FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8211Y

Calculation Name: 3D5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D5N

Chain ID: A

ChEMBL ID:

UniProt ID: Q97W15

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1938980.156528
FMO2-HF: Nuclear repulsion 1868976.481071
FMO2-HF: Total energy -70003.675457
FMO2-MP2: Total energy -70207.232322


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.
-10.57-4.9057.871-4.293-9.244-0.018
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 : -0.009 / q_NPA : 0.003
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].
3A3ILE0-0.010-0.0163.3580.2213.2220.709-1.154-2.5560.003
4A4GLY00.0560.0375.700-0.701-0.675-0.001-0.012-0.0130.000
5A5VAL0-0.059-0.0239.4260.3000.3000.0000.0000.0000.000
6A6ILE00.0050.00011.992-0.052-0.0520.0000.0000.0000.000
7A7ILE0-0.013-0.01315.0520.0480.0480.0000.0000.0000.000
8A8LEU0-0.019-0.01518.002-0.014-0.0140.0000.0000.0000.000
9A9ALA00.0310.00220.6740.0090.0090.0000.0000.0000.000
10A10ALA0-0.0400.00024.073-0.004-0.0040.0000.0000.0000.000
11A11GLY00.063-0.00326.4030.0050.0050.0000.0000.0000.000
12A12GLU-1-0.872-0.87525.172-0.024-0.0240.0000.0000.0000.000
13A13GLY00.0520.02029.0370.0050.0050.0000.0000.0000.000
14A14LYS10.8720.93031.182-0.005-0.0050.0000.0000.0000.000
15A15ARG10.8490.91625.577-0.009-0.0090.0000.0000.0000.000
16A16PHE00.0530.00728.284-0.005-0.0050.0000.0000.0000.000
17A17GLY00.057-0.00128.730-0.002-0.0020.0000.0000.0000.000
18A18GLY0-0.041-0.04229.3300.0010.0010.0000.0000.0000.000
19A19ASP-1-0.759-0.89831.235-0.024-0.0240.0000.0000.0000.000
20A20LYS10.8830.95331.5740.0080.0080.0000.0000.0000.000
21A21LEU0-0.055-0.02426.1980.0010.0010.0000.0000.0000.000
22A22LEU00.0180.01429.270-0.006-0.0060.0000.0000.0000.000
23A23ALA0-0.0160.01131.8650.0000.0000.0000.0000.0000.000
24A24LYS10.9010.94931.2600.0310.0310.0000.0000.0000.000
25A25ILE00.0260.01428.4100.0050.0050.0000.0000.0000.000
26A26ASP-1-0.898-0.93629.827-0.013-0.0130.0000.0000.0000.000
27A27ASN0-0.027-0.03731.414-0.003-0.0030.0000.0000.0000.000
28A28THR0-0.054-0.02527.597-0.007-0.0070.0000.0000.0000.000
29A29PRO00.0420.01328.4070.0060.0060.0000.0000.0000.000
30A30ILE00.0240.01726.199-0.005-0.0050.0000.0000.0000.000
31A31ILE00.0290.02323.042-0.002-0.0020.0000.0000.0000.000
32A32MET00.0170.00723.080-0.007-0.0070.0000.0000.0000.000
33A33ARG10.8930.96222.6020.0070.0070.0000.0000.0000.000
34A34THR0-0.007-0.04220.060-0.006-0.0060.0000.0000.0000.000
35A35ILE00.0290.01818.166-0.006-0.0060.0000.0000.0000.000
36A36ARG10.9320.98117.4770.0370.0370.0000.0000.0000.000
37A37ILE0-0.061-0.03015.665-0.026-0.0260.0000.0000.0000.000
38A38TYR0-0.003-0.01012.7920.0250.0250.0000.0000.0000.000
39A39GLY0-0.036-0.02712.539-0.093-0.0930.0000.0000.0000.000
40A40ASP-1-0.941-0.9679.746-0.590-0.5900.0000.0000.0000.000
41A41LEU00.0120.0247.332-0.148-0.1480.0000.0000.0000.000
42A42GLU-1-0.820-0.9008.212-1.228-1.2280.0000.0000.0000.000
43A43LYS10.8600.95110.8180.4340.4340.0000.0000.0000.000
44A44ILE00.0530.03214.172-0.014-0.0140.0000.0000.0000.000
45A45ILE0-0.0180.00217.0770.0340.0340.0000.0000.0000.000
46A46ILE0-0.034-0.00718.956-0.002-0.0020.0000.0000.0000.000
47A47VAL00.0340.02022.1670.0160.0160.0000.0000.0000.000
48A48GLY00.0580.01125.854-0.002-0.0020.0000.0000.0000.000
49A49LYS10.8860.96728.7320.0200.0200.0000.0000.0000.000
50A50TYR00.0430.06330.9220.0030.0030.0000.0000.0000.000
51A51VAL00.029-0.00829.139-0.003-0.0030.0000.0000.0000.000
52A52ASN0-0.050-0.02930.931-0.003-0.0030.0000.0000.0000.000
53A53GLU-1-0.849-0.91633.183-0.045-0.0450.0000.0000.0000.000
54A54MET0-0.050-0.00927.804-0.002-0.0020.0000.0000.0000.000
55A55LEU00.0550.01526.739-0.005-0.0050.0000.0000.0000.000
56A56PRO0-0.0090.00628.106-0.009-0.0090.0000.0000.0000.000
57A57LEU0-0.027-0.02227.5570.0000.0000.0000.0000.0000.000
58A58LEU0-0.058-0.04023.078-0.006-0.0060.0000.0000.0000.000
59A59MET0-0.030-0.00624.055-0.012-0.0120.0000.0000.0000.000
60A60ASP-1-0.889-0.92821.836-0.171-0.1710.0000.0000.0000.000
61A61GLN0-0.059-0.03118.461-0.047-0.0470.0000.0000.0000.000
62A62ILE00.0230.02516.4370.0150.0150.0000.0000.0000.000
63A63VAL0-0.019-0.02020.0060.0040.0040.0000.0000.0000.000
64A64ILE0-0.0130.00119.7410.0020.0020.0000.0000.0000.000
65A65TYR0-0.005-0.01323.6800.0120.0120.0000.0000.0000.000
66A66ASN00.045-0.00425.089-0.005-0.0050.0000.0000.0000.000
67A67PRO0-0.031-0.01026.9840.0070.0070.0000.0000.0000.000
68A68PHE00.024-0.00228.2870.0040.0040.0000.0000.0000.000
69A69TRP00.0430.01527.8310.0080.0080.0000.0000.0000.000
70A70ASN0-0.040-0.02628.8240.0080.0080.0000.0000.0000.000
71A71GLU-1-0.983-0.97829.457-0.029-0.0290.0000.0000.0000.000
72A72GLY0-0.019-0.02728.2940.0050.0050.0000.0000.0000.000
73A73ILE00.015-0.02522.235-0.004-0.0040.0000.0000.0000.000
74A74SER0-0.095-0.04622.046-0.005-0.0050.0000.0000.0000.000
75A75THR00.0530.03122.126-0.011-0.0110.0000.0000.0000.000
76A76SER0-0.032-0.06022.455-0.015-0.0150.0000.0000.0000.000
77A77LEU0-0.052-0.02116.218-0.013-0.0130.0000.0000.0000.000
78A78LYS10.9260.97817.8530.0300.0300.0000.0000.0000.000
79A79LEU0-0.056-0.00519.089-0.021-0.0210.0000.0000.0000.000
80A80GLY00.022-0.00517.448-0.023-0.0230.0000.0000.0000.000
81A81LEU00.0100.00512.214-0.031-0.0310.0000.0000.0000.000
82A82ARG10.9110.95114.5830.1050.1050.0000.0000.0000.000
83A83PHE0-0.020-0.01213.685-0.007-0.0070.0000.0000.0000.000
84A84PHE00.0430.04510.470-0.021-0.0210.0000.0000.0000.000
85A85LYS10.9420.98410.7240.2260.2260.0000.0000.0000.000
86A86ASP-1-0.949-0.99710.702-0.568-0.5680.0000.0000.0000.000
87A87TYR0-0.021-0.0307.079-0.100-0.1000.0000.0000.0000.000
88A88ASP-1-0.873-0.9432.312-7.173-4.5983.727-2.419-3.884-0.026
89A89ALA0-0.040-0.0364.366-0.1280.106-0.001-0.020-0.2130.000
90A90VAL00.0090.0176.279-0.182-0.1820.0000.0000.0000.000
91A91LEU0-0.004-0.0219.1830.1250.1250.0000.0000.0000.000
92A92VAL0-0.029-0.01510.749-0.135-0.1350.0000.0000.0000.000
93A93ALA0-0.0010.00314.3590.0170.0170.0000.0000.0000.000
94A94LEU0-0.005-0.00316.692-0.018-0.0180.0000.0000.0000.000
95A95GLY00.0630.01720.478-0.004-0.0040.0000.0000.0000.000
96A96ASP-1-0.907-0.94422.7480.0050.0050.0000.0000.0000.000
97A97MET00.0150.00821.3010.0150.0150.0000.0000.0000.000
98A98PRO0-0.037-0.00421.402-0.001-0.0010.0000.0000.0000.000
99A99PHE00.000-0.02723.239-0.005-0.0050.0000.0000.0000.000
100A100VAL0-0.0030.04116.8550.0080.0080.0000.0000.0000.000
101A101THR00.005-0.04018.926-0.021-0.0210.0000.0000.0000.000
102A102LYS10.9740.96914.7160.1430.1430.0000.0000.0000.000
103A103GLU-1-0.895-0.95014.2000.0870.0870.0000.0000.0000.000
104A104ASP-1-0.765-0.79614.5740.1540.1540.0000.0000.0000.000
105A105VAL00.0410.01110.7200.0710.0710.0000.0000.0000.000
106A106ASN00.0200.01310.2470.0120.0120.0000.0000.0000.000
107A107LYS10.9220.9599.910-0.085-0.0850.0000.0000.0000.000
108A108ILE00.0130.01110.0280.1120.1120.0000.0000.0000.000
109A109ILE00.0130.0065.0740.3120.3120.0000.0000.0000.000
110A110ASN0-0.025-0.0086.1190.5960.5960.0000.0000.0000.000
111A111THR0-0.089-0.0538.109-0.023-0.0230.0000.0000.0000.000
112A112PHE0-0.029-0.0112.156-1.558-1.7293.437-0.688-2.5780.005
113A113LYS10.9410.9695.486-0.726-0.7260.0000.0000.0000.000
114A114PRO00.0370.0045.0350.0260.0260.0000.0000.0000.000
115A115ASN0-0.0030.0006.668-0.016-0.0160.0000.0000.0000.000
116A116CYS0-0.097-0.0258.087-0.039-0.0390.0000.0000.0000.000
117A117LYS10.9460.9868.171-0.080-0.0800.0000.0000.0000.000
118A118ALA00.0070.0039.9500.0130.0130.0000.0000.0000.000
119A119VAL0-0.0120.0178.818-0.051-0.0510.0000.0000.0000.000
120A120ILE0-0.076-0.04811.509-0.050-0.0500.0000.0000.0000.000
121A121PRO00.0360.03014.230-0.007-0.0070.0000.0000.0000.000
122A122THR0-0.045-0.04516.414-0.027-0.0270.0000.0000.0000.000
123A123HIS0-0.001-0.00519.906-0.008-0.0080.0000.0000.0000.000
124A124LYS10.9410.97223.053-0.093-0.0930.0000.0000.0000.000
125A125GLY00.0080.01825.052-0.010-0.0100.0000.0000.0000.000
126A126GLU-1-0.953-0.97124.7010.0910.0910.0000.0000.0000.000
127A127ARG10.9600.96419.726-0.155-0.1550.0000.0000.0000.000
128A128GLY00.000-0.01719.638-0.021-0.0210.0000.0000.0000.000
129A129ASN0-0.113-0.03517.2840.0390.0390.0000.0000.0000.000
130A130PRO00.0350.00314.045-0.014-0.0140.0000.0000.0000.000
131A131VAL00.0450.00213.4950.0480.0480.0000.0000.0000.000
132A132LEU0-0.0230.0075.925-0.130-0.1300.0000.0000.0000.000
133A133ILE00.0040.00010.1430.0310.0310.0000.0000.0000.000
134A134SER00.039-0.0036.3380.0320.0320.0000.0000.0000.000
135A135LYS10.9490.9666.6830.5540.5540.0000.0000.0000.000
136A136SER0-0.096-0.0498.492-0.035-0.0350.0000.0000.0000.000
137A137LEU00.001-0.01910.515-0.023-0.0230.0000.0000.0000.000
138A138PHE00.0080.0258.401-0.011-0.0110.0000.0000.0000.000
139A139ASN0-0.002-0.00913.209-0.003-0.0030.0000.0000.0000.000
140A140GLU-1-0.844-0.91815.7900.0210.0210.0000.0000.0000.000
141A141ILE0-0.0080.00814.660-0.002-0.0020.0000.0000.0000.000
142A142GLU-1-0.889-0.96117.202-0.076-0.0760.0000.0000.0000.000
143A143LYS10.7850.88419.3910.0060.0060.0000.0000.0000.000
144A144LEU0-0.070-0.01719.6310.0010.0010.0000.0000.0000.000
145A145ARG10.9570.96322.8170.0010.0010.0000.0000.0000.000
146A146GLY00.0890.04526.2830.0070.0070.0000.0000.0000.000
147A147ASP-1-0.763-0.83726.5530.0030.0030.0000.0000.0000.000
148A148VAL0-0.080-0.01423.6670.0070.0070.0000.0000.0000.000
149A149GLY00.0630.02022.043-0.003-0.0030.0000.0000.0000.000
150A150ALA00.0890.02316.863-0.002-0.0020.0000.0000.0000.000
151A151ARG10.9560.98218.759-0.067-0.0670.0000.0000.0000.000
152A152VAL0-0.006-0.00320.5930.0020.0020.0000.0000.0000.000
153A153ILE00.0110.00116.767-0.003-0.0030.0000.0000.0000.000
154A154LEU00.0230.02014.5850.0040.0040.0000.0000.0000.000
155A155ASN0-0.097-0.04818.141-0.003-0.0030.0000.0000.0000.000
156A156LYS10.9440.97820.312-0.059-0.0590.0000.0000.0000.000
157A157ILE0-0.0060.01414.836-0.008-0.0080.0000.0000.0000.000
158A158LYS10.9300.95418.615-0.080-0.0800.0000.0000.0000.000
159A159ILE00.0520.02517.4860.0200.0200.0000.0000.0000.000
160A160GLU-1-0.855-0.91617.9430.1350.1350.0000.0000.0000.000
161A161GLU-1-0.925-0.98613.8110.1150.1150.0000.0000.0000.000
162A162LEU0-0.054-0.00212.8240.0510.0510.0000.0000.0000.000
163A164PHE00.0250.02013.6520.0440.0440.0000.0000.0000.000
164A165ILE00.003-0.00312.8550.0210.0210.0000.0000.0000.000
165A166GLU-1-0.822-0.90516.6420.1430.1430.0000.0000.0000.000
166A167CYS0-0.105-0.03816.3900.0200.0200.0000.0000.0000.000
167A168SER0-0.022-0.07618.955-0.016-0.0160.0000.0000.0000.000
168A169GLU-1-0.876-0.95421.8950.0640.0640.0000.0000.0000.000
169A170GLY00.0130.00722.620-0.003-0.0030.0000.0000.0000.000
170A171VAL0-0.0240.00318.245-0.003-0.0030.0000.0000.0000.000
171A172LEU0-0.040-0.01520.8590.0080.0080.0000.0000.0000.000
172A173ILE0-0.077-0.02224.009-0.010-0.0100.0000.0000.0000.000
173A174ASP-1-0.823-0.90624.7420.0320.0320.0000.0000.0000.000
174A175ILE0-0.028-0.04126.579-0.002-0.0020.0000.0000.0000.000
175A176ASP-1-0.893-0.94129.5220.0080.0080.0000.0000.0000.000
176A177LYS10.7870.91027.273-0.059-0.0590.0000.0000.0000.000
177A178LYS10.9150.96929.645-0.034-0.0340.0000.0000.0000.000