Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 76GJK

Calculation Name: 5BRL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BRL

Chain ID: A

ChEMBL ID:

UniProt ID: Q99JV5

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2610734.389754
FMO2-HF: Nuclear repulsion 2525317.136286
FMO2-HF: Total energy -85417.253468
FMO2-MP2: Total energy -85663.495683


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:13:ARG)


Summations of interaction energy for fragment #1(A:13:ARG)
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.
-95.43-93.968-0.015-0.583-0.8630.001
Interaction energy analysis for fragmet #1(A:13:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.957
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].
3A15ILE00.0570.0333.780-1.1850.277-0.015-0.583-0.8630.001
4A16LYS10.9290.9894.92331.09331.0930.0000.0000.0000.000
5A17LEU0-0.029-0.0219.080-1.204-1.2040.0000.0000.0000.000
6A18GLU-1-0.904-0.95710.512-19.421-19.4210.0000.0000.0000.000
7A19GLY00.0270.01913.3391.1941.1940.0000.0000.0000.000
8A20LEU00.0270.00314.340-0.784-0.7840.0000.0000.0000.000
9A21SER00.0190.00812.4320.1490.1490.0000.0000.0000.000
10A22ASP-1-0.830-0.8939.975-24.307-24.3070.0000.0000.0000.000
11A23VAL00.0620.02610.822-1.450-1.4500.0000.0000.0000.000
12A24ALA0-0.0020.02213.493-0.003-0.0030.0000.0000.0000.000
13A25SER0-0.034-0.0399.178-0.549-0.5490.0000.0000.0000.000
14A26ILE0-0.040-0.0206.646-1.760-1.7600.0000.0000.0000.000
15A27SER00.0290.00610.4210.2950.2950.0000.0000.0000.000
16A28THR0-0.020-0.00913.297-0.095-0.0950.0000.0000.0000.000
17A29LYS10.9400.9775.33237.33137.3310.0000.0000.0000.000
18A30LEU00.0150.01210.853-0.383-0.3830.0000.0000.0000.000
19A31GLN00.0550.03812.7770.4710.4710.0000.0000.0000.000
20A32ASN0-0.007-0.01812.5081.7311.7310.0000.0000.0000.000
21A33THR0-0.055-0.03710.479-0.826-0.8260.0000.0000.0000.000
22A34LEU0-0.010-0.00312.7730.8240.8240.0000.0000.0000.000
23A35ILE00.0130.00816.1601.0291.0290.0000.0000.0000.000
24A36GLN0-0.0150.00712.505-0.153-0.1530.0000.0000.0000.000
25A37TYR00.0250.00111.6411.0621.0620.0000.0000.0000.000
26A38HIS00.0370.04717.5150.5610.5610.0000.0000.0000.000
27A39SER0-0.086-0.03018.6150.7730.7730.0000.0000.0000.000
28A40ILE00.0070.01116.5570.3810.3810.0000.0000.0000.000
29A41LYS10.8860.92620.58613.91613.9160.0000.0000.0000.000
30A42GLU-1-0.930-0.97923.890-10.607-10.6070.0000.0000.0000.000
31A43ASP-1-0.895-0.94425.621-11.035-11.0350.0000.0000.0000.000
32A44GLU-1-0.983-0.98619.838-15.209-15.2090.0000.0000.0000.000
33A45TRP0-0.091-0.03919.711-0.375-0.3750.0000.0000.0000.000
34A46ARG10.9700.98124.77511.44011.4400.0000.0000.0000.000
35A47VAL0-0.019-0.01327.205-0.218-0.2180.0000.0000.0000.000
36A48ALA0-0.054-0.02426.6220.1170.1170.0000.0000.0000.000
37A49LYS10.9530.96228.7799.5429.5420.0000.0000.0000.000
38A50LYS10.9610.99531.4528.8508.8500.0000.0000.0000.000
39A51VAL0-0.019-0.00234.1930.2660.2660.0000.0000.0000.000
40A52LYS10.8620.90636.5627.5387.5380.0000.0000.0000.000
41A53ASP-1-0.803-0.88036.596-8.007-8.0070.0000.0000.0000.000
42A54VAL00.0010.01430.349-0.177-0.1770.0000.0000.0000.000
43A55THR0-0.049-0.01430.3650.3150.3150.0000.0000.0000.000
44A56VAL00.0190.00825.967-0.266-0.2660.0000.0000.0000.000
45A57TRP00.014-0.00525.3850.3110.3110.0000.0000.0000.000
46A58ARG10.8740.93522.55311.63411.6340.0000.0000.0000.000
47A59LYS10.9020.96516.21518.36618.3660.0000.0000.0000.000
48A60PRO00.0170.00517.929-0.252-0.2520.0000.0000.0000.000
49A61SER0-0.006-0.01613.450-0.787-0.7870.0000.0000.0000.000
50A62GLU-1-0.903-0.95910.703-21.721-21.7210.0000.0000.0000.000
51A63GLU-1-0.974-0.9808.258-35.821-35.8210.0000.0000.0000.000
52A64PHE0-0.029-0.0279.025-0.809-0.8090.0000.0000.0000.000
53A65ASN0-0.026-0.00911.5430.7790.7790.0000.0000.0000.000
54A66GLY00.0290.01315.0070.9370.9370.0000.0000.0000.000
55A67TYR0-0.068-0.02816.967-0.366-0.3660.0000.0000.0000.000
56A68LEU00.0130.02515.933-0.179-0.1790.0000.0000.0000.000
57A69TYR0-0.026-0.04018.0801.1981.1980.0000.0000.0000.000
58A70LYS10.9701.00120.88712.45812.4580.0000.0000.0000.000
59A71ALA0-0.018-0.00723.4830.5310.5310.0000.0000.0000.000
60A72GLN00.0280.02726.524-0.565-0.5650.0000.0000.0000.000
61A73GLY00.0210.00429.2270.3050.3050.0000.0000.0000.000
62A74VAL00.0120.01931.901-0.207-0.2070.0000.0000.0000.000
63A75MET0-0.0060.01131.9350.0800.0800.0000.0000.0000.000
64A76ASP-1-0.895-0.94435.105-7.569-7.5690.0000.0000.0000.000
65A77ASP-1-0.746-0.85935.568-8.241-8.2410.0000.0000.0000.000
66A78VAL00.0040.02835.902-0.195-0.1950.0000.0000.0000.000
67A79VAL00.030-0.00629.737-0.125-0.1250.0000.0000.0000.000
68A80ASN0-0.036-0.02030.984-0.294-0.2940.0000.0000.0000.000
69A81ASN00.020-0.00431.619-0.217-0.2170.0000.0000.0000.000
70A82VAL00.0130.00729.296-0.118-0.1180.0000.0000.0000.000
71A83ILE0-0.001-0.01825.173-0.257-0.2570.0000.0000.0000.000
72A84ASP-1-0.853-0.92627.313-10.228-10.2280.0000.0000.0000.000
73A85HIS0-0.054-0.02029.2630.0930.0930.0000.0000.0000.000
74A86ILE0-0.042-0.01123.932-0.122-0.1220.0000.0000.0000.000
75A87ARG10.8920.95723.74510.81610.8160.0000.0000.0000.000
76A88PRO0-0.006-0.00520.9010.3580.3580.0000.0000.0000.000
77A89GLY00.0740.03223.9930.0760.0760.0000.0000.0000.000
78A90PRO00.001-0.01927.293-0.049-0.0490.0000.0000.0000.000
79A91TRP00.0370.03230.6080.0900.0900.0000.0000.0000.000
80A92ARG10.7820.89623.22111.76611.7660.0000.0000.0000.000
81A93LEU0-0.036-0.03427.747-0.005-0.0050.0000.0000.0000.000
82A94ASP-1-0.915-0.94629.377-8.500-8.5000.0000.0000.0000.000
83A95TRP0-0.083-0.05427.6580.1800.1800.0000.0000.0000.000
84A96ASP-1-0.807-0.89626.041-10.883-10.8830.0000.0000.0000.000
85A97ARG10.8270.87729.4018.9268.9260.0000.0000.0000.000
86A98LEU0-0.079-0.02423.7540.0780.0780.0000.0000.0000.000
87A99MET0-0.041-0.01322.620-0.168-0.1680.0000.0000.0000.000
88A100THR0-0.0050.00326.5700.2070.2070.0000.0000.0000.000
89A101SER0-0.025-0.02825.8080.2320.2320.0000.0000.0000.000
90A102LEU00.007-0.01623.798-0.448-0.4480.0000.0000.0000.000
91A103ASP-1-0.835-0.88723.818-10.229-10.2290.0000.0000.0000.000
92A104VAL0-0.014-0.02122.366-0.562-0.5620.0000.0000.0000.000
93A105LEU0-0.084-0.04818.2740.3520.3520.0000.0000.0000.000
94A106GLU-1-0.876-0.95319.585-13.451-13.4510.0000.0000.0000.000
95A107HIS0-0.063-0.02220.910-0.515-0.5150.0000.0000.0000.000
96A108PHE0-0.032-0.03115.915-0.292-0.2920.0000.0000.0000.000
97A109GLU-1-0.902-0.95920.879-12.093-12.0930.0000.0000.0000.000
98A110GLU-1-0.863-0.93323.264-10.589-10.5890.0000.0000.0000.000
99A111ASN0-0.118-0.06421.7040.1860.1860.0000.0000.0000.000
100A112CYS0-0.073-0.02917.592-0.941-0.9410.0000.0000.0000.000
101A113CYS00.0370.03618.9100.4950.4950.0000.0000.0000.000
102A114VAL00.0520.03715.122-1.024-1.0240.0000.0000.0000.000
103A115MET0-0.038-0.00317.9070.7540.7540.0000.0000.0000.000
104A116ARG10.8740.92118.20010.94610.9460.0000.0000.0000.000
105A117TYR00.0130.01618.4180.4390.4390.0000.0000.0000.000
106A118THR00.0150.00520.841-0.446-0.4460.0000.0000.0000.000
107A119THR00.001-0.00421.8560.0310.0310.0000.0000.0000.000
108A120ALA0-0.005-0.00224.4860.1110.1110.0000.0000.0000.000
109A121GLY00.0070.00526.310-0.329-0.3290.0000.0000.0000.000
110A122GLN0-0.011-0.02523.2740.2610.2610.0000.0000.0000.000
111A123LEU0-0.068-0.04327.9500.0490.0490.0000.0000.0000.000
112A124ASP-1-0.864-0.93230.728-8.118-8.1180.0000.0000.0000.000
113A125ASN0-0.043-0.02429.734-0.106-0.1060.0000.0000.0000.000
114A126ILE0-0.0270.00227.633-0.114-0.1140.0000.0000.0000.000
115A127ILE0-0.063-0.02023.199-0.288-0.2880.0000.0000.0000.000
116A128SER00.0530.02824.6510.0220.0220.0000.0000.0000.000
117A129PRO00.0180.00524.021-0.310-0.3100.0000.0000.0000.000
118A130ARG10.7730.88618.82712.32812.3280.0000.0000.0000.000
119A131GLU-1-0.703-0.83118.360-12.380-12.3800.0000.0000.0000.000
120A132PHE0-0.037-0.01215.004-0.519-0.5190.0000.0000.0000.000
121A133VAL00.0280.00414.6540.7590.7590.0000.0000.0000.000
122A134ASP-1-0.757-0.84713.689-18.322-18.3220.0000.0000.0000.000
123A135PHE0-0.002-0.00412.6690.5720.5720.0000.0000.0000.000
124A136SER0-0.041-0.02114.6050.0740.0740.0000.0000.0000.000
125A137TYR00.0340.00716.6750.3460.3460.0000.0000.0000.000
126A138THR0-0.0030.00318.4860.1410.1410.0000.0000.0000.000
127A139VAL00.0040.01319.9090.1920.1920.0000.0000.0000.000
128A140GLY00.0300.02222.8160.1910.1910.0000.0000.0000.000
129A141TYR0-0.080-0.08322.109-0.905-0.9050.0000.0000.0000.000
130A142GLU-1-0.888-0.92325.091-11.260-11.2600.0000.0000.0000.000
131A143GLU-1-0.907-0.95127.852-9.247-9.2470.0000.0000.0000.000
132A144GLY0-0.043-0.03228.8570.3240.3240.0000.0000.0000.000
133A145LEU0-0.043-0.01325.824-0.168-0.1680.0000.0000.0000.000
134A146LEU0-0.025-0.01318.453-0.081-0.0810.0000.0000.0000.000
135A147SER0-0.018-0.01221.027-0.139-0.1390.0000.0000.0000.000
136A148CYS0-0.068-0.04216.135-0.300-0.3000.0000.0000.0000.000
137A149GLY00.0920.03414.8410.4260.4260.0000.0000.0000.000
138A150VAL0-0.046-0.0248.777-1.065-1.0650.0000.0000.0000.000
139A151SER00.0320.00310.4210.8970.8970.0000.0000.0000.000
140A152VAL0-0.082-0.0409.308-2.420-2.4200.0000.0000.0000.000
141A153GLU-1-0.879-0.9307.454-21.612-21.6120.0000.0000.0000.000
142A154TRP00.0560.00710.740-0.199-0.1990.0000.0000.0000.000
143A155SER0-0.046-0.03414.4100.5960.5960.0000.0000.0000.000
144A156GLU-1-0.905-0.93016.155-11.898-11.8980.0000.0000.0000.000
145A157THR00.0040.01618.4450.7510.7510.0000.0000.0000.000
146A158ARG10.8000.86420.1209.8619.8610.0000.0000.0000.000
147A159PRO0-0.045-0.00919.3160.0590.0590.0000.0000.0000.000
148A160GLU-1-0.872-0.90821.410-9.470-9.4700.0000.0000.0000.000
149A161PHE0-0.022-0.02221.7190.2490.2490.0000.0000.0000.000
150A162VAL00.001-0.00317.419-0.458-0.4580.0000.0000.0000.000
151A163ARG10.8380.91314.68114.61114.6110.0000.0000.0000.000
152A164GLY00.0200.02614.928-0.374-0.3740.0000.0000.0000.000
153A165TYR0-0.040-0.0426.741-0.524-0.5240.0000.0000.0000.000
154A166ASN0-0.017-0.01412.2500.3230.3230.0000.0000.0000.000
155A167HIS00.0080.0118.145-2.787-2.7870.0000.0000.0000.000
156A168PRO0-0.008-0.0049.4051.5161.5160.0000.0000.0000.000
157A169CYS0-0.028-0.00912.2051.0151.0150.0000.0000.0000.000
158A170GLY00.0500.00415.940-0.378-0.3780.0000.0000.0000.000
159A171TRP0-0.0130.00218.9390.5150.5150.0000.0000.0000.000
160A172PHE00.0400.01719.485-0.083-0.0830.0000.0000.0000.000
161A173CYS0-0.0190.00824.5660.4700.4700.0000.0000.0000.000
162A174VAL00.0270.01927.816-0.063-0.0630.0000.0000.0000.000
163A175PRO00.0760.03530.4820.1730.1730.0000.0000.0000.000
164A176LEU0-0.046-0.01733.938-0.173-0.1730.0000.0000.0000.000
165A177LYS10.8930.91935.5918.2438.2430.0000.0000.0000.000
166A178ASP-1-0.880-0.93037.148-7.703-7.7030.0000.0000.0000.000
167A179SER0-0.062-0.03139.4000.2970.2970.0000.0000.0000.000
168A180PRO00.0530.01138.001-0.130-0.1300.0000.0000.0000.000
169A181SER0-0.032-0.02438.215-0.084-0.0840.0000.0000.0000.000
170A182GLN0-0.0230.01737.7390.0000.0000.0000.0000.0000.000
171A183SER00.019-0.01432.326-0.160-0.1600.0000.0000.0000.000
172A184LEU0-0.068-0.02830.2200.1170.1170.0000.0000.0000.000
173A185LEU00.0180.00826.757-0.287-0.2870.0000.0000.0000.000
174A186THR0-0.020-0.02124.3080.2640.2640.0000.0000.0000.000
175A187GLY00.0110.02722.879-0.337-0.3370.0000.0000.0000.000
176A188TYR0-0.037-0.04618.5380.0780.0780.0000.0000.0000.000
177A189ILE00.0340.01518.187-0.333-0.3330.0000.0000.0000.000
178A190GLN00.0310.02213.0180.1880.1880.0000.0000.0000.000
179A191THR00.012-0.00614.006-0.843-0.8430.0000.0000.0000.000
180A192ASP-1-0.870-0.92812.606-17.318-17.3180.0000.0000.0000.000
181A193LEU00.028-0.00514.7530.0650.0650.0000.0000.0000.000
182A194ARG10.8480.94311.90817.32917.3290.0000.0000.0000.000
183A195GLY00.0020.00916.3430.7020.7020.0000.0000.0000.000
184A196MET0-0.025-0.01419.062-0.340-0.3400.0000.0000.0000.000
185A197ILE00.0310.00720.9530.5290.5290.0000.0000.0000.000
186A198PRO00.0200.01322.883-0.320-0.3200.0000.0000.0000.000
187A199GLN00.0440.00520.416-0.186-0.1860.0000.0000.0000.000
188A200SER00.0110.00223.714-0.144-0.1440.0000.0000.0000.000
189A201ALA00.0180.01826.2150.1420.1420.0000.0000.0000.000
190A202VAL00.0580.02619.9600.0940.0940.0000.0000.0000.000
191A203ASP-1-0.786-0.89422.686-12.973-12.9730.0000.0000.0000.000
192A204THR0-0.083-0.04624.4610.2120.2120.0000.0000.0000.000
193A205ALA00.013-0.00124.6470.1870.1870.0000.0000.0000.000
194A206MET00.0190.03119.6490.1080.1080.0000.0000.0000.000
195A207ALA00.0080.00023.7480.0190.0190.0000.0000.0000.000
196A208SER0-0.072-0.04026.5350.3220.3220.0000.0000.0000.000
197A209THR00.0290.01223.2510.2650.2650.0000.0000.0000.000
198A210LEU00.0140.00722.3160.1290.1290.0000.0000.0000.000
199A211ALA0-0.036-0.02426.3290.2310.2310.0000.0000.0000.000
200A212ASN0-0.023-0.02429.5660.5520.5520.0000.0000.0000.000
201A213PHE00.0780.06224.5660.2760.2760.0000.0000.0000.000
202A214TYR00.001-0.02827.2360.1280.1280.0000.0000.0000.000
203A215SER0-0.071-0.02731.3440.3280.3280.0000.0000.0000.000
204A216ASP-1-0.764-0.84631.408-8.668-8.6680.0000.0000.0000.000
205A217LEU00.0630.04529.1730.1910.1910.0000.0000.0000.000
206A218ARG10.7810.86832.5539.0539.0530.0000.0000.0000.000
207A219LYS10.8100.88635.5468.5188.5180.0000.0000.0000.000
208A220GLY00.0090.00834.8660.1780.1780.0000.0000.0000.000
209A221LEU0-0.027-0.01133.1680.0790.0790.0000.0000.0000.000
210A222ARG10.9040.97336.6347.6107.6100.0000.0000.0000.000