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

tag_button

FMODB ID: MMG5Z

Calculation Name: 1I8D-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I8D

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFU8

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2274255.940039
FMO2-HF: Nuclear repulsion 2193495.595508
FMO2-HF: Total energy -80760.344531
FMO2-MP2: Total energy -80992.840354


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.
3.943-6.88528.921-4.274-13.823-0.013
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 : 0.001 / q_NPA : 0.027
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].
3A3THR 00.005-0.0123.7940.1142.794-0.017-1.394-1.2690.007
4A4GLY 00.031-0.0096.3660.6960.6960.0000.0000.0000.000
5A5ILE 0-0.048-0.0059.2100.3450.3450.0000.0000.0000.000
6A6VAL 0-0.020-0.01811.061-0.226-0.2260.0000.0000.0000.000
7A7GLN 00.0200.0228.8660.2990.2990.0000.0000.0000.000
8A8GLY 00.0400.01013.8750.1450.1450.0000.0000.0000.000
9A9THR 0-0.0110.00915.304-0.054-0.0540.0000.0000.0000.000
10A10ALA 00.0150.01616.8510.0310.0310.0000.0000.0000.000
11A11LYS 10.9370.97118.4870.3940.3940.0000.0000.0000.000
12A12LEU 0-0.059-0.02319.713-0.022-0.0220.0000.0000.0000.000
13A13VAL 00.0130.00321.7390.0470.0470.0000.0000.0000.000
14A14SER 0-0.025-0.01723.1990.0430.0430.0000.0000.0000.000
15A15ILE 00.008-0.01522.744-0.030-0.0300.0000.0000.0000.000
16A16ASP -1-0.891-0.92723.569-0.211-0.2110.0000.0000.0000.000
17A17GLU -1-0.870-0.94124.170-0.233-0.2330.0000.0000.0000.000
18A18LYS 10.9240.96224.5290.2050.2050.0000.0000.0000.000
19A19PRO 00.000-0.01926.0300.0010.0010.0000.0000.0000.000
20A20ASN 0-0.012-0.01423.2690.0150.0150.0000.0000.0000.000
21A21PHE 00.009-0.02019.8410.0050.0050.0000.0000.0000.000
22A22ARG 10.8590.93420.2820.3200.3200.0000.0000.0000.000
23A23THR 00.016-0.00119.653-0.024-0.0240.0000.0000.0000.000
24A24HIS 0-0.049-0.00417.3270.0740.0740.0000.0000.0000.000
25A25VAL 00.0490.03118.318-0.047-0.0470.0000.0000.0000.000
26A26VAL 00.002-0.01415.9420.0300.0300.0000.0000.0000.000
27A27GLU -1-0.965-0.96219.250-0.427-0.4270.0000.0000.0000.000
28A28LEU 0-0.015-0.02914.087-0.034-0.0340.0000.0000.0000.000
29A29PRO 00.014-0.01016.6200.0490.0490.0000.0000.0000.000
30A30ASP -1-0.784-0.89718.130-0.555-0.5550.0000.0000.0000.000
31A31HIS 0-0.078-0.03116.0060.0610.0610.0000.0000.0000.000
32A32MET 0-0.062-0.04312.137-0.037-0.0370.0000.0000.0000.000
33A33LEU 0-0.0040.02314.414-0.129-0.1290.0000.0000.0000.000
34A34ASP -1-0.869-0.92816.449-0.659-0.6590.0000.0000.0000.000
35A35GLY 00.0340.02014.472-0.127-0.1270.0000.0000.0000.000
36A36LEU 0-0.142-0.06711.927-0.119-0.1190.0000.0000.0000.000
37A37GLU -1-0.869-0.93413.271-0.465-0.4650.0000.0000.0000.000
38A38THR 0-0.054-0.04313.546-0.114-0.1140.0000.0000.0000.000
39A39GLY 0-0.004-0.00512.6610.0240.0240.0000.0000.0000.000
40A40ALA 0-0.0280.0009.403-0.109-0.1090.0000.0000.0000.000
41A41SER 00.0210.0105.1630.3350.3350.0000.0000.0000.000
42A42VAL 0-0.035-0.0256.601-0.677-0.6770.0000.0000.0000.000
43A43ALA 0-0.0060.0146.4980.3100.3100.0000.0000.0000.000
44A44HIS 00.015-0.0028.1680.3770.3770.0000.0000.0000.000
45A45ASN 0-0.051-0.03911.8000.0720.0720.0000.0000.0000.000
46A46GLY 00.0650.0178.9120.1780.1780.0000.0000.0000.000
47A47CYS 0-0.046-0.0128.4280.0240.0240.0000.0000.0000.000
48A48CYS 0-0.042-0.0064.761-0.582-0.5150.000-0.008-0.0600.000
49A49LEU 0-0.019-0.0117.1470.5080.5080.0000.0000.0000.000
50A50THR 00.007-0.0568.615-0.295-0.2950.0000.0000.0000.000
51A51VAL 0-0.0450.03210.6730.1620.1620.0000.0000.0000.000
52A52THR 0-0.004-0.00213.3570.0470.0470.0000.0000.0000.000
53A53GLU -1-0.927-0.96916.743-0.299-0.2990.0000.0000.0000.000
54A54ILE 00.0260.00816.109-0.064-0.0640.0000.0000.0000.000
55A55ASN 0-0.042-0.01619.8280.0620.0620.0000.0000.0000.000
56A56GLY 00.0370.03023.1720.0090.0090.0000.0000.0000.000
57A57ASN 00.0250.01420.806-0.027-0.0270.0000.0000.0000.000
58A58HIS 0-0.039-0.02020.469-0.015-0.0150.0000.0000.0000.000
59A59VAL 00.0010.00615.0030.0060.0060.0000.0000.0000.000
60A60SER 00.001-0.00917.786-0.002-0.0020.0000.0000.0000.000
61A61PHE 00.0720.02911.163-0.095-0.0950.0000.0000.0000.000
62A62ASP -1-0.804-0.88315.522-0.310-0.3100.0000.0000.0000.000
63A63LEU 0-0.047-0.02715.026-0.021-0.0210.0000.0000.0000.000
64A64MET 00.0440.02716.3580.0750.0750.0000.0000.0000.000
65A65LYS 10.8790.92418.2090.1730.1730.0000.0000.0000.000
66A66GLU -1-0.881-0.92816.4310.0160.0160.0000.0000.0000.000
67A67THR 00.0670.02413.8740.0410.0410.0000.0000.0000.000
68A68LEU 0-0.0570.00316.375-0.013-0.0130.0000.0000.0000.000
69A69ARG 10.9000.96419.2870.0190.0190.0000.0000.0000.000
70A70ILE 0-0.079-0.04215.3070.0160.0160.0000.0000.0000.000
71A71THR 0-0.0060.00413.687-0.022-0.0220.0000.0000.0000.000
72A72ASN 0-0.067-0.05016.819-0.033-0.0330.0000.0000.0000.000
73A73LEU 00.0530.01413.3060.0110.0110.0000.0000.0000.000
74A74GLY 00.020-0.00617.9010.0040.0040.0000.0000.0000.000
75A75ASP -1-0.944-0.95620.830-0.165-0.1650.0000.0000.0000.000
76A76LEU 0-0.140-0.04317.9820.0040.0040.0000.0000.0000.000
77A77LYS 10.9250.94322.3830.2300.2300.0000.0000.0000.000
78A78VAL 00.0350.02024.373-0.022-0.0220.0000.0000.0000.000
79A79GLY 0-0.072-0.03824.8830.0220.0220.0000.0000.0000.000
80A80ASP -1-0.866-0.91922.627-0.300-0.3000.0000.0000.0000.000
81A81TRP 0-0.011-0.01920.660-0.024-0.0240.0000.0000.0000.000
82A82VAL 0-0.044-0.01114.7470.0240.0240.0000.0000.0000.000
83A83ASN 00.007-0.00913.7360.0420.0420.0000.0000.0000.000
84A84VAL 00.007-0.00711.652-0.072-0.0720.0000.0000.0000.000
85A85GLU -1-0.765-0.8817.528-2.773-2.7730.0000.0000.0000.000
86A86ARG 10.8150.9027.8081.1051.1050.0000.0000.0000.000
87A87ALA 0-0.011-0.0112.833-0.677-0.2080.073-0.176-0.3660.000
88A88ALA 00.0110.0232.6631.2302.2390.218-0.370-0.858-0.001
89A89LYS 10.9050.9544.2971.1881.3220.000-0.050-0.0840.000
90A90PHE 0-0.007-0.0196.5170.2080.2080.0000.0000.0000.000
91A91SER 0-0.042-0.0178.1560.1730.1730.0000.0000.0000.000
92A92ASP -1-0.859-0.9207.544-1.799-1.7990.0000.0000.0000.000
93A93GLU -1-0.972-0.9778.953-0.316-0.3160.0000.0000.0000.000
94A94ILE 0-0.002-0.0336.529-0.225-0.2250.0000.0000.0000.000
95A95GLY 0-0.001-0.0018.9000.1710.1710.0000.0000.0000.000
96A96GLY 0-0.028-0.0119.6430.0820.0820.0000.0000.0000.000
97A97HIS 0-0.039-0.0358.3290.2440.2440.0000.0000.0000.000
98A98LEU 0-0.016-0.0192.2681.236-3.40010.460-1.884-3.9400.000
99A99MET 0-0.0100.0434.0980.4100.9330.004-0.109-0.4180.000
100A100SER 00.004-0.0281.859-2.949-5.75618.224-9.707-5.711-0.011
101A101GLY 00.0100.0092.7336.556-1.818-0.0419.433-1.019-0.008
102A102HIS 0-0.057-0.0265.5620.2520.2520.0000.0000.0000.000
103A103ILE 00.0000.0067.2410.1420.1420.0000.0000.0000.000
104A104MET 0-0.009-0.00210.7170.0060.0060.0000.0000.0000.000
105A105THR 00.0150.00113.128-0.013-0.0130.0000.0000.0000.000
106A106THR 0-0.0070.01814.816-0.056-0.0560.0000.0000.0000.000
107A107ALA 0-0.019-0.01317.5800.0480.0480.0000.0000.0000.000
108A108GLU -1-0.842-0.92320.007-0.097-0.0970.0000.0000.0000.000
109A109VAL 0-0.0060.01622.9930.0230.0230.0000.0000.0000.000
110A110ALA 0-0.010-0.00824.8300.0050.0050.0000.0000.0000.000
111A111LYS 10.9200.93127.4230.0240.0240.0000.0000.0000.000
112A112ILE 00.0160.00826.932-0.002-0.0020.0000.0000.0000.000
113A113LEU 0-0.0200.00129.2450.0030.0030.0000.0000.0000.000
114A114THR 0-0.014-0.01730.431-0.010-0.0100.0000.0000.0000.000
115A115SER 0-0.006-0.00231.9300.0090.0090.0000.0000.0000.000
116A116GLU -1-0.874-0.94133.137-0.084-0.0840.0000.0000.0000.000
117A117ASN 0-0.030-0.01031.518-0.002-0.0020.0000.0000.0000.000
118A118ASN 0-0.034-0.01228.755-0.003-0.0030.0000.0000.0000.000
119A119ARG 10.9730.98225.8310.1700.1700.0000.0000.0000.000
120A120GLN 00.0430.04225.8070.0100.0100.0000.0000.0000.000
121A121ILE 0-0.041-0.01722.8220.0020.0020.0000.0000.0000.000
122A122TRP 00.0010.02624.0670.0160.0160.0000.0000.0000.000
123A123PHE 00.0180.00020.366-0.022-0.0220.0000.0000.0000.000
124A124LYS 10.8150.90422.9580.0610.0610.0000.0000.0000.000
125A125VAL 00.0160.01019.295-0.020-0.0200.0000.0000.0000.000
126A126GLN 00.0120.01619.827-0.014-0.0140.0000.0000.0000.000
127A127ASP -1-0.772-0.91518.5980.2050.2050.0000.0000.0000.000
128A128SER 0-0.044-0.01019.8020.0240.0240.0000.0000.0000.000
129A129GLN 0-0.035-0.01820.0780.0270.0270.0000.0000.0000.000
130A130LEU 00.0680.00914.9560.0390.0390.0000.0000.0000.000
131A131MET 0-0.092-0.02217.1150.0210.0210.0000.0000.0000.000
132A132LYS 10.8910.95617.517-0.358-0.3580.0000.0000.0000.000
133A133TYR 0-0.045-0.02113.6210.0240.0240.0000.0000.0000.000
134A134ILE 0-0.048-0.01214.7730.0280.0280.0000.0000.0000.000
135A135LEU 00.0320.01217.076-0.039-0.0390.0000.0000.0000.000
136A136TYR 0-0.035-0.02319.066-0.018-0.0180.0000.0000.0000.000
137A137LYS 10.8950.94220.482-0.058-0.0580.0000.0000.0000.000
138A138GLY 00.0250.03216.7700.0220.0220.0000.0000.0000.000
139A139PHE 00.0160.01912.048-0.081-0.0810.0000.0000.0000.000
140A140ILE 0-0.028-0.03012.6590.0710.0710.0000.0000.0000.000
141A141GLY 00.0510.02710.779-0.097-0.0970.0000.0000.0000.000
142A142ILE 0-0.039-0.04711.7030.0400.0400.0000.0000.0000.000
143A143ASP -1-0.747-0.84613.694-0.506-0.5060.0000.0000.0000.000
144A144GLY 00.0490.0169.615-0.117-0.1170.0000.0000.0000.000
145A145ILE 0-0.081-0.02010.130-0.157-0.1570.0000.0000.0000.000
146A146SER 00.0590.06210.0070.2030.2030.0000.0000.0000.000
147A147LEU 0-0.085-0.04711.9750.0000.0000.0000.0000.0000.000
148A148THR 00.0430.02115.2300.0560.0560.0000.0000.0000.000
149A149VAL 0-0.055-0.01516.708-0.043-0.0430.0000.0000.0000.000
150A150GLY 0-0.004-0.00619.3400.0130.0130.0000.0000.0000.000
151A151GLU -1-0.892-0.96822.9020.0640.0640.0000.0000.0000.000
152A152VAL 00.0330.00720.905-0.014-0.0140.0000.0000.0000.000
153A153THR 0-0.081-0.04024.152-0.003-0.0030.0000.0000.0000.000
154A154PRO 00.0670.01324.2480.0090.0090.0000.0000.0000.000
155A155THR 00.0040.00124.6380.0030.0030.0000.0000.0000.000
156A156ARG 10.9600.97023.392-0.017-0.0170.0000.0000.0000.000
157A157PHE 00.0660.05218.0030.0240.0240.0000.0000.0000.000
158A158CYS 0-0.015-0.00522.772-0.022-0.0220.0000.0000.0000.000
159A159VAL 00.0260.01218.8120.0190.0190.0000.0000.0000.000
160A160HIS 0-0.011-0.00822.154-0.026-0.0260.0000.0000.0000.000
161A161LEU 0-0.025-0.02120.627-0.013-0.0130.0000.0000.0000.000
162A162ILE 00.0300.02420.1350.0180.0180.0000.0000.0000.000
163A163PRO 00.0680.00023.084-0.026-0.0260.0000.0000.0000.000
164A164GLU -1-0.735-0.85920.412-0.367-0.3670.0000.0000.0000.000
165A165THR 0-0.014-0.00318.245-0.041-0.0410.0000.0000.0000.000
166A166LEU 0-0.102-0.04720.150-0.029-0.0290.0000.0000.0000.000
167A167GLU -1-0.961-0.96722.824-0.272-0.2720.0000.0000.0000.000
168A168ARG 10.8670.93817.8500.4950.4950.0000.0000.0000.000
169A169THR 0-0.037-0.00416.262-0.052-0.0520.0000.0000.0000.000
170A170THR 0-0.013-0.01418.2750.0760.0760.0000.0000.0000.000
171A171LEU 00.0260.01018.4380.0560.0560.0000.0000.0000.000
172A172GLY 00.017-0.01220.5950.0430.0430.0000.0000.0000.000
173A173LYS 10.8920.94223.4900.3290.3290.0000.0000.0000.000
174A174LYS 10.8530.93718.9420.3890.3890.0000.0000.0000.000
175A175LYS 10.9500.97624.6070.1660.1660.0000.0000.0000.000
176A176LEU 00.0280.00726.574-0.003-0.0030.0000.0000.0000.000
177A177GLY 0-0.023-0.01027.606-0.004-0.0040.0000.0000.0000.000
178A178ALA 0-0.032-0.00423.404-0.003-0.0030.0000.0000.0000.000
179A179ARG 10.9580.97320.6490.1670.1670.0000.0000.0000.000
180A180VAL 0-0.077-0.03417.417-0.041-0.0410.0000.0000.0000.000
181A181ASN 00.016-0.01413.3010.1540.1540.0000.0000.0000.000
182A182ILE 0-0.035-0.03113.524-0.035-0.0350.0000.0000.0000.000
183A183GLU -1-0.770-0.9015.9720.2470.2470.0000.0000.0000.000
184A184ILE 0-0.0010.00110.276-0.025-0.0250.0000.0000.0000.000
185A185ASP -1-0.762-0.8838.4651.4521.4520.0000.0000.0000.000
186A186PRO 00.0450.0244.559-0.185-0.0780.000-0.009-0.0980.000
187A187GLN 0-0.011-0.0047.074-0.327-0.3270.0000.0000.0000.000
188A188THR 0-0.015-0.0199.336-0.267-0.2670.0000.0000.0000.000
189A189GLN 0-0.020-0.0069.755-0.041-0.0410.0000.0000.0000.000
190A190ALA 0-0.0040.0079.827-0.107-0.1070.0000.0000.0000.000
191A191VAL 0-0.0090.01311.711-0.151-0.1510.0000.0000.0000.000
192A192VAL 00.000-0.00514.660-0.101-0.1010.0000.0000.0000.000
193A193ASP -1-0.817-0.91413.7530.6340.6340.0000.0000.0000.000
194A194THR 0-0.122-0.08614.839-0.051-0.0510.0000.0000.0000.000
195A195VAL 0-0.014-0.01417.273-0.064-0.0640.0000.0000.0000.000
196A196GLU -1-0.879-0.93119.6200.3510.3510.0000.0000.0000.000
197A197ARG 10.9630.98314.051-0.771-0.7710.0000.0000.0000.000
198A198VAL 0-0.0160.00521.234-0.040-0.0400.0000.0000.0000.000
199A199LEU 0-0.013-0.03023.365-0.036-0.0360.0000.0000.0000.000
200A200ALA 00.0250.02624.445-0.026-0.0260.0000.0000.0000.000
201A201ALA 0-0.028-0.01725.049-0.023-0.0230.0000.0000.0000.000
202A202ARG 10.8680.91526.764-0.324-0.3240.0000.0000.0000.000
203A203GLU -1-0.926-0.95328.9810.1940.1940.0000.0000.0000.000
204A204ASN 00.0070.00028.695-0.023-0.0230.0000.0000.0000.000
205A205ALA 0-0.094-0.02631.227-0.013-0.0130.0000.0000.0000.000
206A206MET 0-0.026-0.01432.929-0.007-0.0070.0000.0000.0000.000
207A207NME 0-0.057-0.01434.757-0.013-0.0130.0000.0000.0000.000