# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:55:10 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCNc1cc(nc(n1)c2ccccn2)N3CCc4ccccc4CC3
#
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
 S2I  S2I  3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propan-1-ol  ligand  53  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S2I
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
 S2I  C01   C  CH2   0  -0.502   4.3775   3.2865  -0.3310
 S2I  C02   C  CH2   0  -0.256   3.0638   2.6450   0.0848
 S2I  N03   N  NH1   0  -0.669   3.1129   1.2186  -0.1210
 S2I  C04   C  CR6   0   0.544   2.1018   0.3741   0.1446
 S2I  C05   C  CR16  0  -0.537   0.8618   0.8140   0.6134
 S2I  C06   C  CR6   0   0.561  -0.1116  -0.1653   0.8417
 S2I  N07   N  N     0  -0.490   0.1492  -1.4599   0.5991
 S2I  C08   C  CR6   0   0.357   1.3552  -1.7630   0.1622
 S2I  C09   C  CR6   0   0.141   1.6412  -3.2063  -0.0892
 S2I  C10   C  CR16  0  -0.297   2.8682  -3.5986  -0.6201
 S2I  C11   C  CR16  0  -0.154   3.1015  -4.9462  -0.8397
 S2I  C12   C  CR16  0  -0.314   2.1075  -5.8579  -0.5215
 S2I  C13   C  CR16  0  -0.087   0.9195  -5.3684   0.0037
 S2I  N14   N  N     0  -0.402   0.6873  -4.0815   0.2146
 S2I  N15   N  N     0  -0.511   2.3482  -0.9272  -0.0794
 S2I  N16   N  NT    0  -0.477  -1.3487   0.1206   1.3329
 S2I  C17   C  CH2   0  -0.329  -2.4157  -0.8514   1.1863
 S2I  C18   C  CH2   0  -0.531  -3.1117  -0.7712  -0.1768
 S2I  C19   C  CR6   0   0.103  -4.0906   0.3648  -0.3292
 S2I  C20   C  CR16  0  -0.317  -5.4143   0.0695  -0.6485
 S2I  C21   C  CR16  0  -0.257  -6.3688   1.0650  -0.8074
 S2I  C22   C  CR16  0  -0.259  -6.0017   2.3908  -0.6436
 S2I  C23   C  CR16  0  -0.316  -4.6866   2.6983  -0.3222
 S2I  C24   C  CR6   0   0.102  -3.7197   1.7081  -0.1618
 S2I  C25   C  CH2   0  -0.530  -2.3156   2.1213   0.1966
 S2I  C26   C  CH2   0  -0.352  -1.7829   1.4911   1.4881
 S2I  C27   C  CH2   0  -0.137   4.3417   4.7889  -0.1279
 S2I  O28   O  OH1   0  -0.672   5.5810   5.3264  -0.5328
 S2I  H01   H  HCH2  0   0.240   5.1962   2.8568   0.2535
 S2I  H01A  H  HCH2  0   0.240   4.5749   3.0652  -1.3838
 S2I  H02   H  HCH2  0   0.231   2.8585   2.8704   1.1379
 S2I  H02A  H  HCH2  0   0.230   2.2441   3.0826  -0.4960
 S2I  HN03  H  HNH1  0   0.388   3.9707   0.8016  -0.4444
 S2I  H05   H  HCR6  0   0.276   0.6742   1.8644   0.7671
 S2I  H10   H  HCR6  0   0.269   3.6186  -2.8574  -0.8523
 S2I  H11   H  HCR6  0   0.273   4.0449  -5.2781  -1.2526
 S2I  H12   H  HCR6  0   0.272   2.2434  -6.9198  -0.6731
 S2I  H13   H  HCR6  0   0.260   0.1193  -6.0518   0.2670
 S2I  H17   H  HCH2  0   0.274  -2.0000  -1.8463   1.3166
 S2I  H17A  H  HCH2  0   0.248  -3.1383  -0.6847   1.9881
 S2I  H18   H  HCH2  0   0.251  -2.3430  -0.7209  -0.9553
 S2I  H18A  H  HCH2  0   0.255  -3.6438  -1.7108  -0.3395
 S2I  H20   H  HCR6  0   0.246  -5.7024  -0.9672  -0.7784
 S2I  H21   H  HCR6  0   0.251  -7.3891   0.8021  -1.0550
 S2I  H22   H  HCR6  0   0.251  -6.7299   3.1829  -0.7614
 S2I  H23   H  HCR6  0   0.247  -4.4005   3.7353  -0.1904
 S2I  H25   H  HCH2  0   0.254  -1.6225   1.8953  -0.6217
 S2I  H25A  H  HCH2  0   0.259  -2.2921   3.2065   0.3157
 S2I  H26   H  HCH2  0   0.265  -2.5599   1.5110   2.2553
 S2I  H26A  H  HCH2  0   0.266  -0.9636   2.0924   1.8795
 S2I  H27   H  HCH2  0   0.195   3.5109   5.2122  -0.7077
 S2I  H27A  H  HCH2  0   0.194   4.1341   5.0072   0.9279
 S2I  HO28  H  HOH1  0   0.454   5.5490   6.2793  -0.4111

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
 S2I  C01  C02   single    1.520  0.020  1.520
 S2I  C01  C27   single    1.516  0.020  1.516
 S2I  C02  N03   single    1.442  0.020  1.442
 S2I  N03  C04   single    1.344  0.020  1.344
 S2I  C04  C05   aromatic  1.397  0.020  1.397
 S2I  C04  N15   aromatic  1.343  0.020  1.343
 S2I  C05  C06   aromatic  1.400  0.020  1.400
 S2I  C06  N07   aromatic  1.343  0.020  1.343
 S2I  C06  N16   single    1.361  0.020  1.361
 S2I  N07  C08   aromatic  1.318  0.020  1.318
 S2I  C08  C09   single    1.493  0.020  1.493
 S2I  C08  N15   aromatic  1.320  0.020  1.320
 S2I  C09  C10   aromatic  1.393  0.020  1.393
 S2I  C09  N14   aromatic  1.330  0.020  1.330
 S2I  C10  C11   aromatic  1.385  0.020  1.385
 S2I  C11  C12   aromatic  1.386  0.020  1.386
 S2I  C12  C13   aromatic  1.388  0.020  1.388
 S2I  C13  N14   aromatic  1.325  0.020  1.325
 S2I  N16  C17   single    1.451  0.020  1.451
 S2I  N16  C26   single    1.446  0.020  1.446
 S2I  C17  C18   single    1.533  0.020  1.533
 S2I  C18  C19   single    1.507  0.020  1.507
 S2I  C19  C20   aromatic  1.393  0.020  1.393
 S2I  C19  C24   aromatic  1.404  0.020  1.404
 S2I  C20  C21   aromatic  1.388  0.020  1.388
 S2I  C21  C22   aromatic  1.385  0.020  1.385
 S2I  C22  C23   aromatic  1.388  0.020  1.388
 S2I  C23  C24   aromatic  1.393  0.020  1.393
 S2I  C24  C25   single    1.507  0.020  1.507
 S2I  C25  C26   single    1.533  0.020  1.533
 S2I  C27  O28   single    1.410  0.020  1.410
 S2I  C01  H01   single    0.970  0.020  1.090
 S2I  C01  H01A  single    0.970  0.020  1.090
 S2I  C02  H02   single    0.970  0.020  1.090
 S2I  C02  H02A  single    0.970  0.020  1.090
 S2I  N03  HN03  single    0.860  0.020  1.020
 S2I  C05  H05   single    0.930  0.020  1.080
 S2I  C10  H10   single    0.930  0.020  1.080
 S2I  C11  H11   single    0.930  0.020  1.080
 S2I  C12  H12   single    0.930  0.020  1.080
 S2I  C13  H13   single    0.930  0.020  1.080
 S2I  C17  H17   single    0.970  0.020  1.090
 S2I  C17  H17A  single    0.970  0.020  1.090
 S2I  C18  H18   single    0.970  0.020  1.090
 S2I  C18  H18A  single    0.970  0.020  1.090
 S2I  C20  H20   single    0.930  0.020  1.080
 S2I  C21  H21   single    0.930  0.020  1.080
 S2I  C22  H22   single    0.930  0.020  1.080
 S2I  C23  H23   single    0.930  0.020  1.080
 S2I  C25  H25   single    0.970  0.020  1.090
 S2I  C25  H25A  single    0.970  0.020  1.090
 S2I  C26  H26   single    0.970  0.020  1.090
 S2I  C26  H26A  single    0.970  0.020  1.090
 S2I  C27  H27   single    0.970  0.020  1.090
 S2I  C27  H27A  single    0.970  0.020  1.090
 S2I  O28  HO28  single    0.850  0.020  0.980

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
 S2I  H01A  C01  H01  107.44  3.000
 S2I  H01A  C01  C27  109.49  3.000
 S2I  H01   C01  C27  109.59  3.000
 S2I  H01A  C01  C02  109.50  3.000
 S2I  H01   C01  C02  109.57  3.000
 S2I  C27   C01  C02  111.17  3.000
 S2I  H02A  C02  H02  106.67  3.000
 S2I  H02A  C02  N03  110.17  3.000
 S2I  H02   C02  N03  110.29  3.000
 S2I  H02A  C02  C01  109.46  3.000
 S2I  H02   C02  C01  109.75  3.000
 S2I  N03   C02  C01  110.43  3.000
 S2I  HN03  N03  C04  116.36  3.000
 S2I  HN03  N03  C02  118.97  3.000
 S2I  C04   N03  C02  124.60  3.000
 S2I  N15   C04  C05  121.60  3.000
 S2I  N15   C04  N03  115.96  3.000
 S2I  C05   C04  N03  122.44  3.000
 S2I  H05   C05  C06  122.51  3.000
 S2I  H05   C05  C04  120.61  3.000
 S2I  C06   C05  C04  116.86  3.000
 S2I  N16   C06  N07  116.37  3.000
 S2I  N16   C06  C05  122.95  3.000
 S2I  N07   C06  C05  120.67  3.000
 S2I  C08   N07  C06  117.35  3.000
 S2I  N15   C08  C09  115.93  3.000
 S2I  N15   C08  N07  127.10  3.000
 S2I  C09   C08  N07  116.97  3.000
 S2I  N14   C09  C10  122.24  3.000
 S2I  N14   C09  C08  117.42  3.000
 S2I  C10   C09  C08  120.34  3.000
 S2I  H10   C10  C11  121.10  3.000
 S2I  H10   C10  C09  120.04  3.000
 S2I  C11   C10  C09  118.86  3.000
 S2I  H11   C11  C12  120.74  3.000
 S2I  H11   C11  C10  120.39  3.000
 S2I  C12   C11  C10  118.87  3.000
 S2I  H12   C12  C13  120.46  3.000
 S2I  H12   C12  C11  121.59  3.000
 S2I  C13   C12  C11  117.95  3.000
 S2I  H13   C13  N14  116.37  3.000
 S2I  H13   C13  C12  120.06  3.000
 S2I  N14   C13  C12  123.56  3.000
 S2I  C13   N14  C09  118.51  3.000
 S2I  C08   N15  C04  116.41  3.000
 S2I  C26   N16  C17  115.15  3.000
 S2I  C26   N16  C06  120.70  3.000
 S2I  C17   N16  C06  119.41  3.000
 S2I  H17A  C17  H17  107.76  3.000
 S2I  H17A  C17  C18  110.15  3.000
 S2I  H17   C17  C18  109.17  3.000
 S2I  H17A  C17  N16  108.07  3.000
 S2I  H17   C17  N16  108.67  3.000
 S2I  C18   C17  N16  112.88  3.000
 S2I  H18A  C18  H18  106.00  3.000
 S2I  H18A  C18  C19  108.48  3.000
 S2I  H18   C18  C19  110.45  3.000
 S2I  H18A  C18  C17  107.98  3.000
 S2I  H18   C18  C17  108.41  3.000
 S2I  C19   C18  C17  115.10  3.000
 S2I  C24   C19  C20  118.76  3.000
 S2I  C24   C19  C18  122.52  3.000
 S2I  C20   C19  C18  118.72  3.000
 S2I  H20   C20  C21  119.30  3.000
 S2I  H20   C20  C19  118.86  3.000
 S2I  C21   C20  C19  121.84  3.000
 S2I  H21   C21  C22  120.61  3.000
 S2I  H21   C21  C20  120.01  3.000
 S2I  C22   C21  C20  119.37  3.000
 S2I  H22   C22  C23  120.03  3.000
 S2I  H22   C22  C21  120.61  3.000
 S2I  C23   C22  C21  119.36  3.000
 S2I  H23   C23  C24  118.87  3.000
 S2I  H23   C23  C22  119.35  3.000
 S2I  C24   C23  C22  121.78  3.000
 S2I  C25   C24  C23  118.63  3.000
 S2I  C25   C24  C19  122.48  3.000
 S2I  C23   C24  C19  118.89  3.000
 S2I  H25A  C25  H25  105.83  3.000
 S2I  H25A  C25  C26  108.01  3.000
 S2I  H25   C25  C26  108.94  3.000
 S2I  H25A  C25  C24  108.57  3.000
 S2I  H25   C25  C24  110.81  3.000
 S2I  C26   C25  C24  114.30  3.000
 S2I  H26A  C26  H26  105.82  3.000
 S2I  H26A  C26  C25  109.71  3.000
 S2I  H26   C26  C25  109.71  3.000
 S2I  H26A  C26  N16  109.63  3.000
 S2I  H26   C26  N16  107.83  3.000
 S2I  C25   C26  N16  113.81  3.000
 S2I  H27A  C27  H27  106.74  3.000
 S2I  H27A  C27  O28  111.50  3.000
 S2I  H27   C27  O28  111.49  3.000
 S2I  H27A  C27  C01  109.28  3.000
 S2I  H27   C27  C01  109.21  3.000
 S2I  O28   C27  C01  108.57  3.000
 S2I  HO28  O28  C27  108.20  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
 S2I  CONST_01  N07   C06  C05  C04     0.00   0.0  0
 S2I  CONST_02  N07   C08  N15  C04     0.00   0.0  0
 S2I  CONST_03  C09   C08  N15  C04   180.00   0.0  0
 S2I  CONST_04  C08   N15  C04  C05     0.00   0.0  0
 S2I  CONST_05  C08   N07  C06  C05     0.00   0.0  0
 S2I  CONST_06  N15   C04  C05  C06     0.00   0.0  0
 S2I  CONST_07  C09   C08  N07  C06   180.00   0.0  0
 S2I  CONST_08  N15   C08  N07  C06     0.00   0.0  0
 S2I  CONST_09  C10   C09  C08  N07   180.00   0.0  0
 S2I  CONST_10  N14   C09  C08  N07     0.00   0.0  0
 S2I  CONST_11  C11   C10  C09  C08   180.00   0.0  0
 S2I  CONST_12  C13   N14  C09  C08   180.00   0.0  0
 S2I  CONST_13  C12   C11  C10  C09     0.00   0.0  0
 S2I  CONST_14  C12   C13  N14  C09     0.00   0.0  0
 S2I  CONST_15  N15   C08  C09  C10     0.00   0.0  0
 S2I  CONST_16  C13   N14  C09  C10     0.00   0.0  0
 S2I  CONST_17  C13   C12  C11  C10     0.00   0.0  0
 S2I  CONST_18  N14   C09  C10  C11     0.00   0.0  0
 S2I  CONST_19  N14   C13  C12  C11     0.00   0.0  0
 S2I  CONST_20  N15   C08  C09  N14   180.00   0.0  0
 S2I  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 S2I  CONST_22  C23   C22  C21  C20     0.00   0.0  0
 S2I  CONST_23  C24   C23  C22  C21     0.00   0.0  0
 S2I  CONST_24  N16   C06  C05  C04   180.00   0.0  0
 S2I  CONST_25  N16   C06  N07  C08   180.00   0.0  0
 S2I  CONST_26  C06   C05  C04  N03   180.00   0.0  0
 S2I  CONST_27  C08   N15  C04  N03   180.00   0.0  0
 S2I  CONST_28  H05   C05  C06  N07   180.00   0.0  0
 S2I  CONST_29  H10   C10  C09  C08     0.00   0.0  0
 S2I  CONST_30  H11   C11  C10  C09   180.00   0.0  0
 S2I  CONST_31  H13   C13  N14  C09   180.00   0.0  0
 S2I  CONST_32  H12   C12  C11  C10   180.00   0.0  0
 S2I  CONST_33  H21   C21  C20  C19   180.00   0.0  0
 S2I  CONST_34  H22   C22  C21  C20   180.00   0.0  0
 S2I  CONST_35  H23   C23  C22  C21   180.00   0.0  0
 S2I  CONST_36  H20   C20  C21  C22   180.00   0.0  0
 S2I  CONST_37  C05   C04  N03  C02     0.00   0.0  0
 S2I  CONST_38  N15   C04  N03  C02   180.00   0.0  0
 S2I  CONST_39  HN03  N03  C04  C05   180.00   0.0  0
 S2I  Var_01    C04   N03  C02  C01  -179.60  30.0  3
 S2I  Var_02    O28   C27  C01  C02  -179.83  30.0  3
 S2I  Var_03    C27   C01  C02  N03   179.72  30.0  1

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
 S2I  plan-1  N03   0.020
 S2I  plan-1  C04   0.020
 S2I  plan-1  C05   0.020
 S2I  plan-1  C06   0.020
 S2I  plan-1  N07   0.020
 S2I  plan-1  C08   0.020
 S2I  plan-1  C09   0.020
 S2I  plan-1  N15   0.020
 S2I  plan-1  N16   0.020
 S2I  plan-1  H05   0.020
 S2I  plan-2  C08   0.020
 S2I  plan-2  C09   0.020
 S2I  plan-2  C10   0.020
 S2I  plan-2  C11   0.020
 S2I  plan-2  C12   0.020
 S2I  plan-2  C13   0.020
 S2I  plan-2  N14   0.020
 S2I  plan-2  H10   0.020
 S2I  plan-2  H11   0.020
 S2I  plan-2  H12   0.020
 S2I  plan-2  H13   0.020
 S2I  plan-3  C18   0.020
 S2I  plan-3  C19   0.020
 S2I  plan-3  C20   0.020
 S2I  plan-3  C21   0.020
 S2I  plan-3  C22   0.020
 S2I  plan-3  C23   0.020
 S2I  plan-3  C24   0.020
 S2I  plan-3  C25   0.020
 S2I  plan-3  H20   0.020
 S2I  plan-3  H21   0.020
 S2I  plan-3  H22   0.020
 S2I  plan-3  H23   0.020
 S2I  plan-4  C02   0.020
 S2I  plan-4  N03   0.020
 S2I  plan-4  C04   0.020
 S2I  plan-4  HN03  0.020

