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: 72ZLK

Calculation Name: 5IFH-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFH

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptH
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1656935.545048
FMO2-HF: Nuclear repulsion 1588758.073196
FMO2-HF: Total energy -68177.471852
FMO2-MP2: Total energy -68374.313469


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(H:2:VAL)


Summations of interaction energy for fragment #1(H:2:VAL)
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.
-8.287-5.89816.64-6.486-12.542-0.034
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.037
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].
3H4LEU0-0.026-0.0173.809-0.6531.828-0.040-1.257-1.1840.002
4H5VAL00.0300.0216.558-0.157-0.1570.0000.0000.0000.000
5H6GLU-1-0.765-0.87410.148-0.145-0.1450.0000.0000.0000.000
6H7SER0-0.045-0.02713.1360.0180.0180.0000.0000.0000.000
7H8GLY00.0220.00316.7190.0010.0010.0000.0000.0000.000
8H9GLY0-0.0010.01619.499-0.005-0.0050.0000.0000.0000.000
9H10GLY00.0310.00221.1470.0080.0080.0000.0000.0000.000
10H11LEU0-0.042-0.00724.608-0.009-0.0090.0000.0000.0000.000
11H12VAL0-0.005-0.00427.0710.0090.0090.0000.0000.0000.000
12H13LYS10.9270.98029.799-0.011-0.0110.0000.0000.0000.000
13H14PRO00.0350.00632.4250.0030.0030.0000.0000.0000.000
14H15GLY0-0.034-0.01033.0120.0020.0020.0000.0000.0000.000
15H16GLY0-0.0230.00031.8780.0050.0050.0000.0000.0000.000
16H17SER0-0.035-0.03828.440-0.003-0.0030.0000.0000.0000.000
17H18LEU0-0.009-0.00823.3990.0020.0020.0000.0000.0000.000
18H19ARG10.9240.98820.494-0.136-0.1360.0000.0000.0000.000
19H20LEU0-0.0010.01517.5430.0050.0050.0000.0000.0000.000
20H21SER0-0.013-0.01815.2250.0270.0270.0000.0000.0000.000
21H22CYS0-0.075-0.02810.0330.0360.0360.0000.0000.0000.000
22H23ALA00.0090.00710.1570.0560.0560.0000.0000.0000.000
23H24ALA00.0270.0095.972-0.094-0.0940.0000.0000.0000.000
24H25SER0-0.032-0.0194.3870.1560.370-0.001-0.081-0.1310.000
25H26GLY00.1000.0432.165-0.019-0.2848.301-4.887-3.149-0.019
26H27PHE0-0.027-0.0162.159-3.751-5.0606.2080.519-5.418-0.014
27H28THR00.009-0.0033.746-0.227-0.0940.010-0.035-0.1090.000
28H29PHE00.0770.0357.412-0.180-0.1800.0000.0000.0000.000
29H30ARG10.9780.9808.463-0.488-0.4880.0000.0000.0000.000
30H31SER0-0.051-0.0279.451-0.064-0.0640.0000.0000.0000.000
31H32TYR00.0340.0296.4490.0270.0270.0000.0000.0000.000
32H33SER0-0.010-0.0059.7660.0570.0570.0000.0000.0000.000
33H34MET0-0.0430.0007.6320.0090.0090.0000.0000.0000.000
34H35ASN0-0.0180.00511.3440.0390.0390.0000.0000.0000.000
35H36TRP00.0250.01012.774-0.017-0.0170.0000.0000.0000.000
36H37VAL00.0060.00214.4350.0100.0100.0000.0000.0000.000
37H38ARG10.8030.90416.1140.0630.0630.0000.0000.0000.000
38H39GLN00.0260.00518.725-0.027-0.0270.0000.0000.0000.000
39H40ALA00.0410.03220.7380.0050.0050.0000.0000.0000.000
40H41PRO00.0380.00024.061-0.013-0.0130.0000.0000.0000.000
41H42GLY00.0120.01124.6550.0080.0080.0000.0000.0000.000
42H43LYS10.8720.94424.8600.1010.1010.0000.0000.0000.000
43H44GLY00.0440.02022.636-0.014-0.0140.0000.0000.0000.000
44H45LEU0-0.012-0.00616.2510.0110.0110.0000.0000.0000.000
45H46GLU-1-0.799-0.88819.835-0.075-0.0750.0000.0000.0000.000
46H47TRP0-0.024-0.02716.965-0.003-0.0030.0000.0000.0000.000
47H48VAL0-0.0100.00018.5530.0160.0160.0000.0000.0000.000
48H49SER0-0.006-0.03418.4060.0220.0220.0000.0000.0000.000
49H50SER00.001-0.00215.982-0.018-0.0180.0000.0000.0000.000
50H51ILE0-0.0210.00314.4240.0140.0140.0000.0000.0000.000
51H52ILE00.0130.00514.5530.0030.0030.0000.0000.0000.000
52H53SER00.0330.02012.8280.0210.0210.0000.0000.0000.000
53H54SER0-0.062-0.02314.836-0.025-0.0250.0000.0000.0000.000
54H55SER00.019-0.00517.6040.0070.0070.0000.0000.0000.000
55H56SER0-0.051-0.01618.2270.0070.0070.0000.0000.0000.000
56H57TYR00.0190.01319.171-0.003-0.0030.0000.0000.0000.000
57H58ILE0-0.001-0.00819.555-0.002-0.0020.0000.0000.0000.000
58H59TYR0-0.0010.00719.833-0.006-0.0060.0000.0000.0000.000
59H60TYR0-0.004-0.01121.1260.0050.0050.0000.0000.0000.000
60H61ALA00.0800.05423.290-0.002-0.0020.0000.0000.0000.000
61H62ASP-1-0.897-0.96524.831-0.030-0.0300.0000.0000.0000.000
62H63SER0-0.065-0.01926.6320.0060.0060.0000.0000.0000.000
63H64VAL0-0.029-0.02923.4970.0030.0030.0000.0000.0000.000
64H65LYS10.9941.00126.8410.0240.0240.0000.0000.0000.000
65H66GLY0-0.009-0.00128.102-0.001-0.0010.0000.0000.0000.000
66H67ARG10.7760.88128.1750.0160.0160.0000.0000.0000.000
67H68PHE00.0180.00222.3380.0070.0070.0000.0000.0000.000
68H69THR0-0.037-0.01622.7880.0020.0020.0000.0000.0000.000
69H70ILE00.0010.02415.4840.0100.0100.0000.0000.0000.000
70H71SER0-0.021-0.02117.7620.0110.0110.0000.0000.0000.000
71H72ARG10.8740.94510.989-0.255-0.2550.0000.0000.0000.000
72H73ASP-1-0.870-0.93414.7750.3070.3070.0000.0000.0000.000
73H74ASN0-0.028-0.04113.2870.0800.0800.0000.0000.0000.000
74H75ALA00.0090.02313.4620.0710.0710.0000.0000.0000.000
75H76LYS10.9290.96614.064-0.314-0.3140.0000.0000.0000.000
76H77ASN0-0.042-0.0067.890-0.109-0.1090.0000.0000.0000.000
77H78SER00.0250.02010.1010.0430.0430.0000.0000.0000.000
78H79LEU00.007-0.01211.638-0.026-0.0260.0000.0000.0000.000
79H80TYR0-0.023-0.02413.437-0.004-0.0040.0000.0000.0000.000
80H81LEU00.0320.00316.927-0.015-0.0150.0000.0000.0000.000
81H82GLN0-0.039-0.02719.2520.0080.0080.0000.0000.0000.000
82H83MET0-0.0240.00222.419-0.013-0.0130.0000.0000.0000.000
83H84ASN00.0960.05124.9880.0060.0060.0000.0000.0000.000
84H85SER00.0100.00128.766-0.006-0.0060.0000.0000.0000.000
85H86LEU0-0.0130.01125.949-0.006-0.0060.0000.0000.0000.000
86H87ARG11.0040.99929.7370.0230.0230.0000.0000.0000.000
87H88ALA00.0640.02529.904-0.002-0.0020.0000.0000.0000.000
88H89GLU-1-0.905-0.96829.652-0.039-0.0390.0000.0000.0000.000
89H90ASP-1-0.817-0.88725.817-0.035-0.0350.0000.0000.0000.000
90H91THR0-0.033-0.00124.7430.0000.0000.0000.0000.0000.000
91H92ALA0-0.017-0.01321.670-0.009-0.0090.0000.0000.0000.000
92H93LEU0-0.0180.01216.5530.0210.0210.0000.0000.0000.000
93H94TYR0-0.045-0.04917.040-0.014-0.0140.0000.0000.0000.000
94H95TYR00.014-0.00212.2350.0010.0010.0000.0000.0000.000
95H97ALA00.0570.0178.247-0.122-0.1220.0000.0000.0000.000
96H98ARG10.8240.9033.200-0.6570.3490.505-0.385-1.126-0.002
97H99ASP-1-0.871-0.9127.963-0.327-0.3270.0000.0000.0000.000
98H100GLN0-0.005-0.0149.7620.0220.0220.0000.0000.0000.000
99H101ASN0-0.033-0.01112.864-0.022-0.0220.0000.0000.0000.000
100H102ALA00.003-0.01712.3520.0010.0010.0000.0000.0000.000
101H103MET0-0.0130.0059.987-0.006-0.0060.0000.0000.0000.000
102H104ASP-1-0.763-0.8815.546-0.879-0.8790.0000.0000.0000.000
103H105VAL0-0.055-0.0252.384-0.809-0.7241.658-0.360-1.383-0.001
104H106TRP00.003-0.0165.3860.3460.390-0.0010.000-0.0420.000
105H107GLY00.0320.0266.798-0.306-0.3060.0000.0000.0000.000
106H108GLN0-0.055-0.0468.7080.0600.0600.0000.0000.0000.000
107H109GLY00.0220.03111.8600.0500.0500.0000.0000.0000.000
108H110THR0-0.048-0.01913.8500.0330.0330.0000.0000.0000.000
109H111THR00.028-0.00317.083-0.010-0.0100.0000.0000.0000.000
110H112VAL0-0.0140.00420.6280.0200.0200.0000.0000.0000.000
111H113THR0-0.028-0.02323.220-0.012-0.0120.0000.0000.0000.000
112H114VAL0-0.0030.00626.8350.0100.0100.0000.0000.0000.000
113H115SER00.0280.00129.578-0.004-0.0040.0000.0000.0000.000
114H116SER00.019-0.00732.8920.0050.0050.0000.0000.0000.000
115H117ASP-1-0.920-0.94335.055-0.014-0.0140.0000.0000.0000.000
116H118SER0-0.043-0.03734.7270.0020.0020.0000.0000.0000.000
117H119ALA00.0090.00731.821-0.003-0.0030.0000.0000.0000.000
118H120SER0-0.030-0.01633.1370.0020.0020.0000.0000.0000.000
119H121ALA0-0.003-0.00432.699-0.003-0.0030.0000.0000.0000.000
120H122PRO00.0110.01731.435-0.001-0.0010.0000.0000.0000.000
121H123THR0-0.0080.00034.4270.0060.0060.0000.0000.0000.000
122H124LEU0-0.025-0.02133.571-0.003-0.0030.0000.0000.0000.000
123H125PHE0-0.008-0.00637.6340.0040.0040.0000.0000.0000.000
124H126PRO0-0.0110.00239.389-0.003-0.0030.0000.0000.0000.000
125H127LEU0-0.0170.00038.6820.0000.0000.0000.0000.0000.000
126H128VAL00.017-0.00341.3750.0000.0000.0000.0000.0000.000
127H129SER00.0220.02343.6350.0000.0000.0000.0000.0000.000
128H142VAL0-0.011-0.01137.1330.0010.0010.0000.0000.0000.000
129H143GLY00.0310.00736.892-0.005-0.0050.0000.0000.0000.000
130H144CYS0-0.072-0.02732.6680.0020.0020.0000.0000.0000.000
131H145LEU00.0130.02035.470-0.005-0.0050.0000.0000.0000.000
132H146ALA00.0370.03033.3260.0050.0050.0000.0000.0000.000
133H147GLN0-0.016-0.02535.378-0.006-0.0060.0000.0000.0000.000
134H148ASP-1-0.833-0.93636.463-0.012-0.0120.0000.0000.0000.000
135H149PHE0-0.0520.00429.7510.0050.0050.0000.0000.0000.000
136H150LEU0-0.0180.00431.088-0.007-0.0070.0000.0000.0000.000
137H151PRO00.0590.00726.6140.0070.0070.0000.0000.0000.000
138H152ASP-1-0.810-0.91227.456-0.065-0.0650.0000.0000.0000.000
139H153SER0-0.069-0.03523.555-0.008-0.0080.0000.0000.0000.000
140H154ILE00.0090.01425.0370.0120.0120.0000.0000.0000.000
141H155THR0-0.0220.00422.232-0.017-0.0170.0000.0000.0000.000
142H156PHE00.025-0.00425.2860.0130.0130.0000.0000.0000.000
143H157SER0-0.060-0.02525.517-0.003-0.0030.0000.0000.0000.000
144H158TRP00.0550.00727.2320.0070.0070.0000.0000.0000.000
145H171GLY0-0.007-0.02127.8340.0040.0040.0000.0000.0000.000
146H172PHE0-0.028-0.00428.871-0.007-0.0070.0000.0000.0000.000
147H173PRO0-0.0040.00728.3420.0020.0020.0000.0000.0000.000
148H174SER0-0.018-0.02728.8170.0070.0070.0000.0000.0000.000
149H175VAL0-0.030-0.00130.961-0.004-0.0040.0000.0000.0000.000
150H176LEU0-0.015-0.01233.5730.0040.0040.0000.0000.0000.000
151H177ARG10.9280.94735.3070.0320.0320.0000.0000.0000.000
152H178GLY00.0380.02238.8250.0020.0020.0000.0000.0000.000
153H179GLY00.0300.02036.9110.0030.0030.0000.0000.0000.000
154H180LYS10.8660.93634.9320.0110.0110.0000.0000.0000.000
155H181TYR00.0400.02030.420-0.002-0.0020.0000.0000.0000.000
156H182ALA0-0.052-0.02333.7400.0060.0060.0000.0000.0000.000
157H183ALA00.0300.01530.924-0.006-0.0060.0000.0000.0000.000
158H184THR00.0270.00532.9280.0080.0080.0000.0000.0000.000
159H185SER0-0.0180.01530.321-0.005-0.0050.0000.0000.0000.000
160H186GLN00.030-0.01132.3200.0020.0020.0000.0000.0000.000
161H187VAL0-0.0100.01731.589-0.005-0.0050.0000.0000.0000.000
162H203VAL0-0.033-0.02533.0650.0000.0000.0000.0000.0000.000
163H205LYS10.9710.98229.499-0.020-0.0200.0000.0000.0000.000
164H206VAL00.0210.02128.409-0.007-0.0070.0000.0000.0000.000
165H207GLN0-0.019-0.02523.8380.0030.0030.0000.0000.0000.000
166H208HIS00.0490.01326.181-0.005-0.0050.0000.0000.0000.000
167H209PRO00.0180.01924.8410.0100.0100.0000.0000.0000.000
168H210ASN0-0.008-0.01126.5040.0050.0050.0000.0000.0000.000
169H211GLY0-0.035-0.02429.6450.0040.0040.0000.0000.0000.000
170H212ASN0-0.026-0.00625.970-0.004-0.0040.0000.0000.0000.000
171H213LYS10.9490.98630.115-0.013-0.0130.0000.0000.0000.000
172H214GLU-1-0.898-0.95231.9760.0170.0170.0000.0000.0000.000
173H215LYS10.9420.97534.1190.0020.0020.0000.0000.0000.000
174H216ASN0-0.006-0.00236.496-0.001-0.0010.0000.0000.0000.000
175H217VAL00.0200.00737.372-0.001-0.0010.0000.0000.0000.000
176H218PRO00.0070.02139.9540.0000.0000.0000.0000.0000.000