# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:53:42 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: N-[(1R)-2-[(2S)-2-{[(6-carbamimidoylpyridin-3-yl)methyl]carbamoyl}-2,5-dihydro-1H-pyrrol-1-yl]-1-(cyclohexylmethyl)-2-oxoethyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2C=CCN2C(=O)[C@@H](CC3CCCCC3)NCC(O)=O)cn1
#
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
 CDO  CDO  N-[(1R)-2-[(2S)-2-{[(6-carbamimidoylpyridin-3-yl)methyl]carbamoyl}-2,5-dihydro-1H-pyrrol-1-yl]-1-(cyclohexylmethyl)-2-oxoethyl]glycine  ligand  65  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CDO
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
 CDO  C1    C  CR16  0  -0.305   6.3466   0.8361   0.6429
 CDO  C2    C  CR6   0   0.189   7.3458   0.1670  -0.0570
 CDO  N3    N  N     0  -0.439   7.0997  -0.9490  -0.7316
 CDO  C4    C  CR16  0  -0.103   5.8714  -1.4440  -0.7318
 CDO  C5    C  CR6   0   0.038   4.8059  -0.8591  -0.0605
 CDO  C6    C  CR16  0  -0.172   5.0661   0.3145   0.6377
 CDO  C7    C  CH2   0  -0.385   3.4322  -1.4710  -0.1059
 CDO  C8    C  C     0   0.334   8.7612   0.6691  -0.0919
 CDO  N9    N  N     0  -0.648   9.2309   1.5967   0.6518
 CDO  N10   N  NH2   0  -0.809   9.5305   0.0650  -1.0260
 CDO  N11   N  NH1   0  -0.623   2.4402  -0.5576  -0.6225
 CDO  C12   C  C     0   0.576   1.5352   0.0769   0.1369
 CDO  C13   C  CR15  0  -0.239   0.6598   1.0765  -0.6256
 CDO  O14   O  O     0  -0.482   1.4328  -0.0568   1.3435
 CDO  C15   C  CR15  0  -0.216   1.1527   2.4733  -0.3835
 CDO  C16   C  CR15  0  -0.241   0.2618   3.1854   0.2902
 CDO  C17   C  CH2   0  -0.296  -0.9691   2.3923   0.5857
 CDO  N18   N  NR5   0  -0.489  -0.6774   1.1247  -0.0726
 CDO  C19   C  C     0   0.561  -1.4462   0.0210  -0.1060
 CDO  C20   C  CH1   0  -0.206  -2.8590   0.1269   0.4734
 CDO  O21   O  O     0  -0.489  -1.0279  -1.0112  -0.6152
 CDO  N22   N  NH1   0  -0.593  -3.3366  -1.0969   1.0757
 CDO  C23   C  CH2   0  -0.409  -3.5608  -2.2564   0.2545
 CDO  C24   C  C     0   0.529  -4.4928  -3.2296   0.9363
 CDO  O25   O  OH1   0  -0.598  -4.7279  -4.2839   0.1594
 CDO  O26   O  O     0  -0.442  -4.9574  -3.1052   2.0401
 CDO  C27   C  CH2   0  -0.445  -3.7797   0.6977  -0.6162
 CDO  C28   C  CH1   0  -0.213  -5.1626   1.1700  -0.1565
 CDO  C29   C  CH2   0  -0.421  -5.7268   2.1554  -1.1848
 CDO  C30   C  CH2   0  -0.431  -7.1169   2.6593  -0.8134
 CDO  C31   C  CH2   0  -0.428  -8.0879   1.5036  -0.5993
 CDO  C32   C  CH2   0  -0.428  -7.5459   0.5290   0.4387
 CDO  C33   C  CH2   0  -0.429  -6.1548   0.0258   0.0662
 CDO  H1    H  HCR6  0   0.274   6.5446   1.7545   1.1783
 CDO  H4    H  HCR6  0   0.269   5.7189  -2.3556  -1.3007
 CDO  H6    H  HCR6  0   0.273   4.2778   0.8213   1.1809
 CDO  H71   H  HCH2  0   0.279   3.4475  -2.3666  -0.7285
 CDO  H72   H  HCH2  0   0.279   3.1268  -1.7816   0.8930
 CDO  HN9   H  H     0   0.334   8.5330   1.9605   1.2871
 CDO  H101  H  HNH2  0   0.385  10.5253   0.2067  -0.9846
 CDO  H102  H  HNH2  0   0.396   9.2051  -0.7962  -1.4305
 CDO  H11   H  HNH1  0   0.408   2.4415  -0.3912  -1.6164
 CDO  H13   H  HCR5  0   0.291   0.6427   0.8289  -1.6930
 CDO  H15   H  HCR5  0   0.277   2.1221   2.8076  -0.7240
 CDO  H16   H  HCR5  0   0.269   0.3728   4.2134   0.6037
 CDO  H171  H  HCH2  0   0.265  -1.1249   2.2728   1.6625
 CDO  H172  H  HCH2  0   0.255  -1.8652   2.8717   0.1796
 CDO  H20   H  HCH1  0   0.266  -2.8434   0.8576   1.2889
 CDO  H22   H  HNH1  0   0.358  -2.7717  -1.3326   1.8797
 CDO  H231  H  HCH2  0   0.270  -4.0244  -1.9685  -0.6913
 CDO  H232  H  HCH2  0   0.273  -2.6552  -2.8077  -0.0238
 CDO  H25   H  HOH1  0   0.480  -5.3100  -4.9082   0.6170
 CDO  H271  H  HCH2  0   0.246  -3.2610   1.5558  -1.0564
 CDO  H272  H  HCH2  0   0.238  -3.8868  -0.0178  -1.4375
 CDO  H28   H  HCH1  0   0.207  -5.0414   1.7103   0.7931
 CDO  H291  H  HCH2  0   0.223  -5.0401   2.9994  -1.2968
 CDO  H292  H  HCH2  0   0.206  -5.7697   1.6601  -2.1629
 CDO  H301  H  HCH2  0   0.207  -7.0547   3.2532   0.1053
 CDO  H302  H  HCH2  0   0.224  -7.4903   3.3317  -1.5899
 CDO  H311  H  HCH2  0   0.223  -9.0673   1.8810  -0.2941
 CDO  H312  H  HCH2  0   0.205  -8.2402   0.9775  -1.5484
 CDO  H321  H  HCH2  0   0.206  -7.5015   1.0278   1.4136
 CDO  H322  H  HCH2  0   0.223  -8.2270  -0.3176   0.5567
 CDO  H331  H  HCH2  0   0.197  -6.2207  -0.5640  -0.8574
 CDO  H332  H  HCH2  0   0.245  -5.7804  -0.6424   0.8409

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
 CDO  C1   C2    aromatic  1.391  0.020  1.391
 CDO  C1   C6    aromatic  1.383  0.020  1.383
 CDO  C1   H1    single    0.930  0.020  1.080
 CDO  C2   N3    aromatic  1.327  0.020  1.327
 CDO  C2   C8    single    1.502  0.020  1.502
 CDO  N3   C4    aromatic  1.324  0.020  1.324
 CDO  C4   C5    aromatic  1.389  0.020  1.389
 CDO  C4   H4    single    0.930  0.020  1.080
 CDO  C5   C6    aromatic  1.390  0.020  1.390
 CDO  C5   C7    single    1.504  0.020  1.504
 CDO  C6   H6    single    0.930  0.020  1.080
 CDO  C7   N11   single    1.444  0.020  1.444
 CDO  C7   H71   single    0.970  0.020  1.090
 CDO  C7   H72   single    0.970  0.020  1.090
 CDO  C8   N9    double    1.278  0.020  1.278
 CDO  C8   N10   single    1.352  0.020  1.352
 CDO  N9   HN9   single    0.890  0.020  1.040
 CDO  N10  H101  single    0.890  0.020  1.040
 CDO  N10  H102  single    0.890  0.020  1.040
 CDO  N11  C12   single    1.341  0.020  1.341
 CDO  N11  H11   single    0.860  0.020  1.020
 CDO  C12  C13   single    1.532  0.020  1.532
 CDO  C12  O14   double    1.218  0.020  1.218
 CDO  C13  C15   single    1.501  0.020  1.501
 CDO  C13  N18   single    1.448  0.020  1.448
 CDO  C13  H13   single    0.970  0.020  1.090
 CDO  C15  C16   double    1.325  0.020  1.325
 CDO  C15  H15   single    0.930  0.020  1.080
 CDO  C16  C17   single    1.494  0.020  1.494
 CDO  C16  H16   single    0.930  0.020  1.080
 CDO  C17  N18   single    1.458  0.020  1.458
 CDO  C17  H171  single    0.970  0.020  1.090
 CDO  C17  H172  single    0.970  0.020  1.090
 CDO  N18  C19   single    1.346  0.020  1.346
 CDO  C19  C20   single    1.531  0.020  1.531
 CDO  C19  O21   double    1.225  0.020  1.225
 CDO  C20  N22   single    1.445  0.020  1.445
 CDO  C20  C27   single    1.536  0.020  1.536
 CDO  C20  H20   single    0.970  0.020  1.090
 CDO  N22  C23   single    1.438  0.020  1.438
 CDO  N22  H22   single    0.890  0.020  1.040
 CDO  C23  C24   single    1.510  0.020  1.510
 CDO  C23  H231  single    0.970  0.020  1.090
 CDO  C23  H232  single    0.970  0.020  1.090
 CDO  C24  O25   single    1.331  0.020  1.331
 CDO  C24  O26   double    1.204  0.020  1.204
 CDO  O25  H25   single    0.850  0.020  0.980
 CDO  C27  C28   single    1.532  0.020  1.532
 CDO  C27  H271  single    0.970  0.020  1.090
 CDO  C27  H272  single    0.970  0.020  1.090
 CDO  C28  C29   single    1.532  0.020  1.532
 CDO  C28  C33   single    1.531  0.020  1.531
 CDO  C28  H28   single    0.970  0.020  1.090
 CDO  C29  C30   single    1.525  0.020  1.525
 CDO  C29  H291  single    0.970  0.020  1.090
 CDO  C29  H292  single    0.970  0.020  1.090
 CDO  C30  C31   single    1.525  0.020  1.525
 CDO  C30  H301  single    0.970  0.020  1.090
 CDO  C30  H302  single    0.970  0.020  1.090
 CDO  C31  C32   single    1.523  0.020  1.523
 CDO  C31  H311  single    0.970  0.020  1.090
 CDO  C31  H312  single    0.970  0.020  1.090
 CDO  C32  C33   single    1.525  0.020  1.525
 CDO  C32  H321  single    0.970  0.020  1.090
 CDO  C32  H322  single    0.970  0.020  1.090
 CDO  C33  H331  single    0.970  0.020  1.090
 CDO  C33  H332  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
 CDO  H1    C1   C6    119.46  3.000
 CDO  H1    C1   C2    121.73  3.000
 CDO  C6    C1   C2    118.80  3.000
 CDO  C8    C2   N3    116.36  3.000
 CDO  C8    C2   C1    121.85  3.000
 CDO  N3    C2   C1    121.80  3.000
 CDO  C4    N3   C2    119.10  3.000
 CDO  H4    C4   C5    119.96  3.000
 CDO  H4    C4   N3    116.38  3.000
 CDO  C5    C4   N3    123.66  3.000
 CDO  C7    C5   C6    121.96  3.000
 CDO  C7    C5   C4    120.98  3.000
 CDO  C6    C5   C4    117.05  3.000
 CDO  H6    C6   C5    120.71  3.000
 CDO  H6    C6   C1    119.70  3.000
 CDO  C5    C6   C1    119.58  3.000
 CDO  H72   C7   H71   107.04  3.000
 CDO  H72   C7   N11   108.40  3.000
 CDO  H71   C7   N11   108.95  3.000
 CDO  H72   C7   C5    110.13  3.000
 CDO  H71   C7   C5    109.78  3.000
 CDO  N11   C7   C5    112.39  3.000
 CDO  N10   C8   N9    121.12  3.000
 CDO  N10   C8   C2    113.75  3.000
 CDO  N9    C8   C2    125.11  3.000
 CDO  HN9   N9   C8    111.89  3.000
 CDO  H102  N10  H101  117.21  3.000
 CDO  H102  N10  C8    118.44  3.000
 CDO  H101  N10  C8    118.12  3.000
 CDO  H11   N11  C12   118.76  3.000
 CDO  H11   N11  C7    117.16  3.000
 CDO  C12   N11  C7    124.08  3.000
 CDO  O14   C12  C13   121.10  3.000
 CDO  O14   C12  N11   124.44  3.000
 CDO  C13   C12  N11   114.36  3.000
 CDO  H13   C13  N18   111.42  3.000
 CDO  H13   C13  C15   111.87  3.000
 CDO  N18   C13  C15   102.16  3.000
 CDO  H13   C13  C12   110.26  3.000
 CDO  N18   C13  C12   111.06  3.000
 CDO  C15   C13  C12   109.83  3.000
 CDO  H15   C15  C16   126.68  3.000
 CDO  H15   C15  C13   122.13  3.000
 CDO  C16   C15  C13   111.19  3.000
 CDO  H16   C16  C17   122.17  3.000
 CDO  H16   C16  C15   126.16  3.000
 CDO  C17   C16  C15   111.67  3.000
 CDO  H172  C17  H171  107.23  3.000
 CDO  H172  C17  N18   112.16  3.000
 CDO  H171  C17  N18   112.20  3.000
 CDO  H172  C17  C16   111.64  3.000
 CDO  H171  C17  C16   111.70  3.000
 CDO  N18   C17  C16   101.97  3.000
 CDO  C19   N18  C17   127.59  3.000
 CDO  C19   N18  C13   119.40  3.000
 CDO  C17   N18  C13   112.72  3.000
 CDO  O21   C19  C20   122.07  3.000
 CDO  O21   C19  N18   120.43  3.000
 CDO  C20   C19  N18   117.47  3.000
 CDO  H20   C20  C27   106.78  3.000
 CDO  H20   C20  N22   105.04  3.000
 CDO  C27   C20  N22   114.34  3.000
 CDO  H20   C20  C19   108.35  3.000
 CDO  C27   C20  C19   108.08  3.000
 CDO  N22   C20  C19   113.84  3.000
 CDO  H22   N22  C23   110.69  3.000
 CDO  H22   N22  C20   110.14  3.000
 CDO  C23   N22  C20   119.75  3.000
 CDO  H232  C23  H231  105.27  3.000
 CDO  H232  C23  C24   107.48  3.000
 CDO  H231  C23  C24   107.40  3.000
 CDO  H232  C23  N22   114.93  3.000
 CDO  H231  C23  N22   110.38  3.000
 CDO  C24   C23  N22   110.98  3.000
 CDO  O26   C24  O25   123.29  3.000
 CDO  O26   C24  C23   125.84  3.000
 CDO  O25   C24  C23   110.86  3.000
 CDO  H25   O25  C24   109.95  3.000
 CDO  H272  C27  H271  104.89  3.000
 CDO  H272  C27  C28   109.78  3.000
 CDO  H271  C27  C28   107.86  3.000
 CDO  H272  C27  C20   110.36  3.000
 CDO  H271  C27  C20   107.00  3.000
 CDO  C28   C27  C20   116.27  3.000
 CDO  H28   C28  C33   108.25  3.000
 CDO  H28   C28  C29   107.72  3.000
 CDO  C33   C28  C29   109.86  3.000
 CDO  H28   C28  C27   108.14  3.000
 CDO  C33   C28  C27   113.48  3.000
 CDO  C29   C28  C27   109.23  3.000
 CDO  H292  C29  H291  106.36  3.000
 CDO  H292  C29  C30   109.31  3.000
 CDO  H291  C29  C30   110.02  3.000
 CDO  H292  C29  C28   108.81  3.000
 CDO  H291  C29  C28   109.51  3.000
 CDO  C30   C29  C28   112.63  3.000
 CDO  H302  C30  H301  106.35  3.000
 CDO  H302  C30  C31   110.40  3.000
 CDO  H301  C30  C31   109.23  3.000
 CDO  H302  C30  C29   109.98  3.000
 CDO  H301  C30  C29   109.37  3.000
 CDO  C31   C30  C29   111.37  3.000
 CDO  H312  C31  H311  106.45  3.000
 CDO  H312  C31  C32   109.42  3.000
 CDO  H311  C31  C32   110.45  3.000
 CDO  H312  C31  C30   109.32  3.000
 CDO  H311  C31  C30   110.37  3.000
 CDO  C32   C31  C30   110.73  3.000
 CDO  H322  C32  H321  106.37  3.000
 CDO  H322  C32  C33   109.82  3.000
 CDO  H321  C32  C33   109.29  3.000
 CDO  H322  C32  C31   110.33  3.000
 CDO  H321  C32  C31   109.23  3.000
 CDO  C33   C32  C31   111.66  3.000
 CDO  H332  C33  H331  106.81  3.000
 CDO  H332  C33  C32   110.00  3.000
 CDO  H331  C33  C32   109.15  3.000
 CDO  H332  C33  C28   109.83  3.000
 CDO  H331  C33  C28   108.55  3.000
 CDO  C32   C33  C28   112.34  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
 CDO  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 CDO  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CDO  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 CDO  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 CDO  CONST_05  C6    C1   C2   N3      0.00   0.0  0
 CDO  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 CDO  CONST_07  C7    C5   C6   C1    180.00   0.0  0
 CDO  CONST_08  C7    C5   C4   N3    180.00   0.0  0
 CDO  CONST_09  C8    C2   N3   C4    180.00   0.0  0
 CDO  CONST_10  C8    C2   C1   C6    180.00   0.0  0
 CDO  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 CDO  CONST_12  H4    C4   N3   C2    180.00   0.0  0
 CDO  CONST_13  H1    C1   C2   N3    180.00   0.0  0
 CDO  CONST_14  C20   C19  N18  C13   180.00   0.0  0
 CDO  CONST_15  O21   C19  N18  C13     0.00   0.0  0
 CDO  CONST_16  C20   C19  N18  C17     0.00   0.0  0
 CDO  CONST_17  O21   C19  N18  C17   180.00   0.0  0
 CDO  CONST_18  C13   C12  N11  C7    180.00   0.0  0
 CDO  CONST_19  H11   N11  C12  C13     0.00   0.0  0
 CDO  CONST_20  HN9   N9   C8   C2      0.00   0.0  0
 CDO  CONST_21  H101  N10  C8   C2    180.00   0.0  0
 CDO  CONST_23  O14   C12  N11  C7      0.00   0.0  0
 CDO  CONST_24  H25   O25  C24  C23   180.00   0.0  0
 CDO  Var_01    C17   C16  C15  C13    -0.90  30.0  1
 CDO  Var_02    C16   C17  N18  C13     4.90  30.0  1
 CDO  Var_03    N18   C17  C16  C15    -2.35  30.0  1
 CDO  Var_04    C31   C30  C29  C28   -55.44  30.0  1
 CDO  Var_05    C31   C32  C33  C28    55.50  30.0  1
 CDO  Var_06    C32   C31  C30  C29    55.06  30.0  1
 CDO  Var_07    C33   C32  C31  C30   -55.23  30.0  1
 CDO  Var_08    N9    C8   C2   C1     11.40  30.0  2
 CDO  Var_09    N11   C7   C5   C4   -122.38  30.0  2
 CDO  Var_10    C12   N11  C7   C5   -104.62  30.0  3
 CDO  Var_11    C24   C23  N22  C20  -159.67  30.0  3
 CDO  Var_12    O25   C24  C23  N22   178.28  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
 CDO  chir_01  C13  C12  C15  N18  positiv
 CDO  chir_02  C20  N22  C27  C19  positiv
 CDO  chir_03  C28  C27  C29  C33  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
 CDO  plan-1  C1    0.020
 CDO  plan-1  C2    0.020
 CDO  plan-1  N3    0.020
 CDO  plan-1  C4    0.020
 CDO  plan-1  C5    0.020
 CDO  plan-1  C6    0.020
 CDO  plan-1  C7    0.020
 CDO  plan-1  C8    0.020
 CDO  plan-1  H1    0.020
 CDO  plan-1  H4    0.020
 CDO  plan-1  H6    0.020
 CDO  plan-2  C13   0.020
 CDO  plan-2  C17   0.020
 CDO  plan-2  N18   0.020
 CDO  plan-2  C19   0.020
 CDO  plan-2  C20   0.020
 CDO  plan-2  O21   0.020
 CDO  plan-3  C7    0.020
 CDO  plan-3  N11   0.020
 CDO  plan-3  C12   0.020
 CDO  plan-3  C13   0.020
 CDO  plan-3  O14   0.020
 CDO  plan-3  H11   0.020
 CDO  plan-4  C2    0.020
 CDO  plan-4  C8    0.020
 CDO  plan-4  N9    0.020
 CDO  plan-4  N10   0.020
 CDO  plan-4  HN9   0.020
 CDO  plan-4  H101  0.020
 CDO  plan-4  H102  0.020
 CDO  plan-5  C23   0.020
 CDO  plan-5  C24   0.020
 CDO  plan-5  O25   0.020
 CDO  plan-5  O26   0.020
 CDO  plan-5  H25   0.020

