# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 20:01:18 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(C1CC1)N2CCCc3ccc(Nc4ccnc(NCC#C)n4)cc23
#
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
 WCV  WCV  cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone  ligand  47  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WCV
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
 WCV  C23  C  CR16  0  -0.026   -7.3655  26.9150  -23.2944
 WCV  C25  C  CR16  0  -0.400   -7.8220  26.4893  -29.2141
 WCV  C26  C  CR6   0   0.323   -7.9811  27.0002  -30.4994
 WCV  C10  C  CR6   0   0.030   -8.0344  28.3814  -30.7042
 WCV  C02  C  C     0   0.562   -7.5069  24.9692  -31.8184
 WCV  C03  C  CH1   0  -0.435   -6.2954  24.6910  -30.9986
 WCV  C04  C  CH2   0  -0.465   -5.3532  23.6241  -31.4821
 WCV  C05  C  CH2   0  -0.466   -6.2095  23.3558  -30.2988
 WCV  C07  C  CH2   0  -0.336   -9.0652  26.6660  -32.6333
 WCV  C08  C  CH2   0  -0.451   -8.4575  27.9546  -33.1627
 WCV  C09  C  CH2   0  -0.481   -8.3578  28.9868  -32.0455
 WCV  C11  C  CR16  0  -0.304   -7.8374  29.2005  -29.5975
 WCV  C12  C  CR16  0  -0.307   -7.6047  28.7085  -28.3255
 WCV  C13  C  CR6   0   0.362   -7.6088  27.3267  -28.1223
 WCV  C15  C  CR6   0   0.564   -7.5254  27.1871  -25.6294
 WCV  C17  C  CR6   0   0.602   -8.0926  28.8457  -24.1882
 WCV  C19  C  CH2   0  -0.431   -8.8054  31.0070  -25.1021
 WCV  C20  C  CSP   0   0.232   -7.5754  31.5356  -25.7010
 WCV  C21  C  CSP1  0  -0.497   -6.5694  31.9733  -26.1922
 WCV  C24  C  CR16  0  -0.465   -7.2021  26.3575  -24.5397
 WCV  N06  N  NT    0  -0.579   -8.1890  26.1354  -31.5934
 WCV  N14  N  NH1   0  -0.780   -7.3829  26.7075  -26.8924
 WCV  N16  N  N     0  -0.517   -7.9669  28.4213  -25.4443
 WCV  N18  N  NH1   0  -0.652   -8.5781  30.0956  -24.0127
 WCV  N22  N  N     0  -0.489   -7.8050  28.1536  -23.0845
 WCV  O01  O  O     0  -0.482   -7.8654  24.1908  -32.6899
 WCV  H1   H  HCR6  0   0.266   -7.1281  26.3349  -22.4091
 WCV  H2   H  HCR6  0   0.285   -7.8731  25.4189  -29.0578
 WCV  H3   H  HCH1  0   0.299   -5.8421  25.5270  -30.4841
 WCV  H4   H  HCH2  0   0.257   -5.5913  23.1237  -32.4105
 WCV  H5   H  HCH2  0   0.262   -4.2998  23.8102  -31.3201
 WCV  H6   H  HCH2  0   0.260   -7.0469  22.6806  -30.4183
 WCV  H7   H  HCH2  0   0.264   -5.7596  23.3467  -29.3147
 WCV  H8   H  HCH2  0   0.250  -10.0586  26.8460  -32.2136
 WCV  H9   H  HCH2  0   0.271   -9.1697  25.9234  -33.4178
 WCV  H10  H  HCH2  0   0.238   -7.4714  27.7318  -33.5771
 WCV  H11  H  HCH2  0   0.247   -9.0647  28.3450  -33.9808
 WCV  H12  H  HCH2  0   0.257   -7.6216  29.7538  -32.2963
 WCV  H13  H  HCH2  0   0.250   -9.3151  29.5094  -31.9561
 WCV  H14  H  HCR6  0   0.249   -7.8586  30.2754  -29.7379
 WCV  H15  H  HCR6  0   0.295   -7.4404  29.3922  -27.5086
 WCV  H16  H  HCH2  0   0.296   -9.4031  31.8360  -24.7223
 WCV  H17  H  HCH2  0   0.279   -9.3993  30.5223  -25.8785
 WCV  H18  H  H     0   0.282   -5.6765  32.3629  -26.6248
 WCV  H19  H  HCR6  0   0.273   -6.8389  25.3478  -24.6683
 WCV  H20  H  HNH1  0   0.411   -7.1427  25.7302  -26.9479
 WCV  H21  H  HNH1  0   0.398   -8.5480  30.4683  -23.0784

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
 WCV  C08  C07  single    1.520  0.020  1.520
 WCV  C08  C09  single    1.524  0.020  1.524
 WCV  O01  C02  double    1.222  0.020  1.222
 WCV  C07  N06  single    1.460  0.020  1.460
 WCV  C09  C10  single    1.507  0.020  1.507
 WCV  C02  N06  single    1.370  0.020  1.370
 WCV  C02  C03  single    1.489  0.020  1.489
 WCV  N06  C26  single    1.410  0.020  1.410
 WCV  C04  C03  single    1.503  0.020  1.503
 WCV  C04  C05  single    1.485  0.020  1.485
 WCV  C03  C05  single    1.510  0.020  1.510
 WCV  C10  C26  aromatic  1.397  0.020  1.397
 WCV  C10  C11  aromatic  1.391  0.020  1.391
 WCV  C26  C25  aromatic  1.392  0.020  1.392
 WCV  C11  C12  aromatic  1.384  0.020  1.384
 WCV  C25  C13  aromatic  1.392  0.020  1.392
 WCV  C12  C13  aromatic  1.397  0.020  1.397
 WCV  C13  N14  single    1.395  0.020  1.395
 WCV  N14  C15  single    1.358  0.020  1.358
 WCV  C21  C20  triple    1.202  0.020  1.202
 WCV  C15  N16  aromatic  1.324  0.020  1.324
 WCV  C15  C24  aromatic  1.407  0.020  1.407
 WCV  C20  C19  single    1.467  0.020  1.467
 WCV  N16  C17  aromatic  1.332  0.020  1.332
 WCV  C19  N18  single    1.438  0.020  1.438
 WCV  C24  C23  aromatic  1.374  0.020  1.374
 WCV  C17  N18  single    1.352  0.020  1.352
 WCV  C17  N22  aromatic  1.334  0.020  1.334
 WCV  C23  N22  aromatic  1.331  0.020  1.331
 WCV  C23  H1   single    0.929  0.020  1.085
 WCV  C25  H2   single    0.929  0.020  1.085
 WCV  C03  H3   single    0.939  0.020  1.096
 WCV  C04  H4   single    0.939  0.020  1.096
 WCV  C04  H5   single    0.939  0.020  1.096
 WCV  C05  H6   single    0.939  0.020  1.096
 WCV  C05  H7   single    0.939  0.020  1.096
 WCV  C07  H8   single    0.939  0.020  1.096
 WCV  C07  H9   single    0.939  0.020  1.096
 WCV  C08  H10  single    0.939  0.020  1.096
 WCV  C08  H11  single    0.939  0.020  1.096
 WCV  C09  H12  single    0.939  0.020  1.096
 WCV  C09  H13  single    0.939  0.020  1.096
 WCV  C11  H14  single    0.929  0.020  1.085
 WCV  C12  H15  single    0.929  0.020  1.085
 WCV  C19  H16  single    0.939  0.020  1.096
 WCV  C19  H17  single    0.939  0.020  1.096
 WCV  C21  H18  single    0.913  0.020  1.066
 WCV  C24  H19  single    0.929  0.020  1.085
 WCV  N14  H20  single    0.868  0.020  1.013
 WCV  N18  H21  single    0.868  0.020  1.013

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
 WCV  H1   C23  N22  116.18  3.000
 WCV  H1   C23  C24  119.78  3.000
 WCV  N22  C23  C24  124.04  3.000
 WCV  H2   C25  C13  119.24  3.000
 WCV  H2   C25  C26  119.38  3.000
 WCV  C13  C25  C26  121.38  3.000
 WCV  N06  C26  C10  119.14  3.000
 WCV  C10  C26  C25  120.16  3.000
 WCV  N06  C26  C25  120.54  3.000
 WCV  C11  C10  C09  120.14  3.000
 WCV  C11  C10  C26  117.39  3.000
 WCV  C09  C10  C26  122.40  3.000
 WCV  O01  C02  N06  120.88  3.000
 WCV  N06  C02  C03  118.28  3.000
 WCV  O01  C02  C03  120.82  3.000
 WCV  H3   C03  C05  116.06  3.000
 WCV  H3   C03  C04  116.04  3.000
 WCV  C05  C03  C04   59.05  3.000
 WCV  H3   C03  C02  117.30  3.000
 WCV  C05  C03  C02  117.82  3.000
 WCV  C04  C03  C02  117.74  3.000
 WCV  H5   C04  H4   115.00  3.000
 WCV  H5   C04  C05  118.24  3.000
 WCV  H4   C04  C05  118.27  3.000
 WCV  H5   C04  C03  116.10  3.000
 WCV  H4   C04  C03  117.82  3.000
 WCV  C05  C04  C03   60.70  3.000
 WCV  H7   C05  H6   114.63  3.000
 WCV  H7   C05  C04  119.11  3.000
 WCV  H6   C05  C04  118.09  3.000
 WCV  H7   C05  C03  116.91  3.000
 WCV  H6   C05  C03  117.16  3.000
 WCV  C04  C05  C03   60.25  3.000
 WCV  H9   C07  H8   107.61  3.000
 WCV  H9   C07  N06  108.91  3.000
 WCV  H8   C07  N06  109.38  3.000
 WCV  H9   C07  C08  111.52  3.000
 WCV  H8   C07  C08  110.94  3.000
 WCV  N06  C07  C08  108.44  3.000
 WCV  H11  C08  H10  106.91  3.000
 WCV  H11  C08  C09  110.10  3.000
 WCV  H10  C08  C09  110.92  3.000
 WCV  H11  C08  C07  110.00  3.000
 WCV  H10  C08  C07  108.67  3.000
 WCV  C09  C08  C07  110.18  3.000
 WCV  H13  C09  H12  105.84  3.000
 WCV  H13  C09  C08  109.03  3.000
 WCV  H12  C09  C08  110.57  3.000
 WCV  H13  C09  C10  107.87  3.000
 WCV  H12  C09  C10  109.99  3.000
 WCV  C08  C09  C10  113.23  3.000
 WCV  H14  C11  C12  118.35  3.000
 WCV  H14  C11  C10  118.56  3.000
 WCV  C12  C11  C10  123.09  3.000
 WCV  H15  C12  C13  121.18  3.000
 WCV  H15  C12  C11  119.80  3.000
 WCV  C13  C12  C11  119.01  3.000
 WCV  N14  C13  C12  124.52  3.000
 WCV  N14  C13  C25  116.68  3.000
 WCV  C12  C13  C25  118.78  3.000
 WCV  N16  C15  N14  119.62  3.000
 WCV  N16  C15  C24  121.20  3.000
 WCV  N14  C15  C24  119.19  3.000
 WCV  N22  C17  N18  116.71  3.000
 WCV  N22  C17  N16  126.49  3.000
 WCV  N18  C17  N16  116.79  3.000
 WCV  H17  C19  H16  106.69  3.000
 WCV  H17  C19  N18  110.09  3.000
 WCV  H16  C19  N18  107.73  3.000
 WCV  H17  C19  C20  109.03  3.000
 WCV  H16  C19  C20  109.14  3.000
 WCV  N18  C19  C20  113.90  3.000
 WCV  C21  C20  C19  180.00  3.000
 WCV  H18  C21  C20  180.00  3.000
 WCV  H19  C24  C15  122.41  3.000
 WCV  H19  C24  C23  121.79  3.000
 WCV  C15  C24  C23  115.80  3.000
 WCV  C07  N06  C02  119.44  3.000
 WCV  C02  N06  C26  125.19  3.000
 WCV  C07  N06  C26  114.73  3.000
 WCV  H20  N14  C15  114.74  3.000
 WCV  H20  N14  C13  114.85  3.000
 WCV  C15  N14  C13  130.22  3.000
 WCV  C17  N16  C15  117.41  3.000
 WCV  H21  N18  C19  118.25  3.000
 WCV  H21  N18  C17  116.87  3.000
 WCV  C19  N18  C17  122.96  3.000
 WCV  C17  N22  C23  115.06  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
 WCV  CONST_01  N16  C15  C24  C23     0.00   0.0  0
 WCV  CONST_02  N16  C17  N22  C23     0.00   0.0  0
 WCV  CONST_03  C11  C10  C26  C25     0.00   0.0  0
 WCV  CONST_04  C11  C12  C13  C25     0.00   0.0  0
 WCV  CONST_05  C12  C11  C10  C26     0.00   0.0  0
 WCV  CONST_06  C12  C13  C25  C26     0.00   0.0  0
 WCV  CONST_07  C13  C25  C26  C10     0.00   0.0  0
 WCV  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 WCV  CONST_09  N22  C17  N16  C15     0.00   0.0  0
 WCV  CONST_10  N22  C23  C24  C15     0.00   0.0  0
 WCV  CONST_11  C24  C15  N16  C17     0.00   0.0  0
 WCV  CONST_12  C24  C23  N22  C17     0.00   0.0  0
 WCV  CONST_13  N14  C15  C24  C23   180.00   0.0  0
 WCV  CONST_14  N18  C17  N22  C23   180.00   0.0  0
 WCV  CONST_15  N14  C13  C25  C26   180.00   0.0  0
 WCV  CONST_16  N14  C13  C12  C11   180.00   0.0  0
 WCV  CONST_17  N18  C17  N16  C15   180.00   0.0  0
 WCV  CONST_18  N14  C15  N16  C17   180.00   0.0  0
 WCV  CONST_19  C03  C02  N06  C26     0.00   0.0  0
 WCV  CONST_21  H15  C12  C13  C25   180.00   0.0  0
 WCV  CONST_22  H14  C11  C10  C26   180.00   0.0  0
 WCV  CONST_23  H2   C25  C26  C10   180.00   0.0  0
 WCV  CONST_24  H1   C23  C24  C15   180.00   0.0  0
 WCV  CONST_25  H19  C24  C15  N16   180.00   0.0  0
 WCV  CONST_26  O01  C02  N06  C26   180.00   0.0  0
 WCV  CONST_28  N16  C17  N18  C19     0.00   0.0  0
 WCV  CONST_29  N22  C17  N18  C19   180.00   0.0  0
 WCV  CONST_30  H21  N18  C17  N16   180.00   0.0  0
 WCV  Var_01    C07  N06  C26  C25   145.81  30.0  1
 WCV  Var_02    C08  C07  N06  C26    59.22  30.0  1
 WCV  Var_03    C08  C09  C10  C26    -6.57  30.0  1
 WCV  Var_04    C07  C08  C09  C10    35.64  30.0  1
 WCV  Var_05    N06  C07  C08  C09   -61.54  30.0  1
 WCV  Var_06    C15  N14  C13  C25  -158.63  30.0  2
 WCV  Var_07    C05  C04  C03  C02  -107.43  30.0  1
 WCV  Var_08    N06  C02  C03  C04  -163.87  30.0  1
 WCV  Var_09    N16  C15  N14  C13     1.41  30.0  2
 WCV  Var_10    H6   C05  C04  C03   106.91  30.0  1
 WCV  Var_11    C20  C19  N18  C17   -71.66  30.0  1
 WCV  Var_12    N18  C19  C20  C21  -138.84  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
 WCV  chir_01  C03  C02  C04  C05  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
 WCV  plan-1  C23  0.020
 WCV  plan-1  C15  0.020
 WCV  plan-1  C17  0.020
 WCV  plan-1  C24  0.020
 WCV  plan-1  N14  0.020
 WCV  plan-1  N16  0.020
 WCV  plan-1  N18  0.020
 WCV  plan-1  N22  0.020
 WCV  plan-1  H1   0.020
 WCV  plan-1  H19  0.020
 WCV  plan-2  C25  0.020
 WCV  plan-2  C26  0.020
 WCV  plan-2  C10  0.020
 WCV  plan-2  C09  0.020
 WCV  plan-2  C11  0.020
 WCV  plan-2  C12  0.020
 WCV  plan-2  C13  0.020
 WCV  plan-2  N06  0.020
 WCV  plan-2  N14  0.020
 WCV  plan-2  H2   0.020
 WCV  plan-2  H14  0.020
 WCV  plan-2  H15  0.020
 WCV  plan-3  C26  0.020
 WCV  plan-3  C02  0.020
 WCV  plan-3  C03  0.020
 WCV  plan-3  C07  0.020
 WCV  plan-3  N06  0.020
 WCV  plan-3  O01  0.020
 WCV  plan-4  C17  0.020
 WCV  plan-4  C19  0.020
 WCV  plan-4  N18  0.020
 WCV  plan-4  H21  0.020

