FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

tag_button

FMODB ID: YVR12

Calculation Name: 2QYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QYB

Chain ID: A

ChEMBL ID:

UniProt ID: Q74D90

Base Structure: X-ray

Registration Date: 2023-09-23

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 151
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1466883.699529
FMO2-HF: Nuclear repulsion 1407892.748894
FMO2-HF: Total energy -58990.950634
FMO2-MP2: Total energy -59164.754236


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:7:SER)


Summations of interaction energy for fragment #1(A:7: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.
-6.5-2.1370.601-1.98-2.9830.007
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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].
3A9ILE00.0820.0343.374-1.1700.9050.105-0.949-1.2310.005
4A10MET0-0.0170.0112.593-2.113-1.0100.475-0.515-1.0630.000
5A11ASN0-0.021-0.0273.587-2.314-1.1290.021-0.516-0.6890.002
6A12ARG10.9020.9366.014-1.111-1.1110.0000.0000.0000.000
7A13THR0-0.035-0.0297.515-0.283-0.2830.0000.0000.0000.000
8A14LEU0-0.036-0.0187.060-0.210-0.2100.0000.0000.0000.000
9A15ASP-1-0.879-0.9439.9790.6960.6960.0000.0000.0000.000
10A16LEU0-0.040-0.02311.824-0.118-0.1180.0000.0000.0000.000
11A17GLN0-0.084-0.07012.697-0.040-0.0400.0000.0000.0000.000
12A18ILE00.0320.01813.736-0.074-0.0740.0000.0000.0000.000
13A19ILE0-0.016-0.00215.461-0.062-0.0620.0000.0000.0000.000
14A20MET0-0.064-0.03015.370-0.057-0.0570.0000.0000.0000.000
15A21ASP-1-0.737-0.84018.1160.3380.3380.0000.0000.0000.000
16A22ASP-1-0.864-0.93520.1620.2470.2470.0000.0000.0000.000
17A23LEU0-0.046-0.01721.315-0.032-0.0320.0000.0000.0000.000
18A24LEU0-0.041-0.00923.220-0.029-0.0290.0000.0000.0000.000
19A25ASN0-0.034-0.01322.734-0.031-0.0310.0000.0000.0000.000
20A26LEU0-0.046-0.02525.293-0.020-0.0200.0000.0000.0000.000
21A27LEU00.0080.01027.789-0.015-0.0150.0000.0000.0000.000
22A28LEU0-0.002-0.01829.051-0.013-0.0130.0000.0000.0000.000
23A29LYS10.8590.94730.091-0.144-0.1440.0000.0000.0000.000
24A30GLU-1-0.952-0.96032.1960.1210.1210.0000.0000.0000.000
25A31PHE00.0150.00833.651-0.010-0.0100.0000.0000.0000.000
26A32LYS10.9580.99035.196-0.080-0.0800.0000.0000.0000.000
27A33LEU0-0.0050.00131.918-0.004-0.0040.0000.0000.0000.000
28A34ASP-1-0.768-0.87034.1470.1070.1070.0000.0000.0000.000
29A35LEU0-0.059-0.03228.3760.0010.0010.0000.0000.0000.000
30A36ALA00.0090.01627.511-0.008-0.0080.0000.0000.0000.000
31A37VAL00.004-0.01024.4020.0080.0080.0000.0000.0000.000
32A38ILE00.0260.02720.306-0.014-0.0140.0000.0000.0000.000
33A39ARG10.7990.88321.643-0.185-0.1850.0000.0000.0000.000
34A40LEU00.014-0.00816.643-0.004-0.0040.0000.0000.0000.000
35A41VAL0-0.0110.00120.112-0.006-0.0060.0000.0000.0000.000
36A42ASP-1-0.820-0.89416.9520.3560.3560.0000.0000.0000.000
37A43GLU-1-0.840-0.92315.4340.3230.3230.0000.0000.0000.000
38A44LYS10.7620.87217.744-0.324-0.3240.0000.0000.0000.000
39A45GLY00.0050.00521.408-0.022-0.0220.0000.0000.0000.000
40A46VAL0-0.014-0.00422.435-0.006-0.0060.0000.0000.0000.000
41A47LEU0-0.016-0.00621.9940.0310.0310.0000.0000.0000.000
42A48ARG10.7870.86918.936-0.299-0.2990.0000.0000.0000.000
43A49VAL00.003-0.01520.7330.0180.0180.0000.0000.0000.000
44A50ARG10.8640.94115.719-0.441-0.4410.0000.0000.0000.000
45A51SER00.018-0.00517.6650.0190.0190.0000.0000.0000.000
46A52TYR0-0.016-0.02719.992-0.035-0.0350.0000.0000.0000.000
47A53SER00.0420.02623.316-0.001-0.0010.0000.0000.0000.000
48A54GLY00.0420.02426.066-0.010-0.0100.0000.0000.0000.000
49A55LYS10.9290.95528.640-0.103-0.1030.0000.0000.0000.000
50A56GLY00.0870.02130.682-0.007-0.0070.0000.0000.0000.000
51A57ILE00.0060.02524.759-0.006-0.0060.0000.0000.0000.000
52A58ALA0-0.016-0.00228.0480.0030.0030.0000.0000.0000.000
53A59GLY00.0110.01529.836-0.008-0.0080.0000.0000.0000.000
54A60ILE0-0.057-0.05031.7090.0070.0070.0000.0000.0000.000
55A61ALA00.0070.00231.7070.0030.0030.0000.0000.0000.000
56A62GLY0-0.0170.00127.8940.0100.0100.0000.0000.0000.000
57A63LYS10.9660.99826.433-0.113-0.1130.0000.0000.0000.000
58A64ASP-1-0.729-0.84522.7140.2610.2610.0000.0000.0000.000
59A65TRP0-0.034-0.02025.538-0.021-0.0210.0000.0000.0000.000
60A66GLU-1-0.892-0.93926.6360.1550.1550.0000.0000.0000.000
61A67PRO0-0.051-0.02627.110-0.007-0.0070.0000.0000.0000.000
62A68GLU-1-0.855-0.92130.0210.1000.1000.0000.0000.0000.000
63A69ILE00.0060.00733.8370.0030.0030.0000.0000.0000.000
64A70GLU-1-0.875-0.93736.6100.0870.0870.0000.0000.0000.000
65A71THR0-0.087-0.04333.9060.0000.0000.0000.0000.0000.000
66A72TYR00.026-0.01535.6070.0010.0010.0000.0000.0000.000
67A73ILE00.0120.01228.1320.0010.0010.0000.0000.0000.000
68A74GLY00.0390.02331.0140.0090.0090.0000.0000.0000.000
69A75GLU-1-0.787-0.89132.0980.1060.1060.0000.0000.0000.000
70A76ALA0-0.027-0.00931.856-0.001-0.0010.0000.0000.0000.000
71A77PHE0-0.021-0.00924.8560.0030.0030.0000.0000.0000.000
72A78LEU0-0.022-0.02129.9420.0010.0010.0000.0000.0000.000
73A79SER0-0.040-0.01232.048-0.004-0.0040.0000.0000.0000.000
74A80ASN00.001-0.00629.5940.0060.0060.0000.0000.0000.000
75A81ARG10.8560.91931.802-0.103-0.1030.0000.0000.0000.000
76A82LEU00.0240.01033.5550.0050.0050.0000.0000.0000.000
77A83GLN0-0.051-0.01134.473-0.011-0.0110.0000.0000.0000.000
78A84PHE0-0.037-0.03035.6840.0070.0070.0000.0000.0000.000
79A85VAL00.0060.01138.174-0.006-0.0060.0000.0000.0000.000
80A86ASN00.019-0.00840.5530.0040.0040.0000.0000.0000.000
81A87ASP-1-0.790-0.87842.5940.0710.0710.0000.0000.0000.000
82A88THR0-0.031-0.04040.866-0.002-0.0020.0000.0000.0000.000
83A89GLN0-0.029-0.01443.756-0.003-0.0030.0000.0000.0000.000
84A90TYR00.0010.00147.009-0.004-0.0040.0000.0000.0000.000
85A91MET0-0.050-0.00140.3780.0010.0010.0000.0000.0000.000
86A92THR00.0150.00045.318-0.001-0.0010.0000.0000.0000.000
87A93LYS10.9090.96339.969-0.089-0.0890.0000.0000.0000.000
88A94PRO00.0520.02144.0300.0030.0030.0000.0000.0000.000
89A95LEU00.0400.02042.4230.0000.0000.0000.0000.0000.000
90A96THR00.023-0.00138.5370.0010.0010.0000.0000.0000.000
91A97ARG10.8300.91540.909-0.062-0.0620.0000.0000.0000.000
92A98GLU-1-0.830-0.90743.1560.0670.0670.0000.0000.0000.000
93A99LEU0-0.022-0.01538.9240.0000.0000.0000.0000.0000.000
94A100MET0-0.017-0.00436.2760.0030.0030.0000.0000.0000.000
95A101GLN0-0.007-0.01139.7980.0010.0010.0000.0000.0000.000
96A102LYS10.9190.97641.618-0.073-0.0730.0000.0000.0000.000
97A103GLU-1-0.891-0.94035.2510.1140.1140.0000.0000.0000.000
98A104GLY0-0.018-0.01239.2040.0030.0030.0000.0000.0000.000
99A105ILE0-0.047-0.03635.9490.0000.0000.0000.0000.0000.000
100A106LYS10.8320.92139.787-0.086-0.0860.0000.0000.0000.000
101A107SER00.002-0.01139.434-0.002-0.0020.0000.0000.0000.000
102A108PHE0-0.047-0.03835.1220.0040.0040.0000.0000.0000.000
103A109ALA00.0240.01734.235-0.007-0.0070.0000.0000.0000.000
104A110HIS00.0230.02631.1070.0160.0160.0000.0000.0000.000
105A111ILE00.0390.01529.638-0.011-0.0110.0000.0000.0000.000
106A112PRO00.0140.01628.1200.0160.0160.0000.0000.0000.000
107A113ILE0-0.0210.00921.7750.0010.0010.0000.0000.0000.000
108A114SER00.0250.01124.0960.0120.0120.0000.0000.0000.000
109A115ARG10.9000.95723.237-0.197-0.1970.0000.0000.0000.000
110A116LYS10.9670.96025.340-0.127-0.1270.0000.0000.0000.000
111A117GLY0-0.009-0.00428.709-0.004-0.0040.0000.0000.0000.000
112A118GLU-1-0.844-0.89322.9930.2090.2090.0000.0000.0000.000
113A119PRO00.0300.00225.313-0.002-0.0020.0000.0000.0000.000
114A120PRO0-0.0270.00424.9350.0160.0160.0000.0000.0000.000
115A121PHE00.005-0.00320.0140.0000.0000.0000.0000.0000.000
116A122GLY00.0400.00420.9970.0370.0370.0000.0000.0000.000
117A123ILE0-0.059-0.01323.236-0.023-0.0230.0000.0000.0000.000
118A124LEU00.0320.03725.0130.0170.0170.0000.0000.0000.000
119A125SER0-0.023-0.03126.682-0.013-0.0130.0000.0000.0000.000
120A126VAL0-0.004-0.00528.7180.0090.0090.0000.0000.0000.000
121A127PHE00.0410.00430.057-0.011-0.0110.0000.0000.0000.000
122A128SER00.038-0.00134.3150.0010.0010.0000.0000.0000.000
123A129ARG10.7520.86133.787-0.120-0.1200.0000.0000.0000.000
124A130THR0-0.037-0.00838.601-0.007-0.0070.0000.0000.0000.000
125A131ILE0-0.078-0.04040.582-0.005-0.0050.0000.0000.0000.000
126A132VAL00.0390.02041.9000.0030.0030.0000.0000.0000.000
127A133GLY0-0.014-0.01843.870-0.001-0.0010.0000.0000.0000.000
128A134LEU0-0.015-0.00737.316-0.001-0.0010.0000.0000.0000.000
129A135PHE00.0110.01134.6440.0030.0030.0000.0000.0000.000
130A136ASN00.0230.02439.583-0.002-0.0020.0000.0000.0000.000
131A137GLU-1-0.813-0.92840.0140.0900.0900.0000.0000.0000.000
132A138PRO0-0.027-0.00239.2410.0050.0050.0000.0000.0000.000
133A139PHE00.0180.01733.9570.0060.0060.0000.0000.0000.000
134A140LEU00.0050.00435.3040.0090.0090.0000.0000.0000.000
135A141ASN00.009-0.01334.5770.0070.0070.0000.0000.0000.000
136A142LEU0-0.0230.01931.6350.0070.0070.0000.0000.0000.000
137A143LEU00.008-0.00630.8730.0120.0120.0000.0000.0000.000
138A144GLU-1-0.897-0.95629.7200.1400.1400.0000.0000.0000.000
139A145SER0-0.070-0.04129.3950.0090.0090.0000.0000.0000.000
140A146LEU0-0.031-0.01125.1230.0120.0120.0000.0000.0000.000
141A147ALA00.0350.01225.3470.0210.0210.0000.0000.0000.000
142A148GLY00.0370.01924.7660.0180.0180.0000.0000.0000.000
143A149GLN0-0.057-0.03423.8460.0200.0200.0000.0000.0000.000
144A150LEU00.0150.01320.7320.0270.0270.0000.0000.0000.000
145A151ALA00.0120.00919.9680.0390.0390.0000.0000.0000.000
146A152GLN0-0.025-0.01419.266-0.009-0.0090.0000.0000.0000.000
147A153ALA00.0270.01217.4250.0180.0180.0000.0000.0000.000
148A154VAL00.0390.01115.6560.0610.0610.0000.0000.0000.000
149A155LYS10.7820.87114.928-0.186-0.1860.0000.0000.0000.000
150A156ILE0-0.0460.00613.597-0.012-0.0120.0000.0000.0000.000
151A157VAL0-0.065-0.0229.5230.0890.0890.0000.0000.0000.000