# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:43:55 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(ncc1N(CC2CC2)c3cccc4ccccc34)C(=O)[C@H]5C[C@@H]5C(O)=O
#
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
 JUQ  JUQ  '(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid'  ligand  54  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JUQ
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
 JUQ  C1   C  CR16  0  -0.252   1.7745   3.5088   0.2583
 JUQ  C2   C  CR16  0  -0.259   2.6729   4.1133   1.1603
 JUQ  C3   C  CR16  0  -0.312   3.6875   3.3784   1.7074
 JUQ  C7   C  CR6   0   0.253   3.0695   0.0002   0.2335
 JUQ  C8   C  CR16  0  -0.296   4.1325  -0.6919   0.7494
 JUQ  C9   C  CR16  0  -0.264   5.0687  -0.0616   1.5882
 JUQ  C10  C  CR16  0  -0.321   4.9180   1.2555   1.9213
 JUQ  C12  C  CR6   0   0.167   0.8114  -0.6968  -0.3560
 JUQ  C13  C  CR16  0  -0.111  -0.1623  -0.7583  -1.3475
 JUQ  C15  C  CR6   0   0.255  -1.8337  -0.7629   0.1721
 JUQ  C16  C  C     0   0.381  -3.2934  -0.7930   0.4881
 JUQ  C19  C  CH1   0  -0.377  -5.5767  -0.0480  -0.3787
 JUQ  C20  C  C     0   0.572  -6.1349   0.7892  -1.4662
 JUQ  C27  C  CH3   0  -0.413   0.6459  -0.6817   3.3001
 JUQ  C30  C  CH2   0  -0.489   3.3040  -3.1552  -3.2832
 JUQ  C31  C  CH2   0  -0.482   3.4221  -3.5230  -1.8341
 JUQ  C4   C  CR66  0   0.087   3.8428   2.0069   1.3948
 JUQ  C5   C  CR66  0   0.140   2.9141   1.3866   0.5151
 JUQ  C6   C  CR16  0  -0.318   1.8920   2.1823  -0.0566
 JUQ  N11  N  NT    0  -0.576   2.1558  -0.6676  -0.6224
 JUQ  N14  N  N     0  -0.408  -1.4679  -0.7841  -1.0885
 JUQ  C17  C  CH1   0  -0.403  -4.2400  -0.7114  -0.6524
 JUQ  C18  C  CH2   0  -0.438  -5.4959  -1.5219  -0.5920
 JUQ  O21  O  OH1   0  -0.592  -6.7849   1.8424  -0.9903
 JUQ  O22  O  O     0  -0.450  -6.0217   0.5492  -2.6439
 JUQ  O23  O  O     0  -0.392  -3.6721  -0.8835   1.6354
 JUQ  N24  N  N     0  -0.433  -0.9983  -0.7348   1.2099
 JUQ  C25  C  CR6   0   0.517   0.2840  -0.7096   0.9709
 JUQ  O26  O  O2    0  -0.446   1.1472  -0.7075   1.9684
 JUQ  C28  C  CH2   0  -0.357   2.6305  -1.0483  -1.9534
 JUQ  C29  C  CH1   0  -0.250   2.4159  -2.5047  -2.2688
 JUQ  H1   H  HCR6  0   0.260   0.9900   4.1009  -0.1944
 JUQ  H2   H  HCR6  0   0.259   2.5638   5.1612   1.4069
 JUQ  H3   H  HCR6  0   0.256   4.3936   3.8418   2.3859
 JUQ  H4   H  HCR6  0   0.264   4.2386  -1.7454   0.5252
 JUQ  H5   H  HCR6  0   0.260   5.8957  -0.6352   1.9853
 JUQ  H6   H  HCR6  0   0.256   5.6251   1.7414   2.5827
 JUQ  H7   H  HCR6  0   0.283   0.1106  -0.7786  -2.3945
 JUQ  H8   H  HCH1  0   0.300  -5.7468   0.2968   0.6336
 JUQ  H9   H  HCH3  0   0.236   0.0304   0.1999   3.4783
 JUQ  H10  H  HCH3  0   0.236   0.0606  -1.5734   3.5248
 JUQ  H11  H  HCH3  0   0.251   1.5224  -0.6500   3.9408
 JUQ  H12  H  HCH2  0   0.247   4.0970  -2.5575  -3.7167
 JUQ  H13  H  HCH2  0   0.255   2.8633  -3.8704  -3.9656
 JUQ  H14  H  HCH2  0   0.254   3.0621  -4.4935  -1.5181
 JUQ  H15  H  HCH2  0   0.245   4.3018  -3.1822  -1.3009
 JUQ  H16  H  HCR6  0   0.257   1.2009   1.7505  -0.7671
 JUQ  H17  H  HCH1  0   0.298  -3.8118  -0.5495  -1.6308
 JUQ  H18  H  HCH2  0   0.281  -5.6537  -2.1479   0.2761
 JUQ  H19  H  HCH2  0   0.282  -5.8650  -1.9227  -1.5264
 JUQ  H20  H  HOH1  0   0.483  -7.1423   2.3697  -1.7209
 JUQ  H21  H  HCH2  0   0.263   2.1666  -0.4168  -2.7200
 JUQ  H22  H  HCH2  0   0.273   3.6957  -0.8201  -1.9885
 JUQ  H23  H  HCH1  0   0.267   1.3828  -2.8359  -2.2734

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
 JUQ  C2   C1   aromatic  1.409  0.020  1.409
 JUQ  C2   C3   aromatic  1.367  0.020  1.367
 JUQ  C1   C6   aromatic  1.368  0.020  1.368
 JUQ  C31  C30  single    1.500  0.020  1.500
 JUQ  C31  C29  single    1.496  0.020  1.496
 JUQ  C3   C4   aromatic  1.415  0.020  1.415
 JUQ  C6   C5   aromatic  1.416  0.020  1.416
 JUQ  C30  C29  single    1.497  0.020  1.497
 JUQ  C4   C5   aromatic  1.422  0.020  1.422
 JUQ  C4   C10  aromatic  1.413  0.020  1.413
 JUQ  C29  C28  single    1.505  0.020  1.505
 JUQ  C5   C7   aromatic  1.423  0.020  1.423
 JUQ  C10  C9   aromatic  1.367  0.020  1.367
 JUQ  C7   N11  single    1.419  0.020  1.419
 JUQ  C7   C8   aromatic  1.369  0.020  1.369
 JUQ  C28  N11  single    1.464  0.020  1.464
 JUQ  C13  N14  aromatic  1.331  0.020  1.331
 JUQ  C13  C12  aromatic  1.391  0.020  1.391
 JUQ  N11  C12  single    1.371  0.020  1.371
 JUQ  N14  C15  aromatic  1.313  0.020  1.313
 JUQ  C12  C25  aromatic  1.428  0.020  1.428
 JUQ  C18  C17  single    1.496  0.020  1.496
 JUQ  C18  C19  single    1.491  0.020  1.491
 JUQ  C9   C8   aromatic  1.406  0.020  1.406
 JUQ  C15  C16  single    1.494  0.020  1.494
 JUQ  C15  N24  aromatic  1.333  0.020  1.333
 JUQ  C25  N24  aromatic  1.305  0.020  1.305
 JUQ  C25  O26  single    1.319  0.020  1.319
 JUQ  C17  C16  single    1.484  0.020  1.484
 JUQ  C17  C19  single    1.517  0.020  1.517
 JUQ  C16  O23  double    1.211  0.020  1.211
 JUQ  O26  C27  single    1.423  0.020  1.423
 JUQ  C19  C20  single    1.482  0.020  1.482
 JUQ  O22  C20  double    1.207  0.020  1.207
 JUQ  C20  O21  single    1.326  0.020  1.326
 JUQ  C1   H1   single    0.930  0.020  1.080
 JUQ  C2   H2   single    0.930  0.020  1.080
 JUQ  C3   H3   single    0.930  0.020  1.080
 JUQ  C8   H4   single    0.930  0.020  1.080
 JUQ  C9   H5   single    0.930  0.020  1.080
 JUQ  C10  H6   single    0.930  0.020  1.080
 JUQ  C13  H7   single    0.930  0.020  1.080
 JUQ  C19  H8   single    0.970  0.020  1.090
 JUQ  C27  H9   single    0.970  0.020  1.090
 JUQ  C27  H10  single    0.970  0.020  1.090
 JUQ  C27  H11  single    0.970  0.020  1.090
 JUQ  C30  H12  single    0.970  0.020  1.090
 JUQ  C30  H13  single    0.970  0.020  1.090
 JUQ  C31  H14  single    0.970  0.020  1.090
 JUQ  C31  H15  single    0.970  0.020  1.090
 JUQ  C6   H16  single    0.930  0.020  1.080
 JUQ  C17  H17  single    0.970  0.020  1.090
 JUQ  C18  H18  single    0.970  0.020  1.090
 JUQ  C18  H19  single    0.970  0.020  1.090
 JUQ  O21  H20  single    0.850  0.020  0.980
 JUQ  C28  H21  single    0.970  0.020  1.090
 JUQ  C28  H22  single    0.970  0.020  1.090
 JUQ  C29  H23  single    0.970  0.020  1.090

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
 JUQ  H1   C1   C6   119.76  3.000
 JUQ  H1   C1   C2   119.69  3.000
 JUQ  C6   C1   C2   120.56  3.000
 JUQ  H2   C2   C3   120.28  3.000
 JUQ  H2   C2   C1   119.80  3.000
 JUQ  C3   C2   C1   119.91  3.000
 JUQ  H3   C3   C4   118.77  3.000
 JUQ  H3   C3   C2   120.30  3.000
 JUQ  C4   C3   C2   120.93  3.000
 JUQ  N11  C7   C5   120.50  3.000
 JUQ  N11  C7   C8   119.30  3.000
 JUQ  C5   C7   C8   120.17  3.000
 JUQ  H4   C8   C9   119.64  3.000
 JUQ  H4   C8   C7   119.34  3.000
 JUQ  C9   C8   C7   121.00  3.000
 JUQ  H5   C9   C10  120.37  3.000
 JUQ  H5   C9   C8   119.36  3.000
 JUQ  C10  C9   C8   120.25  3.000
 JUQ  H6   C10  C4   119.05  3.000
 JUQ  H6   C10  C9   120.60  3.000
 JUQ  C4   C10  C9   120.35  3.000
 JUQ  C25  C12  N11  122.88  3.000
 JUQ  C25  C12  C13  113.79  3.000
 JUQ  N11  C12  C13  123.30  3.000
 JUQ  H7   C13  N14  115.79  3.000
 JUQ  H7   C13  C12  120.93  3.000
 JUQ  N14  C13  C12  123.27  3.000
 JUQ  N24  C15  N14  124.99  3.000
 JUQ  N24  C15  C16  116.63  3.000
 JUQ  N14  C15  C16  118.37  3.000
 JUQ  O23  C16  C17  122.17  3.000
 JUQ  O23  C16  C15  120.48  3.000
 JUQ  C17  C16  C15  117.35  3.000
 JUQ  H8   C19  C18  117.18  3.000
 JUQ  H8   C19  C17  116.50  3.000
 JUQ  C18  C19  C17   59.62  3.000
 JUQ  H8   C19  C20  116.56  3.000
 JUQ  C17  C19  C20  116.53  3.000
 JUQ  C18  C19  C20  118.29  3.000
 JUQ  O22  C20  O21  123.64  3.000
 JUQ  O21  C20  C19  111.72  3.000
 JUQ  O22  C20  C19  124.63  3.000
 JUQ  H11  C27  H10  109.61  3.000
 JUQ  H11  C27  H9   109.61  3.000
 JUQ  H10  C27  H9   108.95  3.000
 JUQ  H11  C27  O26  105.56  3.000
 JUQ  H10  C27  O26  111.54  3.000
 JUQ  H9   C27  O26  111.50  3.000
 JUQ  H13  C30  H12  114.23  3.000
 JUQ  H13  C30  C29  118.22  3.000
 JUQ  H12  C30  C29  117.74  3.000
 JUQ  H13  C30  C31  118.64  3.000
 JUQ  H12  C30  C31  117.66  3.000
 JUQ  C29  C30  C31   59.90  3.000
 JUQ  H15  C31  H14  114.10  3.000
 JUQ  H15  C31  C29  118.35  3.000
 JUQ  H14  C31  C29  118.13  3.000
 JUQ  H15  C31  C30  117.53  3.000
 JUQ  H14  C31  C30  118.41  3.000
 JUQ  C29  C31  C30   59.96  3.000
 JUQ  C5   C4   C10  119.71  3.000
 JUQ  C10  C4   C3   121.09  3.000
 JUQ  C5   C4   C3   119.19  3.000
 JUQ  C6   C5   C4   118.45  3.000
 JUQ  C4   C5   C7   118.43  3.000
 JUQ  C6   C5   C7   123.12  3.000
 JUQ  H16  C6   C5   120.16  3.000
 JUQ  H16  C6   C1   118.92  3.000
 JUQ  C5   C6   C1   120.92  3.000
 JUQ  C28  N11  C12  119.29  3.000
 JUQ  C12  N11  C7   121.63  3.000
 JUQ  C28  N11  C7   117.53  3.000
 JUQ  C15  N14  C13  117.37  3.000
 JUQ  H17  C17  C18  116.78  3.000
 JUQ  H17  C17  C19  116.55  3.000
 JUQ  C18  C17  C19   59.33  3.000
 JUQ  H17  C17  C16  116.83  3.000
 JUQ  C19  C17  C16  116.57  3.000
 JUQ  C18  C17  C16  118.33  3.000
 JUQ  H19  C18  H18  115.40  3.000
 JUQ  H19  C18  C17  116.90  3.000
 JUQ  H18  C18  C17  117.93  3.000
 JUQ  H19  C18  C19  118.12  3.000
 JUQ  H18  C18  C19  116.69  3.000
 JUQ  C17  C18  C19   61.04  3.000
 JUQ  H20  O21  C20  110.02  3.000
 JUQ  C25  N24  C15  118.29  3.000
 JUQ  O26  C25  N24  120.31  3.000
 JUQ  O26  C25  C12  117.45  3.000
 JUQ  N24  C25  C12  122.23  3.000
 JUQ  C25  O26  C27  118.50  3.000
 JUQ  H22  C28  H21  105.69  3.000
 JUQ  H22  C28  C29  109.58  3.000
 JUQ  H21  C28  C29  110.51  3.000
 JUQ  H22  C28  N11  106.97  3.000
 JUQ  H21  C28  N11  110.42  3.000
 JUQ  C29  C28  N11  113.33  3.000
 JUQ  H23  C29  C28  115.60  3.000
 JUQ  H23  C29  C31  115.71  3.000
 JUQ  C28  C29  C31  120.11  3.000
 JUQ  H23  C29  C30  115.43  3.000
 JUQ  C28  C29  C30  118.54  3.000
 JUQ  C31  C29  C30   60.14  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
 JUQ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 JUQ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 JUQ  CONST_03  C7   C5   C6   C1    180.00   0.0  0
 JUQ  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 JUQ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 JUQ  CONST_06  C10  C4   C3   C2    180.00   0.0  0
 JUQ  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 JUQ  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 JUQ  CONST_09  C7   C5   C4   C3    180.00   0.0  0
 JUQ  CONST_10  C9   C10  C4   C3    180.00   0.0  0
 JUQ  CONST_11  C10  C4   C5   C7      0.00   0.0  0
 JUQ  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 JUQ  CONST_13  C6   C5   C7   C8    180.00   0.0  0
 JUQ  CONST_14  C4   C5   C7   C8      0.00   0.0  0
 JUQ  CONST_15  C4   C10  C9   C8      0.00   0.0  0
 JUQ  CONST_16  C5   C4   C10  C9      0.00   0.0  0
 JUQ  CONST_17  C5   C7   C8   C9      0.00   0.0  0
 JUQ  CONST_18  C6   C5   C4   C10   180.00   0.0  0
 JUQ  CONST_19  C15  N14  C13  C12     0.00   0.0  0
 JUQ  CONST_20  C15  N24  C25  C12     0.00   0.0  0
 JUQ  CONST_21  N24  C15  N14  C13     0.00   0.0  0
 JUQ  CONST_22  N24  C25  C12  C13     0.00   0.0  0
 JUQ  CONST_23  C25  C12  C13  N14     0.00   0.0  0
 JUQ  CONST_24  C25  N24  C15  N14     0.00   0.0  0
 JUQ  CONST_25  N11  C7   C8   C9    180.00   0.0  0
 JUQ  CONST_26  C16  C15  N14  C13   180.00   0.0  0
 JUQ  CONST_27  O26  C25  C12  C13   180.00   0.0  0
 JUQ  CONST_28  O26  C25  N24  C15   180.00   0.0  0
 JUQ  CONST_29  C25  N24  C15  C16   180.00   0.0  0
 JUQ  CONST_30  N11  C7   C5   C4    180.00   0.0  0
 JUQ  CONST_31  N11  C7   C5   C6      0.00   0.0  0
 JUQ  CONST_32  N14  C13  C12  N11   180.00   0.0  0
 JUQ  CONST_33  N24  C25  C12  N11   180.00   0.0  0
 JUQ  CONST_34  H3   C3   C2   C1    180.00   0.0  0
 JUQ  CONST_35  H16  C6   C1   C2    180.00   0.0  0
 JUQ  CONST_36  H1   C1   C2   C3    180.00   0.0  0
 JUQ  CONST_37  H6   C10  C4   C3      0.00   0.0  0
 JUQ  CONST_38  H5   C9   C8   C7    180.00   0.0  0
 JUQ  CONST_39  H4   C8   C9   C10   180.00   0.0  0
 JUQ  CONST_40  H7   C13  N14  C15   180.00   0.0  0
 JUQ  CONST_41  H2   C2   C3   C4    180.00   0.0  0
 JUQ  CONST_42  H20  O21  C20  C19   180.00   0.0  0
 JUQ  Var_01    C13  C12  N11  C7    149.57  30.0  2
 JUQ  Var_02    C12  N11  C7   C8    124.52  30.0  2
 JUQ  Var_03    C18  C17  C16  C15   142.68  30.0  1
 JUQ  Var_04    C19  C18  C17  C16   105.73  30.0  1
 JUQ  Var_05    C17  C18  C19  C20   105.81  30.0  1
 JUQ  Var_06    C28  C29  C31  C30  -107.69  30.0  1
 JUQ  Var_07    C17  C16  C15  N14    -5.82  30.0  2
 JUQ  Var_08    C29  C28  N11  C7    127.03  30.0  1
 JUQ  Var_09    N24  C25  O26  C27    -2.35  30.0  1
 JUQ  Var_10    N11  C28  C29  C30  -155.25  30.0  3
 JUQ  Var_11    O22  C20  C19  C17    35.49  30.0  3
 JUQ  Var_12    H9   C27  O26  C25   -59.13  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
 JUQ  chir_01  C19  C18  C17  C20  both
 JUQ  chir_02  C17  C19  C16  C18  both
 JUQ  chir_03  C29  C31  C30  C28  both

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
 JUQ  plan-1  C12  0.020
 JUQ  plan-1  C13  0.020
 JUQ  plan-1  C15  0.020
 JUQ  plan-1  C16  0.020
 JUQ  plan-1  N11  0.020
 JUQ  plan-1  N14  0.020
 JUQ  plan-1  N24  0.020
 JUQ  plan-1  C25  0.020
 JUQ  plan-1  O26  0.020
 JUQ  plan-1  H7   0.020
 JUQ  plan-2  C1   0.020
 JUQ  plan-2  C2   0.020
 JUQ  plan-2  C3   0.020
 JUQ  plan-2  C7   0.020
 JUQ  plan-2  C8   0.020
 JUQ  plan-2  C9   0.020
 JUQ  plan-2  C10  0.020
 JUQ  plan-2  C4   0.020
 JUQ  plan-2  C5   0.020
 JUQ  plan-2  C6   0.020
 JUQ  plan-2  N11  0.020
 JUQ  plan-2  H1   0.020
 JUQ  plan-2  H2   0.020
 JUQ  plan-2  H3   0.020
 JUQ  plan-2  H4   0.020
 JUQ  plan-2  H5   0.020
 JUQ  plan-2  H6   0.020
 JUQ  plan-2  H16  0.020
 JUQ  plan-3  C15  0.020
 JUQ  plan-3  C16  0.020
 JUQ  plan-3  C17  0.020
 JUQ  plan-3  O23  0.020
 JUQ  plan-4  C19  0.020
 JUQ  plan-4  C20  0.020
 JUQ  plan-4  O21  0.020
 JUQ  plan-4  O22  0.020
 JUQ  plan-4  H20  0.020

