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: RY8R8

Calculation Name: 3BRU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BRU

Chain ID: A

ChEMBL ID:

UniProt ID: Q3J6K8

Base Structure: X-ray

Registration Date: 2023-09-27

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2047072.097135
FMO2-HF: Nuclear repulsion 1972562.703712
FMO2-HF: Total energy -74509.393422
FMO2-MP2: Total energy -74728.938216


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:24:ASP)


Summations of interaction energy for fragment #1(A:24:ASP)
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.
-146.743-154.70434.675-14.152-12.5610.148
Interaction energy analysis for fragmet #1(A:24:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.820 / q_NPA : -0.897
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].
3A26SER0-0.064-0.0431.609-43.457-55.74530.044-11.044-6.7120.102
4A27LEU00.0230.0152.228-32.329-28.3264.629-2.984-5.6490.045
5A28ALA00.0340.0274.181-12.397-12.0900.003-0.117-0.1930.001
6A29HIS00.0250.0146.069-3.096-3.0960.0000.0000.0000.000
7A30GLN00.0550.0155.589-5.470-5.4700.0000.0000.0000.000
8A31SER0-0.023-0.0245.163-2.471-2.4710.0000.0000.0000.000
9A32LEU0-0.031-0.0077.779-2.928-2.9280.0000.0000.0000.000
10A33ILE00.0260.01710.854-1.926-1.9260.0000.0000.0000.000
11A34ARG10.8890.93910.251-22.448-22.4480.0000.0000.0000.000
12A35ALA00.002-0.00111.256-1.665-1.6650.0000.0000.0000.000
13A36GLY00.005-0.01313.088-1.381-1.3810.0000.0000.0000.000
14A37LEU00.0320.01515.590-1.032-1.0320.0000.0000.0000.000
15A38GLU-1-0.827-0.86914.24217.87817.8780.0000.0000.0000.000
16A39HIS10.8130.88014.862-17.317-17.3170.0000.0000.0000.000
17A40LEU0-0.0070.00718.830-0.649-0.6490.0000.0000.0000.000
18A41THR00.0280.00820.140-0.531-0.5310.0000.0000.0000.000
19A42GLU-1-0.802-0.86820.52413.10313.1030.0000.0000.0000.000
20A43LYS10.8000.87421.008-13.421-13.4210.0000.0000.0000.000
21A44GLY00.0880.04323.873-0.297-0.2970.0000.0000.0000.000
22A45TYR00.0350.00123.1820.5270.5270.0000.0000.0000.000
23A46SER0-0.055-0.05624.0200.2480.2480.0000.0000.0000.000
24A47SER0-0.050-0.00624.933-0.257-0.2570.0000.0000.0000.000
25A48VAL0-0.0020.01518.8870.2710.2710.0000.0000.0000.000
26A49GLY00.0150.01820.229-0.268-0.2680.0000.0000.0000.000
27A50VAL00.0500.00615.7770.5270.5270.0000.0000.0000.000
28A51ASP-1-0.799-0.89315.15416.74416.7440.0000.0000.0000.000
29A52GLU-1-0.813-0.87114.73814.62914.6290.0000.0000.0000.000
30A53ILE0-0.0100.00512.5820.5640.5640.0000.0000.0000.000
31A54LEU00.0000.00410.7051.2371.2370.0000.0000.0000.000
32A55LYS10.9610.9809.697-14.158-14.1580.0000.0000.0000.000
33A56ALA0-0.032-0.01310.6110.5750.5750.0000.0000.0000.000
34A57ALA0-0.0010.0047.7990.8980.8980.0000.0000.0000.000
35A58ARG10.8530.9305.414-23.252-23.2520.0000.0000.0000.000
36A59VAL00.0400.0314.7883.6883.705-0.001-0.007-0.0070.000
37A60PRO00.0320.0186.808-2.985-2.9850.0000.0000.0000.000
38A61LYS10.8960.9069.896-15.870-15.8700.0000.0000.0000.000
39A62GLY00.0250.01013.110-0.507-0.5070.0000.0000.0000.000
40A63SER00.024-0.0028.9790.0560.0560.0000.0000.0000.000
41A64PHE0-0.013-0.00310.9740.4670.4670.0000.0000.0000.000
42A65TYR0-0.008-0.01613.225-0.311-0.3110.0000.0000.0000.000
43A66HIS0-0.054-0.00512.855-0.924-0.9240.0000.0000.0000.000
44A67TYR0-0.034-0.0169.251-0.203-0.2030.0000.0000.0000.000
45A68PHE00.0240.01213.376-0.490-0.4900.0000.0000.0000.000
46A69ARG10.8870.93418.135-13.282-13.2820.0000.0000.0000.000
47A70ASN0-0.004-0.01720.838-0.255-0.2550.0000.0000.0000.000
48A71LYS10.8520.90820.108-12.024-12.0240.0000.0000.0000.000
49A72ALA00.0290.02821.1530.1840.1840.0000.0000.0000.000
50A73ASP-1-0.766-0.87621.23714.36614.3660.0000.0000.0000.000
51A74PHE00.0150.00114.5610.1800.1800.0000.0000.0000.000
52A75GLY00.003-0.00519.2210.3190.3190.0000.0000.0000.000
53A76LEU00.0300.01521.680-0.086-0.0860.0000.0000.0000.000
54A77ALA00.0580.03418.2070.0410.0410.0000.0000.0000.000
55A78LEU0-0.081-0.03816.1600.5740.5740.0000.0000.0000.000
56A79ILE00.0060.01019.437-0.009-0.0090.0000.0000.0000.000
57A80GLU-1-0.894-0.94021.03513.94513.9450.0000.0000.0000.000
58A81ALA0-0.036-0.00917.0390.1420.1420.0000.0000.0000.000
59A82TYR0-0.004-0.01919.0430.2300.2300.0000.0000.0000.000
60A83ASP-1-0.819-0.90821.19011.64711.6470.0000.0000.0000.000
61A84THR0-0.026-0.02019.705-0.187-0.1870.0000.0000.0000.000
62A85TYR0-0.085-0.04815.0630.5060.5060.0000.0000.0000.000
63A86PHE00.0160.00521.267-0.274-0.2740.0000.0000.0000.000
64A87ALA00.0450.02224.487-0.467-0.4670.0000.0000.0000.000
65A88ARG10.9170.96120.044-15.280-15.2800.0000.0000.0000.000
66A89LEU0-0.018-0.00224.777-0.227-0.2270.0000.0000.0000.000
67A90LEU00.006-0.00226.337-0.428-0.4280.0000.0000.0000.000
68A91ASP-1-0.853-0.90827.23911.07611.0760.0000.0000.0000.000
69A92GLN0-0.064-0.03925.3660.0290.0290.0000.0000.0000.000
70A93ALA00.0000.01929.513-0.260-0.2600.0000.0000.0000.000
71A94PHE0-0.012-0.02832.441-0.284-0.2840.0000.0000.0000.000
72A95LEU0-0.0010.00531.336-0.283-0.2830.0000.0000.0000.000
73A96ASP-1-0.812-0.86934.1638.9368.9360.0000.0000.0000.000
74A97GLY00.003-0.00835.555-0.239-0.2390.0000.0000.0000.000
75A98SER0-0.124-0.07537.371-0.277-0.2770.0000.0000.0000.000
76A99LEU0-0.045-0.01536.486-0.236-0.2360.0000.0000.0000.000
77A100ALA00.0350.02040.2510.0030.0030.0000.0000.0000.000
78A101PRO00.0460.02140.7140.1890.1890.0000.0000.0000.000
79A102LEU00.0530.01340.0860.2210.2210.0000.0000.0000.000
80A103ALA0-0.086-0.02540.4520.0740.0740.0000.0000.0000.000
81A104ARG10.8170.90536.366-8.059-8.0590.0000.0000.0000.000
82A105LEU00.0050.01135.6430.2940.2940.0000.0000.0000.000
83A106ARG10.8650.92236.254-7.323-7.3230.0000.0000.0000.000
84A107LEU00.0250.01932.3930.1490.1490.0000.0000.0000.000
85A108PHE00.0210.00229.7170.3020.3020.0000.0000.0000.000
86A109THR0-0.041-0.01931.5010.1670.1670.0000.0000.0000.000
87A110ARG10.8840.93032.705-9.058-9.0580.0000.0000.0000.000
88A111MET00.0210.00828.0980.2930.2930.0000.0000.0000.000
89A112ALA0-0.0200.00227.6550.4670.4670.0000.0000.0000.000
90A113GLU-1-0.825-0.91128.1619.2479.2470.0000.0000.0000.000
91A114GLU-1-0.845-0.92727.87310.49810.4980.0000.0000.0000.000
92A115GLY0-0.047-0.00524.5220.4630.4630.0000.0000.0000.000
93A116MET0-0.030-0.01124.3560.3190.3190.0000.0000.0000.000
94A117ALA00.0150.01426.3650.1280.1280.0000.0000.0000.000
95A118ARG10.8590.91821.919-12.781-12.7810.0000.0000.0000.000
96A119HIS0-0.017-0.01318.5330.3260.3260.0000.0000.0000.000
97A120GLY00.0020.00223.779-0.128-0.1280.0000.0000.0000.000
98A121PHE00.017-0.00627.350-0.243-0.2430.0000.0000.0000.000
99A122ARG10.8530.92421.432-12.799-12.7990.0000.0000.0000.000
100A123ARG10.7360.85017.302-14.978-14.9780.0000.0000.0000.000
101A124GLY00.0530.02424.710-0.282-0.2820.0000.0000.0000.000
102A125CYS0-0.083-0.02624.9180.6890.6890.0000.0000.0000.000
103A126LEU0-0.0090.00221.217-0.131-0.1310.0000.0000.0000.000
104A127VAL00.0300.00824.803-0.123-0.1230.0000.0000.0000.000
105A128GLY00.0960.05027.800-0.303-0.3030.0000.0000.0000.000
106A129ASN0-0.122-0.06725.064-0.603-0.6030.0000.0000.0000.000
107A130LEU0-0.014-0.01924.157-0.157-0.1570.0000.0000.0000.000
108A131GLY00.0270.01328.417-0.215-0.2150.0000.0000.0000.000
109A132GLN0-0.0060.00331.843-0.287-0.2870.0000.0000.0000.000
110A133GLU-1-0.741-0.83727.17110.86010.8600.0000.0000.0000.000
111A134MET0-0.0090.02031.8610.1710.1710.0000.0000.0000.000
112A135GLY0-0.023-0.02433.094-0.264-0.2640.0000.0000.0000.000
113A136ALA0-0.055-0.02231.361-0.156-0.1560.0000.0000.0000.000
114A137LEU0-0.052-0.01726.9490.3170.3170.0000.0000.0000.000
115A138PRO00.010-0.00927.602-0.276-0.2760.0000.0000.0000.000
116A139ASP-1-0.767-0.86130.6978.8678.8670.0000.0000.0000.000
117A140ASP-1-0.911-0.93929.06010.39310.3930.0000.0000.0000.000
118A141PHE0-0.033-0.03324.3430.2250.2250.0000.0000.0000.000
119A142ARG10.8070.87129.589-8.669-8.6690.0000.0000.0000.000
120A143ALA00.0190.00832.557-0.120-0.1200.0000.0000.0000.000
121A144ALA0-0.0060.00227.556-0.005-0.0050.0000.0000.0000.000
122A145LEU0-0.014-0.02227.5150.1450.1450.0000.0000.0000.000
123A146ILE00.0250.02030.289-0.029-0.0290.0000.0000.0000.000
124A147GLY00.0580.03532.413-0.101-0.1010.0000.0000.0000.000
125A148VAL0-0.0250.00227.0840.0150.0150.0000.0000.0000.000
126A149LEU00.0160.00830.273-0.070-0.0700.0000.0000.0000.000
127A150GLU-1-0.823-0.90132.8878.4988.4980.0000.0000.0000.000
128A151THR0-0.053-0.03330.849-0.250-0.2500.0000.0000.0000.000
129A152TRP0-0.027-0.03626.860-0.060-0.0600.0000.0000.0000.000
130A153GLN0-0.037-0.00533.087-0.025-0.0250.0000.0000.0000.000
131A154ARG10.8850.92634.079-9.181-9.1810.0000.0000.0000.000
132A155ARG10.8320.89429.432-10.536-10.5360.0000.0000.0000.000
133A156THR0-0.004-0.00935.827-0.031-0.0310.0000.0000.0000.000
134A157ALA00.0370.02737.875-0.182-0.1820.0000.0000.0000.000
135A158GLN0-0.110-0.05237.820-0.088-0.0880.0000.0000.0000.000
136A159LEU00.0050.01937.164-0.174-0.1740.0000.0000.0000.000
137A160PHE00.007-0.01840.486-0.158-0.1580.0000.0000.0000.000
138A161ARG10.8620.89942.361-7.507-7.5070.0000.0000.0000.000
139A162GLU-1-0.824-0.88940.3957.8877.8870.0000.0000.0000.000
140A163ALA00.0300.00244.379-0.124-0.1240.0000.0000.0000.000
141A164GLN0-0.073-0.05245.975-0.061-0.0610.0000.0000.0000.000
142A165ALA0-0.060-0.02247.524-0.150-0.1500.0000.0000.0000.000
143A166CYS0-0.112-0.05046.911-0.025-0.0250.0000.0000.0000.000
144A167GLY00.0280.02249.741-0.088-0.0880.0000.0000.0000.000
145A168GLU-1-0.827-0.92944.7367.1847.1840.0000.0000.0000.000
146A169LEU0-0.028-0.01345.7370.0340.0340.0000.0000.0000.000
147A170SER00.0440.02549.492-0.030-0.0300.0000.0000.0000.000
148A171ALA0-0.009-0.01951.6660.0990.0990.0000.0000.0000.000
149A172ASP-1-0.959-0.97253.6755.7395.7390.0000.0000.0000.000
150A173HIS0-0.0120.00248.8580.0500.0500.0000.0000.0000.000
151A174ASP-1-0.809-0.89447.4386.7566.7560.0000.0000.0000.000
152A175PRO0-0.001-0.01144.6750.1130.1130.0000.0000.0000.000
153A176ASP-1-0.775-0.87842.9137.6097.6090.0000.0000.0000.000
154A177ALA00.0160.01142.9680.1650.1650.0000.0000.0000.000
155A178LEU0-0.027-0.00144.0780.0950.0950.0000.0000.0000.000
156A179ALA0-0.002-0.01239.4560.1490.1490.0000.0000.0000.000
157A180GLU-1-0.908-0.95239.4087.8337.8330.0000.0000.0000.000
158A181ALA0-0.005-0.00440.2220.1210.1210.0000.0000.0000.000
159A182PHE0-0.036-0.02235.4270.0590.0590.0000.0000.0000.000
160A183TRP0-0.005-0.02631.1480.2600.2600.0000.0000.0000.000
161A184ILE0-0.0060.00736.2040.1810.1810.0000.0000.0000.000
162A185GLY0-0.013-0.00638.2290.0250.0250.0000.0000.0000.000
163A186TRP0-0.012-0.00231.752-0.024-0.0240.0000.0000.0000.000
164A187GLU-1-0.764-0.89130.87610.35110.3510.0000.0000.0000.000
165A188GLY00.0120.01533.7900.1110.1110.0000.0000.0000.000
166A189ALA0-0.025-0.01736.039-0.025-0.0250.0000.0000.0000.000
167A190ILE00.0430.00429.4770.1310.1310.0000.0000.0000.000
168A191LEU0-0.049-0.01131.7830.1600.1600.0000.0000.0000.000
169A192ARG10.8350.88733.128-7.727-7.7270.0000.0000.0000.000
170A193ALA00.0170.00532.497-0.046-0.0460.0000.0000.0000.000
171A194LYS10.8220.92126.330-10.998-10.9980.0000.0000.0000.000
172A195LEU0-0.069-0.03230.9720.0290.0290.0000.0000.0000.000
173A196GLU-1-0.799-0.87933.9227.7477.7470.0000.0000.0000.000
174A197LEU0-0.049-0.01629.269-0.040-0.0400.0000.0000.0000.000
175A198ARG10.7860.88932.348-7.812-7.8120.0000.0000.0000.000
176A199PRO00.0590.03033.6270.0340.0340.0000.0000.0000.000
177A200ASP-1-0.816-0.90534.7977.9147.9140.0000.0000.0000.000
178A201PRO0-0.020-0.01636.289-0.215-0.2150.0000.0000.0000.000
179A202LEU00.0390.02732.093-0.115-0.1150.0000.0000.0000.000
180A203HIS0-0.083-0.03436.281-0.433-0.4330.0000.0000.0000.000
181A204SER0-0.060-0.02839.525-0.227-0.2270.0000.0000.0000.000
182A205PHE00.0300.03438.422-0.182-0.1820.0000.0000.0000.000
183A206THR00.006-0.01637.712-0.195-0.1950.0000.0000.0000.000
184A207ARG10.9120.96040.865-7.412-7.4120.0000.0000.0000.000
185A208THR0-0.051-0.03044.087-0.235-0.2350.0000.0000.0000.000
186A209PHE0-0.008-0.01042.493-0.131-0.1310.0000.0000.0000.000
187A210GLY00.0180.00444.434-0.052-0.0520.0000.0000.0000.000
188A211ARG10.8820.93445.629-6.268-6.2680.0000.0000.0000.000
189A212HIS00.0140.02145.467-0.239-0.2390.0000.0000.0000.000
190A213PHE0-0.014-0.00742.7630.0000.0000.0000.0000.0000.000
191A214VAL0-0.0220.00548.733-0.142-0.1420.0000.0000.0000.000