# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 22:29:10 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-{[2'-hydroxy-3'-(1H-pyrrolo[3,2-c]pyridin-2-yl)biphenyl-3-yl]methyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)NCc1cccc(c1)c2cccc(c2O)c3[nH]c4ccncc4c3
#
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
 7NH  7NH  1-{[2'-hydroxy-3'-(1H-pyrrolo[3,2-c]pyridin-2-yl)biphenyl-3-yl]methyl}urea  ligand  45  27  .  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_7NH
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
 7NH  N1    N  N     0  -0.424  -6.7782   2.4631  -0.0330
 7NH  C2    C  CR16  0  -0.103  -7.3735   1.2587  -0.0588
 7NH  C3    C  CR16  0  -0.380  -6.7076   0.0517   0.0017
 7NH  C4    C  CR56  0   0.433  -5.3206   0.1251   0.0991
 7NH  C5    C  CR56  0  -0.013  -4.6677   1.3746   0.1187
 7NH  C6    C  CR16  0  -0.135  -5.4622   2.5206   0.0520
 7NH  N3    N  NR15  0  -0.741  -4.3658  -0.8316   0.1853
 7NH  CN4   C  CR15  0  -0.451  -3.2693   1.1160   0.2061
 7NH  C8    C  CR5   0   0.381  -3.1166  -0.2464   0.2475
 7NH  C1'   C  CR6   0  -0.054  -1.9303  -1.0871   0.4061
 7NH  C2'   C  CR16  0  -0.312  -2.0234  -2.2970   1.0972
 7NH  C3'   C  CR16  0  -0.257  -0.9204  -3.1128   1.2786
 7NH  C4'   C  CR16  0  -0.288   0.3038  -2.7271   0.7558
 7NH  C5'   C  CR6   0  -0.031   0.4353  -1.5373   0.0487
 7NH  C6'   C  CR6   0   0.281  -0.6827  -0.7097  -0.1143
 7NH  O6'   O  OH1   0  -0.606  -0.6051   0.4649  -0.7617
 7NH  C1B   C  CR6   0   0.009   1.7474  -1.1389  -0.5137
 7NH  C2B   C  CR16  0  -0.314   1.9283  -1.0109  -1.8895
 7NH  C3B   C  CR16  0  -0.222   3.1689  -0.6457  -2.3987
 7NH  C4B   C  CR16  0  -0.300   4.2321  -0.4022  -1.5448
 7NH  C5B   C  CR6   0   0.146   4.0706  -0.5265  -0.1656
 7NH  C6B   C  CR16  0  -0.338   2.8284  -0.8940   0.3343
 7NH  C51   C  CH2   0  -0.387   5.2139  -0.2296   0.7753
 7NH  N52   N  NH1   0  -0.643   5.5268   1.1771   0.8556
 7NH  C53   C  C     0   0.678   6.4895   1.7663   0.0992
 7NH  O53   O  O     0  -0.545   7.2460   1.1320  -0.6302
 7NH  N54   N  NH2   0  -0.842   6.5967   3.1153   0.2587
 7NH  H2    H  HCR6  0   0.256  -8.4551   1.2661  -0.1312
 7NH  H3    H  HCR6  0   0.272  -7.2453  -0.8865  -0.0224
 7NH  H6    H  HCR6  0   0.255  -5.0114   3.5083   0.0684
 7NH  HN3   H  HNR5  0   0.416  -4.5363  -1.8224   0.1241
 7NH  HN4   H  HCR5  0   0.253  -2.4846   1.8503   0.2639
 7NH  H2'   H  HCR6  0   0.260  -2.9712  -2.5954   1.5276
 7NH  H3'   H  HCR6  0   0.259  -1.0143  -4.0399   1.8272
 7NH  H4'   H  HCR6  0   0.261   1.1740  -3.3582   0.8859
 7NH  H6'   H  HOH1  0   0.479   0.3084   0.6589  -1.0092
 7NH  H2B   H  HCR6  0   0.267   1.1108  -1.2230  -2.5685
 7NH  H3B   H  HCR6  0   0.261   3.3045  -0.5592  -3.4689
 7NH  H4B   H  HCR6  0   0.256   5.1955  -0.1175  -1.9493
 7NH  H6B   H  HCR6  0   0.254   2.6896  -0.9853   1.4059
 7NH  H511  H  HCH2  0   0.266   6.1091  -0.7655   0.4627
 7NH  H512  H  HCH2  0   0.265   4.9640  -0.5839   1.7763
 7NH  H52   H  HNH1  0   0.394   4.8759   1.7578   1.3587
 7NH  H541  H  HNH2  0   0.394   7.1404   3.6067  -0.4302
 7NH  H542  H  HNH2  0   0.393   5.8374   3.6437   0.6553

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
 7NH  N1   C2    aromatic  1.344  0.020  1.344
 7NH  N1   C6    aromatic  1.320  0.020  1.320
 7NH  C2   C3    aromatic  1.380  0.020  1.380
 7NH  C2   H2    single    0.930  0.020  1.080
 7NH  C3   C4    aromatic  1.392  0.020  1.392
 7NH  C3   H3    single    0.930  0.020  1.080
 7NH  C4   C5    aromatic  1.410  0.020  1.410
 7NH  C4   N3    aromatic  1.354  0.020  1.354
 7NH  C5   C6    aromatic  1.396  0.020  1.396
 7NH  C5   CN4   aromatic  1.425  0.020  1.425
 7NH  C6   H6    single    0.930  0.020  1.080
 7NH  N3   C8    aromatic  1.381  0.020  1.381
 7NH  N3   HN3   single    0.860  0.020  1.020
 7NH  CN4  C8    aromatic  1.372  0.020  1.372
 7NH  CN4  HN4   single    0.930  0.020  1.080
 7NH  C8   C1'   single    1.463  0.020  1.463
 7NH  C1'  C2'   aromatic  1.397  0.020  1.397
 7NH  C1'  C6'   aromatic  1.403  0.020  1.403
 7NH  C2'  C3'   aromatic  1.384  0.020  1.384
 7NH  C2'  H2'   single    0.930  0.020  1.080
 7NH  C3'  C4'   aromatic  1.386  0.020  1.386
 7NH  C3'  H3'   single    0.930  0.020  1.080
 7NH  C4'  C5'   aromatic  1.390  0.020  1.390
 7NH  C4'  H4'   single    0.930  0.020  1.080
 7NH  C5'  C6'   aromatic  1.400  0.020  1.400
 7NH  C5'  C1B   single    1.482  0.020  1.482
 7NH  C6'  O6'   single    1.343  0.020  1.343
 7NH  O6'  H6'   single    0.850  0.020  0.980
 7NH  C1B  C2B   aromatic  1.394  0.020  1.394
 7NH  C1B  C6B   aromatic  1.396  0.020  1.396
 7NH  C2B  C3B   aromatic  1.390  0.020  1.390
 7NH  C2B  H2B   single    0.930  0.020  1.080
 7NH  C3B  C4B   aromatic  1.385  0.020  1.385
 7NH  C3B  H3B   single    0.930  0.020  1.080
 7NH  C4B  C5B   aromatic  1.394  0.020  1.394
 7NH  C4B  H4B   single    0.930  0.020  1.080
 7NH  C5B  C6B   aromatic  1.388  0.020  1.388
 7NH  C5B  C51   single    1.510  0.020  1.510
 7NH  C6B  H6B   single    0.930  0.020  1.080
 7NH  C51  N52   single    1.443  0.020  1.443
 7NH  C51  H511  single    0.970  0.020  1.090
 7NH  C51  H512  single    0.970  0.020  1.090
 7NH  N52  C53   single    1.359  0.020  1.359
 7NH  N52  H52   single    0.860  0.020  1.020
 7NH  C53  O53   double    1.227  0.020  1.227
 7NH  C53  N54   single    1.363  0.020  1.363
 7NH  N54  H541  single    0.890  0.020  1.040
 7NH  N54  H542  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
 7NH  C6    N1   C2    118.81  3.000
 7NH  H2    C2   C3    119.37  3.000
 7NH  H2    C2   N1    115.93  3.000
 7NH  C3    C2   N1    124.71  3.000
 7NH  H3    C3   C4    122.85  3.000
 7NH  H3    C3   C2    121.19  3.000
 7NH  C4    C3   C2    115.96  3.000
 7NH  N3    C4   C5    107.37  3.000
 7NH  N3    C4   C3    132.03  3.000
 7NH  C5    C4   C3    120.59  3.000
 7NH  CN4   C5   C6    135.27  3.000
 7NH  CN4   C5   C4    107.13  3.000
 7NH  C6    C5   C4    117.60  3.000
 7NH  H6    C6   C5    120.65  3.000
 7NH  H6    C6   N1    117.03  3.000
 7NH  C5    C6   N1    122.33  3.000
 7NH  HN3   N3   C8    124.94  3.000
 7NH  HN3   N3   C4    124.86  3.000
 7NH  C8    N3   C4    109.96  3.000
 7NH  HN4   CN4  C8    126.51  3.000
 7NH  HN4   CN4  C5    126.52  3.000
 7NH  C8    CN4  C5    106.94  3.000
 7NH  C1'   C8   CN4   131.64  3.000
 7NH  C1'   C8   N3    119.68  3.000
 7NH  CN4   C8   N3    108.59  3.000
 7NH  C6'   C1'  C2'   118.41  3.000
 7NH  C6'   C1'  C8    121.75  3.000
 7NH  C2'   C1'  C8    119.84  3.000
 7NH  H2'   C2'  C3'   118.89  3.000
 7NH  H2'   C2'  C1'   119.59  3.000
 7NH  C3'   C2'  C1'   121.50  3.000
 7NH  H3'   C3'  C4'   120.44  3.000
 7NH  H3'   C3'  C2'   120.18  3.000
 7NH  C4'   C3'  C2'   119.38  3.000
 7NH  H4'   C4'  C5'   118.94  3.000
 7NH  H4'   C4'  C3'   120.16  3.000
 7NH  C5'   C4'  C3'   120.90  3.000
 7NH  C1B   C5'  C6'   120.25  3.000
 7NH  C1B   C5'  C4'   120.45  3.000
 7NH  C6'   C5'  C4'   119.30  3.000
 7NH  O6'   C6'  C5'   121.78  3.000
 7NH  O6'   C6'  C1'   117.72  3.000
 7NH  C5'   C6'  C1'   120.50  3.000
 7NH  H6'   O6'  C6'   110.71  3.000
 7NH  C6B   C1B  C2B   118.89  3.000
 7NH  C6B   C1B  C5'   120.16  3.000
 7NH  C2B   C1B  C5'   120.95  3.000
 7NH  H2B   C2B  C3B   119.68  3.000
 7NH  H2B   C2B  C1B   120.18  3.000
 7NH  C3B   C2B  C1B   120.11  3.000
 7NH  H3B   C3B  C4B   119.95  3.000
 7NH  H3B   C3B  C2B   119.68  3.000
 7NH  C4B   C3B  C2B   120.36  3.000
 7NH  H4B   C4B  C5B   119.74  3.000
 7NH  H4B   C4B  C3B   119.92  3.000
 7NH  C5B   C4B  C3B   120.34  3.000
 7NH  C51   C5B  C6B   120.34  3.000
 7NH  C51   C5B  C4B   120.73  3.000
 7NH  C6B   C5B  C4B   118.91  3.000
 7NH  H6B   C6B  C5B   119.51  3.000
 7NH  H6B   C6B  C1B   119.11  3.000
 7NH  C5B   C6B  C1B   121.38  3.000
 7NH  H512  C51  H511  106.97  3.000
 7NH  H512  C51  N52   108.37  3.000
 7NH  H511  C51  N52   108.50  3.000
 7NH  H512  C51  C5B   109.53  3.000
 7NH  H511  C51  C5B   110.29  3.000
 7NH  N52   C51  C5B   112.98  3.000
 7NH  H52   N52  C53   119.08  3.000
 7NH  H52   N52  C51   116.72  3.000
 7NH  C53   N52  C51   123.04  3.000
 7NH  N54   C53  O53   122.19  3.000
 7NH  N54   C53  N52   114.83  3.000
 7NH  O53   C53  N52   122.91  3.000
 7NH  H542  N54  H541  114.91  3.000
 7NH  H542  N54  C53   120.43  3.000
 7NH  H541  N54  C53   116.49  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
 7NH  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 7NH  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 7NH  CONST_03  CN4  C5   C6   N1   180.00   0.0  0
 7NH  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 7NH  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 7NH  CONST_06  N3   C4   C3   C2   180.00   0.0  0
 7NH  CONST_07  C6   N1   C2   C3     0.00   0.0  0
 7NH  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 7NH  CONST_09  CN4  C5   C4   C3   180.00   0.0  0
 7NH  CONST_10  C8   N3   C4   C3   180.00   0.0  0
 7NH  CONST_11  C8   CN4  C5   C4     0.00   0.0  0
 7NH  CONST_12  CN4  C8   N3   C4     0.00   0.0  0
 7NH  CONST_13  C1'  C8   N3   C4   180.00   0.0  0
 7NH  CONST_14  C8   N3   C4   C5     0.00   0.0  0
 7NH  CONST_15  N3   C8   CN4  C5     0.00   0.0  0
 7NH  CONST_16  C1'  C8   CN4  C5   180.00   0.0  0
 7NH  CONST_17  N3   C4   C5   C6   180.00   0.0  0
 7NH  CONST_18  C8   CN4  C5   C6   180.00   0.0  0
 7NH  CONST_19  CN4  C5   C4   N3     0.00   0.0  0
 7NH  CONST_24  C3'  C2'  C1'  C8   180.00   0.0  0
 7NH  CONST_25  C5'  C6'  C1'  C8   180.00   0.0  0
 7NH  CONST_26  C4'  C3'  C2'  C1'    0.00   0.0  0
 7NH  CONST_27  C4'  C5'  C6'  C1'    0.00   0.0  0
 7NH  CONST_28  C1B  C5'  C6'  C1'  180.00   0.0  0
 7NH  CONST_29  C5'  C6'  C1'  C2'    0.00   0.0  0
 7NH  CONST_30  C5'  C4'  C3'  C2'    0.00   0.0  0
 7NH  CONST_31  C6'  C1'  C2'  C3'    0.00   0.0  0
 7NH  CONST_32  C6'  C5'  C4'  C3'    0.00   0.0  0
 7NH  CONST_33  C1B  C5'  C4'  C3'  180.00   0.0  0
 7NH  CONST_36  C3B  C2B  C1B  C5'  180.00   0.0  0
 7NH  CONST_37  C5B  C6B  C1B  C5'  180.00   0.0  0
 7NH  CONST_40  C4B  C3B  C2B  C1B    0.00   0.0  0
 7NH  CONST_41  C4B  C5B  C6B  C1B    0.00   0.0  0
 7NH  CONST_42  C5B  C6B  C1B  C2B    0.00   0.0  0
 7NH  CONST_43  C5B  C4B  C3B  C2B    0.00   0.0  0
 7NH  CONST_44  C6B  C1B  C2B  C3B    0.00   0.0  0
 7NH  CONST_45  C6B  C5B  C4B  C3B    0.00   0.0  0
 7NH  CONST_46  O6'  C6'  C1'  C8     0.00   0.0  0
 7NH  CONST_47  O6'  C6'  C1'  C2'  180.00   0.0  0
 7NH  CONST_48  O6'  C6'  C5'  C4'  180.00   0.0  0
 7NH  CONST_49  C1B  C5'  C6'  O6'    0.00   0.0  0
 7NH  CONST_50  C51  C5B  C6B  C1B  180.00   0.0  0
 7NH  CONST_51  C51  C5B  C4B  C3B  180.00   0.0  0
 7NH  CONST_52  H3   C3   C2   N1   180.00   0.0  0
 7NH  CONST_53  H6   C6   N1   C2   180.00   0.0  0
 7NH  CONST_54  HN3  N3   C4   C3     0.00   0.0  0
 7NH  CONST_55  H2   C2   C3   C4   180.00   0.0  0
 7NH  CONST_56  HN4  CN4  C5   C4   180.00   0.0  0
 7NH  CONST_57  H2'  C2'  C1'  C8     0.00   0.0  0
 7NH  CONST_58  H3'  C3'  C2'  C1'  180.00   0.0  0
 7NH  CONST_59  H4'  C4'  C3'  C2'  180.00   0.0  0
 7NH  CONST_60  H2B  C2B  C1B  C5'    0.00   0.0  0
 7NH  CONST_61  H6B  C6B  C1B  C5'    0.00   0.0  0
 7NH  CONST_62  H3B  C3B  C2B  C1B  180.00   0.0  0
 7NH  CONST_63  H4B  C4B  C3B  C2B  180.00   0.0  0
 7NH  CONST_64  O53  C53  N52  C51    0.00   0.0  0
 7NH  CONST_65  N54  C53  N52  C51  180.00   0.0  0
 7NH  CONST_66  H52  N52  C53  O53  180.00   0.0  0
 7NH  Var_01    N52  C51  C5B  C4B   71.09  30.0  2
 7NH  Var_02    C53  N52  C51  C5B  -94.61  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
 7NH  plan-1  C8    0.020
 7NH  plan-1  C1'   0.020
 7NH  plan-1  C2'   0.020
 7NH  plan-1  C3'   0.020
 7NH  plan-1  C4'   0.020
 7NH  plan-1  C5'   0.020
 7NH  plan-1  C6'   0.020
 7NH  plan-1  O6'   0.020
 7NH  plan-1  C1B   0.020
 7NH  plan-1  H2'   0.020
 7NH  plan-1  H3'   0.020
 7NH  plan-1  H4'   0.020
 7NH  plan-2  C5'   0.020
 7NH  plan-2  C1B   0.020
 7NH  plan-2  C2B   0.020
 7NH  plan-2  C3B   0.020
 7NH  plan-2  C4B   0.020
 7NH  plan-2  C5B   0.020
 7NH  plan-2  C6B   0.020
 7NH  plan-2  C51   0.020
 7NH  plan-2  H2B   0.020
 7NH  plan-2  H3B   0.020
 7NH  plan-2  H4B   0.020
 7NH  plan-2  H6B   0.020
 7NH  plan-3  N1    0.020
 7NH  plan-3  C2    0.020
 7NH  plan-3  C3    0.020
 7NH  plan-3  C4    0.020
 7NH  plan-3  C5    0.020
 7NH  plan-3  C6    0.020
 7NH  plan-3  N3    0.020
 7NH  plan-3  CN4   0.020
 7NH  plan-3  C8    0.020
 7NH  plan-3  C1'   0.020
 7NH  plan-3  H2    0.020
 7NH  plan-3  H3    0.020
 7NH  plan-3  H6    0.020
 7NH  plan-3  HN3   0.020
 7NH  plan-3  HN4   0.020
 7NH  plan-4  C51   0.020
 7NH  plan-4  N52   0.020
 7NH  plan-4  C53   0.020
 7NH  plan-4  O53   0.020
 7NH  plan-4  N54   0.020
 7NH  plan-4  H52   0.020
 7NH  plan-4  H541  0.020
 7NH  plan-4  H542  0.020

