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: 3J74L

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014664.692126
FMO2-HF: Nuclear repulsion 1941988.625094
FMO2-HF: Total energy -72676.067032
FMO2-MP2: Total energy -72889.072984


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.
-42.181-28.36716.065-11.845-18.039-0.094
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 : -0.024 / q_NPA : -0.026
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].
3A201LYS10.8650.9452.510-1.5291.2460.164-1.329-1.6110.004
4A202LEU00.0220.0283.499-3.468-2.9950.041-0.227-0.288-0.001
5A203ALA0-0.007-0.0015.9941.2531.2530.0000.0000.0000.000
6A204VAL0-0.010-0.0118.701-0.302-0.3020.0000.0000.0000.000
7A205ILE00.0200.00211.2650.3420.3420.0000.0000.0000.000
8A206GLY00.0010.00113.9150.0770.0770.0000.0000.0000.000
9A207ALA00.008-0.00516.852-0.080-0.0800.0000.0000.0000.000
10A208GLY00.0230.01018.7430.1090.1090.0000.0000.0000.000
11A209GLY0-0.021-0.02820.731-0.040-0.0400.0000.0000.0000.000
12A210HIS00.0230.00118.032-0.018-0.0180.0000.0000.0000.000
13A211GLY00.1140.04216.783-0.068-0.0680.0000.0000.0000.000
14A212LYS10.9130.96416.6260.5670.5670.0000.0000.0000.000
15A213VAL00.0140.01418.243-0.015-0.0150.0000.0000.0000.000
16A214VAL00.0220.00813.066-0.016-0.0160.0000.0000.0000.000
17A215ALA0-0.0030.00513.277-0.169-0.1690.0000.0000.0000.000
18A216GLU-1-0.882-0.93914.137-0.797-0.7970.0000.0000.0000.000
19A217LEU0-0.079-0.02312.9990.0690.0690.0000.0000.0000.000
20A218ALA00.0280.00110.0130.0040.0040.0000.0000.0000.000
21A219ALA0-0.016-0.01911.119-0.018-0.0180.0000.0000.0000.000
22A220ALA0-0.038-0.01713.2990.1280.1280.0000.0000.0000.000
23A221LEU0-0.047-0.0219.2750.1200.1200.0000.0000.0000.000
24A222GLY0-0.0150.01111.7270.1510.1510.0000.0000.0000.000
25A223THR0-0.018-0.0146.6470.3760.3760.0000.0000.0000.000
26A224TYR0-0.072-0.0413.5831.3211.6310.003-0.076-0.2380.000
27A225GLY0-0.041-0.0356.8290.6980.6980.0000.0000.0000.000
28A226GLU-1-0.955-1.0117.613-0.462-0.4620.0000.0000.0000.000
29A227ILE00.0250.0317.724-0.733-0.7330.0000.0000.0000.000
30A228VAL00.0080.0119.4150.4160.4160.0000.0000.0000.000
31A229PHE0-0.029-0.01611.462-0.286-0.2860.0000.0000.0000.000
32A230LEU0-0.0040.00611.7920.0840.0840.0000.0000.0000.000
33A231ASP-1-0.785-0.89915.039-0.890-0.8900.0000.0000.0000.000
34A232ASP-1-0.758-0.88218.645-0.805-0.8050.0000.0000.0000.000
35A233ARG10.7590.87419.7030.8900.8900.0000.0000.0000.000
36A234THR0-0.0490.00121.0870.0710.0710.0000.0000.0000.000
37A235GLN00.0460.00821.580-0.039-0.0390.0000.0000.0000.000
38A236GLY00.0150.01921.5100.0190.0190.0000.0000.0000.000
39A237SER0-0.024-0.00919.396-0.047-0.0470.0000.0000.0000.000
40A238VAL00.0030.00019.2440.0630.0630.0000.0000.0000.000
41A239ASN0-0.085-0.06819.200-0.005-0.0050.0000.0000.0000.000
42A240GLY00.0380.02619.910-0.019-0.0190.0000.0000.0000.000
43A241PHE0-0.0040.01113.847-0.002-0.0020.0000.0000.0000.000
44A242PRO00.0020.00513.8550.0640.0640.0000.0000.0000.000
45A243VAL0-0.006-0.01614.940-0.186-0.1860.0000.0000.0000.000
46A244ILE0-0.020-0.01011.0470.1220.1220.0000.0000.0000.000
47A245GLY00.0280.00915.3200.1070.1070.0000.0000.0000.000
48A246THR00.0080.01117.068-0.103-0.1030.0000.0000.0000.000
49A247THR0-0.033-0.05715.611-0.074-0.0740.0000.0000.0000.000
50A248LEU00.0350.03415.804-0.055-0.0550.0000.0000.0000.000
51A249LEU0-0.009-0.00413.4370.0340.0340.0000.0000.0000.000
52A250LEU0-0.052-0.0059.832-0.092-0.0920.0000.0000.0000.000
53A251GLU-1-0.880-0.95411.503-1.107-1.1070.0000.0000.0000.000
54A252ASN0-0.096-0.04414.1100.2030.2030.0000.0000.0000.000
55A253SER0-0.071-0.03913.1780.1450.1450.0000.0000.0000.000
56A254LEU0-0.033-0.0088.2090.1970.1970.0000.0000.0000.000
57A255SER00.0630.0356.8040.0000.0000.0000.0000.0000.000
58A256PRO00.0800.0314.024-0.419-0.228-0.001-0.098-0.0930.000
59A257GLU-1-0.901-0.9482.070-8.641-7.5773.486-2.060-2.490-0.028
60A258GLN0-0.071-0.0362.8845.6667.4711.683-0.840-2.6480.002
61A259PHE0-0.016-0.0242.474-4.741-2.7141.918-1.611-2.335-0.021
62A260ASP-1-0.762-0.8602.025-38.539-34.3297.022-4.804-6.428-0.057
63A261ILE0-0.019-0.0123.4173.5723.7630.022-0.007-0.2060.000
64A262THR00.0360.0146.9930.2790.2790.0000.0000.0000.000
65A263VAL00.0290.01310.1720.2100.2100.0000.0000.0000.000
66A264ALA0-0.0250.01413.5030.1670.1670.0000.0000.0000.000
67A265VAL0-0.001-0.00716.2100.1680.1680.0000.0000.0000.000
68A266GLY00.0270.00519.1580.0030.0030.0000.0000.0000.000
69A267ASN0-0.026-0.01922.0720.0180.0180.0000.0000.0000.000
70A268ASN00.0520.00621.828-0.112-0.1120.0000.0000.0000.000
71A269ARG10.8990.96021.5980.5140.5140.0000.0000.0000.000
72A270ILE00.022-0.00619.894-0.030-0.0300.0000.0000.0000.000
73A271ARG10.7800.90016.5790.9990.9990.0000.0000.0000.000
74A272ARG10.8440.92516.9170.5520.5520.0000.0000.0000.000
75A273GLN0-0.025-0.02217.745-0.068-0.0680.0000.0000.0000.000
76A274ILE00.0240.00713.837-0.022-0.0220.0000.0000.0000.000
77A275THR0-0.016-0.01712.525-0.230-0.2300.0000.0000.0000.000
78A276GLU-1-0.870-0.93412.969-0.983-0.9830.0000.0000.0000.000
79A277ASN0-0.019-0.00414.759-0.061-0.0610.0000.0000.0000.000
80A278ALA00.0400.0129.450-0.004-0.0040.0000.0000.0000.000
81A279ALA00.007-0.0069.833-0.221-0.2210.0000.0000.0000.000
82A280ALA0-0.042-0.01411.0680.1000.1000.0000.0000.0000.000
83A281LEU0-0.047-0.01210.5050.1970.1970.0000.0000.0000.000
84A282GLY00.0070.0108.4360.0700.0700.0000.0000.0000.000
85A283PHE0-0.066-0.0295.068-0.685-0.6850.0000.0000.0000.000
86A284LYS10.8740.9512.3344.7225.4691.728-0.793-1.6820.007
87A285LEU00.007-0.0085.040-1.180-1.159-0.0010.000-0.0200.000
88A286PRO00.0110.0135.4271.1741.1740.0000.0000.0000.000
89A287VAL0-0.0090.0048.1440.3080.3080.0000.0000.0000.000
90A288LEU0-0.045-0.0158.4910.0090.0090.0000.0000.0000.000
91A289ILE00.023-0.00511.8130.2050.2050.0000.0000.0000.000
92A290HIS00.0370.02214.3080.0070.0070.0000.0000.0000.000
93A291PRO00.0380.01515.2190.0680.0680.0000.0000.0000.000
94A292ASP-1-0.916-0.95717.492-0.424-0.4240.0000.0000.0000.000
95A293ALA0-0.094-0.03918.8440.0390.0390.0000.0000.0000.000
96A294THR0-0.024-0.01520.5210.0460.0460.0000.0000.0000.000
97A295VAL00.0120.00018.069-0.008-0.0080.0000.0000.0000.000
98A296SER00.0170.02020.7590.0420.0420.0000.0000.0000.000
99A297PRO00.0320.00320.437-0.034-0.0340.0000.0000.0000.000
100A298SER0-0.042-0.02321.3340.0220.0220.0000.0000.0000.000
101A299ALA0-0.0210.00920.7590.0040.0040.0000.0000.0000.000
102A300ILE0-0.002-0.00218.784-0.007-0.0070.0000.0000.0000.000
103A301ILE0-0.016-0.01915.980-0.005-0.0050.0000.0000.0000.000
104A302GLY00.0170.02315.442-0.047-0.0470.0000.0000.0000.000
105A303GLN00.003-0.00810.506-0.342-0.3420.0000.0000.0000.000
106A304GLY00.0320.00510.9310.2130.2130.0000.0000.0000.000
107A305SER0-0.055-0.01412.0830.1800.1800.0000.0000.0000.000
108A306VAL0-0.030-0.01413.919-0.183-0.1830.0000.0000.0000.000
109A307VAL0-0.008-0.00315.9470.1690.1690.0000.0000.0000.000
110A308MET0-0.0030.00417.505-0.053-0.0530.0000.0000.0000.000
111A309ALA00.0680.03119.7080.0570.0570.0000.0000.0000.000
112A310LYS10.9440.94521.4480.4500.4500.0000.0000.0000.000
113A311ALA0-0.0470.01621.5800.0430.0430.0000.0000.0000.000
114A312VAL00.006-0.00723.0300.0080.0080.0000.0000.0000.000
115A313VAL0-0.0080.00121.147-0.008-0.0080.0000.0000.0000.000
116A314GLN00.0510.02223.7570.0120.0120.0000.0000.0000.000
117A315ALA0-0.028-0.03625.598-0.019-0.0190.0000.0000.0000.000
118A316GLY00.0660.04025.8650.0030.0030.0000.0000.0000.000
119A317SER0-0.0120.01824.673-0.001-0.0010.0000.0000.0000.000
120A318VAL0-0.037-0.01622.243-0.019-0.0190.0000.0000.0000.000
121A319LEU0-0.013-0.01019.8930.0090.0090.0000.0000.0000.000
122A320LYS10.9510.97719.4810.4780.4780.0000.0000.0000.000
123A321ASP-1-0.809-0.90615.494-1.205-1.2050.0000.0000.0000.000
124A322GLY00.0120.00815.2630.1050.1050.0000.0000.0000.000
125A323VAL0-0.0100.00716.3860.0910.0910.0000.0000.0000.000
126A324ILE0-0.035-0.00317.884-0.116-0.1160.0000.0000.0000.000
127A325VAL00.0350.01820.0820.1050.1050.0000.0000.0000.000
128A326ASN00.003-0.01721.202-0.054-0.0540.0000.0000.0000.000
129A327THR00.025-0.01723.1640.0280.0280.0000.0000.0000.000
130A328ALA0-0.007-0.00424.5220.0410.0410.0000.0000.0000.000
131A329ALA0-0.076-0.00625.2230.0440.0440.0000.0000.0000.000
132A330THR00.0210.00125.721-0.010-0.0100.0000.0000.0000.000
133A331VAL0-0.0070.00224.7050.0090.0090.0000.0000.0000.000
134A332ASP-1-0.855-0.93927.002-0.294-0.2940.0000.0000.0000.000
135A333HIS0-0.059-0.04028.580-0.015-0.0150.0000.0000.0000.000
136A334ASP-1-0.876-0.93928.806-0.238-0.2380.0000.0000.0000.000
137A335CYS0-0.077-0.00927.6190.0100.0100.0000.0000.0000.000
138A336LEU0-0.020-0.00825.174-0.008-0.0080.0000.0000.0000.000
139A337LEU0-0.032-0.01723.7870.0110.0110.0000.0000.0000.000
140A338ASP-1-0.828-0.93323.204-0.511-0.5110.0000.0000.0000.000
141A339ALA0-0.016-0.02019.967-0.039-0.0390.0000.0000.0000.000
142A340PHE00.015-0.00316.2550.0600.0600.0000.0000.0000.000
143A341VAL00.0200.03620.7510.0340.0340.0000.0000.0000.000
144A342HIS0-0.024-0.00422.027-0.079-0.0790.0000.0000.0000.000
145A343ILE00.0170.00823.9960.0640.0640.0000.0000.0000.000
146A344SER0-0.036-0.02025.237-0.047-0.0470.0000.0000.0000.000
147A345PRO0-0.005-0.01526.0360.0170.0170.0000.0000.0000.000
148A346GLY00.0270.00727.7570.0330.0330.0000.0000.0000.000
149A347ALA0-0.0500.00029.2780.0330.0330.0000.0000.0000.000
150A348HIS10.8540.90829.5990.3450.3450.0000.0000.0000.000
151A349LEU0-0.004-0.00128.2950.0170.0170.0000.0000.0000.000
152A350SER00.005-0.00831.5630.0060.0060.0000.0000.0000.000
153A351GLY00.0690.05132.480-0.016-0.0160.0000.0000.0000.000
154A352ASN0-0.031-0.03032.3230.0190.0190.0000.0000.0000.000
155A353THR0-0.008-0.00231.4800.0150.0150.0000.0000.0000.000
156A354ARG10.8830.92830.0200.2530.2530.0000.0000.0000.000
157A355ILE0-0.025-0.01627.5310.0140.0140.0000.0000.0000.000
158A356GLY00.0580.03127.436-0.029-0.0290.0000.0000.0000.000
159A357GLU-1-0.841-0.94323.954-0.585-0.5850.0000.0000.0000.000
160A358GLU-1-0.793-0.89323.692-0.587-0.5870.0000.0000.0000.000
161A359SER0-0.0140.02825.2600.0090.0090.0000.0000.0000.000
162A360ARG10.9150.96226.5030.4320.4320.0000.0000.0000.000
163A361ILE00.0290.01328.1110.0430.0430.0000.0000.0000.000
164A362GLY0-0.001-0.00329.297-0.029-0.0290.0000.0000.0000.000
165A363THR00.043-0.01530.529-0.006-0.0060.0000.0000.0000.000
166A364GLY0-0.0040.00931.6320.0260.0260.0000.0000.0000.000
167A365ALA0-0.0530.00433.0120.0220.0220.0000.0000.0000.000
168A366CYS0-0.008-0.01233.664-0.005-0.0050.0000.0000.0000.000
169A367SER00.0200.01634.0510.0030.0030.0000.0000.0000.000
170A368ARG10.9210.97336.0300.2140.2140.0000.0000.0000.000
171A369GLN00.0110.00236.520-0.014-0.0140.0000.0000.0000.000
172A370GLN0-0.032-0.02736.3300.0170.0170.0000.0000.0000.000
173A371THR0-0.0420.00036.1750.0020.0020.0000.0000.0000.000
174A372THR00.0050.00333.586-0.016-0.0160.0000.0000.0000.000
175A373VAL0-0.027-0.01231.9960.0150.0150.0000.0000.0000.000
176A374GLY00.0690.03831.986-0.016-0.0160.0000.0000.0000.000
177A375SER0-0.028-0.01729.223-0.023-0.0230.0000.0000.0000.000
178A376GLY00.0550.01828.9900.0260.0260.0000.0000.0000.000
179A377VAL0-0.0310.00430.3570.0210.0210.0000.0000.0000.000
180A378THR0-0.060-0.02530.863-0.043-0.0430.0000.0000.0000.000
181A379ALA00.0150.00932.4010.0290.0290.0000.0000.0000.000
182A380GLY0-0.024-0.02133.249-0.022-0.0220.0000.0000.0000.000
183A381ALA00.008-0.02034.293-0.002-0.0020.0000.0000.0000.000
184A382GLY0-0.041-0.01535.1840.0180.0180.0000.0000.0000.000
185A383ALA0-0.069-0.01536.1410.0180.0180.0000.0000.0000.000
186A384VAL00.0350.01737.084-0.009-0.0090.0000.0000.0000.000
187A385ILE00.0180.00334.4340.0150.0150.0000.0000.0000.000
188A386VAL00.0320.00938.5080.0000.0000.0000.0000.0000.000
189A387CYS0-0.041-0.02040.4740.0150.0150.0000.0000.0000.000
190A388ASP-1-0.817-0.90138.222-0.248-0.2480.0000.0000.0000.000
191A389ILE0-0.078-0.04236.0110.0090.0090.0000.0000.0000.000
192A390PRO00.0270.00136.275-0.014-0.0140.0000.0000.0000.000
193A391ASP-1-0.796-0.90233.845-0.327-0.3270.0000.0000.0000.000
194A392GLY0-0.039-0.00833.7200.0170.0170.0000.0000.0000.000
195A393MET0-0.0430.01034.9480.0090.0090.0000.0000.0000.000
196A394THR00.0270.00435.500-0.026-0.0260.0000.0000.0000.000
197A395VAL0-0.007-0.00636.6320.0200.0200.0000.0000.0000.000
198A396ALA00.021-0.00537.563-0.020-0.0200.0000.0000.0000.000
199A397GLY00.0230.01939.7800.0140.0140.0000.0000.0000.000
200A398ASN0-0.0010.02041.401-0.006-0.0060.0000.0000.0000.000
201A399PRO00.0580.01143.2200.0090.0090.0000.0000.0000.000
202A400ALA0-0.057-0.03739.3750.0020.0020.0000.0000.0000.000
203A401LYS10.9080.96041.3540.2170.2170.0000.0000.0000.000
204A402PRO00.0610.00341.433-0.012-0.0120.0000.0000.0000.000
205A403LEU0-0.041-0.00139.6480.0120.0120.0000.0000.0000.000