# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 07:39:59 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  64  33  .  2021-08-07  2021-08-07  
;
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  -0.309   6.0220   1.0419  -0.4078
 CDO  C2    C  CR6    0   0.187   6.4044   0.5185   0.8219
 CDO  N3    N  N      0  -0.440   5.8876  -0.6106   1.2930
 CDO  C4    C  CR16   0  -0.098   4.9982  -1.2652   0.5628
 CDO  C5    C  CR6    0   0.028   4.5641  -0.8394  -0.6858
 CDO  C6    C  CR16   0  -0.170   5.0924   0.3520  -1.1653
 CDO  C7    C  CH2    0  -0.364   3.5629  -1.6372  -1.4778
 CDO  C8    C  C      0   0.333   7.4195   1.2028   1.6904
 CDO  N9    N  N      0  -0.648   8.2209   2.1195   1.2995
 CDO  N10   N  NH2    0  -0.808   7.4066   0.7853   2.9767
 CDO  N11   N  NH1    0  -0.634   2.4518  -0.8358  -1.9325
 CDO  C12   C  C      0   0.578   1.5707  -0.3041  -1.0732
 CDO  C13   C  CR15   0  -0.242   0.5592   0.6559  -1.7042
 CDO  O14   O  O      0  -0.472   1.6078  -0.4985   0.1281
 CDO  C15   C  CR15   0  -0.217   1.0538   2.0648  -1.5435
 CDO  C16   C  CR15   0  -0.237   0.2756   2.7521  -0.7211
 CDO  C17   C  CH2    0  -0.298  -0.8689   1.9279  -0.2306
 CDO  N18   N  NR5    0  -0.486  -0.6799   0.6793  -0.9588
 CDO  C19   C  C      0   0.540  -1.4160  -0.4478  -0.8472
 CDO  C20   C  CH1    0  -0.199  -2.6847  -0.3530   0.0084
 CDO  O21   O  O      0  -0.486  -1.0622  -1.4755  -1.4073
 CDO  N22   N  NH1    0  -0.594  -3.1643  -1.6353   0.4631
 CDO  C23   C  CH2    0  -0.419  -3.8589  -2.4883  -0.4776
 CDO  C24   C  C      0   0.394  -3.7363  -3.9811  -0.1163
 CDO  O25   O  OC    -1  -0.625  -4.4704  -4.7510  -0.7671
 CDO  O26   O  O      0  -0.606  -2.9128  -4.3019   0.7632
 CDO  C27   C  CH2    0  -0.445  -3.7540   0.4760  -0.7314
 CDO  C28   C  CH1    0  -0.233  -4.6776   1.2936   0.1711
 CDO  C29   C  CH2    0  -0.416  -5.5476   2.2237  -0.6762
 CDO  C30   C  CH2    0  -0.432  -6.4863   3.0711   0.1760
 CDO  C31   C  CH2    0  -0.429  -7.3535   2.1991   1.0780
 CDO  C32   C  CH2    0  -0.429  -6.4932   1.2755   1.9337
 CDO  C33   C  CH2    0  -0.411  -5.5556   0.4301   1.0769
 CDO  H1    H  HCR6   0   0.272   6.4203   1.9781  -0.7738
 CDO  H4    H  HCR6   0   0.265   4.6007  -2.1787   0.9933
 CDO  H6    H  HCR6   0   0.272   4.7801   0.7479  -2.1240
 CDO  H71   H  HCH2   0   0.286   4.0432  -2.0529  -2.3633
 CDO  H72   H  HCH2   0   0.266   3.2073  -2.4814  -0.8836
 CDO  HN9   H  H      0   0.333   8.1011   2.3273   0.3166
 CDO  H101  H  HNH2   0   0.385   8.1732   1.0528   3.5700
 CDO  H102  H  HNH2   0   0.396   6.9350  -0.0754   3.1960
 CDO  H11   H  HNH1   0   0.411   2.3550  -0.6636  -2.9195
 CDO  H13   H  HCR5   0   0.291   0.3945   0.3944  -2.7556
 CDO  H15   H  HCR5   0   0.274   1.9463   2.4239  -2.0360
 CDO  H16   H  HCR5   0   0.268   0.4169   3.7797  -0.4185
 CDO  H171  H  HCH2   0   0.261  -0.8288   1.7861   0.8549
 CDO  H172  H  HCH2   0   0.256  -1.8308   2.3959  -0.4578
 CDO  H20   H  HCH1   0   0.252  -2.4020   0.2110   0.9083
 CDO  H22   H  HNH1   0   0.337  -2.4097  -2.1745   0.8679
 CDO  H231  H  HCH2   0   0.210  -4.9254  -2.2384  -0.5058
 CDO  H232  H  HCH2   0   0.209  -3.5032  -2.3865  -1.5118
 CDO  H271  H  HCH2   0   0.240  -3.2607   1.1698  -1.4185
 CDO  H272  H  HCH2   0   0.251  -4.3501  -0.1789  -1.3728
 CDO  H28   H  HCH1   0   0.205  -4.0426   1.9224   0.8139
 CDO  H291  H  HCH2   0   0.221  -4.9097   2.8687  -1.2882
 CDO  H292  H  HCH2   0   0.205  -6.1383   1.6185  -1.3755
 CDO  H301  H  HCH2   0   0.207  -5.8951   3.7555   0.7948
 CDO  H302  H  HCH2   0   0.224  -7.1126   3.6967  -0.4648
 CDO  H311  H  HCH2   0   0.223  -7.9899   2.8227   1.7109
 CDO  H312  H  HCH2   0   0.206  -8.0268   1.5956   0.4587
 CDO  H321  H  HCH2   0   0.205  -5.9016   1.8780   2.6325
 CDO  H322  H  HCH2   0   0.223  -7.1257   0.6274   2.5455
 CDO  H331  H  HCH2   0   0.199  -6.1477  -0.2475   0.4488
 CDO  H332  H  HCH2   0   0.238  -4.9306  -0.2068   1.7042

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  1.390  0.020  1.390
 CDO  C1   C6    aromatic  1.383  0.020  1.383
 CDO  C1   H1    single    0.930  0.020  1.080
 CDO  C2   N3    aromatic  1.328  0.020  1.328
 CDO  C2   C8    single    1.501  0.020  1.501
 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  1.389  0.020  1.389
 CDO  C5   C7    single    1.505  0.020  1.505
 CDO  C6   H6    single    0.930  0.020  1.080
 CDO  C7   N11   single    1.443  0.020  1.443
 CDO  C7   H71   single    0.970  0.020  1.090
 CDO  C7   H72   single    0.970  0.020  1.090
 CDO  C8   N9    double    1.279  0.020  1.279
 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    1.531  0.020  1.531
 CDO  C12  O14   double    1.217  0.020  1.217
 CDO  C13  C15   single    1.502  0.020  1.502
 CDO  C13  N18   single    1.446  0.020  1.446
 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    1.493  0.020  1.493
 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    1.351  0.020  1.351
 CDO  C19  C20   single    1.533  0.020  1.533
 CDO  C19  O21   double    1.223  0.020  1.223
 CDO  C20  N22   single    1.443  0.020  1.443
 CDO  C20  C27   single    1.542  0.020  1.542
 CDO  C20  H20   single    0.970  0.020  1.090
 CDO  N22  C23   single    1.447  0.020  1.447
 CDO  N22  H22   single    0.890  0.020  1.040
 CDO  C23  C24   single    1.541  0.020  1.541
 CDO  C23  H231  single    0.970  0.020  1.090
 CDO  C23  H232  single    0.970  0.020  1.090
 CDO  C24  O25   deloc     1.247  0.020  1.247
 CDO  C24  O26   deloc     1.247  0.020  1.247
 CDO  C27  C28   single    1.528  0.020  1.528
 CDO  C27  H271  single    0.970  0.020  1.090
 CDO  C27  H272  single    0.970  0.020  1.090
 CDO  C28  C29   single    1.530  0.020  1.530
 CDO  C28  C33   single    1.529  0.020  1.529
 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    1.525  0.020  1.525
 CDO  C31  H311  single    0.970  0.020  1.090
 CDO  C31  H312  single    0.970  0.020  1.090
 CDO  C32  C33   single    1.526  0.020  1.526
 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    119.60  3.000
 CDO  H1    C1   C2    121.61  3.000
 CDO  C6    C1   C2    118.78  3.000
 CDO  C8    C2   N3    116.46  3.000
 CDO  C8    C2   C1    121.75  3.000
 CDO  N3    C2   C1    121.79  3.000
 CDO  C4    N3   C2    119.08  3.000
 CDO  H4    C4   C5    120.01  3.000
 CDO  H4    C4   N3    116.32  3.000
 CDO  C5    C4   N3    123.66  3.000
 CDO  C7    C5   C6    121.73  3.000
 CDO  C7    C5   C4    121.23  3.000
 CDO  C6    C5   C4    117.04  3.000
 CDO  H6    C6   C5    120.63  3.000
 CDO  H6    C6   C1    119.74  3.000
 CDO  C5    C6   C1    119.63  3.000
 CDO  H72   C7   H71   106.91  3.000
 CDO  H72   C7   N11   110.48  3.000
 CDO  H71   C7   N11   107.16  3.000
 CDO  H72   C7   C5    109.88  3.000
 CDO  H71   C7   C5    109.67  3.000
 CDO  N11   C7   C5    112.55  3.000
 CDO  N10   C8   N9    121.20  3.000
 CDO  N10   C8   C2    113.78  3.000
 CDO  N9    C8   C2    125.01  3.000
 CDO  HN9   N9   C8    111.72  3.000
 CDO  H102  N10  H101  117.16  3.000
 CDO  H102  N10  C8    118.43  3.000
 CDO  H101  N10  C8    118.15  3.000
 CDO  H11   N11  C12   119.83  3.000
 CDO  H11   N11  C7    118.55  3.000
 CDO  C12   N11  C7    121.61  3.000
 CDO  O14   C12  C13   121.81  3.000
 CDO  O14   C12  N11   123.30  3.000
 CDO  C13   C12  N11   114.76  3.000
 CDO  H13   C13  N18   111.69  3.000
 CDO  H13   C13  C15   112.09  3.000
 CDO  N18   C13  C15   102.23  3.000
 CDO  H13   C13  C12   110.19  3.000
 CDO  N18   C13  C12   111.34  3.000
 CDO  C15   C13  C12   109.07  3.000
 CDO  H15   C15  C16   126.57  3.000
 CDO  H15   C15  C13   122.34  3.000
 CDO  C16   C15  C13   111.08  3.000
 CDO  H16   C16  C17   122.22  3.000
 CDO  H16   C16  C15   126.19  3.000
 CDO  C17   C16  C15   111.58  3.000
 CDO  H172  C17  H171  107.06  3.000
 CDO  H172  C17  N18   112.14  3.000
 CDO  H171  C17  N18   112.30  3.000
 CDO  H172  C17  C16   111.70  3.000
 CDO  H171  C17  C16   111.65  3.000
 CDO  N18   C17  C16   102.08  3.000
 CDO  C19   N18  C17   127.07  3.000
 CDO  C19   N18  C13   119.74  3.000
 CDO  C17   N18  C13   112.48  3.000
 CDO  O21   C19  C20   123.16  3.000
 CDO  O21   C19  N18   120.38  3.000
 CDO  C20   C19  N18   116.46  3.000
 CDO  H20   C20  C27   107.17  3.000
 CDO  H20   C20  N22   106.48  3.000
 CDO  C27   C20  N22   113.48  3.000
 CDO  H20   C20  C19   106.01  3.000
 CDO  C27   C20  C19   109.83  3.000
 CDO  N22   C20  C19   113.34  3.000
 CDO  H22   N22  C23   107.68  3.000
 CDO  H22   N22  C20   110.59  3.000
 CDO  C23   N22  C20   118.59  3.000
 CDO  H232  C23  H231  105.65  3.000
 CDO  H232  C23  C24   106.55  3.000
 CDO  H231  C23  C24   107.73  3.000
 CDO  H232  C23  N22   113.70  3.000
 CDO  H231  C23  N22   110.44  3.000
 CDO  C24   C23  N22   112.36  3.000
 CDO  O26   C24  O25   126.73  3.000
 CDO  O26   C24  C23   117.85  3.000
 CDO  O25   C24  C23   115.40  3.000
 CDO  H272  C27  H271  104.91  3.000
 CDO  H272  C27  C28   109.71  3.000
 CDO  H271  C27  C28   107.70  3.000
 CDO  H272  C27  C20   109.72  3.000
 CDO  H271  C27  C20   109.24  3.000
 CDO  C28   C27  C20   115.05  3.000
 CDO  H28   C28  C33   107.93  3.000
 CDO  H28   C28  C29   107.71  3.000
 CDO  C33   C28  C29   110.19  3.000
 CDO  H28   C28  C27   107.56  3.000
 CDO  C33   C28  C27   113.25  3.000
 CDO  C29   C28  C27   109.99  3.000
 CDO  H292  C29  H291  106.41  3.000
 CDO  H292  C29  C30   109.34  3.000
 CDO  H291  C29  C30   110.11  3.000
 CDO  H292  C29  C28   108.89  3.000
 CDO  H291  C29  C28   109.67  3.000
 CDO  C30   C29  C28   112.24  3.000
 CDO  H302  C30  H301  106.43  3.000
 CDO  H302  C30  C31   110.38  3.000
 CDO  H301  C30  C31   109.26  3.000
 CDO  H302  C30  C29   110.07  3.000
 CDO  H301  C30  C29   109.30  3.000
 CDO  C31   C30  C29   111.27  3.000
 CDO  H312  C31  H311  106.48  3.000
 CDO  H312  C31  C32   109.28  3.000
 CDO  H311  C31  C32   110.44  3.000
 CDO  H312  C31  C30   109.26  3.000
 CDO  H311  C31  C30   110.32  3.000
 CDO  C32   C31  C30   110.94  3.000
 CDO  H322  C32  H321  106.35  3.000
 CDO  H322  C32  C33   109.96  3.000
 CDO  H321  C32  C33   109.33  3.000
 CDO  H322  C32  C31   110.29  3.000
 CDO  H321  C32  C31   109.23  3.000
 CDO  C33   C32  C31   111.54  3.000
 CDO  H332  C33  H331  106.13  3.000
 CDO  H332  C33  C32   110.65  3.000
 CDO  H331  C33  C32   109.39  3.000
 CDO  H332  C33  C28   109.97  3.000
 CDO  H331  C33  C28   108.64  3.000
 CDO  C32   C33  C28   111.88  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  Var_01    C17   C16  C15  C13   -1.27  30.0  1
 CDO  Var_02    C16   C17  N18  C13    6.84  30.0  1
 CDO  Var_03    N18   C17  C16  C15   -3.27  30.0  1
 CDO  Var_04    C31   C30  C29  C28  -55.45  30.0  1
 CDO  Var_05    C31   C32  C33  C28   55.62  30.0  1
 CDO  Var_06    C32   C31  C30  C29   54.94  30.0  1
 CDO  Var_07    C33   C32  C31  C30  -55.19  30.0  1
 CDO  Var_08    N9    C8   C2   C1   -15.89  30.0  2
 CDO  Var_09    N11   C7   C5   C4   128.84  30.0  2
 CDO  Var_10    C12   N11  C7   C5   -66.68  30.0  3
 CDO  Var_11    C24   C23  N22  C20  153.48  30.0  3
 CDO  Var_12    O25   C24  C23  N22  169.84  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
 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

