Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4J7QN

Calculation Name: 3VX8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX8

Chain ID: B

ChEMBL ID:

UniProt ID: Q0WWQ1

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2024803.146192
FMO2-HF: Nuclear repulsion 1951417.997461
FMO2-HF: Total energy -73385.148732
FMO2-MP2: Total energy -73595.984862


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:23:PRO)


Summations of interaction energy for fragment #1(B:23:PRO)
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.
-18.191-12.6512.17-7.92-9.792-0.046
Interaction energy analysis for fragmet #1(B:23:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.016
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].
3B25MET00.0080.0112.864-3.1260.6920.107-1.892-2.0330.004
4B26ALA0-0.007-0.0122.098-0.917-0.7423.814-1.411-2.5780.001
5B27PHE00.0150.0063.694-0.1160.3110.005-0.032-0.4010.000
6B28LYS10.8870.9285.6381.1811.1810.0000.0000.0000.000
7B29GLU-1-0.902-0.9386.9040.2850.2850.0000.0000.0000.000
8B30LYS10.8700.9184.976-0.340-0.3400.0000.0000.0000.000
9B31GLY00.0230.0417.9960.0840.0840.0000.0000.0000.000
10B32VAL0-0.072-0.0283.985-0.0320.1040.000-0.020-0.1160.000
11B33LEU00.0030.0075.032-0.734-0.7340.0000.0000.0000.000
12B34SER0-0.002-0.0072.5711.2311.9540.267-0.265-0.7260.001
13B35VAL00.0360.0014.662-0.075-0.051-0.001-0.009-0.0130.000
14B36SER00.0160.0115.913-0.004-0.0040.0000.0000.0000.000
15B37GLU-1-0.725-0.8421.996-17.249-17.1967.979-4.248-3.784-0.052
16B38PHE0-0.032-0.0156.2350.0120.0120.0000.0000.0000.000
17B39VAL00.006-0.0039.1920.0700.0700.0000.0000.0000.000
18B40LEU00.0250.0208.6140.0310.0310.0000.0000.0000.000
19B41ALA0-0.001-0.0089.4390.0690.0690.0000.0000.0000.000
20B42GLY0-0.008-0.02011.1630.0860.0860.0000.0000.0000.000
21B43ASP-1-0.790-0.86613.702-0.155-0.1550.0000.0000.0000.000
22B44ASN0-0.032-0.02413.4840.1260.1260.0000.0000.0000.000
23B45LEU0-0.024-0.01315.4450.0270.0270.0000.0000.0000.000
24B46VAL00.0080.01017.3140.0320.0320.0000.0000.0000.000
25B47SER0-0.050-0.01018.6020.0190.0190.0000.0000.0000.000
26B48LYS10.8530.92118.2300.3080.3080.0000.0000.0000.000
27B49CYS0-0.0290.00320.9260.0100.0100.0000.0000.0000.000
28B50PRO00.0450.02022.671-0.004-0.0040.0000.0000.0000.000
29B51THR0-0.007-0.02024.5610.0110.0110.0000.0000.0000.000
30B52TRP0-0.079-0.03620.7210.0020.0020.0000.0000.0000.000
31B53SER00.0000.00422.5960.0090.0090.0000.0000.0000.000
32B54TRP0-0.022-0.02913.985-0.013-0.0130.0000.0000.0000.000
33B55GLU-1-0.848-0.90420.793-0.087-0.0870.0000.0000.0000.000
34B56SER00.023-0.00521.268-0.004-0.0040.0000.0000.0000.000
35B57GLY0-0.046-0.02523.0330.0020.0020.0000.0000.0000.000
36B58ASP-1-0.866-0.93025.120-0.042-0.0420.0000.0000.0000.000
37B59ALA00.009-0.00925.2890.0010.0010.0000.0000.0000.000
38B60SER0-0.013-0.01525.6390.0040.0040.0000.0000.0000.000
39B61LYS10.8250.92323.7070.0610.0610.0000.0000.0000.000
40B62ARG10.9220.98719.543-0.013-0.0130.0000.0000.0000.000
41B63LYS10.9080.95415.8590.0890.0890.0000.0000.0000.000
42B64PRO0-0.010-0.01317.355-0.005-0.0050.0000.0000.0000.000
43B65TYR0-0.006-0.00912.1350.0280.0280.0000.0000.0000.000
44B66LEU0-0.011-0.00111.9490.0000.0000.0000.0000.0000.000
45B67PRO00.0760.04014.0190.0200.0200.0000.0000.0000.000
46B68SER0-0.0080.00317.247-0.017-0.0170.0000.0000.0000.000
47B69ASP-1-0.898-0.94420.300-0.063-0.0630.0000.0000.0000.000
48B70LYS10.8230.89616.4890.1310.1310.0000.0000.0000.000
49B71GLN0-0.039-0.01716.689-0.013-0.0130.0000.0000.0000.000
50B72PHE0-0.045-0.04217.140-0.021-0.0210.0000.0000.0000.000
51B73LEU00.0240.03415.2820.0090.0090.0000.0000.0000.000
52B74ILE0-0.030-0.02419.511-0.002-0.0020.0000.0000.0000.000
53B75THR00.0030.00023.0160.0020.0020.0000.0000.0000.000
54B76ARG10.8960.91925.4600.1060.1060.0000.0000.0000.000
55B77ASN0-0.033-0.01929.1940.0020.0020.0000.0000.0000.000
56B78VAL00.0470.03727.3110.0020.0020.0000.0000.0000.000
57B79PRO00.0090.01630.7580.0040.0040.0000.0000.0000.000
58B80CYS0-0.0280.00332.363-0.006-0.0060.0000.0000.0000.000
59B81LEU00.0210.00734.2510.0080.0080.0000.0000.0000.000
60B82ARG10.9420.98135.5240.1060.1060.0000.0000.0000.000
61B83ARG10.8680.89635.6790.0840.0840.0000.0000.0000.000
62B84ALA00.0390.02532.794-0.001-0.0010.0000.0000.0000.000
63B85ALA0-0.049-0.00734.583-0.002-0.0020.0000.0000.0000.000
64B86SER0-0.071-0.03336.5680.0060.0060.0000.0000.0000.000
65B190LEU0-0.009-0.01541.914-0.001-0.0010.0000.0000.0000.000
66B191ARG10.8850.93241.8250.0610.0610.0000.0000.0000.000
67B192THR00.0030.00739.059-0.003-0.0030.0000.0000.0000.000
68B193ARG10.8060.88935.4870.0870.0870.0000.0000.0000.000
69B194THR00.0200.00934.005-0.005-0.0050.0000.0000.0000.000
70B195TYR0-0.043-0.06929.1790.0030.0030.0000.0000.0000.000
71B196ASP-1-0.807-0.87228.490-0.105-0.1050.0000.0000.0000.000
72B197LEU0-0.032-0.02323.7200.0020.0020.0000.0000.0000.000
73B198SER00.0110.00521.816-0.005-0.0050.0000.0000.0000.000
74B199ILE00.003-0.00415.790-0.012-0.0120.0000.0000.0000.000
75B200THR00.0370.02917.2240.0120.0120.0000.0000.0000.000
76B201TYR0-0.038-0.0477.1280.1050.1050.0000.0000.0000.000
77B202ASP-1-0.848-0.93313.524-0.096-0.0960.0000.0000.0000.000
78B203LYS10.9540.9648.999-0.152-0.1520.0000.0000.0000.000
79B204TYR0-0.0190.00510.8660.0400.0400.0000.0000.0000.000
80B205TYR00.0330.00611.7370.0340.0340.0000.0000.0000.000
81B206GLN0-0.067-0.0146.0630.0210.0210.0000.0000.0000.000
82B207THR00.0510.0258.132-0.227-0.2270.0000.0000.0000.000
83B208PRO0-0.0020.00210.8530.0890.0890.0000.0000.0000.000
84B209ARG10.8080.90313.6640.1740.1740.0000.0000.0000.000
85B210VAL00.0460.03217.2140.0030.0030.0000.0000.0000.000
86B211TRP0-0.042-0.02919.6870.0260.0260.0000.0000.0000.000
87B212LEU00.0210.00523.593-0.005-0.0050.0000.0000.0000.000
88B213THR0-0.032-0.01126.8950.0100.0100.0000.0000.0000.000
89B214GLY00.0790.03630.252-0.003-0.0030.0000.0000.0000.000
90B215TYR0-0.059-0.04431.9720.0080.0080.0000.0000.0000.000
91B216ASP-1-0.848-0.94736.325-0.063-0.0630.0000.0000.0000.000
92B217GLU-1-0.843-0.89439.572-0.061-0.0610.0000.0000.0000.000
93B218SER0-0.069-0.03941.8090.0000.0000.0000.0000.0000.000
94B219ARG10.7720.88032.6880.0870.0870.0000.0000.0000.000
95B220MET00.0490.03639.7820.0020.0020.0000.0000.0000.000
96B221LEU0-0.010-0.00234.283-0.003-0.0030.0000.0000.0000.000
97B222LEU00.0120.02435.5180.0030.0030.0000.0000.0000.000
98B223GLN00.010-0.00136.085-0.001-0.0010.0000.0000.0000.000
99B224PRO00.0250.00231.998-0.004-0.0040.0000.0000.0000.000
100B225GLU-1-0.895-0.95532.961-0.069-0.0690.0000.0000.0000.000
101B226LEU00.0110.00235.083-0.001-0.0010.0000.0000.0000.000
102B227VAL00.0090.00830.062-0.003-0.0030.0000.0000.0000.000
103B228MET0-0.039-0.01830.056-0.010-0.0100.0000.0000.0000.000
104B229GLU-1-0.845-0.90532.786-0.076-0.0760.0000.0000.0000.000
105B230ASP-1-0.749-0.84531.907-0.099-0.0990.0000.0000.0000.000
106B231VAL0-0.054-0.01327.905-0.012-0.0120.0000.0000.0000.000
107B232SER00.0290.01628.7250.0130.0130.0000.0000.0000.000
108B233GLN0-0.050-0.04229.939-0.003-0.0030.0000.0000.0000.000
109B234ASP-1-0.755-0.86529.355-0.123-0.1230.0000.0000.0000.000
110B235HIS0-0.054-0.04428.150-0.009-0.0090.0000.0000.0000.000
111B236ALA0-0.002-0.00125.366-0.007-0.0070.0000.0000.0000.000
112B237ARG10.9070.96324.2200.0950.0950.0000.0000.0000.000
113B238LYS10.7950.88921.6030.1620.1620.0000.0000.0000.000
114B239THR00.0030.00823.9350.0130.0130.0000.0000.0000.000
115B240VAL0-0.006-0.00424.249-0.011-0.0110.0000.0000.0000.000
116B241THR0-0.024-0.00924.7390.0130.0130.0000.0000.0000.000
117B242ILE00.0220.01126.869-0.008-0.0080.0000.0000.0000.000
118B243GLU-1-0.853-0.93323.761-0.093-0.0930.0000.0000.0000.000
119B244ASP-1-0.862-0.90926.961-0.059-0.0590.0000.0000.0000.000
120B245HIS00.0550.03122.4750.0060.0060.0000.0000.0000.000
121B246PRO0-0.040-0.03319.7230.0130.0130.0000.0000.0000.000
122B247HIS0-0.015-0.02119.046-0.007-0.0070.0000.0000.0000.000
123B248LEU00.0440.03523.5820.0060.0060.0000.0000.0000.000
124B249PRO00.0680.04027.0450.0020.0020.0000.0000.0000.000
125B250GLY00.0420.03130.257-0.006-0.0060.0000.0000.0000.000
126B251LYS10.8310.89429.7170.0550.0550.0000.0000.0000.000
127B252HIS10.8410.90626.7850.0920.0920.0000.0000.0000.000
128B253ALA00.0760.05327.7190.0010.0010.0000.0000.0000.000
129B254SER0-0.038-0.03722.290-0.012-0.0120.0000.0000.0000.000
130B255VAL00.0440.02221.1540.0110.0110.0000.0000.0000.000
131B256HIS00.0610.03619.542-0.031-0.0310.0000.0000.0000.000
132B257PRO00.0320.00215.095-0.010-0.0100.0000.0000.0000.000
133B258CYS0-0.052-0.01615.531-0.030-0.0300.0000.0000.0000.000
134B259ARG10.9380.95416.1320.1480.1480.0000.0000.0000.000
135B260HIS00.0330.02614.157-0.012-0.0120.0000.0000.0000.000
136B261GLY00.0550.04711.231-0.059-0.0590.0000.0000.0000.000
137B262ALA0-0.005-0.01912.087-0.036-0.0360.0000.0000.0000.000
138B263VAL0-0.048-0.01714.731-0.001-0.0010.0000.0000.0000.000
139B264MET0-0.004-0.00511.324-0.019-0.0190.0000.0000.0000.000
140B265LYS10.9600.99211.1280.1940.1940.0000.0000.0000.000
141B266LYS10.9600.98912.8340.2400.2400.0000.0000.0000.000
142B267ILE0-0.015-0.01215.4260.0250.0250.0000.0000.0000.000
143B268ILE00.0040.00310.5100.0170.0170.0000.0000.0000.000
144B269ASP-1-0.873-0.93713.824-0.295-0.2950.0000.0000.0000.000
145B270VAL0-0.057-0.03815.5720.0320.0320.0000.0000.0000.000
146B271LEU0-0.082-0.05015.4500.0370.0370.0000.0000.0000.000
147B272MET00.0450.02312.270-0.012-0.0120.0000.0000.0000.000
148B273SER0-0.0210.00716.2440.0350.0350.0000.0000.0000.000
149B274ARG10.8750.93919.5680.2830.2830.0000.0000.0000.000
150B275GLY00.0420.03519.6530.0200.0200.0000.0000.0000.000
151B276VAL0-0.073-0.03016.384-0.007-0.0070.0000.0000.0000.000
152B277GLU-1-0.811-0.90613.082-0.450-0.4500.0000.0000.0000.000
153B278PRO0-0.067-0.01711.871-0.009-0.0090.0000.0000.0000.000
154B279GLU-1-0.814-0.9088.790-0.844-0.8440.0000.0000.0000.000
155B280VAL00.008-0.0103.7030.4020.587-0.001-0.043-0.1410.000
156B281ASP-1-0.784-0.8717.052-0.621-0.6210.0000.0000.0000.000
157B282LYS10.7970.8709.7870.8740.8740.0000.0000.0000.000
158B283TYR0-0.035-0.0287.7580.2540.2540.0000.0000.0000.000
159B284LEU00.0290.00210.8340.1180.1180.0000.0000.0000.000
160B285PHE00.0510.04113.8360.0680.0680.0000.0000.0000.000
161B286LEU0-0.028-0.00912.3500.0740.0740.0000.0000.0000.000
162B287PHE0-0.018-0.03913.7410.0610.0610.0000.0000.0000.000
163B288LEU00.0160.01015.6760.0520.0520.0000.0000.0000.000
164B289LYS10.9801.01118.2420.4110.4110.0000.0000.0000.000
165B290PHE0-0.056-0.02218.0930.0310.0310.0000.0000.0000.000
166B291MET00.0170.01219.2330.0320.0320.0000.0000.0000.000
167B292ALA00.0450.04121.6040.0260.0260.0000.0000.0000.000
168B293SER0-0.079-0.04023.4370.0220.0220.0000.0000.0000.000
169B294VAL0-0.055-0.03122.5150.0170.0170.0000.0000.0000.000
170B295ILE0-0.019-0.01324.3030.0160.0160.0000.0000.0000.000
171B296PRO00.0130.01527.635-0.003-0.0030.0000.0000.0000.000
172B297THR0-0.020-0.01429.394-0.002-0.0020.0000.0000.0000.000
173B298ILE0-0.045-0.01427.9310.0070.0070.0000.0000.0000.000
174B299GLU-1-0.938-0.96428.203-0.130-0.1300.0000.0000.0000.000
175B300TYR0-0.019-0.02522.1750.0060.0060.0000.0000.0000.000
176B301ASP-1-0.819-0.88224.370-0.176-0.1760.0000.0000.0000.000
177B302TYR00.006-0.03120.193-0.033-0.0330.0000.0000.0000.000
178B303THR00.0210.01820.6990.0110.0110.0000.0000.0000.000
179B304MET0-0.024-0.00816.886-0.036-0.0360.0000.0000.0000.000