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: KGKV3

Calculation Name: 2BDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BDQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DYB9

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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2478804.093259
FMO2-HF: Nuclear repulsion 2396916.502957
FMO2-HF: Total energy -81887.590302
FMO2-MP2: Total energy -82125.372565


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.
-2.609-0.173-0.009-0.946-1.4780.003
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 : 0.003 / q_NPA : 0.014
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].
3A3LEU0-0.039-0.0103.893-2.277-0.486-0.004-0.902-0.8840.003
4A4ARG10.8610.9276.0081.4391.4390.0000.0000.0000.000
5A5GLU-1-0.710-0.8278.483-0.269-0.2690.0000.0000.0000.000
6A6PHE00.019-0.00211.9940.0200.0200.0000.0000.0000.000
7A7CYS0-0.081-0.04414.6460.0250.0250.0000.0000.0000.000
8A8ALA00.0310.00718.2270.0020.0020.0000.0000.0000.000
9A9GLU-1-0.837-0.90221.073-0.113-0.1130.0000.0000.0000.000
10A10ASN0-0.048-0.05124.8900.0090.0090.0000.0000.0000.000
11A11LEU00.0500.00023.732-0.011-0.0110.0000.0000.0000.000
12A12THR0-0.028-0.00324.2530.0020.0020.0000.0000.0000.000
13A13ASP-1-0.872-0.94621.093-0.162-0.1620.0000.0000.0000.000
14A14LEU00.0140.01919.036-0.014-0.0140.0000.0000.0000.000
15A15THR0-0.0080.00419.775-0.002-0.0020.0000.0000.0000.000
16A16ARG10.8470.91118.9320.1500.1500.0000.0000.0000.000
17A17LEU00.0240.03214.988-0.016-0.0160.0000.0000.0000.000
18A18ASP-1-0.772-0.87913.166-0.074-0.0740.0000.0000.0000.000
19A19LYS10.9360.95711.271-0.011-0.0110.0000.0000.0000.000
20A20ALA0-0.055-0.0178.986-0.062-0.0620.0000.0000.0000.000
21A21ILE0-0.088-0.0437.701-0.032-0.0320.0000.0000.0000.000
22A22ILE0-0.033-0.0188.233-0.232-0.2320.0000.0000.0000.000
23A23SER00.0380.0257.3950.1080.1080.0000.0000.0000.000
24A24ARG10.8140.8879.9880.5260.5260.0000.0000.0000.000
25A25VAL0-0.003-0.01312.687-0.048-0.0480.0000.0000.0000.000
26A26GLU-1-0.779-0.87315.692-0.184-0.1840.0000.0000.0000.000
27A27LEU0-0.022-0.00118.489-0.003-0.0030.0000.0000.0000.000
28A28CYS0-0.046-0.02221.7330.0110.0110.0000.0000.0000.000
29A29ASP-1-0.775-0.88624.780-0.096-0.0960.0000.0000.0000.000
30A30ASN00.0290.00727.895-0.005-0.0050.0000.0000.0000.000
31A31LEU00.0610.00722.650-0.001-0.0010.0000.0000.0000.000
32A32ALA0-0.070-0.01726.690-0.002-0.0020.0000.0000.0000.000
33A33VAL0-0.0300.00129.8060.0050.0050.0000.0000.0000.000
34A34GLY0-0.024-0.01626.3030.0050.0050.0000.0000.0000.000
35A35GLY0-0.0080.00825.518-0.007-0.0070.0000.0000.0000.000
36A36THR0-0.027-0.00626.5160.0070.0070.0000.0000.0000.000
37A37THR00.000-0.03427.658-0.010-0.0100.0000.0000.0000.000
38A38PRO0-0.0530.00625.5360.0040.0040.0000.0000.0000.000
39A39SER00.0450.00928.7060.0070.0070.0000.0000.0000.000
40A40TYR0-0.005-0.03130.236-0.004-0.0040.0000.0000.0000.000
41A41GLY00.0230.01230.7600.0000.0000.0000.0000.0000.000
42A42VAL0-0.027-0.01126.729-0.002-0.0020.0000.0000.0000.000
43A43ILE00.0200.01425.903-0.007-0.0070.0000.0000.0000.000
44A44LYS10.8590.92725.9040.0480.0480.0000.0000.0000.000
45A45GLU-1-0.834-0.91526.712-0.060-0.0600.0000.0000.0000.000
46A46ALA0-0.019-0.00822.852-0.004-0.0040.0000.0000.0000.000
47A47ASN0-0.015-0.03121.995-0.021-0.0210.0000.0000.0000.000
48A48GLN00.0330.03422.2030.0020.0020.0000.0000.0000.000
49A49TYR00.008-0.00522.079-0.005-0.0050.0000.0000.0000.000
50A50LEU0-0.041-0.02617.526-0.006-0.0060.0000.0000.0000.000
51A51HIS10.8100.87918.3630.0890.0890.0000.0000.0000.000
52A52GLU-1-0.966-0.96919.583-0.050-0.0500.0000.0000.0000.000
53A53LYS10.8060.90017.5330.1560.1560.0000.0000.0000.000
54A54GLY0-0.038-0.01015.795-0.003-0.0030.0000.0000.0000.000
55A55ILE0-0.101-0.04913.640-0.027-0.0270.0000.0000.0000.000
56A56SER0-0.014-0.01813.8580.0190.0190.0000.0000.0000.000
57A57VAL0-0.043-0.04115.603-0.043-0.0430.0000.0000.0000.000
58A58ALA0-0.049-0.02317.0380.0130.0130.0000.0000.0000.000
59A59VAL00.0410.02318.991-0.009-0.0090.0000.0000.0000.000
60A60MET0-0.048-0.02722.6420.0080.0080.0000.0000.0000.000
61A61ILE00.0110.01224.4910.0080.0080.0000.0000.0000.000
62A62ARG10.8060.87027.5330.0950.0950.0000.0000.0000.000
63A63PRO00.0410.03429.778-0.003-0.0030.0000.0000.0000.000
64A64ARG10.7200.82033.1260.0590.0590.0000.0000.0000.000
65A65GLY00.0480.01732.260-0.003-0.0030.0000.0000.0000.000
66A66GLY0-0.019-0.00932.9960.0050.0050.0000.0000.0000.000
67A67ASN00.007-0.00332.193-0.007-0.0070.0000.0000.0000.000
68A68PHE00.0660.03527.2650.0000.0000.0000.0000.0000.000
69A69VAL0-0.0020.02632.0660.0020.0020.0000.0000.0000.000
70A70TYR00.002-0.01430.028-0.004-0.0040.0000.0000.0000.000
71A71ASN00.0130.01036.8000.0040.0040.0000.0000.0000.000
72A72ASP-1-0.822-0.92638.913-0.030-0.0300.0000.0000.0000.000
73A73LEU0-0.027-0.00340.0270.0000.0000.0000.0000.0000.000
74A74GLU-1-0.808-0.88636.390-0.050-0.0500.0000.0000.0000.000
75A75LEU00.0330.01434.337-0.004-0.0040.0000.0000.0000.000
76A76ARG10.7570.84835.5100.0330.0330.0000.0000.0000.000
77A77ILE0-0.027-0.01334.3760.0000.0000.0000.0000.0000.000
78A78MET0-0.021-0.00529.577-0.001-0.0010.0000.0000.0000.000
79A79GLU-1-0.825-0.89731.652-0.033-0.0330.0000.0000.0000.000
80A80GLU-1-0.830-0.88733.243-0.036-0.0360.0000.0000.0000.000
81A81ASP-1-0.842-0.91530.230-0.065-0.0650.0000.0000.0000.000
82A82ILE0-0.025-0.01027.837-0.005-0.0050.0000.0000.0000.000
83A83LEU0-0.0030.00029.2190.0000.0000.0000.0000.0000.000
84A84ARG10.7330.82431.3950.0400.0400.0000.0000.0000.000
85A85ALA00.0280.01725.945-0.002-0.0020.0000.0000.0000.000
86A86VAL00.0020.01026.446-0.004-0.0040.0000.0000.0000.000
87A87GLU-1-0.813-0.85027.522-0.038-0.0380.0000.0000.0000.000
88A88LEU0-0.056-0.02127.6420.0020.0020.0000.0000.0000.000
89A89GLU-1-0.913-0.94523.740-0.060-0.0600.0000.0000.0000.000
90A90SER0-0.008-0.02822.180-0.011-0.0110.0000.0000.0000.000
91A91ASP-1-0.773-0.83917.331-0.130-0.1300.0000.0000.0000.000
92A92ALA0-0.061-0.03617.659-0.003-0.0030.0000.0000.0000.000
93A93LEU00.0200.02419.706-0.002-0.0020.0000.0000.0000.000
94A94VAL0-0.039-0.02419.562-0.003-0.0030.0000.0000.0000.000
95A95LEU00.0470.02022.2030.0060.0060.0000.0000.0000.000
96A96GLY00.016-0.00724.468-0.004-0.0040.0000.0000.0000.000
97A97ILE0-0.0100.00527.059-0.001-0.0010.0000.0000.0000.000
98A98LEU0-0.065-0.02728.5220.0020.0020.0000.0000.0000.000
99A99THR00.0930.04532.392-0.001-0.0010.0000.0000.0000.000
100A100SER0-0.032-0.02735.344-0.002-0.0020.0000.0000.0000.000
101A101ASN0-0.045-0.02736.5390.0000.0000.0000.0000.0000.000
102A102ASN0-0.029-0.01431.345-0.002-0.0020.0000.0000.0000.000
103A103HIS00.0540.03430.778-0.003-0.0030.0000.0000.0000.000
104A104ILE00.016-0.00426.138-0.003-0.0030.0000.0000.0000.000
105A105ASP-1-0.868-0.94430.755-0.027-0.0270.0000.0000.0000.000
106A106THR0-0.0090.00031.524-0.002-0.0020.0000.0000.0000.000
107A107GLU-1-0.838-0.92432.830-0.021-0.0210.0000.0000.0000.000
108A108ALA00.0070.00634.1920.0000.0000.0000.0000.0000.000
109A109ILE0-0.040-0.02928.084-0.004-0.0040.0000.0000.0000.000
110A110GLU-1-0.928-0.97331.220-0.014-0.0140.0000.0000.0000.000
111A111GLN0-0.042-0.02933.015-0.001-0.0010.0000.0000.0000.000
112A112LEU00.0100.01230.6720.0000.0000.0000.0000.0000.000
113A113LEU0-0.0150.01327.558-0.003-0.0030.0000.0000.0000.000
114A114PRO0-0.029-0.02230.1670.0000.0000.0000.0000.0000.000
115A115ALA00.0230.01432.0340.0000.0000.0000.0000.0000.000
116A116THR0-0.017-0.02225.600-0.005-0.0050.0000.0000.0000.000
117A117GLN0-0.070-0.03327.045-0.003-0.0030.0000.0000.0000.000
118A118GLY00.0020.00725.9640.0030.0030.0000.0000.0000.000
119A119LEU0-0.0140.00222.448-0.001-0.0010.0000.0000.0000.000
120A120PRO0-0.019-0.01317.9900.0010.0010.0000.0000.0000.000
121A121LEU00.0390.03620.143-0.011-0.0110.0000.0000.0000.000
122A122VAL0-0.062-0.04417.380-0.007-0.0070.0000.0000.0000.000
123A123PHE00.0420.03619.7840.0020.0020.0000.0000.0000.000
124A124HIS00.0500.02620.635-0.015-0.0150.0000.0000.0000.000
125A125MET00.0450.01218.8970.0100.0100.0000.0000.0000.000
126A126ALA00.0120.02522.7230.0070.0070.0000.0000.0000.000
127A127PHE00.032-0.01320.6650.0090.0090.0000.0000.0000.000
128A128ASP-1-0.773-0.89520.664-0.092-0.0920.0000.0000.0000.000
129A129VAL0-0.0110.00123.8620.0040.0040.0000.0000.0000.000
130A130ILE0-0.0150.03025.6050.0050.0050.0000.0000.0000.000
131A131PRO00.0060.01327.133-0.002-0.0020.0000.0000.0000.000
132A132LYS10.7920.87522.8490.0690.0690.0000.0000.0000.000
133A133SER0-0.030-0.03126.2020.0040.0040.0000.0000.0000.000
134A134ASP-1-0.812-0.88928.624-0.008-0.0080.0000.0000.0000.000
135A135GLN00.0710.07122.273-0.004-0.0040.0000.0000.0000.000
136A136LYS10.8960.95221.231-0.034-0.0340.0000.0000.0000.000
137A137LYS10.8760.92224.7440.0070.0070.0000.0000.0000.000
138A138SER00.0570.02225.7320.0000.0000.0000.0000.0000.000
139A139ILE0-0.025-0.00519.918-0.003-0.0030.0000.0000.0000.000
140A140ASP-1-0.775-0.85123.4740.0260.0260.0000.0000.0000.000
141A141GLN0-0.030-0.01226.0430.0010.0010.0000.0000.0000.000
142A142LEU00.0080.00922.564-0.002-0.0020.0000.0000.0000.000
143A143VAL0-0.035-0.01921.528-0.001-0.0010.0000.0000.0000.000
144A144ALA0-0.043-0.01823.9550.0010.0010.0000.0000.0000.000
145A145LEU0-0.022-0.00726.4950.0000.0000.0000.0000.0000.000
146A146GLY00.0090.01423.933-0.005-0.0050.0000.0000.0000.000
147A147PHE0-0.011-0.02021.159-0.009-0.0090.0000.0000.0000.000
148A148THR00.0130.00515.7080.0060.0060.0000.0000.0000.000
149A149ARG10.8240.88613.5360.2340.2340.0000.0000.0000.000
150A150ILE00.0050.01016.7230.0020.0020.0000.0000.0000.000
151A151LEU0-0.035-0.01016.481-0.013-0.0130.0000.0000.0000.000
152A152LEU0-0.016-0.01215.6960.0190.0190.0000.0000.0000.000
153A153HIS10.7900.87216.3700.1410.1410.0000.0000.0000.000
154A154GLY0-0.022-0.01017.600-0.004-0.0040.0000.0000.0000.000
155A155SER0-0.043-0.06019.1680.0080.0080.0000.0000.0000.000
156A156SER00.000-0.02422.457-0.010-0.0100.0000.0000.0000.000
157A157ASN0-0.069-0.03325.3400.0040.0040.0000.0000.0000.000
158A158GLY00.0110.01424.1010.0000.0000.0000.0000.0000.000
159A159GLU-1-0.790-0.85122.126-0.104-0.1040.0000.0000.0000.000
160A160PRO00.0310.01219.235-0.016-0.0160.0000.0000.0000.000
161A161ILE0-0.0050.00713.0300.0050.0050.0000.0000.0000.000
162A162ILE0-0.007-0.01413.4060.0060.0060.0000.0000.0000.000
163A163GLU-1-0.905-0.95615.258-0.104-0.1040.0000.0000.0000.000
164A164ASN0-0.047-0.03117.0350.0280.0280.0000.0000.0000.000
165A165ILE0-0.0020.00611.9590.0240.0240.0000.0000.0000.000
166A166LYS10.9630.97214.7670.0800.0800.0000.0000.0000.000
167A167HIS0-0.0180.00217.1450.0280.0280.0000.0000.0000.000
168A168ILE00.0270.00612.9080.0150.0150.0000.0000.0000.000
169A169LYS10.8040.89213.003-0.087-0.0870.0000.0000.0000.000
170A170ALA0-0.0030.01314.5490.0240.0240.0000.0000.0000.000
171A171LEU0-0.014-0.00617.2050.0030.0030.0000.0000.0000.000
172A172VAL00.0180.01711.835-0.006-0.0060.0000.0000.0000.000
173A173GLU-1-0.815-0.90415.1750.1420.1420.0000.0000.0000.000
174A174TYR0-0.093-0.07517.0580.0010.0010.0000.0000.0000.000
175A175ALA00.0270.02016.625-0.006-0.0060.0000.0000.0000.000
176A176ASN0-0.039-0.02416.5650.0200.0200.0000.0000.0000.000
177A177ASN0-0.049-0.03713.0130.0230.0230.0000.0000.0000.000
178A178ARG10.7730.88915.650-0.068-0.0680.0000.0000.0000.000
179A179ILE00.0250.02617.509-0.015-0.0150.0000.0000.0000.000
180A180GLU-1-0.800-0.88110.034-0.034-0.0340.0000.0000.0000.000
181A181ILE0-0.003-0.00213.089-0.016-0.0160.0000.0000.0000.000
182A182MET0-0.068-0.02012.050-0.043-0.0430.0000.0000.0000.000
183A183VAL00.0330.03310.2750.0150.0150.0000.0000.0000.000
184A184GLY00.0660.01413.156-0.067-0.0670.0000.0000.0000.000
185A185GLY00.0240.02315.6250.0290.0290.0000.0000.0000.000
186A186GLY00.022-0.00517.4020.0070.0070.0000.0000.0000.000
187A187VAL0-0.0350.00711.371-0.017-0.0170.0000.0000.0000.000
188A188THR0-0.036-0.06012.974-0.002-0.0020.0000.0000.0000.000
189A189ALA00.001-0.01110.576-0.079-0.0790.0000.0000.0000.000
190A190GLU-1-0.903-0.92310.093-0.455-0.4550.0000.0000.0000.000
191A191ASN0-0.008-0.01110.473-0.064-0.0640.0000.0000.0000.000
192A192TYR00.0240.0135.6950.0800.0800.0000.0000.0000.000
193A193GLN00.0060.0084.285-0.480-0.290-0.001-0.014-0.1750.000
194A194TYR0-0.031-0.0184.609-0.236-0.153-0.001-0.006-0.0750.000
195A195ILE00.0360.0007.1900.1420.1420.0000.0000.0000.000
196A196CYS0-0.0420.0084.4580.0210.107-0.001-0.006-0.0790.000
197A197GLN0-0.025-0.0214.4680.0620.184-0.001-0.008-0.1120.000
198A198GLU-1-0.878-0.9125.8810.0300.0300.0000.0000.0000.000
199A199THR0-0.084-0.0818.7580.0460.0460.0000.0000.0000.000
200A200GLY00.0260.0218.284-0.013-0.0130.0000.0000.0000.000
201A201VAL0-0.025-0.0108.7460.0560.0560.0000.0000.0000.000
202A202LYS10.8990.9405.856-0.1030.061-0.001-0.010-0.1530.000
203A203GLN00.006-0.0076.416-0.741-0.7410.0000.0000.0000.000
204A204ALA00.0060.0038.8010.1500.1500.0000.0000.0000.000
205A205HIS10.8090.89610.6820.2090.2090.0000.0000.0000.000
206A206GLY00.004-0.01313.9250.0370.0370.0000.0000.0000.000
207A207THR00.0290.02515.772-0.032-0.0320.0000.0000.0000.000
208A208ARG10.9580.97616.6470.2430.2430.0000.0000.0000.000
209A209ILE00.0380.03210.677-0.028-0.0280.0000.0000.0000.000
210A210THR00.0140.01411.234-0.110-0.1100.0000.0000.0000.000