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: MN3MZ

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2609713.060559
FMO2-HF: Nuclear repulsion 2524296.632014
FMO2-HF: Total energy -85416.428546
FMO2-MP2: Total energy -85662.635248


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.
-93.303-91.58-0.02-0.615-1.0860.001
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 : 0.942 / q_NPA : 0.953
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].
3A15ILE00.0210.0173.780-1.3020.245-0.018-0.611-0.9170.001
4A16LYS11.0081.0214.78431.20831.311-0.001-0.004-0.0980.000
5A17LEU0-0.021-0.0159.064-1.212-1.2120.0000.0000.0000.000
6A18GLU-1-0.922-0.95811.134-19.348-19.3480.0000.0000.0000.000
7A19GLY00.0260.01513.2451.2031.2030.0000.0000.0000.000
8A20LEU00.0370.00814.214-0.841-0.8410.0000.0000.0000.000
9A21SER00.0220.00312.1080.0530.0530.0000.0000.0000.000
10A22ASP-1-0.846-0.8959.589-25.463-25.4630.0000.0000.0000.000
11A23VAL00.0550.02210.668-1.538-1.5380.0000.0000.0000.000
12A24ALA00.0000.01413.331-0.030-0.0300.0000.0000.0000.000
13A25SER0-0.034-0.0369.003-0.616-0.6160.0000.0000.0000.000
14A26ILE0-0.043-0.0226.660-1.899-1.8990.0000.0000.0000.000
15A27SER00.0240.00710.2450.2770.2770.0000.0000.0000.000
16A28THR0-0.016-0.00312.981-0.132-0.1320.0000.0000.0000.000
17A29LYS10.9450.9754.76744.98845.061-0.0010.000-0.0710.000
18A30LEU00.0290.00810.525-0.406-0.4060.0000.0000.0000.000
19A31GLN00.0330.03312.3700.4120.4120.0000.0000.0000.000
20A32ASN0-0.014-0.02312.2601.7821.7820.0000.0000.0000.000
21A33THR0-0.047-0.01310.122-0.558-0.5580.0000.0000.0000.000
22A34LEU0-0.014-0.01012.4700.8920.8920.0000.0000.0000.000
23A35ILE00.0090.00815.8091.0801.0800.0000.0000.0000.000
24A36GLN0-0.0100.01112.281-0.361-0.3610.0000.0000.0000.000
25A37TYR00.030-0.01111.4610.9230.9230.0000.0000.0000.000
26A38HIS00.0360.03917.0050.5340.5340.0000.0000.0000.000
27A39SER0-0.094-0.03118.1940.8050.8050.0000.0000.0000.000
28A40ILE0-0.0040.01216.2310.3370.3370.0000.0000.0000.000
29A41LYS10.8830.92120.12213.96313.9630.0000.0000.0000.000
30A42GLU-1-0.952-0.99123.457-10.636-10.6360.0000.0000.0000.000
31A43ASP-1-0.877-0.93025.467-11.031-11.0310.0000.0000.0000.000
32A44GLU-1-0.997-0.99020.501-14.840-14.8400.0000.0000.0000.000
33A45TRP0-0.105-0.04219.382-0.423-0.4230.0000.0000.0000.000
34A46ARG10.9800.98524.30511.45011.4500.0000.0000.0000.000
35A47VAL0-0.033-0.02226.696-0.234-0.2340.0000.0000.0000.000
36A48ALA0-0.059-0.02626.6100.1160.1160.0000.0000.0000.000
37A49LYS10.9690.96728.7809.6309.6300.0000.0000.0000.000
38A50LYS10.9751.00231.4538.8038.8030.0000.0000.0000.000
39A51VAL0-0.027-0.00634.1940.2730.2730.0000.0000.0000.000
40A52LYS10.9380.96336.4997.4637.4630.0000.0000.0000.000
41A53ASP-1-0.869-0.93236.382-8.153-8.1530.0000.0000.0000.000
42A54VAL0-0.0120.00930.320-0.177-0.1770.0000.0000.0000.000
43A55THR0-0.052-0.01729.9760.3260.3260.0000.0000.0000.000
44A56VAL00.0180.01025.910-0.279-0.2790.0000.0000.0000.000
45A57TRP00.0270.00124.9160.3050.3050.0000.0000.0000.000
46A58ARG10.8840.94622.50811.88111.8810.0000.0000.0000.000
47A59LYS10.9630.99115.85718.49018.4900.0000.0000.0000.000
48A60PRO00.0160.00417.683-0.295-0.2950.0000.0000.0000.000
49A61SER0-0.017-0.02713.401-0.753-0.7530.0000.0000.0000.000
50A62GLU-1-0.956-0.97810.392-24.459-24.4590.0000.0000.0000.000
51A63GLU-1-0.963-0.9757.842-38.069-38.0690.0000.0000.0000.000
52A64PHE0-0.054-0.0399.025-0.733-0.7330.0000.0000.0000.000
53A65ASN0-0.026-0.00711.5430.8250.8250.0000.0000.0000.000
54A66GLY00.0410.02115.0070.9440.9440.0000.0000.0000.000
55A67TYR0-0.068-0.02816.968-0.387-0.3870.0000.0000.0000.000
56A68LEU00.0150.02015.549-0.236-0.2360.0000.0000.0000.000
57A69TYR00.002-0.02118.0801.2231.2230.0000.0000.0000.000
58A70LYS10.9841.00920.74512.40712.4070.0000.0000.0000.000
59A71ALA0-0.015-0.00523.1360.5340.5340.0000.0000.0000.000
60A72GLN00.0240.01926.242-0.568-0.5680.0000.0000.0000.000
61A73GLY00.0180.00128.8650.3070.3070.0000.0000.0000.000
62A74VAL00.0130.01931.721-0.214-0.2140.0000.0000.0000.000
63A75MET0-0.020-0.00231.9490.0710.0710.0000.0000.0000.000
64A76ASP-1-0.922-0.96235.086-7.625-7.6250.0000.0000.0000.000
65A77ASP-1-0.727-0.83935.588-8.241-8.2410.0000.0000.0000.000
66A78VAL0-0.0030.02235.883-0.205-0.2050.0000.0000.0000.000
67A79VAL00.0380.00029.715-0.121-0.1210.0000.0000.0000.000
68A80ASN0-0.009-0.01430.985-0.452-0.4520.0000.0000.0000.000
69A81ASN00.024-0.00831.620-0.226-0.2260.0000.0000.0000.000
70A82VAL00.0060.00029.212-0.122-0.1220.0000.0000.0000.000
71A83ILE0-0.014-0.02325.282-0.261-0.2610.0000.0000.0000.000
72A84ASP-1-0.902-0.94927.309-10.166-10.1660.0000.0000.0000.000
73A85HIS0-0.064-0.02529.2570.0890.0890.0000.0000.0000.000
74A86ILE0-0.035-0.00223.903-0.127-0.1270.0000.0000.0000.000
75A87ARG10.9010.96423.74011.18211.1820.0000.0000.0000.000
76A88PRO0-0.006-0.00521.0140.3610.3610.0000.0000.0000.000
77A89GLY00.0640.02823.9820.0740.0740.0000.0000.0000.000
78A90PRO00.002-0.02127.282-0.049-0.0490.0000.0000.0000.000
79A91TRP00.0540.04330.5910.0920.0920.0000.0000.0000.000
80A92ARG10.8030.91523.02911.97511.9750.0000.0000.0000.000
81A93LEU0-0.041-0.03527.547-0.013-0.0130.0000.0000.0000.000
82A94ASP-1-0.917-0.94529.378-8.637-8.6370.0000.0000.0000.000
83A95TRP0-0.091-0.06327.7530.1840.1840.0000.0000.0000.000
84A96ASP-1-0.818-0.91026.071-10.972-10.9720.0000.0000.0000.000
85A97ARG10.8520.89829.4039.0039.0030.0000.0000.0000.000
86A98LEU0-0.086-0.03123.6980.0770.0770.0000.0000.0000.000
87A99MET0-0.046-0.01822.611-0.166-0.1660.0000.0000.0000.000
88A100THR0-0.0070.01426.5690.2000.2000.0000.0000.0000.000
89A101SER0-0.021-0.02325.7800.2390.2390.0000.0000.0000.000
90A102LEU00.021-0.01523.705-0.470-0.4700.0000.0000.0000.000
91A103ASP-1-0.892-0.92823.823-10.277-10.2770.0000.0000.0000.000
92A104VAL0-0.025-0.02522.291-0.590-0.5900.0000.0000.0000.000
93A105LEU0-0.080-0.05018.3620.3600.3600.0000.0000.0000.000
94A106GLU-1-0.876-0.95119.398-13.595-13.5950.0000.0000.0000.000
95A107HIS0-0.034-0.00420.714-0.489-0.4890.0000.0000.0000.000
96A108PHE0-0.025-0.02415.924-0.237-0.2370.0000.0000.0000.000
97A109GLU-1-0.898-0.95920.699-12.169-12.1690.0000.0000.0000.000
98A110GLU-1-0.898-0.95323.081-10.642-10.6420.0000.0000.0000.000
99A111ASN0-0.089-0.04021.7420.2310.2310.0000.0000.0000.000
100A112CYS0-0.066-0.03117.371-0.949-0.9490.0000.0000.0000.000
101A113CYS00.0350.03218.7640.3740.3740.0000.0000.0000.000
102A114VAL00.0310.03614.850-1.075-1.0750.0000.0000.0000.000
103A115MET0-0.0110.00317.7530.7640.7640.0000.0000.0000.000
104A116ARG10.9480.97618.20111.01011.0100.0000.0000.0000.000
105A117TYR00.0100.02018.4520.3890.3890.0000.0000.0000.000
106A118THR0-0.002-0.01820.842-0.458-0.4580.0000.0000.0000.000
107A119THR00.0060.00021.9060.0270.0270.0000.0000.0000.000
108A120ALA00.0130.00424.4880.1210.1210.0000.0000.0000.000
109A121GLY0-0.013-0.00526.312-0.326-0.3260.0000.0000.0000.000
110A122GLN0-0.003-0.02123.1270.2370.2370.0000.0000.0000.000
111A123LEU0-0.071-0.04227.7290.0430.0430.0000.0000.0000.000
112A124ASP-1-0.891-0.94330.730-8.139-8.1390.0000.0000.0000.000
113A125ASN00.000-0.00429.756-0.025-0.0250.0000.0000.0000.000
114A126ILE0-0.033-0.00227.467-0.114-0.1140.0000.0000.0000.000
115A127ILE0-0.069-0.02423.209-0.293-0.2930.0000.0000.0000.000
116A128SER00.0460.02224.4690.0350.0350.0000.0000.0000.000
117A129PRO00.0130.00124.023-0.320-0.3200.0000.0000.0000.000
118A130ARG10.7550.85918.76312.54212.5420.0000.0000.0000.000
119A131GLU-1-0.717-0.81818.463-12.360-12.3600.0000.0000.0000.000
120A132PHE0-0.035-0.01415.099-0.582-0.5820.0000.0000.0000.000
121A133VAL00.0140.00214.5420.8080.8080.0000.0000.0000.000
122A134ASP-1-0.743-0.84513.691-18.718-18.7180.0000.0000.0000.000
123A135PHE0-0.004-0.00712.6650.6150.6150.0000.0000.0000.000
124A136SER0-0.036-0.01514.6040.0560.0560.0000.0000.0000.000
125A137TYR00.0450.00916.6300.3840.3840.0000.0000.0000.000
126A138THR00.0000.00318.5010.1290.1290.0000.0000.0000.000
127A139VAL00.0000.00219.7000.1930.1930.0000.0000.0000.000
128A140GLY00.0300.02022.7000.1920.1920.0000.0000.0000.000
129A141TYR0-0.052-0.04422.188-0.909-0.9090.0000.0000.0000.000
130A142GLU-1-0.922-0.95824.756-11.172-11.1720.0000.0000.0000.000
131A143GLU-1-0.903-0.95227.558-9.312-9.3120.0000.0000.0000.000
132A144GLY0-0.043-0.03128.5130.3280.3280.0000.0000.0000.000
133A145LEU0-0.049-0.01425.743-0.188-0.1880.0000.0000.0000.000
134A146LEU0-0.014-0.01017.968-0.079-0.0790.0000.0000.0000.000
135A147SER0-0.028-0.01321.036-0.148-0.1480.0000.0000.0000.000
136A148CYS0-0.059-0.03716.001-0.274-0.2740.0000.0000.0000.000
137A149GLY00.0850.02514.8380.4420.4420.0000.0000.0000.000
138A150VAL0-0.052-0.0288.726-1.108-1.1080.0000.0000.0000.000
139A151SER00.0260.01810.3290.9380.9380.0000.0000.0000.000
140A152VAL0-0.075-0.0379.306-2.517-2.5170.0000.0000.0000.000
141A153GLU-1-0.977-1.0037.958-20.860-20.8600.0000.0000.0000.000
142A154TRP00.035-0.00310.740-0.146-0.1460.0000.0000.0000.000
143A155SER0-0.046-0.03414.4100.6210.6210.0000.0000.0000.000
144A156GLU-1-0.911-0.92816.162-11.881-11.8810.0000.0000.0000.000
145A157THR0-0.0160.00718.4390.8010.8010.0000.0000.0000.000
146A158ARG10.9200.94420.1209.9839.9830.0000.0000.0000.000
147A159PRO0-0.055-0.01519.3300.0680.0680.0000.0000.0000.000
148A160GLU-1-1.003-1.00821.412-9.583-9.5830.0000.0000.0000.000
149A161PHE0-0.012-0.02021.6720.2270.2270.0000.0000.0000.000
150A162VAL0-0.015-0.01017.454-0.479-0.4790.0000.0000.0000.000
151A163ARG10.9010.94214.56414.98314.9830.0000.0000.0000.000
152A164GLY00.0200.03314.931-0.360-0.3600.0000.0000.0000.000
153A165TYR0-0.030-0.0376.568-0.646-0.6460.0000.0000.0000.000
154A166ASN0-0.024-0.03212.2520.3290.3290.0000.0000.0000.000
155A167HIS00.0160.0117.777-2.708-2.7080.0000.0000.0000.000
156A168PRO0-0.005-0.0019.3201.6321.6320.0000.0000.0000.000
157A169CYS0-0.022-0.00212.1781.0421.0420.0000.0000.0000.000
158A170GLY00.0430.00215.914-0.384-0.3840.0000.0000.0000.000
159A171TRP0-0.0100.00918.9230.5020.5020.0000.0000.0000.000
160A172PHE00.0330.01419.178-0.090-0.0900.0000.0000.0000.000
161A173CYS0-0.0370.00324.1950.5010.5010.0000.0000.0000.000
162A174VAL00.0420.02427.476-0.077-0.0770.0000.0000.0000.000
163A175PRO00.0830.03630.1120.1790.1790.0000.0000.0000.000
164A176LEU0-0.045-0.01533.595-0.176-0.1760.0000.0000.0000.000
165A177LYS10.9380.96335.2538.4268.4260.0000.0000.0000.000
166A178ASP-1-0.918-0.97136.836-7.694-7.6940.0000.0000.0000.000
167A179SER0-0.072-0.03339.0640.3010.3010.0000.0000.0000.000
168A180PRO00.0600.01537.633-0.142-0.1420.0000.0000.0000.000
169A181SER0-0.007-0.00737.885-0.084-0.0840.0000.0000.0000.000
170A182GLN0-0.059-0.00437.4980.0170.0170.0000.0000.0000.000
171A183SER00.028-0.00632.190-0.158-0.1580.0000.0000.0000.000
172A184LEU0-0.070-0.02929.9920.1240.1240.0000.0000.0000.000
173A185LEU00.0220.01026.569-0.291-0.2910.0000.0000.0000.000
174A186THR0-0.023-0.01623.7810.2610.2610.0000.0000.0000.000
175A187GLY00.0080.01922.856-0.345-0.3450.0000.0000.0000.000
176A188TYR0-0.045-0.05018.2190.0780.0780.0000.0000.0000.000
177A189ILE00.0440.02018.173-0.348-0.3480.0000.0000.0000.000
178A190GLN00.0280.02512.813-0.094-0.0940.0000.0000.0000.000
179A191THR00.011-0.00414.007-0.835-0.8350.0000.0000.0000.000
180A192ASP-1-0.859-0.92312.770-17.418-17.4180.0000.0000.0000.000
181A193LEU00.034-0.00114.7540.0680.0680.0000.0000.0000.000
182A194ARG10.8460.93912.10117.19217.1920.0000.0000.0000.000
183A195GLY0-0.0010.01716.3450.7360.7360.0000.0000.0000.000
184A196MET0-0.020-0.01219.063-0.328-0.3280.0000.0000.0000.000
185A197ILE00.0260.00520.7640.5350.5350.0000.0000.0000.000
186A198PRO00.0190.01322.885-0.326-0.3260.0000.0000.0000.000
187A199GLN00.0390.00519.856-0.118-0.1180.0000.0000.0000.000
188A200SER00.0160.00923.715-0.144-0.1440.0000.0000.0000.000
189A201ALA00.0120.01226.1070.1440.1440.0000.0000.0000.000
190A202VAL00.0510.02319.9720.0830.0830.0000.0000.0000.000
191A203ASP-1-0.833-0.92722.739-12.818-12.8180.0000.0000.0000.000
192A204THR0-0.067-0.03524.4620.2140.2140.0000.0000.0000.000
193A205ALA00.012-0.00124.6680.1810.1810.0000.0000.0000.000
194A206MET00.0020.02419.9090.0500.0500.0000.0000.0000.000
195A207ALA00.0110.00123.7490.0060.0060.0000.0000.0000.000
196A208SER0-0.076-0.04226.5360.3080.3080.0000.0000.0000.000
197A209THR00.0320.01123.3150.2500.2500.0000.0000.0000.000
198A210LEU00.0130.00722.3340.1160.1160.0000.0000.0000.000
199A211ALA0-0.035-0.02126.3300.2360.2360.0000.0000.0000.000
200A212ASN0-0.036-0.03529.4950.4960.4960.0000.0000.0000.000
201A213PHE00.0630.06124.9220.2610.2610.0000.0000.0000.000
202A214TYR0-0.003-0.02527.2470.1140.1140.0000.0000.0000.000
203A215SER0-0.083-0.04031.3250.3360.3360.0000.0000.0000.000
204A216ASP-1-0.771-0.86931.301-8.888-8.8880.0000.0000.0000.000
205A217LEU00.0470.02929.2240.1940.1940.0000.0000.0000.000
206A218ARG10.8070.88732.5249.0829.0820.0000.0000.0000.000
207A219LYS10.8800.93735.8338.4528.4520.0000.0000.0000.000
208A220GLY00.0110.00934.8400.1830.1830.0000.0000.0000.000
209A221LEU0-0.017-0.00733.2940.0770.0770.0000.0000.0000.000
210A222ARG10.9040.97236.6157.6417.6410.0000.0000.0000.000