# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 06:01:48 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-[2-(phenylcarbamoyl)-5-(1H-pyrazol-4-yl)phenoxy]propan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCCOc1cc(ccc1C(=O)Nc2ccccc2)c3c[nH]nc3
#
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
 3I7  3I7  3-[2-(phenylcarbamoyl)-5-(1H-pyrazol-4-yl)phenoxy]propan-1-aminium  ligand  46  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3I7
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
 3I7  N1    N  NT3   1  -0.776   0.9268   6.3958  -0.4134
 3I7  C2    C  CH2   0  -0.308   1.6393   5.1043  -0.2485
 3I7  C3    C  CH2   0  -0.486   0.6533   3.9550  -0.1807
 3I7  C4    C  CH2   0  -0.179   1.3975   2.6400  -0.0554
 3I7  O5    O  O2    0  -0.460   0.4234   1.6233   0.0903
 3I7  C6    C  CR6   0   0.433   0.8125   0.3470   0.2250
 3I7  C7    C  CR16  0  -0.495   2.1345  -0.0689   0.1234
 3I7  C8    C  CR6   0   0.151   2.4760  -1.4194   0.2329
 3I7  C9    C  CR16  0  -0.362   1.4641  -2.3550   0.4400
 3I7  C10   C  CR16  0  -0.232   0.1473  -1.9404   0.5325
 3I7  C11   C  CR6   0  -0.201  -0.2027  -0.5985   0.4374
 3I7  C12   C  C     0   0.513  -1.6186  -0.1711   0.6433
 3I7  O13   O  O     0  -0.451  -1.9247   0.7173   1.4167
 3I7  N14   N  NH1   0  -0.739  -2.5117  -0.8879  -0.0880
 3I7  C15   C  CR6   0   0.372  -3.9104  -0.8624  -0.0478
 3I7  C16   C  CR16  0  -0.315  -4.6613   0.1020   0.6264
 3I7  C17   C  CR16  0  -0.245  -6.0487   0.0341   0.5976
 3I7  C18   C  CR16  0  -0.271  -6.7078  -0.9714  -0.0933
 3I7  C19   C  CR16  0  -0.244  -5.9579  -1.9260  -0.7689
 3I7  C20   C  CR16  0  -0.348  -4.5752  -1.8744  -0.7463
 3I7  C21   C  CR5   0  -0.112   3.8711  -1.8306   0.1232
 3I7  C22   C  CR15  0  -0.115   5.0331  -1.0293   0.1794
 3I7  N23   N  N     0  -0.259   6.1278  -1.7481   0.0374
 3I7  N24   N  NR15  0  -0.425   5.6991  -2.9959  -0.1129
 3I7  C25   C  CR15  0   0.001   4.3670  -3.1079  -0.0693
 3I7  HN1   H  HNT3  0   0.481   1.5763   7.1814  -0.4264
 3I7  HN1A  H  HNT3  0   0.472   0.4004   6.4323  -1.2861
 3I7  HN1B  H  HNT3  0   0.471   0.2674   6.5690   0.3452
 3I7  HN24  H  HNR5  0   0.426   6.3627  -3.7412  -0.2538
 3I7  H2    H  HCH2  0   0.298   2.3170   5.0106  -1.0943
 3I7  H2A   H  HCH2  0   0.299   2.2298   5.1838   0.6616
 3I7  H3    H  HCH2  0   0.267  -0.0075   4.0845   0.6795
 3I7  H3A   H  HCH2  0   0.267   0.0327   3.9415  -1.0802
 3I7  H4    H  HCH2  0   0.237   2.0123   2.4684  -0.9456
 3I7  H4A   H  HCH2  0   0.238   2.0645   2.6574   0.8139
 3I7  H7    H  HCR6  0   0.278   2.9183   0.6537  -0.0570
 3I7  H9    H  HCR6  0   0.253   1.6964  -3.4061   0.5463
 3I7  H10   H  HCR6  0   0.270  -0.6211  -2.6815   0.7154
 3I7  HN14  H  HNH1  0   0.420  -2.1189  -1.5583  -0.7315
 3I7  H16   H  HCR6  0   0.279  -4.1807   0.9024   1.1635
 3I7  H17   H  HCR6  0   0.258  -6.6170   0.7895   1.1250
 3I7  H18   H  HCR6  0   0.256  -7.7888  -1.0115  -0.1073
 3I7  H19   H  HCR6  0   0.260  -6.4496  -2.7212  -1.3140
 3I7  H20   H  HCR6  0   0.270  -4.0025  -2.6311  -1.2701
 3I7  H22   H  HCR5  0   0.260   5.1045   0.0377   0.3290
 3I7  H25   H  HCR5  0   0.294   3.8753  -4.0597  -0.1875

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
 3I7  N1   C2    single    1.484  0.020  1.484
 3I7  N1   HN1   single    0.890  0.020  1.040
 3I7  N1   HN1A  single    0.890  0.020  1.040
 3I7  N1   HN1B  single    0.890  0.020  1.040
 3I7  C2   C3    single    1.516  0.020  1.516
 3I7  C2   H2    single    0.970  0.020  1.090
 3I7  C2   H2A   single    0.970  0.020  1.090
 3I7  C3   C4    single    1.516  0.020  1.516
 3I7  C3   H3    single    0.970  0.020  1.090
 3I7  C3   H3A   single    0.970  0.020  1.090
 3I7  C4   O5    single    1.416  0.020  1.416
 3I7  C4   H4    single    0.970  0.020  1.090
 3I7  C4   H4A   single    0.970  0.020  1.090
 3I7  O5   C6    single    1.341  0.020  1.341
 3I7  C6   C7    aromatic  1.390  0.020  1.390
 3I7  C6   C11   aromatic  1.403  0.020  1.403
 3I7  C7   C8    aromatic  1.397  0.020  1.397
 3I7  C7   H7    single    0.930  0.020  1.080
 3I7  C8   C9    aromatic  1.394  0.020  1.394
 3I7  C8   C21   single    1.459  0.020  1.459
 3I7  C9   C10   aromatic  1.384  0.020  1.384
 3I7  C9   H9    single    0.930  0.020  1.080
 3I7  C10  C11   aromatic  1.390  0.020  1.390
 3I7  C10  H10   single    0.930  0.020  1.080
 3I7  C11  C12   single    1.493  0.020  1.493
 3I7  C12  O13   double    1.217  0.020  1.217
 3I7  C12  N14   single    1.359  0.020  1.359
 3I7  N14  C15   single    1.400  0.020  1.400
 3I7  N14  HN14  single    0.860  0.020  1.020
 3I7  C15  C16   aromatic  1.396  0.020  1.396
 3I7  C15  C20   aromatic  1.398  0.020  1.398
 3I7  C16  C17   aromatic  1.389  0.020  1.389
 3I7  C16  H16   single    0.930  0.020  1.080
 3I7  C17  C18   aromatic  1.387  0.020  1.387
 3I7  C17  H17   single    0.930  0.020  1.080
 3I7  C18  C19   aromatic  1.389  0.020  1.389
 3I7  C18  H18   single    0.930  0.020  1.080
 3I7  C19  C20   aromatic  1.384  0.020  1.384
 3I7  C19  H19   single    0.930  0.020  1.080
 3I7  C20  H20   single    0.930  0.020  1.080
 3I7  C21  C22   aromatic  1.413  0.020  1.413
 3I7  C21  C25   aromatic  1.384  0.020  1.384
 3I7  C22  N23   aromatic  1.317  0.020  1.317
 3I7  C22  H22   single    0.930  0.020  1.080
 3I7  N23  N24   aromatic  1.328  0.020  1.328
 3I7  N24  C25   aromatic  1.338  0.020  1.338
 3I7  N24  HN24  single    0.860  0.020  1.020
 3I7  C25  H25   single    0.930  0.020  1.080

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
 3I7  HN1B  N1   HN1A  107.26  3.000
 3I7  HN1B  N1   HN1   106.89  3.000
 3I7  HN1A  N1   HN1   106.88  3.000
 3I7  HN1B  N1   C2    112.05  3.000
 3I7  HN1A  N1   C2    111.96  3.000
 3I7  HN1   N1   C2    111.48  3.000
 3I7  H2A   C2   H2    108.58  3.000
 3I7  H2A   C2   C3    111.79  3.000
 3I7  H2    C2   C3    112.01  3.000
 3I7  H2A   C2   N1    106.85  3.000
 3I7  H2    C2   N1    106.71  3.000
 3I7  C3    C2   N1    110.64  3.000
 3I7  H3A   C3   H3    107.82  3.000
 3I7  H3A   C3   C4    109.64  3.000
 3I7  H3    C3   C4    109.55  3.000
 3I7  H3A   C3   C2    110.00  3.000
 3I7  H3    C3   C2    109.80  3.000
 3I7  C4    C3   C2    110.00  3.000
 3I7  H4A   C4   H4    107.79  3.000
 3I7  H4A   C4   O5    110.41  3.000
 3I7  H4    C4   O5    110.94  3.000
 3I7  H4A   C4   C3    110.52  3.000
 3I7  H4    C4   C3    110.13  3.000
 3I7  O5    C4   C3    107.08  3.000
 3I7  C6    O5   C4    119.62  3.000
 3I7  C11   C6   C7    119.84  3.000
 3I7  C11   C6   O5    116.51  3.000
 3I7  C7    C6   O5    123.61  3.000
 3I7  H7    C7   C8    118.80  3.000
 3I7  H7    C7   C6    120.12  3.000
 3I7  C8    C7   C6    121.07  3.000
 3I7  C21   C8   C9    121.09  3.000
 3I7  C21   C8   C7    120.03  3.000
 3I7  C9    C8   C7    118.88  3.000
 3I7  H9    C9   C10   119.27  3.000
 3I7  H9    C9   C8    120.73  3.000
 3I7  C10   C9   C8    119.99  3.000
 3I7  H10   C10  C11   119.56  3.000
 3I7  H10   C10  C9    118.78  3.000
 3I7  C11   C10  C9    121.62  3.000
 3I7  C12   C11  C10   120.37  3.000
 3I7  C12   C11  C6    120.93  3.000
 3I7  C10   C11  C6    118.59  3.000
 3I7  N14   C12  O13   124.18  3.000
 3I7  N14   C12  C11   113.46  3.000
 3I7  O13   C12  C11   122.34  3.000
 3I7  HN14  N14  C15   114.80  3.000
 3I7  HN14  N14  C12   115.97  3.000
 3I7  C15   N14  C12   129.19  3.000
 3I7  C20   C15  C16   119.06  3.000
 3I7  C20   C15  N14   116.60  3.000
 3I7  C16   C15  N14   124.34  3.000
 3I7  H16   C16  C17   119.49  3.000
 3I7  H16   C16  C15   120.94  3.000
 3I7  C17   C16  C15   119.57  3.000
 3I7  H17   C17  C18   119.95  3.000
 3I7  H17   C17  C16   118.69  3.000
 3I7  C18   C17  C16   121.36  3.000
 3I7  H18   C18  C19   120.50  3.000
 3I7  H18   C18  C17   120.55  3.000
 3I7  C19   C18  C17   118.95  3.000
 3I7  H19   C19  C20   119.32  3.000
 3I7  H19   C19  C18   120.30  3.000
 3I7  C20   C19  C18   120.38  3.000
 3I7  H20   C20  C19   119.60  3.000
 3I7  H20   C20  C15   119.71  3.000
 3I7  C19   C20  C15   120.69  3.000
 3I7  C25   C21  C22   103.55  3.000
 3I7  C25   C21  C8    127.85  3.000
 3I7  C22   C21  C8    128.60  3.000
 3I7  H22   C22  N23   119.95  3.000
 3I7  H22   C22  C21   128.35  3.000
 3I7  N23   C22  C21   111.70  3.000
 3I7  N24   N23  C22   104.87  3.000
 3I7  HN24  N24  C25   126.76  3.000
 3I7  HN24  N24  N23   119.88  3.000
 3I7  C25   N24  N23   113.36  3.000
 3I7  H25   C25  N24   121.65  3.000
 3I7  H25   C25  C21   131.84  3.000
 3I7  N24   C25  C21   106.51  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
 3I7  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 3I7  CONST_02  C21   C8   C7   C6   180.00   0.0  0
 3I7  CONST_03  C9    C10  C11  C6     0.00   0.0  0
 3I7  CONST_04  C10   C11  C6   C7     0.00   0.0  0
 3I7  CONST_05  C10   C9   C8   C7     0.00   0.0  0
 3I7  CONST_06  C22   C21  C8   C7     0.00   0.0  0
 3I7  CONST_07  C25   C21  C8   C7   180.00   0.0  0
 3I7  CONST_08  C11   C6   C7   C8     0.00   0.0  0
 3I7  CONST_09  C11   C10  C9   C8     0.00   0.0  0
 3I7  CONST_10  N23   C22  C21  C8   180.00   0.0  0
 3I7  CONST_11  N24   C25  C21  C8   180.00   0.0  0
 3I7  CONST_12  C22   C21  C8   C9   180.00   0.0  0
 3I7  CONST_13  C25   C21  C8   C9     0.00   0.0  0
 3I7  CONST_14  C21   C8   C9   C10  180.00   0.0  0
 3I7  CONST_15  C18   C17  C16  C15    0.00   0.0  0
 3I7  CONST_16  C18   C19  C20  C15    0.00   0.0  0
 3I7  CONST_17  C19   C20  C15  C16    0.00   0.0  0
 3I7  CONST_18  C19   C18  C17  C16    0.00   0.0  0
 3I7  CONST_19  C20   C15  C16  C17    0.00   0.0  0
 3I7  CONST_20  C20   C19  C18  C17    0.00   0.0  0
 3I7  CONST_21  N24   N23  C22  C21    0.00   0.0  0
 3I7  CONST_22  N23   N24  C25  C21    0.00   0.0  0
 3I7  CONST_23  N24   C25  C21  C22    0.00   0.0  0
 3I7  CONST_24  C25   N24  N23  C22    0.00   0.0  0
 3I7  CONST_25  C25   C21  C22  N23    0.00   0.0  0
 3I7  CONST_26  C8    C7   C6   O5   180.00   0.0  0
 3I7  CONST_27  C10   C11  C6   O5   180.00   0.0  0
 3I7  CONST_28  C12   C11  C6   C7   180.00   0.0  0
 3I7  CONST_29  C12   C11  C10  C9   180.00   0.0  0
 3I7  CONST_30  C17   C16  C15  N14  180.00   0.0  0
 3I7  CONST_31  C19   C20  C15  N14  180.00   0.0  0
 3I7  CONST_32  H10   C10  C11  C6   180.00   0.0  0
 3I7  CONST_33  H9    C9   C8   C7   180.00   0.0  0
 3I7  CONST_34  H22   C22  C21  C8     0.00   0.0  0
 3I7  CONST_35  H25   C25  C21  C8     0.00   0.0  0
 3I7  CONST_36  H7    C7   C8   C9   180.00   0.0  0
 3I7  CONST_37  H17   C17  C16  C15  180.00   0.0  0
 3I7  CONST_38  H19   C19  C20  C15  180.00   0.0  0
 3I7  CONST_39  H20   C20  C15  C16  180.00   0.0  0
 3I7  CONST_40  H18   C18  C17  C16  180.00   0.0  0
 3I7  CONST_41  H16   C16  C17  C18  180.00   0.0  0
 3I7  CONST_42  HN24  N24  C25  C21  180.00   0.0  0
 3I7  CONST_43  C15   N14  C12  C11  180.00   0.0  0
 3I7  CONST_44  C16   C15  N14  C12    0.00   0.0  0
 3I7  CONST_45  C20   C15  N14  C12  180.00   0.0  0
 3I7  CONST_46  HN14  N14  C15  C16  180.00   0.0  0
 3I7  CONST_47  C15   N14  C12  O13    0.00   0.0  0
 3I7  Var_01    C7    C6   O5   C4    -5.40  30.0  2
 3I7  Var_02    O13   C12  C11  C6   -47.60  30.0  2
 3I7  Var_03    H4    C4   O5   C6    59.93  30.0  1
 3I7  Var_04    C4    C3   C2   N1   178.26  30.0  3
 3I7  Var_05    O5    C4   C3   C2   176.27  30.0  3
 3I7  Var_06    HN1   N1   C2   C3   177.93  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
 3I7  plan-1  C8    0.020
 3I7  plan-1  C21   0.020
 3I7  plan-1  C22   0.020
 3I7  plan-1  N23   0.020
 3I7  plan-1  N24   0.020
 3I7  plan-1  C25   0.020
 3I7  plan-1  HN24  0.020
 3I7  plan-1  H22   0.020
 3I7  plan-1  H25   0.020
 3I7  plan-2  O5    0.020
 3I7  plan-2  C6    0.020
 3I7  plan-2  C7    0.020
 3I7  plan-2  C8    0.020
 3I7  plan-2  C9    0.020
 3I7  plan-2  C10   0.020
 3I7  plan-2  C11   0.020
 3I7  plan-2  C12   0.020
 3I7  plan-2  C21   0.020
 3I7  plan-2  H7    0.020
 3I7  plan-2  H9    0.020
 3I7  plan-2  H10   0.020
 3I7  plan-3  N14   0.020
 3I7  plan-3  C15   0.020
 3I7  plan-3  C16   0.020
 3I7  plan-3  C17   0.020
 3I7  plan-3  C18   0.020
 3I7  plan-3  C19   0.020
 3I7  plan-3  C20   0.020
 3I7  plan-3  H16   0.020
 3I7  plan-3  H17   0.020
 3I7  plan-3  H18   0.020
 3I7  plan-3  H19   0.020
 3I7  plan-3  H20   0.020
 3I7  plan-4  C11   0.020
 3I7  plan-4  C12   0.020
 3I7  plan-4  O13   0.020
 3I7  plan-4  N14   0.020
 3I7  plan-4  C15   0.020
 3I7  plan-4  HN14  0.020

