FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 2JK4R

Calculation Name: 5MQH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MQH

Chain ID: A

ChEMBL ID:

UniProt ID: P37475

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2735261.22313
FMO2-HF: Nuclear repulsion 2644843.160994
FMO2-HF: Total energy -90418.062136
FMO2-MP2: Total energy -90677.731605


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:587:HIS)


Summations of interaction energy for fragment #1(A:587:HIS)
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.
0.6452.432-0.015-0.781-0.9910.001
Interaction energy analysis for fragmet #1(A:587:HIS)
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 : -0.017
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].
3A589HIS00.000-0.0083.8600.8952.595-0.014-0.757-0.9290.001
4A590SER00.0330.0065.9600.4010.4010.0000.0000.0000.000
5A591TYR0-0.059-0.0128.6830.2750.2750.0000.0000.0000.000
6A592ARG10.8530.92710.2650.9840.9840.0000.0000.0000.000
7A593VAL00.0110.01112.5770.1660.1660.0000.0000.0000.000
8A594SER0-0.053-0.01115.669-0.013-0.0130.0000.0000.0000.000
9A595THR00.0370.00618.3950.0220.0220.0000.0000.0000.000
10A596GLY0-0.006-0.00521.0380.0020.0020.0000.0000.0000.000
11A597ALA0-0.021-0.02124.536-0.006-0.0060.0000.0000.0000.000
12A598ALA00.0180.03527.2610.0070.0070.0000.0000.0000.000
13A599HIS00.0470.01829.006-0.014-0.0140.0000.0000.0000.000
14A600ALA0-0.036-0.00933.1340.0060.0060.0000.0000.0000.000
15A601ALA00.0260.01336.831-0.002-0.0020.0000.0000.0000.000
16A602LYS10.8940.92339.1210.1110.1110.0000.0000.0000.000
17A603GLY0-0.062-0.03642.7100.0030.0030.0000.0000.0000.000
18A604GLY0-0.027-0.00142.2110.0040.0040.0000.0000.0000.000
19A605GLY0-0.0210.00141.9290.0030.0030.0000.0000.0000.000
20A606LEU0-0.025-0.03838.684-0.005-0.0050.0000.0000.0000.000
21A607VAL0-0.056-0.03135.469-0.006-0.0060.0000.0000.0000.000
22A608SER00.0110.01633.9810.0050.0050.0000.0000.0000.000
23A609GLY0-0.053-0.03735.4230.0010.0010.0000.0000.0000.000
24A610ASP-1-0.756-0.83132.824-0.183-0.1830.0000.0000.0000.000
25A611SER0-0.106-0.04629.575-0.001-0.0010.0000.0000.0000.000
26A612TYR00.000-0.03425.253-0.016-0.0160.0000.0000.0000.000
27A613SER0-0.0070.00022.5050.0170.0170.0000.0000.0000.000
28A614MET0-0.031-0.02019.725-0.013-0.0130.0000.0000.0000.000
29A615MET0-0.031-0.00716.8960.0060.0060.0000.0000.0000.000
30A616GLU-1-0.916-0.96710.379-1.540-1.5400.0000.0000.0000.000
31A617LEU0-0.0360.00712.562-0.054-0.0540.0000.0000.0000.000
32A618GLY0-0.005-0.00911.305-0.046-0.0460.0000.0000.0000.000
33A619ALA0-0.009-0.0156.002-0.118-0.1180.0000.0000.0000.000
34A620ARG10.8710.9086.5670.5500.5500.0000.0000.0000.000
35A621LYS10.8270.9358.2390.7530.7530.0000.0000.0000.000
36A622TYR00.0560.03711.806-0.060-0.0600.0000.0000.0000.000
37A623ALA0-0.0040.01114.3700.0590.0590.0000.0000.0000.000
38A624ILE0-0.009-0.01017.906-0.005-0.0050.0000.0000.0000.000
39A625ALA00.012-0.00221.2850.0190.0190.0000.0000.0000.000
40A626ILE00.0180.00824.574-0.004-0.0040.0000.0000.0000.000
41A627SER00.017-0.01428.1860.0010.0010.0000.0000.0000.000
42A628ASP-1-0.800-0.88230.977-0.140-0.1400.0000.0000.0000.000
43A629GLY00.0100.00334.6870.0040.0040.0000.0000.0000.000
44A630MET0-0.0790.02330.7550.0000.0000.0000.0000.0000.000
45A631GLY00.0450.02334.0210.0110.0110.0000.0000.0000.000
46A632ASN0-0.024-0.01436.004-0.005-0.0050.0000.0000.0000.000
47A633GLY00.041-0.00136.4580.0080.0080.0000.0000.0000.000
48A634ALA0-0.027-0.01033.695-0.007-0.0070.0000.0000.0000.000
49A635ARG10.9390.95932.7050.0380.0380.0000.0000.0000.000
50A636ALA00.0530.03633.4640.0000.0000.0000.0000.0000.000
51A637HIS00.1260.06029.760-0.010-0.0100.0000.0000.0000.000
52A638PHE0-0.081-0.02827.509-0.008-0.0080.0000.0000.0000.000
53A639GLU-1-0.925-0.97628.935-0.070-0.0700.0000.0000.0000.000
54A640SER00.053-0.01629.5850.0000.0000.0000.0000.0000.000
55A641ASN00.0250.00524.891-0.016-0.0160.0000.0000.0000.000
56A642GLU-1-0.894-0.91224.845-0.095-0.0950.0000.0000.0000.000
57A643THR00.015-0.01225.902-0.005-0.0050.0000.0000.0000.000
58A644ILE00.0640.03322.942-0.005-0.0050.0000.0000.0000.000
59A645LYS10.8650.92721.0500.0820.0820.0000.0000.0000.000
60A646LEU0-0.102-0.04622.061-0.006-0.0060.0000.0000.0000.000
61A647LEU00.0270.00323.862-0.008-0.0080.0000.0000.0000.000
62A648GLU-1-0.876-0.94719.210-0.357-0.3570.0000.0000.0000.000
63A649LYS10.8790.94016.8180.1610.1610.0000.0000.0000.000
64A650ILE0-0.015-0.00320.562-0.001-0.0010.0000.0000.0000.000
65A651LEU00.0750.05420.7080.0000.0000.0000.0000.0000.000
66A652GLU-1-0.864-0.93116.122-0.513-0.5130.0000.0000.0000.000
67A653SER0-0.104-0.05617.560-0.003-0.0030.0000.0000.0000.000
68A654GLY0-0.019-0.00719.9570.0140.0140.0000.0000.0000.000
69A655ILE0-0.071-0.01920.4260.0220.0220.0000.0000.0000.000
70A656ASP-1-0.802-0.92524.108-0.152-0.1520.0000.0000.0000.000
71A657GLU-1-0.847-0.92825.042-0.222-0.2220.0000.0000.0000.000
72A658LYS10.9490.97227.6070.1350.1350.0000.0000.0000.000
73A659ILE0-0.024-0.01528.7340.0070.0070.0000.0000.0000.000
74A660ALA00.0470.04226.0290.0080.0080.0000.0000.0000.000
75A661ILE00.0730.04427.9640.0040.0040.0000.0000.0000.000
76A662LYS10.9550.99730.8150.0960.0960.0000.0000.0000.000
77A663THR0-0.113-0.07528.5840.0130.0130.0000.0000.0000.000
78A664ILE00.0220.01326.2760.0070.0070.0000.0000.0000.000
79A665ASN00.001-0.01630.4760.0070.0070.0000.0000.0000.000
80A666SER0-0.028-0.02033.5110.0080.0080.0000.0000.0000.000
81A667ILE0-0.095-0.05128.2760.0070.0070.0000.0000.0000.000
82A668LEU0-0.0070.01231.2180.0020.0020.0000.0000.0000.000
83A669SER00.033-0.00234.0020.0020.0020.0000.0000.0000.000
84A670LEU0-0.070-0.02534.1470.0080.0080.0000.0000.0000.000
85A671ARG10.8480.91830.0560.0810.0810.0000.0000.0000.000
86A672THR0-0.010-0.01135.247-0.009-0.0090.0000.0000.0000.000
87A673THR0-0.078-0.03437.6450.0060.0060.0000.0000.0000.000
88A674ASP-1-0.828-0.91640.977-0.068-0.0680.0000.0000.0000.000
89A675GLU-1-0.926-0.95243.547-0.067-0.0670.0000.0000.0000.000
90A676ILE0-0.095-0.03738.170-0.002-0.0020.0000.0000.0000.000
91A677TYR0-0.058-0.04439.750-0.001-0.0010.0000.0000.0000.000
92A678SER0-0.041-0.00934.784-0.003-0.0030.0000.0000.0000.000
93A679THR0-0.0070.00432.9020.0020.0020.0000.0000.0000.000
94A680LEU0-0.063-0.04926.749-0.003-0.0030.0000.0000.0000.000
95A681ASP-1-0.839-0.89827.855-0.235-0.2350.0000.0000.0000.000
96A682LEU0-0.040-0.03121.485-0.012-0.0120.0000.0000.0000.000
97A683SER00.024-0.00921.4580.0170.0170.0000.0000.0000.000
98A684ILE0-0.027-0.01715.812-0.035-0.0350.0000.0000.0000.000
99A685ILE00.001-0.00814.1530.0190.0190.0000.0000.0000.000
100A686ASP-1-0.774-0.87210.065-1.276-1.2760.0000.0000.0000.000
101A687LEU00.009-0.0128.7290.0060.0060.0000.0000.0000.000
102A688GLN0-0.052-0.0303.7630.3490.436-0.001-0.024-0.0620.000
103A689ASP-1-0.815-0.8958.486-0.621-0.6210.0000.0000.0000.000
104A690ALA0-0.0030.02212.0700.1040.1040.0000.0000.0000.000
105A691SER0-0.045-0.03014.2020.0960.0960.0000.0000.0000.000
106A692CYS0-0.027-0.02115.796-0.084-0.0840.0000.0000.0000.000
107A693LYS10.8320.91817.6380.4440.4440.0000.0000.0000.000
108A694PHE00.036-0.00120.615-0.037-0.0370.0000.0000.0000.000
109A695LEU0-0.023-0.01623.7260.0190.0190.0000.0000.0000.000
110A696LYS10.8230.89826.4060.1750.1750.0000.0000.0000.000
111A697VAL00.0260.02329.8450.0110.0110.0000.0000.0000.000
112A698GLY00.1330.06832.851-0.001-0.0010.0000.0000.0000.000
113A699SER0-0.014-0.01735.594-0.002-0.0020.0000.0000.0000.000
114A700THR0-0.0040.00133.5810.0060.0060.0000.0000.0000.000
115A701PRO0-0.058-0.00932.631-0.009-0.0090.0000.0000.0000.000
116A702SER00.0580.02227.345-0.014-0.0140.0000.0000.0000.000
117A703PHE0-0.034-0.04228.5150.0170.0170.0000.0000.0000.000
118A704ILE00.0430.03524.034-0.025-0.0250.0000.0000.0000.000
119A705LYS10.8610.92826.3510.2990.2990.0000.0000.0000.000
120A706ARG10.8060.88222.4620.3400.3400.0000.0000.0000.000
121A707GLY00.0000.00226.9460.0230.0230.0000.0000.0000.000
122A708ASP-1-0.836-0.92029.259-0.225-0.2250.0000.0000.0000.000
123A709GLN0-0.114-0.05130.3910.0110.0110.0000.0000.0000.000
124A710VAL00.016-0.00730.508-0.014-0.0140.0000.0000.0000.000
125A711MET0-0.043-0.00727.5040.0230.0230.0000.0000.0000.000
126A712LYS10.8870.94629.9680.1570.1570.0000.0000.0000.000
127A713VAL0-0.037-0.01226.2290.0070.0070.0000.0000.0000.000
128A714GLN0-0.009-0.01829.4070.0070.0070.0000.0000.0000.000
129A715ALA00.0160.02530.328-0.004-0.0040.0000.0000.0000.000
130A716SER0-0.056-0.03631.9150.0050.0050.0000.0000.0000.000
131A717ASN00.0100.01234.7990.0020.0020.0000.0000.0000.000
132A718LEU00.008-0.00334.3590.0010.0010.0000.0000.0000.000
133A719PRO0-0.020-0.01536.7490.0040.0040.0000.0000.0000.000
134A720ILE00.0730.03440.1310.0010.0010.0000.0000.0000.000
135A721GLY0-0.024-0.01043.3450.0030.0030.0000.0000.0000.000
136A722ILE0-0.082-0.03637.4340.0040.0040.0000.0000.0000.000
137A723ILE00.0050.00540.118-0.003-0.0030.0000.0000.0000.000
138A724ASN0-0.016-0.01834.770-0.003-0.0030.0000.0000.0000.000
139A725GLU-1-0.880-0.90938.115-0.083-0.0830.0000.0000.0000.000
140A726PHE00.0300.01435.3330.0010.0010.0000.0000.0000.000
141A727ASP-1-0.958-0.97835.939-0.124-0.1240.0000.0000.0000.000
142A728VAL0-0.026-0.01230.312-0.010-0.0100.0000.0000.0000.000
143A729GLU-1-0.855-0.91230.704-0.179-0.1790.0000.0000.0000.000
144A730VAL00.000-0.01425.054-0.010-0.0100.0000.0000.0000.000
145A731VAL00.0010.02025.7960.0130.0130.0000.0000.0000.000
146A732SER0-0.010-0.02121.544-0.034-0.0340.0000.0000.0000.000
147A733GLU-1-0.929-0.95621.654-0.263-0.2630.0000.0000.0000.000
148A734GLN0-0.114-0.06216.093-0.014-0.0140.0000.0000.0000.000
149A735LEU0-0.009-0.00817.9960.0380.0380.0000.0000.0000.000
150A736LYS10.9240.94918.2280.3430.3430.0000.0000.0000.000
151A737ALA00.0330.01416.992-0.010-0.0100.0000.0000.0000.000
152A738GLY0-0.052-0.02718.6750.0590.0590.0000.0000.0000.000
153A739ASP-1-0.773-0.85420.996-0.393-0.3930.0000.0000.0000.000
154A740LEU0-0.004-0.00921.855-0.040-0.0400.0000.0000.0000.000
155A741LEU00.0190.02320.9860.0270.0270.0000.0000.0000.000
156A742ILE0-0.020-0.02224.337-0.013-0.0130.0000.0000.0000.000
157A743MET0-0.0150.01724.696-0.004-0.0040.0000.0000.0000.000
158A744MET0-0.007-0.02128.4140.0020.0020.0000.0000.0000.000
159A745SER00.0570.02431.619-0.001-0.0010.0000.0000.0000.000
160A746ASP-1-0.788-0.92133.777-0.159-0.1590.0000.0000.0000.000
161A747GLY00.0510.04037.1300.0050.0050.0000.0000.0000.000
162A748ILE0-0.073-0.05034.5490.0050.0050.0000.0000.0000.000
163A749PHE0-0.037-0.03636.1540.0000.0000.0000.0000.0000.000
164A750GLU-1-0.937-0.97137.922-0.128-0.1280.0000.0000.0000.000
165A751GLY00.0100.02540.6700.0080.0080.0000.0000.0000.000
166A752PRO0-0.064-0.02940.9430.0070.0070.0000.0000.0000.000
167A753LYS10.8720.93043.9670.1070.1070.0000.0000.0000.000
168A754HIS0-0.056-0.03847.774-0.002-0.0020.0000.0000.0000.000
169A755VAL0-0.0010.00643.924-0.001-0.0010.0000.0000.0000.000
170A756GLU-1-0.915-0.94146.664-0.105-0.1050.0000.0000.0000.000
171A757ASN0-0.025-0.02142.396-0.007-0.0070.0000.0000.0000.000
172A758HIS00.1120.04840.458-0.005-0.0050.0000.0000.0000.000
173A759ASP-1-0.816-0.89537.518-0.179-0.1790.0000.0000.0000.000
174A760LEU0-0.039-0.03437.985-0.009-0.0090.0000.0000.0000.000
175A761TRP00.0270.00839.120-0.005-0.0050.0000.0000.0000.000
176A762MET00.0610.03835.587-0.007-0.0070.0000.0000.0000.000
177A763LYS10.9060.95434.9260.1700.1700.0000.0000.0000.000
178A764ARG10.8890.94736.3430.1340.1340.0000.0000.0000.000
179A765LYS10.8330.91537.6200.1540.1540.0000.0000.0000.000
180A766MET00.0100.02031.971-0.009-0.0090.0000.0000.0000.000
181A767LYS10.8630.91033.8790.1860.1860.0000.0000.0000.000
182A768GLY0-0.0210.00435.496-0.001-0.0010.0000.0000.0000.000
183A769LEU00.0040.02331.8520.0080.0080.0000.0000.0000.000
184A770LYS10.8500.90933.7470.1930.1930.0000.0000.0000.000
185A771THR0-0.037-0.04429.847-0.018-0.0180.0000.0000.0000.000
186A772ASN00.0390.00624.9710.0210.0210.0000.0000.0000.000
187A773ASP-1-0.835-0.91924.958-0.452-0.4520.0000.0000.0000.000
188A774PRO00.002-0.01022.0300.0290.0290.0000.0000.0000.000
189A775GLN00.015-0.00425.321-0.005-0.0050.0000.0000.0000.000
190A776GLU-1-0.878-0.90027.117-0.256-0.2560.0000.0000.0000.000
191A777ILE0-0.056-0.03527.4700.0260.0260.0000.0000.0000.000
192A778ALA0-0.011-0.00128.3450.0190.0190.0000.0000.0000.000
193A779ASP-1-0.818-0.91430.365-0.234-0.2340.0000.0000.0000.000
194A780LEU0-0.068-0.03333.0590.0200.0200.0000.0000.0000.000
195A781LEU0-0.043-0.02431.9230.0160.0160.0000.0000.0000.000
196A782MET00.0430.03034.1240.0180.0180.0000.0000.0000.000
197A783GLU-1-0.777-0.85236.554-0.142-0.1420.0000.0000.0000.000
198A784GLU-1-0.787-0.87538.629-0.148-0.1480.0000.0000.0000.000
199A785VAL0-0.0050.00238.7170.0100.0100.0000.0000.0000.000
200A786ILE00.0170.02139.3760.0110.0110.0000.0000.0000.000
201A787ARG10.7210.81841.5680.1570.1570.0000.0000.0000.000
202A788THR0-0.096-0.05343.9620.0080.0080.0000.0000.0000.000
203A789ARG10.7640.86543.4880.1260.1260.0000.0000.0000.000
204A790SER0-0.066-0.04247.5150.0060.0060.0000.0000.0000.000
205A791GLY0-0.013-0.00145.5240.0050.0050.0000.0000.0000.000
206A792GLN0-0.072-0.03945.654-0.005-0.0050.0000.0000.0000.000
207A793ILE00.0440.02040.819-0.004-0.0040.0000.0000.0000.000
208A794GLU-1-0.713-0.82044.416-0.097-0.0970.0000.0000.0000.000
209A795ASP-1-0.867-0.93240.863-0.112-0.1120.0000.0000.0000.000
210A796ASP-1-0.793-0.87637.013-0.135-0.1350.0000.0000.0000.000
211A797MET0-0.058-0.01936.770-0.001-0.0010.0000.0000.0000.000
212A798THR00.032-0.02130.415-0.006-0.0060.0000.0000.0000.000
213A799VAL0-0.024-0.01030.0010.0010.0010.0000.0000.0000.000
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