FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 98M22

Calculation Name: 4M98-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M98

Chain ID: A

ChEMBL ID:

UniProt ID: Q5FAE1

Base Structure: X-ray

Registration Date: 2023-09-22

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2013926.988491
FMO2-HF: Nuclear repulsion 1941250.293597
FMO2-HF: Total energy -72676.694894
FMO2-MP2: Total energy -72889.654052


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:199:ASN)


Summations of interaction energy for fragment #1(A:199:ASN)
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.
-49.211-40.85822.861-11.372-19.842-0.082
Interaction energy analysis for fragmet #1(A:199:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.033
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].
3A201LYS10.8070.9182.750-3.841-1.5090.077-1.058-1.3510.003
4A202LEU00.0240.0232.870-4.503-3.3890.314-0.676-0.753-0.008
5A203ALA0-0.013-0.0095.6511.2181.2180.0000.0000.0000.000
6A204VAL0-0.016-0.0128.367-0.352-0.3520.0000.0000.0000.000
7A205ILE00.0230.00510.9750.3620.3620.0000.0000.0000.000
8A206GLY00.0090.00013.7450.0100.0100.0000.0000.0000.000
9A207ALA00.007-0.01016.691-0.071-0.0710.0000.0000.0000.000
10A208GLY00.0070.00518.4180.0830.0830.0000.0000.0000.000
11A209GLY0-0.008-0.01620.537-0.038-0.0380.0000.0000.0000.000
12A210HIS0-0.008-0.01117.9750.0420.0420.0000.0000.0000.000
13A211GLY00.1080.03916.739-0.082-0.0820.0000.0000.0000.000
14A212LYS10.8110.89216.3790.4840.4840.0000.0000.0000.000
15A213VAL00.0200.01917.577-0.038-0.0380.0000.0000.0000.000
16A214VAL00.0090.00612.615-0.031-0.0310.0000.0000.0000.000
17A215ALA00.0290.02112.902-0.195-0.1950.0000.0000.0000.000
18A216GLU-1-0.852-0.93213.936-0.646-0.6460.0000.0000.0000.000
19A217LEU0-0.063-0.02012.9780.0750.0750.0000.0000.0000.000
20A218ALA00.0260.0059.9310.0040.0040.0000.0000.0000.000
21A219ALA0-0.029-0.02311.5470.0100.0100.0000.0000.0000.000
22A220ALA0-0.045-0.02313.8130.1210.1210.0000.0000.0000.000
23A221LEU0-0.018-0.0089.3510.1000.1000.0000.0000.0000.000
24A222GLY0-0.0190.00111.9740.0830.0830.0000.0000.0000.000
25A223THR0-0.023-0.0126.7910.3840.3840.0000.0000.0000.000
26A224TYR0-0.072-0.0443.2901.6482.0010.012-0.076-0.2890.000
27A225GLY0-0.025-0.0106.9900.4390.4390.0000.0000.0000.000
28A226GLU-1-0.802-0.9227.6000.8120.8120.0000.0000.0000.000
29A227ILE00.0100.0227.268-0.629-0.6290.0000.0000.0000.000
30A228VAL0-0.018-0.0068.6710.3730.3730.0000.0000.0000.000
31A229PHE0-0.021-0.00811.009-0.292-0.2920.0000.0000.0000.000
32A230LEU0-0.0080.00911.9800.1230.1230.0000.0000.0000.000
33A231ASP-1-0.779-0.90714.613-0.730-0.7300.0000.0000.0000.000
34A232ASP-1-0.731-0.84718.360-0.582-0.5820.0000.0000.0000.000
35A233ARG10.7030.84519.8780.6700.6700.0000.0000.0000.000
36A234THR0-0.036-0.00620.8360.0530.0530.0000.0000.0000.000
37A235GLN00.0430.00820.768-0.002-0.0020.0000.0000.0000.000
38A236GLY00.0420.03020.5880.0060.0060.0000.0000.0000.000
39A237SER0-0.066-0.02718.604-0.006-0.0060.0000.0000.0000.000
40A238VAL00.0360.02118.5120.0280.0280.0000.0000.0000.000
41A239ASN0-0.036-0.02518.448-0.015-0.0150.0000.0000.0000.000
42A240GLY00.0410.03118.839-0.018-0.0180.0000.0000.0000.000
43A241PHE0-0.0010.01113.3550.0280.0280.0000.0000.0000.000
44A242PRO00.0140.00313.3760.0220.0220.0000.0000.0000.000
45A243VAL0-0.031-0.02614.355-0.132-0.1320.0000.0000.0000.000
46A244ILE0-0.022-0.00810.8500.0970.0970.0000.0000.0000.000
47A245GLY00.0320.01615.2180.1050.1050.0000.0000.0000.000
48A246THR0-0.0040.00116.711-0.097-0.0970.0000.0000.0000.000
49A247THR0-0.002-0.04515.653-0.008-0.0080.0000.0000.0000.000
50A248LEU00.0270.03015.077-0.070-0.0700.0000.0000.0000.000
51A249LEU00.0160.01413.3260.0660.0660.0000.0000.0000.000
52A250LEU0-0.049-0.0149.5960.0460.0460.0000.0000.0000.000
53A251GLU-1-0.820-0.91611.243-0.731-0.7310.0000.0000.0000.000
54A252ASN0-0.078-0.03713.9430.1730.1730.0000.0000.0000.000
55A253SER0-0.077-0.04912.8080.1170.1170.0000.0000.0000.000
56A254LEU0-0.040-0.0027.9540.2820.2820.0000.0000.0000.000
57A255SER00.0380.0146.437-0.022-0.0220.0000.0000.0000.000
58A256PRO00.0560.0183.8631.2861.5070.000-0.107-0.1130.000
59A257GLU-1-0.859-0.9102.070-10.540-8.8263.622-2.529-2.806-0.026
60A258GLN0-0.049-0.0262.957-0.8650.3702.239-0.815-2.6600.012
61A259PHE0-0.037-0.0282.986-5.643-4.2311.026-0.023-2.415-0.002
62A260ASP-1-0.738-0.8381.823-37.065-38.31714.184-5.570-7.363-0.063
63A261ILE0-0.036-0.0183.2094.1274.1670.0680.203-0.3110.001
64A262THR00.0350.0096.720-0.035-0.0350.0000.0000.0000.000
65A263VAL00.0380.0219.8130.2950.2950.0000.0000.0000.000
66A264ALA0-0.0160.02413.3960.1300.1300.0000.0000.0000.000
67A265VAL0-0.012-0.01416.1410.1810.1810.0000.0000.0000.000
68A266GLY00.0400.01818.988-0.013-0.0130.0000.0000.0000.000
69A267ASN0-0.027-0.01421.8360.0160.0160.0000.0000.0000.000
70A268ASN00.0640.01021.204-0.108-0.1080.0000.0000.0000.000
71A269ARG10.8700.92820.8730.5170.5170.0000.0000.0000.000
72A270ILE00.012-0.00619.583-0.029-0.0290.0000.0000.0000.000
73A271ARG10.7750.88016.0381.0351.0350.0000.0000.0000.000
74A272ARG10.7880.88316.3470.6170.6170.0000.0000.0000.000
75A273GLN0-0.024-0.02417.066-0.075-0.0750.0000.0000.0000.000
76A274ILE00.0050.00013.383-0.009-0.0090.0000.0000.0000.000
77A275THR0-0.013-0.02311.829-0.219-0.2190.0000.0000.0000.000
78A276GLU-1-0.807-0.88312.508-1.070-1.0700.0000.0000.0000.000
79A277ASN0-0.083-0.03613.801-0.056-0.0560.0000.0000.0000.000
80A278ALA00.0470.0109.1220.0150.0150.0000.0000.0000.000
81A279ALA00.014-0.0029.299-0.250-0.2500.0000.0000.0000.000
82A280ALA0-0.043-0.01510.9080.0810.0810.0000.0000.0000.000
83A281LEU0-0.037-0.01010.1810.1930.1930.0000.0000.0000.000
84A282GLY00.0130.0138.3180.1890.1890.0000.0000.0000.000
85A283PHE0-0.037-0.0244.715-0.714-0.604-0.001-0.001-0.1070.000
86A284LYS10.8210.9202.2314.3535.3471.321-0.712-1.6030.001
87A285LEU00.0180.0064.274-0.904-0.824-0.001-0.008-0.0710.000
88A286PRO00.0110.0134.9081.2751.2750.0000.0000.0000.000
89A287VAL0-0.017-0.0017.6680.5150.5150.0000.0000.0000.000
90A288LEU0-0.024-0.0148.6130.1010.1010.0000.0000.0000.000
91A289ILE00.0200.00412.2890.2450.2450.0000.0000.0000.000
92A290HIS00.0530.01414.654-0.018-0.0180.0000.0000.0000.000
93A291PRO00.008-0.00215.3480.0670.0670.0000.0000.0000.000
94A292ASP-1-0.806-0.87617.825-0.396-0.3960.0000.0000.0000.000
95A293ALA0-0.0160.00919.4460.0400.0400.0000.0000.0000.000
96A294THR0-0.048-0.03321.3840.0600.0600.0000.0000.0000.000
97A295VAL00.0180.00918.627-0.006-0.0060.0000.0000.0000.000
98A296SER00.0240.01621.0210.0340.0340.0000.0000.0000.000
99A297PRO0-0.005-0.00720.533-0.051-0.0510.0000.0000.0000.000
100A298SER0-0.011-0.01621.6170.0200.0200.0000.0000.0000.000
101A299ALA0-0.0170.01321.1840.0220.0220.0000.0000.0000.000
102A300ILE0-0.023-0.01919.055-0.024-0.0240.0000.0000.0000.000
103A301ILE0-0.012-0.01415.7900.0310.0310.0000.0000.0000.000
104A302GLY00.0410.04015.069-0.068-0.0680.0000.0000.0000.000
105A303GLN0-0.001-0.00210.019-0.430-0.4300.0000.0000.0000.000
106A304GLY00.0280.00210.1320.2900.2900.0000.0000.0000.000
107A305SER0-0.078-0.02911.1760.2500.2500.0000.0000.0000.000
108A306VAL0-0.047-0.02513.462-0.188-0.1880.0000.0000.0000.000
109A307VAL0-0.0010.00215.8650.1710.1710.0000.0000.0000.000
110A308MET00.0070.01417.901-0.038-0.0380.0000.0000.0000.000
111A309ALA00.0570.02419.8330.0410.0410.0000.0000.0000.000
112A310LYS10.8020.85221.9630.4540.4540.0000.0000.0000.000
113A311ALA0-0.0540.01121.9800.0400.0400.0000.0000.0000.000
114A312VAL0-0.007-0.01923.385-0.005-0.0050.0000.0000.0000.000
115A313VAL0-0.001-0.00121.517-0.004-0.0040.0000.0000.0000.000
116A314GLN0-0.0040.01023.908-0.011-0.0110.0000.0000.0000.000
117A315ALA0-0.011-0.01525.471-0.033-0.0330.0000.0000.0000.000
118A316GLY00.0470.03526.2800.0110.0110.0000.0000.0000.000
119A317SER0-0.038-0.01425.047-0.001-0.0010.0000.0000.0000.000
120A318VAL0-0.034-0.01622.030-0.046-0.0460.0000.0000.0000.000
121A319LEU0-0.002-0.00219.4960.0320.0320.0000.0000.0000.000
122A320LYS10.9080.96718.8150.6210.6210.0000.0000.0000.000
123A321ASP-1-0.789-0.89914.794-1.552-1.5520.0000.0000.0000.000
124A322GLY00.0200.00714.4940.1530.1530.0000.0000.0000.000
125A323VAL0-0.0240.00815.6830.1250.1250.0000.0000.0000.000
126A324ILE0-0.045-0.01917.563-0.109-0.1090.0000.0000.0000.000
127A325VAL00.0200.01219.7640.1090.1090.0000.0000.0000.000
128A326ASN00.016-0.00321.247-0.036-0.0360.0000.0000.0000.000
129A327THR00.038-0.00522.9080.0210.0210.0000.0000.0000.000
130A328ALA0-0.004-0.00924.3620.0440.0440.0000.0000.0000.000
131A329ALA0-0.070-0.00725.4150.0440.0440.0000.0000.0000.000
132A330THR00.005-0.00325.925-0.015-0.0150.0000.0000.0000.000
133A331VAL0-0.029-0.00524.6650.0160.0160.0000.0000.0000.000
134A332ASP-1-0.792-0.90027.328-0.374-0.3740.0000.0000.0000.000
135A333HIS0-0.038-0.05128.883-0.020-0.0200.0000.0000.0000.000
136A334ASP-1-0.847-0.91729.240-0.339-0.3390.0000.0000.0000.000
137A335CYS0-0.071-0.00827.6080.0190.0190.0000.0000.0000.000
138A336LEU0-0.038-0.01624.944-0.022-0.0220.0000.0000.0000.000
139A337LEU0-0.022-0.01623.3080.0250.0250.0000.0000.0000.000
140A338ASP-1-0.820-0.94122.507-0.670-0.6700.0000.0000.0000.000
141A339ALA00.002-0.00619.596-0.035-0.0350.0000.0000.0000.000
142A340PHE00.0310.00415.4810.0910.0910.0000.0000.0000.000
143A341VAL00.0040.02520.0500.0410.0410.0000.0000.0000.000
144A342HIS0-0.058-0.02621.408-0.076-0.0760.0000.0000.0000.000
145A343ILE00.0150.01223.4770.0710.0710.0000.0000.0000.000
146A344SER0-0.012-0.03124.763-0.046-0.0460.0000.0000.0000.000
147A345PRO0-0.001-0.01225.7460.0140.0140.0000.0000.0000.000
148A346GLY00.0170.00327.5000.0350.0350.0000.0000.0000.000
149A347ALA0-0.0380.00329.1170.0320.0320.0000.0000.0000.000
150A348HIS10.8360.89429.7100.3850.3850.0000.0000.0000.000
151A349LEU00.0070.01027.8770.0240.0240.0000.0000.0000.000
152A350SER00.013-0.00231.349-0.004-0.0040.0000.0000.0000.000
153A351GLY00.0740.05532.714-0.017-0.0170.0000.0000.0000.000
154A352ASN0-0.048-0.03432.4030.0320.0320.0000.0000.0000.000
155A353THR0-0.015-0.01231.0450.0170.0170.0000.0000.0000.000
156A354ARG10.8780.92929.7040.3120.3120.0000.0000.0000.000
157A355ILE0-0.029-0.01627.0780.0240.0240.0000.0000.0000.000
158A356GLY00.0670.03626.879-0.038-0.0380.0000.0000.0000.000
159A357GLU-1-0.837-0.93223.413-0.625-0.6250.0000.0000.0000.000
160A358GLU-1-0.755-0.86022.773-0.613-0.6130.0000.0000.0000.000
161A359SER0-0.0320.01224.5780.0140.0140.0000.0000.0000.000
162A360ARG10.9070.95425.8820.4390.4390.0000.0000.0000.000
163A361ILE00.0420.02327.7260.0470.0470.0000.0000.0000.000
164A362GLY00.0230.03128.782-0.031-0.0310.0000.0000.0000.000
165A363THR00.029-0.01630.539-0.006-0.0060.0000.0000.0000.000
166A364GLY00.0010.00731.4500.0280.0280.0000.0000.0000.000
167A365ALA0-0.072-0.00532.6490.0220.0220.0000.0000.0000.000
168A366CYS0-0.024-0.01733.207-0.009-0.0090.0000.0000.0000.000
169A367SER00.0350.01433.7580.0040.0040.0000.0000.0000.000
170A368ARG10.8320.92235.8170.2600.2600.0000.0000.0000.000
171A369GLN00.0190.00736.201-0.013-0.0130.0000.0000.0000.000
172A370GLN0-0.017-0.00635.9940.0200.0200.0000.0000.0000.000
173A371THR0-0.018-0.00435.4770.0090.0090.0000.0000.0000.000
174A372THR0-0.029-0.03233.374-0.024-0.0240.0000.0000.0000.000
175A373VAL0-0.034-0.01231.4820.0200.0200.0000.0000.0000.000
176A374GLY00.0680.03931.379-0.021-0.0210.0000.0000.0000.000
177A375SER0-0.035-0.02828.647-0.024-0.0240.0000.0000.0000.000
178A376GLY00.0350.00228.2600.0320.0320.0000.0000.0000.000
179A377VAL0-0.0390.00029.5830.0220.0220.0000.0000.0000.000
180A378THR0-0.063-0.02930.229-0.041-0.0410.0000.0000.0000.000
181A379ALA00.0190.00931.9290.0300.0300.0000.0000.0000.000
182A380GLY0-0.003-0.02032.681-0.021-0.0210.0000.0000.0000.000
183A381ALA0-0.012-0.02034.049-0.008-0.0080.0000.0000.0000.000
184A382GLY0-0.029-0.00934.9430.0190.0190.0000.0000.0000.000
185A383ALA0-0.052-0.00935.7070.0170.0170.0000.0000.0000.000
186A384VAL00.0060.00236.760-0.012-0.0120.0000.0000.0000.000
187A385ILE00.0390.01333.9070.0170.0170.0000.0000.0000.000
188A386VAL00.0290.01338.055-0.003-0.0030.0000.0000.0000.000
189A387CYS0-0.033-0.01340.2500.0130.0130.0000.0000.0000.000
190A388ASP-1-0.764-0.86137.794-0.302-0.3020.0000.0000.0000.000
191A389ILE0-0.062-0.03235.6270.0140.0140.0000.0000.0000.000
192A390PRO00.030-0.00435.652-0.019-0.0190.0000.0000.0000.000
193A391ASP-1-0.772-0.87132.632-0.374-0.3740.0000.0000.0000.000
194A392GLY0-0.0350.00033.0030.0200.0200.0000.0000.0000.000
195A393MET0-0.0510.00434.2260.0120.0120.0000.0000.0000.000
196A394THR00.015-0.00934.894-0.027-0.0270.0000.0000.0000.000
197A395VAL00.0010.00136.2100.0200.0200.0000.0000.0000.000
198A396ALA00.0190.00037.008-0.020-0.0200.0000.0000.0000.000
199A397GLY00.0490.03039.1320.0140.0140.0000.0000.0000.000
200A398ASN00.0360.02540.838-0.011-0.0110.0000.0000.0000.000
201A399PRO00.0490.00842.7930.0110.0110.0000.0000.0000.000
202A400ALA0-0.048-0.01838.6780.0040.0040.0000.0000.0000.000
203A401LYS10.8800.93940.6520.2270.2270.0000.0000.0000.000
204A402PRO00.0460.00341.002-0.010-0.0100.0000.0000.0000.000
205A403LEU0-0.0350.00638.8220.0130.0130.0000.0000.0000.000