FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5JM6Z

Calculation Name: 4NA2-B-Xray372

Preferred Name:

Target Type:

Ligand Name: (2s)-2-amino-3-oxopropyl 4-{[(2s)-2-hydroxy-4-methylpentanoyl]amino}butanoate

ligand 3-letter code: 2JF

PDB ID: 4NA2

Chain ID: B

ChEMBL ID:

UniProt ID: P40806

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 585
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12858136.902528
FMO2-HF: Nuclear repulsion 12628644.005915
FMO2-HF: Total energy -229492.896614
FMO2-MP2: Total energy -230160.497903


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:4:PHE)


Summations of interaction energy for fragment #1(B:4:PHE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-15.2870.0779999999999987.355-6.546-16.175-0.01
Interaction energy analysis for fragmet #1(B:4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.006
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B6PRO00.0200.0082.622-0.2383.3570.815-1.639-2.7710.007
4B7VAL00.0180.0083.6390.3560.6260.0050.113-0.3880.000
5B8ALA0-0.017-0.0065.927-0.098-0.0980.0000.0000.0000.000
6B9ILE00.010-0.0059.1830.1050.1050.0000.0000.0000.000
7B10VAL00.010-0.00611.4390.0290.0290.0000.0000.0000.000
8B11GLY00.0100.01814.6460.0390.0390.0000.0000.0000.000
9B12ILE0-0.047-0.01415.295-0.009-0.0090.0000.0000.0000.000
10B13SER0-0.019-0.01517.8220.0220.0220.0000.0000.0000.000
11B14GLY00.0240.00020.159-0.002-0.0020.0000.0000.0000.000
12B15ARG10.8330.94222.6740.0730.0730.0000.0000.0000.000
13B16PHE00.013-0.00320.6570.0030.0030.0000.0000.0000.000
14B17PRO00.0250.01826.4790.0000.0000.0000.0000.0000.000
15B18GLY00.0200.01429.614-0.002-0.0020.0000.0000.0000.000
16B19ALA0-0.067-0.02727.400-0.003-0.0030.0000.0000.0000.000
17B20MET00.0380.01828.6110.0000.0000.0000.0000.0000.000
18B21ASP-1-0.875-0.95526.508-0.120-0.1200.0000.0000.0000.000
19B22ILE00.024-0.00720.5990.0040.0040.0000.0000.0000.000
20B23ASP-1-0.787-0.87324.317-0.159-0.1590.0000.0000.0000.000
21B24GLU-1-0.900-0.93827.013-0.077-0.0770.0000.0000.0000.000
22B25PHE00.002-0.01121.0800.0070.0070.0000.0000.0000.000
23B26TRP00.0390.00622.9930.0010.0010.0000.0000.0000.000
24B27LYS10.9020.94525.8710.0860.0860.0000.0000.0000.000
25B28ASN00.0260.00829.1020.0100.0100.0000.0000.0000.000
26B29LEU0-0.0190.00123.2420.0060.0060.0000.0000.0000.000
27B30GLU-1-0.884-0.92827.458-0.096-0.0960.0000.0000.0000.000
28B31GLU-1-0.822-0.88229.073-0.069-0.0690.0000.0000.0000.000
29B32GLY0-0.0180.00430.3130.0060.0060.0000.0000.0000.000
30B33LYS10.7920.88831.3380.0700.0700.0000.0000.0000.000
31B34ASP-1-0.788-0.88331.053-0.028-0.0280.0000.0000.0000.000
32B35SER0-0.011-0.01830.619-0.001-0.0010.0000.0000.0000.000
33B36ILE0-0.063-0.01130.5540.0010.0010.0000.0000.0000.000
34B37THR0-0.001-0.00234.106-0.001-0.0010.0000.0000.0000.000
35B38GLU-1-0.855-0.92137.122-0.006-0.0060.0000.0000.0000.000
36B39VAL0-0.025-0.01537.474-0.003-0.0030.0000.0000.0000.000
37B40PRO0-0.0030.02237.6990.0010.0010.0000.0000.0000.000
38B41LYS10.8760.89940.6360.0110.0110.0000.0000.0000.000
39B42ASP-1-0.876-0.94439.024-0.021-0.0210.0000.0000.0000.000
40B43ARG10.7500.88033.4140.0250.0250.0000.0000.0000.000
41B44TRP00.0460.00735.9920.0020.0020.0000.0000.0000.000
42B45ASP-1-0.821-0.89842.348-0.007-0.0070.0000.0000.0000.000
43B46TRP00.000-0.02542.1950.0030.0030.0000.0000.0000.000
44B47ARG10.9290.96443.9700.0090.0090.0000.0000.0000.000
45B48GLU-1-0.941-0.94947.2080.0030.0030.0000.0000.0000.000
46B49HIS0-0.050-0.03843.9880.0040.0040.0000.0000.0000.000
47B50TYR0-0.0090.00743.9330.0020.0020.0000.0000.0000.000
48B51GLY00.007-0.00546.2750.0000.0000.0000.0000.0000.000
49B52ASN0-0.002-0.01845.7870.0000.0000.0000.0000.0000.000
50B53PRO00.0250.03541.7850.0010.0010.0000.0000.0000.000
51B54ASP-1-0.884-0.93043.1220.0340.0340.0000.0000.0000.000
52B55THR0-0.093-0.05845.2010.0010.0010.0000.0000.0000.000
53B56ASP-1-0.862-0.90347.7550.0170.0170.0000.0000.0000.000
54B57VAL0-0.010-0.01846.7360.0010.0010.0000.0000.0000.000
55B58ASN0-0.053-0.03644.3700.0000.0000.0000.0000.0000.000
56B59LYS10.8700.95745.052-0.014-0.0140.0000.0000.0000.000
57B60THR0-0.002-0.02040.2450.0020.0020.0000.0000.0000.000
58B61ASP-1-0.821-0.90841.2440.0150.0150.0000.0000.0000.000
59B62ILE0-0.049-0.01836.184-0.003-0.0030.0000.0000.0000.000
60B63LYS10.8480.91939.6150.0040.0040.0000.0000.0000.000
61B64TRP00.0270.00136.489-0.003-0.0030.0000.0000.0000.000
62B65GLY00.007-0.00633.2220.0040.0040.0000.0000.0000.000
63B66GLY00.0470.02430.483-0.003-0.0030.0000.0000.0000.000
64B67PHE0-0.001-0.00430.5840.0010.0010.0000.0000.0000.000
65B68ILE0-0.020-0.00228.039-0.004-0.0040.0000.0000.0000.000
66B69ASP-1-0.871-0.93431.589-0.048-0.0480.0000.0000.0000.000
67B70GLY0-0.019-0.01932.466-0.004-0.0040.0000.0000.0000.000
68B71VAL00.0240.00931.036-0.003-0.0030.0000.0000.0000.000
69B72ALA0-0.008-0.00933.0130.0010.0010.0000.0000.0000.000
70B73GLU-1-0.847-0.89933.736-0.059-0.0590.0000.0000.0000.000
71B74PHE0-0.029-0.02930.076-0.001-0.0010.0000.0000.0000.000
72B75ASP-1-0.798-0.90033.324-0.064-0.0640.0000.0000.0000.000
73B76PRO00.0120.00734.012-0.003-0.0030.0000.0000.0000.000
74B77LEU00.0330.00535.3260.0000.0000.0000.0000.0000.000
75B78PHE0-0.068-0.01329.409-0.001-0.0010.0000.0000.0000.000
76B79PHE0-0.014-0.02527.648-0.005-0.0050.0000.0000.0000.000
77B80GLY0-0.0280.00832.3400.0020.0020.0000.0000.0000.000
78B81ILE0-0.044-0.02131.7610.0040.0040.0000.0000.0000.000
79B82SER0-0.030-0.05836.248-0.001-0.0010.0000.0000.0000.000
80B83PRO00.045-0.00739.3280.0020.0020.0000.0000.0000.000
81B84ARG10.8750.95140.9240.0120.0120.0000.0000.0000.000
82B85GLU-1-0.820-0.88437.535-0.023-0.0230.0000.0000.0000.000
83B86ALA0-0.0020.00136.2910.0010.0010.0000.0000.0000.000
84B87ASP-1-0.823-0.90836.681-0.022-0.0220.0000.0000.0000.000
85B88TYR0-0.102-0.07537.9510.0030.0030.0000.0000.0000.000
86B89VAL0-0.046-0.00931.7750.0030.0030.0000.0000.0000.000
87B90ASP-1-0.815-0.91430.437-0.011-0.0110.0000.0000.0000.000
88B91PRO00.0470.02630.671-0.005-0.0050.0000.0000.0000.000
89B92GLN0-0.0010.00825.022-0.011-0.0110.0000.0000.0000.000
90B93GLN00.001-0.00425.971-0.011-0.0110.0000.0000.0000.000
91B94ARG10.8250.91227.1510.0220.0220.0000.0000.0000.000
92B95LEU00.0400.02526.240-0.009-0.0090.0000.0000.0000.000
93B96LEU00.0000.00921.785-0.011-0.0110.0000.0000.0000.000
94B97MET00.016-0.00823.384-0.010-0.0100.0000.0000.0000.000
95B98THR0-0.034-0.02725.333-0.010-0.0100.0000.0000.0000.000
96B99TYR00.004-0.02122.287-0.005-0.0050.0000.0000.0000.000
97B100VAL00.0080.01519.401-0.018-0.0180.0000.0000.0000.000
98B101TRP00.009-0.00221.069-0.017-0.0170.0000.0000.0000.000
99B102LYS10.8460.90823.5260.1060.1060.0000.0000.0000.000
100B103ALA0-0.0160.00317.999-0.011-0.0110.0000.0000.0000.000
101B104LEU00.0350.02118.715-0.026-0.0260.0000.0000.0000.000
102B105GLU-1-0.723-0.84520.693-0.148-0.1480.0000.0000.0000.000
103B106ASP-1-0.775-0.82819.818-0.260-0.2600.0000.0000.0000.000
104B107ALA00.0370.01617.710-0.015-0.0150.0000.0000.0000.000
105B108GLY0-0.065-0.01519.290-0.017-0.0170.0000.0000.0000.000
106B109CYS0-0.025-0.01319.322-0.010-0.0100.0000.0000.0000.000
107B110SER00.0450.02921.4670.0190.0190.0000.0000.0000.000
108B111PRO00.0460.02323.748-0.009-0.0090.0000.0000.0000.000
109B112GLN00.003-0.00224.9960.0050.0050.0000.0000.0000.000
110B113SER0-0.071-0.04122.868-0.003-0.0030.0000.0000.0000.000
111B114LEU00.0210.00118.373-0.013-0.0130.0000.0000.0000.000
112B115SER00.0220.04122.1970.0110.0110.0000.0000.0000.000
113B116GLY0-0.021-0.00624.532-0.005-0.0050.0000.0000.0000.000
114B117THR0-0.045-0.01619.1950.0010.0010.0000.0000.0000.000
115B118GLY00.0650.01717.7760.0180.0180.0000.0000.0000.000
116B119THR0-0.029-0.02915.702-0.014-0.0140.0000.0000.0000.000
117B120GLY00.0600.03714.4070.0300.0300.0000.0000.0000.000
118B121ILE0-0.064-0.03815.333-0.032-0.0320.0000.0000.0000.000
119B122PHE00.0190.01312.0520.0240.0240.0000.0000.0000.000
120B123ILE0-0.011-0.00815.177-0.023-0.0230.0000.0000.0000.000
121B124GLY00.0270.01417.6640.0240.0240.0000.0000.0000.000
122B125THR0-0.021-0.02218.968-0.011-0.0110.0000.0000.0000.000
123B126GLY00.0490.01922.6340.0130.0130.0000.0000.0000.000
124B127ASN0-0.017-0.01325.583-0.011-0.0110.0000.0000.0000.000
125B128THR00.0120.00328.0260.0050.0050.0000.0000.0000.000
126B129GLY00.0490.02930.726-0.002-0.0020.0000.0000.0000.000
127B130TYR00.018-0.00933.549-0.002-0.0020.0000.0000.0000.000
128B131LYS10.9070.94635.028-0.021-0.0210.0000.0000.0000.000
129B132ASP-1-0.842-0.92836.1830.0190.0190.0000.0000.0000.000
130B133LEU0-0.0060.00237.6710.0000.0000.0000.0000.0000.000
131B134PHE00.009-0.00438.481-0.001-0.0010.0000.0000.0000.000
132B135HIS0-0.025-0.00441.6390.0000.0000.0000.0000.0000.000
133B136ARG10.8030.86941.393-0.006-0.0060.0000.0000.0000.000
134B137ALA0-0.0120.00044.6110.0000.0000.0000.0000.0000.000
135B138ASN0-0.094-0.04846.4690.0000.0000.0000.0000.0000.000
136B139LEU0-0.0030.01943.8020.0000.0000.0000.0000.0000.000
137B140PRO0-0.014-0.00445.7330.0020.0020.0000.0000.0000.000
138B141ILE00.0170.00341.948-0.001-0.0010.0000.0000.0000.000
139B142GLU-1-0.802-0.88242.583-0.005-0.0050.0000.0000.0000.000
140B143GLY00.008-0.00941.1130.0020.0020.0000.0000.0000.000
141B144HIS00.0110.00138.5440.0010.0010.0000.0000.0000.000
142B145ALA00.0360.02236.806-0.001-0.0010.0000.0000.0000.000
143B146ALA00.0010.00435.3600.0010.0010.0000.0000.0000.000
144B147THR00.011-0.00832.1290.0010.0010.0000.0000.0000.000
145B148GLY00.0270.02632.028-0.004-0.0040.0000.0000.0000.000
146B149HIS0-0.068-0.05632.2620.0000.0000.0000.0000.0000.000
147B150MET0-0.0210.00133.1690.0030.0030.0000.0000.0000.000
148B151ILE0-0.0050.00227.8550.0060.0060.0000.0000.0000.000
149B152PRO00.0380.01725.368-0.006-0.0060.0000.0000.0000.000
150B153SER00.0320.01523.531-0.008-0.0080.0000.0000.0000.000
151B154VAL00.0140.01024.157-0.006-0.0060.0000.0000.0000.000
152B155GLY00.0230.01725.184-0.007-0.0070.0000.0000.0000.000
153B156PRO00.0030.00120.309-0.009-0.0090.0000.0000.0000.000
154B157ASN0-0.012-0.01822.208-0.009-0.0090.0000.0000.0000.000
155B158ARG10.8610.93224.0530.0230.0230.0000.0000.0000.000
156B159MET0-0.0310.00022.673-0.001-0.0010.0000.0000.0000.000
157B160SER00.0370.00621.315-0.015-0.0150.0000.0000.0000.000
158B161TYR0-0.045-0.02023.200-0.003-0.0030.0000.0000.0000.000
159B162PHE0-0.053-0.02526.728-0.004-0.0040.0000.0000.0000.000
160B163LEU0-0.013-0.00521.588-0.006-0.0060.0000.0000.0000.000
161B164ASN0-0.048-0.02224.938-0.001-0.0010.0000.0000.0000.000
162B165ILE0-0.0410.00018.995-0.009-0.0090.0000.0000.0000.000
163B166HIS0-0.034-0.03320.5180.0220.0220.0000.0000.0000.000
164B167GLY00.0060.02916.4370.0150.0150.0000.0000.0000.000
165B168PRO0-0.028-0.01313.8230.0060.0060.0000.0000.0000.000
166B169SER00.0380.03216.531-0.023-0.0230.0000.0000.0000.000
167B170GLU-1-0.812-0.88514.8600.0970.0970.0000.0000.0000.000
168B171PRO0-0.051-0.01917.974-0.019-0.0190.0000.0000.0000.000
169B172VAL0-0.025-0.03114.5240.0170.0170.0000.0000.0000.000
170B173GLU-1-0.862-0.94117.8030.0640.0640.0000.0000.0000.000
171B174THR00.000-0.01216.3950.0160.0160.0000.0000.0000.000
172B175ALA00.0360.01419.4030.0090.0090.0000.0000.0000.000
173B1762JF0-0.043-0.03520.869-0.003-0.0030.0000.0000.0000.000
174B177SER0-0.0030.01115.855-0.017-0.0170.0000.0000.0000.000
175B178SER00.0290.01515.5310.0040.0040.0000.0000.0000.000
176B179SER00.006-0.02815.490-0.006-0.0060.0000.0000.0000.000
177B180LEU0-0.071-0.02611.234-0.042-0.0420.0000.0000.0000.000
178B181VAL00.0180.00610.833-0.007-0.0070.0000.0000.0000.000
179B182ALA0-0.0140.00810.9610.0020.0020.0000.0000.0000.000
180B183ILE00.0070.0107.198-0.028-0.0280.0000.0000.0000.000
181B184HIS00.0480.0456.581-0.128-0.1280.0000.0000.0000.000
182B185ARG10.7820.8826.666-0.141-0.1410.0000.0000.0000.000
183B186ALA00.001-0.0048.9160.0140.0140.0000.0000.0000.000
184B187VAL00.013-0.0142.538-0.788-0.1590.756-0.242-1.143-0.001
185B188THR0-0.047-0.0384.6930.0160.152-0.001-0.011-0.1240.000
186B189ALA00.0050.0095.5490.1510.1510.0000.0000.0000.000
187B190MET0-0.061-0.0236.633-0.007-0.0070.0000.0000.0000.000
188B191GLN0-0.033-0.0122.691-3.946-0.4412.698-1.949-4.254-0.016
189B192ASN0-0.085-0.0556.1290.0100.0100.0000.0000.0000.000
190B193GLY00.0050.0049.028-0.009-0.0090.0000.0000.0000.000
191B194ASP-1-0.887-0.92411.1290.1400.1400.0000.0000.0000.000
192B195CYS0-0.098-0.04611.059-0.029-0.0290.0000.0000.0000.000
193B196GLU-1-0.833-0.90611.533-0.386-0.3860.0000.0000.0000.000
194B197MET0-0.047-0.01711.854-0.094-0.0940.0000.0000.0000.000
195B198ALA00.0310.00710.7750.0610.0610.0000.0000.0000.000
196B199ILE0-0.0220.00412.832-0.042-0.0420.0000.0000.0000.000
197B200ALA00.0310.01411.7940.0360.0360.0000.0000.0000.000
198B201GLY00.0500.00713.830-0.022-0.0220.0000.0000.0000.000
199B202GLY0-0.033-0.00916.0400.0270.0270.0000.0000.0000.000
200B203VAL0-0.032-0.01019.117-0.013-0.0130.0000.0000.0000.000
201B204ASN0-0.029-0.00322.8960.0170.0170.0000.0000.0000.000
202B205THR00.021-0.01025.430-0.004-0.0040.0000.0000.0000.000
203B206ILE0-0.040-0.02829.1990.0080.0080.0000.0000.0000.000
204B207LEU0-0.019-0.00432.195-0.003-0.0030.0000.0000.0000.000
205B208THR00.0160.01335.110-0.001-0.0010.0000.0000.0000.000
206B209GLU-1-0.761-0.84636.2980.0080.0080.0000.0000.0000.000
207B210GLU-1-0.942-0.97636.9760.0270.0270.0000.0000.0000.000
208B211ALA0-0.005-0.00732.4660.0030.0030.0000.0000.0000.000
209B212HIS00.0260.00333.7400.0050.0050.0000.0000.0000.000
210B213ILE00.0210.00936.1060.0030.0030.0000.0000.0000.000
211B214SER0-0.016-0.00635.6260.0030.0030.0000.0000.0000.000
212B215TYR00.035-0.00929.1130.0060.0060.0000.0000.0000.000
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