J0C  N3   C2   C8   116.09  3.000
 J0C  N6   C4   N5   116.36  3.000
 J0C  N6   C4   N3   123.76  3.000
 J0C  N5   C4   N3   119.85  3.000
 J0C  N22  C7   N6   127.54  3.000
 J0C  N22  C7   C8   109.89  3.000
 J0C  N6   C7   C8   122.57  3.000
 J0C  C9   C8   C7   106.26  3.000
 J0C  C9   C8   C2   135.45  3.000
 J0C  C7   C8   C2   118.25  3.000
 J0C  C8   C9   C21  106.38  3.000
 J0C  C21  C9   C10  125.53  3.000
 J0C  C8   C9   C10  128.02  3.000
 J0C  H10  C12  H9   105.80  3.000
 J0C  H10  C12  N11  108.34  3.000
 J0C  H9   C12  N11  113.34  3.000
 J0C  H10  C12  C13  109.84  3.000
 J0C  H9   C12  C13  108.43  3.000
 J0C  N11  C12  C13  110.94  3.000
 J0C  N16  C14  N15   49.23  3.000
 J0C  N16  C14  C17  116.22  3.000
 J0C  N15  C14  C17  116.72  3.000
 J0C  N16  C14  C13  116.79  3.000
 J0C  N15  C14  C13  117.57  3.000
 J0C  C17  C14  C13  120.46  3.000
 J0C  H12  C18  H11  106.03  3.000
 J0C  H12  C18  C19  109.31  3.000
 J0C  H11  C18  C19  108.33  3.000
 J0C  H12  C18  C17  109.81  3.000
 J0C  H11  C18  C17  108.57  3.000
 J0C  C19  C18  C17  114.44  3.000
 J0C  C18  C19  C20  180.00  3.000
 J0C  C4   N3   C2   122.35  3.000
 J0C  H15  N6   C7   121.49  3.000
 J0C  H15  N6   C4   121.59  3.000
 J0C  C7   N6   C4   116.92  3.000
 J0C  H16  N11  C12  109.32  3.000
 J0C  H16  N11  C10  108.70  3.000
 J0C  C12  N11  C10  113.11  3.000
 J0C  N16  N15  C14   65.51  3.000
 J0C  N15  N16  C14   65.26  3.000
 J0C  H20  N22  C7   126.27  3.000
 J0C  H20  N22  C21  125.54  3.000
 J0C  C7   N22  C21  108.19  3.000
 J0C  H14  N5   H13  115.86  3.000
 J0C  H14  N5   C4   120.64  3.000
 J0C  H13  N5   C4   116.54  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
 J0C  CONST_01  C7   C8   C9   C21     0.00   0.0  0
 J0C  CONST_02  C8   C7   N22  C21     0.00   0.0  0
 J0C  CONST_03  C9   C21  N22  C7      0.00   0.0  0
 J0C  CONST_04  N22  C21  C9   C8      0.00   0.0  0
 J0C  CONST_05  N22  C7   C8   C9      0.00   0.0  0
 J0C  CONST_06  N6   C4   N3   C2      0.00   0.0  0
 J0C  CONST_07  N3   C4   N6   C7      0.00   0.0  0
 J0C  CONST_08  C2   C8   C9   C10     0.00   0.0  0
 J0C  CONST_09  C7   C8   C9   C10   180.00   0.0  0
 J0C  CONST_10  N22  C21  C9   C10   180.00   0.0  0
 J0C  CONST_11  N5   C4   N3   C2    180.00   0.0  0
 J0C  CONST_12  N5   C4   N6   C7    180.00   0.0  0
 J0C  CONST_13  H8   C21  N22  C7    180.00   0.0  0
 J0C  CONST_14  H20  N22  C7   C8    180.00   0.0  0
 J0C  CONST_15  H8   C21  C9   C8    180.00   0.0  0
 J0C  CONST_16  H20  N22  C21  C9    180.00   0.0  0
 J0C  CONST_17  H20  N22  C7   N6      0.00   0.0  0
 J0C  CONST_18  H15  N6   C4   N3    180.00   0.0  0
 J0C  CONST_19  H13  N5   C4   N3      0.00   0.0  0
 J0C  CONST_21  H15  N6   C4   N5      0.00   0.0  0
 J0C  CONST_22  H13  N5   C4   N6    180.00   0.0  0
 J0C  Var_01    N16  N15  C14  C13   102.77  30.0  1
 J0C  Var_02    N16  N15  C14  C17  -102.66  30.0  1
 J0C  Var_03    O1   C2   N3   C4    177.57  30.0  1
 J0C  Var_04    O1   C2   C8   C7   -176.92  30.0  1
 J0C  Var_05    O1   C2   C8   C9      0.43  30.0  1
 J0C  Var_06    N11  C10  C9   C21  -104.46  30.0  2
 J0C  Var_07    N11  C10  C9   C8     72.16  30.0  2
 J0C  Var_08    N15  C14  C13  C12   103.42  30.0  1
 J0C  Var_09    N16  C14  C13  C12   159.24  30.0  1
 J0C  Var_10    N15  C14  C17  C18   125.89  30.0  3
 J0C  Var_11    N16  C14  C17  C18    70.44  30.0  3
 J0C  Var_12    H1   C10  C9   C21   136.25  30.0  2
 J0C  Var_13    H2   C10  C9   C21    20.08  30.0  2
 J0C  Var_14    H1   C10  C9   C8    -47.13  30.0  2
 J0C  Var_15    H2   C10  C9   C8   -163.30  30.0  2
 J0C  Var_16    H5   C17  C14  N15     6.18  30.0  1
 J0C  Var_17    H6   C17  C14  N15  -109.95  30.0  1
 J0C  Var_18    H3   C13  C14  N15  -134.48  30.0  3
 J0C  Var_19    H4   C13  C14  N15   -18.59  30.0  3
 J0C  Var_20    H5   C17  C14  N16   -49.27  30.0  1
 J0C  Var_21    H6   C17  C14  N16  -165.41  30.0  1
 J0C  Var_22    H3   C13  C14  N16   -78.65  30.0  3
 J0C  Var_23    H4   C13  C14  N16    37.23  30.0  3
 J0C  Var_24    C18  C17  C14  C13   -80.32  30.0  1
 J0C  Var_25    C12  C13  C14  C17   -50.16  30.0  3
 J0C  Var_26    C12  N11  C10  C9   -179.41  30.0  2
 J0C  Var_27    C19  C18  C17  C14    69.59  30.0  2
 J0C  Var_28    N11  C12  C13  C14   -53.16  30.0  3
 J0C  Var_29    H5   C17  C14  C13   159.97  30.0  1
 J0C  Var_30    H6   C17  C14  C13    43.84  30.0  1
 J0C  Var_31    H3   C13  C14  C17    71.95  30.0  3
 J0C  Var_32    H4   C13  C14  C17  -172.17  30.0  3
 J0C  Var_33    H16  N11  C10  C9     58.97  30.0  2
 J0C  Var_34    H11  C18  C17  C14  -169.26  30.0  2
 J0C  Var_35    H12  C18  C17  C14   -53.76  30.0  2
 J0C  Var_36    H9   C12  C13  C14  -178.23  30.0  3
 J0C  Var_37    H10  C12  C13  C14    66.59  30.0  3
 J0C  Var_38    C13  C12  N11  C10   179.54  30.0  3
 J0C  Var_39    C20  C19  C18  C17   110.54  30.0  3
 J0C  Var_40    H9   C12  N11  C10   -58.20  30.0  3
 J0C  Var_41    H10  C12  N11  C10    58.90  30.0  3
 J0C  Var_42    H16  N11  C12  C13   -59.19  30.0  1
 J0C  Var_43    H11  C18  C19  C20   -10.73  30.0  2
 J0C  Var_44    H12  C18  C19  C20  -125.84  30.0  2
 J0C  Var_45    H1   C10  N11  C12   -58.85  30.0  3
 J0C  Var_46    H2   C10  N11  C12    58.14  30.0  3
 J0C  Var_47    H5   C17  C18  C19  -169.78  30.0  3
 J0C  Var_48    H6   C17  C18  C19   -54.75  30.0  3
 J0C  Var_49    H3   C13  C12  N11  -175.85  30.0  1
 J0C  Var_50    H4   C13  C12  N11    68.59  30.0  1

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
 J0C  chir_01  C14  N15  N16  C13  both

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
 J0C  plan-1  C2   0.020
 J0C  plan-1  C8   0.020
 J0C  plan-1  N3   0.020
 J0C  plan-1  O1   0.020
 J0C  plan-2  C10  0.020
 J0C  plan-2  C21  0.020
 J0C  plan-2  C2   0.020
 J0C  plan-2  C4   0.020
 J0C  plan-2  C7   0.020
 J0C  plan-2  C8   0.020
 J0C  plan-2  C9   0.020
 J0C  plan-2  N3   0.020
 J0C  plan-2  N6   0.020
 J0C  plan-2  N22  0.020
 J0C  plan-2  H8   0.020
 J0C  plan-2  H13  0.020
 J0C  plan-2  H14  0.020
 J0C  plan-2  H15  0.020
 J0C  plan-2  H20  0.020
 J0C  plan-2  N5   0.020

