# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 08:14:47 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: N-[(2R,3S)-1-[N-(cyclopentylcarbamoyl)-L-valyl]-2-(1-formylcyclobutyl)pyrrolidin-3-yl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)NC1CCCC1)C(=O)N2CC[C@H](NC(=O)C3CC3)[C@H]2C4(CCC4)C=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
 CPX  CPX  N-[(2R,3S)-1-[N-(cyclopentylcarbamoyl)-L-valyl]-2-(1-formylcyclobutyl)pyrrolidin-3-yl]cyclopropanecarboxamide  ligand  70  32  .  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_CPX
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
 CPX  O27   O  O     0  -0.534  -2.4230   0.9365   0.7442
 CPX  C17   C  CH2   0  -0.467   5.3051   4.2035  -1.0126
 CPX  C16   C  CH2   0  -0.466   5.7648   3.1127  -1.9089
 CPX  C12   C  CH1   0  -0.426   4.3688   3.0717  -1.3453
 CPX  C26   C  C     0   0.741  -3.1939   0.0885   0.3040
 CPX  N4    N  NH1   0  -0.690  -4.2337   0.3764  -0.5156
 CPX  C29   C  CH1   0  -0.057  -4.6569   1.7225  -0.8132
 CPX  C30   C  CH2   0  -0.456  -5.3018   1.8351  -2.2032
 CPX  C32   C  CH2   0  -0.447  -6.2880   3.0179  -2.1102
 CPX  C31   C  CH2   0  -0.456  -6.2262   3.5064  -0.6504
 CPX  C28   C  CH2   0  -0.438  -5.7149   2.3008   0.1286
 CPX  N3    N  NH1   0  -0.683  -3.0585  -1.2356   0.6153
 CPX  C13   C  CH1   0  -0.145  -1.8548  -1.6945   1.2676
 CPX  C19   C  CH1   0  -0.264  -1.9853  -3.1917   1.5929
 CPX  C22   C  CH3   0  -0.675  -0.6842  -3.7505   2.1555
 CPX  C18   C  CH3   0  -0.654  -3.1292  -3.4262   2.5752
 CPX  C14   C  C     0   0.560  -0.6546  -1.4506   0.3461
 CPX  O15   O  O     0  -0.489  -0.7150  -1.8519  -0.8078
 CPX  N2    N  NR5   0  -0.486   0.4441  -0.8357   0.8297
 CPX  C6    C  CR15  0  -0.050   1.5693  -0.5437  -0.0660
 CPX  C8    C  CR15  0  -0.119   2.3092   0.6224   0.6326
 CPX  C9    C  CH2   0  -0.443   1.2830   1.1946   1.6055
 CPX  C7    C  CH2   0  -0.304   0.5126  -0.0324   2.0508
 CPX  N1    N  NH1   0  -0.659   2.8238   1.5785  -0.3100
 CPX  C10   C  C     0   0.606   4.0784   2.0708  -0.2849
 CPX  O11   O  O     0  -0.505   4.9185   1.7206   0.5343
 CPX  C25   C  C     0  -0.189   2.4652  -1.7541  -0.3391
 CPX  C24   C  C1    0   0.204   2.7981  -2.4636   0.9406
 CPX  O5    O  O     0  -0.376   2.8544  -3.6603   1.0795
 CPX  C23   C  C     0  -0.408   2.1246  -2.7212  -1.4896
 CPX  C21   C  C     0  -0.449   3.6116  -2.7577  -1.8801
 CPX  C20   C  C     0  -0.443   3.8109  -1.4610  -1.0792
 CPX  H172  H  HCH2  0   0.257   5.7035   4.2384  -0.0072
 CPX  H161  H  HCH2  0   0.257   6.4759   2.3984  -1.5151
 CPX  H162  H  HCH2  0   0.263   5.8587   3.3127  -2.9678
 CPX  H12   H  HCH1  0   0.278   3.5603   3.2961  -2.0318
 CPX  HN4   H  HNH1  0   0.385  -4.8940  -0.3573  -0.7245
 CPX  H29   H  HCH1  0   0.246  -3.7737   2.3626  -0.7748
 CPX  H301  H  HCH2  0   0.241  -4.5510   1.9686  -2.9824
 CPX  H302  H  HCH2  0   0.229  -5.8348   0.9103  -2.4387
 CPX  H321  H  HCH2  0   0.232  -6.0424   3.8154  -2.8116
 CPX  H322  H  HCH2  0   0.229  -7.2976   2.6866  -2.3561
 CPX  H311  H  HCH2  0   0.223  -5.5125   4.3293  -0.5584
 CPX  H312  H  HCH2  0   0.234  -7.1872   3.8732  -0.2891
 CPX  H281  H  HCH2  0   0.217  -6.5146   1.5665   0.2714
 CPX  H282  H  HCH2  0   0.235  -5.3112   2.5509   1.1110
 CPX  HN3   H  HNH1  0   0.388  -3.5213  -1.9053   0.0184
 CPX  H13   H  HCH1  0   0.258  -1.7550  -1.1681   2.2171
 CPX  H19   H  HCH1  0   0.234  -2.2091  -3.7179   0.6578
 CPX  H221  H  HCH3  0   0.240  -0.8194  -4.7880   2.4624
 CPX  H222  H  HCH3  0   0.242   0.1253  -3.7358   1.4280
 CPX  H223  H  HCH3  0   0.222  -0.3599  -3.1884   3.0343
 CPX  H181  H  HCH3  0   0.220  -2.9137  -2.9558   3.5376
 CPX  H182  H  HCH3  0   0.234  -4.0768  -3.0281   2.2142
 CPX  H183  H  HCH3  0   0.234  -3.2655  -4.4936   2.7520
 CPX  H6    H  HCR5  0   0.267   1.1809  -0.1939  -1.0288
 CPX  H8    H  HCR5  0   0.269   3.1641   0.2462   1.1955
 CPX  H91   H  HCH2  0   0.246   0.6091   1.8791   1.0835
 CPX  H92   H  HCH2  0   0.261   1.7465   1.7317   2.4319
 CPX  H71   H  HCH2  0   0.273  -0.4747   0.2272   2.4159
 CPX  H72   H  HCH2  0   0.245   1.0372  -0.5741   2.8426
 CPX  HN1   H  HNH1  0   0.400   2.1769   1.9541  -0.9864
 CPX  H24   H  H     0   0.199   3.0512  -1.8042   1.7927
 CPX  H231  H  H     0   0.235   1.6325  -3.6569  -1.2286
 CPX  H232  H  H     0   0.240   1.5279  -2.2132  -2.2457
 CPX  H211  H  H     0   0.233   4.1422  -3.6043  -1.4447
 CPX  H212  H  H     0   0.236   3.8459  -2.7129  -2.9429
 CPX  H201  H  H     0   0.251   3.7078  -0.5802  -1.7137
 CPX  H202  H  H     0   0.249   4.7104  -1.3471  -0.4720
 CPX  H171  H  HCH2  0   0.262   5.0743   5.1685  -1.4435

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
 CPX  O27  C26   double  1.228  0.020  1.228
 CPX  C17  C16   single  1.485  0.020  1.485
 CPX  C17  C12   single  1.506  0.020  1.506
 CPX  C17  H171  single  0.970  0.020  1.090
 CPX  C17  H172  single  0.970  0.020  1.090
 CPX  C16  C12   single  1.506  0.020  1.506
 CPX  C16  H161  single  0.970  0.020  1.090
 CPX  C16  H162  single  0.970  0.020  1.090
 CPX  C12  C10   single  1.487  0.020  1.487
 CPX  C12  H12   single  0.970  0.020  1.090
 CPX  C26  N4    single  1.355  0.020  1.355
 CPX  C26  N3    single  1.367  0.020  1.367
 CPX  N4   C29   single  1.442  0.020  1.442
 CPX  N4   HN4   single  0.860  0.020  1.020
 CPX  C29  C30   single  1.536  0.020  1.536
 CPX  C29  C28   single  1.530  0.020  1.530
 CPX  C29  H29   single  0.970  0.020  1.090
 CPX  C30  C32   single  1.543  0.020  1.543
 CPX  C30  H301  single  0.970  0.020  1.090
 CPX  C30  H302  single  0.970  0.020  1.090
 CPX  C32  C31   single  1.541  0.020  1.541
 CPX  C32  H321  single  0.970  0.020  1.090
 CPX  C32  H322  single  0.970  0.020  1.090
 CPX  C31  C28   single  1.524  0.020  1.524
 CPX  C31  H311  single  0.970  0.020  1.090
 CPX  C31  H312  single  0.970  0.020  1.090
 CPX  C28  H281  single  0.970  0.020  1.090
 CPX  C28  H282  single  0.970  0.020  1.090
 CPX  N3   C13   single  1.444  0.020  1.444
 CPX  N3   HN3   single  0.890  0.020  1.040
 CPX  C13  C19   single  1.538  0.020  1.538
 CPX  C13  C14   single  1.533  0.020  1.533
 CPX  C13  H13   single  0.970  0.020  1.090
 CPX  C19  C22   single  1.524  0.020  1.524
 CPX  C19  C18   single  1.526  0.020  1.526
 CPX  C19  H19   single  0.970  0.020  1.090
 CPX  C22  H221  single  0.970  0.020  1.090
 CPX  C22  H222  single  0.970  0.020  1.090
 CPX  C22  H223  single  0.970  0.020  1.090
 CPX  C18  H181  single  0.970  0.020  1.090
 CPX  C18  H182  single  0.970  0.020  1.090
 CPX  C18  H183  single  0.970  0.020  1.090
 CPX  C14  O15   double  1.223  0.020  1.223
 CPX  C14  N2    single  1.349  0.020  1.349
 CPX  N2   C6    single  1.467  0.020  1.467
 CPX  N2   C7    single  1.463  0.020  1.463
 CPX  C6   C8    single  1.548  0.020  1.548
 CPX  C6   C25   single  1.530  0.020  1.530
 CPX  C6   H6    single  0.970  0.020  1.090
 CPX  C8   C9    single  1.526  0.020  1.526
 CPX  C8   N1    single  1.438  0.020  1.438
 CPX  C8   H8    single  0.970  0.020  1.090
 CPX  C9   C7    single  1.516  0.020  1.516
 CPX  C9   H91   single  0.970  0.020  1.090
 CPX  C9   H92   single  0.970  0.020  1.090
 CPX  C7   H71   single  0.970  0.020  1.090
 CPX  C7   H72   single  0.970  0.020  1.090
 CPX  N1   C10   single  1.348  0.020  1.348
 CPX  N1   HN1   single  0.860  0.020  1.020
 CPX  C10  O11   double  1.225  0.020  1.225
 CPX  C25  C24   single  1.501  0.020  1.501
 CPX  C25  C23   single  1.541  0.020  1.541
 CPX  C25  C20   single  1.564  0.020  1.564
 CPX  C24  O5    double  1.206  0.020  1.206
 CPX  C24  H24   single  0.930  0.020  1.080
 CPX  C23  C21   single  1.538  0.020  1.538
 CPX  C23  H231  single  0.970  0.020  1.090
 CPX  C23  H232  single  0.970  0.020  1.090
 CPX  C21  C20   single  1.537  0.020  1.537
 CPX  C21  H211  single  0.970  0.020  1.090
 CPX  C21  H212  single  0.970  0.020  1.090
 CPX  C20  H201  single  0.970  0.020  1.090
 CPX  C20  H202  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
 CPX  H172  C17  H171  114.83  3.000
 CPX  H172  C17  C12   117.29  3.000
 CPX  H171  C17  C12   116.72  3.000
 CPX  H172  C17  C16   118.08  3.000
 CPX  H171  C17  C16   118.75  3.000
 CPX  C12   C17  C16    60.47  3.000
 CPX  H162  C16  H161  114.91  3.000
 CPX  H162  C16  C12   116.86  3.000
 CPX  H161  C16  C12   117.07  3.000
 CPX  H162  C16  C17   118.81  3.000
 CPX  H161  C16  C17   117.95  3.000
 CPX  C12   C16  C17    60.47  3.000
 CPX  H12   C12  C10   116.44  3.000
 CPX  H12   C12  C16   116.66  3.000
 CPX  C10   C12  C16   117.79  3.000
 CPX  H12   C12  C17   116.62  3.000
 CPX  C10   C12  C17   118.02  3.000
 CPX  C16   C12  C17    59.06  3.000
 CPX  N3    C26  N4    114.81  3.000
 CPX  N3    C26  O27   121.68  3.000
 CPX  N4    C26  O27   123.51  3.000
 CPX  HN4   N4   C29   116.36  3.000
 CPX  HN4   N4   C26   118.23  3.000
 CPX  C29   N4   C26   123.26  3.000
 CPX  H29   C29  C28   108.44  3.000
 CPX  H29   C29  C30   109.18  3.000
 CPX  C28   C29  C30   103.82  3.000
 CPX  H29   C29  N4    107.62  3.000
 CPX  C28   C29  N4    115.39  3.000
 CPX  C30   C29  N4    112.23  3.000
 CPX  H302  C30  H301  106.58  3.000
 CPX  H302  C30  C32   110.49  3.000
 CPX  H301  C30  C32   112.92  3.000
 CPX  H302  C30  C29   109.73  3.000
 CPX  H301  C30  C29   111.49  3.000
 CPX  C32   C30  C29   105.66  3.000
 CPX  H322  C32  H321  106.60  3.000
 CPX  H322  C32  C31   110.31  3.000
 CPX  H321  C32  C31   111.64  3.000
 CPX  H322  C32  C30   110.19  3.000
 CPX  H321  C32  C30   112.21  3.000
 CPX  C31   C32  C30   105.94  3.000
 CPX  H312  C31  H311  107.12  3.000
 CPX  H312  C31  C28   113.12  3.000
 CPX  H311  C31  C28   109.49  3.000
 CPX  H312  C31  C32   112.66  3.000
 CPX  H311  C31  C32   110.16  3.000
 CPX  C28   C31  C32   104.30  3.000
 CPX  H282  C28  H281  107.85  3.000
 CPX  H282  C28  C31   113.77  3.000
 CPX  H281  C28  C31   110.63  3.000
 CPX  H282  C28  C29   112.64  3.000
 CPX  H281  C28  C29   109.38  3.000
 CPX  C31   C28  C29   102.50  3.000
 CPX  HN3   N3   C13   116.01  3.000
 CPX  HN3   N3   C26   117.55  3.000
 CPX  C13   N3   C26   119.56  3.000
 CPX  H13   C13  C14   112.03  3.000
 CPX  H13   C13  C19   107.08  3.000
 CPX  C14   C13  C19   110.40  3.000
 CPX  H13   C13  N3    108.44  3.000
 CPX  C14   C13  N3    109.30  3.000
 CPX  C19   C13  N3    109.52  3.000
 CPX  H19   C19  C18   108.81  3.000
 CPX  H19   C19  C22   108.26  3.000
 CPX  C18   C19  C22   110.25  3.000
 CPX  H19   C19  C13   107.72  3.000
 CPX  C18   C19  C13   110.45  3.000
 CPX  C22   C19  C13   111.26  3.000
 CPX  H223  C22  H222  108.05  3.000
 CPX  H223  C22  H221  107.46  3.000
 CPX  H222  C22  H221  107.05  3.000
 CPX  H223  C22  C19   111.21  3.000
 CPX  H222  C22  C19   112.54  3.000
 CPX  H221  C22  C19   110.30  3.000
 CPX  H183  C18  H182  107.61  3.000
 CPX  H183  C18  H181  107.65  3.000
 CPX  H182  C18  H181  107.82  3.000
 CPX  H183  C18  C19   110.40  3.000
 CPX  H182  C18  C19   112.50  3.000
 CPX  H181  C18  C19   110.67  3.000
 CPX  N2    C14  O15   121.87  3.000
 CPX  N2    C14  C13   119.66  3.000
 CPX  O15   C14  C13   118.44  3.000
 CPX  C7    N2   C6    111.36  3.000
 CPX  C7    N2   C14   125.99  3.000
 CPX  C6    N2   C14   119.77  3.000
 CPX  H6    C6   C25   107.65  3.000
 CPX  H6    C6   C8    109.01  3.000
 CPX  C25   C6   C8    113.36  3.000
 CPX  H6    C6   N2    109.15  3.000
 CPX  C25   C6   N2    113.60  3.000
 CPX  C8    C6   N2    103.95  3.000
 CPX  H8    C8   N1    106.69  3.000
 CPX  H8    C8   C9    109.12  3.000
 CPX  N1    C8   C9    114.17  3.000
 CPX  H8    C8   C6    110.36  3.000
 CPX  N1    C8   C6    112.10  3.000
 CPX  C9    C8   C6    104.41  3.000
 CPX  H92   C9   H91   108.42  3.000
 CPX  H92   C9   C7    113.12  3.000
 CPX  H91   C9   C7    109.50  3.000
 CPX  H92   C9   C8    112.49  3.000
 CPX  H91   C9   C8    110.18  3.000
 CPX  C7    C9   C8    103.04  3.000
 CPX  H72   C7   H71   108.16  3.000
 CPX  H72   C7   C9    111.71  3.000
 CPX  H71   C7   C9    111.58  3.000
 CPX  H72   C7   N2    110.78  3.000
 CPX  H71   C7   N2    111.71  3.000
 CPX  C9    C7   N2    102.89  3.000
 CPX  HN1   N1   C10   118.26  3.000
 CPX  HN1   N1   C8    117.25  3.000
 CPX  C10   N1   C8    124.31  3.000
 CPX  O11   C10  N1    123.13  3.000
 CPX  O11   C10  C12   122.39  3.000
 CPX  N1    C10  C12   114.48  3.000
 CPX  C20   C25  C23    87.39  3.000
 CPX  C20   C25  C24   107.54  3.000
 CPX  C23   C25  C24   112.89  3.000
 CPX  C20   C25  C6    116.10  3.000
 CPX  C23   C25  C6    120.01  3.000
 CPX  C24   C25  C6    110.59  3.000
 CPX  H24   C24  O5    119.46  3.000
 CPX  H24   C24  C25   115.19  3.000
 CPX  O5    C24  C25   125.28  3.000
 CPX  H232  C23  H231  108.64  3.000
 CPX  H232  C23  C21   111.39  3.000
 CPX  H231  C23  C21   118.52  3.000
 CPX  H232  C23  C25   110.28  3.000
 CPX  H231  C23  C25   117.39  3.000
 CPX  C21   C23  C25    89.47  3.000
 CPX  H212  C21  H211  108.48  3.000
 CPX  H212  C21  C20   116.48  3.000
 CPX  H211  C21  C20   112.59  3.000
 CPX  H212  C21  C23   117.05  3.000
 CPX  H211  C21  C23   112.82  3.000
 CPX  C20   C21  C23    88.46  3.000
 CPX  H202  C20  H201  108.51  3.000
 CPX  H202  C20  C21   119.00  3.000
 CPX  H201  C20  C21   111.47  3.000
 CPX  H202  C20  C25   117.75  3.000
 CPX  H201  C20  C25   110.21  3.000
 CPX  C21   C20  C25    88.68  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
 CPX  CONST_01  C8    N1   C10  C12   180.00   0.0  0
 CPX  CONST_02  C6    N2   C14  C13   180.00   0.0  0
 CPX  CONST_04  C6    N2   C14  O15     0.00   0.0  0
 CPX  CONST_06  C29   N4   C26  O27     0.00   0.0  0
 CPX  CONST_07  O11   C10  N1   C8      0.00   0.0  0
 CPX  CONST_08  N3    C26  N4   C29   180.00   0.0  0
 CPX  CONST_09  HN1   N1   C10  C12     0.00   0.0  0
 CPX  CONST_10  C13   N3   C26  O27     0.00   0.0  0
 CPX  CONST_11  C13   N3   C26  N4    180.00   0.0  0
 CPX  CONST_12  HN4   N4   C26  O27   180.00   0.0  0
 CPX  Var_01    C31   C32  C30  C29    -2.55  30.0  1
 CPX  Var_02    C28   C31  C32  C30   -22.94  30.0  1
 CPX  Var_03    C8    C9   C7   N2    -37.15  30.0  1
 CPX  Var_04    C9    C7   N2   C6     26.66  30.0  1
 CPX  Var_05    C20   C21  C23  C25   -18.62  30.0  1
 CPX  Var_06    C10   C12  C16  C17  -107.65  30.0  1
 CPX  Var_07    N1    C10  C12  C17   145.56  30.0  3
 CPX  Var_08    H221  C22  C19  C13   175.01  30.0  3
 CPX  Var_09    H181  C18  C19  C13   -64.82  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
 CPX  chir_02  C29  N4   C30  C28  negativ
 CPX  chir_03  C13  N3   C19  C14  negativ
 CPX  chir_04  C6   N2   C8   C25  negativ
 CPX  chir_05  C8   N1   C9   C6   negativ
 CPX  chir_06  C25  C23  C20  C6   negativ
 CPX  chir_07  C12  C17  C16  C10  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
 CPX  plan-1  C25  0.020
 CPX  plan-1  C24  0.020
 CPX  plan-1  O5   0.020
 CPX  plan-1  H24  0.020
 CPX  plan-2  O27  0.020
 CPX  plan-2  C26  0.020
 CPX  plan-2  N4   0.020
 CPX  plan-2  C29  0.020
 CPX  plan-2  N3   0.020
 CPX  plan-2  C13  0.020
 CPX  plan-2  HN4  0.020
 CPX  plan-2  HN3  0.020
 CPX  plan-3  C13  0.020
 CPX  plan-3  C14  0.020
 CPX  plan-3  O15  0.020
 CPX  plan-3  N2   0.020
 CPX  plan-3  C6   0.020
 CPX  plan-3  C7   0.020
 CPX  plan-4  C12  0.020
 CPX  plan-4  C8   0.020
 CPX  plan-4  N1   0.020
 CPX  plan-4  C10  0.020
 CPX  plan-4  O11  0.020
 CPX  plan-4  HN1  0.020

