# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 15:54:11 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (1~{R},2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(Nc2nc(N[C@H]3CCCC[C@H]3C(O)=O)nc4ccccc24)c1
#
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
 E7W  E7W  '(1~{R},2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]cyclohexane-1-carboxylic acid'  ligand  54  29  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E7W
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
 E7W  N1   N  NH1   0  -0.674  -2.1054   0.3638   0.1047
 E7W  C5   C  CH1   0  -0.399  -4.3341   1.2786  -0.2615
 E7W  C7   C  CH2   0  -0.438  -4.1400   2.5998   0.4835
 E7W  C10  C  CH2   0  -0.434  -4.4550   2.4319   1.9676
 E7W  C13  C  CH2   0  -0.443  -3.6262   1.3181   2.5974
 E7W  C26  C  CR66  0  -0.065   0.7687  -2.4780  -0.1192
 E7W  C19  C  C     0   0.571  -4.0660   1.3098  -1.7504
 E7W  O20  O  OH1   0  -0.582  -3.6039   2.4709  -2.1919
 E7W  C16  C  CH2   0  -0.431  -3.8264   0.0047   1.8516
 E7W  C3   C  CH1   0  -0.085  -3.5130   0.1357   0.3597
 E7W  C23  C  CR6   0   0.603  -1.1836  -0.6251   0.0568
 E7W  N28  N  N     0  -0.531   0.0955  -0.1818   0.0290
 E7W  C27  C  CR6   0   0.547   1.0570  -1.0629  -0.0444
 E7W  C47  C  CR16  0  -0.310   1.7297  -3.4972  -0.2327
 E7W  C49  C  CR16  0  -0.267   1.3490  -4.8156  -0.2891
 E7W  C51  C  CR16  0  -0.246  -0.0133  -5.1496  -0.2312
 E7W  C53  C  CR16  0  -0.322  -0.9689  -4.1714  -0.1241
 E7W  C25  C  CR66  0   0.263  -0.6028  -2.8097  -0.0693
 E7W  N24  N  N     0  -0.532  -1.5777  -1.8747   0.0285
 E7W  N29  N  NH1   0  -0.784   2.3464  -0.6571  -0.0451
 E7W  C31  C  CR6   0   0.399   2.9092   0.6207   0.0305
 E7W  C39  C  CR16  0  -0.325   2.1988   1.8177  -0.0497
 E7W  C37  C  CR16  0  -0.235   2.8937   3.0195   0.0188
 E7W  C35  C  CR16  0  -0.318   4.2692   3.0534   0.1639
 E7W  C34  C  CR6   0   0.089   4.9869   1.8607   0.2516
 E7W  C32  C  CR16  0  -0.428   4.3006   0.6600   0.1826
 E7W  C41  C  CH2   0  -0.325   6.4827   1.9031   0.4480
 E7W  N44  N  NH2   0  -0.797   7.1315   0.6512   0.1104
 E7W  H1   H  HNH1  0   0.388  -1.7229   1.2796   0.2791
 E7W  H2   H  HCH1  0   0.291  -5.3867   0.9878  -0.1601
 E7W  H3   H  HCH2  0   0.224  -3.1175   2.9720   0.3697
 E7W  H4   H  HCH2  0   0.252  -4.7862   3.3671   0.0537
 E7W  H5   H  HCH2  0   0.237  -4.2792   3.3766   2.4861
 E7W  H6   H  HCH2  0   0.217  -5.5193   2.2023   2.0875
 E7W  H7   H  HCH2  0   0.214  -2.5672   1.5961   2.5862
 E7W  H8   H  HCH2  0   0.238  -3.8964   1.1928   3.6480
 E7W  H9   H  HOH1  0   0.481  -3.4548   2.4231  -3.1487
 E7W  H10  H  HCH2  0   0.241  -3.2059  -0.7881   2.2755
 E7W  H11  H  HCH2  0   0.226  -4.8664  -0.3206   1.9571
 E7W  H12  H  HCH1  0   0.269  -3.7821  -0.7951  -0.1376
 E7W  H13  H  HCR6  0   0.253   2.7878  -3.2727  -0.2849
 E7W  H14  H  HCR6  0   0.263   2.0962  -5.5919  -0.3783
 E7W  H15  H  HCR6  0   0.263  -0.3106  -6.1896  -0.2739
 E7W  H16  H  HCR6  0   0.255  -2.0214  -4.4212  -0.0825
 E7W  H17  H  HNH1  0   0.427   3.0352  -1.3909  -0.0506
 E7W  H18  H  HCR6  0   0.285   1.1288   1.8181  -0.1650
 E7W  H19  H  HCR6  0   0.253   2.3374   3.9457  -0.0519
 E7W  H20  H  HCR6  0   0.244   4.7898   4.0028   0.2076
 E7W  H21  H  HCR6  0   0.262   4.8622  -0.2656   0.2474
 E7W  H22  H  HCH2  0   0.217   6.8752   2.7698  -0.1011
 E7W  H23  H  HCH2  0   0.245   6.6803   2.1114   1.5037
 E7W  H24  H  HNH2  0   0.346   7.1243   0.5243  -0.8939
 E7W  H25  H  HNH2  0   0.358   8.1053   0.6975   0.3793
 E7W  O21  O  O     0  -0.452  -4.2578   0.3633  -2.4749

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
 E7W  C16  C13  single    1.524  0.020  1.524
 E7W  C16  C3   single    1.530  0.020  1.530
 E7W  C13  C10  single    1.525  0.020  1.525
 E7W  C10  C7   single    1.526  0.020  1.526
 E7W  C3   N1   single    1.449  0.020  1.449
 E7W  C3   C5   single    1.538  0.020  1.538
 E7W  C41  C34  single    1.509  0.020  1.509
 E7W  C41  N44  single    1.450  0.020  1.450
 E7W  C34  C32  aromatic  1.385  0.020  1.385
 E7W  C34  C35  aromatic  1.395  0.020  1.395
 E7W  N1   C23  single    1.353  0.020  1.353
 E7W  C32  C31  aromatic  1.400  0.020  1.400
 E7W  C35  C37  aromatic  1.384  0.020  1.384
 E7W  C5   C7   single    1.529  0.020  1.529
 E7W  C5   C19  single    1.513  0.020  1.513
 E7W  N28  C23  aromatic  1.354  0.020  1.354
 E7W  N28  C27  aromatic  1.306  0.020  1.306
 E7W  C23  N24  aromatic  1.311  0.020  1.311
 E7W  N24  C25  aromatic  1.354  0.020  1.354
 E7W  C31  N29  single    1.398  0.020  1.398
 E7W  C31  C39  aromatic  1.394  0.020  1.394
 E7W  C27  N29  single    1.352  0.020  1.352
 E7W  C27  C26  aromatic  1.446  0.020  1.446
 E7W  C37  C39  aromatic  1.390  0.020  1.390
 E7W  C25  C26  aromatic  1.412  0.020  1.412
 E7W  C25  C53  aromatic  1.411  0.020  1.411
 E7W  C26  C47  aromatic  1.405  0.020  1.405
 E7W  C53  C51  aromatic  1.372  0.020  1.372
 E7W  C47  C49  aromatic  1.373  0.020  1.373
 E7W  C51  C49  aromatic  1.404  0.020  1.404
 E7W  O21  C19  double    1.207  0.020  1.207
 E7W  C19  O20  single    1.325  0.020  1.325
 E7W  N1   H1   single    0.890  0.020  1.040
 E7W  C5   H2   single    0.970  0.020  1.090
 E7W  C7   H3   single    0.970  0.020  1.090
 E7W  C7   H4   single    0.970  0.020  1.090
 E7W  C10  H5   single    0.970  0.020  1.090
 E7W  C10  H6   single    0.970  0.020  1.090
 E7W  C13  H7   single    0.970  0.020  1.090
 E7W  C13  H8   single    0.970  0.020  1.090
 E7W  O20  H9   single    0.850  0.020  0.980
 E7W  C16  H10  single    0.970  0.020  1.090
 E7W  C16  H11  single    0.970  0.020  1.090
 E7W  C3   H12  single    0.970  0.020  1.090
 E7W  C47  H13  single    0.930  0.020  1.080
 E7W  C49  H14  single    0.930  0.020  1.080
 E7W  C51  H15  single    0.930  0.020  1.080
 E7W  C53  H16  single    0.930  0.020  1.080
 E7W  N29  H17  single    0.860  0.020  1.020
 E7W  C39  H18  single    0.930  0.020  1.080
 E7W  C37  H19  single    0.930  0.020  1.080
 E7W  C35  H20  single    0.930  0.020  1.080
 E7W  C32  H21  single    0.930  0.020  1.080
 E7W  C41  H22  single    0.970  0.020  1.090
 E7W  C41  H23  single    0.970  0.020  1.090
 E7W  N44  H24  single    0.890  0.020  1.040
 E7W  N44  H25  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
 E7W  H1   N1   C23  114.32  3.000
 E7W  H1   N1   C3   118.78  3.000
 E7W  C23  N1   C3   123.60  3.000
 E7W  H2   C5   C3   106.14  3.000
 E7W  H2   C5   C19  105.45  3.000
 E7W  C3   C5   C19  108.55  3.000
 E7W  H2   C5   C7   107.81  3.000
 E7W  C19  C5   C7   116.04  3.000
 E7W  C3   C5   C7   112.18  3.000
 E7W  H4   C7   H3   105.86  3.000
 E7W  H4   C7   C10  109.76  3.000
 E7W  H3   C7   C10  109.35  3.000
 E7W  H4   C7   C5   109.91  3.000
 E7W  H3   C7   C5   111.22  3.000
 E7W  C10  C7   C5   110.64  3.000
 E7W  H6   C10  H5   106.61  3.000
 E7W  H6   C10  C13  109.26  3.000
 E7W  H5   C10  C13  110.39  3.000
 E7W  H6   C10  C7   109.27  3.000
 E7W  H5   C10  C7   109.47  3.000
 E7W  C13  C10  C7   111.71  3.000
 E7W  H8   C13  H7   106.16  3.000
 E7W  H8   C13  C16  109.85  3.000
 E7W  H7   C13  C16  109.93  3.000
 E7W  H8   C13  C10  110.29  3.000
 E7W  H7   C13  C10  109.64  3.000
 E7W  C16  C13  C10  110.86  3.000
 E7W  C25  C26  C47  119.78  3.000
 E7W  C47  C26  C27  125.28  3.000
 E7W  C25  C26  C27  114.94  3.000
 E7W  O20  C19  O21  122.84  3.000
 E7W  O20  C19  C5   114.06  3.000
 E7W  O21  C19  C5   123.11  3.000
 E7W  H9   O20  C19  109.83  3.000
 E7W  H11  C16  H10  106.65  3.000
 E7W  H11  C16  C3   108.30  3.000
 E7W  H10  C16  C3   108.92  3.000
 E7W  H11  C16  C13  109.50  3.000
 E7W  H10  C16  C13  111.17  3.000
 E7W  C3   C16  C13  112.12  3.000
 E7W  H12  C3   C16  108.75  3.000
 E7W  H12  C3   C5   108.59  3.000
 E7W  C16  C3   C5   110.37  3.000
 E7W  H12  C3   N1   107.11  3.000
 E7W  C5   C3   N1   109.30  3.000
 E7W  C16  C3   N1   112.59  3.000
 E7W  N24  C23  N28  126.57  3.000
 E7W  N24  C23  N1   119.53  3.000
 E7W  N28  C23  N1   113.90  3.000
 E7W  C27  N28  C23  118.40  3.000
 E7W  N29  C27  N28  119.98  3.000
 E7W  N29  C27  C26  118.94  3.000
 E7W  N28  C27  C26  121.08  3.000
 E7W  H13  C47  C49  117.90  3.000
 E7W  H13  C47  C26  121.44  3.000
 E7W  C49  C47  C26  120.66  3.000
 E7W  H14  C49  C51  120.22  3.000
 E7W  H14  C49  C47  120.07  3.000
 E7W  C51  C49  C47  119.71  3.000
 E7W  H15  C51  C53  119.79  3.000
 E7W  H15  C51  C49  119.57  3.000
 E7W  C53  C51  C49  120.64  3.000
 E7W  H16  C53  C25  118.25  3.000
 E7W  H16  C53  C51  121.05  3.000
 E7W  C25  C53  C51  120.70  3.000
 E7W  N24  C25  C53  118.84  3.000
 E7W  C53  C25  C26  118.51  3.000
 E7W  N24  C25  C26  122.66  3.000
 E7W  C25  N24  C23  116.32  3.000
 E7W  H17  N29  C31  113.03  3.000
 E7W  H17  N29  C27  115.71  3.000
 E7W  C31  N29  C27  131.17  3.000
 E7W  C32  C31  C39  119.24  3.000
 E7W  C39  C31  N29  125.19  3.000
 E7W  C32  C31  N29  115.56  3.000
 E7W  H18  C39  C37  120.14  3.000
 E7W  H18  C39  C31  120.87  3.000
 E7W  C37  C39  C31  118.99  3.000
 E7W  H19  C37  C35  119.78  3.000
 E7W  H19  C37  C39  118.65  3.000
 E7W  C35  C37  C39  121.56  3.000
 E7W  H20  C35  C34  119.96  3.000
 E7W  H20  C35  C37  120.22  3.000
 E7W  C34  C35  C37  119.82  3.000
 E7W  C41  C34  C32  121.47  3.000
 E7W  C32  C34  C35  118.90  3.000
 E7W  C41  C34  C35  119.62  3.000
 E7W  H21  C32  C34  118.71  3.000
 E7W  H21  C32  C31  119.81  3.000
 E7W  C34  C32  C31  121.48  3.000
 E7W  H23  C41  H22  105.52  3.000
 E7W  H23  C41  N44  107.95  3.000
 E7W  H22  C41  N44  113.89  3.000
 E7W  H23  C41  C34  108.05  3.000
 E7W  H22  C41  C34  108.13  3.000
 E7W  N44  C41  C34  112.89  3.000
 E7W  H25  N44  H24  106.03  3.000
 E7W  H25  N44  C41  109.24  3.000
 E7W  H24  N44  C41  109.64  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
 E7W  CONST_01  C23  N28  C27  C26     0.00   0.0  0
 E7W  CONST_02  C23  N24  C25  C26     0.00   0.0  0
 E7W  CONST_03  C51  C53  C25  C26     0.00   0.0  0
 E7W  CONST_04  C51  C49  C47  C26     0.00   0.0  0
 E7W  CONST_05  C53  C25  N24  C23   180.00   0.0  0
 E7W  CONST_06  C25  N24  C23  N28     0.00   0.0  0
 E7W  CONST_07  C25  C26  C27  N28     0.00   0.0  0
 E7W  CONST_08  C47  C26  C27  N28   180.00   0.0  0
 E7W  CONST_09  N24  C23  N28  C27     0.00   0.0  0
 E7W  CONST_10  N24  C25  C26  C27     0.00   0.0  0
 E7W  CONST_11  C53  C25  C26  C27   180.00   0.0  0
 E7W  CONST_12  C49  C47  C26  C27   180.00   0.0  0
 E7W  CONST_13  N24  C25  C26  C47   180.00   0.0  0
 E7W  CONST_14  C53  C25  C26  C47     0.00   0.0  0
 E7W  CONST_15  C53  C51  C49  C47     0.00   0.0  0
 E7W  CONST_16  C25  C26  C47  C49     0.00   0.0  0
 E7W  CONST_17  C25  C53  C51  C49     0.00   0.0  0
 E7W  CONST_18  N24  C25  C53  C51   180.00   0.0  0
 E7W  CONST_19  C35  C34  C32  C31     0.00   0.0  0
 E7W  CONST_20  C35  C37  C39  C31     0.00   0.0  0
 E7W  CONST_21  C34  C32  C31  C39     0.00   0.0  0
 E7W  CONST_22  C34  C35  C37  C39     0.00   0.0  0
 E7W  CONST_23  C32  C34  C35  C37     0.00   0.0  0
 E7W  CONST_24  C32  C31  C39  C37     0.00   0.0  0
 E7W  CONST_25  C27  N28  C23  N1    180.00   0.0  0
 E7W  CONST_26  C25  N24  C23  N1    180.00   0.0  0
 E7W  CONST_27  N29  C27  N28  C23   180.00   0.0  0
 E7W  CONST_28  N29  C27  C26  C47     0.00   0.0  0
 E7W  CONST_29  N29  C27  C26  C25   180.00   0.0  0
 E7W  CONST_30  C34  C32  C31  N29   180.00   0.0  0
 E7W  CONST_31  C37  C39  C31  N29   180.00   0.0  0
 E7W  CONST_32  C41  C34  C32  C31   180.00   0.0  0
 E7W  CONST_33  C41  C34  C35  C37   180.00   0.0  0
 E7W  CONST_34  N28  C23  N1   C3    180.00   0.0  0
 E7W  CONST_35  N24  C23  N1   C3      0.00   0.0  0
 E7W  CONST_36  H16  C53  C25  C26   180.00   0.0  0
 E7W  CONST_37  H14  C49  C47  C26   180.00   0.0  0
 E7W  CONST_38  H13  C47  C26  C27     0.00   0.0  0
 E7W  CONST_39  H15  C51  C49  C47   180.00   0.0  0
 E7W  CONST_40  H19  C37  C39  C31   180.00   0.0  0
 E7W  CONST_41  H21  C32  C31  C39   180.00   0.0  0
 E7W  CONST_42  H20  C35  C37  C39   180.00   0.0  0
 E7W  CONST_43  H18  C39  C37  C35   180.00   0.0  0
 E7W  CONST_44  H1   N1   C23  N28     0.00   0.0  0
 E7W  CONST_45  H9   O20  C19  C5    180.00   0.0  0
 E7W  Var_01    C13  C10  C7   C5     55.59  30.0  1
 E7W  Var_02    C16  C13  C10  C7    -55.98  30.0  1
 E7W  Var_03    C3   C16  C13  C10    55.67  30.0  1
 E7W  Var_04    C31  N29  C27  C26  -179.26  30.0  2
 E7W  Var_05    C32  C31  N29  C27   171.82  30.0  2
 E7W  Var_06    N44  C41  C34  C35  -162.02  30.0  1
 E7W  Var_07    H24  N44  C41  C34    71.85  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
 E7W  chir_01  C5  C3  C7   C19  negativ
 E7W  chir_02  C3  N1  C16  C5   negativ

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
 E7W  plan-1  N29  0.020
 E7W  plan-1  C31  0.020
 E7W  plan-1  C39  0.020
 E7W  plan-1  C37  0.020
 E7W  plan-1  C35  0.020
 E7W  plan-1  C34  0.020
 E7W  plan-1  C32  0.020
 E7W  plan-1  C41  0.020
 E7W  plan-1  H18  0.020
 E7W  plan-1  H19  0.020
 E7W  plan-1  H20  0.020
 E7W  plan-1  H21  0.020
 E7W  plan-2  N1   0.020
 E7W  plan-2  C26  0.020
 E7W  plan-2  C23  0.020
 E7W  plan-2  N28  0.020
 E7W  plan-2  C27  0.020
 E7W  plan-2  C47  0.020
 E7W  plan-2  C49  0.020
 E7W  plan-2  C51  0.020
 E7W  plan-2  C53  0.020
 E7W  plan-2  C25  0.020
 E7W  plan-2  N24  0.020
 E7W  plan-2  N29  0.020
 E7W  plan-2  H13  0.020
 E7W  plan-2  H14  0.020
 E7W  plan-2  H15  0.020
 E7W  plan-2  H16  0.020
 E7W  plan-3  N1   0.020
 E7W  plan-3  C3   0.020
 E7W  plan-3  C23  0.020
 E7W  plan-3  H1   0.020
 E7W  plan-4  C5   0.020
 E7W  plan-4  C19  0.020
 E7W  plan-4  O20  0.020
 E7W  plan-4  H9   0.020
 E7W  plan-4  O21  0.020

