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: 6GY9Z

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2034628.819938
FMO2-HF: Nuclear repulsion 1960120.572203
FMO2-HF: Total energy -74508.247735
FMO2-MP2: Total energy -74727.699798


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.
-77.128-73.2584.895-3.702-5.0620.021
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 : -0.896 / q_NPA : -0.963
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].
3A26SER0-0.0050.0003.845-6.235-3.963-0.016-1.015-1.2410.004
4A27LEU00.0120.0092.041-11.674-10.1794.913-2.677-3.7310.017
5A28ALA00.0140.0194.125-4.683-4.566-0.001-0.007-0.1090.000
6A29HIS00.0530.0206.447-1.261-1.2610.0000.0000.0000.000
7A30GLN00.0550.0145.661-5.532-5.5320.0000.0000.0000.000
8A31SER0-0.0080.0005.356-0.989-0.9890.0000.0000.0000.000
9A32LEU0-0.030-0.0137.975-2.251-2.2510.0000.0000.0000.000
10A33ILE00.0460.02611.120-1.503-1.5030.0000.0000.0000.000
11A34ARG10.8870.95410.555-21.872-21.8720.0000.0000.0000.000
12A35ALA00.0010.00111.602-1.431-1.4310.0000.0000.0000.000
13A36GLY00.017-0.00313.466-1.237-1.2370.0000.0000.0000.000
14A37LEU00.000-0.00715.713-0.978-0.9780.0000.0000.0000.000
15A38GLU-1-0.922-0.95114.37818.96618.9660.0000.0000.0000.000
16A39HIS10.8380.90315.172-17.011-17.0110.0000.0000.0000.000
17A40LEU00.0080.00119.169-0.657-0.6570.0000.0000.0000.000
18A41THR0-0.015-0.00320.500-0.615-0.6150.0000.0000.0000.000
19A42GLU-1-0.941-0.96321.29813.05013.0500.0000.0000.0000.000
20A43LYS10.8440.92721.685-13.073-13.0730.0000.0000.0000.000
21A44GLY00.0750.03924.237-0.309-0.3090.0000.0000.0000.000
22A45TYR00.013-0.00923.4060.5340.5340.0000.0000.0000.000
23A46SER0-0.063-0.05024.3190.2200.2200.0000.0000.0000.000
24A47SER0-0.033-0.00824.704-0.103-0.1030.0000.0000.0000.000
25A48VAL0-0.0340.00719.1380.2440.2440.0000.0000.0000.000
26A49GLY00.0150.00720.691-0.144-0.1440.0000.0000.0000.000
27A50VAL00.050-0.00216.0270.5010.5010.0000.0000.0000.000
28A51ASP-1-0.822-0.90515.57815.57815.5780.0000.0000.0000.000
29A52GLU-1-0.854-0.91815.06114.71314.7130.0000.0000.0000.000
30A53ILE00.0050.01112.9910.7890.7890.0000.0000.0000.000
31A54LEU0-0.009-0.00611.0971.2771.2770.0000.0000.0000.000
32A55LYS10.9560.98010.005-14.379-14.3790.0000.0000.0000.000
33A56ALA0-0.046-0.02310.9120.7480.7480.0000.0000.0000.000
34A57ALA0-0.006-0.0018.4841.3401.3400.0000.0000.0000.000
35A58ARG10.8950.9565.648-25.026-25.0260.0000.0000.0000.000
36A59VAL00.0230.0235.1413.4793.465-0.001-0.0030.0190.000
37A60PRO00.0270.0076.718-2.773-2.7730.0000.0000.0000.000
38A61LYS10.9380.9469.703-15.500-15.5000.0000.0000.0000.000
39A62GLY00.0150.00812.931-0.650-0.6500.0000.0000.0000.000
40A63SER00.009-0.0039.1520.1220.1220.0000.0000.0000.000
41A64PHE0-0.010-0.00211.188-0.150-0.1500.0000.0000.0000.000
42A65TYR0-0.036-0.03713.213-0.489-0.4890.0000.0000.0000.000
43A66HIS0-0.0490.00613.429-1.125-1.1250.0000.0000.0000.000
44A67TYR0-0.039-0.01510.4430.5420.5420.0000.0000.0000.000
45A68PHE00.0420.02713.813-0.381-0.3810.0000.0000.0000.000
46A69ARG10.9940.99218.253-11.775-11.7750.0000.0000.0000.000
47A70ASN0-0.024-0.02820.961-0.064-0.0640.0000.0000.0000.000
48A71LYS10.8920.95420.286-11.754-11.7540.0000.0000.0000.000
49A72ALA00.0310.02421.3200.1870.1870.0000.0000.0000.000
50A73ASP-1-0.839-0.91921.28913.48413.4840.0000.0000.0000.000
51A74PHE0-0.003-0.00714.7780.2650.2650.0000.0000.0000.000
52A75GLY00.003-0.01319.4640.3010.3010.0000.0000.0000.000
53A76LEU00.0230.01121.8620.0020.0020.0000.0000.0000.000
54A77ALA00.0610.04818.0370.0200.0200.0000.0000.0000.000
55A78LEU0-0.102-0.04916.2730.4910.4910.0000.0000.0000.000
56A79ILE00.0160.01119.4840.0550.0550.0000.0000.0000.000
57A80GLU-1-0.895-0.94221.25012.85912.8590.0000.0000.0000.000
58A81ALA0-0.047-0.02417.2310.1740.1740.0000.0000.0000.000
59A82TYR0-0.017-0.03619.2460.2520.2520.0000.0000.0000.000
60A83ASP-1-0.881-0.94921.42611.12011.1200.0000.0000.0000.000
61A84THR0-0.0200.00720.290-0.210-0.2100.0000.0000.0000.000
62A85TYR0-0.096-0.06915.2690.0500.0500.0000.0000.0000.000
63A86PHE00.0290.01421.144-0.131-0.1310.0000.0000.0000.000
64A87ALA00.0260.02024.467-0.412-0.4120.0000.0000.0000.000
65A88ARG10.9680.97919.295-14.761-14.7610.0000.0000.0000.000
66A89LEU0-0.0020.01025.049-0.123-0.1230.0000.0000.0000.000
67A90LEU0-0.016-0.01626.287-0.347-0.3470.0000.0000.0000.000
68A91ASP-1-0.845-0.89527.63910.61510.6150.0000.0000.0000.000
69A92GLN0-0.051-0.02126.1360.0840.0840.0000.0000.0000.000
70A93ALA0-0.0070.00829.741-0.265-0.2650.0000.0000.0000.000
71A94PHE0-0.028-0.03932.702-0.285-0.2850.0000.0000.0000.000
72A95LEU0-0.022-0.00531.554-0.276-0.2760.0000.0000.0000.000
73A96ASP-1-0.841-0.89433.9708.9468.9460.0000.0000.0000.000
74A97GLY0-0.005-0.01335.442-0.234-0.2340.0000.0000.0000.000
75A98SER0-0.108-0.05137.187-0.277-0.2770.0000.0000.0000.000
76A99LEU0-0.049-0.01836.172-0.192-0.1920.0000.0000.0000.000
77A100ALA00.0280.01540.245-0.022-0.0220.0000.0000.0000.000
78A101PRO00.0630.01441.0180.2000.2000.0000.0000.0000.000
79A102LEU00.009-0.00640.4810.2160.2160.0000.0000.0000.000
80A103ALA0-0.073-0.04240.5400.1050.1050.0000.0000.0000.000
81A104ARG10.9040.98136.513-7.900-7.9000.0000.0000.0000.000
82A105LEU00.0060.01235.8080.2980.2980.0000.0000.0000.000
83A106ARG10.9400.96036.498-7.345-7.3450.0000.0000.0000.000
84A107LEU00.0120.01432.6080.1270.1270.0000.0000.0000.000
85A108PHE00.0380.01729.5730.2790.2790.0000.0000.0000.000
86A109THR0-0.038-0.01431.5760.2180.2180.0000.0000.0000.000
87A110ARG10.9650.99633.140-8.994-8.9940.0000.0000.0000.000
88A111MET00.0210.00728.4550.2450.2450.0000.0000.0000.000
89A112ALA0-0.034-0.00527.9960.4540.4540.0000.0000.0000.000
90A113GLU-1-0.848-0.92428.3699.3499.3490.0000.0000.0000.000
91A114GLU-1-0.931-0.97127.94410.57510.5750.0000.0000.0000.000
92A115GLY0-0.055-0.02424.6930.4400.4400.0000.0000.0000.000
93A116MET0-0.039-0.02024.6620.3010.3010.0000.0000.0000.000
94A117ALA00.0080.00226.5890.1610.1610.0000.0000.0000.000
95A118ARG10.9180.96821.367-13.452-13.4520.0000.0000.0000.000
96A119HIS0-0.057-0.03318.9130.4240.4240.0000.0000.0000.000
97A120GLY0-0.001-0.00823.786-0.098-0.0980.0000.0000.0000.000
98A121PHE00.0260.01427.340-0.284-0.2840.0000.0000.0000.000
99A122ARG10.9911.00122.851-12.513-12.5130.0000.0000.0000.000
100A123ARG10.8810.95117.620-15.208-15.2080.0000.0000.0000.000
101A124GLY00.013-0.00324.794-0.258-0.2580.0000.0000.0000.000
102A125CYS0-0.077-0.02425.1460.6520.6520.0000.0000.0000.000
103A126LEU00.0050.00221.605-0.105-0.1050.0000.0000.0000.000
104A127VAL00.0490.01424.958-0.105-0.1050.0000.0000.0000.000
105A128GLY00.0680.03927.897-0.312-0.3120.0000.0000.0000.000
106A129ASN0-0.127-0.08225.529-0.583-0.5830.0000.0000.0000.000
107A130LEU0-0.017-0.01524.417-0.126-0.1260.0000.0000.0000.000
108A131GLY00.0120.00828.596-0.229-0.2290.0000.0000.0000.000
109A132GLN00.0070.00331.988-0.348-0.3480.0000.0000.0000.000
110A133GLU-1-0.793-0.88927.81210.47610.4760.0000.0000.0000.000
111A134MET0-0.0200.00832.2450.1560.1560.0000.0000.0000.000
112A135GLY0-0.016-0.01333.574-0.254-0.2540.0000.0000.0000.000
113A136ALA0-0.053-0.02931.467-0.103-0.1030.0000.0000.0000.000
114A137LEU0-0.071-0.02927.6920.3620.3620.0000.0000.0000.000
115A138PRO00.003-0.00627.501-0.241-0.2410.0000.0000.0000.000
116A139ASP-1-0.841-0.95130.8428.5458.5450.0000.0000.0000.000
117A140ASP-1-0.908-0.93829.1369.9379.9370.0000.0000.0000.000
118A141PHE0-0.040-0.03024.8680.2030.2030.0000.0000.0000.000
119A142ARG10.9390.99029.851-8.302-8.3020.0000.0000.0000.000
120A143ALA00.0410.01333.057-0.034-0.0340.0000.0000.0000.000
121A144ALA00.0120.01727.7320.0280.0280.0000.0000.0000.000
122A145LEU0-0.034-0.04027.5230.1610.1610.0000.0000.0000.000
123A146ILE0-0.004-0.00230.3230.0120.0120.0000.0000.0000.000
124A147GLY00.0500.03331.934-0.120-0.1200.0000.0000.0000.000
125A148VAL0-0.033-0.01327.074-0.028-0.0280.0000.0000.0000.000
126A149LEU00.013-0.00130.133-0.039-0.0390.0000.0000.0000.000
127A150GLU-1-0.875-0.94032.9338.1018.1010.0000.0000.0000.000
128A151THR0-0.054-0.02330.499-0.288-0.2880.0000.0000.0000.000
129A152TRP00.007-0.00826.970-0.085-0.0850.0000.0000.0000.000
130A153GLN00.0220.02733.204-0.100-0.1000.0000.0000.0000.000
131A154ARG10.9940.99433.915-8.970-8.9700.0000.0000.0000.000
132A155ARG10.7910.87929.253-10.188-10.1880.0000.0000.0000.000
133A156THR00.000-0.00535.844-0.051-0.0510.0000.0000.0000.000
134A157ALA00.0620.04037.980-0.151-0.1510.0000.0000.0000.000
135A158GLN0-0.081-0.03137.958-0.062-0.0620.0000.0000.0000.000
136A159LEU00.0060.02337.337-0.139-0.1390.0000.0000.0000.000
137A160PHE00.006-0.01040.514-0.144-0.1440.0000.0000.0000.000
138A161ARG10.9760.98142.055-7.398-7.3980.0000.0000.0000.000
139A162GLU-1-0.913-0.96141.0837.6577.6570.0000.0000.0000.000
140A163ALA00.011-0.00844.396-0.099-0.0990.0000.0000.0000.000
141A164GLN0-0.057-0.03446.035-0.076-0.0760.0000.0000.0000.000
142A165ALA0-0.056-0.01448.053-0.143-0.1430.0000.0000.0000.000
143A166CYS0-0.078-0.02947.101-0.050-0.0500.0000.0000.0000.000
144A167GLY0-0.0050.00049.968-0.044-0.0440.0000.0000.0000.000
145A168GLU-1-0.844-0.92645.3097.0347.0340.0000.0000.0000.000
146A169LEU0-0.030-0.01646.8420.0160.0160.0000.0000.0000.000
147A170SER00.0130.00649.615-0.050-0.0500.0000.0000.0000.000
148A171ALA0-0.003-0.02152.0970.0780.0780.0000.0000.0000.000
149A172ASP-1-0.948-0.97554.0195.6505.6500.0000.0000.0000.000
150A173HIS0-0.0180.01149.1990.0540.0540.0000.0000.0000.000
151A174ASP-1-0.822-0.91748.1736.5646.5640.0000.0000.0000.000
152A175PRO0-0.022-0.02444.8790.1380.1380.0000.0000.0000.000
153A176ASP-1-0.876-0.95343.3397.3437.3430.0000.0000.0000.000
154A177ALA00.0250.02543.3180.1500.1500.0000.0000.0000.000
155A178LEU0-0.0040.00644.4150.1100.1100.0000.0000.0000.000
156A179ALA0-0.019-0.02039.6960.1680.1680.0000.0000.0000.000
157A180GLU-1-0.942-0.96539.5337.5467.5460.0000.0000.0000.000
158A181ALA00.000-0.00640.4220.1150.1150.0000.0000.0000.000
159A182PHE0-0.045-0.03135.2320.0840.0840.0000.0000.0000.000
160A183TRP0-0.017-0.03631.4350.2740.2740.0000.0000.0000.000
161A184ILE00.0020.01736.2940.1990.1990.0000.0000.0000.000
162A185GLY0-0.029-0.01938.2670.0620.0620.0000.0000.0000.000
163A186TRP0-0.013-0.02031.414-0.005-0.0050.0000.0000.0000.000
164A187GLU-1-0.739-0.86231.12410.14310.1430.0000.0000.0000.000
165A188GLY0-0.0140.00634.1570.1240.1240.0000.0000.0000.000
166A189ALA0-0.008-0.01536.158-0.040-0.0400.0000.0000.0000.000
167A190ILE00.0360.00729.6530.1380.1380.0000.0000.0000.000
168A191LEU0-0.091-0.02532.2990.1580.1580.0000.0000.0000.000
169A192ARG10.8710.91533.663-7.645-7.6450.0000.0000.0000.000
170A193ALA00.0190.01932.682-0.063-0.0630.0000.0000.0000.000
171A194LYS10.9240.96927.637-10.312-10.3120.0000.0000.0000.000
172A195LEU0-0.061-0.02131.2990.0750.0750.0000.0000.0000.000
173A196GLU-1-0.833-0.92634.1727.8077.8070.0000.0000.0000.000
174A197LEU0-0.069-0.01829.7910.0030.0030.0000.0000.0000.000
175A198ARG10.8530.93532.776-7.923-7.9230.0000.0000.0000.000
176A199PRO00.0500.02333.8080.0170.0170.0000.0000.0000.000
177A200ASP-1-0.858-0.92835.1437.9547.9540.0000.0000.0000.000
178A201PRO0-0.022-0.02336.591-0.211-0.2110.0000.0000.0000.000
179A202LEU00.0300.02332.429-0.097-0.0970.0000.0000.0000.000
180A203HIS0-0.065-0.04736.357-0.380-0.3800.0000.0000.0000.000
181A204SER0-0.072-0.03539.840-0.238-0.2380.0000.0000.0000.000
182A205PHE00.0350.02038.382-0.170-0.1700.0000.0000.0000.000
183A206THR00.0010.00237.975-0.195-0.1950.0000.0000.0000.000
184A207ARG10.9350.97941.215-7.399-7.3990.0000.0000.0000.000
185A208THR0-0.045-0.02944.345-0.210-0.2100.0000.0000.0000.000
186A209PHE00.0040.00342.717-0.126-0.1260.0000.0000.0000.000
187A210GLY00.022-0.00244.583-0.059-0.0590.0000.0000.0000.000
188A211ARG10.9020.95145.583-6.249-6.2490.0000.0000.0000.000
189A212HIS0-0.0090.00545.960-0.217-0.2170.0000.0000.0000.000
190A213PHE0-0.039-0.00942.963-0.003-0.0030.0000.0000.0000.000
191A214VAL0-0.0150.00848.860-0.102-0.1020.0000.0000.0000.000