# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 21:44:04 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-[(6-carbamimidoylpyridin-3-yl)methyl]-N~2~-methyl-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N(C)C(=O)[C@@H](CC1CCCCC1)NCC(O)=O)C(=O)NCc2ccc(nc2)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
 NA9  NA9  N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-[(6-carbamimidoylpyridin-3-yl)methyl]-N~2~-methyl-L-alaninamide  ligand  66  32  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NA9
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
 NA9  C1    C  CR16  0  -0.275   7.2340  -5.2224   2.8081
 NA9  C2    C  CR6   0   0.125   5.9466  -4.7436   3.0099
 NA9  N3    N  N     0  -0.411   5.6257  -3.4693   2.8067
 NA9  C4    C  CR16  0  -0.105   6.5579  -2.6402   2.3744
 NA9  C5    C  CR6   0   0.043   7.8670  -3.0248   2.0955
 NA9  C6    C  CR16  0  -0.200   8.2005  -4.3478   2.3345
 NA9  C7    C  CH2   0  -0.360   8.8487  -2.0330   1.5290
 NA9  C8    C  C     0   0.351   4.8087  -5.6372   3.3879
 NA9  N9    N  NH2   0  -0.812   5.1512  -6.7720   4.0583
 NA9  N10   N  N     0  -0.636   3.6014  -5.3960   3.0559
 NA9  N11   N  NH1   0  -0.642   8.2717  -1.2631   0.4505
 NA9  C12   C  C     0   0.567   7.9371  -1.8362  -0.7170
 NA9  C13   C  CH1   0  -0.237   7.2785  -0.9159  -1.7519
 NA9  O14   O  O     0  -0.462   8.1792  -3.0048  -0.9642
 NA9  C15   C  CH3   0  -0.697   6.4017   0.1970  -1.1796
 NA9  N17   N  NT    0  -0.448   6.6619  -1.6925  -2.8147
 NA9  C18   C  C     0   0.566   5.7456  -2.6749  -2.6275
 NA9  C19   C  CH1   0  -0.209   4.8855  -2.7244  -1.3523
 NA9  O20   O  O     0  -0.497   5.5008  -3.4818  -3.5146
 NA9  N21   N  NH1   0  -0.565   4.4795  -4.0630  -1.0084
 NA9  C22   C  CH2   0  -0.384   5.5315  -4.9595  -0.6140
 NA9  C23   C  C     0   0.530   4.9602  -6.2797  -0.1645
 NA9  O24   O  OH1   0  -0.593   5.8794  -7.0279   0.4360
 NA9  O25   O  O     0  -0.441   3.8271  -6.6420  -0.3501
 NA9  C26   C  CH2   0  -0.438   3.6288  -1.8814  -1.6234
 NA9  C27   C  CH1   0  -0.201   2.5942  -1.8907  -0.4996
 NA9  C28   C  CH2   0  -0.458   3.1514  -1.3929   0.8310
 NA9  C29   C  CH2   0  -0.425   2.0872  -1.3784   1.9242
 NA9  C30   C  CH2   0  -0.428   0.8685  -0.5601   1.5120
 NA9  C31   C  CH2   0  -0.431   0.3051  -1.0513   0.1828
 NA9  C32   C  CH2   0  -0.414   1.3754  -1.0599  -0.9038
 NA9  H1    H  HCR6  0   0.273   7.4716  -6.2652   2.9631
 NA9  H4    H  HCR6  0   0.261   6.2484  -1.6104   2.2240
 NA9  H6    H  HCR6  0   0.273   9.2016  -4.7067   2.1286
 NA9  H71   H  HCH2  0   0.288   9.1588  -1.3270   2.2995
 NA9  H72   H  HCH2  0   0.268   9.7477  -2.5510   1.1919
 NA9  HN91  H  HNH2  0   0.385   4.3867  -7.3214   4.4169
 NA9  HN92  H  HNH2  0   0.391   5.9563  -6.7487   4.6616
 NA9  HN10  H  H     0   0.332   3.5665  -4.5475   2.4994
 NA9  HN11  H  HNH1  0   0.415   8.0490  -0.2985   0.6266
 NA9  H13   H  HCH1  0   0.312   8.1232  -0.4068  -2.2242
 NA9  H151  H  HCH3  0   0.242   5.6289  -0.1629  -0.5040
 NA9  H152  H  HCH3  0   0.255   7.0038   0.9289  -0.6414
 NA9  H153  H  HCH3  0   0.265   5.9194   0.7322  -1.9957
 NA9  H161  H  HCH3  0   0.251   6.6456  -1.8596  -4.9099
 NA9  H162  H  HCH3  0   0.236   8.1496  -2.4004  -4.1530
 NA9  H163  H  HCH3  0   0.244   7.7683  -0.6759  -4.2553
 NA9  H19   H  HCH1  0   0.236   5.4138  -2.3108  -0.4895
 NA9  HN21  H  HNH1  0   0.343   3.9416  -4.4620  -1.7673
 NA9  H221  H  HCH2  0   0.268   6.0971  -4.5214   0.2104
 NA9  H222  H  HCH2  0   0.248   6.2773  -5.1751  -1.3951
 NA9  HO24  H  HOH1  0   0.478   5.4945  -7.8755   0.7030
 NA9  H261  H  HCH2  0   0.237   3.1567  -2.2583  -2.5374
 NA9  H262  H  HCH2  0   0.237   3.9229  -0.8520  -1.8432
 NA9  H27   H  HCH1  0   0.215   2.2664  -2.9258  -0.3534
 NA9  H281  H  HCH2  0   0.199   3.5527  -0.3788   0.7029
 NA9  H282  H  HCH2  0   0.253   3.9808  -2.0259   1.1532
 NA9  H291  H  HCH2  0   0.224   2.5117  -0.9903   2.8536
 NA9  H292  H  HCH2  0   0.206   1.7765  -2.4081   2.1351
 NA9  H301  H  HCH2  0   0.224   0.1015  -0.6018   2.2894
 NA9  H302  H  HCH2  0   0.206   1.1565   0.4928   1.4158
 NA9  H311  H  HCH2  0   0.207  -0.0888  -2.0661   0.3093
 NA9  H312  H  HCH2  0   0.223  -0.5392  -0.4294  -0.1260
 NA9  H321  H  HCH2  0   0.221   0.9574  -1.4417  -1.8405
 NA9  H322  H  HCH2  0   0.202   1.6947  -0.0303  -1.1068
 NA9  C16   C  CH3   0  -0.529   7.3431  -1.6649  -4.1000

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
 NA9  C1   C6    aromatic  1.387  0.020  1.387
 NA9  C1   C2    aromatic  1.388  0.020  1.388
 NA9  C1   H1    single    0.930  0.020  1.080
 NA9  C2   N3    aromatic  1.330  0.020  1.330
 NA9  C2   C8    single    1.495  0.020  1.495
 NA9  N3   C4    aromatic  1.320  0.020  1.320
 NA9  C4   C5    aromatic  1.393  0.020  1.393
 NA9  C4   H4    single    0.930  0.020  1.080
 NA9  C5   C7    single    1.506  0.020  1.506
 NA9  C5   C6    aromatic  1.385  0.020  1.385
 NA9  C6   H6    single    0.930  0.020  1.080
 NA9  C7   N11   single    1.445  0.020  1.445
 NA9  C7   H71   single    0.970  0.020  1.090
 NA9  C7   H72   single    0.970  0.020  1.090
 NA9  C8   N9    single    1.362  0.020  1.362
 NA9  C8   N10   double    1.275  0.020  1.275
 NA9  N9   HN91  single    0.890  0.020  1.040
 NA9  N9   HN92  single    0.890  0.020  1.040
 NA9  N10  HN10  single    0.890  0.020  1.040
 NA9  N11  C12   single    1.343  0.020  1.343
 NA9  N11  HN11  single    0.860  0.020  1.020
 NA9  C12  O14   double    1.219  0.020  1.219
 NA9  C12  C13   single    1.534  0.020  1.534
 NA9  C13  C15   single    1.528  0.020  1.528
 NA9  C13  N17   single    1.454  0.020  1.454
 NA9  C13  H13   single    0.970  0.020  1.090
 NA9  C15  H151  single    0.970  0.020  1.090
 NA9  C15  H152  single    0.970  0.020  1.090
 NA9  C15  H153  single    0.970  0.020  1.090
 NA9  C16  N17   single    1.455  0.020  1.455
 NA9  C16  H161  single    0.970  0.020  1.090
 NA9  C16  H162  single    0.970  0.020  1.090
 NA9  C16  H163  single    0.970  0.020  1.090
 NA9  N17  C18   single    1.356  0.020  1.356
 NA9  C18  O20   double    1.224  0.020  1.224
 NA9  C18  C19   single    1.539  0.020  1.539
 NA9  C19  N21   single    1.441  0.020  1.441
 NA9  C19  C26   single    1.537  0.020  1.537
 NA9  C19  H19   single    0.970  0.020  1.090
 NA9  N21  C22   single    1.437  0.020  1.437
 NA9  N21  HN21  single    0.890  0.020  1.040
 NA9  C22  C23   single    1.507  0.020  1.507
 NA9  C22  H221  single    0.970  0.020  1.090
 NA9  C22  H222  single    0.970  0.020  1.090
 NA9  C23  O25   double    1.204  0.020  1.204
 NA9  C23  O24   single    1.329  0.020  1.329
 NA9  O24  HO24  single    0.850  0.020  0.980
 NA9  C26  C27   single    1.527  0.020  1.527
 NA9  C26  H261  single    0.970  0.020  1.090
 NA9  C26  H262  single    0.970  0.020  1.090
 NA9  C27  C28   single    1.526  0.020  1.526
 NA9  C27  C32   single    1.529  0.020  1.529
 NA9  C27  H27   single    0.970  0.020  1.090
 NA9  C28  C29   single    1.526  0.020  1.526
 NA9  C28  H281  single    0.970  0.020  1.090
 NA9  C28  H282  single    0.970  0.020  1.090
 NA9  C29  C30   single    1.525  0.020  1.525
 NA9  C29  H291  single    0.970  0.020  1.090
 NA9  C29  H292  single    0.970  0.020  1.090
 NA9  C30  C31   single    1.525  0.020  1.525
 NA9  C30  H301  single    0.970  0.020  1.090
 NA9  C30  H302  single    0.970  0.020  1.090
 NA9  C31  C32   single    1.525  0.020  1.525
 NA9  C31  H311  single    0.970  0.020  1.090
 NA9  C31  H312  single    0.970  0.020  1.090
 NA9  C32  H321  single    0.970  0.020  1.090
 NA9  C32  H322  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
 NA9  H1    C1   C6    120.29  3.000
 NA9  H1    C1   C2    121.05  3.000
 NA9  C6    C1   C2    118.58  3.000
 NA9  C8    C2   N3    115.32  3.000
 NA9  C8    C2   C1    122.43  3.000
 NA9  N3    C2   C1    122.14  3.000
 NA9  C4    N3   C2    118.78  3.000
 NA9  H4    C4   C5    120.14  3.000
 NA9  H4    C4   N3    116.09  3.000
 NA9  C5    C4   N3    123.77  3.000
 NA9  C7    C5   C6    122.48  3.000
 NA9  C6    C5   C4    117.10  3.000
 NA9  C7    C5   C4    120.41  3.000
 NA9  H6    C6   C5    120.41  3.000
 NA9  H6    C6   C1    120.00  3.000
 NA9  C5    C6   C1    119.57  3.000
 NA9  H72   C7   H71   106.95  3.000
 NA9  H72   C7   N11   110.57  3.000
 NA9  H71   C7   N11   107.22  3.000
 NA9  H72   C7   C5    109.92  3.000
 NA9  H71   C7   C5    110.25  3.000
 NA9  N11   C7   C5    111.79  3.000
 NA9  N10   C8   N9    121.59  3.000
 NA9  N10   C8   C2    122.80  3.000
 NA9  N9    C8   C2    115.53  3.000
 NA9  HN92  N9   HN91  113.98  3.000
 NA9  HN92  N9   C8    118.50  3.000
 NA9  HN91  N9   C8    116.03  3.000
 NA9  HN10  N10  C8    109.47  3.000
 NA9  HN11  N11  C12   120.43  3.000
 NA9  HN11  N11  C7    117.95  3.000
 NA9  C12   N11  C7    121.39  3.000
 NA9  O14   C12  C13   121.59  3.000
 NA9  C13   C12  N11   115.95  3.000
 NA9  O14   C12  N11   122.41  3.000
 NA9  H13   C13  N17   105.11  3.000
 NA9  H13   C13  C15   105.42  3.000
 NA9  N17   C13  C15   114.81  3.000
 NA9  H13   C13  C12   103.83  3.000
 NA9  N17   C13  C12   110.79  3.000
 NA9  C15   C13  C12   115.52  3.000
 NA9  H153  C15  H152  106.55  3.000
 NA9  H153  C15  H151  108.27  3.000
 NA9  H152  C15  H151  107.93  3.000
 NA9  H153  C15  C13   109.36  3.000
 NA9  H152  C15  C13   110.92  3.000
 NA9  H151  C15  C13   113.53  3.000
 NA9  C18   N17  C16   116.87  3.000
 NA9  C18   N17  C13   124.93  3.000
 NA9  C16   N17  C13   115.92  3.000
 NA9  O20   C18  C19   117.88  3.000
 NA9  C19   C18  N17   121.01  3.000
 NA9  O20   C18  N17   120.84  3.000
 NA9  H19   C19  C26   109.07  3.000
 NA9  H19   C19  N21   107.42  3.000
 NA9  C26   C19  N21   108.74  3.000
 NA9  H19   C19  C18   111.83  3.000
 NA9  C26   C19  C18   107.05  3.000
 NA9  N21   C19  C18   112.66  3.000
 NA9  HN21  N21  C22   110.42  3.000
 NA9  HN21  N21  C19   109.70  3.000
 NA9  C22   N21  C19   116.03  3.000
 NA9  H222  C22  H221  105.27  3.000
 NA9  H222  C22  C23   107.26  3.000
 NA9  H221  C22  C23   108.83  3.000
 NA9  H222  C22  N21   115.03  3.000
 NA9  H221  C22  N21   109.64  3.000
 NA9  C23   C22  N21   110.53  3.000
 NA9  O25   C23  O24   123.45  3.000
 NA9  O24   C23  C22   111.46  3.000
 NA9  O25   C23  C22   125.06  3.000
 NA9  HO24  O24  C23   110.03  3.000
 NA9  H262  C26  H261  105.80  3.000
 NA9  H262  C26  C27   109.63  3.000
 NA9  H261  C26  C27   108.65  3.000
 NA9  H262  C26  C19   109.39  3.000
 NA9  H261  C26  C19   108.10  3.000
 NA9  C27   C26  C19   114.87  3.000
 NA9  H27   C27  C32   108.06  3.000
 NA9  H27   C27  C28   107.52  3.000
 NA9  C32   C27  C28   110.13  3.000
 NA9  H27   C27  C26   107.86  3.000
 NA9  C32   C27  C26   110.00  3.000
 NA9  C28   C27  C26   113.09  3.000
 NA9  H282  C28  H281  106.99  3.000
 NA9  H282  C28  C29   108.90  3.000
 NA9  H281  C28  C29   109.25  3.000
 NA9  H282  C28  C27   110.21  3.000
 NA9  H281  C28  C27   109.45  3.000
 NA9  C29   C28  C27   111.91  3.000
 NA9  H292  C29  H291  106.26  3.000
 NA9  H292  C29  C30   109.25  3.000
 NA9  H291  C29  C30   110.47  3.000
 NA9  H292  C29  C28   109.07  3.000
 NA9  H291  C29  C28   109.99  3.000
 NA9  C30   C29  C28   111.65  3.000
 NA9  H302  C30  H301  106.48  3.000
 NA9  H302  C30  C31   109.27  3.000
 NA9  H301  C30  C31   110.39  3.000
 NA9  H302  C30  C29   109.23  3.000
 NA9  H301  C30  C29   110.37  3.000
 NA9  C31   C30  C29   110.98  3.000
 NA9  H312  C31  H311  106.36  3.000
 NA9  H312  C31  C32   110.11  3.000
 NA9  H311  C31  C32   109.22  3.000
 NA9  H312  C31  C30   110.39  3.000
 NA9  H311  C31  C30   109.30  3.000
 NA9  C32   C31  C30   111.32  3.000
 NA9  H322  C32  H321  106.27  3.000
 NA9  H322  C32  C31   109.31  3.000
 NA9  H321  C32  C31   110.11  3.000
 NA9  H322  C32  C27   109.08  3.000
 NA9  H321  C32  C27   109.94  3.000
 NA9  C31   C32  C27   111.96  3.000
 NA9  H163  C16  H162  108.45  3.000
 NA9  H163  C16  H161  107.91  3.000
 NA9  H162  C16  H161  108.49  3.000
 NA9  H163  C16  N17   109.05  3.000
 NA9  H162  C16  N17   112.06  3.000
 NA9  H161  C16  N17   110.77  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
 NA9  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 NA9  CONST_02  C4    N3   C2   C1      0.00   0.0  0
 NA9  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 NA9  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 NA9  CONST_05  C6    C1   C2   N3      0.00   0.0  0
 NA9  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 NA9  CONST_07  C7    C5   C6   C1    180.00   0.0  0
 NA9  CONST_08  C7    C5   C4   N3    180.00   0.0  0
 NA9  CONST_09  C8    C2   N3   C4    180.00   0.0  0
 NA9  CONST_10  C8    C2   C1   C6    180.00   0.0  0
 NA9  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 NA9  CONST_12  H4    C4   N3   C2    180.00   0.0  0
 NA9  CONST_13  H1    C1   C2   N3    180.00   0.0  0
 NA9  CONST_14  HN91  N9   C8   C2    180.00   0.0  0
 NA9  CONST_16  HN10  N10  C8   C2      0.00   0.0  0
 NA9  CONST_17  O14   C12  N11  C7      0.00   0.0  0
 NA9  CONST_18  C13   C12  N11  C7    180.00   0.0  0
 NA9  CONST_21  O20   C18  N17  C16     0.00   0.0  0
 NA9  CONST_22  C19   C18  N17  C16   180.00   0.0  0
 NA9  CONST_23  HN11  N11  C12  C13     0.00   0.0  0
 NA9  CONST_24  HO24  O24  C23  C22   180.00   0.0  0
 NA9  Var_01    C30   C29  C28  C27   -55.36  30.0  1
 NA9  Var_02    C30   C31  C32  C27    55.79  30.0  1
 NA9  Var_03    C31   C30  C29  C28    54.66  30.0  1
 NA9  Var_04    C32   C31  C30  C29   -54.79  30.0  1
 NA9  Var_05    N9    C8   C2   C1     26.73  30.0  2
 NA9  Var_06    N11   C7   C5   C4    -45.54  30.0  2
 NA9  Var_07    C12   N11  C7   C5    -66.99  30.0  3
 NA9  Var_08    C23   C22  N21  C19   174.91  30.0  3
 NA9  Var_09    O25   C23  C22  N21    13.67  30.0  3
 NA9  Var_10    H161  C16  N17  C13  -154.36  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
 NA9  chir_01  C13  C12  C15  N17  positiv
 NA9  chir_02  C19  N21  C26  C18  positiv
 NA9  chir_03  C27  C26  C28  C32  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
 NA9  plan-1  C1    0.020
 NA9  plan-1  C2    0.020
 NA9  plan-1  N3    0.020
 NA9  plan-1  C4    0.020
 NA9  plan-1  C5    0.020
 NA9  plan-1  C6    0.020
 NA9  plan-1  C7    0.020
 NA9  plan-1  C8    0.020
 NA9  plan-1  H1    0.020
 NA9  plan-1  H4    0.020
 NA9  plan-1  H6    0.020
 NA9  plan-2  C7    0.020
 NA9  plan-2  N11   0.020
 NA9  plan-2  C12   0.020
 NA9  plan-2  C13   0.020
 NA9  plan-2  O14   0.020
 NA9  plan-2  HN11  0.020
 NA9  plan-3  C13   0.020
 NA9  plan-3  N17   0.020
 NA9  plan-3  C18   0.020
 NA9  plan-3  C19   0.020
 NA9  plan-3  O20   0.020
 NA9  plan-3  C16   0.020
 NA9  plan-4  C2    0.020
 NA9  plan-4  C8    0.020
 NA9  plan-4  N9    0.020
 NA9  plan-4  N10   0.020
 NA9  plan-4  HN91  0.020
 NA9  plan-4  HN92  0.020
 NA9  plan-4  HN10  0.020
 NA9  plan-5  C22   0.020
 NA9  plan-5  C23   0.020
 NA9  plan-5  O24   0.020
 NA9  plan-5  O25   0.020
 NA9  plan-5  HO24  0.020

