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: 2N2KR

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2610739.447658
FMO2-HF: Nuclear repulsion 2525321.931118
FMO2-HF: Total energy -85417.51654
FMO2-MP2: Total energy -85663.753316


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.
-97.53-96.457-0.002-0.406-0.6650.001
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 : 0.963 / 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].
3A15ILE00.0660.0393.886-0.9380.135-0.002-0.406-0.6650.001
4A16LYS10.8540.9395.20930.48230.4820.0000.0000.0000.000
5A17LEU0-0.034-0.0318.694-1.220-1.2200.0000.0000.0000.000
6A18GLU-1-0.896-0.94810.826-19.212-19.2120.0000.0000.0000.000
7A19GLY00.0140.00813.3971.1691.1690.0000.0000.0000.000
8A20LEU00.0310.00214.241-0.873-0.8730.0000.0000.0000.000
9A21SER0-0.008-0.01912.5890.3380.3380.0000.0000.0000.000
10A22ASP-1-0.802-0.8599.860-23.655-23.6550.0000.0000.0000.000
11A23VAL00.0570.02911.157-1.139-1.1390.0000.0000.0000.000
12A24ALA00.0300.03513.778-0.052-0.0520.0000.0000.0000.000
13A25SER0-0.029-0.0249.574-0.460-0.4600.0000.0000.0000.000
14A26ILE0-0.031-0.0166.807-1.875-1.8750.0000.0000.0000.000
15A27SER00.0110.00010.5470.4820.4820.0000.0000.0000.000
16A28THR0-0.019-0.02213.405-0.133-0.1330.0000.0000.0000.000
17A29LYS10.9140.9556.03834.90534.9050.0000.0000.0000.000
18A30LEU0-0.0020.02111.070-0.087-0.0870.0000.0000.0000.000
19A31GLN00.0800.04813.1260.4470.4470.0000.0000.0000.000
20A32ASN00.002-0.00812.9611.6801.6800.0000.0000.0000.000
21A33THR0-0.033-0.02710.717-0.902-0.9020.0000.0000.0000.000
22A34LEU0-0.0130.00513.0000.7000.7000.0000.0000.0000.000
23A35ILE00.0170.01316.4240.9620.9620.0000.0000.0000.000
24A36GLN0-0.027-0.00412.533-0.221-0.2210.0000.0000.0000.000
25A37TYR0-0.003-0.01011.5931.2901.2900.0000.0000.0000.000
26A38HIS00.0400.04117.5050.5560.5560.0000.0000.0000.000
27A39SER0-0.081-0.03718.9610.7630.7630.0000.0000.0000.000
28A40ILE0-0.0080.00916.9780.5350.5350.0000.0000.0000.000
29A41LYS10.8970.93721.29413.50813.5080.0000.0000.0000.000
30A42GLU-1-0.875-0.94324.505-10.661-10.6610.0000.0000.0000.000
31A43ASP-1-0.899-0.94725.733-11.218-11.2180.0000.0000.0000.000
32A44GLU-1-0.935-0.97120.013-15.262-15.2620.0000.0000.0000.000
33A45TRP0-0.081-0.04319.700-0.360-0.3600.0000.0000.0000.000
34A46ARG10.9790.98625.11011.53311.5330.0000.0000.0000.000
35A47VAL0-0.009-0.01126.910-0.207-0.2070.0000.0000.0000.000
36A48ALA0-0.055-0.02626.3170.0440.0440.0000.0000.0000.000
37A49LYS10.9380.96028.4429.4439.4430.0000.0000.0000.000
38A50LYS10.9490.98131.2248.9778.9770.0000.0000.0000.000
39A51VAL00.0070.00934.0260.2450.2450.0000.0000.0000.000
40A52LYS10.8400.89536.3397.4987.4980.0000.0000.0000.000
41A53ASP-1-0.799-0.86836.317-7.832-7.8320.0000.0000.0000.000
42A54VAL00.0060.01330.030-0.154-0.1540.0000.0000.0000.000
43A55THR0-0.056-0.01930.3460.3330.3330.0000.0000.0000.000
44A56VAL00.0260.01525.985-0.263-0.2630.0000.0000.0000.000
45A57TRP0-0.054-0.04425.4840.3160.3160.0000.0000.0000.000
46A58ARG10.8590.93222.27911.54611.5460.0000.0000.0000.000
47A59LYS10.8580.94416.81118.08718.0870.0000.0000.0000.000
48A60PRO00.004-0.00918.473-0.289-0.2890.0000.0000.0000.000
49A61SER00.001-0.01413.128-0.742-0.7420.0000.0000.0000.000
50A62GLU-1-0.866-0.93111.100-20.987-20.9870.0000.0000.0000.000
51A63GLU-1-0.941-0.9597.990-35.244-35.2440.0000.0000.0000.000
52A64PHE0-0.022-0.0298.575-0.975-0.9750.0000.0000.0000.000
53A65ASN0-0.025-0.01111.0330.9690.9690.0000.0000.0000.000
54A66GLY00.0170.00714.3500.9280.9280.0000.0000.0000.000
55A67TYR0-0.057-0.02316.499-0.231-0.2310.0000.0000.0000.000
56A68LEU00.0080.03015.757-0.025-0.0250.0000.0000.0000.000
57A69TYR0-0.034-0.06217.7081.1971.1970.0000.0000.0000.000
58A70LYS10.9440.99120.33212.44912.4490.0000.0000.0000.000
59A71ALA0-0.016-0.01623.0090.5160.5160.0000.0000.0000.000
60A72GLN00.0210.02726.158-0.523-0.5230.0000.0000.0000.000
61A73GLY00.0140.00228.9560.2950.2950.0000.0000.0000.000
62A74VAL00.0100.01831.958-0.191-0.1910.0000.0000.0000.000
63A75MET00.0050.01231.8150.1270.1270.0000.0000.0000.000
64A76ASP-1-0.872-0.94335.014-7.516-7.5160.0000.0000.0000.000
65A77ASP-1-0.753-0.86735.597-8.333-8.3330.0000.0000.0000.000
66A78VAL00.0030.02035.791-0.205-0.2050.0000.0000.0000.000
67A79VAL00.027-0.00729.708-0.105-0.1050.0000.0000.0000.000
68A80ASN0-0.034-0.02030.782-0.268-0.2680.0000.0000.0000.000
69A81ASN00.002-0.00531.206-0.206-0.2060.0000.0000.0000.000
70A82VAL00.0400.01929.615-0.125-0.1250.0000.0000.0000.000
71A83ILE0-0.003-0.01125.258-0.273-0.2730.0000.0000.0000.000
72A84ASP-1-0.828-0.91227.251-10.373-10.3730.0000.0000.0000.000
73A85HIS0-0.055-0.01929.2520.1310.1310.0000.0000.0000.000
74A86ILE0-0.042-0.02023.878-0.102-0.1020.0000.0000.0000.000
75A87ARG10.8690.93623.71210.84410.8440.0000.0000.0000.000
76A88PRO0-0.019-0.01420.8330.3380.3380.0000.0000.0000.000
77A89GLY00.0850.04223.8740.0800.0800.0000.0000.0000.000
78A90PRO0-0.008-0.01327.419-0.037-0.0370.0000.0000.0000.000
79A91TRP00.0420.02430.702-0.002-0.0020.0000.0000.0000.000
80A92ARG10.7920.90623.09011.70611.7060.0000.0000.0000.000
81A93LEU0-0.003-0.02227.665-0.017-0.0170.0000.0000.0000.000
82A94ASP-1-0.925-0.95829.508-8.506-8.5060.0000.0000.0000.000
83A95TRP0-0.094-0.05827.4690.2340.2340.0000.0000.0000.000
84A96ASP-1-0.810-0.90125.854-10.876-10.8760.0000.0000.0000.000
85A97ARG10.8190.87429.0388.8448.8440.0000.0000.0000.000
86A98LEU0-0.069-0.01423.5730.0940.0940.0000.0000.0000.000
87A99MET0-0.045-0.01922.401-0.142-0.1420.0000.0000.0000.000
88A100THR0-0.013-0.02926.2020.3300.3300.0000.0000.0000.000
89A101SER0-0.0210.00426.2290.1650.1650.0000.0000.0000.000
90A102LEU0-0.019-0.01223.900-0.453-0.4530.0000.0000.0000.000
91A103ASP-1-0.800-0.86623.551-10.315-10.3150.0000.0000.0000.000
92A104VAL0-0.011-0.02322.431-0.575-0.5750.0000.0000.0000.000
93A105LEU0-0.074-0.03318.0580.3560.3560.0000.0000.0000.000
94A106GLU-1-0.870-0.95219.694-13.478-13.4780.0000.0000.0000.000
95A107HIS0-0.070-0.03620.986-0.510-0.5100.0000.0000.0000.000
96A108PHE0-0.029-0.02416.219-0.085-0.0850.0000.0000.0000.000
97A109GLU-1-0.885-0.94621.133-12.080-12.0800.0000.0000.0000.000
98A110GLU-1-0.873-0.92823.447-10.598-10.5980.0000.0000.0000.000
99A111ASN0-0.107-0.06021.6830.2500.2500.0000.0000.0000.000
100A112CYS0-0.090-0.04217.655-0.917-0.9170.0000.0000.0000.000
101A113CYS00.0150.02218.7510.4900.4900.0000.0000.0000.000
102A114VAL00.0400.02215.034-1.102-1.1020.0000.0000.0000.000
103A115MET0-0.047-0.00817.6670.7410.7410.0000.0000.0000.000
104A116ARG10.8490.89317.89811.04211.0420.0000.0000.0000.000
105A117TYR00.0140.02118.4300.3930.3930.0000.0000.0000.000
106A118THR00.000-0.00820.641-0.342-0.3420.0000.0000.0000.000
107A119THR00.001-0.00821.914-0.093-0.0930.0000.0000.0000.000
108A120ALA00.0450.02524.5060.0830.0830.0000.0000.0000.000
109A121GLY00.0110.00925.792-0.376-0.3760.0000.0000.0000.000
110A122GLN0-0.036-0.03823.2800.2830.2830.0000.0000.0000.000
111A123LEU0-0.066-0.04727.7830.0330.0330.0000.0000.0000.000
112A124ASP-1-0.850-0.92330.415-8.144-8.1440.0000.0000.0000.000
113A125ASN0-0.045-0.02929.125-0.125-0.1250.0000.0000.0000.000
114A126ILE0-0.0350.00327.680-0.145-0.1450.0000.0000.0000.000
115A127ILE0-0.062-0.01322.906-0.313-0.3130.0000.0000.0000.000
116A128SER00.0710.03124.3560.0490.0490.0000.0000.0000.000
117A129PRO00.0130.00223.852-0.330-0.3300.0000.0000.0000.000
118A130ARG10.7710.88318.56312.23012.2300.0000.0000.0000.000
119A131GLU-1-0.697-0.83618.126-12.373-12.3730.0000.0000.0000.000
120A132PHE0-0.042-0.01214.971-0.568-0.5680.0000.0000.0000.000
121A133VAL00.0270.00414.6540.7610.7610.0000.0000.0000.000
122A134ASP-1-0.743-0.82813.549-18.368-18.3680.0000.0000.0000.000
123A135PHE00.0000.00612.5980.5880.5880.0000.0000.0000.000
124A136SER0-0.007-0.01514.544-0.262-0.2620.0000.0000.0000.000
125A137TYR00.0180.00116.7140.5100.5100.0000.0000.0000.000
126A138THR0-0.030-0.01818.5480.3450.3450.0000.0000.0000.000
127A139VAL0-0.0090.01520.4500.1450.1450.0000.0000.0000.000
128A140GLY00.0460.02423.2210.2370.2370.0000.0000.0000.000
129A141TYR0-0.080-0.08922.455-0.942-0.9420.0000.0000.0000.000
130A142GLU-1-0.866-0.91425.419-11.139-11.1390.0000.0000.0000.000
131A143GLU-1-0.934-0.96328.326-9.212-9.2120.0000.0000.0000.000
132A144GLY0-0.026-0.02529.4010.3340.3340.0000.0000.0000.000
133A145LEU0-0.0220.00425.950-0.201-0.2010.0000.0000.0000.000
134A146LEU0-0.023-0.00818.687-0.090-0.0900.0000.0000.0000.000
135A147SER0-0.018-0.00921.123-0.071-0.0710.0000.0000.0000.000
136A148CYS0-0.052-0.03516.266-0.253-0.2530.0000.0000.0000.000
137A149GLY00.0990.03914.4890.2260.2260.0000.0000.0000.000
138A150VAL0-0.041-0.0188.445-0.867-0.8670.0000.0000.0000.000
139A151SER00.019-0.01810.4860.7640.7640.0000.0000.0000.000
140A152VAL0-0.063-0.0259.153-2.686-2.6860.0000.0000.0000.000
141A153GLU-1-0.830-0.8997.111-22.140-22.1400.0000.0000.0000.000
142A154TRP00.0600.02010.450-0.106-0.1060.0000.0000.0000.000
143A155SER0-0.038-0.03114.2700.5140.5140.0000.0000.0000.000
144A156GLU-1-0.920-0.94015.919-11.961-11.9610.0000.0000.0000.000
145A157THR00.0020.02018.2060.7520.7520.0000.0000.0000.000
146A158ARG10.8030.85519.6839.8359.8350.0000.0000.0000.000
147A159PRO0-0.035-0.00619.1350.0020.0020.0000.0000.0000.000
148A160GLU-1-0.844-0.88521.201-9.470-9.4700.0000.0000.0000.000
149A161PHE0-0.026-0.02021.6990.2790.2790.0000.0000.0000.000
150A162VAL0-0.014-0.01117.258-0.462-0.4620.0000.0000.0000.000
151A163ARG10.8110.89814.20414.49114.4910.0000.0000.0000.000
152A164GLY00.0440.03714.729-0.328-0.3280.0000.0000.0000.000
153A165TYR0-0.105-0.0926.940-1.570-1.5700.0000.0000.0000.000
154A166ASN0-0.008-0.00911.9890.1720.1720.0000.0000.0000.000
155A167HIS00.0200.0197.913-2.847-2.8470.0000.0000.0000.000
156A168PRO0-0.035-0.0148.9511.6031.6030.0000.0000.0000.000
157A169CYS0-0.024-0.00411.8201.0521.0520.0000.0000.0000.000
158A170GLY00.041-0.00215.605-0.345-0.3450.0000.0000.0000.000
159A171TRP0-0.014-0.00318.7280.4950.4950.0000.0000.0000.000
160A172PHE00.0450.02919.724-0.083-0.0830.0000.0000.0000.000
161A173CYS0-0.037-0.00824.4570.4360.4360.0000.0000.0000.000
162A174VAL00.0280.02228.060-0.059-0.0590.0000.0000.0000.000
163A175PRO00.0700.02730.8170.1610.1610.0000.0000.0000.000
164A176LEU0-0.054-0.02234.471-0.150-0.1500.0000.0000.0000.000
165A177LYS10.8410.88836.0938.1538.1530.0000.0000.0000.000
166A178ASP-1-0.850-0.91437.628-7.648-7.6480.0000.0000.0000.000
167A179SER0-0.042-0.01540.0400.2910.2910.0000.0000.0000.000
168A180PRO00.033-0.00238.337-0.104-0.1040.0000.0000.0000.000
169A181SER0-0.024-0.01838.446-0.078-0.0780.0000.0000.0000.000
170A182GLN0-0.0300.03037.791-0.006-0.0060.0000.0000.0000.000
171A183SER00.012-0.01932.357-0.145-0.1450.0000.0000.0000.000
172A184LEU0-0.071-0.01830.3690.1190.1190.0000.0000.0000.000
173A185LEU00.0280.01526.843-0.234-0.2340.0000.0000.0000.000
174A186THR0-0.017-0.02424.6460.3150.3150.0000.0000.0000.000
175A187GLY00.0250.02522.799-0.361-0.3610.0000.0000.0000.000
176A188TYR0-0.034-0.04518.3300.0970.0970.0000.0000.0000.000
177A189ILE00.0190.00717.949-0.303-0.3030.0000.0000.0000.000
178A190GLN00.0290.01412.6530.1370.1370.0000.0000.0000.000
179A191THR00.005-0.00913.740-0.848-0.8480.0000.0000.0000.000
180A192ASP-1-0.866-0.92212.136-17.330-17.3300.0000.0000.0000.000
181A193LEU00.031-0.00314.4050.1440.1440.0000.0000.0000.000
182A194ARG10.8360.92911.51217.50417.5040.0000.0000.0000.000
183A195GLY00.0220.02215.9190.7290.7290.0000.0000.0000.000
184A196MET0-0.028-0.01518.529-0.246-0.2460.0000.0000.0000.000
185A197ILE00.0430.01620.3220.4540.4540.0000.0000.0000.000
186A198PRO00.0100.00522.607-0.281-0.2810.0000.0000.0000.000
187A199GLN00.0410.00819.774-0.098-0.0980.0000.0000.0000.000
188A200SER00.0080.00323.302-0.136-0.1360.0000.0000.0000.000
189A201ALA00.0200.01825.9240.1750.1750.0000.0000.0000.000
190A202VAL00.0570.02719.5620.0920.0920.0000.0000.0000.000
191A203ASP-1-0.757-0.85422.089-13.154-13.1540.0000.0000.0000.000
192A204THR0-0.069-0.03823.9920.2340.2340.0000.0000.0000.000
193A205ALA00.0030.00124.2390.2210.2210.0000.0000.0000.000
194A206MET00.0220.03319.4560.1490.1490.0000.0000.0000.000
195A207ALA00.0160.00123.4630.0920.0920.0000.0000.0000.000
196A208SER0-0.067-0.03326.4380.3610.3610.0000.0000.0000.000
197A209THR00.0300.01623.1210.2540.2540.0000.0000.0000.000
198A210LEU00.000-0.00422.1650.1560.1560.0000.0000.0000.000
199A211ALA0-0.035-0.02326.2010.2450.2450.0000.0000.0000.000
200A212ASN0-0.029-0.02229.5600.5430.5430.0000.0000.0000.000
201A213PHE00.0980.06924.4750.3120.3120.0000.0000.0000.000
202A214TYR0-0.015-0.03826.9980.1150.1150.0000.0000.0000.000
203A215SER0-0.087-0.04431.2490.3760.3760.0000.0000.0000.000
204A216ASP-1-0.788-0.84431.517-8.570-8.5700.0000.0000.0000.000
205A217LEU00.0820.05429.0030.2050.2050.0000.0000.0000.000
206A218ARG10.7660.85332.2758.9668.9660.0000.0000.0000.000
207A219LYS10.8140.89435.6068.4698.4690.0000.0000.0000.000
208A220GLY00.0030.00134.5020.1790.1790.0000.0000.0000.000
209A221LEU0-0.032-0.01332.9610.1070.1070.0000.0000.0000.000
210A222ARG10.9070.97236.5677.6317.6310.0000.0000.0000.000