# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 09:22:35 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[(6-aminopyridin-3-yl)methyl]-3-[4-(phenylsulfonyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(CNC(=O)Nc2ccc(cc2)[S](=O)(=O)c3ccccc3)cn1
#
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
 1LJ  1LJ  1-[(6-aminopyridin-3-yl)methyl]-3-[4-(phenylsulfonyl)phenyl]urea  ligand  45  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1LJ
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
 1LJ  C4   C  CR6   0  -0.164  -5.2939   0.5219  -0.2134
 1LJ  C5   C  CR16  0  -0.235  -5.4721   1.3021  -1.3483
 1LJ  C6   C  CR16  0  -0.241  -5.9167   2.6075  -1.2025
 1LJ  C10  C  CR6   0  -0.200  -2.9541  -0.9993  -0.3329
 1LJ  C13  C  CR6   0   0.403  -0.1794  -0.7522  -0.2244
 1LJ  C15  C  CR16  0  -0.223  -2.2297  -0.8591  -1.5108
 1LJ  C17  C  C     0   0.757   2.0975  -0.5640   0.7644
 1LJ  C20  C  CH2   0  -0.327   4.4886  -0.5160   1.2912
 1LJ  C21  C  CR6   0  -0.044   5.7213   0.0496   0.6530
 1LJ  C22  C  CR16  0  -0.168   5.8158   1.3957   0.2836
 1LJ  C24  C  CR6   0   0.448   8.0261   0.9743  -0.5294
 1LJ  C26  C  CR16  0  -0.099   6.8228  -0.7405   0.3826
 1LJ  C1   C  CR16  0  -0.236  -6.1790   3.1181   0.0622
 1LJ  C2   C  CR16  0  -0.241  -5.9999   2.3251   1.1883
 1LJ  C3   C  CR16  0  -0.238  -5.5568   1.0176   1.0569
 1LJ  S7   S  S     0   1.222  -4.7092  -1.1452  -0.3894
 1LJ  O8   O  OS    0  -0.655  -5.1417  -1.8957   0.7865
 1LJ  O9   O  OS    0  -0.655  -5.0863  -1.6127  -1.7205
 1LJ  C11  C  CR16  0  -0.219  -2.2985  -1.0224   0.8905
 1LJ  C12  C  CR16  0  -0.307  -0.9228  -0.8966   0.9538
 1LJ  C14  C  CR16  0  -0.345  -0.8582  -0.7372  -1.4520
 1LJ  N16  N  NH1   0  -0.790   1.1956  -0.6372  -0.2785
 1LJ  O18  O  O     0  -0.513   1.7679  -0.5293   1.9391
 1LJ  N19  N  NH1   0  -0.677   3.3840  -0.5108   0.3517
 1LJ  C23  C  CR16  0  -0.376   6.9623   1.8704  -0.3055
 1LJ  N25  N  N     0  -0.458   7.9435  -0.3080  -0.1877
 1LJ  N27  N  NH2   0  -0.832   9.2012   1.4037  -1.0690
 1LJ  H1   H  HCR6  0   0.282  -5.2727   0.9063  -2.3349
 1LJ  H2   H  HCR6  0   0.274  -6.0618   3.2235  -2.0796
 1LJ  H3   H  HCR6  0   0.283  -2.7213  -0.8481  -2.4742
 1LJ  H4   H  HCH2  0   0.249   4.6952  -1.5285   1.6533
 1LJ  H5   H  HCH2  0   0.261   4.2032   0.0776   2.1601
 1LJ  H6   H  HCR6  0   0.264   4.9859   2.0698   0.4607
 1LJ  H7   H  HCR6  0   0.253   6.8023  -1.7955   0.6420
 1LJ  H8   H  HCR6  0   0.273  -6.5269   4.1369   0.1707
 1LJ  H9   H  HCR6  0   0.274  -6.2092   2.7221   2.1722
 1LJ  H10  H  HCR6  0   0.282  -5.4256   0.4001   1.9351
 1LJ  H11  H  HCR6  0   0.281  -2.8506  -1.1453   1.8127
 1LJ  H12  H  HCR6  0   0.293  -0.4399  -0.9189   1.9156
 1LJ  H13  H  HCR6  0   0.283  -0.2976  -0.6322  -2.3731
 1LJ  H14  H  HNH1  0   0.416   1.5764  -0.5808  -1.2109
 1LJ  H15  H  HNH1  0   0.402   3.6071  -0.7187  -0.6093
 1LJ  H16  H  HCR6  0   0.269   7.0528   2.9103  -0.5920
 1LJ  H17  H  HNH2  0   0.391   9.1890   2.2564  -1.6029
 1LJ  H18  H  HNH2  0   0.383   9.8093   0.6917  -1.4388

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
 1LJ  C1   C6   aromatic  1.389  0.020  1.389
 1LJ  C1   C2   aromatic  1.389  0.020  1.389
 1LJ  C6   C5   aromatic  1.387  0.020  1.387
 1LJ  C2   C3   aromatic  1.387  0.020  1.387
 1LJ  C5   C4   aromatic  1.389  0.020  1.389
 1LJ  C3   C4   aromatic  1.389  0.020  1.389
 1LJ  C4   S7   single    1.775  0.020  1.775
 1LJ  O8   S7   double    1.461  0.020  1.461
 1LJ  S7   O9   double    1.460  0.020  1.460
 1LJ  S7   C10  single    1.762  0.020  1.762
 1LJ  C10  C11  aromatic  1.388  0.020  1.388
 1LJ  C10  C15  aromatic  1.390  0.020  1.390
 1LJ  C11  C12  aromatic  1.383  0.020  1.383
 1LJ  C15  C14  aromatic  1.378  0.020  1.378
 1LJ  C12  C13  aromatic  1.401  0.020  1.401
 1LJ  C14  C13  aromatic  1.403  0.020  1.403
 1LJ  C13  N16  single    1.381  0.020  1.381
 1LJ  N16  C17  single    1.381  0.020  1.381
 1LJ  O18  C17  double    1.221  0.020  1.221
 1LJ  C17  N19  single    1.352  0.020  1.352
 1LJ  N19  C20  single    1.450  0.020  1.450
 1LJ  C20  C21  single    1.499  0.020  1.499
 1LJ  C21  C22  aromatic  1.399  0.020  1.399
 1LJ  C21  C26  aromatic  1.382  0.020  1.382
 1LJ  C22  C23  aromatic  1.374  0.020  1.374
 1LJ  C26  N25  aromatic  1.330  0.020  1.330
 1LJ  C23  C24  aromatic  1.409  0.020  1.409
 1LJ  N25  C24  aromatic  1.330  0.020  1.330
 1LJ  C24  N27  single    1.363  0.020  1.363
 1LJ  C5   H1   single    0.930  0.020  1.080
 1LJ  C6   H2   single    0.930  0.020  1.080
 1LJ  C15  H3   single    0.930  0.020  1.080
 1LJ  C20  H4   single    0.970  0.020  1.090
 1LJ  C20  H5   single    0.970  0.020  1.090
 1LJ  C22  H6   single    0.930  0.020  1.080
 1LJ  C26  H7   single    0.930  0.020  1.080
 1LJ  C1   H8   single    0.930  0.020  1.080
 1LJ  C2   H9   single    0.930  0.020  1.080
 1LJ  C3   H10  single    0.930  0.020  1.080
 1LJ  C11  H11  single    0.930  0.020  1.080
 1LJ  C12  H12  single    0.930  0.020  1.080
 1LJ  C14  H13  single    0.930  0.020  1.080
 1LJ  N16  H14  single    0.860  0.020  1.020
 1LJ  N19  H15  single    0.860  0.020  1.020
 1LJ  C23  H16  single    0.930  0.020  1.080
 1LJ  N27  H17  single    0.890  0.020  1.040
 1LJ  N27  H18  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
 1LJ  S7   C4   C3   119.23  3.000
 1LJ  S7   C4   C5   119.26  3.000
 1LJ  C3   C4   C5   121.51  3.000
 1LJ  H1   C5   C6   119.97  3.000
 1LJ  H1   C5   C4   121.07  3.000
 1LJ  C6   C5   C4   118.95  3.000
 1LJ  H2   C6   C1   120.25  3.000
 1LJ  H2   C6   C5   119.60  3.000
 1LJ  C1   C6   C5   120.15  3.000
 1LJ  C11  C10  S7   119.83  3.000
 1LJ  C11  C10  C15  120.16  3.000
 1LJ  S7   C10  C15  120.02  3.000
 1LJ  N16  C13  C14  116.53  3.000
 1LJ  N16  C13  C12  124.76  3.000
 1LJ  C14  C13  C12  118.71  3.000
 1LJ  H3   C15  C14  119.30  3.000
 1LJ  H3   C15  C10  121.27  3.000
 1LJ  C14  C15  C10  119.43  3.000
 1LJ  N19  C17  O18  123.34  3.000
 1LJ  N19  C17  N16  113.14  3.000
 1LJ  O18  C17  N16  123.51  3.000
 1LJ  H5   C20  H4   106.82  3.000
 1LJ  H5   C20  N19  108.36  3.000
 1LJ  H4   C20  N19  111.18  3.000
 1LJ  H5   C20  C21  110.43  3.000
 1LJ  H4   C20  C21  109.55  3.000
 1LJ  N19  C20  C21  110.44  3.000
 1LJ  C26  C21  C22  116.39  3.000
 1LJ  C26  C21  C20  121.53  3.000
 1LJ  C22  C21  C20  122.08  3.000
 1LJ  H6   C22  C23  119.63  3.000
 1LJ  H6   C22  C21  120.23  3.000
 1LJ  C23  C22  C21  120.14  3.000
 1LJ  N27  C24  N25  117.34  3.000
 1LJ  N27  C24  C23  120.91  3.000
 1LJ  N25  C24  C23  121.71  3.000
 1LJ  H7   C26  N25  115.72  3.000
 1LJ  H7   C26  C21  119.56  3.000
 1LJ  N25  C26  C21  124.72  3.000
 1LJ  H8   C1   C2   119.85  3.000
 1LJ  H8   C1   C6   119.88  3.000
 1LJ  C2   C1   C6   120.27  3.000
 1LJ  H9   C2   C3   119.61  3.000
 1LJ  H9   C2   C1   120.21  3.000
 1LJ  C3   C2   C1   120.18  3.000
 1LJ  H10  C3   C2   120.01  3.000
 1LJ  H10  C3   C4   121.06  3.000
 1LJ  C2   C3   C4   118.93  3.000
 1LJ  O9   S7   O8   119.53  3.000
 1LJ  O9   S7   C10  108.24  3.000
 1LJ  O8   S7   C10  108.16  3.000
 1LJ  C10  S7   C4   104.31  3.000
 1LJ  O9   S7   C4   107.82  3.000
 1LJ  O8   S7   C4   107.77  3.000
 1LJ  H11  C11  C12  118.62  3.000
 1LJ  H11  C11  C10  120.80  3.000
 1LJ  C12  C11  C10  120.58  3.000
 1LJ  H12  C12  C11  119.03  3.000
 1LJ  H12  C12  C13  121.04  3.000
 1LJ  C11  C12  C13  119.93  3.000
 1LJ  H13  C14  C15  119.16  3.000
 1LJ  H13  C14  C13  119.64  3.000
 1LJ  C15  C14  C13  121.19  3.000
 1LJ  H14  N16  C17  116.66  3.000
 1LJ  H14  N16  C13  114.63  3.000
 1LJ  C17  N16  C13  128.70  3.000
 1LJ  H15  N19  C20  116.63  3.000
 1LJ  H15  N19  C17  119.56  3.000
 1LJ  C20  N19  C17  121.79  3.000
 1LJ  H16  C23  C24  120.39  3.000
 1LJ  H16  C23  C22  121.01  3.000
 1LJ  C24  C23  C22  118.60  3.000
 1LJ  C26  N25  C24  118.44  3.000
 1LJ  H18  N27  H17  114.32  3.000
 1LJ  H18  N27  C24  116.33  3.000
 1LJ  H17  N27  C24  117.83  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
 1LJ  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 1LJ  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 1LJ  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 1LJ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 1LJ  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 1LJ  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 1LJ  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 1LJ  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 1LJ  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 1LJ  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 1LJ  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 1LJ  CONST_12  C24  N25  C26  C21     0.00   0.0  0
 1LJ  CONST_13  N25  C26  C21  C22     0.00   0.0  0
 1LJ  CONST_14  N25  C24  C23  C22     0.00   0.0  0
 1LJ  CONST_15  C23  C22  C21  C26     0.00   0.0  0
 1LJ  CONST_16  C23  C24  N25  C26     0.00   0.0  0
 1LJ  CONST_17  C14  C15  C10  C11     0.00   0.0  0
 1LJ  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 1LJ  CONST_19  S7   C4   C5   C6    180.00   0.0  0
 1LJ  CONST_20  N16  C13  C14  C15   180.00   0.0  0
 1LJ  CONST_21  C23  C22  C21  C20   180.00   0.0  0
 1LJ  CONST_22  N25  C26  C21  C20   180.00   0.0  0
 1LJ  CONST_23  N27  C24  C23  C22   180.00   0.0  0
 1LJ  CONST_24  N27  C24  N25  C26   180.00   0.0  0
 1LJ  CONST_25  S7   C4   C3   C2    180.00   0.0  0
 1LJ  CONST_26  C12  C11  C10  S7    180.00   0.0  0
 1LJ  CONST_27  C14  C15  C10  S7    180.00   0.0  0
 1LJ  CONST_28  N16  C13  C12  C11   180.00   0.0  0
 1LJ  CONST_29  H2   C6   C5   C4    180.00   0.0  0
 1LJ  CONST_30  H9   C2   C3   C4    180.00   0.0  0
 1LJ  CONST_31  H8   C1   C6   C5    180.00   0.0  0
 1LJ  CONST_32  H10  C3   C4   C5    180.00   0.0  0
 1LJ  CONST_33  H12  C12  C11  C10   180.00   0.0  0
 1LJ  CONST_34  H13  C14  C15  C10   180.00   0.0  0
 1LJ  CONST_35  H11  C11  C12  C13   180.00   0.0  0
 1LJ  CONST_36  H3   C15  C14  C13   180.00   0.0  0
 1LJ  CONST_37  H16  C23  C22  C21   180.00   0.0  0
 1LJ  CONST_38  H7   C26  C21  C22   180.00   0.0  0
 1LJ  CONST_39  H6   C22  C23  C24   180.00   0.0  0
 1LJ  CONST_40  H1   C5   C6   C1    180.00   0.0  0
 1LJ  CONST_41  C12  C13  N16  C17     0.00   0.0  0
 1LJ  CONST_42  C14  C13  N16  C17   180.00   0.0  0
 1LJ  CONST_43  H14  N16  C13  C12   180.00   0.0  0
 1LJ  CONST_46  O18  C17  N16  C13     0.00   0.0  0
 1LJ  CONST_47  N19  C17  N16  C13   180.00   0.0  0
 1LJ  CONST_48  O18  C17  N19  C20     0.00   0.0  0
 1LJ  CONST_49  N16  C17  N19  C20   180.00   0.0  0
 1LJ  CONST_50  H15  N19  C17  O18   180.00   0.0  0
 1LJ  Var_01    C11  C10  S7   C4     87.33  30.0  2
 1LJ  Var_02    C10  S7   C4   C5     89.10  30.0  2
 1LJ  Var_03    N19  C20  C21  C22    67.13  30.0  3
 1LJ  Var_04    C21  C20  N19  C17  -158.95  30.0  3

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
 1LJ  plan-1  C10  0.020
 1LJ  plan-1  C13  0.020
 1LJ  plan-1  C15  0.020
 1LJ  plan-1  S7   0.020
 1LJ  plan-1  C11  0.020
 1LJ  plan-1  C12  0.020
 1LJ  plan-1  C14  0.020
 1LJ  plan-1  N16  0.020
 1LJ  plan-1  H3   0.020
 1LJ  plan-1  H11  0.020
 1LJ  plan-1  H12  0.020
 1LJ  plan-1  H13  0.020
 1LJ  plan-2  C20  0.020
 1LJ  plan-2  C21  0.020
 1LJ  plan-2  C22  0.020
 1LJ  plan-2  C24  0.020
 1LJ  plan-2  C26  0.020
 1LJ  plan-2  C23  0.020
 1LJ  plan-2  N25  0.020
 1LJ  plan-2  N27  0.020
 1LJ  plan-2  H6   0.020
 1LJ  plan-2  H7   0.020
 1LJ  plan-2  H16  0.020
 1LJ  plan-3  C4   0.020
 1LJ  plan-3  C5   0.020
 1LJ  plan-3  C6   0.020
 1LJ  plan-3  C1   0.020
 1LJ  plan-3  C2   0.020
 1LJ  plan-3  C3   0.020
 1LJ  plan-3  S7   0.020
 1LJ  plan-3  H1   0.020
 1LJ  plan-3  H2   0.020
 1LJ  plan-3  H8   0.020
 1LJ  plan-3  H9   0.020
 1LJ  plan-3  H10  0.020
 1LJ  plan-4  C13  0.020
 1LJ  plan-4  C17  0.020
 1LJ  plan-4  C20  0.020
 1LJ  plan-4  N16  0.020
 1LJ  plan-4  O18  0.020
 1LJ  plan-4  N19  0.020
 1LJ  plan-4  H14  0.020
 1LJ  plan-4  H15  0.020
 1LJ  plan-5  C24  0.020
 1LJ  plan-5  N27  0.020
 1LJ  plan-5  H17  0.020
 1LJ  plan-5  H18  0.020

