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: 3JK8L

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 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 391
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6424287.856567
FMO2-HF: Nuclear repulsion 6265785.140186
FMO2-HF: Total energy -158502.716381
FMO2-MP2: Total energy -158943.577726


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.
-1.2671.036-0.001-1.08-1.220
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 : 0.029 / q_NPA : -0.005
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].
3A26GLY00.0090.0063.2350.2032.2470.001-1.046-0.9990.000
4A27CYS0-0.043-0.0194.0761.5311.715-0.001-0.034-0.1480.000
5A28SER00.0600.0237.632-0.141-0.1410.0000.0000.0000.000
6A29ASN0-0.076-0.03710.1940.1970.1970.0000.0000.0000.000
7A30SER00.0280.01011.634-0.185-0.1850.0000.0000.0000.000
8A31GLY0-0.038-0.00913.9210.0540.0540.0000.0000.0000.000
9A32ILE0-0.070-0.02811.5940.0940.0940.0000.0000.0000.000
10A33THR00.003-0.02810.826-0.165-0.1650.0000.0000.0000.000
11A34ASP-1-0.789-0.9025.246-4.186-4.1860.0000.0000.0000.000
12A35SER00.0090.0057.0800.1170.1170.0000.0000.0000.000
13A36ASP-1-0.776-0.8739.142-0.610-0.6100.0000.0000.0000.000
14A37ARG10.7490.8377.0342.2952.2950.0000.0000.0000.000
15A38GLN0-0.066-0.0495.162-0.155-0.080-0.0010.000-0.0730.000
16A39ALA00.0180.0147.8540.2350.2350.0000.0000.0000.000
17A40PHE00.028-0.01311.6310.1420.1420.0000.0000.0000.000
18A41LEU0-0.0130.0047.2220.1360.1360.0000.0000.0000.000
19A42ASP-1-0.818-0.9049.826-0.132-0.1320.0000.0000.0000.000
20A43PHE0-0.043-0.00711.8870.0680.0680.0000.0000.0000.000
21A44HIS00.0140.00014.4350.0590.0590.0000.0000.0000.000
22A45ASN00.0240.01011.3800.0320.0320.0000.0000.0000.000
23A46ASN0-0.014-0.00913.8950.0600.0600.0000.0000.0000.000
24A47ALA00.0010.01216.8800.0140.0140.0000.0000.0000.000
25A48ARG10.8140.87117.100-0.024-0.0240.0000.0000.0000.000
26A49ARG10.8600.92414.517-0.145-0.1450.0000.0000.0000.000
27A50ARG10.8810.92020.0970.0420.0420.0000.0000.0000.000
28A51VAL0-0.0060.01122.8020.0010.0010.0000.0000.0000.000
29A52ALA00.0260.01722.5610.0020.0020.0000.0000.0000.000
30A53LYS10.8000.87121.252-0.072-0.0720.0000.0000.0000.000
31A54GLY00.0130.02325.702-0.001-0.0010.0000.0000.0000.000
32A55LEU0-0.039-0.02324.497-0.005-0.0050.0000.0000.0000.000
33A56GLU-1-0.791-0.85624.998-0.062-0.0620.0000.0000.0000.000
34A57ASP-1-0.834-0.88527.230-0.037-0.0370.0000.0000.0000.000
35A58SER00.004-0.00429.625-0.005-0.0050.0000.0000.0000.000
36A59ASN00.002-0.00232.4040.0000.0000.0000.0000.0000.000
37A60SER0-0.049-0.00435.3740.0010.0010.0000.0000.0000.000
38A61GLY00.0880.03235.9770.0010.0010.0000.0000.0000.000
39A62LYS10.7730.86829.3640.0180.0180.0000.0000.0000.000
40A63LEU0-0.033-0.02327.6520.0020.0020.0000.0000.0000.000
41A64ASN0-0.026-0.02030.6400.0050.0050.0000.0000.0000.000
42A65PRO00.0240.01828.146-0.001-0.0010.0000.0000.0000.000
43A66ALA0-0.033-0.01325.107-0.001-0.0010.0000.0000.0000.000
44A67LYS10.8670.94325.942-0.047-0.0470.0000.0000.0000.000
45A68ASN0-0.011-0.02824.2330.0060.0060.0000.0000.0000.000
46A69MET00.0090.02720.446-0.005-0.0050.0000.0000.0000.000
47A70TYR0-0.037-0.02618.1890.0160.0160.0000.0000.0000.000
48A71LYS10.8080.90310.165-0.650-0.6500.0000.0000.0000.000
49A72LEU0-0.045-0.02513.4490.0170.0170.0000.0000.0000.000
50A73SER00.007-0.0019.8300.1540.1540.0000.0000.0000.000
51A74TRP00.026-0.0267.681-0.027-0.0270.0000.0000.0000.000
52A75ASP-1-0.777-0.8819.389-0.078-0.0780.0000.0000.0000.000
53A77ALA00.0280.02810.911-0.004-0.0040.0000.0000.0000.000
54A78MET0-0.102-0.05014.1720.0430.0430.0000.0000.0000.000
55A79GLU-1-0.686-0.81010.785-1.273-1.2730.0000.0000.0000.000
56A80GLN0-0.065-0.03814.125-0.070-0.0700.0000.0000.0000.000
57A81GLN00.0560.02115.7250.0670.0670.0000.0000.0000.000
58A82LEU00.0080.00317.6890.0300.0300.0000.0000.0000.000
59A83GLN0-0.006-0.00616.842-0.036-0.0360.0000.0000.0000.000
60A84ASP-1-0.865-0.92219.091-0.343-0.3430.0000.0000.0000.000
61A85ALA0-0.040-0.00921.4420.0290.0290.0000.0000.0000.000
62A86ILE0-0.032-0.02019.9780.0270.0270.0000.0000.0000.000
63A87GLN00.006-0.00420.6550.0060.0060.0000.0000.0000.000
64A88SER00.0240.00524.865-0.002-0.0020.0000.0000.0000.000
65A89CYS0-0.110-0.05724.3560.0100.0100.0000.0000.0000.000
66A90PRO00.0460.04826.5040.0150.0150.0000.0000.0000.000
67A91SER0-0.005-0.01628.868-0.008-0.0080.0000.0000.0000.000
68A92GLY0-0.0050.00830.9140.0040.0040.0000.0000.0000.000
69A93PHE0-0.040-0.02926.799-0.011-0.0110.0000.0000.0000.000
70A94ALA00.000-0.00924.8990.0040.0040.0000.0000.0000.000
71A95GLY00.0110.01626.8980.0040.0040.0000.0000.0000.000
72A96ILE0-0.027-0.00521.3780.0050.0050.0000.0000.0000.000
73A97GLN0-0.013-0.00423.4440.0290.0290.0000.0000.0000.000
74A98GLY00.009-0.00422.893-0.010-0.0100.0000.0000.0000.000
75A99VAL0-0.071-0.03719.9020.0100.0100.0000.0000.0000.000
76A100ALA00.0150.02822.8470.0010.0010.0000.0000.0000.000
77A101GLN00.030-0.00322.2590.0000.0000.0000.0000.0000.000
78A102ASN00.0080.02521.5770.0280.0280.0000.0000.0000.000
79A103THR00.0010.00022.423-0.033-0.0330.0000.0000.0000.000
80A104MET00.0220.03023.8570.0240.0240.0000.0000.0000.000
81A105SER00.0280.00125.099-0.020-0.0200.0000.0000.0000.000
82A106TRP00.0180.00623.6350.0240.0240.0000.0000.0000.000
83A107SER0-0.005-0.01228.221-0.004-0.0040.0000.0000.0000.000
84A108SER0-0.007-0.00129.9680.0090.0090.0000.0000.0000.000
85A109SER00.0210.00231.934-0.008-0.0080.0000.0000.0000.000
86A110GLY00.0090.00832.2760.0030.0030.0000.0000.0000.000
87A111GLY0-0.0110.00929.551-0.006-0.0060.0000.0000.0000.000
88A112TYR0-0.020-0.03924.1050.0030.0030.0000.0000.0000.000
89A113PRO00.0050.00724.193-0.022-0.0220.0000.0000.0000.000
90A114ASP-1-0.808-0.88819.303-0.433-0.4330.0000.0000.0000.000
91A115PRO0-0.009-0.01619.0060.0170.0170.0000.0000.0000.000
92A116SER00.0180.01015.7710.0130.0130.0000.0000.0000.000
93A117VAL0-0.0010.00217.5750.0160.0160.0000.0000.0000.000
94A118LYS10.8460.92720.2590.2430.2430.0000.0000.0000.000
95A119ILE0-0.0030.01914.2850.0310.0310.0000.0000.0000.000
96A120GLU-1-0.854-0.93118.298-0.173-0.1730.0000.0000.0000.000
97A121PRO00.0360.02819.5090.0240.0240.0000.0000.0000.000
98A122THR0-0.060-0.04220.5930.0250.0250.0000.0000.0000.000
99A123LEU0-0.0050.01016.1890.0190.0190.0000.0000.0000.000
100A124SER0-0.008-0.01820.5910.0300.0300.0000.0000.0000.000
101A125GLY0-0.019-0.00823.1100.0200.0200.0000.0000.0000.000
102A126TRP0-0.048-0.04319.1140.0130.0130.0000.0000.0000.000
103A127TRP00.044-0.00322.0350.0130.0130.0000.0000.0000.000
104A128SER0-0.110-0.04524.4990.0160.0160.0000.0000.0000.000
105A129GLY00.0470.02327.8460.0060.0060.0000.0000.0000.000
106A130ALA00.0370.01928.4860.0060.0060.0000.0000.0000.000
107A131LYS10.8420.90729.7020.0600.0600.0000.0000.0000.000
108A132LYS10.8950.93530.4680.0930.0930.0000.0000.0000.000
109A133ASN0-0.041-0.01532.8640.0030.0030.0000.0000.0000.000
110A134GLY00.0120.03133.7450.0040.0040.0000.0000.0000.000
111A135VAL0-0.017-0.01730.544-0.002-0.0020.0000.0000.0000.000
112A136GLY00.0320.01534.0240.0020.0020.0000.0000.0000.000
113A137PRO00.0380.01335.4830.0010.0010.0000.0000.0000.000
114A138ASP-1-0.842-0.89735.9910.0070.0070.0000.0000.0000.000
115A139ASN0-0.029-0.03330.736-0.001-0.0010.0000.0000.0000.000
116A140LYS10.8230.92131.770-0.003-0.0030.0000.0000.0000.000
117A141TYR00.0250.02330.804-0.007-0.0070.0000.0000.0000.000
118A142THR00.0470.01433.3010.0010.0010.0000.0000.0000.000
119A143GLY0-0.0050.01233.980-0.002-0.0020.0000.0000.0000.000
120A144GLY00.0360.00834.583-0.001-0.0010.0000.0000.0000.000
121A145GLY00.0010.00233.379-0.001-0.0010.0000.0000.0000.000
122A146LEU0-0.0070.00130.331-0.006-0.0060.0000.0000.0000.000
123A147PHE0-0.030-0.00627.0860.0010.0010.0000.0000.0000.000
124A148ALA00.0290.01925.3820.0000.0000.0000.0000.0000.000
125A149PHE00.0550.02024.379-0.004-0.0040.0000.0000.0000.000
126A150SER0-0.010-0.02624.6220.0060.0060.0000.0000.0000.000
127A151ASN0-0.030-0.03122.5450.0220.0220.0000.0000.0000.000
128A152MET0-0.064-0.00319.1840.0050.0050.0000.0000.0000.000
129A153VAL00.0120.01620.0900.0140.0140.0000.0000.0000.000
130A154TYR0-0.078-0.04522.6830.0140.0140.0000.0000.0000.000
131A155SER00.0500.02422.0230.0030.0030.0000.0000.0000.000
132A156GLU-1-0.874-0.93121.9310.0620.0620.0000.0000.0000.000
133A157THR0-0.020-0.00918.2090.0120.0120.0000.0000.0000.000
134A158THR00.0300.01316.2410.0130.0130.0000.0000.0000.000
135A159LYS10.8390.91113.3900.0210.0210.0000.0000.0000.000
136A160LEU00.0170.01212.127-0.018-0.0180.0000.0000.0000.000
137A161GLY00.0340.02112.829-0.043-0.0430.0000.0000.0000.000
138A162CYS0-0.049-0.00313.3560.0330.0330.0000.0000.0000.000
139A163ALA00.0690.03413.980-0.109-0.1090.0000.0000.0000.000
140A164TYR0-0.038-0.02215.1560.1020.1020.0000.0000.0000.000
141A165LYS10.8730.93919.0410.2890.2890.0000.0000.0000.000
142A166VAL00.0480.01821.7820.0270.0270.0000.0000.0000.000
143A168GLY00.0380.01727.9240.0170.0170.0000.0000.0000.000
144A169THR00.0080.00429.500-0.008-0.0080.0000.0000.0000.000
145A170LYS10.8650.93228.6410.1850.1850.0000.0000.0000.000
146A171LEU0-0.0170.01021.465-0.013-0.0130.0000.0000.0000.000
147A172ALA00.0070.01924.1070.0190.0190.0000.0000.0000.000
148A173VAL00.026-0.00118.753-0.038-0.0380.0000.0000.0000.000
149A174SER0-0.048-0.04319.4970.0400.0400.0000.0000.0000.000
150A176ILE00.0100.00217.7810.0360.0360.0000.0000.0000.000
151A177TYR00.000-0.03117.627-0.016-0.0160.0000.0000.0000.000
152A178ASN00.0460.02918.216-0.001-0.0010.0000.0000.0000.000
153A179GLY00.0240.00820.2970.0230.0230.0000.0000.0000.000
154A180VAL0-0.025-0.00823.173-0.016-0.0160.0000.0000.0000.000
155A181GLY00.0410.02026.1790.0100.0100.0000.0000.0000.000
156A182TYR0-0.021-0.01526.9280.0000.0000.0000.0000.0000.000
157A183ILE0-0.020-0.00530.242-0.002-0.0020.0000.0000.0000.000
158A184THR00.007-0.02032.7810.0010.0010.0000.0000.0000.000
159A185ASN0-0.036-0.03036.0370.0020.0020.0000.0000.0000.000
160A186GLN0-0.0150.00729.2630.0070.0070.0000.0000.0000.000
161A187PRO0-0.023-0.01031.577-0.006-0.0060.0000.0000.0000.000
162A188MET0-0.029-0.02227.365-0.002-0.0020.0000.0000.0000.000
163A189TRP00.0370.00226.2580.0010.0010.0000.0000.0000.000
164A190GLU-1-0.810-0.88628.0900.0490.0490.0000.0000.0000.000
165A191THR00.0550.01429.5840.0040.0040.0000.0000.0000.000
166A192GLY0-0.025-0.01030.5430.0030.0030.0000.0000.0000.000
167A193GLN0-0.034-0.01228.720-0.006-0.0060.0000.0000.0000.000
168A194ALA00.0270.03523.9780.0060.0060.0000.0000.0000.000
169A195CYS0-0.062-0.03119.060-0.025-0.0250.0000.0000.0000.000
170A196GLN0-0.063-0.04923.966-0.001-0.0010.0000.0000.0000.000
171A197THR00.005-0.01123.4420.0170.0170.0000.0000.0000.000
172A198GLY00.020-0.00322.438-0.003-0.0030.0000.0000.0000.000
173A199ALA0-0.020-0.01323.010-0.004-0.0040.0000.0000.0000.000
174A200ASP-1-0.818-0.89725.8680.1120.1120.0000.0000.0000.000
175A201CYS0-0.082-0.02018.5040.0180.0180.0000.0000.0000.000
176A202SER00.0330.00225.0100.0050.0050.0000.0000.0000.000
177A203THR0-0.060-0.01923.846-0.001-0.0010.0000.0000.0000.000
178A204TYR0-0.030-0.02321.060-0.006-0.0060.0000.0000.0000.000
179A205LYS11.0121.01423.291-0.102-0.1020.0000.0000.0000.000
180A206ASN0-0.020-0.01721.5450.0020.0020.0000.0000.0000.000
181A207SER00.0220.02619.4160.0300.0300.0000.0000.0000.000
182A208GLY00.0080.01018.125-0.007-0.0070.0000.0000.0000.000
183A210GLU-1-0.785-0.86712.6810.5370.5370.0000.0000.0000.000
184A211ASP-1-0.793-0.87317.3230.0790.0790.0000.0000.0000.000
185A212GLY00.0350.01619.663-0.019-0.0190.0000.0000.0000.000
186A213LEU0-0.018-0.00815.729-0.016-0.0160.0000.0000.0000.000
187A215THR00.004-0.00514.6590.0020.0020.0000.0000.0000.000
188A216LYS10.8370.92116.116-0.226-0.2260.0000.0000.0000.000
189A217GLY00.0550.03414.9500.0600.0600.0000.0000.0000.000
190A218PRO0-0.007-0.03014.254-0.026-0.0260.0000.0000.0000.000
191A219ASP-1-0.890-0.92416.0320.1670.1670.0000.0000.0000.000
192A220VAL00.0170.01318.7760.0130.0130.0000.0000.0000.000
193A221PRO0-0.028-0.02721.679-0.016-0.0160.0000.0000.0000.000
194A222GLU-1-0.795-0.83623.5430.0760.0760.0000.0000.0000.000
195A223THR0-0.008-0.02026.4680.0010.0010.0000.0000.0000.000
196A224ASN00.005-0.00529.862-0.005-0.0050.0000.0000.0000.000
197A225GLN0-0.023-0.01833.411-0.001-0.0010.0000.0000.0000.000
198A226GLN0-0.088-0.04334.984-0.007-0.0070.0000.0000.0000.000
199A227CYS00.009-0.01237.606-0.004-0.0040.0000.0000.0000.000
200A228PRO00.0410.02037.865-0.002-0.0020.0000.0000.0000.000
201A229SER0-0.007-0.00138.9530.0000.0000.0000.0000.0000.000
202A230ASN0-0.067-0.02238.921-0.005-0.0050.0000.0000.0000.000
203A231THR00.014-0.00535.1100.0040.0040.0000.0000.0000.000
204A232GLY00.0200.00333.535-0.004-0.0040.0000.0000.0000.000
205A233MET0-0.085-0.01433.056-0.003-0.0030.0000.0000.0000.000
206A234THR0-0.029-0.03528.752-0.002-0.0020.0000.0000.0000.000
207A235ASP-1-0.698-0.84431.4430.0630.0630.0000.0000.0000.000
208A236SER0-0.004-0.00927.239-0.004-0.0040.0000.0000.0000.000
209A237VAL00.012-0.00629.380-0.003-0.0030.0000.0000.0000.000
210A238ARG10.7390.84431.381-0.048-0.0480.0000.0000.0000.000
211A239ASP-1-0.820-0.91332.3150.0650.0650.0000.0000.0000.000
212A240THR0-0.0340.01430.0540.0010.0010.0000.0000.0000.000
213A241PHE00.000-0.00532.742-0.004-0.0040.0000.0000.0000.000
214A242LEU00.0130.01736.020-0.003-0.0030.0000.0000.0000.000
215A243SER0-0.038-0.04134.176-0.002-0.0020.0000.0000.0000.000
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