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: ZNV3N

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2037304.590289
FMO2-HF: Nuclear repulsion 1962795.437646
FMO2-HF: Total energy -74509.152643
FMO2-MP2: Total energy -74728.643466


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.
-120.133-110.4826.552-7.378-8.8240.082
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 : -0.870 / q_NPA : -0.949
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].
3A26SER0-0.037-0.0052.025-33.648-28.9084.071-4.424-4.3870.055
4A27LEU00.0230.0162.344-21.241-16.4742.483-2.923-4.3260.027
5A28ALA00.0130.0184.537-8.559-8.412-0.001-0.026-0.1200.000
6A29HIS00.0470.0156.698-2.204-2.2040.0000.0000.0000.000
7A30GLN00.0440.0135.561-5.378-5.3780.0000.0000.0000.000
8A31SER0-0.017-0.0165.432-1.869-1.8690.0000.0000.0000.000
9A32LEU0-0.030-0.0077.994-2.700-2.7000.0000.0000.0000.000
10A33ILE00.0430.02411.176-1.772-1.7720.0000.0000.0000.000
11A34ARG10.9000.94610.470-22.504-22.5040.0000.0000.0000.000
12A35ALA0-0.002-0.00411.577-1.598-1.5980.0000.0000.0000.000
13A36GLY00.013-0.00713.384-1.312-1.3120.0000.0000.0000.000
14A37LEU00.006-0.00215.912-1.069-1.0690.0000.0000.0000.000
15A38GLU-1-0.847-0.88814.20218.10018.1000.0000.0000.0000.000
16A39HIS10.8280.89515.174-17.104-17.1040.0000.0000.0000.000
17A40LEU00.0060.00319.168-0.659-0.6590.0000.0000.0000.000
18A41THR00.0160.00720.417-0.631-0.6310.0000.0000.0000.000
19A42GLU-1-0.812-0.87720.86813.17913.1790.0000.0000.0000.000
20A43LYS10.7800.87521.471-13.221-13.2210.0000.0000.0000.000
21A44GLY00.0700.03924.258-0.308-0.3080.0000.0000.0000.000
22A45TYR00.031-0.00823.5640.6110.6110.0000.0000.0000.000
23A46SER0-0.055-0.05624.3170.2580.2580.0000.0000.0000.000
24A47SER0-0.046-0.00825.064-0.160-0.1600.0000.0000.0000.000
25A48VAL0-0.0120.01119.1340.2070.2070.0000.0000.0000.000
26A49GLY00.0180.01720.690-0.121-0.1210.0000.0000.0000.000
27A50VAL00.0550.00216.0780.4950.4950.0000.0000.0000.000
28A51ASP-1-0.810-0.88915.57716.19116.1910.0000.0000.0000.000
29A52GLU-1-0.802-0.86415.05914.62914.6290.0000.0000.0000.000
30A53ILE00.0130.01313.1360.7300.7300.0000.0000.0000.000
31A54LEU00.0030.00211.1051.2501.2500.0000.0000.0000.000
32A55LYS10.9530.97910.004-14.069-14.0690.0000.0000.0000.000
33A56ALA0-0.045-0.02310.9100.6110.6110.0000.0000.0000.000
34A57ALA0-0.006-0.0088.5031.1641.1640.0000.0000.0000.000
35A58ARG10.8880.9555.722-23.308-23.3080.0000.0000.0000.000
36A59VAL00.0240.0265.1393.4723.469-0.001-0.0050.0090.000
37A60PRO00.0360.0146.806-2.878-2.8780.0000.0000.0000.000
38A61LYS10.8930.9089.702-15.727-15.7270.0000.0000.0000.000
39A62GLY00.0240.01312.936-0.620-0.6200.0000.0000.0000.000
40A63SER00.012-0.0039.1190.1730.1730.0000.0000.0000.000
41A64PHE0-0.015-0.00611.187-0.045-0.0450.0000.0000.0000.000
42A65TYR0-0.034-0.03413.212-0.458-0.4580.0000.0000.0000.000
43A66HIS0-0.0450.00713.389-0.984-0.9840.0000.0000.0000.000
44A67TYR0-0.038-0.01310.3750.7420.7420.0000.0000.0000.000
45A68PHE00.0230.01413.777-0.485-0.4850.0000.0000.0000.000
46A69ARG10.9040.93818.253-12.800-12.8000.0000.0000.0000.000
47A70ASN00.001-0.02120.928-0.098-0.0980.0000.0000.0000.000
48A71LYS10.8450.90420.288-11.975-11.9750.0000.0000.0000.000
49A72ALA00.0270.02521.3190.2040.2040.0000.0000.0000.000
50A73ASP-1-0.767-0.87021.26313.84413.8440.0000.0000.0000.000
51A74PHE00.006-0.00714.8640.2410.2410.0000.0000.0000.000
52A75GLY00.007-0.00819.4710.3130.3130.0000.0000.0000.000
53A76LEU00.0250.01121.970-0.004-0.0040.0000.0000.0000.000
54A77ALA00.0580.04118.3360.0240.0240.0000.0000.0000.000
55A78LEU0-0.093-0.04016.3040.5150.5150.0000.0000.0000.000
56A79ILE00.0130.00919.6260.0350.0350.0000.0000.0000.000
57A80GLU-1-0.898-0.93821.41613.54213.5420.0000.0000.0000.000
58A81ALA0-0.044-0.01917.4280.1850.1850.0000.0000.0000.000
59A82TYR0-0.013-0.02919.4560.2490.2490.0000.0000.0000.000
60A83ASP-1-0.844-0.93921.56411.34711.3470.0000.0000.0000.000
61A84THR0-0.041-0.00720.546-0.221-0.2210.0000.0000.0000.000
62A85TYR0-0.092-0.06615.3890.0910.0910.0000.0000.0000.000
63A86PHE00.0130.00721.313-0.186-0.1860.0000.0000.0000.000
64A87ALA00.0370.02724.598-0.442-0.4420.0000.0000.0000.000
65A88ARG10.9720.98219.625-15.241-15.2410.0000.0000.0000.000
66A89LEU0-0.0190.00624.847-0.160-0.1600.0000.0000.0000.000
67A90LEU00.001-0.01226.398-0.383-0.3830.0000.0000.0000.000
68A91ASP-1-0.827-0.89527.55810.95410.9540.0000.0000.0000.000
69A92GLN0-0.068-0.02525.8450.0720.0720.0000.0000.0000.000
70A93ALA0-0.0060.00929.832-0.276-0.2760.0000.0000.0000.000
71A94PHE0-0.015-0.03432.809-0.288-0.2880.0000.0000.0000.000
72A95LEU0-0.028-0.01231.444-0.274-0.2740.0000.0000.0000.000
73A96ASP-1-0.820-0.86533.9058.9728.9720.0000.0000.0000.000
74A97GLY00.003-0.01035.364-0.235-0.2350.0000.0000.0000.000
75A98SER0-0.121-0.07637.020-0.277-0.2770.0000.0000.0000.000
76A99LEU0-0.049-0.01536.565-0.209-0.2090.0000.0000.0000.000
77A100ALA00.0230.00940.260-0.022-0.0220.0000.0000.0000.000
78A101PRO00.0610.01741.1450.1960.1960.0000.0000.0000.000
79A102LEU00.012-0.01140.5820.2200.2200.0000.0000.0000.000
80A103ALA0-0.077-0.03940.6670.0990.0990.0000.0000.0000.000
81A104ARG10.8670.95136.629-8.001-8.0010.0000.0000.0000.000
82A105LEU0-0.0070.00535.8810.3030.3030.0000.0000.0000.000
83A106ARG10.9040.94936.533-7.339-7.3390.0000.0000.0000.000
84A107LEU00.0140.01232.7620.1340.1340.0000.0000.0000.000
85A108PHE00.0350.01229.7820.2940.2940.0000.0000.0000.000
86A109THR00.0070.00331.5820.2170.2170.0000.0000.0000.000
87A110ARG10.8800.94033.091-9.052-9.0520.0000.0000.0000.000
88A111MET00.0250.00928.4400.2590.2590.0000.0000.0000.000
89A112ALA0-0.037-0.00727.9680.4470.4470.0000.0000.0000.000
90A113GLU-1-0.826-0.90628.2939.2829.2820.0000.0000.0000.000
91A114GLU-1-0.878-0.93227.95510.49810.4980.0000.0000.0000.000
92A115GLY0-0.052-0.02624.5840.4140.4140.0000.0000.0000.000
93A116MET0-0.034-0.01924.5230.2880.2880.0000.0000.0000.000
94A117ALA00.0090.00426.4270.1290.1290.0000.0000.0000.000
95A118ARG10.8910.95821.583-13.058-13.0580.0000.0000.0000.000
96A119HIS0-0.051-0.02718.4000.2960.2960.0000.0000.0000.000
97A120GLY00.012-0.00223.679-0.095-0.0950.0000.0000.0000.000
98A121PHE00.0180.00827.160-0.284-0.2840.0000.0000.0000.000
99A122ARG10.9070.95121.745-12.800-12.8000.0000.0000.0000.000
100A123ARG10.7430.85817.275-15.154-15.1540.0000.0000.0000.000
101A124GLY00.0310.00524.634-0.256-0.2560.0000.0000.0000.000
102A125CYS0-0.068-0.01525.0800.6640.6640.0000.0000.0000.000
103A126LEU0-0.002-0.00521.376-0.105-0.1050.0000.0000.0000.000
104A127VAL00.0400.01024.962-0.100-0.1000.0000.0000.0000.000
105A128GLY00.0830.04627.947-0.316-0.3160.0000.0000.0000.000
106A129ASN0-0.114-0.07025.336-0.624-0.6240.0000.0000.0000.000
107A130LEU0-0.017-0.01124.375-0.120-0.1200.0000.0000.0000.000
108A131GLY00.0150.00628.605-0.225-0.2250.0000.0000.0000.000
109A132GLN00.0140.00732.020-0.329-0.3290.0000.0000.0000.000
110A133GLU-1-0.767-0.84227.62910.67810.6780.0000.0000.0000.000
111A134MET0-0.0200.00832.2440.1720.1720.0000.0000.0000.000
112A135GLY0-0.009-0.01133.548-0.240-0.2400.0000.0000.0000.000
113A136ALA0-0.055-0.03031.487-0.110-0.1100.0000.0000.0000.000
114A137LEU0-0.058-0.02227.6550.3620.3620.0000.0000.0000.000
115A138PRO00.009-0.00627.541-0.245-0.2450.0000.0000.0000.000
116A139ASP-1-0.773-0.87630.8418.7348.7340.0000.0000.0000.000
117A140ASP-1-0.911-0.94029.51010.17610.1760.0000.0000.0000.000
118A141PHE0-0.033-0.02824.7210.2230.2230.0000.0000.0000.000
119A142ARG10.8480.91229.994-8.517-8.5170.0000.0000.0000.000
120A143ALA00.0480.01633.281-0.037-0.0370.0000.0000.0000.000
121A144ALA00.0010.01527.9110.0340.0340.0000.0000.0000.000
122A145LEU0-0.036-0.04227.6600.1720.1720.0000.0000.0000.000
123A146ILE00.0140.00430.4630.0040.0040.0000.0000.0000.000
124A147GLY00.0520.03332.151-0.131-0.1310.0000.0000.0000.000
125A148VAL0-0.039-0.01827.134-0.036-0.0360.0000.0000.0000.000
126A149LEU00.0160.00530.314-0.048-0.0480.0000.0000.0000.000
127A150GLU-1-0.884-0.93833.0738.3028.3020.0000.0000.0000.000
128A151THR0-0.056-0.03030.847-0.263-0.2630.0000.0000.0000.000
129A152TRP0-0.009-0.01427.074-0.089-0.0890.0000.0000.0000.000
130A153GLN0-0.029-0.00233.362-0.026-0.0260.0000.0000.0000.000
131A154ARG10.9640.98134.097-9.209-9.2090.0000.0000.0000.000
132A155ARG10.8020.88729.628-10.412-10.4120.0000.0000.0000.000
133A156THR0-0.002-0.00636.053-0.070-0.0700.0000.0000.0000.000
134A157ALA00.0380.03038.128-0.162-0.1620.0000.0000.0000.000
135A158GLN0-0.099-0.04438.367-0.076-0.0760.0000.0000.0000.000
136A159LEU00.0220.02137.572-0.145-0.1450.0000.0000.0000.000
137A160PHE00.007-0.01840.676-0.159-0.1590.0000.0000.0000.000
138A161ARG10.8220.87542.416-7.474-7.4740.0000.0000.0000.000
139A162GLU-1-0.852-0.90740.9487.8057.8050.0000.0000.0000.000
140A163ALA00.0270.00644.478-0.109-0.1090.0000.0000.0000.000
141A164GLN0-0.066-0.04546.173-0.062-0.0620.0000.0000.0000.000
142A165ALA0-0.055-0.01348.190-0.150-0.1500.0000.0000.0000.000
143A166CYS0-0.098-0.04847.243-0.047-0.0470.0000.0000.0000.000
144A167GLY0-0.007-0.00250.123-0.049-0.0490.0000.0000.0000.000
145A168GLU-1-0.818-0.91145.3107.1117.1110.0000.0000.0000.000
146A169LEU0-0.030-0.01246.0940.0170.0170.0000.0000.0000.000
147A170SER00.0240.01349.718-0.034-0.0340.0000.0000.0000.000
148A171ALA0-0.012-0.02552.2190.0780.0780.0000.0000.0000.000
149A172ASP-1-0.955-0.97954.1655.7135.7130.0000.0000.0000.000
150A173HIS0-0.0090.01449.2640.0450.0450.0000.0000.0000.000
151A174ASP-1-0.817-0.90448.0666.6726.6720.0000.0000.0000.000
152A175PRO0-0.018-0.01944.9580.1280.1280.0000.0000.0000.000
153A176ASP-1-0.742-0.86943.5007.4887.4880.0000.0000.0000.000
154A177ALA00.0300.03343.4570.1570.1570.0000.0000.0000.000
155A178LEU0-0.0080.00844.3070.1090.1090.0000.0000.0000.000
156A179ALA0-0.011-0.01539.8960.1630.1630.0000.0000.0000.000
157A180GLU-1-0.903-0.94439.6337.7427.7420.0000.0000.0000.000
158A181ALA0-0.006-0.00740.4980.1160.1160.0000.0000.0000.000
159A182PHE0-0.042-0.03435.4130.0800.0800.0000.0000.0000.000
160A183TRP0-0.004-0.02631.3940.2800.2800.0000.0000.0000.000
161A184ILE0-0.0060.01036.3300.1880.1880.0000.0000.0000.000
162A185GLY0-0.023-0.01538.2680.0540.0540.0000.0000.0000.000
163A186TRP0-0.006-0.01431.674-0.020-0.0200.0000.0000.0000.000
164A187GLU-1-0.750-0.87431.16410.26710.2670.0000.0000.0000.000
165A188GLY0-0.0090.00734.1080.1190.1190.0000.0000.0000.000
166A189ALA0-0.021-0.01936.077-0.052-0.0520.0000.0000.0000.000
167A190ILE00.0430.00829.7230.1260.1260.0000.0000.0000.000
168A191LEU0-0.073-0.01832.1790.1340.1340.0000.0000.0000.000
169A192ARG10.8430.89233.556-7.681-7.6810.0000.0000.0000.000
170A193ALA00.0150.01332.569-0.075-0.0750.0000.0000.0000.000
171A194LYS10.8760.94127.411-10.629-10.6290.0000.0000.0000.000
172A195LEU0-0.064-0.02431.1200.0610.0610.0000.0000.0000.000
173A196GLU-1-0.807-0.88633.9717.7737.7730.0000.0000.0000.000
174A197LEU0-0.063-0.01629.552-0.015-0.0150.0000.0000.0000.000
175A198ARG10.7960.89032.635-7.864-7.8640.0000.0000.0000.000
176A199PRO00.0510.02433.6880.0210.0210.0000.0000.0000.000
177A200ASP-1-0.819-0.90534.9737.8967.8960.0000.0000.0000.000
178A201PRO0-0.015-0.01936.478-0.200-0.2000.0000.0000.0000.000
179A202LEU00.0360.02632.296-0.095-0.0950.0000.0000.0000.000
180A203HIS0-0.080-0.05036.239-0.400-0.4000.0000.0000.0000.000
181A204SER0-0.075-0.03839.731-0.236-0.2360.0000.0000.0000.000
182A205PHE00.0360.02938.456-0.180-0.1800.0000.0000.0000.000
183A206THR00.015-0.00238.029-0.181-0.1810.0000.0000.0000.000
184A207ARG10.9200.97341.172-7.363-7.3630.0000.0000.0000.000
185A208THR0-0.051-0.03244.281-0.209-0.2090.0000.0000.0000.000
186A209PHE0-0.007-0.00442.682-0.125-0.1250.0000.0000.0000.000
187A210GLY00.0230.00544.570-0.054-0.0540.0000.0000.0000.000
188A211ARG10.8990.94845.581-6.268-6.2680.0000.0000.0000.000
189A212HIS0-0.0070.00945.755-0.236-0.2360.0000.0000.0000.000
190A213PHE0-0.027-0.01042.8940.0030.0030.0000.0000.0000.000
191A214VAL0-0.0030.01448.908-0.112-0.1120.0000.0000.0000.000