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: R9JM8

Calculation Name: 3BQ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BQ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7T925

Base Structure: X-ray

Registration Date: 2023-09-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2081778.093432
FMO2-HF: Nuclear repulsion 2006423.921481
FMO2-HF: Total energy -75354.171951
FMO2-MP2: Total energy -75572.647115


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:131:ILE)


Summations of interaction energy for fragment #1(A:131:ILE)
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.
-7.413-0.9740.416-1.688-5.1660.003
Interaction energy analysis for fragmet #1(A:131:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.024
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].
3A133THR0-0.071-0.0262.926-1.3881.0270.085-0.495-2.0050.009
4A134LEU00.0800.0654.507-0.541-0.284-0.001-0.019-0.2370.000
5A135TRP0-0.009-0.0207.0130.3360.3360.0000.0000.0000.000
6A136THR00.0800.0619.886-0.066-0.0660.0000.0000.0000.000
7A137GLY0-0.063-0.02511.566-0.007-0.0070.0000.0000.0000.000
8A138ILE00.024-0.01012.506-0.016-0.0160.0000.0000.0000.000
9A139ASN0-0.052-0.01614.796-0.037-0.0370.0000.0000.0000.000
10A140PRO00.0030.02416.435-0.005-0.0050.0000.0000.0000.000
11A141PRO00.013-0.00418.1560.0070.0070.0000.0000.0000.000
12A142PRO00.009-0.01820.881-0.007-0.0070.0000.0000.0000.000
13A143ASN00.0190.02518.262-0.009-0.0090.0000.0000.0000.000
14A144CYS00.0230.01621.335-0.019-0.0190.0000.0000.0000.000
15A145GLN00.0150.02423.584-0.002-0.0020.0000.0000.0000.000
16A146ILE0-0.009-0.00826.401-0.005-0.0050.0000.0000.0000.000
17A147VAL00.0060.01428.315-0.002-0.0020.0000.0000.0000.000
18A148GLU-1-0.956-0.97231.074-0.045-0.0450.0000.0000.0000.000
19A149ASN0-0.052-0.03932.127-0.003-0.0030.0000.0000.0000.000
20A150THR0-0.049-0.01230.403-0.003-0.0030.0000.0000.0000.000
21A151ASN00.0550.03731.180-0.003-0.0030.0000.0000.0000.000
22A152THR0-0.074-0.05129.421-0.002-0.0020.0000.0000.0000.000
23A153ASN00.008-0.01323.852-0.004-0.0040.0000.0000.0000.000
24A154ASP-1-0.770-0.89527.139-0.010-0.0100.0000.0000.0000.000
25A155GLY00.1030.01625.6920.0060.0060.0000.0000.0000.000
26A156LYS10.8100.91520.815-0.097-0.0970.0000.0000.0000.000
27A157LEU00.0320.00218.1050.0110.0110.0000.0000.0000.000
28A158THR0-0.060-0.03215.2980.0140.0140.0000.0000.0000.000
29A159LEU00.0540.01813.5400.0020.0020.0000.0000.0000.000
30A160VAL0-0.050-0.0439.8340.0130.0130.0000.0000.0000.000
31A161LEU00.0180.0088.9150.0230.0230.0000.0000.0000.000
32A162VAL0-0.015-0.0256.8500.0060.0060.0000.0000.0000.000
33A163LYS10.8960.9664.3970.5520.704-0.001-0.010-0.1400.000
34A164ASN0-0.063-0.0266.2600.2890.2890.0000.0000.0000.000
35A165GLY00.0550.0308.469-0.020-0.0200.0000.0000.0000.000
36A166GLY00.0220.0029.803-0.110-0.1100.0000.0000.0000.000
37A167LEU0-0.006-0.00111.815-0.025-0.0250.0000.0000.0000.000
38A168VAL00.0090.0099.217-0.030-0.0300.0000.0000.0000.000
39A169ASN0-0.047-0.02110.4140.0860.0860.0000.0000.0000.000
40A170GLY00.0660.00711.602-0.001-0.0010.0000.0000.0000.000
41A171TYR0-0.031-0.02714.2000.0410.0410.0000.0000.0000.000
42A172VAL00.0170.01115.655-0.012-0.0120.0000.0000.0000.000
43A173SER0-0.059-0.01518.4030.0090.0090.0000.0000.0000.000
44A174LEU00.0430.02920.399-0.007-0.0070.0000.0000.0000.000
45A175VAL0-0.017-0.01023.0810.0080.0080.0000.0000.0000.000
46A176GLY00.0690.04325.287-0.010-0.0100.0000.0000.0000.000
47A177VAL0-0.093-0.01426.0860.0070.0070.0000.0000.0000.000
48A178SER00.0450.01329.1270.0020.0020.0000.0000.0000.000
49A179ASP-1-0.874-0.94632.3670.0070.0070.0000.0000.0000.000
50A180THR0-0.021-0.00434.4840.0000.0000.0000.0000.0000.000
51A181VAL0-0.0110.00229.4940.0000.0000.0000.0000.0000.000
52A182ASN00.018-0.01131.6790.0050.0050.0000.0000.0000.000
53A183GLN0-0.064-0.00633.8400.0040.0040.0000.0000.0000.000
54A184MET00.001-0.00233.654-0.004-0.0040.0000.0000.0000.000
55A185PHE0-0.041-0.02730.992-0.001-0.0010.0000.0000.0000.000
56A186THR00.0630.02936.4230.0030.0030.0000.0000.0000.000
57A187GLN0-0.024-0.00239.058-0.003-0.0030.0000.0000.0000.000
58A188LYS10.9310.96639.175-0.005-0.0050.0000.0000.0000.000
59A189THR0-0.050-0.05438.105-0.001-0.0010.0000.0000.0000.000
60A190ALA00.0020.01734.164-0.001-0.0010.0000.0000.0000.000
61A191ASN00.0460.01531.5260.0030.0030.0000.0000.0000.000
62A192ILE0-0.0120.01527.302-0.003-0.0030.0000.0000.0000.000
63A193GLN00.0260.00826.3710.0070.0070.0000.0000.0000.000
64A194LEU0-0.028-0.00822.351-0.001-0.0010.0000.0000.0000.000
65A195ARG10.8510.90422.2490.0790.0790.0000.0000.0000.000
66A196LEU0-0.005-0.00615.9290.0000.0000.0000.0000.0000.000
67A197TYR00.0300.00618.6290.0000.0000.0000.0000.0000.000
68A198PHE00.031-0.02813.327-0.008-0.0080.0000.0000.0000.000
69A199ASP-1-0.695-0.82714.397-0.445-0.4450.0000.0000.0000.000
70A200SER00.013-0.03314.597-0.045-0.0450.0000.0000.0000.000
71A201SER0-0.072-0.04411.980-0.028-0.0280.0000.0000.0000.000
72A202GLY0-0.010-0.03110.054-0.105-0.1050.0000.0000.0000.000
73A203ASN00.005-0.00810.825-0.121-0.1210.0000.0000.0000.000
74A204LEU0-0.049-0.00512.9130.0460.0460.0000.0000.0000.000
75A205LEU0-0.0250.01015.341-0.002-0.0020.0000.0000.0000.000
76A206THR0-0.029-0.03118.3320.0170.0170.0000.0000.0000.000
77A207GLU-1-0.975-0.97720.335-0.098-0.0980.0000.0000.0000.000
78A208GLU-1-0.829-0.92722.275-0.166-0.1660.0000.0000.0000.000
79A209SER0-0.054-0.00319.8390.0020.0020.0000.0000.0000.000
80A210ASP-1-0.753-0.85422.094-0.073-0.0730.0000.0000.0000.000
81A211LEU0-0.066-0.02816.4350.0140.0140.0000.0000.0000.000
82A212LYS10.8570.92420.0910.0800.0800.0000.0000.0000.000
83A213ILE0-0.043-0.02416.0160.0060.0060.0000.0000.0000.000
84A214PRO00.0170.00713.719-0.002-0.0020.0000.0000.0000.000
85A215LEU00.0080.01810.3040.0490.0490.0000.0000.0000.000
86A216LYS10.9700.9748.738-0.062-0.0620.0000.0000.0000.000
87A217ASN00.1400.0873.4950.2770.6580.012-0.077-0.3160.000
88A218LYS10.9240.9714.348-1.738-1.532-0.001-0.021-0.1840.000
89A219SER00.001-0.0243.107-1.5680.3170.184-0.739-1.330-0.007
90A220SER0-0.0400.0105.368-0.265-0.254-0.001-0.003-0.0070.000
91A221THR0-0.034-0.0229.1570.0770.0770.0000.0000.0000.000
92A222ALA0-0.046-0.01410.437-0.065-0.0650.0000.0000.0000.000
93A223THR0-0.004-0.0417.1660.0910.0910.0000.0000.0000.000
94A224SER0-0.020-0.0063.9410.0950.2040.000-0.015-0.0940.000
95A225GLU-1-0.877-0.9366.110-0.570-0.5700.0000.0000.0000.000
96A226THR0-0.061-0.0366.117-0.139-0.1390.0000.0000.0000.000
97A227VAL00.0470.0117.335-0.129-0.1290.0000.0000.0000.000
98A228ALA0-0.054-0.0175.1770.0930.0930.0000.0000.0000.000
99A229SER00.0480.0177.3350.0090.0090.0000.0000.0000.000
100A230SER00.0030.0115.861-0.493-0.4930.0000.0000.0000.000
101A231LYS10.9630.9746.9510.7180.7180.0000.0000.0000.000
102A232ALA00.0410.0454.6940.0690.118-0.001-0.001-0.0470.000
103A233PHE0-0.043-0.0132.933-0.7110.2630.140-0.308-0.8060.001
104A234MET0-0.0640.0297.8450.1880.1880.0000.0000.0000.000
105A235PRO0-0.018-0.01011.1740.0030.0030.0000.0000.0000.000
106A236SER00.0690.02414.1440.0200.0200.0000.0000.0000.000
107A237THR0-0.063-0.02815.6700.0460.0460.0000.0000.0000.000
108A238THR00.0100.00918.6300.0200.0200.0000.0000.0000.000
109A239ALA0-0.054-0.02419.2420.0220.0220.0000.0000.0000.000
110A240TYR0-0.0160.00016.5860.0230.0230.0000.0000.0000.000
111A241PRO00.0110.00220.938-0.018-0.0180.0000.0000.0000.000
112A242PHE00.0530.03919.9040.0090.0090.0000.0000.0000.000
113A243ASN0-0.024-0.03024.7170.0140.0140.0000.0000.0000.000
114A244THR0-0.0330.00028.162-0.002-0.0020.0000.0000.0000.000
115A245THR00.1130.07230.5170.0020.0020.0000.0000.0000.000
116A246THR0-0.141-0.07731.942-0.005-0.0050.0000.0000.0000.000
117A247ARG10.8740.90324.8530.1000.1000.0000.0000.0000.000
118A248ASP-1-0.931-0.97229.207-0.063-0.0630.0000.0000.0000.000
119A249SER00.0300.04027.9020.0060.0060.0000.0000.0000.000
120A250GLU-1-0.917-0.92726.973-0.076-0.0760.0000.0000.0000.000
121A251ASN0-0.046-0.03722.4960.0140.0140.0000.0000.0000.000
122A252TYR00.0840.03323.404-0.007-0.0070.0000.0000.0000.000
123A253ILE0-0.062-0.02619.3810.0100.0100.0000.0000.0000.000
124A254HIS00.0400.01123.4440.0060.0060.0000.0000.0000.000
125A255GLY0-0.008-0.00325.9310.0060.0060.0000.0000.0000.000
126A256ILE00.0040.00526.919-0.005-0.0050.0000.0000.0000.000
127A257CYS0-0.073-0.00125.5400.0090.0090.0000.0000.0000.000
128A258TYR00.027-0.03527.570-0.009-0.0090.0000.0000.0000.000
129A259TYR00.0730.05328.7090.0040.0040.0000.0000.0000.000
130A260MET0-0.038-0.01830.7640.0000.0000.0000.0000.0000.000
131A261THR0-0.017-0.01532.8660.0000.0000.0000.0000.0000.000
132A262SER00.0050.00035.5590.0050.0050.0000.0000.0000.000
133A263TYR0-0.028-0.00336.5400.0040.0040.0000.0000.0000.000
134A264ASP-1-0.815-0.91039.4300.0550.0550.0000.0000.0000.000
135A265ARG10.8790.92234.329-0.073-0.0730.0000.0000.0000.000
136A266SER00.0120.02235.9820.0060.0060.0000.0000.0000.000
137A267LEU0-0.015-0.01532.1140.0010.0010.0000.0000.0000.000
138A268PHE00.0310.00834.258-0.004-0.0040.0000.0000.0000.000
139A269PRO0-0.015-0.01632.8010.0030.0030.0000.0000.0000.000
140A270LEU0-0.0380.00029.254-0.005-0.0050.0000.0000.0000.000
141A271ASN0-0.018-0.00529.5730.0040.0040.0000.0000.0000.000
142A272ILE00.0080.01522.558-0.002-0.0020.0000.0000.0000.000
143A273SER0-0.010-0.01725.084-0.001-0.0010.0000.0000.0000.000
144A274ILE0-0.029-0.02618.755-0.004-0.0040.0000.0000.0000.000
145A275MET0-0.050-0.01522.166-0.005-0.0050.0000.0000.0000.000
146A276LEU0-0.0140.00116.989-0.005-0.0050.0000.0000.0000.000
147A277ASN0-0.030-0.02217.450-0.011-0.0110.0000.0000.0000.000
148A278SER00.0100.01820.7250.0090.0090.0000.0000.0000.000
149A279ARG10.9750.94224.1790.0960.0960.0000.0000.0000.000
150A280MET00.0000.00321.2850.0030.0030.0000.0000.0000.000
151A281ILE0-0.0520.00624.3890.0060.0060.0000.0000.0000.000
152A282SER00.028-0.00724.1320.0080.0080.0000.0000.0000.000
153A283SER0-0.014-0.00824.558-0.012-0.0120.0000.0000.0000.000
154A284ASN00.000-0.00421.447-0.003-0.0030.0000.0000.0000.000
155A285VAL00.0040.03320.043-0.016-0.0160.0000.0000.0000.000
156A286ALA0-0.070-0.02816.4400.0070.0070.0000.0000.0000.000
157A287TYR0-0.020-0.02614.044-0.022-0.0220.0000.0000.0000.000
158A288ALA00.0060.00517.2300.0050.0050.0000.0000.0000.000
159A289ILE0-0.0170.01313.7720.0050.0050.0000.0000.0000.000
160A290GLN00.0100.00118.394-0.008-0.0080.0000.0000.0000.000
161A291PHE0-0.0040.00616.6770.0090.0090.0000.0000.0000.000
162A292GLU-1-0.901-0.97222.557-0.041-0.0410.0000.0000.0000.000
163A293TRP0-0.0050.00221.6700.0030.0030.0000.0000.0000.000
164A294ASN00.0520.01628.135-0.002-0.0020.0000.0000.0000.000
165A295LEU0-0.035-0.01231.8150.0050.0050.0000.0000.0000.000
166A296ASN0-0.027-0.02634.670-0.006-0.0060.0000.0000.0000.000
167A297ALA00.0140.01537.9900.0010.0010.0000.0000.0000.000
168A298SER0-0.036-0.04240.253-0.002-0.0020.0000.0000.0000.000
169A299GLU-1-0.925-0.94942.9210.0200.0200.0000.0000.0000.000
170A300SER0-0.042-0.00937.6290.0030.0030.0000.0000.0000.000
171A301PRO0-0.053-0.04536.734-0.001-0.0010.0000.0000.0000.000
172A302GLU-1-0.963-0.95039.3040.0190.0190.0000.0000.0000.000
173A303SER0-0.010-0.00240.6240.0020.0020.0000.0000.0000.000
174A304ASN00.021-0.01337.7710.0000.0000.0000.0000.0000.000
175A305ILE00.0030.01735.4210.0020.0020.0000.0000.0000.000
176A306ALA00.0050.00034.4110.0050.0050.0000.0000.0000.000
177A307THR0-0.031-0.00528.904-0.002-0.0020.0000.0000.0000.000
178A308LEU00.0000.01027.953-0.001-0.0010.0000.0000.0000.000
179A309THR0-0.033-0.05325.4720.0050.0050.0000.0000.0000.000
180A310THR00.0170.03223.9010.0010.0010.0000.0000.0000.000
181A311SER0-0.0010.01424.6540.0080.0080.0000.0000.0000.000
182A312PRO0-0.047-0.05119.695-0.008-0.0080.0000.0000.0000.000
183A313PHE00.0350.03320.8490.0030.0030.0000.0000.0000.000
184A314PHE0-0.008-0.01818.1650.0070.0070.0000.0000.0000.000
185A315PHE00.0200.04415.087-0.014-0.0140.0000.0000.0000.000
186A316SER0-0.030-0.04114.9640.0430.0430.0000.0000.0000.000
187A317TYR0-0.0270.00211.4340.0360.0360.0000.0000.0000.000
188A318ILE00.023-0.01413.912-0.002-0.0020.0000.0000.0000.000
189A319THR0-0.050-0.0528.796-0.019-0.0190.0000.0000.0000.000
190A320GLU-1-0.823-0.92811.247-0.309-0.3090.0000.0000.0000.000
191A321ASP-1-0.961-0.95810.707-0.416-0.4160.0000.0000.0000.000
192A322ASP-1-1.025-1.0197.992-0.950-0.9500.0000.0000.0000.000