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: 4J7ZN

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 OptH
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 -12848815.883527
FMO2-HF: Nuclear repulsion 12619325.530092
FMO2-HF: Total energy -229490.353435
FMO2-MP2: Total energy -230157.73027


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.
-12.4841.1228.165-5.787-15.985-0.011
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 : -0.050 / q_NPA : -0.041
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].
3B6PRO00.0060.0132.638-0.5182.6430.958-1.281-2.8380.003
4B7VAL00.0240.0083.6120.1530.4690.0160.151-0.4830.001
5B8ALA0-0.012-0.0045.631-0.158-0.1580.0000.0000.0000.000
6B9ILE00.006-0.0059.0030.0750.0750.0000.0000.0000.000
7B10VAL0-0.007-0.01011.2290.0300.0300.0000.0000.0000.000
8B11GLY00.0280.01714.4230.0380.0380.0000.0000.0000.000
9B12ILE0-0.047-0.00715.309-0.022-0.0220.0000.0000.0000.000
10B13SER0-0.019-0.01617.7510.0180.0180.0000.0000.0000.000
11B14GLY00.0200.00020.193-0.009-0.0090.0000.0000.0000.000
12B15ARG10.8450.94622.7160.0820.0820.0000.0000.0000.000
13B16PHE0-0.006-0.01120.590-0.003-0.0030.0000.0000.0000.000
14B17PRO00.0150.01526.5550.0030.0030.0000.0000.0000.000
15B18GLY00.0130.01129.659-0.003-0.0030.0000.0000.0000.000
16B19ALA0-0.058-0.01327.395-0.001-0.0010.0000.0000.0000.000
17B20MET00.0200.00028.636-0.001-0.0010.0000.0000.0000.000
18B21ASP-1-0.870-0.95326.488-0.107-0.1070.0000.0000.0000.000
19B22ILE00.016-0.00821.033-0.001-0.0010.0000.0000.0000.000
20B23ASP-1-0.896-0.94424.232-0.139-0.1390.0000.0000.0000.000
21B24GLU-1-0.885-0.92626.871-0.085-0.0850.0000.0000.0000.000
22B25PHE0-0.004-0.01221.1560.0020.0020.0000.0000.0000.000
23B26TRP00.025-0.00523.068-0.004-0.0040.0000.0000.0000.000
24B27LYS10.9590.99525.7320.0870.0870.0000.0000.0000.000
25B28ASN0-0.012-0.01328.8370.0070.0070.0000.0000.0000.000
26B29LEU0-0.036-0.01123.0370.0030.0030.0000.0000.0000.000
27B30GLU-1-1.012-1.00127.358-0.112-0.1120.0000.0000.0000.000
28B31GLU-1-0.927-0.97728.907-0.080-0.0800.0000.0000.0000.000
29B32GLY0-0.042-0.00830.2230.0050.0050.0000.0000.0000.000
30B33LYS10.8880.94431.2450.0820.0820.0000.0000.0000.000
31B34ASP-1-0.863-0.94031.033-0.070-0.0700.0000.0000.0000.000
32B35SER0-0.010-0.02230.8000.0030.0030.0000.0000.0000.000
33B36ILE0-0.070-0.00930.7350.0020.0020.0000.0000.0000.000
34B37THR0-0.012-0.00934.2100.0010.0010.0000.0000.0000.000
35B38GLU-1-0.920-0.97737.275-0.035-0.0350.0000.0000.0000.000
36B39VAL0-0.017-0.00937.568-0.002-0.0020.0000.0000.0000.000
37B40PRO00.0020.02637.8090.0020.0020.0000.0000.0000.000
38B41LYS10.9010.91940.8140.0280.0280.0000.0000.0000.000
39B42ASP-1-0.912-0.95639.994-0.038-0.0380.0000.0000.0000.000
40B43ARG10.7730.89133.5850.0470.0470.0000.0000.0000.000
41B44TRP00.020-0.00436.3260.0020.0020.0000.0000.0000.000
42B45ASP-1-0.844-0.92342.607-0.027-0.0270.0000.0000.0000.000
43B46TRP00.022-0.00642.4190.0020.0020.0000.0000.0000.000
44B47ARG10.9360.96344.2160.0280.0280.0000.0000.0000.000
45B48GLU-1-0.973-0.96447.568-0.018-0.0180.0000.0000.0000.000
46B49HIS0-0.035-0.02844.2380.0020.0020.0000.0000.0000.000
47B50TYR00.0000.00344.6150.0000.0000.0000.0000.0000.000
48B51GLY0-0.015-0.01646.5370.0020.0020.0000.0000.0000.000
49B52ASN00.010-0.00146.073-0.002-0.0020.0000.0000.0000.000
50B53PRO00.0420.04442.2050.0020.0020.0000.0000.0000.000
51B54ASP-1-0.884-0.93243.266-0.015-0.0150.0000.0000.0000.000
52B55THR0-0.092-0.05445.4890.0010.0010.0000.0000.0000.000
53B56ASP-1-0.885-0.92448.047-0.014-0.0140.0000.0000.0000.000
54B57VAL0-0.010-0.02246.9750.0000.0000.0000.0000.0000.000
55B58ASN0-0.056-0.03644.5680.0000.0000.0000.0000.0000.000
56B59LYS10.9230.98645.4540.0160.0160.0000.0000.0000.000
57B60THR00.0290.00139.8510.0000.0000.0000.0000.0000.000
58B61ASP-1-0.826-0.91041.566-0.026-0.0260.0000.0000.0000.000
59B62ILE0-0.062-0.01836.457-0.002-0.0020.0000.0000.0000.000
60B63LYS10.8740.94439.8640.0350.0350.0000.0000.0000.000
61B64TRP00.017-0.00136.688-0.001-0.0010.0000.0000.0000.000
62B65GLY00.003-0.00833.4170.0020.0020.0000.0000.0000.000
63B66GLY00.0440.02630.633-0.001-0.0010.0000.0000.0000.000
64B67PHE00.004-0.00230.759-0.001-0.0010.0000.0000.0000.000
65B68ILE0-0.021-0.00728.259-0.003-0.0030.0000.0000.0000.000
66B69ASP-1-0.867-0.93031.717-0.058-0.0580.0000.0000.0000.000
67B70GLY0-0.014-0.01832.582-0.003-0.0030.0000.0000.0000.000
68B71VAL00.0070.00431.141-0.002-0.0020.0000.0000.0000.000
69B72ALA0-0.022-0.01633.1950.0010.0010.0000.0000.0000.000
70B73GLU-1-0.941-0.96834.093-0.053-0.0530.0000.0000.0000.000
71B74PHE0-0.045-0.03230.214-0.002-0.0020.0000.0000.0000.000
72B75ASP-1-0.828-0.91833.466-0.042-0.0420.0000.0000.0000.000
73B76PRO00.0100.00534.148-0.001-0.0010.0000.0000.0000.000
74B77LEU00.0340.00235.4960.0020.0020.0000.0000.0000.000
75B78PHE0-0.081-0.01829.3360.0020.0020.0000.0000.0000.000
76B79PHE0-0.013-0.02227.724-0.001-0.0010.0000.0000.0000.000
77B80GLY0-0.0280.00632.4980.0030.0030.0000.0000.0000.000
78B81ILE0-0.034-0.01631.9310.0030.0030.0000.0000.0000.000
79B82SER0-0.037-0.05236.338-0.001-0.0010.0000.0000.0000.000
80B83PRO00.049-0.00439.4530.0000.0000.0000.0000.0000.000
81B84ARG10.9470.99141.1410.0130.0130.0000.0000.0000.000
82B85GLU-1-0.827-0.89837.539-0.014-0.0140.0000.0000.0000.000
83B86ALA00.0090.00836.449-0.001-0.0010.0000.0000.0000.000
84B87ASP-1-0.834-0.91336.869-0.025-0.0250.0000.0000.0000.000
85B88TYR0-0.041-0.03337.9490.0010.0010.0000.0000.0000.000
86B89VAL0-0.033-0.00131.8470.0010.0010.0000.0000.0000.000
87B90ASP-1-0.835-0.92530.416-0.036-0.0360.0000.0000.0000.000
88B91PRO00.0350.02430.856-0.003-0.0030.0000.0000.0000.000
89B92GLN00.0140.03225.386-0.008-0.0080.0000.0000.0000.000
90B93GLN00.0170.00526.240-0.006-0.0060.0000.0000.0000.000
91B94ARG10.8300.91427.3980.0320.0320.0000.0000.0000.000
92B95LEU00.0430.02626.449-0.004-0.0040.0000.0000.0000.000
93B96LEU00.0040.01421.921-0.008-0.0080.0000.0000.0000.000
94B97MET00.011-0.01023.566-0.006-0.0060.0000.0000.0000.000
95B98THR0-0.026-0.02425.470-0.003-0.0030.0000.0000.0000.000
96B99TYR00.013-0.01922.335-0.001-0.0010.0000.0000.0000.000
97B100VAL00.0240.02219.691-0.015-0.0150.0000.0000.0000.000
98B101TRP00.013-0.01121.136-0.008-0.0080.0000.0000.0000.000
99B102LYS10.8840.94423.5330.0890.0890.0000.0000.0000.000
100B103ALA0-0.0100.01018.010-0.007-0.0070.0000.0000.0000.000
101B104LEU00.0190.01318.667-0.016-0.0160.0000.0000.0000.000
102B105GLU-1-0.758-0.88420.664-0.089-0.0890.0000.0000.0000.000
103B106ASP-1-0.793-0.86219.924-0.194-0.1940.0000.0000.0000.000
104B107ALA00.0340.01017.514-0.010-0.0100.0000.0000.0000.000
105B108GLY0-0.067-0.01119.127-0.004-0.0040.0000.0000.0000.000
106B109CYS0-0.041-0.01918.5850.0090.0090.0000.0000.0000.000
107B110SER00.0430.03221.3500.0070.0070.0000.0000.0000.000
108B111PRO00.0730.04223.7000.0010.0010.0000.0000.0000.000
109B112GLN0-0.013-0.00625.0000.0100.0100.0000.0000.0000.000
110B113SER0-0.074-0.05022.7900.0040.0040.0000.0000.0000.000
111B114LEU00.0490.00618.7110.0010.0010.0000.0000.0000.000
112B115SER00.0060.03922.1840.0110.0110.0000.0000.0000.000
113B116GLY0-0.021-0.00624.3470.0030.0030.0000.0000.0000.000
114B117THR0-0.035-0.01618.9640.0100.0100.0000.0000.0000.000
115B118GLY00.0630.01817.663-0.001-0.0010.0000.0000.0000.000
116B119THR0-0.036-0.03315.573-0.003-0.0030.0000.0000.0000.000
117B120GLY00.0530.03114.3490.0160.0160.0000.0000.0000.000
118B121ILE0-0.056-0.03015.252-0.034-0.0340.0000.0000.0000.000
119B122PHE00.0190.01211.9840.0110.0110.0000.0000.0000.000
120B123ILE0-0.020-0.01215.257-0.027-0.0270.0000.0000.0000.000
121B124GLY00.0260.01117.8030.0180.0180.0000.0000.0000.000
122B125THR0-0.023-0.02419.078-0.002-0.0020.0000.0000.0000.000
123B126GLY00.0470.01822.7170.0060.0060.0000.0000.0000.000
124B127ASN0-0.010-0.01025.718-0.004-0.0040.0000.0000.0000.000
125B128THR00.003-0.00128.1900.0020.0020.0000.0000.0000.000
126B129GLY00.0590.03230.839-0.001-0.0010.0000.0000.0000.000
127B130TYR00.011-0.00733.6310.0000.0000.0000.0000.0000.000
128B131LYS10.9730.98335.1310.0090.0090.0000.0000.0000.000
129B132ASP-1-0.886-0.94736.847-0.013-0.0130.0000.0000.0000.000
130B133LEU0-0.032-0.01738.1070.0010.0010.0000.0000.0000.000
131B134PHE0-0.012-0.01138.3910.0010.0010.0000.0000.0000.000
132B135HIS0-0.022-0.00341.7570.0010.0010.0000.0000.0000.000
133B136ARG10.9070.95641.7920.0200.0200.0000.0000.0000.000
134B137ALA0-0.027-0.00444.7000.0000.0000.0000.0000.0000.000
135B138ASN0-0.068-0.03446.5610.0010.0010.0000.0000.0000.000
136B139LEU0-0.0220.00043.9470.0010.0010.0000.0000.0000.000
137B140PRO0-0.0100.00145.8390.0010.0010.0000.0000.0000.000
138B141ILE00.000-0.00742.152-0.001-0.0010.0000.0000.0000.000
139B142GLU-1-0.922-0.95542.515-0.004-0.0040.0000.0000.0000.000
140B143GLY00.002-0.01241.2220.0000.0000.0000.0000.0000.000
141B144HIS00.014-0.00338.5810.0000.0000.0000.0000.0000.000
142B145ALA00.0360.02236.868-0.002-0.0020.0000.0000.0000.000
143B146ALA0-0.0010.00335.417-0.001-0.0010.0000.0000.0000.000
144B147THR00.012-0.00732.217-0.001-0.0010.0000.0000.0000.000
145B148GLY00.0410.03232.075-0.003-0.0030.0000.0000.0000.000
146B149HIS0-0.060-0.05532.341-0.002-0.0020.0000.0000.0000.000
147B150MET0-0.027-0.00733.2890.0010.0010.0000.0000.0000.000
148B151ILE0-0.0100.00227.9420.0020.0020.0000.0000.0000.000
149B152PRO00.0380.01725.564-0.002-0.0020.0000.0000.0000.000
150B153SER00.0310.01023.653-0.006-0.0060.0000.0000.0000.000
151B154VAL0-0.003-0.00224.239-0.001-0.0010.0000.0000.0000.000
152B155GLY00.0210.01325.199-0.002-0.0020.0000.0000.0000.000
153B156PRO00.0160.01120.355-0.003-0.0030.0000.0000.0000.000
154B157ASN00.0300.01122.200-0.002-0.0020.0000.0000.0000.000
155B158ARG10.8300.91324.0690.0270.0270.0000.0000.0000.000
156B159MET0-0.0240.00622.6300.0030.0030.0000.0000.0000.000
157B160SER00.0470.01321.286-0.005-0.0050.0000.0000.0000.000
158B161TYR0-0.050-0.02123.1150.0050.0050.0000.0000.0000.000
159B162PHE0-0.057-0.02826.7020.0010.0010.0000.0000.0000.000
160B163LEU0-0.009-0.00621.661-0.002-0.0020.0000.0000.0000.000
161B164ASN0-0.067-0.02324.8460.0050.0050.0000.0000.0000.000
162B165ILE0-0.034-0.00118.8520.0010.0010.0000.0000.0000.000
163B166HIS0-0.029-0.03020.4490.0060.0060.0000.0000.0000.000
164B167GLY00.0050.02616.3880.0170.0170.0000.0000.0000.000
165B168PRO0-0.027-0.01613.956-0.008-0.0080.0000.0000.0000.000
166B169SER00.0480.02916.550-0.028-0.0280.0000.0000.0000.000
167B170GLU-1-0.909-0.96415.3620.0210.0210.0000.0000.0000.000
168B171PRO0-0.063-0.02218.057-0.017-0.0170.0000.0000.0000.000
169B172VAL0-0.019-0.02614.6780.0080.0080.0000.0000.0000.000
170B173GLU-1-0.870-0.95617.981-0.025-0.0250.0000.0000.0000.000
171B174THR0-0.002-0.01716.7300.0080.0080.0000.0000.0000.000
172B175ALA00.0220.01619.673-0.002-0.0020.0000.0000.0000.000
173B1762JF0-0.033-0.02121.041-0.012-0.0120.0000.0000.0000.000
174B177SER00.0220.02616.068-0.011-0.0110.0000.0000.0000.000
175B178SER00.0100.00515.717-0.011-0.0110.0000.0000.0000.000
176B179SER00.0170.00815.612-0.015-0.0150.0000.0000.0000.000
177B180LEU0-0.052-0.02311.448-0.032-0.0320.0000.0000.0000.000
178B181VAL00.0040.00111.151-0.037-0.0370.0000.0000.0000.000
179B182ALA0-0.0080.01011.149-0.013-0.0130.0000.0000.0000.000
180B183ILE00.0050.0077.458-0.020-0.0200.0000.0000.0000.000
181B184HIS00.0540.0606.734-0.173-0.1730.0000.0000.0000.000
182B185ARG10.8690.9546.886-0.060-0.0600.0000.0000.0000.000
183B186ALA00.0070.0009.0540.0370.0370.0000.0000.0000.000
184B187VAL00.013-0.0102.790-0.767-0.1250.481-0.191-0.9330.000
185B188THR0-0.052-0.0424.682-0.0710.050-0.001-0.012-0.1080.000
186B189ALA0-0.016-0.0065.7970.2050.2050.0000.0000.0000.000
187B190MET0-0.067-0.0186.4310.0390.0390.0000.0000.0000.000
188B191GLN0-0.027-0.0222.930-2.8690.0333.063-1.831-4.134-0.013
189B192ASN0-0.030-0.0195.9960.3080.3080.0000.0000.0000.000
190B193GLY00.0010.0019.024-0.044-0.0440.0000.0000.0000.000
191B194ASP-1-0.936-0.94611.2200.1380.1380.0000.0000.0000.000
192B195CYS0-0.089-0.04311.475-0.057-0.0570.0000.0000.0000.000
193B196GLU-1-0.879-0.93411.4020.1950.1950.0000.0000.0000.000
194B197MET0-0.019-0.00911.735-0.065-0.0650.0000.0000.0000.000
195B198ALA00.0240.00010.8940.0350.0350.0000.0000.0000.000
196B199ILE0-0.0060.01612.912-0.038-0.0380.0000.0000.0000.000
197B200ALA00.0250.01112.0570.0200.0200.0000.0000.0000.000
198B201GLY00.0540.00614.060-0.013-0.0130.0000.0000.0000.000
199B202GLY0-0.035-0.01116.2660.0140.0140.0000.0000.0000.000
200B203VAL0-0.026-0.00719.385-0.005-0.0050.0000.0000.0000.000
201B204ASN0-0.042-0.01723.1590.0110.0110.0000.0000.0000.000
202B205THR00.012-0.02225.706-0.001-0.0010.0000.0000.0000.000
203B206ILE0-0.013-0.01229.4690.0040.0040.0000.0000.0000.000
204B207LEU0-0.011-0.00732.4750.0000.0000.0000.0000.0000.000
205B208THR00.0040.00535.4050.0010.0010.0000.0000.0000.000
206B209GLU-1-0.812-0.91136.612-0.024-0.0240.0000.0000.0000.000
207B210GLU-1-0.956-0.98137.064-0.014-0.0140.0000.0000.0000.000
208B211ALA0-0.004-0.00632.7800.0010.0010.0000.0000.0000.000
209B212HIS00.0270.01033.9840.0010.0010.0000.0000.0000.000
210B213ILE0-0.010-0.00136.4220.0010.0010.0000.0000.0000.000
211B214SER0-0.012-0.00535.8720.0010.0010.0000.0000.0000.000
212B215TYR00.039-0.00529.8560.0000.0000.0000.0000.0000.000
213B216SER0-0.046-0.01634.8190.0000.0000.0000.0000.0000.000
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