# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 07:21:21 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (1S,2S)-N-{4-[(1S)-1-(propanoylamino)ethyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@@H](C)c1ccc(NC(=O)[C@H]2C[C@@H]2c3cccnc3)cc1
#
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
 CVJ  CVJ  (1S,2S)-N-{4-[(1S)-1-(propanoylamino)ethyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide  ligand  48  25  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CVJ
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
 CVJ  C1   C  CR16  0  -0.336  -1.0469   0.0428   1.6098
 CVJ  C2   C  CR6   0   0.362  -0.3520  -0.0260   0.4015
 CVJ  C3   C  CR16  0  -0.300  -1.0215   0.3104  -0.7761
 CVJ  C11  C  C     0   0.561  -6.5348   0.0097  -0.2864
 CVJ  C12  C  CH2   0  -0.574  -7.2684  -1.3162  -0.2510
 CVJ  C14  C  CH3   0  -0.659  -8.3015  -1.4588  -1.3557
 CVJ  C15  C  C     0   0.605   1.8369  -0.7467  -0.5378
 CVJ  C16  C  CH1   0  -0.429   3.2099  -1.0885  -0.0757
 CVJ  C18  C  CH1   0  -0.355   4.3626  -0.6962  -0.9804
 CVJ  C19  C  CR6   0   0.125   5.6070  -0.1415  -0.4010
 CVJ  C20  C  CR16  0  -0.207   6.2518   0.9263  -1.0168
 CVJ  C21  C  CR16  0  -0.313   7.4132   1.4377  -0.4606
 CVJ  C22  C  CR16  0  -0.079   7.8966   0.8641   0.7046
 CVJ  C24  C  CR16  0  -0.135   6.1873  -0.6394   0.7650
 CVJ  C25  C  CH2   0  -0.449   3.9798  -2.1287  -0.8319
 CVJ  C4   C  CR16  0  -0.290  -2.3504   0.7035  -0.7194
 CVJ  C5   C  CR6   0   0.103  -3.0498   0.7813   0.4797
 CVJ  C6   C  CR16  0  -0.289  -2.3720   0.4400   1.6457
 CVJ  C7   C  CH1   0  -0.147  -4.5053   1.1899   0.4797
 CVJ  N8   N  NH1   0  -0.759   0.9924  -0.4047   0.4673
 CVJ  N9   N  NH1   0  -0.631  -5.3231  -0.0005   0.2971
 CVJ  C10  C  CH3   0  -0.663  -4.9265   1.9757   1.7173
 CVJ  O13  O  O     0  -0.507  -7.0180   1.0145  -0.7910
 CVJ  O17  O  O     0  -0.474   1.5232  -0.7734  -1.7163
 CVJ  N23  N  N     0  -0.397   7.2959  -0.1560   1.3076
 CVJ  H1   H  HCR6  0   0.270  -0.5445  -0.2141   2.5349
 CVJ  H2   H  HCR6  0   0.278  -0.5215   0.2760  -1.7298
 CVJ  H3   H  HCH2  0   0.252  -6.5524  -2.1402  -0.2884
 CVJ  H4   H  HCH2  0   0.269  -7.7555  -1.3884   0.7269
 CVJ  H5   H  HCH3  0   0.229  -9.0494  -0.6694  -1.3084
 CVJ  H6   H  HCH3  0   0.227  -7.8390  -1.4254  -2.3422
 CVJ  H7   H  HCH3  0   0.234  -8.8186  -2.4136  -1.2661
 CVJ  H8   H  HCH1  0   0.294   3.3973  -1.0227   0.9909
 CVJ  H9   H  HCH1  0   0.279   4.0642  -0.2299  -1.9129
 CVJ  H10  H  HCR6  0   0.269   5.8482   1.3545  -1.9264
 CVJ  H11  H  HCR6  0   0.271   7.9350   2.2656  -0.9206
 CVJ  H12  H  HCR6  0   0.263   8.8012   1.2402   1.1686
 CVJ  H13  H  HCR6  0   0.256   5.7323  -1.4732   1.2917
 CVJ  H14  H  HCH2  0   0.274   4.6221  -2.7798  -0.2528
 CVJ  H15  H  HCH2  0   0.276   3.4898  -2.6025  -1.6724
 CVJ  H16  H  HCR6  0   0.255  -2.8494   0.9651  -1.6453
 CVJ  H17  H  HCR6  0   0.256  -2.8706   0.4849   2.6053
 CVJ  H18  H  HCH1  0   0.258  -4.6687   1.8250  -0.3936
 CVJ  H19  H  HNH1  0   0.418   1.3644  -0.4738   1.4023
 CVJ  H20  H  HNH1  0   0.398  -5.0005  -0.8563   0.7208
 CVJ  H21  H  HCH3  0   0.229  -4.8845   1.3669   2.6208
 CVJ  H22  H  HCH3  0   0.236  -4.2847   2.8452   1.8607
 CVJ  H23  H  HCH3  0   0.244  -5.9511   2.3285   1.6051

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
 CVJ  C24  N23  aromatic  1.326  0.020  1.326
 CVJ  C24  C19  aromatic  1.394  0.020  1.394
 CVJ  N23  C22  aromatic  1.329  0.020  1.329
 CVJ  C25  C18  single    1.490  0.020  1.490
 CVJ  C25  C16  single    1.499  0.020  1.499
 CVJ  C18  C19  single    1.481  0.020  1.481
 CVJ  C18  C16  single    1.517  0.020  1.517
 CVJ  C19  C20  aromatic  1.391  0.020  1.391
 CVJ  C22  C21  aromatic  1.386  0.020  1.386
 CVJ  O17  C15  double    1.220  0.020  1.220
 CVJ  C16  C15  single    1.488  0.020  1.488
 CVJ  C20  C21  aromatic  1.386  0.020  1.386
 CVJ  C15  N8   single    1.357  0.020  1.357
 CVJ  N8   C2   single    1.398  0.020  1.398
 CVJ  C3   C2   aromatic  1.396  0.020  1.396
 CVJ  C3   C4   aromatic  1.387  0.020  1.387
 CVJ  C2   C1   aromatic  1.396  0.020  1.396
 CVJ  C4   C5   aromatic  1.390  0.020  1.390
 CVJ  C1   C6   aromatic  1.384  0.020  1.384
 CVJ  C5   C6   aromatic  1.391  0.020  1.391
 CVJ  C5   C7   single    1.512  0.020  1.512
 CVJ  C10  C7   single    1.525  0.020  1.525
 CVJ  C7   N9   single    1.456  0.020  1.456
 CVJ  N9   C11  single    1.345  0.020  1.345
 CVJ  O13  C11  double    1.224  0.020  1.224
 CVJ  C11  C12  single    1.516  0.020  1.516
 CVJ  C12  C14  single    1.519  0.020  1.519
 CVJ  C1   H1   single    0.930  0.020  1.080
 CVJ  C3   H2   single    0.930  0.020  1.080
 CVJ  C12  H3   single    0.970  0.020  1.090
 CVJ  C12  H4   single    0.970  0.020  1.090
 CVJ  C14  H5   single    0.970  0.020  1.090
 CVJ  C14  H6   single    0.970  0.020  1.090
 CVJ  C14  H7   single    0.970  0.020  1.090
 CVJ  C16  H8   single    0.970  0.020  1.090
 CVJ  C18  H9   single    0.970  0.020  1.090
 CVJ  C20  H10  single    0.930  0.020  1.080
 CVJ  C21  H11  single    0.930  0.020  1.080
 CVJ  C22  H12  single    0.930  0.020  1.080
 CVJ  C24  H13  single    0.930  0.020  1.080
 CVJ  C25  H14  single    0.970  0.020  1.090
 CVJ  C25  H15  single    0.970  0.020  1.090
 CVJ  C4   H16  single    0.930  0.020  1.080
 CVJ  C6   H17  single    0.930  0.020  1.080
 CVJ  C7   H18  single    0.970  0.020  1.090
 CVJ  N8   H19  single    0.860  0.020  1.020
 CVJ  N9   H20  single    0.860  0.020  1.020
 CVJ  C10  H21  single    0.970  0.020  1.090
 CVJ  C10  H22  single    0.970  0.020  1.090
 CVJ  C10  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
 CVJ  H1   C1   C6   119.33  3.000
 CVJ  H1   C1   C2   119.78  3.000
 CVJ  C6   C1   C2   120.89  3.000
 CVJ  N8   C2   C3   124.49  3.000
 CVJ  C3   C2   C1   118.67  3.000
 CVJ  N8   C2   C1   116.83  3.000
 CVJ  H2   C3   C4   119.33  3.000
 CVJ  H2   C3   C2   121.10  3.000
 CVJ  C4   C3   C2   119.57  3.000
 CVJ  O13  C11  N9   122.74  3.000
 CVJ  O13  C11  C12  122.47  3.000
 CVJ  N9   C11  C12  114.79  3.000
 CVJ  H4   C12  H3   105.81  3.000
 CVJ  H4   C12  C14  109.92  3.000
 CVJ  H3   C12  C14  110.50  3.000
 CVJ  H4   C12  C11  107.09  3.000
 CVJ  H3   C12  C11  109.99  3.000
 CVJ  C14  C12  C11  113.22  3.000
 CVJ  H7   C14  H6   107.61  3.000
 CVJ  H7   C14  H5   107.81  3.000
 CVJ  H6   C14  H5   107.98  3.000
 CVJ  H7   C14  C12  110.20  3.000
 CVJ  H6   C14  C12  111.51  3.000
 CVJ  H5   C14  C12  111.57  3.000
 CVJ  O17  C15  N8   124.14  3.000
 CVJ  N8   C15  C16  113.71  3.000
 CVJ  O17  C15  C16  122.15  3.000
 CVJ  H8   C16  C25  116.70  3.000
 CVJ  H8   C16  C18  116.07  3.000
 CVJ  C25  C16  C18   59.22  3.000
 CVJ  H8   C16  C15  116.78  3.000
 CVJ  C18  C16  C15  117.15  3.000
 CVJ  C25  C16  C15  118.46  3.000
 CVJ  H9   C18  C25  115.36  3.000
 CVJ  H9   C18  C19  114.00  3.000
 CVJ  C25  C18  C19  122.48  3.000
 CVJ  H9   C18  C16  114.52  3.000
 CVJ  C19  C18  C16  120.14  3.000
 CVJ  C25  C18  C16   59.78  3.000
 CVJ  C24  C19  C20  116.83  3.000
 CVJ  C20  C19  C18  120.26  3.000
 CVJ  C24  C19  C18  122.91  3.000
 CVJ  H10  C20  C21  120.23  3.000
 CVJ  H10  C20  C19  120.16  3.000
 CVJ  C21  C20  C19  119.62  3.000
 CVJ  H11  C21  C22  120.42  3.000
 CVJ  H11  C21  C20  121.09  3.000
 CVJ  C22  C21  C20  118.50  3.000
 CVJ  H12  C22  N23  116.71  3.000
 CVJ  H12  C22  C21  120.49  3.000
 CVJ  N23  C22  C21  122.80  3.000
 CVJ  H13  C24  N23  115.58  3.000
 CVJ  H13  C24  C19  120.35  3.000
 CVJ  N23  C24  C19  124.07  3.000
 CVJ  H15  C25  H14  114.88  3.000
 CVJ  H15  C25  C18  117.38  3.000
 CVJ  H14  C25  C18  118.63  3.000
 CVJ  H15  C25  C16  117.59  3.000
 CVJ  H14  C25  C16  116.89  3.000
 CVJ  C18  C25  C16   60.99  3.000
 CVJ  H16  C4   C5   119.45  3.000
 CVJ  H16  C4   C3   118.33  3.000
 CVJ  C5   C4   C3   122.21  3.000
 CVJ  C7   C5   C6   122.37  3.000
 CVJ  C7   C5   C4   119.97  3.000
 CVJ  C6   C5   C4   117.64  3.000
 CVJ  H17  C6   C5   120.56  3.000
 CVJ  H17  C6   C1   118.43  3.000
 CVJ  C5   C6   C1   121.01  3.000
 CVJ  H18  C7   C10  107.94  3.000
 CVJ  H18  C7   N9   106.92  3.000
 CVJ  C10  C7   N9   111.59  3.000
 CVJ  H18  C7   C5   107.53  3.000
 CVJ  N9   C7   C5   108.66  3.000
 CVJ  C10  C7   C5   113.90  3.000
 CVJ  H19  N8   C15  116.10  3.000
 CVJ  H19  N8   C2   114.64  3.000
 CVJ  C15  N8   C2   129.19  3.000
 CVJ  H20  N9   C7   117.49  3.000
 CVJ  H20  N9   C11  118.50  3.000
 CVJ  C7   N9   C11  123.67  3.000
 CVJ  H23  C10  H22  108.00  3.000
 CVJ  H23  C10  H21  107.60  3.000
 CVJ  H22  C10  H21  108.29  3.000
 CVJ  H23  C10  C7   110.06  3.000
 CVJ  H22  C10  C7   110.79  3.000
 CVJ  H21  C10  C7   111.96  3.000
 CVJ  C24  N23  C22  118.19  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
 CVJ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 CVJ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 CVJ  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 CVJ  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 CVJ  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 CVJ  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 CVJ  CONST_07  C22  N23  C24  C19     0.00   0.0  0
 CVJ  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 CVJ  CONST_09  N23  C24  C19  C20     0.00   0.0  0
 CVJ  CONST_10  N23  C22  C21  C20     0.00   0.0  0
 CVJ  CONST_11  C24  N23  C22  C21     0.00   0.0  0
 CVJ  CONST_12  C24  C19  C20  C21     0.00   0.0  0
 CVJ  CONST_13  N23  C24  C19  C18   180.00   0.0  0
 CVJ  CONST_14  C21  C20  C19  C18   180.00   0.0  0
 CVJ  CONST_15  C7   C5   C6   C1    180.00   0.0  0
 CVJ  CONST_16  C7   C5   C4   C3    180.00   0.0  0
 CVJ  CONST_17  N8   C2   C3   C4    180.00   0.0  0
 CVJ  CONST_18  N8   C2   C1   C6    180.00   0.0  0
 CVJ  CONST_19  H2   C3   C2   C1    180.00   0.0  0
 CVJ  CONST_20  H16  C4   C3   C2    180.00   0.0  0
 CVJ  CONST_21  H17  C6   C1   C2    180.00   0.0  0
 CVJ  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 CVJ  CONST_23  H13  C24  C19  C18     0.00   0.0  0
 CVJ  CONST_24  H10  C20  C19  C18     0.00   0.0  0
 CVJ  CONST_25  H11  C21  C20  C19   180.00   0.0  0
 CVJ  CONST_26  H12  C22  C21  C20   180.00   0.0  0
 CVJ  CONST_27  C16  C15  N8   C2    180.00   0.0  0
 CVJ  CONST_28  C15  N8   C2   C1    180.00   0.0  0
 CVJ  CONST_29  C15  N8   C2   C3      0.00   0.0  0
 CVJ  CONST_30  H19  N8   C2   C1      0.00   0.0  0
 CVJ  CONST_31  O17  C15  N8   C2      0.00   0.0  0
 CVJ  CONST_32  C7   N9   C11  C12   180.00   0.0  0
 CVJ  CONST_33  O13  C11  N9   C7      0.00   0.0  0
 CVJ  CONST_34  H20  N9   C11  C12     0.00   0.0  0
 CVJ  Var_01    C19  C18  C25  C16   108.55  30.0  1
 CVJ  Var_02    C24  C19  C18  C16    41.03  30.0  2
 CVJ  Var_03    C18  C25  C16  C15   106.34  30.0  1
 CVJ  Var_04    O17  C15  C16  C18    34.89  30.0  3
 CVJ  Var_05    N9   C11  C12  C14  -155.99  30.0  1
 CVJ  Var_06    H5   C14  C12  C11   -58.56  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
 CVJ  chir_03  C7   C5   C10  N9   positiv
 CVJ  chir_04  C16  C25  C18  C15  both
 CVJ  chir_05  C18  C16  C19  C25  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
 CVJ  plan-1  C1   0.020
 CVJ  plan-1  C2   0.020
 CVJ  plan-1  C3   0.020
 CVJ  plan-1  C4   0.020
 CVJ  plan-1  C5   0.020
 CVJ  plan-1  C6   0.020
 CVJ  plan-1  C7   0.020
 CVJ  plan-1  N8   0.020
 CVJ  plan-1  H1   0.020
 CVJ  plan-1  H2   0.020
 CVJ  plan-1  H16  0.020
 CVJ  plan-1  H17  0.020
 CVJ  plan-2  C18  0.020
 CVJ  plan-2  C19  0.020
 CVJ  plan-2  C20  0.020
 CVJ  plan-2  C21  0.020
 CVJ  plan-2  C22  0.020
 CVJ  plan-2  C24  0.020
 CVJ  plan-2  N23  0.020
 CVJ  plan-2  H10  0.020
 CVJ  plan-2  H11  0.020
 CVJ  plan-2  H12  0.020
 CVJ  plan-2  H13  0.020
 CVJ  plan-3  C2   0.020
 CVJ  plan-3  C15  0.020
 CVJ  plan-3  C16  0.020
 CVJ  plan-3  N8   0.020
 CVJ  plan-3  O17  0.020
 CVJ  plan-3  H19  0.020
 CVJ  plan-4  C11  0.020
 CVJ  plan-4  C12  0.020
 CVJ  plan-4  C7   0.020
 CVJ  plan-4  N9   0.020
 CVJ  plan-4  O13  0.020
 CVJ  plan-4  H20  0.020

