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: GYQM1

Calculation Name: 2IAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAD

Chain ID: A

ChEMBL ID:

UniProt ID: P04228

Base Structure: X-ray

Registration Date: 2023-09-26

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1932547.501511
FMO2-HF: Nuclear repulsion 1859290.351659
FMO2-HF: Total energy -73257.149852
FMO2-MP2: Total energy -73475.528856


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:ILE)


Summations of interaction energy for fragment #1(A:1:ILE)
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.
-3.825-1.0410.122-1.316-1.589-0.002
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.013
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].
3A2ALA00.000-0.0113.137-2.1710.5360.123-1.308-1.521-0.002
4A3ASP-1-0.941-0.9584.683-1.522-1.445-0.001-0.008-0.0680.000
5A4HIS10.7710.8547.2041.6161.6160.0000.0000.0000.000
6A5VAL00.0090.0116.024-0.451-0.4510.0000.0000.0000.000
7A6GLY00.0170.0167.8640.2520.2520.0000.0000.0000.000
8A7PHE0-0.059-0.0117.4890.0510.0510.0000.0000.0000.000
9A8TYR0-0.011-0.02811.6370.0080.0080.0000.0000.0000.000
10A9GLY00.0710.02713.8440.0350.0350.0000.0000.0000.000
11A10THR0-0.024-0.01513.2670.0420.0420.0000.0000.0000.000
12A11THR0-0.032-0.01915.718-0.032-0.0320.0000.0000.0000.000
13A12VAL00.0180.01918.2190.0370.0370.0000.0000.0000.000
14A13TYR0-0.022-0.05320.749-0.024-0.0240.0000.0000.0000.000
15A14GLN00.009-0.01023.9960.0290.0290.0000.0000.0000.000
16A15SER00.0380.01926.715-0.012-0.0120.0000.0000.0000.000
17A16PRO0-0.045-0.01629.387-0.009-0.0090.0000.0000.0000.000
18A17GLY00.0470.01232.041-0.004-0.0040.0000.0000.0000.000
19A18ASP-1-0.850-0.90231.0410.0630.0630.0000.0000.0000.000
20A19ILE00.0280.03627.639-0.008-0.0080.0000.0000.0000.000
21A20GLY00.017-0.01025.1420.0170.0170.0000.0000.0000.000
22A21GLN0-0.036-0.01919.648-0.014-0.0140.0000.0000.0000.000
23A22TYR0-0.024-0.02518.4850.0280.0280.0000.0000.0000.000
24A23THR00.0570.01317.6090.0020.0020.0000.0000.0000.000
25A24HIS0-0.0120.04316.1830.0480.0480.0000.0000.0000.000
26A25GLU-1-0.822-0.91813.368-0.215-0.2150.0000.0000.0000.000
27A26PHE0-0.026-0.03711.522-0.043-0.0430.0000.0000.0000.000
28A27ASP-1-0.798-0.87510.601-1.201-1.2010.0000.0000.0000.000
29A28GLY0-0.0060.00511.654-0.014-0.0140.0000.0000.0000.000
30A29ASP-1-0.887-0.92812.505-0.267-0.2670.0000.0000.0000.000
31A30GLU-1-0.763-0.87116.044-0.160-0.1600.0000.0000.0000.000
32A31LEU0-0.029-0.01516.0940.0060.0060.0000.0000.0000.000
33A32PHE0-0.032-0.02819.6560.0240.0240.0000.0000.0000.000
34A33TYR00.0540.04020.7280.0010.0010.0000.0000.0000.000
35A34VAL0-0.039-0.01923.196-0.004-0.0040.0000.0000.0000.000
36A35ASP-1-0.777-0.86425.529-0.022-0.0220.0000.0000.0000.000
37A36LEU00.010-0.01425.6580.0010.0010.0000.0000.0000.000
38A37ASP-1-0.893-0.92229.630-0.008-0.0080.0000.0000.0000.000
39A38LYS10.8010.85633.1920.0310.0310.0000.0000.0000.000
40A39LYS10.9000.96330.744-0.006-0.0060.0000.0000.0000.000
41A40LYS10.8970.93430.1690.0490.0490.0000.0000.0000.000
42A41THR00.004-0.00424.1720.0100.0100.0000.0000.0000.000
43A42VAL0-0.037-0.00926.130-0.003-0.0030.0000.0000.0000.000
44A43TRP00.018-0.00220.644-0.008-0.0080.0000.0000.0000.000
45A44ARG10.8740.94322.0510.2090.2090.0000.0000.0000.000
46A45LEU00.0330.02722.6100.0050.0050.0000.0000.0000.000
47A46PRO00.012-0.00425.593-0.002-0.0020.0000.0000.0000.000
48A47GLU-1-0.879-0.93726.143-0.197-0.1970.0000.0000.0000.000
49A48PHE00.010-0.00920.461-0.002-0.0020.0000.0000.0000.000
50A49GLY00.0240.01124.8100.0030.0030.0000.0000.0000.000
51A50GLN0-0.097-0.05426.7630.0200.0200.0000.0000.0000.000
52A51LEU0-0.059-0.02725.2930.0050.0050.0000.0000.0000.000
53A52ILE0-0.056-0.01520.449-0.004-0.0040.0000.0000.0000.000
54A53LEU00.0030.00224.1380.0060.0060.0000.0000.0000.000
55A54PHE00.0230.00319.704-0.009-0.0090.0000.0000.0000.000
56A55GLU-1-0.870-0.92423.516-0.063-0.0630.0000.0000.0000.000
57A56PRO0-0.012-0.00824.9550.0080.0080.0000.0000.0000.000
58A57GLN0-0.021-0.02325.0830.0010.0010.0000.0000.0000.000
59A58GLY00.0340.02922.8760.0130.0130.0000.0000.0000.000
60A59GLY00.0620.02522.2710.0140.0140.0000.0000.0000.000
61A60LEU0-0.049-0.02923.2740.0180.0180.0000.0000.0000.000
62A61GLN0-0.015-0.00224.3990.0030.0030.0000.0000.0000.000
63A62ASN00.0090.01018.0390.0150.0150.0000.0000.0000.000
64A63ILE00.0110.00922.4080.0220.0220.0000.0000.0000.000
65A64ALA0-0.061-0.02724.7360.0110.0110.0000.0000.0000.000
66A65ALA0-0.008-0.00422.7760.0090.0090.0000.0000.0000.000
67A66GLU-1-0.823-0.91319.8790.2390.2390.0000.0000.0000.000
68A67LYS10.7820.90623.427-0.058-0.0580.0000.0000.0000.000
69A68HIS0-0.041-0.01625.869-0.003-0.0030.0000.0000.0000.000
70A69ASN0-0.026-0.03621.4060.0040.0040.0000.0000.0000.000
71A70LEU00.0380.03124.0800.0150.0150.0000.0000.0000.000
72A71GLY00.0160.02725.3240.0010.0010.0000.0000.0000.000
73A72ILE0-0.018-0.00626.307-0.003-0.0030.0000.0000.0000.000
74A73LEU00.016-0.01321.3840.0040.0040.0000.0000.0000.000
75A74THR0-0.0110.00325.1560.0060.0060.0000.0000.0000.000
76A75LYS10.8520.92327.885-0.139-0.1390.0000.0000.0000.000
77A76ARG10.9280.96622.156-0.282-0.2820.0000.0000.0000.000
78A77SER00.0200.00924.7710.0200.0200.0000.0000.0000.000
79A78ASN0-0.060-0.02626.683-0.007-0.0070.0000.0000.0000.000
80A79PHE0-0.027-0.03029.936-0.010-0.0100.0000.0000.0000.000
81A80THR0-0.0130.00026.076-0.010-0.0100.0000.0000.0000.000
82A81PRO0-0.032-0.00227.1240.0080.0080.0000.0000.0000.000
83A82ALA00.0100.00124.9300.0170.0170.0000.0000.0000.000
84A83THR0-0.023-0.01724.590-0.013-0.0130.0000.0000.0000.000
85A84ASN0-0.048-0.04224.6770.0130.0130.0000.0000.0000.000
86A85GLU-1-0.840-0.90920.9420.1770.1770.0000.0000.0000.000
87A86ALA00.0090.01324.326-0.016-0.0160.0000.0000.0000.000
88A87PRO0-0.0250.00023.418-0.001-0.0010.0000.0000.0000.000
89A88GLN0-0.017-0.00819.5710.0120.0120.0000.0000.0000.000
90A89ALA00.013-0.00823.989-0.009-0.0090.0000.0000.0000.000
91A90THR0-0.033-0.01824.1140.0040.0040.0000.0000.0000.000
92A91VAL0-0.006-0.00826.246-0.007-0.0070.0000.0000.0000.000
93A92PHE0-0.022-0.00923.418-0.001-0.0010.0000.0000.0000.000
94A93PRO00.0280.02128.6310.0010.0010.0000.0000.0000.000
95A94LYS10.9500.97127.3510.1820.1820.0000.0000.0000.000
96A95SER0-0.012-0.02528.436-0.019-0.0190.0000.0000.0000.000
97A96PRO00.0030.00831.0940.0080.0080.0000.0000.0000.000
98A97VAL00.0260.00933.5930.0020.0020.0000.0000.0000.000
99A98LEU0-0.025-0.00536.1760.0050.0050.0000.0000.0000.000
100A99LEU00.0210.01639.423-0.001-0.0010.0000.0000.0000.000
101A100GLY0-0.0130.00042.3140.0000.0000.0000.0000.0000.000
102A101GLN0-0.043-0.02837.820-0.003-0.0030.0000.0000.0000.000
103A102PRO0-0.035-0.02738.518-0.001-0.0010.0000.0000.0000.000
104A103ASN0-0.0010.02132.891-0.015-0.0150.0000.0000.0000.000
105A104THR0-0.041-0.04030.6160.0010.0010.0000.0000.0000.000
106A105LEU0-0.0020.03030.961-0.010-0.0100.0000.0000.0000.000
107A106ILE0-0.007-0.00725.033-0.001-0.0010.0000.0000.0000.000
108A107CYS0-0.052-0.01827.3000.0090.0090.0000.0000.0000.000
109A108PHE0-0.0080.01217.847-0.001-0.0010.0000.0000.0000.000
110A109VAL00.006-0.01322.8190.0130.0130.0000.0000.0000.000
111A110ASP-1-0.811-0.90617.654-0.028-0.0280.0000.0000.0000.000
112A111ASN0-0.066-0.04618.6830.0330.0330.0000.0000.0000.000
113A112ILE0-0.019-0.00119.8490.0110.0110.0000.0000.0000.000
114A113PHE00.0230.01119.6690.0200.0200.0000.0000.0000.000
115A114PRO00.0470.02922.2630.0010.0010.0000.0000.0000.000
116A115PRO0-0.0130.00821.247-0.016-0.0160.0000.0000.0000.000
117A116VAL0-0.043-0.01523.518-0.011-0.0110.0000.0000.0000.000
118A117ILE0-0.021-0.01125.5720.0050.0050.0000.0000.0000.000
119A118ASN0-0.060-0.02828.450-0.010-0.0100.0000.0000.0000.000
120A119ILE00.0290.01626.0790.0030.0030.0000.0000.0000.000
121A120THR0-0.042-0.01330.732-0.003-0.0030.0000.0000.0000.000
122A121TRP00.0610.02830.0080.0010.0010.0000.0000.0000.000
123A122LEU0-0.077-0.04135.5820.0040.0040.0000.0000.0000.000
124A123ARG10.8700.92838.3270.0540.0540.0000.0000.0000.000
125A124ASN0-0.060-0.05140.9180.0030.0030.0000.0000.0000.000
126A125SER0-0.026-0.02241.3990.0030.0030.0000.0000.0000.000
127A126LYS10.8770.94542.6290.0360.0360.0000.0000.0000.000
128A127SER00.0130.00640.221-0.002-0.0020.0000.0000.0000.000
129A128VAL0-0.033-0.01237.7740.0000.0000.0000.0000.0000.000
130A129THR0-0.013-0.00338.092-0.003-0.0030.0000.0000.0000.000
131A130ASP-1-0.855-0.91837.979-0.061-0.0610.0000.0000.0000.000
132A131GLY00.0420.01336.474-0.003-0.0030.0000.0000.0000.000
133A132VAL0-0.049-0.01232.203-0.007-0.0070.0000.0000.0000.000
134A133TYR0-0.044-0.01924.8380.0020.0020.0000.0000.0000.000
135A134GLU-1-0.805-0.88526.198-0.048-0.0480.0000.0000.0000.000
136A135THR0-0.0310.00521.612-0.003-0.0030.0000.0000.0000.000
137A136SER0-0.024-0.03720.7570.0270.0270.0000.0000.0000.000
138A137PHE0-0.042-0.02120.337-0.010-0.0100.0000.0000.0000.000
139A138LEU00.0350.03216.2600.0140.0140.0000.0000.0000.000
140A139VAL0-0.010-0.00911.7260.0450.0450.0000.0000.0000.000
141A140ASN0-0.0040.01212.476-0.141-0.1410.0000.0000.0000.000
142A141ARG10.8290.8836.957-0.405-0.4050.0000.0000.0000.000
143A142ASP-1-0.824-0.8869.7230.5840.5840.0000.0000.0000.000
144A143HIS0-0.037-0.02011.168-0.103-0.1030.0000.0000.0000.000
145A144SER0-0.0100.00714.777-0.067-0.0670.0000.0000.0000.000
146A145PHE0-0.004-0.02415.9140.0080.0080.0000.0000.0000.000
147A146HIS00.002-0.00314.909-0.024-0.0240.0000.0000.0000.000
148A147LYS10.7720.87019.1660.0390.0390.0000.0000.0000.000
149A148LEU00.0030.00919.752-0.003-0.0030.0000.0000.0000.000
150A149SER00.019-0.00723.6720.0000.0000.0000.0000.0000.000
151A150TYR0-0.010-0.01723.915-0.014-0.0140.0000.0000.0000.000
152A151LEU00.0440.02229.7820.0100.0100.0000.0000.0000.000
153A152THR0-0.030-0.00633.494-0.006-0.0060.0000.0000.0000.000
154A153PHE0-0.005-0.01033.9720.0060.0060.0000.0000.0000.000
155A154ILE00.0060.00237.959-0.006-0.0060.0000.0000.0000.000
156A155PRO0-0.039-0.00337.3790.0050.0050.0000.0000.0000.000
157A156SER00.060-0.00640.0670.0000.0000.0000.0000.0000.000
158A157ASP-1-0.870-0.93642.242-0.061-0.0610.0000.0000.0000.000
159A158ASP-1-0.923-0.92044.174-0.044-0.0440.0000.0000.0000.000
160A159ASP-1-0.847-0.91641.720-0.055-0.0550.0000.0000.0000.000
161A160ILE00.0280.02339.818-0.003-0.0030.0000.0000.0000.000
162A161TYR0-0.038-0.03935.963-0.001-0.0010.0000.0000.0000.000
163A162ASP-1-0.801-0.90235.704-0.027-0.0270.0000.0000.0000.000
164A164LYS10.8440.90232.9190.0090.0090.0000.0000.0000.000
165A165VAL00.0300.01427.723-0.002-0.0020.0000.0000.0000.000
166A166GLU-1-0.817-0.89531.0520.0110.0110.0000.0000.0000.000
167A167HIS00.0490.00525.475-0.007-0.0070.0000.0000.0000.000
168A168TRP0-0.020-0.01729.0950.0020.0020.0000.0000.0000.000
169A169GLY00.0080.01028.1540.0070.0070.0000.0000.0000.000
170A170LEU0-0.065-0.02228.971-0.002-0.0020.0000.0000.0000.000
171A171GLU-1-0.924-0.95631.5940.0490.0490.0000.0000.0000.000
172A172GLU-1-0.986-0.99334.8040.0150.0150.0000.0000.0000.000
173A173PRO0-0.054-0.04434.3540.0000.0000.0000.0000.0000.000
174A174VAL00.0510.04330.011-0.005-0.0050.0000.0000.0000.000
175A175LEU00.0080.00432.594-0.007-0.0070.0000.0000.0000.000
176A176LYS10.8070.90228.9550.0230.0230.0000.0000.0000.000
177A177HIS00.0120.00632.570-0.003-0.0030.0000.0000.0000.000
178A178TRP00.0180.00732.592-0.005-0.0050.0000.0000.0000.000
179A179SER0-0.027-0.03635.3080.0060.0060.0000.0000.0000.000
180A180SER0-0.022-0.02037.314-0.007-0.0070.0000.0000.0000.000
181A181ALA00.0570.04239.134-0.003-0.0030.0000.0000.0000.000
182A182ASP-1-0.901-0.92838.080-0.055-0.0550.0000.0000.0000.000
183A183LEU0-0.070-0.03939.0460.0050.0050.0000.0000.0000.000
184A184VAL00.044-0.00338.2440.0000.0000.0000.0000.0000.000
185A185PRO0-0.045-0.02636.6310.0010.0010.0000.0000.0000.000
186A186ARG10.8550.95039.2170.0260.0260.0000.0000.0000.000