# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:26:18 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: [(1R)-3-methyl-1-({(2R)-2-[(morpholin-4-ylcarbonyl)amino]-3-naphthalen-1-ylpropanoyl}amino)butyl]boronic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](Cc1cccc2ccccc12)NC(=O)N3CCOCC3)B(O)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
 M1N  M1N  '[(1R)-3-methyl-1-({(2R)-2-[(morpholin-4-ylcarbonyl)amino]-3-naphthalen-1-ylpropanoyl}amino)butyl]boronic acid (non-preferred name)'  ligand  64  32  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M1N
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
 M1N  O3    O  O     0  -0.507  -1.9125   0.9776   1.3763
 M1N  C2    C  C     0   0.619  -1.5739   0.1211   0.5648
 M1N  N1    N  NH1   0  -0.664  -2.4555  -0.4214  -0.2745
 M1N  C15   C  CH1   0  -0.243  -3.8094   0.1052  -0.3431
 M1N  B     B  B     0   0.508  -4.3139   0.5005   1.1220
 M1N  O17   O  OH1   0  -0.632  -4.3678  -0.4892   2.0591
 M1N  O16   O  OH1   0  -0.623  -4.9083   1.7025   1.3956
 M1N  C22   C  CH2   0  -0.468  -4.7227  -0.9391  -0.9908
 M1N  C23   C  CH1   0  -0.261  -6.1625  -0.4760  -1.2259
 M1N  C25   C  CH3   0  -0.657  -6.2406   0.7132  -2.1795
 M1N  C24   C  CH3   0  -0.648  -6.9940  -1.6362  -1.7655
 M1N  C4    C  CH1   0  -0.183  -0.1472  -0.4303   0.5602
 M1N  N6    N  NH1   0  -0.681   0.7835   0.6238   0.8588
 M1N  C7    C  C     0   0.776   0.9119   1.6773   0.0103
 M1N  N9    N  NT    0  -0.515   1.9343   2.5543   0.2446
 M1N  C14   C  CH2   0  -0.306   2.2469   3.5234  -0.7941
 M1N  C13   C  CH2   0  -0.193   2.9046   4.7459  -0.1869
 M1N  O12   O  O2    0  -0.481   4.0469   4.4049   0.5661
 M1N  C11   C  CH2   0  -0.182   3.6943   3.5383   1.6166
 M1N  C10   C  CH2   0  -0.338   3.0606   2.2524   1.1129
 M1N  O8    O  O     0  -0.539   0.1085   1.8413  -0.9037
 M1N  C5    C  CH2   0  -0.629   0.2307  -1.2458  -0.6968
 M1N  C31   C  CR6   0   0.152   1.7072  -1.5119  -0.7699
 M1N  C36   C  CR16  0  -0.335   2.4868  -0.7612  -1.6139
 M1N  C35   C  CR16  0  -0.240   3.8854  -0.9211  -1.6699
 M1N  C34   C  CR16  0  -0.334   4.5031  -1.8424  -0.8732
 M1N  C33   C  CR66  0   0.114   3.7423  -2.6495   0.0047
 M1N  C40   C  CR16  0  -0.310   4.3633  -3.6175   0.8282
 M1N  C39   C  CR16  0  -0.261   3.6253  -4.4008   1.6725
 M1N  C38   C  CR16  0  -0.249   2.2252  -4.2517   1.7246
 M1N  C37   C  CR16  0  -0.341   1.5971  -3.3228   0.9391
 M1N  C32   C  CR66  0   0.087   2.3303  -2.4901   0.0583
 M1N  HN1   H  HNH1  0   0.407  -2.1467  -1.0313  -1.0145
 M1N  H15   H  HCH1  0   0.239  -3.7911   0.9952  -0.9860
 M1N  H17   H  HOH1  0   0.481  -4.7453  -0.2046   2.8976
 M1N  H16   H  HOH1  0   0.473  -4.8292   2.3314   0.6733
 M1N  H221  H  HCH2  0   0.236  -4.7323  -1.8387  -0.3679
 M1N  H222  H  HCH2  0   0.223  -4.2975  -1.2385  -1.9579
 M1N  H23   H  HCH1  0   0.232  -6.5990  -0.1771  -0.2650
 M1N  H251  H  HCH3  0   0.216  -5.7811   0.4666  -3.1400
 M1N  H252  H  HCH3  0   0.230  -7.2786   0.9893  -2.3713
 M1N  H253  H  HCH3  0   0.224  -5.7408   1.6017  -1.7922
 M1N  H241  H  HCH3  0   0.214  -6.5988  -1.9866  -2.7224
 M1N  H242  H  HCH3  0   0.226  -6.9972  -2.4828  -1.0768
 M1N  H243  H  HCH3  0   0.226  -8.0307  -1.3362  -1.9265
 M1N  H4    H  HCH1  0   0.300  -0.1080  -1.1025   1.4227
 M1N  HN6   H  HNH1  0   0.403   1.5042   0.4025   1.5217
 M1N  H141  H  HCH2  0   0.229   2.9101   3.0764  -1.5459
 M1N  H142  H  HCH2  0   0.265   1.3349   3.8303  -1.2998
 M1N  H131  H  HCH2  0   0.245   3.2220   5.4225  -0.9815
 M1N  H132  H  HCH2  0   0.208   2.1767   5.2768   0.4428
 M1N  H111  H  HCH2  0   0.248   4.6029   3.2983   2.1697
 M1N  H112  H  HCH2  0   0.210   2.9964   4.0349   2.3053
 M1N  H101  H  HCH2  0   0.257   2.7413   1.7030   1.9975
 M1N  H102  H  HCH2  0   0.242   3.8038   1.6405   0.5865
 M1N  H51   H  HCH2  0   0.268  -0.3311  -2.1836  -0.6902
 M1N  H52   H  HCH2  0   0.282  -0.0694  -0.7049  -1.5942
 M1N  H36   H  HCR6  0   0.251   2.0193  -0.0179  -2.2489
 M1N  H35   H  HCR6  0   0.257   4.4652  -0.3074  -2.3468
 M1N  H34   H  HCR6  0   0.254   5.5785  -1.9701  -0.9071
 M1N  H40   H  HCR6  0   0.255   5.4396  -3.7314   0.7773
 M1N  H39   H  HCR6  0   0.258   4.1127  -5.1386   2.2964
 M1N  H38   H  HCR6  0   0.260   1.6420  -4.8779   2.3870
 M1N  H37   H  HCR6  0   0.249   0.5196  -3.2381   0.9892

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
 M1N  O3   C2    double    1.228  0.020  1.228
 M1N  C2   N1    single    1.333  0.020  1.333
 M1N  C2   C4    single    1.530  0.020  1.530
 M1N  N1   C15   single    1.454  0.020  1.454
 M1N  N1   HN1   single    0.860  0.020  1.020
 M1N  C15  B     single    1.599  0.020  1.599
 M1N  C15  C22   single    1.531  0.020  1.531
 M1N  C15  H15   single    0.970  0.020  1.090
 M1N  B    O17   single    1.364  0.020  1.364
 M1N  B    O16   single    1.369  0.020  1.369
 M1N  O17  H17   single    0.850  0.020  0.980
 M1N  O16  H16   single    0.850  0.020  0.980
 M1N  C22  C23   single    1.531  0.020  1.531
 M1N  C22  H221  single    0.970  0.020  1.090
 M1N  C22  H222  single    0.970  0.020  1.090
 M1N  C23  C25   single    1.526  0.020  1.526
 M1N  C23  C24   single    1.526  0.020  1.526
 M1N  C23  H23   single    0.970  0.020  1.090
 M1N  C25  H251  single    0.970  0.020  1.090
 M1N  C25  H252  single    0.970  0.020  1.090
 M1N  C25  H253  single    0.970  0.020  1.090
 M1N  C24  H241  single    0.970  0.020  1.090
 M1N  C24  H242  single    0.970  0.020  1.090
 M1N  C24  H243  single    0.970  0.020  1.090
 M1N  C4   N6    single    1.438  0.020  1.438
 M1N  C4   C5    single    1.545  0.020  1.545
 M1N  C4   H4    single    0.970  0.020  1.090
 M1N  N6   C7    single    1.359  0.020  1.359
 M1N  N6   HN6   single    0.860  0.020  1.020
 M1N  C7   N9    single    1.367  0.020  1.367
 M1N  C7   O8    double    1.228  0.020  1.228
 M1N  N9   C14   single    1.455  0.020  1.455
 M1N  N9   C10   single    1.454  0.020  1.454
 M1N  C14  C13   single    1.515  0.020  1.515
 M1N  C14  H141  single    0.970  0.020  1.090
 M1N  C14  H142  single    0.970  0.020  1.090
 M1N  C13  O12   single    1.410  0.020  1.410
 M1N  C13  H131  single    0.970  0.020  1.090
 M1N  C13  H132  single    0.970  0.020  1.090
 M1N  O12  C11   single    1.407  0.020  1.407
 M1N  C11  C10   single    1.520  0.020  1.520
 M1N  C11  H111  single    0.970  0.020  1.090
 M1N  C11  H112  single    0.970  0.020  1.090
 M1N  C10  H101  single    0.970  0.020  1.090
 M1N  C10  H102  single    0.970  0.020  1.090
 M1N  C5   C31   single    1.502  0.020  1.502
 M1N  C5   H51   single    0.970  0.020  1.090
 M1N  C5   H52   single    0.970  0.020  1.090
 M1N  C31  C36   aromatic  1.372  0.020  1.372
 M1N  C31  C32   aromatic  1.425  0.020  1.425
 M1N  C36  C35   aromatic  1.409  0.020  1.409
 M1N  C36  H36   single    0.930  0.020  1.080
 M1N  C35  C34   aromatic  1.366  0.020  1.366
 M1N  C35  H35   single    0.930  0.020  1.080
 M1N  C34  C33   aromatic  1.415  0.020  1.415
 M1N  C34  H34   single    0.930  0.020  1.080
 M1N  C33  C40   aromatic  1.414  0.020  1.414
 M1N  C33  C32   aromatic  1.422  0.020  1.422
 M1N  C40  C39   aromatic  1.368  0.020  1.368
 M1N  C40  H40   single    0.930  0.020  1.080
 M1N  C39  C38   aromatic  1.409  0.020  1.409
 M1N  C39  H39   single    0.930  0.020  1.080
 M1N  C38  C37   aromatic  1.369  0.020  1.369
 M1N  C38  H38   single    0.930  0.020  1.080
 M1N  C37  C32   aromatic  1.417  0.020  1.417
 M1N  C37  H37   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
 M1N  C4    C2   N1    117.93  3.000
 M1N  C4    C2   O3    120.72  3.000
 M1N  N1    C2   O3    121.19  3.000
 M1N  HN1   N1   C15   118.03  3.000
 M1N  HN1   N1   C2    120.41  3.000
 M1N  C15   N1   C2    119.88  3.000
 M1N  H15   C15  C22   108.36  3.000
 M1N  H15   C15  B     109.96  3.000
 M1N  C22   C15  B     111.59  3.000
 M1N  H15   C15  N1    107.79  3.000
 M1N  C22   C15  N1    109.17  3.000
 M1N  B     C15  N1    109.88  3.000
 M1N  O16   B    O17   118.87  3.000
 M1N  O16   B    C15   122.50  3.000
 M1N  O17   B    C15   117.55  3.000
 M1N  H17   O17  B     113.54  3.000
 M1N  H16   O16  B     112.88  3.000
 M1N  H222  C22  H221  106.30  3.000
 M1N  H222  C22  C23   108.15  3.000
 M1N  H221  C22  C23   109.14  3.000
 M1N  H222  C22  C15   109.12  3.000
 M1N  H221  C22  C15   108.97  3.000
 M1N  C23   C22  C15   114.82  3.000
 M1N  H23   C23  C24   107.47  3.000
 M1N  H23   C23  C25   108.34  3.000
 M1N  C24   C23  C25   110.09  3.000
 M1N  H23   C23  C22   108.80  3.000
 M1N  C24   C23  C22   109.68  3.000
 M1N  C25   C23  C22   112.32  3.000
 M1N  H253  C25  H252  107.00  3.000
 M1N  H253  C25  H251  107.65  3.000
 M1N  H252  C25  H251  107.62  3.000
 M1N  H253  C25  C23   112.92  3.000
 M1N  H252  C25  C23   110.83  3.000
 M1N  H251  C25  C23   110.59  3.000
 M1N  H243  C24  H242  107.67  3.000
 M1N  H243  C24  H241  107.61  3.000
 M1N  H242  C24  H241  107.75  3.000
 M1N  H243  C24  C23   111.15  3.000
 M1N  H242  C24  C23   111.61  3.000
 M1N  H241  C24  C23   110.87  3.000
 M1N  H4    C4   C5    107.96  3.000
 M1N  H4    C4   N6    105.28  3.000
 M1N  C5    C4   N6    113.43  3.000
 M1N  H4    C4   C2    104.63  3.000
 M1N  C5    C4   C2    114.89  3.000
 M1N  N6    C4   C2    109.81  3.000
 M1N  HN6   N6   C7    121.02  3.000
 M1N  HN6   N6   C4    116.13  3.000
 M1N  C7    N6   C4    120.00  3.000
 M1N  O8    C7   N9    122.08  3.000
 M1N  O8    C7   N6    120.43  3.000
 M1N  N9    C7   N6    117.45  3.000
 M1N  C10   N9   C14   113.48  3.000
 M1N  C10   N9   C7    123.26  3.000
 M1N  C14   N9   C7    117.75  3.000
 M1N  H142  C14  H141  107.66  3.000
 M1N  H142  C14  C13   108.84  3.000
 M1N  H141  C14  C13   109.93  3.000
 M1N  H142  C14  N9    109.87  3.000
 M1N  H141  C14  N9    110.34  3.000
 M1N  C13   C14  N9    110.16  3.000
 M1N  H132  C13  H131  108.09  3.000
 M1N  H132  C13  O12   110.33  3.000
 M1N  H131  C13  O12   107.66  3.000
 M1N  H132  C13  C14   109.37  3.000
 M1N  H131  C13  C14   109.56  3.000
 M1N  O12   C13  C14   111.75  3.000
 M1N  C11   O12  C13   110.16  3.000
 M1N  H112  C11  H111  108.10  3.000
 M1N  H112  C11  C10   108.98  3.000
 M1N  H111  C11  C10   109.23  3.000
 M1N  H112  C11  O12   110.42  3.000
 M1N  H111  C11  O12   107.79  3.000
 M1N  C10   C11  O12   112.23  3.000
 M1N  H102  C10  H101  107.87  3.000
 M1N  H102  C10  C11   110.40  3.000
 M1N  H101  C10  C11   106.26  3.000
 M1N  H102  C10  N9    110.74  3.000
 M1N  H101  C10  N9    111.27  3.000
 M1N  C11   C10  N9    110.20  3.000
 M1N  H52   C5   H51   106.81  3.000
 M1N  H52   C5   C31   108.58  3.000
 M1N  H51   C5   C31   110.70  3.000
 M1N  H52   C5   C4    109.91  3.000
 M1N  H51   C5   C4    108.79  3.000
 M1N  C31   C5   C4    111.93  3.000
 M1N  C32   C31  C36   118.98  3.000
 M1N  C32   C31  C5    121.54  3.000
 M1N  C36   C31  C5    119.43  3.000
 M1N  H36   C36  C35   118.87  3.000
 M1N  H36   C36  C31   119.37  3.000
 M1N  C35   C36  C31   121.75  3.000
 M1N  H35   C35  C34   120.34  3.000
 M1N  H35   C35  C36   119.50  3.000
 M1N  C34   C35  C36   120.16  3.000
 M1N  H34   C34  C33   119.07  3.000
 M1N  H34   C34  C35   120.68  3.000
 M1N  C33   C34  C35   120.24  3.000
 M1N  C32   C33  C40   119.39  3.000
 M1N  C32   C33  C34   119.57  3.000
 M1N  C40   C33  C34   121.04  3.000
 M1N  H40   C40  C39   120.31  3.000
 M1N  H40   C40  C33   118.73  3.000
 M1N  C39   C40  C33   120.95  3.000
 M1N  H39   C39  C38   119.89  3.000
 M1N  H39   C39  C40   120.22  3.000
 M1N  C38   C39  C40   119.89  3.000
 M1N  H38   C38  C37   119.77  3.000
 M1N  H38   C38  C39   119.80  3.000
 M1N  C37   C38  C39   120.43  3.000
 M1N  H37   C37  C32   119.88  3.000
 M1N  H37   C37  C38   118.91  3.000
 M1N  C32   C37  C38   121.21  3.000
 M1N  C37   C32  C33   118.13  3.000
 M1N  C37   C32  C31   122.59  3.000
 M1N  C33   C32  C31   119.29  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
 M1N  CONST_01  C34   C35  C36  C31     0.00   0.0  0
 M1N  CONST_02  C34   C33  C32  C31     0.00   0.0  0
 M1N  CONST_03  C40   C33  C32  C31   180.00   0.0  0
 M1N  CONST_04  C38   C37  C32  C31   180.00   0.0  0
 M1N  CONST_05  C33   C32  C31  C36     0.00   0.0  0
 M1N  CONST_06  C37   C32  C31  C36   180.00   0.0  0
 M1N  CONST_07  C33   C34  C35  C36     0.00   0.0  0
 M1N  CONST_08  C32   C31  C36  C35     0.00   0.0  0
 M1N  CONST_09  C40   C33  C34  C35   180.00   0.0  0
 M1N  CONST_10  C32   C33  C34  C35     0.00   0.0  0
 M1N  CONST_11  C39   C40  C33  C34   180.00   0.0  0
 M1N  CONST_12  C37   C32  C33  C34   180.00   0.0  0
 M1N  CONST_13  C38   C39  C40  C33     0.00   0.0  0
 M1N  CONST_14  C38   C37  C32  C33     0.00   0.0  0
 M1N  CONST_15  C37   C32  C33  C40     0.00   0.0  0
 M1N  CONST_16  C37   C38  C39  C40     0.00   0.0  0
 M1N  CONST_17  C32   C33  C40  C39     0.00   0.0  0
 M1N  CONST_18  C32   C37  C38  C39     0.00   0.0  0
 M1N  CONST_19  C35   C36  C31  C5    180.00   0.0  0
 M1N  CONST_20  C33   C32  C31  C5    180.00   0.0  0
 M1N  CONST_21  C37   C32  C31  C5      0.00   0.0  0
 M1N  CONST_22  H35   C35  C36  C31   180.00   0.0  0
 M1N  CONST_23  H37   C37  C32  C31     0.00   0.0  0
 M1N  CONST_24  H34   C34  C35  C36   180.00   0.0  0
 M1N  CONST_25  H36   C36  C35  C34   180.00   0.0  0
 M1N  CONST_26  H40   C40  C33  C34     0.00   0.0  0
 M1N  CONST_27  H39   C39  C40  C33   180.00   0.0  0
 M1N  CONST_28  H38   C38  C39  C40   180.00   0.0  0
 M1N  CONST_29  O8    C7   N9   C14     0.00   0.0  0
 M1N  CONST_30  O8    C7   N9   C10   180.00   0.0  0
 M1N  CONST_31  C14   N9   C7   N6    180.00   0.0  0
 M1N  CONST_33  N9    C7   N6   C4    180.00   0.0  0
 M1N  CONST_34  HN6   N6   C7   N9      0.00   0.0  0
 M1N  CONST_35  C15   N1   C2   O3      0.00   0.0  0
 M1N  CONST_36  C4    C2   N1   C15   180.00   0.0  0
 M1N  CONST_37  O8    C7   N6   C4      0.00   0.0  0
 M1N  CONST_38  HN1   N1   C2   O3    180.00   0.0  0
 M1N  Var_01    O12   C13  C14  N9     55.32  30.0  1
 M1N  Var_02    O12   C11  C10  N9    -54.02  30.0  1
 M1N  Var_03    C11   C10  N9   C14    49.91  30.0  1
 M1N  Var_04    C10   N9   C14  C13   -50.70  30.0  1
 M1N  Var_05    C10   C11  O12  C13    59.53  30.0  1
 M1N  Var_06    C36   C31  C5   C4   -101.92  30.0  2
 M1N  Var_07    C25   C23  C22  C15    61.86  30.0  3
 M1N  Var_08    H251  C25  C23  C22    57.72  30.0  3
 M1N  Var_09    H241  C24  C23  C22   -61.28  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
 M1N  chir_01  C15  N1  B   C22  positiv
 M1N  chir_02  C4   N6  C5  C2   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
 M1N  plan-1  C5   0.020
 M1N  plan-1  C31  0.020
 M1N  plan-1  C36  0.020
 M1N  plan-1  C35  0.020
 M1N  plan-1  C34  0.020
 M1N  plan-1  C33  0.020
 M1N  plan-1  C40  0.020
 M1N  plan-1  C39  0.020
 M1N  plan-1  C38  0.020
 M1N  plan-1  C37  0.020
 M1N  plan-1  C32  0.020
 M1N  plan-1  H36  0.020
 M1N  plan-1  H35  0.020
 M1N  plan-1  H34  0.020
 M1N  plan-1  H40  0.020
 M1N  plan-1  H39  0.020
 M1N  plan-1  H38  0.020
 M1N  plan-1  H37  0.020
 M1N  plan-2  C4   0.020
 M1N  plan-2  N6   0.020
 M1N  plan-2  C7   0.020
 M1N  plan-2  N9   0.020
 M1N  plan-2  C14  0.020
 M1N  plan-2  C10  0.020
 M1N  plan-2  O8   0.020
 M1N  plan-2  HN6  0.020
 M1N  plan-3  O3   0.020
 M1N  plan-3  C2   0.020
 M1N  plan-3  N1   0.020
 M1N  plan-3  C15  0.020
 M1N  plan-3  C4   0.020
 M1N  plan-3  HN1  0.020

