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: QVKLY

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2475187.864745
FMO2-HF: Nuclear repulsion 2393300.670456
FMO2-HF: Total energy -81887.194289
FMO2-MP2: Total energy -82124.988527


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.
-2.646-0.377-0.008-0.962-1.2970.003
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 : 0.006 / q_NPA : 0.016
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].
3A3LEU0-0.048-0.0063.876-2.444-0.621-0.004-0.930-0.8870.003
4A4ARG10.9350.9636.0441.4421.4420.0000.0000.0000.000
5A5GLU-1-0.715-0.8438.558-0.258-0.2580.0000.0000.0000.000
6A6PHE00.009-0.00812.1610.0110.0110.0000.0000.0000.000
7A7CYS0-0.092-0.03914.9240.0320.0320.0000.0000.0000.000
8A8ALA00.0300.00918.3970.0010.0010.0000.0000.0000.000
9A9GLU-1-0.825-0.89421.033-0.115-0.1150.0000.0000.0000.000
10A10ASN0-0.049-0.04524.8120.0080.0080.0000.0000.0000.000
11A11LEU00.033-0.01423.712-0.012-0.0120.0000.0000.0000.000
12A12THR0-0.021-0.00124.6040.0040.0040.0000.0000.0000.000
13A13ASP-1-0.918-0.95521.440-0.159-0.1590.0000.0000.0000.000
14A14LEU00.0320.01619.108-0.018-0.0180.0000.0000.0000.000
15A15THR0-0.011-0.00819.660-0.007-0.0070.0000.0000.0000.000
16A16ARG10.8840.93618.6570.1490.1490.0000.0000.0000.000
17A17LEU0-0.0090.01815.105-0.016-0.0160.0000.0000.0000.000
18A18ASP-1-0.809-0.91713.004-0.087-0.0870.0000.0000.0000.000
19A19LYS10.9901.00711.470-0.034-0.0340.0000.0000.0000.000
20A20ALA0-0.074-0.0239.181-0.043-0.0430.0000.0000.0000.000
21A21ILE0-0.090-0.0527.363-0.050-0.0500.0000.0000.0000.000
22A22ILE0-0.045-0.0217.819-0.253-0.2530.0000.0000.0000.000
23A23SER00.0510.0207.4980.1120.1120.0000.0000.0000.000
24A24ARG10.7940.88110.0840.5180.5180.0000.0000.0000.000
25A25VAL00.0300.00713.032-0.047-0.0470.0000.0000.0000.000
26A26GLU-1-0.851-0.91316.049-0.188-0.1880.0000.0000.0000.000
27A27LEU0-0.011-0.01518.6380.0010.0010.0000.0000.0000.000
28A28CYS0-0.042-0.01421.9160.0100.0100.0000.0000.0000.000
29A29ASP-1-0.782-0.89024.959-0.101-0.1010.0000.0000.0000.000
30A30ASN00.0130.00227.823-0.006-0.0060.0000.0000.0000.000
31A31LEU00.0830.00322.890-0.001-0.0010.0000.0000.0000.000
32A32ALA0-0.073-0.01227.004-0.003-0.0030.0000.0000.0000.000
33A33VAL0-0.038-0.01029.9380.0030.0030.0000.0000.0000.000
34A34GLY0-0.037-0.02726.3910.0050.0050.0000.0000.0000.000
35A35GLY00.0010.01225.560-0.009-0.0090.0000.0000.0000.000
36A36THR0-0.041-0.02126.7480.0060.0060.0000.0000.0000.000
37A37THR00.0280.00327.598-0.011-0.0110.0000.0000.0000.000
38A38PRO0-0.0450.00625.8360.0040.0040.0000.0000.0000.000
39A39SER00.0490.01429.0880.0060.0060.0000.0000.0000.000
40A40TYR00.021-0.01330.344-0.004-0.0040.0000.0000.0000.000
41A41GLY00.0060.00230.853-0.001-0.0010.0000.0000.0000.000
42A42VAL0-0.017-0.00926.726-0.002-0.0020.0000.0000.0000.000
43A43ILE00.0380.02125.790-0.007-0.0070.0000.0000.0000.000
44A44LYS10.8710.94026.0570.0480.0480.0000.0000.0000.000
45A45GLU-1-0.846-0.92127.169-0.058-0.0580.0000.0000.0000.000
46A46ALA0-0.009-0.00223.008-0.003-0.0030.0000.0000.0000.000
47A47ASN0-0.018-0.02122.108-0.021-0.0210.0000.0000.0000.000
48A48GLN00.0210.01922.1990.0000.0000.0000.0000.0000.000
49A49TYR00.016-0.00221.597-0.004-0.0040.0000.0000.0000.000
50A50LEU0-0.023-0.03017.579-0.004-0.0040.0000.0000.0000.000
51A51HIS10.8520.90718.3610.0920.0920.0000.0000.0000.000
52A52GLU-1-0.966-0.95419.278-0.047-0.0470.0000.0000.0000.000
53A53LYS10.7910.90417.3700.1580.1580.0000.0000.0000.000
54A54GLY0-0.049-0.02615.514-0.008-0.0080.0000.0000.0000.000
55A55ILE0-0.086-0.03713.538-0.033-0.0330.0000.0000.0000.000
56A56SER0-0.030-0.02713.7970.0200.0200.0000.0000.0000.000
57A57VAL0-0.027-0.02915.582-0.034-0.0340.0000.0000.0000.000
58A58ALA0-0.052-0.01917.2950.0150.0150.0000.0000.0000.000
59A59VAL00.0480.01819.185-0.010-0.0100.0000.0000.0000.000
60A60MET0-0.031-0.02122.7410.0100.0100.0000.0000.0000.000
61A61ILE0-0.0130.00124.5910.0070.0070.0000.0000.0000.000
62A62ARG10.8220.90427.6670.0990.0990.0000.0000.0000.000
63A63PRO00.0400.02629.924-0.003-0.0030.0000.0000.0000.000
64A64ARG10.7470.84932.7940.0610.0610.0000.0000.0000.000
65A65GLY00.0420.01632.012-0.004-0.0040.0000.0000.0000.000
66A66GLY0-0.028-0.01532.4970.0060.0060.0000.0000.0000.000
67A67ASN0-0.010-0.02532.169-0.006-0.0060.0000.0000.0000.000
68A68PHE00.0720.03927.663-0.003-0.0030.0000.0000.0000.000
69A69VAL0-0.0090.01032.5760.0020.0020.0000.0000.0000.000
70A70TYR0-0.004-0.01430.412-0.002-0.0020.0000.0000.0000.000
71A71ASN00.0120.02037.0420.0040.0040.0000.0000.0000.000
72A72ASP-1-0.815-0.93139.264-0.031-0.0310.0000.0000.0000.000
73A73LEU0-0.019-0.00440.2360.0000.0000.0000.0000.0000.000
74A74GLU-1-0.799-0.88636.619-0.052-0.0520.0000.0000.0000.000
75A75LEU00.0360.01934.758-0.004-0.0040.0000.0000.0000.000
76A76ARG10.7540.85036.0290.0340.0340.0000.0000.0000.000
77A77ILE0-0.028-0.01434.7380.0000.0000.0000.0000.0000.000
78A78MET0-0.019-0.00230.007-0.001-0.0010.0000.0000.0000.000
79A79GLU-1-0.824-0.89132.049-0.033-0.0330.0000.0000.0000.000
80A80GLU-1-0.840-0.89833.548-0.036-0.0360.0000.0000.0000.000
81A81ASP-1-0.867-0.94930.613-0.065-0.0650.0000.0000.0000.000
82A82ILE0-0.047-0.01828.277-0.005-0.0050.0000.0000.0000.000
83A83LEU00.0130.00629.4450.0000.0000.0000.0000.0000.000
84A84ARG10.7530.84631.3820.0400.0400.0000.0000.0000.000
85A85ALA00.0310.01626.128-0.001-0.0010.0000.0000.0000.000
86A86VAL00.0160.01826.523-0.004-0.0040.0000.0000.0000.000
87A87GLU-1-0.809-0.85727.600-0.038-0.0380.0000.0000.0000.000
88A88LEU0-0.084-0.03827.7770.0020.0020.0000.0000.0000.000
89A89GLU-1-0.971-0.97524.289-0.052-0.0520.0000.0000.0000.000
90A90SER0-0.020-0.03222.463-0.011-0.0110.0000.0000.0000.000
91A91ASP-1-0.788-0.85317.472-0.132-0.1320.0000.0000.0000.000
92A92ALA0-0.064-0.04418.018-0.001-0.0010.0000.0000.0000.000
93A93LEU00.0290.03720.064-0.004-0.0040.0000.0000.0000.000
94A94VAL0-0.023-0.01720.064-0.002-0.0020.0000.0000.0000.000
95A95LEU00.0400.02422.6660.0040.0040.0000.0000.0000.000
96A96GLY00.010-0.01325.043-0.003-0.0030.0000.0000.0000.000
97A97ILE0-0.0160.00127.504-0.001-0.0010.0000.0000.0000.000
98A98LEU0-0.046-0.02328.5740.0020.0020.0000.0000.0000.000
99A99THR00.0890.04532.520-0.001-0.0010.0000.0000.0000.000
100A100SER0-0.005-0.01835.232-0.002-0.0020.0000.0000.0000.000
101A101ASN0-0.065-0.03836.6510.0000.0000.0000.0000.0000.000
102A102ASN0-0.037-0.01531.466-0.001-0.0010.0000.0000.0000.000
103A103HIS00.0380.02131.182-0.002-0.0020.0000.0000.0000.000
104A104ILE00.0240.00426.541-0.003-0.0030.0000.0000.0000.000
105A105ASP-1-0.879-0.94231.082-0.029-0.0290.0000.0000.0000.000
106A106THR00.001-0.01132.203-0.001-0.0010.0000.0000.0000.000
107A107GLU-1-0.877-0.93633.299-0.021-0.0210.0000.0000.0000.000
108A108ALA00.0120.01434.4800.0000.0000.0000.0000.0000.000
109A109ILE0-0.039-0.03828.649-0.002-0.0020.0000.0000.0000.000
110A110GLU-1-0.926-0.96931.689-0.014-0.0140.0000.0000.0000.000
111A111GLN0-0.056-0.03133.3480.0000.0000.0000.0000.0000.000
112A112LEU0-0.010-0.00131.3030.0000.0000.0000.0000.0000.000
113A113LEU0-0.020-0.00228.019-0.002-0.0020.0000.0000.0000.000
114A114PRO0-0.015-0.01430.2970.0000.0000.0000.0000.0000.000
115A115ALA00.0230.01632.1420.0010.0010.0000.0000.0000.000
116A116THR0-0.022-0.01225.785-0.005-0.0050.0000.0000.0000.000
117A117GLN0-0.065-0.03427.196-0.003-0.0030.0000.0000.0000.000
118A118GLY0-0.009-0.00226.0910.0020.0020.0000.0000.0000.000
119A119LEU0-0.0090.01522.685-0.001-0.0010.0000.0000.0000.000
120A120PRO0-0.016-0.01518.2580.0010.0010.0000.0000.0000.000
121A121LEU00.0430.03820.409-0.010-0.0100.0000.0000.0000.000
122A122VAL0-0.043-0.03417.917-0.004-0.0040.0000.0000.0000.000
123A123PHE00.0460.03720.3590.0030.0030.0000.0000.0000.000
124A124HIS00.0390.01821.136-0.014-0.0140.0000.0000.0000.000
125A125MET00.0320.01118.9350.0060.0060.0000.0000.0000.000
126A126ALA00.0040.02322.5940.0060.0060.0000.0000.0000.000
127A127PHE00.027-0.00821.2610.0100.0100.0000.0000.0000.000
128A128ASP-1-0.759-0.87521.241-0.105-0.1050.0000.0000.0000.000
129A129VAL0-0.022-0.01423.9340.0030.0030.0000.0000.0000.000
130A130ILE0-0.0190.02425.8530.0050.0050.0000.0000.0000.000
131A131PRO00.0090.01727.215-0.003-0.0030.0000.0000.0000.000
132A132LYS10.8410.90423.1110.0750.0750.0000.0000.0000.000
133A133SER0-0.016-0.00426.3110.0040.0040.0000.0000.0000.000
134A134ASP-1-0.821-0.90528.911-0.011-0.0110.0000.0000.0000.000
135A135GLN00.0250.03822.532-0.006-0.0060.0000.0000.0000.000
136A136LYS10.9770.97721.878-0.023-0.0230.0000.0000.0000.000
137A137LYS10.8710.92824.9040.0120.0120.0000.0000.0000.000
138A138SER00.0520.02325.8780.0000.0000.0000.0000.0000.000
139A139ILE0-0.0090.00420.111-0.002-0.0020.0000.0000.0000.000
140A140ASP-1-0.764-0.84823.8140.0240.0240.0000.0000.0000.000
141A141GLN00.009-0.00126.079-0.001-0.0010.0000.0000.0000.000
142A142LEU00.0110.00823.196-0.002-0.0020.0000.0000.0000.000
143A143VAL0-0.041-0.02021.714-0.001-0.0010.0000.0000.0000.000
144A144ALA0-0.049-0.02324.1920.0020.0020.0000.0000.0000.000
145A145LEU0-0.018-0.00426.9850.0000.0000.0000.0000.0000.000
146A146GLY0-0.0080.00824.441-0.004-0.0040.0000.0000.0000.000
147A147PHE0-0.012-0.01321.654-0.009-0.0090.0000.0000.0000.000
148A148THR0-0.010-0.01115.9890.0050.0050.0000.0000.0000.000
149A149ARG10.8550.90413.9600.2330.2330.0000.0000.0000.000
150A150ILE00.0070.01317.1670.0020.0020.0000.0000.0000.000
151A151LEU0-0.043-0.01016.476-0.015-0.0150.0000.0000.0000.000
152A152LEU0-0.006-0.01116.3340.0190.0190.0000.0000.0000.000
153A153HIS10.7700.86316.6170.1480.1480.0000.0000.0000.000
154A154GLY0-0.013-0.01617.746-0.007-0.0070.0000.0000.0000.000
155A155SER0-0.072-0.07419.1860.0060.0060.0000.0000.0000.000
156A156SER00.019-0.00422.546-0.008-0.0080.0000.0000.0000.000
157A157ASN0-0.043-0.00925.4830.0030.0030.0000.0000.0000.000
158A158GLY00.0000.01423.6590.0000.0000.0000.0000.0000.000
159A159GLU-1-0.809-0.87722.497-0.108-0.1080.0000.0000.0000.000
160A160PRO00.0320.01419.513-0.015-0.0150.0000.0000.0000.000
161A161ILE00.0430.02713.2440.0040.0040.0000.0000.0000.000
162A162ILE0-0.022-0.01513.4780.0050.0050.0000.0000.0000.000
163A163GLU-1-0.929-0.96715.621-0.116-0.1160.0000.0000.0000.000
164A164ASN0-0.044-0.02417.0490.0290.0290.0000.0000.0000.000
165A165ILE0-0.005-0.00212.5010.0230.0230.0000.0000.0000.000
166A166LYS10.9540.96715.0150.0840.0840.0000.0000.0000.000
167A167HIS00.0090.00917.5500.0250.0250.0000.0000.0000.000
168A168ILE00.0370.00813.2160.0150.0150.0000.0000.0000.000
169A169LYS10.8030.90013.188-0.075-0.0750.0000.0000.0000.000
170A170ALA0-0.0110.00514.7730.0290.0290.0000.0000.0000.000
171A171LEU0-0.033-0.02017.3940.0120.0120.0000.0000.0000.000
172A172VAL00.0150.01912.0630.0000.0000.0000.0000.0000.000
173A173GLU-1-0.829-0.91015.4070.1320.1320.0000.0000.0000.000
174A174TYR0-0.111-0.09017.1050.0050.0050.0000.0000.0000.000
175A175ALA00.0330.02216.814-0.003-0.0030.0000.0000.0000.000
176A176ASN0-0.033-0.01117.1320.0190.0190.0000.0000.0000.000
177A177ASN0-0.048-0.03513.4350.0270.0270.0000.0000.0000.000
178A178ARG10.7740.88916.000-0.061-0.0610.0000.0000.0000.000
179A179ILE00.0120.00917.576-0.016-0.0160.0000.0000.0000.000
180A180GLU-1-0.815-0.87710.432-0.028-0.0280.0000.0000.0000.000
181A181ILE00.0240.01613.437-0.022-0.0220.0000.0000.0000.000
182A182MET0-0.085-0.03112.328-0.031-0.0310.0000.0000.0000.000
183A183VAL00.0360.03110.4800.0170.0170.0000.0000.0000.000
184A184GLY00.0580.01513.371-0.062-0.0620.0000.0000.0000.000
185A185GLY00.0160.01215.9380.0240.0240.0000.0000.0000.000
186A186GLY00.023-0.00417.5150.0060.0060.0000.0000.0000.000
187A187VAL0-0.0290.00311.437-0.019-0.0190.0000.0000.0000.000
188A188THR00.013-0.00613.350-0.010-0.0100.0000.0000.0000.000
189A189ALA00.006-0.00810.785-0.080-0.0800.0000.0000.0000.000
190A190GLU-1-0.951-0.97710.648-0.423-0.4230.0000.0000.0000.000
191A191ASN0-0.009-0.00710.653-0.056-0.0560.0000.0000.0000.000
192A192TYR00.0350.0255.7230.0830.0830.0000.0000.0000.000
193A193GLN00.0020.0064.500-0.540-0.366-0.001-0.014-0.1580.000
194A194TYR00.0090.0094.876-0.188-0.124-0.001-0.002-0.0620.000
195A195ILE00.0440.0017.4630.1260.1260.0000.0000.0000.000
196A196CYS0-0.0540.0014.7790.0520.117-0.001-0.003-0.0610.000
197A197GLN0-0.041-0.0264.144-0.0020.141-0.001-0.013-0.1290.000
198A198GLU-1-0.893-0.9315.6720.0040.0040.0000.0000.0000.000
199A199THR0-0.100-0.0798.7540.0690.0690.0000.0000.0000.000
200A200GLY00.0210.0168.2780.0130.0130.0000.0000.0000.000
201A201VAL0-0.029-0.0078.7320.1010.1010.0000.0000.0000.000
202A202LYS10.9000.9326.007-0.073-0.0730.0000.0000.0000.000
203A203GLN0-0.006-0.0206.651-0.659-0.6590.0000.0000.0000.000
204A204ALA00.0070.0088.8710.1320.1320.0000.0000.0000.000
205A205HIS10.8400.91710.7050.2180.2180.0000.0000.0000.000
206A206GLY00.021-0.00814.0770.0200.0200.0000.0000.0000.000
207A207THR00.0320.03016.036-0.025-0.0250.0000.0000.0000.000
208A208ARG10.9480.97116.9980.2410.2410.0000.0000.0000.000
209A209ILE00.0260.01810.875-0.031-0.0310.0000.0000.0000.000
210A210THR00.0090.01211.250-0.100-0.1000.0000.0000.0000.000