# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 21:47:27 2022
#   Inital geometry file: a 161 line input string
#   Ligand name: methyl N-{[(3R)-1-carbamimidoylpiperidin-3-yl]acetyl}-4-(phenylethynyl)-L-phenylalaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1ccc(cc1)C#Cc2ccccc2)NC(=O)C[C@H]3CCCN(C3)C(N)=N
#
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
 FRG  FRG  'methyl N-{[(3R)-1-carbamimidoylpiperidin-3-yl]acetyl}-4-(phenylethynyl)-L-phenylalaninate'  ligand  63  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FRG
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
 FRG  N33   N  N     0  -0.690   0.3377  -1.6322  -1.9034
 FRG  C31   C  C     0   0.560  -0.1911  -2.3038  -0.9490
 FRG  N32   N  NH2   0  -0.838  -1.1747  -3.2676  -1.1098
 FRG  N29   N  NT    0  -0.448   0.2161  -2.1241   0.3517
 FRG  C30   C  CH2   0  -0.279   1.2032  -1.1033   0.6330
 FRG  C28   C  CH2   0  -0.323   0.2873  -3.2367   1.2840
 FRG  C27   C  CH2   0  -0.432   1.6657  -3.8885   1.2477
 FRG  C26   C  CH2   0  -0.425   2.7546  -2.8566   1.5219
 FRG  C24   C  CH1   0  -0.240   2.6338  -1.6429   0.5997
 FRG  C23   C  CH2   0  -0.564   3.6371  -0.5652   1.0206
 FRG  C22   C  C     0   0.545   3.6088   0.6272   0.0947
 FRG  O25   O  O     0  -0.494   3.9986   0.5637  -1.0622
 FRG  N21   N  NH1   0  -0.618   3.0879   1.7512   0.6254
 FRG  C16   C  CH1   0  -0.203   2.8916   2.9572  -0.1215
 FRG  C17   C  C     0   0.606   4.0934   3.8829   0.0168
 FRG  O19   O  O     0  -0.434   5.0609   3.6516   0.6925
 FRG  O18   O  O2    0  -0.452   3.9359   4.9761  -0.7100
 FRG  C20   C  CH3   0  -0.424   4.9807   5.9509  -0.6783
 FRG  C15   C  CH2   0  -0.547   1.5875   3.6553   0.3083
 FRG  C12   C  CR6   0   0.140   0.4196   2.7128   0.2274
 FRG  C13   C  CR16  0  -0.315  -0.2010   2.2378   1.3782
 FRG  C14   C  CR16  0  -0.270  -1.2404   1.3250   1.3042
 FRG  C11   C  CR16  0  -0.291  -0.0389   2.2616  -1.0092
 FRG  C10   C  CR16  0  -0.245  -1.0666   1.3420  -1.0960
 FRG  C9    C  CR6   0  -0.131  -1.6776   0.8563   0.0644
 FRG  C8    C  CSP   0   0.152  -2.7095  -0.1163  -0.0250
 FRG  C7    C  CSP   0   0.133  -3.5742  -0.9544  -0.1169
 FRG  C4    C  CR6   0  -0.119  -4.5724  -1.9589  -0.2477
 FRG  C5    C  CR16  0  -0.305  -4.7848  -2.5805  -1.4837
 FRG  C6    C  CR16  0  -0.245  -5.7502  -3.5658  -1.6127
 FRG  C3    C  CR16  0  -0.298  -5.3448  -2.3461   0.8528
 FRG  C2    C  CR16  0  -0.247  -6.3088  -3.3316   0.7147
 FRG  C1    C  CR16  0  -0.256  -6.5146  -3.9441  -0.5157
 FRG  H33   H  H     0   0.308  -0.1781  -1.7774  -2.7639
 FRG  H321  H  HNH2  0   0.380  -1.8851  -3.2846  -0.3937
 FRG  H322  H  HNH2  0   0.377  -1.5916  -3.2732  -2.0275
 FRG  H301  H  HCH2  0   0.218   0.9904  -0.7063   1.6333
 FRG  H302  H  HCH2  0   0.281   1.0741  -0.2885  -0.0748
 FRG  H281  H  HCH2  0   0.250  -0.4873  -3.9712   1.0761
 FRG  H282  H  HCH2  0   0.228   0.0895  -2.8511   2.2895
 FRG  H271  H  HCH2  0   0.220   1.8187  -4.3467   0.2657
 FRG  H272  H  HCH2  0   0.232   1.7117  -4.6939   1.9849
 FRG  H261  H  HCH2  0   0.234   3.7453  -3.3075   1.4208
 FRG  H262  H  HCH2  0   0.210   2.6702  -2.5183   2.5619
 FRG  H24   H  HCH1  0   0.235   2.8549  -1.9522  -0.4273
 FRG  H231  H  HCH2  0   0.269   4.6468  -0.9835   1.0063
 FRG  H232  H  HCH2  0   0.243   3.4322  -0.2643   2.0521
 FRG  H21   H  HNH1  0   0.402   2.8333   1.7533   1.6003
 FRG  H16   H  HCH1  0   0.299   2.8103   2.6926  -1.1792
 FRG  H201  H  HCH3  0   0.242   5.1492   6.3191   0.3330
 FRG  H202  H  HCH3  0   0.242   5.9110   5.5465  -1.0755
 FRG  H203  H  HCH3  0   0.254   4.6445   6.7687  -1.3084
 FRG  H151  H  HCH2  0   0.271   1.6921   4.0357   1.3278
 FRG  H152  H  HCH2  0   0.282   1.4212   4.5169  -0.3388
 FRG  H13   H  HCR6  0   0.254   0.1370   2.5771   2.3500
 FRG  H14   H  HCR6  0   0.254  -1.7016   0.9564   2.2110
 FRG  H11   H  HCR6  0   0.253   0.4208   2.6254  -1.9208
 FRG  H10   H  HCR6  0   0.248  -1.3943   0.9849  -2.0621
 FRG  H5    H  HCR6  0   0.259  -4.1913  -2.2849  -2.3393
 FRG  H6    H  HCR6  0   0.263  -5.9055  -4.0398  -2.5729
 FRG  H3    H  HCR6  0   0.260  -5.1861  -1.8702   1.8116
 FRG  H2    H  HCR6  0   0.263  -6.9034  -3.6220   1.5710
 FRG  H1    H  HCR6  0   0.264  -7.2687  -4.7131  -0.6183

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
 FRG  N33  C31   double    1.281  0.020  1.281
 FRG  N33  H33   single    0.890  0.020  1.040
 FRG  C31  N32   single    1.386  0.020  1.386
 FRG  C31  N29   single    1.375  0.020  1.375
 FRG  N32  H321  single    0.890  0.020  1.040
 FRG  N32  H322  single    0.890  0.020  1.040
 FRG  N29  C30   single    1.448  0.020  1.448
 FRG  N29  C28   single    1.453  0.020  1.453
 FRG  C30  C24   single    1.529  0.020  1.529
 FRG  C30  H301  single    0.970  0.020  1.090
 FRG  C30  H302  single    0.970  0.020  1.090
 FRG  C28  C27   single    1.525  0.020  1.525
 FRG  C28  H281  single    0.970  0.020  1.090
 FRG  C28  H282  single    0.970  0.020  1.090
 FRG  C27  C26   single    1.525  0.020  1.525
 FRG  C27  H271  single    0.970  0.020  1.090
 FRG  C27  H272  single    0.970  0.020  1.090
 FRG  C26  C24   single    1.529  0.020  1.529
 FRG  C26  H261  single    0.970  0.020  1.090
 FRG  C26  H262  single    0.970  0.020  1.090
 FRG  C24  C23   single    1.531  0.020  1.531
 FRG  C24  H24   single    0.970  0.020  1.090
 FRG  C23  C22   single    1.510  0.020  1.510
 FRG  C23  H231  single    0.970  0.020  1.090
 FRG  C23  H232  single    0.970  0.020  1.090
 FRG  C22  O25   double    1.222  0.020  1.222
 FRG  C22  N21   single    1.348  0.020  1.348
 FRG  N21  C16   single    1.432  0.020  1.432
 FRG  N21  H21   single    0.860  0.020  1.020
 FRG  C16  C17   single    1.523  0.020  1.523
 FRG  C16  C15   single    1.540  0.020  1.540
 FRG  C16  H16   single    0.970  0.020  1.090
 FRG  C17  O19   double    1.203  0.020  1.203
 FRG  C17  O18   single    1.322  0.020  1.322
 FRG  O18  C20   single    1.429  0.020  1.429
 FRG  C20  H201  single    0.970  0.020  1.090
 FRG  C20  H202  single    0.970  0.020  1.090
 FRG  C20  H203  single    0.970  0.020  1.090
 FRG  C15  C12   single    1.503  0.020  1.503
 FRG  C15  H151  single    0.970  0.020  1.090
 FRG  C15  H152  single    0.970  0.020  1.090
 FRG  C12  C13   aromatic  1.391  0.020  1.391
 FRG  C12  C11   aromatic  1.394  0.020  1.394
 FRG  C13  C14   aromatic  1.385  0.020  1.385
 FRG  C13  H13   single    0.930  0.020  1.080
 FRG  C14  C9    aromatic  1.396  0.020  1.396
 FRG  C14  H14   single    0.930  0.020  1.080
 FRG  C11  C10   aromatic  1.382  0.020  1.382
 FRG  C11  H11   single    0.930  0.020  1.080
 FRG  C10  C9    aromatic  1.398  0.020  1.398
 FRG  C10  H10   single    0.930  0.020  1.080
 FRG  C9   C8    single    1.421  0.020  1.421
 FRG  C8   C7    triple    1.208  0.020  1.208
 FRG  C7   C4    single    1.422  0.020  1.422
 FRG  C4   C5    aromatic  1.400  0.020  1.400
 FRG  C4   C3    aromatic  1.399  0.020  1.399
 FRG  C5   C6    aromatic  1.385  0.020  1.385
 FRG  C5   H5    single    0.930  0.020  1.080
 FRG  C6   C1    aromatic  1.390  0.020  1.390
 FRG  C6   H6    single    0.930  0.020  1.080
 FRG  C3   C2    aromatic  1.385  0.020  1.385
 FRG  C3   H3    single    0.930  0.020  1.080
 FRG  C2   C1    aromatic  1.390  0.020  1.390
 FRG  C2   H2    single    0.930  0.020  1.080
 FRG  C1   H1    single    0.930  0.020  1.080

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
 FRG  H33   N33  C31   110.31  3.000
 FRG  N29   C31  N32   114.25  3.000
 FRG  N29   C31  N33   120.93  3.000
 FRG  N32   C31  N33   124.81  3.000
 FRG  H322  N32  H321  110.79  3.000
 FRG  H322  N32  C31   113.75  3.000
 FRG  H321  N32  C31   115.40  3.000
 FRG  C28   N29  C30   112.45  3.000
 FRG  C28   N29  C31   121.42  3.000
 FRG  C30   N29  C31   118.56  3.000
 FRG  H302  C30  H301  107.43  3.000
 FRG  H302  C30  C24   111.19  3.000
 FRG  H301  C30  C24   109.20  3.000
 FRG  H302  C30  N29   108.73  3.000
 FRG  H301  C30  N29   107.46  3.000
 FRG  C24   C30  N29   112.63  3.000
 FRG  H282  C28  H281  106.55  3.000
 FRG  H282  C28  C27   109.61  3.000
 FRG  H281  C28  C27   110.52  3.000
 FRG  H282  C28  N29   108.10  3.000
 FRG  H281  C28  N29   111.07  3.000
 FRG  C27   C28  N29   110.86  3.000
 FRG  H272  C27  H271  106.91  3.000
 FRG  H272  C27  C26   110.32  3.000
 FRG  H271  C27  C26   110.17  3.000
 FRG  H272  C27  C28   109.69  3.000
 FRG  H271  C27  C28   109.07  3.000
 FRG  C26   C27  C28   110.60  3.000
 FRG  H262  C26  H261  106.54  3.000
 FRG  H262  C26  C24   108.72  3.000
 FRG  H261  C26  C24   110.07  3.000
 FRG  H262  C26  C27   108.92  3.000
 FRG  H261  C26  C27   110.57  3.000
 FRG  C24   C26  C27   111.86  3.000
 FRG  H24   C24  C23   108.92  3.000
 FRG  H24   C24  C26   109.00  3.000
 FRG  C23   C24  C26   109.95  3.000
 FRG  H24   C24  C30   107.99  3.000
 FRG  C23   C24  C30   111.01  3.000
 FRG  C26   C24  C30   109.93  3.000
 FRG  H232  C23  H231  106.90  3.000
 FRG  H232  C23  C22   110.95  3.000
 FRG  H231  C23  C22   108.15  3.000
 FRG  H232  C23  C24   109.27  3.000
 FRG  H231  C23  C24   109.41  3.000
 FRG  C22   C23  C24   112.02  3.000
 FRG  N21   C22  O25   122.63  3.000
 FRG  N21   C22  C23   115.11  3.000
 FRG  O25   C22  C23   122.23  3.000
 FRG  H21   N21  C16   117.92  3.000
 FRG  H21   N21  C22   118.71  3.000
 FRG  C16   N21  C22   123.36  3.000
 FRG  H16   C16  C15   108.47  3.000
 FRG  H16   C16  C17   107.07  3.000
 FRG  C15   C16  C17   111.54  3.000
 FRG  H16   C16  N21   108.12  3.000
 FRG  C15   C16  N21   110.62  3.000
 FRG  C17   C16  N21   110.87  3.000
 FRG  O18   C17  O19   124.31  3.000
 FRG  O18   C17  C16   111.01  3.000
 FRG  O19   C17  C16   124.68  3.000
 FRG  C20   O18  C17   117.69  3.000
 FRG  H203  C20  H202  109.42  3.000
 FRG  H203  C20  H201  109.40  3.000
 FRG  H202  C20  H201  109.38  3.000
 FRG  H203  C20  O18   105.93  3.000
 FRG  H202  C20  O18   111.28  3.000
 FRG  H201  C20  O18   111.35  3.000
 FRG  H152  C15  H151  107.04  3.000
 FRG  H152  C15  C12   110.19  3.000
 FRG  H151  C15  C12   110.05  3.000
 FRG  H152  C15  C16   108.76  3.000
 FRG  H151  C15  C16   109.69  3.000
 FRG  C12   C15  C16   111.02  3.000
 FRG  C11   C12  C13   118.46  3.000
 FRG  C11   C12  C15   120.42  3.000
 FRG  C13   C12  C15   121.08  3.000
 FRG  H13   C13  C14   119.24  3.000
 FRG  H13   C13  C12   119.72  3.000
 FRG  C14   C13  C12   121.04  3.000
 FRG  H14   C14  C9    119.77  3.000
 FRG  H14   C14  C13   119.97  3.000
 FRG  C9    C14  C13   120.25  3.000
 FRG  H11   C11  C10   119.08  3.000
 FRG  H11   C11  C12   119.87  3.000
 FRG  C10   C11  C12   121.05  3.000
 FRG  H10   C10  C9    119.64  3.000
 FRG  H10   C10  C11   120.10  3.000
 FRG  C9    C10  C11   120.26  3.000
 FRG  C8    C9   C10   120.19  3.000
 FRG  C8    C9   C14   120.88  3.000
 FRG  C10   C9   C14   118.93  3.000
 FRG  C7    C8   C9    180.00  3.000
 FRG  C4    C7   C8    180.00  3.000
 FRG  C3    C4   C5    119.21  3.000
 FRG  C3    C4   C7    120.70  3.000
 FRG  C5    C4   C7    120.09  3.000
 FRG  H5    C5   C6    120.18  3.000
 FRG  H5    C5   C4    119.58  3.000
 FRG  C6    C5   C4    120.24  3.000
 FRG  H6    C6   C1    120.16  3.000
 FRG  H6    C6   C5    119.61  3.000
 FRG  C1    C6   C5    120.23  3.000
 FRG  H3    C3   C2    120.21  3.000
 FRG  H3    C3   C4    119.62  3.000
 FRG  C2    C3   C4    120.17  3.000
 FRG  H2    C2   C1    120.06  3.000
 FRG  H2    C2   C3    119.62  3.000
 FRG  C1    C2   C3    120.32  3.000
 FRG  H1    C1   C2    120.03  3.000
 FRG  H1    C1   C6    120.14  3.000
 FRG  C2    C1   C6    119.83  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
 FRG  CONST_01  C9    C14  C13  C12    0.00   0.0  0
 FRG  CONST_02  C9    C10  C11  C12    0.00   0.0  0
 FRG  CONST_03  C10   C11  C12  C13    0.00   0.0  0
 FRG  CONST_04  C10   C9   C14  C13    0.00   0.0  0
 FRG  CONST_05  C11   C12  C13  C14    0.00   0.0  0
 FRG  CONST_06  C11   C10  C9   C14    0.00   0.0  0
 FRG  CONST_07  C1    C6   C5   C4     0.00   0.0  0
 FRG  CONST_08  C1    C2   C3   C4     0.00   0.0  0
 FRG  CONST_09  C2    C3   C4   C5     0.00   0.0  0
 FRG  CONST_10  C2    C1   C6   C5     0.00   0.0  0
 FRG  CONST_11  C3    C4   C5   C6     0.00   0.0  0
 FRG  CONST_12  C3    C2   C1   C6     0.00   0.0  0
 FRG  CONST_13  C14   C13  C12  C15  180.00   0.0  0
 FRG  CONST_14  C10   C11  C12  C15  180.00   0.0  0
 FRG  CONST_15  C8    C9   C14  C13  180.00   0.0  0
 FRG  CONST_16  C8    C9   C10  C11  180.00   0.0  0
 FRG  CONST_17  C6    C5   C4   C7   180.00   0.0  0
 FRG  CONST_18  C2    C3   C4   C7   180.00   0.0  0
 FRG  CONST_19  H14   C14  C13  C12  180.00   0.0  0
 FRG  CONST_20  H10   C10  C11  C12  180.00   0.0  0
 FRG  CONST_21  H11   C11  C12  C13  180.00   0.0  0
 FRG  CONST_22  H13   C13  C12  C11  180.00   0.0  0
 FRG  CONST_23  H6    C6   C5   C4   180.00   0.0  0
 FRG  CONST_24  H2    C2   C3   C4   180.00   0.0  0
 FRG  CONST_25  H3    C3   C4   C5   180.00   0.0  0
 FRG  CONST_26  H1    C1   C6   C5   180.00   0.0  0
 FRG  CONST_27  H5    C5   C4   C3   180.00   0.0  0
 FRG  CONST_28  C30   N29  C31  N33    0.00   0.0  0
 FRG  CONST_30  C30   N29  C31  N32  180.00   0.0  0
 FRG  CONST_32  H33   N33  C31  N29  180.00   0.0  0
 FRG  CONST_34  H322  N32  C31  N29  180.00   0.0  0
 FRG  CONST_35  C16   N21  C22  C23  180.00   0.0  0
 FRG  CONST_36  C16   N21  C22  O25    0.00   0.0  0
 FRG  CONST_37  H21   N21  C22  C23    0.00   0.0  0
 FRG  Var_01    C26   C27  C28  N29   55.69  30.0  1
 FRG  Var_02    C27   C28  N29  C30  -58.89  30.0  1
 FRG  Var_03    C24   C30  N29  C28   58.25  30.0  1
 FRG  Var_04    C24   C26  C27  C28  -52.64  30.0  1
 FRG  Var_05    C13   C12  C15  C16  109.63  30.0  2
 FRG  Var_06    O25   C22  C23  C24  -68.47  30.0  3
 FRG  Var_07    H201  C20  O18  C17  -59.51  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
 FRG  chir_01  C24  C30  C26  C23  positiv
 FRG  chir_02  C16  N21  C17  C15  positiv

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
 FRG  plan-1  C15   0.020
 FRG  plan-1  C12   0.020
 FRG  plan-1  C13   0.020
 FRG  plan-1  C14   0.020
 FRG  plan-1  C11   0.020
 FRG  plan-1  C10   0.020
 FRG  plan-1  C9    0.020
 FRG  plan-1  C8    0.020
 FRG  plan-1  C7    0.020
 FRG  plan-1  H13   0.020
 FRG  plan-1  H14   0.020
 FRG  plan-1  H11   0.020
 FRG  plan-1  H10   0.020
 FRG  plan-2  C8    0.020
 FRG  plan-2  C7    0.020
 FRG  plan-2  C4    0.020
 FRG  plan-2  C5    0.020
 FRG  plan-2  C6    0.020
 FRG  plan-2  C3    0.020
 FRG  plan-2  C2    0.020
 FRG  plan-2  C1    0.020
 FRG  plan-2  H5    0.020
 FRG  plan-2  H6    0.020
 FRG  plan-2  H3    0.020
 FRG  plan-2  H2    0.020
 FRG  plan-2  H1    0.020
 FRG  plan-3  C23   0.020
 FRG  plan-3  C22   0.020
 FRG  plan-3  O25   0.020
 FRG  plan-3  N21   0.020
 FRG  plan-3  C16   0.020
 FRG  plan-3  H21   0.020
 FRG  plan-4  N33   0.020
 FRG  plan-4  C31   0.020
 FRG  plan-4  N32   0.020
 FRG  plan-4  N29   0.020
 FRG  plan-4  C30   0.020
 FRG  plan-4  C28   0.020
 FRG  plan-4  H33   0.020
 FRG  plan-4  H321  0.020
 FRG  plan-4  H322  0.020
 FRG  plan-5  C16   0.020
 FRG  plan-5  C17   0.020
 FRG  plan-5  O19   0.020
 FRG  plan-5  O18   0.020

