FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: JQ479

Calculation Name: 3NT8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NT8

Chain ID: A

ChEMBL ID:

UniProt ID: O76744

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 391
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6421035.064463
FMO2-HF: Nuclear repulsion 6262534.06843
FMO2-HF: Total energy -158500.996033
FMO2-MP2: Total energy -158941.851826


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:24:SER)


Summations of interaction energy for fragment #1(A:24:SER)
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.
-2.491-0.474-0.013-0.938-1.0650.001
Interaction energy analysis for fragmet #1(A:24:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.018
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].
3A26GLY00.0200.0133.887-0.3851.455-0.009-0.913-0.9180.001
4A27CYS0-0.056-0.0244.982-0.321-0.182-0.002-0.013-0.1240.000
5A28SER00.0510.0178.5580.0140.0140.0000.0000.0000.000
6A29ASN0-0.077-0.04011.1380.0020.0020.0000.0000.0000.000
7A30SER00.0290.01012.008-0.038-0.0380.0000.0000.0000.000
8A31GLY0-0.033-0.00514.231-0.007-0.0070.0000.0000.0000.000
9A32ILE0-0.053-0.02011.7420.0060.0060.0000.0000.0000.000
10A33THR00.0260.00210.836-0.036-0.0360.0000.0000.0000.000
11A34ASP-1-0.786-0.9124.696-1.554-1.603-0.001-0.0110.0610.000
12A35SER0-0.0010.0027.059-0.066-0.0660.0000.0000.0000.000
13A36ASP-1-0.804-0.8899.145-0.145-0.1450.0000.0000.0000.000
14A37ARG10.7260.8357.0160.5200.5200.0000.0000.0000.000
15A38GLN0-0.062-0.0354.908-0.378-0.291-0.001-0.001-0.0840.000
16A39ALA00.0330.0207.8240.1390.1390.0000.0000.0000.000
17A40PHE00.011-0.01511.5710.0680.0680.0000.0000.0000.000
18A41LEU0-0.023-0.0087.2580.0670.0670.0000.0000.0000.000
19A42ASP-1-0.847-0.9209.6050.0260.0260.0000.0000.0000.000
20A43PHE0-0.047-0.01511.8550.0220.0220.0000.0000.0000.000
21A44HIS00.0180.02914.3970.0120.0120.0000.0000.0000.000
22A45ASN00.0310.01111.325-0.013-0.0130.0000.0000.0000.000
23A46ASN0-0.0060.00014.1640.0210.0210.0000.0000.0000.000
24A47ALA00.0160.01816.853-0.004-0.0040.0000.0000.0000.000
25A48ARG10.8210.86716.935-0.122-0.1220.0000.0000.0000.000
26A49ARG10.8630.93114.658-0.157-0.1570.0000.0000.0000.000
27A50ARG10.9270.96620.062-0.028-0.0280.0000.0000.0000.000
28A51VAL0-0.0050.01322.774-0.005-0.0050.0000.0000.0000.000
29A52ALA00.0330.01522.587-0.004-0.0040.0000.0000.0000.000
30A53LYS10.8230.88821.413-0.068-0.0680.0000.0000.0000.000
31A54GLY00.0150.02225.675-0.004-0.0040.0000.0000.0000.000
32A55LEU0-0.049-0.02624.523-0.005-0.0050.0000.0000.0000.000
33A56GLU-1-0.886-0.94124.2390.0170.0170.0000.0000.0000.000
34A57ASP-1-0.848-0.90427.1990.0110.0110.0000.0000.0000.000
35A58SER00.003-0.00829.5870.0010.0010.0000.0000.0000.000
36A59ASN00.0190.00732.363-0.001-0.0010.0000.0000.0000.000
37A60SER0-0.047-0.01435.332-0.002-0.0020.0000.0000.0000.000
38A61GLY00.0790.03535.886-0.001-0.0010.0000.0000.0000.000
39A62LYS10.7690.86729.532-0.017-0.0170.0000.0000.0000.000
40A63LEU0-0.029-0.02127.5480.0000.0000.0000.0000.0000.000
41A64ASN0-0.037-0.03530.6010.0000.0000.0000.0000.0000.000
42A65PRO00.0180.01528.1060.0020.0020.0000.0000.0000.000
43A66ALA0-0.026-0.00925.031-0.001-0.0010.0000.0000.0000.000
44A67LYS10.9771.00925.895-0.043-0.0430.0000.0000.0000.000
45A68ASN00.008-0.01824.1770.0040.0040.0000.0000.0000.000
46A69MET00.0070.02920.3200.0050.0050.0000.0000.0000.000
47A70TYR0-0.042-0.02118.0890.0070.0070.0000.0000.0000.000
48A71LYS10.8930.96710.448-0.529-0.5290.0000.0000.0000.000
49A72LEU0-0.044-0.01913.3530.0080.0080.0000.0000.0000.000
50A73SER00.009-0.0029.8960.1160.1160.0000.0000.0000.000
51A74TRP00.009-0.0317.554-0.132-0.1320.0000.0000.0000.000
52A75ASP-1-0.801-0.9079.4470.2270.2270.0000.0000.0000.000
53A77ALA00.0170.02710.964-0.031-0.0310.0000.0000.0000.000
54A78MET0-0.082-0.04914.269-0.008-0.0080.0000.0000.0000.000
55A79GLU-1-0.706-0.83010.867-0.169-0.1690.0000.0000.0000.000
56A80GLN0-0.047-0.02014.602-0.015-0.0150.0000.0000.0000.000
57A81GLN00.0260.00416.173-0.007-0.0070.0000.0000.0000.000
58A82LEU0-0.0010.00117.483-0.003-0.0030.0000.0000.0000.000
59A83GLN0-0.013-0.00716.804-0.016-0.0160.0000.0000.0000.000
60A84ASP-1-0.871-0.94219.096-0.001-0.0010.0000.0000.0000.000
61A85ALA0-0.043-0.01321.8600.0000.0000.0000.0000.0000.000
62A86ILE0-0.043-0.02219.9450.0000.0000.0000.0000.0000.000
63A87GLN00.0140.00720.826-0.005-0.0050.0000.0000.0000.000
64A88SER00.0200.00724.922-0.002-0.0020.0000.0000.0000.000
65A89CYS0-0.108-0.05624.3120.0020.0020.0000.0000.0000.000
66A90PRO00.0230.03526.3850.0010.0010.0000.0000.0000.000
67A91SER0-0.002-0.01828.794-0.001-0.0010.0000.0000.0000.000
68A92GLY0-0.0140.00030.8410.0010.0010.0000.0000.0000.000
69A93PHE0-0.047-0.03426.647-0.001-0.0010.0000.0000.0000.000
70A94ALA0-0.001-0.01324.837-0.001-0.0010.0000.0000.0000.000
71A95GLY00.0110.01726.8070.0000.0000.0000.0000.0000.000
72A96ILE0-0.0160.00121.3780.0000.0000.0000.0000.0000.000
73A97GLN0-0.017-0.01023.5230.0000.0000.0000.0000.0000.000
74A98GLY0-0.012-0.01722.9490.0040.0040.0000.0000.0000.000
75A99VAL0-0.067-0.03719.8790.0090.0090.0000.0000.0000.000
76A100ALA00.0140.02422.736-0.007-0.0070.0000.0000.0000.000
77A101GLN00.0340.00922.1650.0050.0050.0000.0000.0000.000
78A102ASN00.0110.02421.495-0.001-0.0010.0000.0000.0000.000
79A103THR0-0.0010.00222.344-0.005-0.0050.0000.0000.0000.000
80A104MET00.0300.02623.8610.0040.0040.0000.0000.0000.000
81A105SER00.0270.00325.036-0.004-0.0040.0000.0000.0000.000
82A106TRP00.0060.00723.7150.0020.0020.0000.0000.0000.000
83A107SER00.004-0.00628.1740.0010.0010.0000.0000.0000.000
84A108SER00.006-0.00529.9740.0010.0010.0000.0000.0000.000
85A109SER00.0170.00431.902-0.001-0.0010.0000.0000.0000.000
86A110GLY00.0160.01132.2610.0010.0010.0000.0000.0000.000
87A111GLY0-0.0060.01129.527-0.001-0.0010.0000.0000.0000.000
88A112TYR0-0.025-0.04024.1090.0000.0000.0000.0000.0000.000
89A113PRO00.0070.00724.173-0.003-0.0030.0000.0000.0000.000
90A114ASP-1-0.826-0.91219.440-0.112-0.1120.0000.0000.0000.000
91A115PRO0-0.014-0.01218.9940.0020.0020.0000.0000.0000.000
92A116SER00.0400.02815.8180.0040.0040.0000.0000.0000.000
93A117VAL00.0010.00617.5570.0020.0020.0000.0000.0000.000
94A118LYS10.8470.92620.2470.0500.0500.0000.0000.0000.000
95A119ILE00.0000.02414.1230.0150.0150.0000.0000.0000.000
96A120GLU-1-0.874-0.95018.262-0.024-0.0240.0000.0000.0000.000
97A121PRO00.0240.02119.4810.0110.0110.0000.0000.0000.000
98A122THR0-0.043-0.04220.5200.0090.0090.0000.0000.0000.000
99A123LEU0-0.0120.00516.1690.0090.0090.0000.0000.0000.000
100A124SER00.0120.00520.5400.0120.0120.0000.0000.0000.000
101A125GLY0-0.014-0.00523.0690.0050.0050.0000.0000.0000.000
102A126TRP0-0.045-0.03619.1300.0040.0040.0000.0000.0000.000
103A127TRP00.0550.01021.4780.0060.0060.0000.0000.0000.000
104A128SER0-0.129-0.05924.4450.0020.0020.0000.0000.0000.000
105A129GLY00.0480.01927.7910.0000.0000.0000.0000.0000.000
106A130ALA00.0380.01428.483-0.001-0.0010.0000.0000.0000.000
107A131LYS10.9170.96429.705-0.004-0.0040.0000.0000.0000.000
108A132LYS10.8980.94030.6670.0010.0010.0000.0000.0000.000
109A133ASN0-0.028-0.00132.916-0.002-0.0020.0000.0000.0000.000
110A134GLY00.0020.02733.6940.0000.0000.0000.0000.0000.000
111A135VAL0-0.010-0.01130.4620.0010.0010.0000.0000.0000.000
112A136GLY00.0220.00833.964-0.001-0.0010.0000.0000.0000.000
113A137PRO00.0320.01335.4220.0020.0020.0000.0000.0000.000
114A138ASP-1-0.881-0.93435.8840.0260.0260.0000.0000.0000.000
115A139ASN0-0.031-0.03330.6900.0000.0000.0000.0000.0000.000
116A140LYS10.8770.96731.700-0.024-0.0240.0000.0000.0000.000
117A141TYR00.0320.03230.474-0.003-0.0030.0000.0000.0000.000
118A142THR00.0500.01133.2240.0000.0000.0000.0000.0000.000
119A143GLY0-0.0110.00433.904-0.002-0.0020.0000.0000.0000.000
120A144GLY00.0330.00934.5110.0000.0000.0000.0000.0000.000
121A145GLY00.0020.00333.309-0.001-0.0010.0000.0000.0000.000
122A146LEU0-0.0070.00230.2680.0000.0000.0000.0000.0000.000
123A147PHE0-0.024-0.00527.1160.0030.0030.0000.0000.0000.000
124A148ALA00.0250.01525.3020.0040.0040.0000.0000.0000.000
125A149PHE00.0620.02224.3060.0040.0040.0000.0000.0000.000
126A150SER0-0.005-0.02024.5530.0060.0060.0000.0000.0000.000
127A151ASN0-0.027-0.02722.3570.0100.0100.0000.0000.0000.000
128A152MET0-0.064-0.00718.8550.0070.0070.0000.0000.0000.000
129A153VAL00.0190.02720.0200.0150.0150.0000.0000.0000.000
130A154TYR0-0.043-0.00922.6150.0070.0070.0000.0000.0000.000
131A155SER00.0160.00321.9450.0120.0120.0000.0000.0000.000
132A156GLU-1-0.915-0.95921.8560.0840.0840.0000.0000.0000.000
133A157THR0-0.027-0.02218.0930.0050.0050.0000.0000.0000.000
134A158THR00.0080.01416.3100.0120.0120.0000.0000.0000.000
135A159LYS10.9160.95513.624-0.126-0.1260.0000.0000.0000.000
136A160LEU00.0160.01312.044-0.038-0.0380.0000.0000.0000.000
137A161GLY00.0380.02212.7310.0230.0230.0000.0000.0000.000
138A162CYS0-0.0390.00113.274-0.006-0.0060.0000.0000.0000.000
139A163ALA00.0780.03913.902-0.024-0.0240.0000.0000.0000.000
140A164TYR0-0.041-0.03715.2150.0280.0280.0000.0000.0000.000
141A165LYS10.8820.94118.9830.0270.0270.0000.0000.0000.000
142A166VAL00.0400.01721.7270.0040.0040.0000.0000.0000.000
143A168GLY00.0340.01427.8760.0020.0020.0000.0000.0000.000
144A169THR0-0.0020.00429.467-0.002-0.0020.0000.0000.0000.000
145A170LYS10.8940.95428.5870.0150.0150.0000.0000.0000.000
146A171LEU0-0.0150.01021.386-0.002-0.0020.0000.0000.0000.000
147A172ALA00.0000.01224.0430.0040.0040.0000.0000.0000.000
148A173VAL00.0300.00118.676-0.008-0.0080.0000.0000.0000.000
149A174SER0-0.060-0.04919.4400.0100.0100.0000.0000.0000.000
150A176ILE00.0130.00617.6750.0000.0000.0000.0000.0000.000
151A177TYR0-0.001-0.05017.5330.0090.0090.0000.0000.0000.000
152A178ASN00.0310.01817.915-0.011-0.0110.0000.0000.0000.000
153A179GLY00.013-0.00320.3540.0020.0020.0000.0000.0000.000
154A180VAL0-0.025-0.00723.079-0.004-0.0040.0000.0000.0000.000
155A181GLY00.0370.01726.0760.0010.0010.0000.0000.0000.000
156A182TYR0-0.017-0.01126.649-0.002-0.0020.0000.0000.0000.000
157A183ILE0-0.018-0.00430.156-0.003-0.0030.0000.0000.0000.000
158A184THR00.009-0.02232.6920.0010.0010.0000.0000.0000.000
159A185ASN00.0060.00435.9520.0010.0010.0000.0000.0000.000
160A186GLN0-0.032-0.00129.3420.0010.0010.0000.0000.0000.000
161A187PRO0-0.011-0.01031.421-0.001-0.0010.0000.0000.0000.000
162A188MET0-0.026-0.01327.2760.0040.0040.0000.0000.0000.000
163A189TRP00.012-0.01126.1400.0080.0080.0000.0000.0000.000
164A190GLU-1-0.911-0.94828.0220.0440.0440.0000.0000.0000.000
165A191THR00.0370.01229.5260.0040.0040.0000.0000.0000.000
166A192GLY0-0.033-0.01430.505-0.001-0.0010.0000.0000.0000.000
167A193GLN0-0.014-0.00728.6590.0010.0010.0000.0000.0000.000
168A194ALA00.0210.03223.9550.0040.0040.0000.0000.0000.000
169A195CYS0-0.067-0.03219.125-0.004-0.0040.0000.0000.0000.000
170A196GLN0-0.058-0.04324.0310.0000.0000.0000.0000.0000.000
171A197THR00.0130.00023.5410.0040.0040.0000.0000.0000.000
172A198GLY00.017-0.00822.4930.0030.0030.0000.0000.0000.000
173A199ALA0-0.016-0.01323.0880.0000.0000.0000.0000.0000.000
174A200ASP-1-0.821-0.89925.9160.0630.0630.0000.0000.0000.000
175A201CYS0-0.064-0.01718.4960.0100.0100.0000.0000.0000.000
176A202SER00.0220.00525.0100.0000.0000.0000.0000.0000.000
177A203THR0-0.041-0.01423.888-0.004-0.0040.0000.0000.0000.000
178A204TYR0-0.007-0.00721.345-0.003-0.0030.0000.0000.0000.000
179A205LYS11.0061.02723.324-0.056-0.0560.0000.0000.0000.000
180A206ASN0-0.024-0.01921.4970.0040.0040.0000.0000.0000.000
181A207SER00.013-0.00119.4420.0170.0170.0000.0000.0000.000
182A208GLY00.0150.01518.143-0.016-0.0160.0000.0000.0000.000
183A210GLU-1-0.872-0.93513.1580.3890.3890.0000.0000.0000.000
184A211ASP-1-0.835-0.89917.3920.0800.0800.0000.0000.0000.000
185A212GLY00.0380.01619.712-0.003-0.0030.0000.0000.0000.000
186A213LEU0-0.034-0.01915.818-0.003-0.0030.0000.0000.0000.000
187A215THR00.014-0.00214.6150.0150.0150.0000.0000.0000.000
188A216LYS10.8700.95516.145-0.177-0.1770.0000.0000.0000.000
189A217GLY00.0480.03314.9840.0410.0410.0000.0000.0000.000
190A218PRO0-0.002-0.02214.4820.0060.0060.0000.0000.0000.000
191A219ASP-1-0.933-0.96316.0600.1290.1290.0000.0000.0000.000
192A220VAL00.0040.00018.810-0.008-0.0080.0000.0000.0000.000
193A221PRO0-0.035-0.02821.364-0.001-0.0010.0000.0000.0000.000
194A222GLU-1-0.827-0.89023.5720.0530.0530.0000.0000.0000.000
195A223THR00.0130.00026.501-0.003-0.0030.0000.0000.0000.000
196A224ASN0-0.007-0.00529.8930.0020.0020.0000.0000.0000.000
197A225GLN0-0.038-0.02433.444-0.002-0.0020.0000.0000.0000.000
198A226GLN0-0.080-0.02634.783-0.003-0.0030.0000.0000.0000.000
199A227CYS0-0.006-0.01537.639-0.001-0.0010.0000.0000.0000.000
200A228PRO00.0470.02237.8970.0000.0000.0000.0000.0000.000
201A229SER0-0.005-0.00238.9850.0000.0000.0000.0000.0000.000
202A230ASN0-0.070-0.02038.989-0.002-0.0020.0000.0000.0000.000
203A231THR00.0210.00235.2370.0010.0010.0000.0000.0000.000
204A232GLY0-0.003-0.01333.577-0.001-0.0010.0000.0000.0000.000
205A233MET0-0.080-0.02433.1000.0030.0030.0000.0000.0000.000
206A234THR0-0.018-0.00328.776-0.002-0.0020.0000.0000.0000.000
207A235ASP-1-0.702-0.86731.4650.0300.0300.0000.0000.0000.000
208A236SER0-0.0070.01627.3910.0000.0000.0000.0000.0000.000
209A237VAL00.0240.00129.3690.0000.0000.0000.0000.0000.000
210A238ARG10.7190.83131.424-0.028-0.0280.0000.0000.0000.000
211A239ASP-1-0.837-0.92632.3030.0350.0350.0000.0000.0000.000
212A240THR0-0.0380.00330.1890.0010.0010.0000.0000.0000.000
213A241PHE0-0.002-0.00532.785-0.001-0.0010.0000.0000.0000.000
214A242LEU00.0080.01036.066-0.002-0.0020.0000.0000.0000.000
215A243SER0-0.048-0.04034.217-0.001-0.0010.0000.0000.0000.000
216A244VAL00.0320.01033.768-0.001-0.0010.0000.0000.0000.000
217A245HIS00.0070.01836.680-0.003-0.0030.0000.0000.0000.000
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