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: 3936L

Calculation Name: 4QT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QT4

Chain ID: A

ChEMBL ID:

UniProt ID: B5XIP6

Base Structure: X-ray

Registration Date: 2023-06-21

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152273.75089
FMO2-HF: Nuclear repulsion 2077627.653291
FMO2-HF: Total energy -74646.0976
FMO2-MP2: Total energy -74862.402352


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.3262.6011.293-3.004-4.212-0.006
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.004
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].
3A3LYS10.8710.9463.8072.4694.436-0.020-0.945-1.0010.002
4A4MET0-0.0040.0076.1750.1050.1050.0000.0000.0000.000
5A5ILE00.0220.0039.7660.1410.1410.0000.0000.0000.000
6A6VAL00.0010.00012.4040.0400.0400.0000.0000.0000.000
7A7GLY00.0210.01215.9000.0140.0140.0000.0000.0000.000
8A8LEU0-0.050-0.04319.2640.0200.0200.0000.0000.0000.000
9A9GLY00.026-0.00622.231-0.002-0.0020.0000.0000.0000.000
10A10ASN0-0.046-0.00925.7150.0080.0080.0000.0000.0000.000
11A11PRO00.0560.04226.733-0.005-0.0050.0000.0000.0000.000
12A12GLY00.0330.00328.4140.0100.0100.0000.0000.0000.000
13A13SER00.0610.01831.699-0.003-0.0030.0000.0000.0000.000
14A14LYS10.9600.98133.9770.0730.0730.0000.0000.0000.000
15A15TYR0-0.042-0.03331.4960.0050.0050.0000.0000.0000.000
16A16GLU-1-0.927-0.92630.084-0.137-0.1370.0000.0000.0000.000
17A17LYS10.9800.99830.8850.0960.0960.0000.0000.0000.000
18A18THR0-0.077-0.05231.7110.0010.0010.0000.0000.0000.000
19A19LYS10.9660.99530.7330.0840.0840.0000.0000.0000.000
20A20HIS10.7410.83528.7280.1030.1030.0000.0000.0000.000
21A21ASN00.0290.02026.796-0.001-0.0010.0000.0000.0000.000
22A22ILE00.0370.03124.697-0.011-0.0110.0000.0000.0000.000
23A23GLY00.0100.00622.026-0.016-0.0160.0000.0000.0000.000
24A24PHE0-0.042-0.02921.492-0.026-0.0260.0000.0000.0000.000
25A25MET00.0230.02023.059-0.013-0.0130.0000.0000.0000.000
26A26ALA00.0070.00620.571-0.009-0.0090.0000.0000.0000.000
27A27ILE00.0180.01316.589-0.024-0.0240.0000.0000.0000.000
28A28ASP-1-0.806-0.89219.550-0.254-0.2540.0000.0000.0000.000
29A29ASN0-0.079-0.04722.2490.0060.0060.0000.0000.0000.000
30A30ILE0-0.015-0.00815.591-0.005-0.0050.0000.0000.0000.000
31A31VAL00.0060.00416.508-0.026-0.0260.0000.0000.0000.000
32A32LYS10.9530.99218.6370.2290.2290.0000.0000.0000.000
33A33ASN0-0.106-0.07020.3650.0240.0240.0000.0000.0000.000
34A34LEU0-0.084-0.03113.948-0.013-0.0130.0000.0000.0000.000
35A35ASP-1-0.920-0.93317.174-0.274-0.2740.0000.0000.0000.000
36A36VAL0-0.049-0.01914.466-0.020-0.0200.0000.0000.0000.000
37A37THR00.0190.00117.2590.0150.0150.0000.0000.0000.000
38A38PHE0-0.048-0.03217.596-0.025-0.0250.0000.0000.0000.000
39A39THR0-0.034-0.01817.1870.0310.0310.0000.0000.0000.000
40A40ASP-1-0.926-0.96718.942-0.171-0.1710.0000.0000.0000.000
41A41ASP-1-0.810-0.88915.814-0.193-0.1930.0000.0000.0000.000
42A42LYS10.9540.96318.6180.1020.1020.0000.0000.0000.000
43A43ASN0-0.0230.01014.8960.0380.0380.0000.0000.0000.000
44A44PHE0-0.063-0.05312.9910.0170.0170.0000.0000.0000.000
45A45LYS10.9590.98818.3440.0950.0950.0000.0000.0000.000
46A46ALA00.013-0.01117.972-0.001-0.0010.0000.0000.0000.000
47A47GLN0-0.037-0.00219.635-0.002-0.0020.0000.0000.0000.000
48A48ILE0-0.018-0.01613.223-0.029-0.0290.0000.0000.0000.000
49A49GLY00.0740.05314.9670.0430.0430.0000.0000.0000.000
50A50SER0-0.060-0.0369.536-0.071-0.0710.0000.0000.0000.000
51A51THR00.0260.0089.8230.1500.1500.0000.0000.0000.000
52A52PHE00.006-0.0014.230-0.512-0.367-0.001-0.015-0.1290.000
53A53ILE0-0.0150.0037.6230.2890.2890.0000.0000.0000.000
54A54ASN00.0250.0157.374-0.147-0.1470.0000.0000.0000.000
55A55HIS00.008-0.0103.355-0.1970.4490.023-0.160-0.5080.000
56A56GLU-1-0.916-0.9532.306-8.296-5.8741.286-1.639-2.069-0.009
57A57LYS10.8840.9793.4951.8582.5560.007-0.225-0.4790.001
58A58VAL00.0300.0065.203-0.514-0.601-0.001-0.0130.1020.000
59A59TYR00.007-0.0106.2010.4750.4750.0000.0000.0000.000
60A60PHE00.001-0.01010.4590.0190.0190.0000.0000.0000.000
61A61VAL00.042-0.00313.4950.0660.0660.0000.0000.0000.000
62A62LYS10.8500.93916.2320.2400.2400.0000.0000.0000.000
63A63PRO0-0.006-0.00819.0440.0180.0180.0000.0000.0000.000
64A64THR00.012-0.00921.1530.0100.0100.0000.0000.0000.000
65A65THR00.0220.01322.5100.0090.0090.0000.0000.0000.000
66A66PHE0-0.024-0.00725.2670.0120.0120.0000.0000.0000.000
67A67MET00.0650.04325.4430.0000.0000.0000.0000.0000.000
68A68ASN0-0.074-0.03725.942-0.006-0.0060.0000.0000.0000.000
69A69ASN00.002-0.00325.7680.0140.0140.0000.0000.0000.000
70A70SER0-0.009-0.01521.533-0.006-0.0060.0000.0000.0000.000
71A71GLY00.003-0.00820.637-0.013-0.0130.0000.0000.0000.000
72A72ILE0-0.0230.00420.1620.0060.0060.0000.0000.0000.000
73A73ALA00.0420.01818.8520.0030.0030.0000.0000.0000.000
74A74VAL0-0.0010.00015.182-0.016-0.0160.0000.0000.0000.000
75A75LYS10.9971.00215.272-0.016-0.0160.0000.0000.0000.000
76A76ALA0-0.0090.01015.2080.0170.0170.0000.0000.0000.000
77A77LEU00.012-0.01012.5670.0040.0040.0000.0000.0000.000
78A78LEU0-0.031-0.02310.889-0.055-0.0550.0000.0000.0000.000
79A79THR0-0.0100.00010.5780.0720.0720.0000.0000.0000.000
80A80TYR0-0.077-0.0339.8760.0460.0460.0000.0000.0000.000
81A81TYR0-0.019-0.0226.387-0.036-0.0360.0000.0000.0000.000
82A82ASN0-0.0240.0066.074-0.057-0.0570.0000.0000.0000.000
83A83ILE0-0.043-0.0126.4010.1990.1990.0000.0000.0000.000
84A84ASP-1-0.776-0.8917.9140.2400.2400.0000.0000.0000.000
85A85ILE0-0.001-0.0099.445-0.094-0.0940.0000.0000.0000.000
86A86THR0-0.083-0.0559.045-0.071-0.0710.0000.0000.0000.000
87A87ASP-1-0.879-0.9264.8481.2791.415-0.001-0.007-0.1280.000
88A88LEU0-0.088-0.0287.409-0.306-0.3060.0000.0000.0000.000
89A89ILE0-0.035-0.02210.6870.0080.0080.0000.0000.0000.000
90A90VAL0-0.0270.00112.931-0.006-0.0060.0000.0000.0000.000
91A91ILE00.007-0.00616.0100.0160.0160.0000.0000.0000.000
92A92TYR0-0.026-0.04418.9280.0160.0160.0000.0000.0000.000
93A93ASP-1-0.679-0.81222.587-0.137-0.1370.0000.0000.0000.000
94A94ASP-1-0.866-0.94626.137-0.110-0.1100.0000.0000.0000.000
95A95LEU0-0.042-0.04127.2470.0030.0030.0000.0000.0000.000
96A96ASP-1-0.834-0.90130.280-0.074-0.0740.0000.0000.0000.000
97A97MET0-0.102-0.01626.1960.0000.0000.0000.0000.0000.000
98A98GLU-1-0.861-0.93931.393-0.091-0.0910.0000.0000.0000.000
99A99VAL00.0140.00531.644-0.011-0.0110.0000.0000.0000.000
100A100SER0-0.0130.00429.225-0.001-0.0010.0000.0000.0000.000
101A101LYS10.9070.98827.9040.1230.1230.0000.0000.0000.000
102A102LEU00.0560.01421.403-0.002-0.0020.0000.0000.0000.000
103A103ARG10.8590.91123.5530.1350.1350.0000.0000.0000.000
104A104LEU00.0390.04816.8820.0000.0000.0000.0000.0000.000
105A105ARG10.8320.90919.2740.1710.1710.0000.0000.0000.000
106A106SER00.1640.07916.660-0.021-0.0210.0000.0000.0000.000
107A107LYS11.0271.03317.9480.0940.0940.0000.0000.0000.000
108A108GLY0-0.029-0.00820.844-0.014-0.0140.0000.0000.0000.000
109A109SER00.0270.01123.681-0.001-0.0010.0000.0000.0000.000
110A110ALA00.0400.00026.095-0.006-0.0060.0000.0000.0000.000
111A111GLY00.0120.02426.984-0.005-0.0050.0000.0000.0000.000
112A112GLY0-0.038-0.02630.209-0.001-0.0010.0000.0000.0000.000
113A113HIS00.0140.00225.3360.0080.0080.0000.0000.0000.000
114A114ASN00.0610.00627.489-0.006-0.0060.0000.0000.0000.000
115A115GLY00.0720.04224.8000.0050.0050.0000.0000.0000.000
116A116ILE00.0050.00221.4770.0040.0040.0000.0000.0000.000
117A117LYS10.9100.94523.4860.0650.0650.0000.0000.0000.000
118A118SER00.0120.03424.6290.0070.0070.0000.0000.0000.000
119A119ILE00.0650.02218.4910.0090.0090.0000.0000.0000.000
120A120ILE0-0.033-0.00820.7220.0130.0130.0000.0000.0000.000
121A121ALA0-0.035-0.02022.2700.0140.0140.0000.0000.0000.000
122A122HIS0-0.062-0.02820.7800.0130.0130.0000.0000.0000.000
123A123ILE0-0.026-0.02116.1030.0090.0090.0000.0000.0000.000
124A124GLY00.0130.02418.6240.0210.0210.0000.0000.0000.000
125A125THR00.0810.03717.1640.0000.0000.0000.0000.0000.000
126A126GLN0-0.013-0.01720.088-0.022-0.0220.0000.0000.0000.000
127A127GLU-1-0.994-0.99917.848-0.067-0.0670.0000.0000.0000.000
128A128PHE00.0730.04014.8240.0160.0160.0000.0000.0000.000
129A129ASN00.0150.00511.4090.0380.0380.0000.0000.0000.000
130A130ARG10.7860.89814.9950.1120.1120.0000.0000.0000.000
131A131ILE00.0330.00815.4270.0010.0010.0000.0000.0000.000
132A132LYS10.8360.91519.0210.1440.1440.0000.0000.0000.000
133A133VAL00.0640.02722.705-0.002-0.0020.0000.0000.0000.000
134A134GLY0-0.026-0.01325.4420.0090.0090.0000.0000.0000.000
135A135ILE00.0050.00529.011-0.003-0.0030.0000.0000.0000.000
136A136GLY00.0500.02531.4840.0060.0060.0000.0000.0000.000
137A137ARG10.8440.90834.1180.0820.0820.0000.0000.0000.000
138A138PRO0-0.0080.02435.1770.0020.0020.0000.0000.0000.000
139A139LEU00.0620.01038.0640.0020.0020.0000.0000.0000.000
140A140LYS10.9870.98341.5290.0450.0450.0000.0000.0000.000
141A141GLY0-0.002-0.00542.8780.0010.0010.0000.0000.0000.000
142A142MET0-0.0270.02039.8170.0000.0000.0000.0000.0000.000
143A143THR0-0.040-0.01439.684-0.001-0.0010.0000.0000.0000.000
144A144VAL00.0610.00333.053-0.003-0.0030.0000.0000.0000.000
145A145ILE00.0250.01135.369-0.005-0.0050.0000.0000.0000.000
146A146ASN00.0280.00036.396-0.005-0.0050.0000.0000.0000.000
147A147HIS00.0290.03733.6640.0010.0010.0000.0000.0000.000
148A148VAL0-0.015-0.02931.315-0.004-0.0040.0000.0000.0000.000
149A149MET0-0.065-0.03832.134-0.006-0.0060.0000.0000.0000.000
150A150GLY00.0310.04335.4370.0010.0010.0000.0000.0000.000
151A151GLN00.001-0.01635.107-0.005-0.0050.0000.0000.0000.000
152A152PHE00.018-0.00629.8260.0020.0020.0000.0000.0000.000
153A153ASN00.0140.03035.7000.0040.0040.0000.0000.0000.000
154A154THR0-0.005-0.01837.632-0.007-0.0070.0000.0000.0000.000
155A155GLU-1-0.852-0.93038.673-0.084-0.0840.0000.0000.0000.000
156A156ASP-1-0.876-0.94434.851-0.101-0.1010.0000.0000.0000.000
157A157ASN0-0.046-0.02533.980-0.012-0.0120.0000.0000.0000.000
158A158ILE00.0440.02032.773-0.010-0.0100.0000.0000.0000.000
159A159ALA00.0410.02732.137-0.009-0.0090.0000.0000.0000.000
160A160ILE00.007-0.00328.559-0.012-0.0120.0000.0000.0000.000
161A161SER0-0.025-0.02428.055-0.015-0.0150.0000.0000.0000.000
162A162LEU00.0220.02027.567-0.014-0.0140.0000.0000.0000.000
163A163THR0-0.086-0.08225.025-0.015-0.0150.0000.0000.0000.000
164A164LEU00.006-0.00723.466-0.022-0.0220.0000.0000.0000.000
165A165ASP-1-0.810-0.88822.608-0.244-0.2440.0000.0000.0000.000
166A166ARG10.8460.91822.2370.1790.1790.0000.0000.0000.000
167A167VAL0-0.020-0.01218.621-0.024-0.0240.0000.0000.0000.000
168A168VAL00.0320.02217.935-0.052-0.0520.0000.0000.0000.000
169A169ASN0-0.008-0.01717.167-0.075-0.0750.0000.0000.0000.000
170A170ALA0-0.016-0.00517.057-0.034-0.0340.0000.0000.0000.000
171A171VAL00.0220.00912.426-0.051-0.0510.0000.0000.0000.000
172A172LYS10.9620.98612.3760.3360.3360.0000.0000.0000.000
173A173PHE0-0.015-0.01113.055-0.056-0.0560.0000.0000.0000.000
174A174TYR00.0450.0187.778-0.114-0.1140.0000.0000.0000.000
175A175LEU0-0.018-0.0207.713-0.089-0.0890.0000.0000.0000.000
176A176GLN0-0.120-0.0648.625-0.161-0.1610.0000.0000.0000.000
177A177GLU-1-0.890-0.94210.792-0.489-0.4890.0000.0000.0000.000
178A178ASN00.0100.0275.054-0.332-0.3320.0000.0000.0000.000
179A179ASP-1-0.803-0.8987.965-0.218-0.2180.0000.0000.0000.000
180A180PHE00.008-0.01310.9540.0350.0350.0000.0000.0000.000
181A181GLU-1-0.924-0.96312.927-0.128-0.1280.0000.0000.0000.000
182A182LYS10.9690.98613.9410.3970.3970.0000.0000.0000.000
183A183THR0-0.013-0.01513.5840.0020.0020.0000.0000.0000.000
184A184MET0-0.060-0.03616.1990.0350.0350.0000.0000.0000.000
185A185GLN0-0.063-0.02518.8280.0330.0330.0000.0000.0000.000
186A186LYS10.9240.98618.7550.2790.2790.0000.0000.0000.000
187A187PHE0-0.025-0.00518.0380.0120.0120.0000.0000.0000.000
188A188ASN0-0.043-0.01121.3090.0130.0130.0000.0000.0000.000
189A189GLY0-0.0080.00523.8660.0080.0080.0000.0000.0000.000