Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 173LZ

Calculation Name: 5DFW-H-Xray372

Preferred Name: CD81 antigen

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DFW

Chain ID: H

ChEMBL ID: CHEMBL1075180

UniProt ID: P60033

Base Structure: X-ray

Registration Date: 2023-06-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2615980.229335
FMO2-HF: Nuclear repulsion 2530237.283566
FMO2-HF: Total energy -85742.945769
FMO2-MP2: Total energy -85994.183754


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(H:102:VAL)


Summations of interaction energy for fragment #1(H:102:VAL)
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.
-1.3530.345-0.014-0.828-0.8550.001
Interaction energy analysis for fragmet #1(H:102:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.017
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].
3H104LEU00.0100.0123.883-2.444-0.942-0.017-0.755-0.7290.001
4H105HIS00.0190.0245.9090.0830.0830.0000.0000.0000.000
5H106GLN00.022-0.0087.5060.1220.1220.0000.0000.0000.000
6H107SER0-0.0380.01411.286-0.028-0.0280.0000.0000.0000.000
7H108ALA00.0460.00814.1780.0400.0400.0000.0000.0000.000
8H109ALA0-0.016-0.00516.2100.0090.0090.0000.0000.0000.000
9H110GLN0-0.024-0.01319.529-0.013-0.0130.0000.0000.0000.000
10H111LEU0-0.0140.00022.8510.0120.0120.0000.0000.0000.000
11H112VAL0-0.003-0.00526.373-0.007-0.0070.0000.0000.0000.000
12H113GLN00.0290.01529.1500.0040.0040.0000.0000.0000.000
13H114PRO0-0.031-0.03632.649-0.002-0.0020.0000.0000.0000.000
14H115GLY00.0070.00833.783-0.003-0.0030.0000.0000.0000.000
15H116ALA0-0.0200.00829.982-0.003-0.0030.0000.0000.0000.000
16H117SER0-0.001-0.01828.6680.0050.0050.0000.0000.0000.000
17H118VAL0-0.019-0.00223.531-0.006-0.0060.0000.0000.0000.000
18H119ARG10.9640.98719.6080.1090.1090.0000.0000.0000.000
19H120LEU0-0.0080.02517.924-0.010-0.0100.0000.0000.0000.000
20H121SER00.019-0.01913.4340.0030.0030.0000.0000.0000.000
21H122CYS0-0.035-0.00111.631-0.002-0.0020.0000.0000.0000.000
22H123THR0-0.0070.0087.6840.0340.0340.0000.0000.0000.000
23H124THR00.004-0.0047.494-0.075-0.0750.0000.0000.0000.000
24H125SER00.0370.0383.372-0.211-0.0150.003-0.073-0.1260.000
25H151GLY00.007-0.0155.651-0.149-0.1490.0000.0000.0000.000
26H152PHE0-0.007-0.0076.6240.3940.3940.0000.0000.0000.000
27H153ASN00.0340.0419.712-0.162-0.1620.0000.0000.0000.000
28H154PHE00.035-0.00111.7890.0300.0300.0000.0000.0000.000
29H155LYS10.8860.94213.7290.1380.1380.0000.0000.0000.000
30H156ASP-1-0.904-0.93116.8850.0070.0070.0000.0000.0000.000
31H196SER0-0.036-0.00615.7000.0350.0350.0000.0000.0000.000
32H197TYR00.0060.01017.250-0.014-0.0140.0000.0000.0000.000
33H198LEU0-0.019-0.01112.9130.0430.0430.0000.0000.0000.000
34H199HIS00.0310.02416.653-0.041-0.0410.0000.0000.0000.000
35H201TRP00.0160.01515.5650.0280.0280.0000.0000.0000.000
36H202VAL0-0.015-0.01018.193-0.008-0.0080.0000.0000.0000.000
37H203LYS10.8650.95819.331-0.074-0.0740.0000.0000.0000.000
38H204GLN00.0630.03720.2670.0260.0260.0000.0000.0000.000
39H205ARG10.8900.95322.593-0.085-0.0850.0000.0000.0000.000
40H206PRO00.0180.01225.4550.0090.0090.0000.0000.0000.000
41H207ALA0-0.042-0.03326.352-0.007-0.0070.0000.0000.0000.000
42H208GLN00.0140.01627.0480.0010.0010.0000.0000.0000.000
43H209GLY00.0140.00625.7980.0120.0120.0000.0000.0000.000
44H210LEU0-0.069-0.02520.162-0.003-0.0030.0000.0000.0000.000
45H211GLU-1-0.839-0.94423.4140.0900.0900.0000.0000.0000.000
46H212TRP00.0140.00321.514-0.001-0.0010.0000.0000.0000.000
47H213ILE0-0.034-0.01321.209-0.015-0.0150.0000.0000.0000.000
48H214GLY00.0870.01422.715-0.014-0.0140.0000.0000.0000.000
49H251ARG10.7630.87420.825-0.055-0.0550.0000.0000.0000.000
50H252ILE0-0.0170.00719.128-0.012-0.0120.0000.0000.0000.000
51H253ASP-1-0.825-0.90320.2030.0540.0540.0000.0000.0000.000
52H254THR0-0.063-0.08017.053-0.002-0.0020.0000.0000.0000.000
53H255GLY00.0730.05620.294-0.016-0.0160.0000.0000.0000.000
54H288ASN0-0.091-0.06722.695-0.009-0.0090.0000.0000.0000.000
55H289GLY00.0270.02523.727-0.004-0.0040.0000.0000.0000.000
56H290ASN00.0110.02224.7500.0110.0110.0000.0000.0000.000
57H291VAL0-0.010-0.00723.9340.0060.0060.0000.0000.0000.000
58H292LYS10.9010.96025.570-0.080-0.0800.0000.0000.0000.000
59H293PHE00.0660.03024.5380.0070.0070.0000.0000.0000.000
60H294ASP-1-0.781-0.86827.5350.0800.0800.0000.0000.0000.000
61H295PRO0-0.002-0.02329.301-0.006-0.0060.0000.0000.0000.000
62H296LYS10.8280.91729.535-0.087-0.0870.0000.0000.0000.000
63H297PHE0-0.053-0.03526.976-0.004-0.0040.0000.0000.0000.000
64H298GLN0-0.068-0.03729.661-0.006-0.0060.0000.0000.0000.000
65H299ASP-1-0.852-0.91931.2860.0180.0180.0000.0000.0000.000
66H301LYS10.8180.91729.250-0.040-0.0400.0000.0000.0000.000
67H302ALA0-0.019-0.00825.510-0.005-0.0050.0000.0000.0000.000
68H303THR00.0440.01424.915-0.005-0.0050.0000.0000.0000.000
69H304ILE0-0.022-0.00519.9270.0000.0000.0000.0000.0000.000
70H305THR00.0070.02020.831-0.003-0.0030.0000.0000.0000.000
71H306THR00.014-0.00917.1220.0000.0000.0000.0000.0000.000
72H307ASP-1-0.851-0.88616.138-0.221-0.2210.0000.0000.0000.000
73H308ILE00.0490.01315.193-0.035-0.0350.0000.0000.0000.000
74H309PRO0-0.022-0.00114.608-0.036-0.0360.0000.0000.0000.000
75H310SER0-0.038-0.03712.575-0.055-0.0550.0000.0000.0000.000
76H311MET0-0.060-0.0328.643-0.085-0.0850.0000.0000.0000.000
77H312THR00.017-0.00110.945-0.054-0.0540.0000.0000.0000.000
78H313ALA00.006-0.00413.2470.0380.0380.0000.0000.0000.000
79H314TYR0-0.031-0.03215.427-0.011-0.0110.0000.0000.0000.000
80H315LEU00.0460.03018.2600.0120.0120.0000.0000.0000.000
81H316HIS0-0.066-0.06320.720-0.006-0.0060.0000.0000.0000.000
82H317LEU00.0060.01223.4030.0090.0090.0000.0000.0000.000
83H318SER00.0400.01926.306-0.006-0.0060.0000.0000.0000.000
84H319ASN00.008-0.01329.9310.0030.0030.0000.0000.0000.000
85H320LEU0-0.0200.01126.8740.0050.0050.0000.0000.0000.000
86H321THR00.0150.00331.236-0.002-0.0020.0000.0000.0000.000
87H322SER00.0580.01030.9220.0030.0030.0000.0000.0000.000
88H323GLU-1-0.971-0.98730.6720.0580.0580.0000.0000.0000.000
89H324ASP-1-0.796-0.89127.3630.0500.0500.0000.0000.0000.000
90H325THR00.0140.03625.9380.0010.0010.0000.0000.0000.000
91H326ALA0-0.019-0.01423.5520.0060.0060.0000.0000.0000.000
92H327VAL0-0.0060.01817.514-0.014-0.0140.0000.0000.0000.000
93H328TYR0-0.004-0.01618.6420.0070.0070.0000.0000.0000.000
94H329TYR00.001-0.01114.2440.0040.0040.0000.0000.0000.000
95H331VAL00.018-0.01412.6510.1030.1030.0000.0000.0000.000
96H332PRO00.0250.02810.060-0.076-0.0760.0000.0000.0000.000
97H351TYR0-0.011-0.03013.3710.0770.0770.0000.0000.0000.000
98H352GLY00.0390.01815.594-0.055-0.0550.0000.0000.0000.000
99H353TYR0-0.031-0.02213.600-0.020-0.0200.0000.0000.0000.000
100H396GLY0-0.0040.00013.5050.0480.0480.0000.0000.0000.000
101H397PHE0-0.046-0.03213.690-0.048-0.0480.0000.0000.0000.000
102H398HIS00.0030.0059.5440.2860.2860.0000.0000.0000.000
103H399SER00.0250.0058.103-0.327-0.3270.0000.0000.0000.000
104H401TRP0-0.008-0.0119.769-0.020-0.0200.0000.0000.0000.000
105H402GLY00.0190.0198.9930.2060.2060.0000.0000.0000.000
106H403ASP-1-0.935-0.9809.6060.2290.2290.0000.0000.0000.000
107H404GLY00.0100.00011.151-0.022-0.0220.0000.0000.0000.000
108H405THR0-0.046-0.01914.327-0.031-0.0310.0000.0000.0000.000
109H406THR0-0.002-0.00816.7790.0140.0140.0000.0000.0000.000
110H407LEU00.0110.02220.120-0.019-0.0190.0000.0000.0000.000
111H408THR0-0.041-0.03523.1440.0080.0080.0000.0000.0000.000
112H409VAL00.0380.02026.470-0.008-0.0080.0000.0000.0000.000
113H410SER0-0.004-0.00729.8080.0060.0060.0000.0000.0000.000
114H411SER00.0010.00032.728-0.005-0.0050.0000.0000.0000.000
115H501ASP-1-0.909-0.97131.8870.0920.0920.0000.0000.0000.000
116H502ILE0-0.0120.00129.343-0.001-0.0010.0000.0000.0000.000
117H503GLN00.0200.03330.2470.0100.0100.0000.0000.0000.000
118H504MET0-0.063-0.01426.7290.0050.0050.0000.0000.0000.000
119H505THR0-0.005-0.00430.171-0.006-0.0060.0000.0000.0000.000
120H506GLN0-0.024-0.05525.8620.0110.0110.0000.0000.0000.000
121H507SER0-0.057-0.01030.301-0.014-0.0140.0000.0000.0000.000
122H508PRO00.0470.02431.2170.0070.0070.0000.0000.0000.000
123H509ALA00.0740.04031.3300.0090.0090.0000.0000.0000.000
124H510SER0-0.016-0.01131.1060.0060.0060.0000.0000.0000.000
125H511LEU0-0.029-0.02430.193-0.005-0.0050.0000.0000.0000.000
126H512SER0-0.035-0.01531.5930.0040.0040.0000.0000.0000.000
127H513VAL0-0.0060.00330.249-0.004-0.0040.0000.0000.0000.000
128H514SER0-0.064-0.05832.1210.0000.0000.0000.0000.0000.000
129H515VAL00.003-0.02528.4930.0030.0030.0000.0000.0000.000
130H516GLY0-0.0060.00129.490-0.009-0.0090.0000.0000.0000.000
131H517GLU-1-0.818-0.87631.0010.1100.1100.0000.0000.0000.000
132H518THR0-0.023-0.01930.0830.0130.0130.0000.0000.0000.000
133H519VAL00.0200.02728.333-0.009-0.0090.0000.0000.0000.000
134H520THR0-0.051-0.05129.1280.0090.0090.0000.0000.0000.000
135H521ILE0-0.0130.02325.558-0.011-0.0110.0000.0000.0000.000
136H522THR00.000-0.01528.9030.0030.0030.0000.0000.0000.000
137H523CYS0-0.048-0.00721.6090.0240.0240.0000.0000.0000.000
138H551ARG10.8950.94829.315-0.103-0.1030.0000.0000.0000.000
139H552ALA00.0620.03529.7130.0010.0010.0000.0000.0000.000
140H553SER00.0310.01531.559-0.004-0.0040.0000.0000.0000.000
141H556GLU-1-0.925-0.95133.0800.0830.0830.0000.0000.0000.000
142H561ASN0-0.019-0.01531.7760.0170.0170.0000.0000.0000.000
143H562ILE00.0420.02126.154-0.003-0.0030.0000.0000.0000.000
144H571TYR0-0.013-0.02027.1190.0100.0100.0000.0000.0000.000
145H596ARG10.8510.92625.111-0.180-0.1800.0000.0000.0000.000
146H597THR0-0.0150.01222.1620.0360.0360.0000.0000.0000.000
147H598LEU00.003-0.00722.541-0.014-0.0140.0000.0000.0000.000
148H599ALA0-0.0090.00017.6870.0250.0250.0000.0000.0000.000
149H601TRP0-0.013-0.00519.138-0.042-0.0420.0000.0000.0000.000
150H602TYR00.007-0.01414.9620.0800.0800.0000.0000.0000.000
151H603LEU00.0040.00517.369-0.057-0.0570.0000.0000.0000.000
152H604GLN00.010-0.00817.3940.0350.0350.0000.0000.0000.000
153H605LYS10.8810.93717.427-0.369-0.3690.0000.0000.0000.000
154H606GLN00.016-0.02119.1460.0160.0160.0000.0000.0000.000
155H607GLY00.0070.00820.0830.0020.0020.0000.0000.0000.000
156H608LYS10.9430.98913.725-0.383-0.3830.0000.0000.0000.000
157H609SER00.0760.04611.402-0.035-0.0350.0000.0000.0000.000
158H610PRO0-0.081-0.03314.4810.0400.0400.0000.0000.0000.000
159H611GLN00.0120.01812.3620.0870.0870.0000.0000.0000.000
160H612LEU0-0.021-0.01511.830-0.112-0.1120.0000.0000.0000.000
161H613LEU0-0.035-0.00313.6150.0590.0590.0000.0000.0000.000
162H614VAL0-0.008-0.01716.3530.0020.0020.0000.0000.0000.000
163H615TYR00.0400.03313.492-0.049-0.0490.0000.0000.0000.000
164H651GLY00.0260.02917.653-0.024-0.0240.0000.0000.0000.000
165H694ALA0-0.016-0.02320.627-0.006-0.0060.0000.0000.0000.000
166H695THR0-0.049-0.05622.598-0.004-0.0040.0000.0000.0000.000
167H696THR0-0.0060.01916.723-0.026-0.0260.0000.0000.0000.000
168H697LEU00.0030.01316.9610.0330.0330.0000.0000.0000.000
169H698ALA00.0000.00012.1190.0050.0050.0000.0000.0000.000
170H699ASP-1-0.929-0.9698.2441.4981.4980.0000.0000.0000.000
171H701GLY00.0120.00310.4230.1590.1590.0000.0000.0000.000
172H702VAL0-0.060-0.01011.888-0.077-0.0770.0000.0000.0000.000
173H703PRO0-0.0040.00014.843-0.051-0.0510.0000.0000.0000.000
174H704SER00.0680.00318.163-0.003-0.0030.0000.0000.0000.000
175H705ARG10.7520.87919.845-0.270-0.2700.0000.0000.0000.000
176H706PHE00.0040.01518.990-0.017-0.0170.0000.0000.0000.000
177H707SER00.002-0.00321.9050.0010.0010.0000.0000.0000.000
178H708GLY00.0630.05322.947-0.012-0.0120.0000.0000.0000.000
179H709SER0-0.054-0.03824.000-0.017-0.0170.0000.0000.0000.000
180H710GLY00.0730.03327.2010.0040.0040.0000.0000.0000.000
181H711SER0-0.021-0.02728.6080.0070.0070.0000.0000.0000.000
182H712GLY00.0580.03930.620-0.005-0.0050.0000.0000.0000.000
183H715THR00.0240.02331.0980.0050.0050.0000.0000.0000.000
184H716GLN0-0.0100.00931.920-0.001-0.0010.0000.0000.0000.000
185H717TYR00.003-0.01526.7450.0070.0070.0000.0000.0000.000
186H718TYR0-0.007-0.02227.759-0.009-0.0090.0000.0000.0000.000
187H719LEU00.0210.02122.0380.0130.0130.0000.0000.0000.000
188H720LYS10.8740.93725.810-0.182-0.1820.0000.0000.0000.000
189H721ILE00.0110.01023.7370.0180.0180.0000.0000.0000.000
190H722ASN0-0.048-0.03725.699-0.031-0.0310.0000.0000.0000.000
191H723SER0-0.001-0.00326.2430.0050.0050.0000.0000.0000.000
192H724LEU0-0.0120.00825.9800.0090.0090.0000.0000.0000.000
193H725GLN00.0530.02023.485-0.004-0.0040.0000.0000.0000.000
194H726SER00.0380.00524.8350.0020.0020.0000.0000.0000.000
195H727GLU-1-0.881-0.91319.1660.2860.2860.0000.0000.0000.000
196H728ASP-1-0.793-0.89119.8400.2840.2840.0000.0000.0000.000
197H729PHE00.0590.02721.801-0.010-0.0100.0000.0000.0000.000
198H730GLY0-0.002-0.01322.6610.0170.0170.0000.0000.0000.000
199H731THR0-0.0100.00722.783-0.024-0.0240.0000.0000.0000.000
200H732TYR0-0.0100.00021.6600.0420.0420.0000.0000.0000.000
201H733HIS00.0240.01820.253-0.037-0.0370.0000.0000.0000.000
202H751GLN00.0470.01619.3880.0210.0210.0000.0000.0000.000
203H752HIS00.0630.03622.5680.0210.0210.0000.0000.0000.000
204H753PHE0-0.028-0.02917.1210.0080.0080.0000.0000.0000.000
205H754TRP0-0.0110.00322.673-0.005-0.0050.0000.0000.0000.000
206H755GLY00.0220.01225.450-0.012-0.0120.0000.0000.0000.000
207H796THR0-0.120-0.05425.1950.0090.0090.0000.0000.0000.000
208H797PRO00.1000.05226.485-0.007-0.0070.0000.0000.0000.000
209H798TRP0-0.026-0.01417.0590.0100.0100.0000.0000.0000.000
210H799THR0-0.022-0.04324.554-0.002-0.0020.0000.0000.0000.000
211H801PHE00.034-0.00720.1640.0180.0180.0000.0000.0000.000
212H802GLY00.0130.00425.489-0.018-0.0180.0000.0000.0000.000
213H803GLY0-0.034-0.02326.8000.0050.0050.0000.0000.0000.000
214H804GLY00.0430.03626.2520.0000.0000.0000.0000.0000.000
215H805THR0-0.058-0.04426.461-0.010-0.0100.0000.0000.0000.000
216H806LYS10.8200.91326.622-0.119-0.1190.0000.0000.0000.000
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