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: 43Q7N

Calculation Name: 1I8D-A-Xray372

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: 2023-03-13

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2272611.057539
FMO2-HF: Nuclear repulsion 2191867.855685
FMO2-HF: Total energy -80743.201854
FMO2-MP2: Total energy -80975.348919


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.
-7.2880.4827.616-5.028-10.357-0.023
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 : -0.004 / q_NPA : 0.011
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].
3A3THR0-0.010-0.0243.794-0.1212.658-0.023-1.448-1.3080.007
4A4GLY00.0410.0006.2940.6740.6740.0000.0000.0000.000
5A5ILE0-0.047-0.0049.1770.3250.3250.0000.0000.0000.000
6A6VAL0-0.032-0.02411.061-0.216-0.2160.0000.0000.0000.000
7A7GLN00.0270.0228.8650.2500.2500.0000.0000.0000.000
8A8GLY00.0500.01913.8750.1290.1290.0000.0000.0000.000
9A9THR0-0.0170.00715.317-0.045-0.0450.0000.0000.0000.000
10A10ALA00.0070.00916.8250.0230.0230.0000.0000.0000.000
11A11LYS10.8120.90018.4980.3760.3760.0000.0000.0000.000
12A12LEU0-0.044-0.02619.624-0.024-0.0240.0000.0000.0000.000
13A13VAL00.0250.00521.7450.0430.0430.0000.0000.0000.000
14A14SER0-0.040-0.02023.2040.0380.0380.0000.0000.0000.000
15A15ILE00.015-0.00322.671-0.027-0.0270.0000.0000.0000.000
16A16ASP-1-0.807-0.88523.568-0.180-0.1800.0000.0000.0000.000
17A17GLU-1-0.822-0.89824.168-0.196-0.1960.0000.0000.0000.000
18A18LYS10.8440.91524.3970.1970.1970.0000.0000.0000.000
19A19PRO00.017-0.00426.0230.0020.0020.0000.0000.0000.000
20A20ASN0-0.002-0.00823.3470.0150.0150.0000.0000.0000.000
21A21PHE00.021-0.00719.9450.0090.0090.0000.0000.0000.000
22A22ARG10.8000.91320.2750.2590.2590.0000.0000.0000.000
23A23THR0-0.001-0.01019.650-0.020-0.0200.0000.0000.0000.000
24A24HIS0-0.030-0.02117.1920.0750.0750.0000.0000.0000.000
25A25VAL00.0270.02818.321-0.045-0.0450.0000.0000.0000.000
26A26VAL00.007-0.00315.8370.0290.0290.0000.0000.0000.000
27A27GLU-1-0.824-0.87819.259-0.393-0.3930.0000.0000.0000.000
28A28LEU0-0.031-0.03614.261-0.026-0.0260.0000.0000.0000.000
29A29PRO00.0320.00216.7120.0430.0430.0000.0000.0000.000
30A30ASP-1-0.791-0.89018.145-0.543-0.5430.0000.0000.0000.000
31A31HIS0-0.075-0.03916.1890.0450.0450.0000.0000.0000.000
32A32MET0-0.070-0.04612.263-0.034-0.0340.0000.0000.0000.000
33A33LEU00.0080.01714.405-0.124-0.1240.0000.0000.0000.000
34A34ASP-1-0.868-0.92716.442-0.667-0.6670.0000.0000.0000.000
35A35GLY00.0260.02314.464-0.129-0.1290.0000.0000.0000.000
36A36LEU0-0.126-0.05811.925-0.110-0.1100.0000.0000.0000.000
37A37GLU-1-0.874-0.92913.259-0.459-0.4590.0000.0000.0000.000
38A38THR0-0.017-0.02713.550-0.092-0.0920.0000.0000.0000.000
39A39GLY0-0.040-0.02612.6640.0270.0270.0000.0000.0000.000
40A40ALA0-0.0240.0039.410-0.099-0.0990.0000.0000.0000.000
41A41SER00.0160.0095.1400.3320.3320.0000.0000.0000.000
42A42VAL0-0.030-0.0236.613-0.667-0.6670.0000.0000.0000.000
43A43ALA0-0.0080.0146.4640.3180.3180.0000.0000.0000.000
44A44HIS00.022-0.0018.1730.3100.3100.0000.0000.0000.000
45A45ASN0-0.045-0.02911.8040.0700.0700.0000.0000.0000.000
46A46GLY00.0600.0148.9460.1850.1850.0000.0000.0000.000
47A47CYS0-0.063-0.0178.4550.0540.0540.0000.0000.0000.000
48A48CYS00.0090.0085.381-0.416-0.4160.0000.0000.0000.000
49A49LEU0-0.045-0.0177.1420.4580.4580.0000.0000.0000.000
50A50THR0-0.002-0.0178.617-0.313-0.3130.0000.0000.0000.000
51A51VAL0-0.031-0.00910.6740.1530.1530.0000.0000.0000.000
52A52THR0-0.050-0.02313.3620.0380.0380.0000.0000.0000.000
53A53GLU-1-0.866-0.92516.746-0.307-0.3070.0000.0000.0000.000
54A54ILE00.0240.01416.101-0.059-0.0590.0000.0000.0000.000
55A55ASN0-0.058-0.02919.8380.0560.0560.0000.0000.0000.000
56A56GLY00.0390.03023.1820.0100.0100.0000.0000.0000.000
57A57ASN0-0.001-0.00620.811-0.021-0.0210.0000.0000.0000.000
58A58HIS0-0.049-0.02520.481-0.009-0.0090.0000.0000.0000.000
59A59VAL00.0030.00914.7600.0030.0030.0000.0000.0000.000
60A60SER0-0.017-0.02417.793-0.001-0.0010.0000.0000.0000.000
61A61PHE00.0740.02811.211-0.097-0.0970.0000.0000.0000.000
62A62ASP-1-0.807-0.88915.532-0.300-0.3000.0000.0000.0000.000
63A63LEU0-0.022-0.01115.119-0.018-0.0180.0000.0000.0000.000
64A64MET00.0440.02516.3200.0670.0670.0000.0000.0000.000
65A65LYS10.8450.88818.1990.1450.1450.0000.0000.0000.000
66A66GLU-1-0.814-0.86016.3690.0600.0600.0000.0000.0000.000
67A67THR00.0520.01913.7480.0190.0190.0000.0000.0000.000
68A68LEU0-0.0630.00016.217-0.008-0.0080.0000.0000.0000.000
69A69ARG10.8340.89519.129-0.032-0.0320.0000.0000.0000.000
70A70ILE0-0.035-0.02514.7010.0110.0110.0000.0000.0000.000
71A71THR0-0.028-0.02113.632-0.013-0.0130.0000.0000.0000.000
72A72ASN0-0.080-0.06416.896-0.039-0.0390.0000.0000.0000.000
73A73LEU00.0490.01613.2840.0050.0050.0000.0000.0000.000
74A74GLY00.0360.01117.898-0.004-0.0040.0000.0000.0000.000
75A75ASP-1-0.937-0.93520.825-0.117-0.1170.0000.0000.0000.000
76A76LEU0-0.075-0.01917.9270.0060.0060.0000.0000.0000.000
77A77LYS10.8530.90622.3830.2020.2020.0000.0000.0000.000
78A78VAL00.0310.01024.377-0.020-0.0200.0000.0000.0000.000
79A79GLY0-0.055-0.02824.8990.0210.0210.0000.0000.0000.000
80A80ASP-1-0.865-0.91722.479-0.259-0.2590.0000.0000.0000.000
81A81TRP0-0.032-0.03020.669-0.028-0.0280.0000.0000.0000.000
82A82VAL0-0.048-0.01115.4200.0300.0300.0000.0000.0000.000
83A83ASN00.005-0.00413.8190.0350.0350.0000.0000.0000.000
84A84VAL00.0240.00411.665-0.051-0.0510.0000.0000.0000.000
85A85GLU-1-0.760-0.8697.648-2.462-2.4620.0000.0000.0000.000
86A86ARG10.8230.9027.8221.1251.1250.0000.0000.0000.000
87A87ALA00.001-0.0073.139-0.603-0.2740.020-0.102-0.2470.000
88A88ALA00.0040.0172.6981.2182.2100.200-0.354-0.8380.000
89A89LYS10.8940.9554.2191.1201.265-0.001-0.058-0.0860.000
90A90PHE0-0.013-0.0246.4530.1660.1660.0000.0000.0000.000
91A91SER0-0.048-0.0178.1180.1710.1710.0000.0000.0000.000
92A92ASP-1-0.851-0.9287.569-1.880-1.8800.0000.0000.0000.000
93A93GLU-1-0.965-0.9698.949-0.380-0.3800.0000.0000.0000.000
94A94ILE00.001-0.0286.265-0.215-0.2150.0000.0000.0000.000
95A95GLY00.0080.0048.7990.1820.1820.0000.0000.0000.000
96A96GLY0-0.025-0.0099.5710.0900.0900.0000.0000.0000.000
97A97HIS0-0.047-0.0378.3290.2810.2810.0000.0000.0000.000
98A98LEU0-0.019-0.0162.552-2.129-0.6121.299-0.499-2.3170.001
99A99MET0-0.0120.0174.1090.5811.0680.001-0.112-0.3750.000
100A100SER0-0.015-0.0562.299-3.217-1.1616.055-3.807-4.304-0.025
101A101GLY00.0090.0023.179-1.601-2.2250.0661.361-0.803-0.006
102A102HIS0-0.053-0.0195.5800.0200.0200.0000.0000.0000.000
103A103ILE0-0.0100.0037.1850.1570.1570.0000.0000.0000.000
104A104MET00.0040.00110.782-0.009-0.0090.0000.0000.0000.000
105A105THR00.0130.00013.227-0.037-0.0370.0000.0000.0000.000
106A106THR00.0330.03615.164-0.043-0.0430.0000.0000.0000.000
107A107ALA0-0.054-0.02117.9490.0410.0410.0000.0000.0000.000
108A108GLU-1-0.791-0.88220.525-0.051-0.0510.0000.0000.0000.000
109A109VAL0-0.0130.01623.0310.0210.0210.0000.0000.0000.000
110A110ALA0-0.002-0.00424.8570.0000.0000.0000.0000.0000.000
111A111LYS10.9170.94327.449-0.009-0.0090.0000.0000.0000.000
112A112ILE00.0120.00626.8490.0010.0010.0000.0000.0000.000
113A113LEU0-0.0200.00329.2740.0010.0010.0000.0000.0000.000
114A114THR00.000-0.01130.461-0.009-0.0090.0000.0000.0000.000
115A115SER0-0.0020.00131.9620.0070.0070.0000.0000.0000.000
116A116GLU-1-0.871-0.93733.150-0.069-0.0690.0000.0000.0000.000
117A117ASN0-0.043-0.02431.399-0.002-0.0020.0000.0000.0000.000
118A118ASN0-0.0210.00128.735-0.002-0.0020.0000.0000.0000.000
119A119ARG10.9390.96525.9250.1330.1330.0000.0000.0000.000
120A120GLN00.0400.04525.8310.0040.0040.0000.0000.0000.000
121A121ILE0-0.034-0.01222.6530.0000.0000.0000.0000.0000.000
122A122TRP0-0.026-0.00824.0920.0210.0210.0000.0000.0000.000
123A123PHE00.017-0.00120.122-0.022-0.0220.0000.0000.0000.000
124A124LYS10.7720.86523.3490.0170.0170.0000.0000.0000.000
125A125VAL00.0200.00919.672-0.018-0.0180.0000.0000.0000.000
126A126GLN00.0060.01520.290-0.021-0.0210.0000.0000.0000.000
127A127ASP-1-0.788-0.91319.0120.2600.2600.0000.0000.0000.000
128A128SER0-0.035-0.01220.3590.0270.0270.0000.0000.0000.000
129A129GLN0-0.015-0.01220.5440.0250.0250.0000.0000.0000.000
130A130LEU00.025-0.01014.8620.0390.0390.0000.0000.0000.000
131A131MET0-0.058-0.01017.8520.0320.0320.0000.0000.0000.000
132A132LYS10.7920.89818.249-0.475-0.4750.0000.0000.0000.000
133A133TYR0-0.063-0.06414.4350.0100.0100.0000.0000.0000.000
134A134ILE0-0.035-0.00515.7050.0400.0400.0000.0000.0000.000
135A135LEU00.0330.01817.976-0.051-0.0510.0000.0000.0000.000
136A136TYR0-0.048-0.05319.750-0.018-0.0180.0000.0000.0000.000
137A137LYS10.8490.93020.476-0.088-0.0880.0000.0000.0000.000
138A138GLY00.0390.03917.0190.0140.0140.0000.0000.0000.000
139A139PHE00.0150.01112.113-0.075-0.0750.0000.0000.0000.000
140A140ILE0-0.027-0.02213.3780.0820.0820.0000.0000.0000.000
141A141GLY00.0570.03710.778-0.102-0.1020.0000.0000.0000.000
142A142ILE0-0.045-0.04611.7260.0320.0320.0000.0000.0000.000
143A143ASP-1-0.761-0.86313.752-0.405-0.4050.0000.0000.0000.000
144A144GLY00.0450.0149.649-0.124-0.1240.0000.0000.0000.000
145A145ILE0-0.089-0.02510.168-0.153-0.1530.0000.0000.0000.000
146A146SER00.0470.05310.0180.2180.2180.0000.0000.0000.000
147A147LEU0-0.083-0.05111.976-0.036-0.0360.0000.0000.0000.000
148A148THR00.0520.02615.2590.0580.0580.0000.0000.0000.000
149A149VAL0-0.066-0.02017.045-0.044-0.0440.0000.0000.0000.000
150A150GLY00.0180.00619.5360.0050.0050.0000.0000.0000.000
151A151GLU-1-0.836-0.92723.1810.1010.1010.0000.0000.0000.000
152A152VAL00.0370.01521.926-0.010-0.0100.0000.0000.0000.000
153A153THR0-0.087-0.05825.093-0.010-0.0100.0000.0000.0000.000
154A154PRO00.0730.02025.0850.0120.0120.0000.0000.0000.000
155A155THR00.0190.00825.3630.0070.0070.0000.0000.0000.000
156A156ARG10.9620.98024.179-0.053-0.0530.0000.0000.0000.000
157A157PHE00.0620.05318.2300.0220.0220.0000.0000.0000.000
158A158CYS0-0.031-0.01023.540-0.021-0.0210.0000.0000.0000.000
159A159VAL00.0250.01818.8460.0200.0200.0000.0000.0000.000
160A160HIS0-0.030-0.03122.179-0.029-0.0290.0000.0000.0000.000
161A161LEU0-0.027-0.01920.470-0.009-0.0090.0000.0000.0000.000
162A162ILE00.0310.03220.0330.0160.0160.0000.0000.0000.000
163A163PRO00.0640.00123.043-0.021-0.0210.0000.0000.0000.000
164A164GLU-1-0.727-0.83620.205-0.353-0.3530.0000.0000.0000.000
165A165THR00.0110.00117.928-0.026-0.0260.0000.0000.0000.000
166A166LEU0-0.098-0.04520.120-0.028-0.0280.0000.0000.0000.000
167A167GLU-1-0.961-0.97022.863-0.249-0.2490.0000.0000.0000.000
168A168ARG10.8400.91118.0030.4580.4580.0000.0000.0000.000
169A169THR0-0.036-0.01416.212-0.046-0.0460.0000.0000.0000.000
170A170THR0-0.022-0.02818.2230.0680.0680.0000.0000.0000.000
171A171LEU00.0190.00618.3350.0520.0520.0000.0000.0000.000
172A172GLY00.0270.00420.6320.0390.0390.0000.0000.0000.000
173A173LYS10.9070.94423.5310.3070.3070.0000.0000.0000.000
174A174LYS10.8600.94519.0680.3080.3080.0000.0000.0000.000
175A175LYS10.9580.98024.6420.1310.1310.0000.0000.0000.000
176A176LEU00.032-0.00126.6050.0000.0000.0000.0000.0000.000
177A177GLY0-0.013-0.00427.644-0.006-0.0060.0000.0000.0000.000
178A178ALA0-0.041-0.01223.402-0.001-0.0010.0000.0000.0000.000
179A179ARG10.9250.95520.3800.1120.1120.0000.0000.0000.000
180A180VAL0-0.066-0.03417.519-0.040-0.0400.0000.0000.0000.000
181A181ASN00.0250.00013.3040.1410.1410.0000.0000.0000.000
182A182ILE0-0.040-0.03414.125-0.034-0.0340.0000.0000.0000.000
183A183GLU-1-0.739-0.8396.3111.0981.0980.0000.0000.0000.000
184A184ILE00.0060.00110.987-0.050-0.0500.0000.0000.0000.000
185A185ASP-1-0.762-0.8639.3291.6821.6820.0000.0000.0000.000
186A186PRO00.0420.0215.298-0.248-0.159-0.001-0.009-0.0790.000
187A187GLN0-0.009-0.0027.981-0.373-0.3730.0000.0000.0000.000
188A188THR0-0.005-0.0329.764-0.296-0.2960.0000.0000.0000.000
189A189GLN0-0.019-0.01110.571-0.073-0.0730.0000.0000.0000.000
190A190ALA0-0.027-0.00110.399-0.142-0.1420.0000.0000.0000.000
191A191VAL0-0.0030.00512.352-0.168-0.1680.0000.0000.0000.000
192A192VAL00.0030.00215.434-0.108-0.1080.0000.0000.0000.000
193A193ASP-1-0.800-0.89214.0270.7340.7340.0000.0000.0000.000
194A194THR0-0.099-0.07115.314-0.067-0.0670.0000.0000.0000.000
195A195VAL00.0010.00117.774-0.069-0.0690.0000.0000.0000.000
196A196GLU-1-0.830-0.88520.0720.4090.4090.0000.0000.0000.000
197A197ARG10.9590.98414.193-0.840-0.8400.0000.0000.0000.000
198A198VAL0-0.0060.00621.693-0.044-0.0440.0000.0000.0000.000
199A199LEU0-0.019-0.02723.804-0.037-0.0370.0000.0000.0000.000
200A200ALA00.0430.03524.734-0.027-0.0270.0000.0000.0000.000
201A201ALA0-0.0020.00125.360-0.026-0.0260.0000.0000.0000.000
202A202ARG10.8820.92427.178-0.321-0.3210.0000.0000.0000.000
203A203GLU-1-0.932-0.95529.3920.2170.2170.0000.0000.0000.000
204A204ASN0-0.051-0.03529.154-0.025-0.0250.0000.0000.0000.000
205A205ALA0-0.0650.00731.469-0.015-0.0150.0000.0000.0000.000
206A206MET0-0.097-0.05833.214-0.024-0.0240.0000.0000.0000.000