# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 21:46:53 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 1-(aminomethyl)-N-(3-{[6-bromo-2-(4-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-7-yl]amino}propyl)cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2[nH]c3ncc(Br)c(NCCCNC(=O)C4(CN)CC4)c3n2
#
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
 1N3  1N3  1-(aminomethyl)-N-(3-{[6-bromo-2-(4-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-7-yl]amino}propyl)cyclopropanecarboxamide  ligand  55  30  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1N3
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
 1N3  C1   C   CH3   0  -0.440   9.0653   3.8533   0.7403
 1N3  O2   O   O2    0  -0.463   7.7020   4.1401   0.4891
 1N3  C3   C   CR6   0   0.387   6.8409   3.1205   0.3650
 1N3  C4   C   CR16  0  -0.326   5.5074   3.4627   0.1135
 1N3  C5   C   CR16  0  -0.272   4.5533   2.4811  -0.0348
 1N3  C6   C   CR6   0  -0.008   4.8921   1.1267   0.0608
 1N3  C7   C   CR16  0  -0.283   6.2195   0.7970   0.3166
 1N3  C8   C   CR16  0  -0.368   7.1906   1.7756   0.4685
 1N3  C9   C   CR5   0   0.506   3.8545   0.1175  -0.1012
 1N3  N10  N   NR15  0  -0.727   4.1153  -1.2184  -0.2133
 1N3  C11  C   CR56  0   0.461   2.9188  -1.8583  -0.3568
 1N3  C12  C   CR56  0   0.017   1.9672  -0.8389  -0.3157
 1N3  N13  N   N     0  -0.484   2.5709   0.3753  -0.1548
 1N3  C14  C   CR6   0   0.418   0.6032  -1.1512  -0.4195
 1N3  C15  C   CR6   0  -0.275   0.3633  -2.5232  -0.5950
 1N3  C16  C   CR16  0  -0.090   1.4062  -3.4566  -0.6052
 1N3  N17  N   N     0  -0.434   2.6904  -3.1544  -0.4812
 1N3  BR1  BR  BR    0  -0.036  -1.3695  -3.1690  -0.9794
 1N3  N19  N   NH1   0  -0.668  -0.3315  -0.1540  -0.4059
 1N3  C20  C   CH2   0  -0.295  -1.4711  -0.1402   0.5062
 1N3  C21  C   CH2   0  -0.485  -2.7030   0.4516  -0.1555
 1N3  C22  C   CH2   0  -0.243  -3.8671   0.5325   0.8188
 1N3  N23  N   NH1   0  -0.668  -5.0138   1.1380   0.1817
 1N3  C24  C   C     0   0.574  -6.1818   1.3010   0.8152
 1N3  O25  O   O     0  -0.517  -6.3756   0.9128   1.9636
 1N3  C26  C   CT    0  -0.172  -7.2425   2.0182   0.0235
 1N3  C27  C   CH2   0  -0.470  -7.8363   3.2303   0.7064
 1N3  C28  C   CH2   0  -0.467  -8.6308   1.9766   0.5926
 1N3  C29  C   CH2   0  -0.310  -7.1241   2.0492  -1.4861
 1N3  N30  N   NH2   0  -0.804  -5.9114   2.7285  -1.9263
 1N3  H1   H   HCH3  0   0.263   9.5777   4.8108   0.7860
 1N3  H2   H   HCH3  0   0.233   9.2025   3.3342   1.6921
 1N3  H3   H   HCH3  0   0.233   9.5078   3.2530  -0.0583
 1N3  H4   H   HCR6  0   0.270   5.2324   4.5067   0.0310
 1N3  H5   H   HCR6  0   0.260   3.5279   2.7622  -0.2342
 1N3  H6   H   HCR6  0   0.252   6.5301  -0.2353   0.4167
 1N3  H7   H   HCR6  0   0.287   8.2072   1.4686   0.6708
 1N3  H8   H   HNR5  0   0.426   5.0202  -1.6628  -0.2279
 1N3  H10  H   HCR6  0   0.274   1.1720  -4.5073  -0.7332
 1N3  H11  H   HNH1  0   0.387   0.1090   0.7548  -0.4497
 1N3  H12  H   HCH2  0   0.248  -1.6801  -1.1468   0.8615
 1N3  H13  H   HCH2  0   0.247  -1.2095   0.4440   1.3950
 1N3  H14  H   HCH2  0   0.236  -2.4656   1.4535  -0.5272
 1N3  H15  H   HCH2  0   0.239  -2.9812  -0.1543  -1.0217
 1N3  H16  H   HCH2  0   0.229  -4.1258  -0.4701   1.1704
 1N3  H17  H   HCH2  0   0.225  -3.5691   1.1060   1.7037
 1N3  H18  H   HNH1  0   0.415  -4.9048   1.6434  -0.7009
 1N3  H19  H   HCH2  0   0.259  -7.4463   3.5028   1.6786
 1N3  H20  H   HCH2  0   0.257  -8.0981   4.0731   0.0777
 1N3  H21  H   HCH2  0   0.256  -9.4496   1.9503  -0.1155
 1N3  H22  H   HCH2  0   0.257  -8.7904   1.3901   1.4867
 1N3  H23  H   HCH2  0   0.244  -7.0906   1.0238  -1.8628
 1N3  H24  H   HCH2  0   0.223  -8.0387   2.4983  -1.8924
 1N3  H25  H   HNH2  0   0.367  -5.8275   2.6667  -2.9326
 1N3  H26  H   HNH2  0   0.355  -5.9643   3.7140  -1.6994

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
 1N3  C7   C8   aromatic  1.387  0.020  1.387
 1N3  C7   C6   aromatic  1.391  0.020  1.391
 1N3  C8   C3   aromatic  1.394  0.020  1.394
 1N3  N10  C11  aromatic  1.364  0.020  1.364
 1N3  N10  C9   aromatic  1.366  0.020  1.366
 1N3  N17  C11  aromatic  1.322  0.020  1.322
 1N3  N17  C16  aromatic  1.325  0.020  1.325
 1N3  C6   C9   single    1.456  0.020  1.456
 1N3  C6   C5   aromatic  1.399  0.020  1.399
 1N3  C11  C12  aromatic  1.395  0.020  1.395
 1N3  O2   C3   single    1.340  0.020  1.340
 1N3  O2   C1   single    1.416  0.020  1.416
 1N3  C3   C4   aromatic  1.399  0.020  1.399
 1N3  C9   N13  aromatic  1.310  0.020  1.310
 1N3  C16  C15  aromatic  1.400  0.020  1.400
 1N3  N13  C12  aromatic  1.365  0.020  1.365
 1N3  C12  C14  aromatic  1.403  0.020  1.403
 1N3  C5   C4   aromatic  1.377  0.020  1.377
 1N3  C15  C14  aromatic  1.404  0.020  1.404
 1N3  C15  BR1  single    1.889  0.020  1.889
 1N3  C14  N19  single    1.367  0.020  1.367
 1N3  N19  C20  single    1.460  0.020  1.460
 1N3  C20  C21  single    1.519  0.020  1.519
 1N3  C21  C22  single    1.520  0.020  1.520
 1N3  O25  C24  double    1.228  0.020  1.228
 1N3  C27  C26  single    1.513  0.020  1.513
 1N3  C27  C28  single    1.489  0.020  1.489
 1N3  C22  N23  single    1.445  0.020  1.445
 1N3  C24  N23  single    1.339  0.020  1.339
 1N3  C24  C26  single    1.505  0.020  1.505
 1N3  C26  C28  single    1.501  0.020  1.501
 1N3  C26  C29  single    1.515  0.020  1.515
 1N3  C29  N30  single    1.458  0.020  1.458
 1N3  C1   H1   single    0.970  0.020  1.090
 1N3  C1   H2   single    0.970  0.020  1.090
 1N3  C1   H3   single    0.970  0.020  1.090
 1N3  C4   H4   single    0.930  0.020  1.080
 1N3  C5   H5   single    0.930  0.020  1.080
 1N3  C7   H6   single    0.930  0.020  1.080
 1N3  C8   H7   single    0.930  0.020  1.080
 1N3  N10  H8   single    0.860  0.020  1.020
 1N3  C16  H10  single    0.930  0.020  1.080
 1N3  N19  H11  single    0.890  0.020  1.040
 1N3  C20  H12  single    0.970  0.020  1.090
 1N3  C20  H13  single    0.970  0.020  1.090
 1N3  C21  H14  single    0.970  0.020  1.090
 1N3  C21  H15  single    0.970  0.020  1.090
 1N3  C22  H16  single    0.970  0.020  1.090
 1N3  C22  H17  single    0.970  0.020  1.090
 1N3  N23  H18  single    0.860  0.020  1.020
 1N3  C27  H19  single    0.970  0.020  1.090
 1N3  C27  H20  single    0.970  0.020  1.090
 1N3  C28  H21  single    0.970  0.020  1.090
 1N3  C28  H22  single    0.970  0.020  1.090
 1N3  C29  H23  single    0.970  0.020  1.090
 1N3  C29  H24  single    0.970  0.020  1.090
 1N3  N30  H25  single    0.890  0.020  1.040
 1N3  N30  H26  single    0.890  0.020  1.040

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
 1N3  H3   C1   H2   108.95  3.000
 1N3  H3   C1   H1   108.89  3.000
 1N3  H2   C1   H1   108.83  3.000
 1N3  H3   C1   O2   111.81  3.000
 1N3  H2   C1   O2   111.82  3.000
 1N3  H1   C1   O2   106.44  3.000
 1N3  C3   O2   C1   118.76  3.000
 1N3  C8   C3   C4   119.24  3.000
 1N3  C4   C3   O2   116.29  3.000
 1N3  C8   C3   O2   124.48  3.000
 1N3  H4   C4   C5   120.21  3.000
 1N3  H4   C4   C3   119.43  3.000
 1N3  C5   C4   C3   120.36  3.000
 1N3  H5   C5   C6   119.57  3.000
 1N3  H5   C5   C4   119.44  3.000
 1N3  C6   C5   C4   120.99  3.000
 1N3  C9   C6   C7   122.41  3.000
 1N3  C9   C6   C5   119.38  3.000
 1N3  C7   C6   C5   118.22  3.000
 1N3  H6   C7   C8   117.50  3.000
 1N3  H6   C7   C6   121.10  3.000
 1N3  C8   C7   C6   121.40  3.000
 1N3  H7   C8   C7   118.59  3.000
 1N3  H7   C8   C3   121.60  3.000
 1N3  C7   C8   C3   119.81  3.000
 1N3  N13  C9   N10  112.10  3.000
 1N3  N13  C9   C6   124.48  3.000
 1N3  N10  C9   C6   123.42  3.000
 1N3  H8   N10  C11  125.37  3.000
 1N3  H8   N10  C9   127.14  3.000
 1N3  C11  N10  C9   107.45  3.000
 1N3  N17  C11  C12  126.97  3.000
 1N3  C12  C11  N10  104.62  3.000
 1N3  N17  C11  N10  128.40  3.000
 1N3  C14  C12  N13  129.52  3.000
 1N3  C14  C12  C11  119.88  3.000
 1N3  N13  C12  C11  110.59  3.000
 1N3  C12  N13  C9   105.25  3.000
 1N3  N19  C14  C15  126.69  3.000
 1N3  N19  C14  C12  120.11  3.000
 1N3  C15  C14  C12  113.13  3.000
 1N3  BR1  C15  C16  117.01  3.000
 1N3  BR1  C15  C14  121.09  3.000
 1N3  C16  C15  C14  121.69  3.000
 1N3  H10  C16  N17  116.20  3.000
 1N3  H10  C16  C15  119.09  3.000
 1N3  N17  C16  C15  124.71  3.000
 1N3  C16  N17  C11  113.57  3.000
 1N3  H11  N19  C20  111.02  3.000
 1N3  H11  N19  C14  110.95  3.000
 1N3  C20  N19  C14  123.16  3.000
 1N3  H13  C20  H12  105.93  3.000
 1N3  H13  C20  C21  109.84  3.000
 1N3  H12  C20  C21  110.31  3.000
 1N3  H13  C20  N19  109.01  3.000
 1N3  H12  C20  N19  110.21  3.000
 1N3  C21  C20  N19  111.39  3.000
 1N3  H15  C21  H14  107.06  3.000
 1N3  H15  C21  C22  110.03  3.000
 1N3  H14  C21  C22  109.57  3.000
 1N3  H15  C21  C20  109.62  3.000
 1N3  H14  C21  C20  109.19  3.000
 1N3  C22  C21  C20  111.27  3.000
 1N3  H17  C22  H16  106.53  3.000
 1N3  H17  C22  N23  110.65  3.000
 1N3  H16  C22  N23  109.77  3.000
 1N3  H17  C22  C21  109.71  3.000
 1N3  H16  C22  C21  109.78  3.000
 1N3  N23  C22  C21  110.33  3.000
 1N3  H18  N23  C24  116.17  3.000
 1N3  H18  N23  C22  120.20  3.000
 1N3  C24  N23  C22  122.33  3.000
 1N3  C26  C24  O25  122.10  3.000
 1N3  C26  C24  N23  115.08  3.000
 1N3  O25  C24  N23  122.81  3.000
 1N3  C29  C26  C28  116.79  3.000
 1N3  C29  C26  C27  117.66  3.000
 1N3  C28  C26  C27   59.20  3.000
 1N3  C29  C26  C24  118.61  3.000
 1N3  C28  C26  C24  116.05  3.000
 1N3  C27  C26  C24  114.90  3.000
 1N3  H20  C27  H19  114.36  3.000
 1N3  H20  C27  C28  118.80  3.000
 1N3  H19  C27  C28  118.23  3.000
 1N3  H20  C27  C26  117.14  3.000
 1N3  H19  C27  C26  117.76  3.000
 1N3  C28  C27  C26   60.01  3.000
 1N3  H22  C28  H21  114.58  3.000
 1N3  H22  C28  C27  118.19  3.000
 1N3  H21  C28  C27  118.30  3.000
 1N3  H22  C28  C26  117.72  3.000
 1N3  H21  C28  C26  116.88  3.000
 1N3  C27  C28  C26   60.79  3.000
 1N3  H24  C29  H23  106.38  3.000
 1N3  H24  C29  N30  113.01  3.000
 1N3  H23  C29  N30  107.91  3.000
 1N3  H24  C29  C26  108.21  3.000
 1N3  H23  C29  C26  109.07  3.000
 1N3  N30  C29  C26  112.05  3.000
 1N3  H26  N30  H25  106.66  3.000
 1N3  H26  N30  C29  110.01  3.000
 1N3  H25  N30  C29  109.93  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
 1N3  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 1N3  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 1N3  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 1N3  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 1N3  CONST_05  C9   C6   C5   C4    180.00   0.0  0
 1N3  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 1N3  CONST_07  N10  C9   C6   C5    180.00   0.0  0
 1N3  CONST_08  N13  C9   C6   C5      0.00   0.0  0
 1N3  CONST_09  C8   C3   C4   C5      0.00   0.0  0
 1N3  CONST_10  C11  N10  C9   C6    180.00   0.0  0
 1N3  CONST_11  C12  N13  C9   C6    180.00   0.0  0
 1N3  CONST_12  N10  C9   C6   C7      0.00   0.0  0
 1N3  CONST_13  N13  C9   C6   C7    180.00   0.0  0
 1N3  CONST_14  C9   C6   C7   C8    180.00   0.0  0
 1N3  CONST_15  N17  C11  N10  C9    180.00   0.0  0
 1N3  CONST_16  C12  C11  N10  C9      0.00   0.0  0
 1N3  CONST_17  C11  C12  N13  C9      0.00   0.0  0
 1N3  CONST_18  C14  C12  N13  C9    180.00   0.0  0
 1N3  CONST_19  C16  N17  C11  N10   180.00   0.0  0
 1N3  CONST_20  N13  C12  C11  N10     0.00   0.0  0
 1N3  CONST_21  C14  C12  C11  N10   180.00   0.0  0
 1N3  CONST_22  C12  N13  C9   N10     0.00   0.0  0
 1N3  CONST_23  N13  C9   N10  C11     0.00   0.0  0
 1N3  CONST_24  C15  C16  N17  C11     0.00   0.0  0
 1N3  CONST_25  C15  C14  C12  C11     0.00   0.0  0
 1N3  CONST_26  C16  N17  C11  C12     0.00   0.0  0
 1N3  CONST_27  C16  C15  C14  C12     0.00   0.0  0
 1N3  CONST_28  N17  C11  C12  N13   180.00   0.0  0
 1N3  CONST_29  C15  C14  C12  N13   180.00   0.0  0
 1N3  CONST_30  N17  C11  C12  C14     0.00   0.0  0
 1N3  CONST_31  N17  C16  C15  C14     0.00   0.0  0
 1N3  CONST_32  C7   C8   C3   O2    180.00   0.0  0
 1N3  CONST_33  C5   C4   C3   O2    180.00   0.0  0
 1N3  CONST_34  N19  C14  C12  C11   180.00   0.0  0
 1N3  CONST_35  BR1  C15  C14  C12   180.00   0.0  0
 1N3  CONST_36  N19  C14  C12  N13     0.00   0.0  0
 1N3  CONST_37  N19  C14  C15  C16   180.00   0.0  0
 1N3  CONST_38  BR1  C15  C16  N17   180.00   0.0  0
 1N3  CONST_39  H6   C7   C8   C3    180.00   0.0  0
 1N3  CONST_40  H5   C5   C4   C3    180.00   0.0  0
 1N3  CONST_41  H7   C8   C3   C4    180.00   0.0  0
 1N3  CONST_42  H8   N10  C9   C6      0.00   0.0  0
 1N3  CONST_43  H4   C4   C5   C6    180.00   0.0  0
 1N3  CONST_44  H10  C16  N17  C11   180.00   0.0  0
 1N3  CONST_47  H11  N19  C14  C12     0.00   0.0  0
 1N3  CONST_48  C26  C24  N23  C22   180.00   0.0  0
 1N3  CONST_49  H18  N23  C24  C26     0.00   0.0  0
 1N3  CONST_50  O25  C24  N23  C22     0.00   0.0  0
 1N3  Var_01    C28  C27  C26  C24  -106.67  30.0  1
 1N3  Var_02    H21  C28  C27  C26  -106.70  30.0  1
 1N3  Var_03    C8   C3   O2   C1      0.13  30.0  2
 1N3  Var_04    C27  C26  C24  N23  -125.34  30.0  3
 1N3  Var_05    N30  C29  C26  C27    84.07  30.0  3
 1N3  Var_06    C21  C20  N19  C14  -144.59  30.0  3
 1N3  Var_07    H1   C1   O2   C3    179.02  30.0  3
 1N3  Var_08    H25  N30  C29  C26   175.53  30.0  3
 1N3  Var_09    C22  C21  C20  N19  -176.99  30.0  3
 1N3  Var_10    N23  C22  C21  C20   178.13  30.0  3
 1N3  Var_11    C24  N23  C22  C21   178.56  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
 1N3  chir_01  C26  C24  C28  C29  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
 1N3  plan-1  O2   0.020
 1N3  plan-1  C3   0.020
 1N3  plan-1  C4   0.020
 1N3  plan-1  C5   0.020
 1N3  plan-1  C6   0.020
 1N3  plan-1  C7   0.020
 1N3  plan-1  C8   0.020
 1N3  plan-1  C9   0.020
 1N3  plan-1  H4   0.020
 1N3  plan-1  H5   0.020
 1N3  plan-1  H6   0.020
 1N3  plan-1  H7   0.020
 1N3  plan-2  C6   0.020
 1N3  plan-2  C9   0.020
 1N3  plan-2  N10  0.020
 1N3  plan-2  C11  0.020
 1N3  plan-2  C12  0.020
 1N3  plan-2  N13  0.020
 1N3  plan-2  C14  0.020
 1N3  plan-2  C15  0.020
 1N3  plan-2  C16  0.020
 1N3  plan-2  N17  0.020
 1N3  plan-2  BR1  0.020
 1N3  plan-2  N19  0.020
 1N3  plan-2  H8   0.020
 1N3  plan-2  H10  0.020
 1N3  plan-3  C14  0.020
 1N3  plan-3  N19  0.020
 1N3  plan-3  C20  0.020
 1N3  plan-3  H11  0.020
 1N3  plan-4  C22  0.020
 1N3  plan-4  N23  0.020
 1N3  plan-4  C24  0.020
 1N3  plan-4  O25  0.020
 1N3  plan-4  C26  0.020
 1N3  plan-4  H18  0.020

