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: G6421

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 OptAll
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 -2615667.592487
FMO2-HF: Nuclear repulsion 2529923.918468
FMO2-HF: Total energy -85743.674018
FMO2-MP2: Total energy -85994.773182


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.
-0.7541.063-0.013-0.812-0.9930.002
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 : 0.004 / 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].
3H104LEU00.0050.0043.882-1.803-0.179-0.017-0.758-0.8500.002
4H105HIS00.0190.0295.8070.1580.1580.0000.0000.0000.000
5H106GLN0-0.001-0.0207.6600.0330.0330.0000.0000.0000.000
6H107SER0-0.037-0.00111.470-0.033-0.0330.0000.0000.0000.000
7H108ALA00.0510.02014.4540.0330.0330.0000.0000.0000.000
8H109ALA0-0.012-0.00616.0500.0030.0030.0000.0000.0000.000
9H110GLN0-0.041-0.02419.273-0.015-0.0150.0000.0000.0000.000
10H111LEU00.002-0.00222.5580.0100.0100.0000.0000.0000.000
11H112VAL0-0.0010.00826.215-0.007-0.0070.0000.0000.0000.000
12H113GLN00.0060.00229.0790.0030.0030.0000.0000.0000.000
13H114PRO0-0.012-0.02832.359-0.001-0.0010.0000.0000.0000.000
14H115GLY00.0000.01334.062-0.003-0.0030.0000.0000.0000.000
15H116ALA0-0.0180.00730.164-0.003-0.0030.0000.0000.0000.000
16H117SER00.001-0.01228.8770.0040.0040.0000.0000.0000.000
17H118VAL0-0.026-0.00323.809-0.004-0.0040.0000.0000.0000.000
18H119ARG10.9420.97919.2870.0670.0670.0000.0000.0000.000
19H120LEU00.0170.03417.822-0.004-0.0040.0000.0000.0000.000
20H121SER00.019-0.02113.707-0.009-0.0090.0000.0000.0000.000
21H122CYS0-0.049-0.00911.594-0.005-0.0050.0000.0000.0000.000
22H123THR0-0.0040.0197.2320.0120.0120.0000.0000.0000.000
23H124THR0-0.018-0.0187.6340.0000.0000.0000.0000.0000.000
24H125SER00.0390.0123.407-0.345-0.1520.004-0.054-0.1430.000
25H151GLY0-0.003-0.0085.7200.1160.1160.0000.0000.0000.000
26H152PHE00.008-0.0026.6980.3250.3250.0000.0000.0000.000
27H153ASN00.0310.0349.919-0.102-0.1020.0000.0000.0000.000
28H154PHE00.0400.00711.3250.0330.0330.0000.0000.0000.000
29H155LYS10.8860.94013.3170.1530.1530.0000.0000.0000.000
30H156ASP-1-0.901-0.93816.528-0.024-0.0240.0000.0000.0000.000
31H196SER0-0.0420.00015.7300.0140.0140.0000.0000.0000.000
32H197TYR0-0.0090.00417.502-0.002-0.0020.0000.0000.0000.000
33H198LEU00.0180.00312.8500.0260.0260.0000.0000.0000.000
34H199HIS00.0330.02616.803-0.026-0.0260.0000.0000.0000.000
35H201TRP00.0110.00015.6230.0230.0230.0000.0000.0000.000
36H202VAL0-0.033-0.01018.386-0.009-0.0090.0000.0000.0000.000
37H203LYS10.8650.95219.470-0.073-0.0730.0000.0000.0000.000
38H204GLN00.0360.03220.5870.0350.0350.0000.0000.0000.000
39H205ARG10.8710.95022.854-0.087-0.0870.0000.0000.0000.000
40H206PRO0-0.001-0.00725.6910.0100.0100.0000.0000.0000.000
41H207ALA0-0.029-0.02426.627-0.007-0.0070.0000.0000.0000.000
42H208GLN00.0320.03026.8230.0000.0000.0000.0000.0000.000
43H209GLY00.0240.00925.5710.0140.0140.0000.0000.0000.000
44H210LEU0-0.056-0.01620.048-0.001-0.0010.0000.0000.0000.000
45H211GLU-1-0.847-0.94823.1330.0920.0920.0000.0000.0000.000
46H212TRP00.002-0.01221.590-0.002-0.0020.0000.0000.0000.000
47H213ILE0-0.021-0.00621.360-0.014-0.0140.0000.0000.0000.000
48H214GLY00.0710.01322.730-0.014-0.0140.0000.0000.0000.000
49H251ARG10.7580.88520.494-0.039-0.0390.0000.0000.0000.000
50H252ILE0-0.0300.01118.926-0.008-0.0080.0000.0000.0000.000
51H253ASP-1-0.828-0.92019.9880.0260.0260.0000.0000.0000.000
52H254THR0-0.042-0.05916.6850.0000.0000.0000.0000.0000.000
53H255GLY00.0550.04919.813-0.014-0.0140.0000.0000.0000.000
54H288ASN0-0.102-0.06422.103-0.003-0.0030.0000.0000.0000.000
55H289GLY00.0400.02423.518-0.001-0.0010.0000.0000.0000.000
56H290ASN00.0100.00824.4960.0100.0100.0000.0000.0000.000
57H291VAL00.0090.00823.6760.0060.0060.0000.0000.0000.000
58H292LYS10.8850.94825.329-0.063-0.0630.0000.0000.0000.000
59H293PHE00.0380.02124.3200.0070.0070.0000.0000.0000.000
60H294ASP-1-0.767-0.85627.5300.0740.0740.0000.0000.0000.000
61H295PRO0-0.010-0.01929.420-0.005-0.0050.0000.0000.0000.000
62H296LYS10.8210.91029.416-0.083-0.0830.0000.0000.0000.000
63H297PHE0-0.029-0.03626.898-0.001-0.0010.0000.0000.0000.000
64H298GLN0-0.065-0.03929.820-0.005-0.0050.0000.0000.0000.000
65H299ASP-1-0.846-0.91130.9390.0220.0220.0000.0000.0000.000
66H301LYS10.8130.90529.629-0.050-0.0500.0000.0000.0000.000
67H302ALA00.0020.01025.618-0.002-0.0020.0000.0000.0000.000
68H303THR00.023-0.00224.884-0.006-0.0060.0000.0000.0000.000
69H304ILE0-0.018-0.00119.6680.0010.0010.0000.0000.0000.000
70H305THR00.0030.01420.542-0.003-0.0030.0000.0000.0000.000
71H306THR00.000-0.01716.7420.0040.0040.0000.0000.0000.000
72H307ASP-1-0.832-0.87315.721-0.181-0.1810.0000.0000.0000.000
73H308ILE00.0400.00814.751-0.026-0.0260.0000.0000.0000.000
74H309PRO0-0.021-0.00314.217-0.033-0.0330.0000.0000.0000.000
75H310SER0-0.049-0.04612.088-0.042-0.0420.0000.0000.0000.000
76H311MET0-0.042-0.0268.112-0.071-0.0710.0000.0000.0000.000
77H312THR00.0470.03110.477-0.030-0.0300.0000.0000.0000.000
78H313ALA00.0150.00212.6510.0240.0240.0000.0000.0000.000
79H314TYR0-0.033-0.03615.078-0.006-0.0060.0000.0000.0000.000
80H315LEU00.0210.01917.8960.0080.0080.0000.0000.0000.000
81H316HIS0-0.028-0.03620.4190.0000.0000.0000.0000.0000.000
82H317LEU0-0.011-0.00223.2510.0080.0080.0000.0000.0000.000
83H318SER00.012-0.00826.246-0.006-0.0060.0000.0000.0000.000
84H319ASN0-0.001-0.00929.9140.0030.0030.0000.0000.0000.000
85H320LEU0-0.0040.01826.8860.0040.0040.0000.0000.0000.000
86H321THR00.020-0.00731.083-0.002-0.0020.0000.0000.0000.000
87H322SER00.0420.01130.9750.0040.0040.0000.0000.0000.000
88H323GLU-1-0.905-0.95730.8600.0610.0610.0000.0000.0000.000
89H324ASP-1-0.787-0.87527.2940.0610.0610.0000.0000.0000.000
90H325THR00.0040.02125.9860.0020.0020.0000.0000.0000.000
91H326ALA0-0.006-0.00323.7370.0030.0030.0000.0000.0000.000
92H327VAL00.0090.01617.785-0.011-0.0110.0000.0000.0000.000
93H328TYR00.001-0.00818.707-0.004-0.0040.0000.0000.0000.000
94H329TYR0-0.001-0.01714.4430.0150.0150.0000.0000.0000.000
95H331VAL00.021-0.00712.7800.0900.0900.0000.0000.0000.000
96H332PRO00.0280.02710.247-0.061-0.0610.0000.0000.0000.000
97H351TYR0-0.029-0.03113.5620.0620.0620.0000.0000.0000.000
98H352GLY00.0620.02915.973-0.048-0.0480.0000.0000.0000.000
99H353TYR0-0.047-0.02913.930-0.002-0.0020.0000.0000.0000.000
100H396GLY00.0210.01813.6780.0380.0380.0000.0000.0000.000
101H397PHE0-0.033-0.02714.402-0.032-0.0320.0000.0000.0000.000
102H398HIS0-0.010-0.0089.8800.1990.1990.0000.0000.0000.000
103H399SER00.013-0.0098.219-0.275-0.2750.0000.0000.0000.000
104H401TRP0-0.015-0.0079.793-0.044-0.0440.0000.0000.0000.000
105H402GLY00.0280.0238.9660.2100.2100.0000.0000.0000.000
106H403ASP-1-0.898-0.9509.4590.3320.3320.0000.0000.0000.000
107H404GLY0-0.020-0.02110.932-0.029-0.0290.0000.0000.0000.000
108H405THR0-0.036-0.01314.004-0.033-0.0330.0000.0000.0000.000
109H406THR0-0.016-0.01216.7620.0080.0080.0000.0000.0000.000
110H407LEU00.0140.02320.073-0.017-0.0170.0000.0000.0000.000
111H408THR0-0.042-0.03323.0910.0060.0060.0000.0000.0000.000
112H409VAL00.0300.01726.601-0.007-0.0070.0000.0000.0000.000
113H410SER0-0.002-0.00229.9630.0030.0030.0000.0000.0000.000
114H411SER00.0220.00332.804-0.004-0.0040.0000.0000.0000.000
115H501ASP-1-0.916-0.97631.7960.0810.0810.0000.0000.0000.000
116H502ILE0-0.0170.00529.9960.0000.0000.0000.0000.0000.000
117H503GLN00.0230.02930.7000.0070.0070.0000.0000.0000.000
118H504MET0-0.035-0.00126.9310.0050.0050.0000.0000.0000.000
119H505THR0-0.031-0.02130.398-0.008-0.0080.0000.0000.0000.000
120H506GLN00.005-0.02325.9260.0090.0090.0000.0000.0000.000
121H507SER0-0.052-0.00930.646-0.012-0.0120.0000.0000.0000.000
122H508PRO00.0580.02731.4330.0050.0050.0000.0000.0000.000
123H509ALA00.0790.04231.2810.0090.0090.0000.0000.0000.000
124H510SER0-0.043-0.02231.0220.0060.0060.0000.0000.0000.000
125H511LEU0-0.021-0.01230.673-0.008-0.0080.0000.0000.0000.000
126H512SER0-0.040-0.01931.6030.0050.0050.0000.0000.0000.000
127H513VAL0-0.0090.00330.269-0.005-0.0050.0000.0000.0000.000
128H514SER0-0.063-0.06831.7580.0030.0030.0000.0000.0000.000
129H515VAL0-0.010-0.01828.0420.0040.0040.0000.0000.0000.000
130H516GLY00.0040.01429.593-0.009-0.0090.0000.0000.0000.000
131H517GLU-1-0.827-0.87731.2210.1040.1040.0000.0000.0000.000
132H518THR0-0.011-0.01430.0230.0130.0130.0000.0000.0000.000
133H519VAL00.0140.02828.401-0.008-0.0080.0000.0000.0000.000
134H520THR0-0.032-0.03929.2050.0070.0070.0000.0000.0000.000
135H521ILE0-0.0200.01225.503-0.010-0.0100.0000.0000.0000.000
136H522THR0-0.005-0.01128.7450.0030.0030.0000.0000.0000.000
137H523CYS0-0.044-0.01821.8610.0230.0230.0000.0000.0000.000
138H551ARG10.8820.93829.543-0.092-0.0920.0000.0000.0000.000
139H552ALA00.0450.02930.1960.0040.0040.0000.0000.0000.000
140H553SER00.0110.00632.144-0.003-0.0030.0000.0000.0000.000
141H556GLU-1-0.918-0.95233.6430.0690.0690.0000.0000.0000.000
142H561ASN0-0.027-0.01632.0590.0150.0150.0000.0000.0000.000
143H562ILE00.0450.02126.627-0.002-0.0020.0000.0000.0000.000
144H571TYR0-0.017-0.01927.2310.0090.0090.0000.0000.0000.000
145H596ARG10.8320.91224.950-0.151-0.1510.0000.0000.0000.000
146H597THR0-0.0060.01022.5350.0240.0240.0000.0000.0000.000
147H598LEU00.002-0.00222.715-0.008-0.0080.0000.0000.0000.000
148H599ALA0-0.045-0.02017.8400.0210.0210.0000.0000.0000.000
149H601TRP0-0.006-0.01019.235-0.036-0.0360.0000.0000.0000.000
150H602TYR0-0.004-0.02315.1860.0660.0660.0000.0000.0000.000
151H603LEU0-0.0210.00017.469-0.052-0.0520.0000.0000.0000.000
152H604GLN00.0070.00417.5580.0340.0340.0000.0000.0000.000
153H605LYS10.8950.94317.393-0.399-0.3990.0000.0000.0000.000
154H606GLN00.021-0.00819.4780.0160.0160.0000.0000.0000.000
155H607GLY00.0070.00719.9820.0030.0030.0000.0000.0000.000
156H608LYS10.9340.97613.304-0.436-0.4360.0000.0000.0000.000
157H609SER00.0800.04811.753-0.034-0.0340.0000.0000.0000.000
158H610PRO0-0.070-0.03614.9680.0250.0250.0000.0000.0000.000
159H611GLN00.0160.02212.8020.0460.0460.0000.0000.0000.000
160H612LEU00.0030.00011.866-0.104-0.1040.0000.0000.0000.000
161H613LEU0-0.040-0.00713.7510.0560.0560.0000.0000.0000.000
162H614VAL00.010-0.00316.219-0.009-0.0090.0000.0000.0000.000
163H615TYR00.0420.01413.856-0.044-0.0440.0000.0000.0000.000
164H651GLY00.0660.04018.331-0.023-0.0230.0000.0000.0000.000
165H694ALA0-0.015-0.01921.140-0.016-0.0160.0000.0000.0000.000
166H695THR0-0.108-0.06121.581-0.023-0.0230.0000.0000.0000.000
167H696THR00.0190.02816.663-0.014-0.0140.0000.0000.0000.000
168H697LEU00.0160.01716.6910.0290.0290.0000.0000.0000.000
169H698ALA00.0020.00111.753-0.010-0.0100.0000.0000.0000.000
170H699ASP-1-0.900-0.9527.7671.4181.4180.0000.0000.0000.000
171H701GLY0-0.006-0.00910.8680.1290.1290.0000.0000.0000.000
172H702VAL0-0.066-0.01711.892-0.075-0.0750.0000.0000.0000.000
173H703PRO00.0060.01614.849-0.051-0.0510.0000.0000.0000.000
174H704SER00.025-0.02218.041-0.007-0.0070.0000.0000.0000.000
175H705ARG10.7640.87519.689-0.268-0.2680.0000.0000.0000.000
176H706PHE00.0100.01418.631-0.017-0.0170.0000.0000.0000.000
177H707SER0-0.0010.00222.233-0.004-0.0040.0000.0000.0000.000
178H708GLY00.0460.03022.888-0.006-0.0060.0000.0000.0000.000
179H709SER0-0.034-0.02123.924-0.017-0.0170.0000.0000.0000.000
180H710GLY00.0760.03026.9840.0040.0040.0000.0000.0000.000
181H711SER0-0.026-0.01728.8510.0020.0020.0000.0000.0000.000
182H712GLY00.0680.04230.729-0.003-0.0030.0000.0000.0000.000
183H715THR00.0220.02331.2140.0040.0040.0000.0000.0000.000
184H716GLN0-0.0110.00231.812-0.001-0.0010.0000.0000.0000.000
185H717TYR00.015-0.01426.7240.0040.0040.0000.0000.0000.000
186H718TYR00.001-0.00727.838-0.005-0.0050.0000.0000.0000.000
187H719LEU0-0.0020.02722.0270.0070.0070.0000.0000.0000.000
188H720LYS10.8670.93325.610-0.166-0.1660.0000.0000.0000.000
189H721ILE00.0170.00423.6720.0180.0180.0000.0000.0000.000
190H722ASN0-0.045-0.03825.878-0.026-0.0260.0000.0000.0000.000
191H723SER00.011-0.00126.6130.0040.0040.0000.0000.0000.000
192H724LEU0-0.0140.00825.6920.0070.0070.0000.0000.0000.000
193H725GLN00.0550.00823.446-0.006-0.0060.0000.0000.0000.000
194H726SER00.031-0.00324.4400.0080.0080.0000.0000.0000.000
195H727GLU-1-0.857-0.88619.0670.2800.2800.0000.0000.0000.000
196H728ASP-1-0.798-0.89819.6740.2780.2780.0000.0000.0000.000
197H729PHE00.0490.04121.678-0.006-0.0060.0000.0000.0000.000
198H730GLY0-0.020-0.01322.3680.0230.0230.0000.0000.0000.000
199H731THR0-0.022-0.01622.709-0.025-0.0250.0000.0000.0000.000
200H732TYR00.006-0.01421.4150.0360.0360.0000.0000.0000.000
201H733HIS00.0120.00020.329-0.036-0.0360.0000.0000.0000.000
202H751GLN00.0590.02819.6870.0190.0190.0000.0000.0000.000
203H752HIS00.0490.02122.6260.0180.0180.0000.0000.0000.000
204H753PHE0-0.016-0.01417.4120.0090.0090.0000.0000.0000.000
205H754TRP00.0030.01222.955-0.009-0.0090.0000.0000.0000.000
206H755GLY00.0260.01325.455-0.010-0.0100.0000.0000.0000.000
207H796THR0-0.123-0.06025.4290.0020.0020.0000.0000.0000.000
208H797PRO00.1030.06526.618-0.006-0.0060.0000.0000.0000.000
209H798TRP0-0.034-0.01817.2620.0110.0110.0000.0000.0000.000
210H799THR0-0.006-0.02524.6880.0000.0000.0000.0000.0000.000
211H801PHE00.037-0.00820.2360.0150.0150.0000.0000.0000.000
212H802GLY00.0120.00025.625-0.016-0.0160.0000.0000.0000.000
213H803GLY0-0.038-0.02426.9140.0060.0060.0000.0000.0000.000
214H804GLY00.0150.02226.317-0.002-0.0020.0000.0000.0000.000
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216H806LYS10.7770.89426.677-0.124-0.1240.0000.0000.0000.000
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