Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QN83Y

Calculation Name: 2FBE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FBE

Chain ID: A

ChEMBL ID:

UniProt ID: A6NLU0

Base Structure: X-ray

Registration Date: 2023-09-26

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2113101.964496
FMO2-HF: Nuclear repulsion 2038135.567595
FMO2-HF: Total energy -74966.396901
FMO2-MP2: Total energy -75182.187638


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-1.1191.9483.613-3.354-3.325-0.018
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.009
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].
3A3LEU0-0.0420.0023.2861.3952.5400.011-0.531-0.6250.000
4A4GLY0-0.002-0.0095.3120.0850.149-0.001-0.005-0.0580.000
5A5SER0-0.037-0.0447.5380.3990.3990.0000.0000.0000.000
6A6PRO00.006-0.0067.285-0.069-0.0690.0000.0000.0000.000
7A7GLU-1-0.834-0.8998.602-0.670-0.6700.0000.0000.0000.000
8A8PHE00.014-0.00510.2570.1250.1250.0000.0000.0000.000
9A9GLN00.0180.0076.5580.0400.0400.0000.0000.0000.000
10A10VAL0-0.064-0.0279.4150.1460.1460.0000.0000.0000.000
11A11ASP-1-0.785-0.86712.017-0.250-0.2500.0000.0000.0000.000
12A12MET0-0.075-0.03412.4580.0550.0550.0000.0000.0000.000
13A13THR00.0510.03515.1460.0090.0090.0000.0000.0000.000
14A14PHE0-0.009-0.00616.595-0.015-0.0150.0000.0000.0000.000
15A15ASP-1-0.834-0.89419.850-0.093-0.0930.0000.0000.0000.000
16A16VAL00.0210.00823.0480.0080.0080.0000.0000.0000.000
17A17ASP-1-0.788-0.87825.527-0.047-0.0470.0000.0000.0000.000
18A18THR0-0.022-0.03224.4870.0020.0020.0000.0000.0000.000
19A19ALA0-0.0190.00124.9740.0030.0030.0000.0000.0000.000
20A20ASN00.0440.01626.2360.0090.0090.0000.0000.0000.000
21A21ASN00.0330.00628.4270.0000.0000.0000.0000.0000.000
22A22TYR0-0.0430.00030.1840.0030.0030.0000.0000.0000.000
23A23LEU0-0.0240.00023.9990.0060.0060.0000.0000.0000.000
24A24ILE0-0.0200.00724.071-0.005-0.0050.0000.0000.0000.000
25A25ILE0-0.004-0.02321.1520.0030.0030.0000.0000.0000.000
26A26SER0-0.040-0.04318.9080.0010.0010.0000.0000.0000.000
27A27GLU-1-0.861-0.94821.7950.0150.0150.0000.0000.0000.000
28A28ASP-1-0.838-0.89116.629-0.015-0.0150.0000.0000.0000.000
29A29LEU0-0.034-0.01518.735-0.021-0.0210.0000.0000.0000.000
30A30ARG10.8450.89712.8420.1500.1500.0000.0000.0000.000
31A31SER00.0130.00515.2280.0140.0140.0000.0000.0000.000
32A32PHE0-0.029-0.01617.470-0.007-0.0070.0000.0000.0000.000
33A33ARG10.9090.94919.887-0.046-0.0460.0000.0000.0000.000
34A34SER00.0470.01622.685-0.006-0.0060.0000.0000.0000.000
35A35GLY0-0.034-0.02325.9890.0090.0090.0000.0000.0000.000
36A36ASP-1-0.816-0.88529.3020.0310.0310.0000.0000.0000.000
37A37LEU0-0.038-0.00632.039-0.002-0.0020.0000.0000.0000.000
38A38SER00.011-0.01032.555-0.002-0.0020.0000.0000.0000.000
39A39GLN00.0230.00329.7660.0010.0010.0000.0000.0000.000
40A40ASN0-0.025-0.00532.662-0.005-0.0050.0000.0000.0000.000
41A41ARG10.8340.92627.2400.0210.0210.0000.0000.0000.000
42A42LYS10.7840.88031.3080.0470.0470.0000.0000.0000.000
43A43GLU-1-0.936-0.96834.254-0.037-0.0370.0000.0000.0000.000
44A44GLN00.023-0.00931.6630.0030.0030.0000.0000.0000.000
45A45ALA00.0600.04333.5300.0000.0000.0000.0000.0000.000
46A46GLU-1-0.845-0.91229.231-0.061-0.0610.0000.0000.0000.000
47A47ARG10.7690.88128.7310.0360.0360.0000.0000.0000.000
48A48PHE00.0160.01424.8120.0020.0020.0000.0000.0000.000
49A49ASP-1-0.783-0.85029.826-0.027-0.0270.0000.0000.0000.000
50A50THR0-0.069-0.05232.4550.0060.0060.0000.0000.0000.000
51A51ALA0-0.009-0.00127.6630.0040.0040.0000.0000.0000.000
52A52LEU0-0.0100.00025.796-0.002-0.0020.0000.0000.0000.000
53A53CYS0-0.033-0.02323.3080.0030.0030.0000.0000.0000.000
54A54VAL00.0140.00020.9070.0050.0050.0000.0000.0000.000
55A55LEU00.0070.01720.561-0.009-0.0090.0000.0000.0000.000
56A56GLY00.0280.01217.6480.0070.0070.0000.0000.0000.000
57A57THR0-0.010-0.02518.6420.0030.0030.0000.0000.0000.000
58A58PRO0-0.030-0.01416.2110.0080.0080.0000.0000.0000.000
59A59ARG10.8930.93119.4400.1350.1350.0000.0000.0000.000
60A60PHE00.0250.00714.8820.0010.0010.0000.0000.0000.000
61A61THR00.0500.02620.5110.0010.0010.0000.0000.0000.000
62A62SER00.0010.00921.7520.0040.0040.0000.0000.0000.000
63A63GLY00.0220.01819.345-0.016-0.0160.0000.0000.0000.000
64A64ARG10.8220.91813.7420.5530.5530.0000.0000.0000.000
65A65HIS10.8380.90512.8870.4080.4080.0000.0000.0000.000
66A66TYR0-0.009-0.0313.041-0.422-0.0760.023-0.155-0.2140.000
67A67TRP00.0210.0237.9610.0420.0420.0000.0000.0000.000
68A68GLU-1-0.769-0.8902.571-2.323-0.6551.113-1.311-1.469-0.015
69A69VAL00.0000.0017.4090.0290.0290.0000.0000.0000.000
70A70ASP-1-0.756-0.8529.4630.5820.5820.0000.0000.0000.000
71A71VAL00.0090.00310.979-0.050-0.0500.0000.0000.0000.000
72A72GLY00.0270.01813.373-0.016-0.0160.0000.0000.0000.000
73A73THR0-0.011-0.02414.9820.0130.0130.0000.0000.0000.000
74A74SER0-0.012-0.00117.717-0.020-0.0200.0000.0000.0000.000
75A75GLN00.012-0.00518.7720.0030.0030.0000.0000.0000.000
76A76VAL0-0.033-0.00721.504-0.009-0.0090.0000.0000.0000.000
77A77TRP00.0100.00514.680-0.007-0.0070.0000.0000.0000.000
78A78ASP-1-0.798-0.87718.899-0.035-0.0350.0000.0000.0000.000
79A79VAL00.006-0.00112.806-0.001-0.0010.0000.0000.0000.000
80A80GLY00.0350.00915.232-0.007-0.0070.0000.0000.0000.000
81A81VAL0-0.042-0.00916.199-0.016-0.0160.0000.0000.0000.000
82A82CYS0-0.0320.00018.7450.0190.0190.0000.0000.0000.000
83A83LYS10.9190.95722.5470.0950.0950.0000.0000.0000.000
84A84GLU-1-0.719-0.83625.399-0.102-0.1020.0000.0000.0000.000
85A85SER0-0.089-0.06326.7520.0100.0100.0000.0000.0000.000
86A86VAL0-0.041-0.00226.2830.0060.0060.0000.0000.0000.000
87A87ASN00.012-0.01329.2790.0020.0020.0000.0000.0000.000
88A88ARG10.7850.86926.9740.0820.0820.0000.0000.0000.000
89A89GLN00.000-0.00530.8980.0020.0020.0000.0000.0000.000
90A90GLY00.0120.00634.195-0.001-0.0010.0000.0000.0000.000
91A91LYS10.8160.88832.6340.0320.0320.0000.0000.0000.000
92A92ILE00.0080.01826.845-0.004-0.0040.0000.0000.0000.000
93A93GLU-1-0.885-0.93829.349-0.037-0.0370.0000.0000.0000.000
94A94LEU0-0.013-0.00223.018-0.006-0.0060.0000.0000.0000.000
95A95SER00.0190.00025.926-0.001-0.0010.0000.0000.0000.000
96A96SER00.0570.01724.684-0.002-0.0020.0000.0000.0000.000
97A97GLU-1-0.988-0.98726.068-0.075-0.0750.0000.0000.0000.000
98A98HIS0-0.011-0.00129.063-0.001-0.0010.0000.0000.0000.000
99A99GLY0-0.0070.00426.8080.0010.0010.0000.0000.0000.000
100A100PHE0-0.010-0.01423.173-0.010-0.0100.0000.0000.0000.000
101A101LEU0-0.033-0.00219.8450.0050.0050.0000.0000.0000.000
102A102THR0-0.034-0.02617.903-0.016-0.0160.0000.0000.0000.000
103A103VAL00.0330.00515.5170.0060.0060.0000.0000.0000.000
104A104GLY00.0340.02317.2210.0010.0010.0000.0000.0000.000
105A105CYS0-0.082-0.02018.2570.0100.0100.0000.0000.0000.000
106A106ARG10.8110.86820.2570.0090.0090.0000.0000.0000.000
107A107GLU-1-0.876-0.95623.3970.0460.0460.0000.0000.0000.000
108A108GLY00.0180.00725.519-0.005-0.0050.0000.0000.0000.000
109A109LYS10.8630.92917.703-0.160-0.1600.0000.0000.0000.000
110A110VAL00.0120.02521.421-0.002-0.0020.0000.0000.0000.000
111A111PHE00.027-0.00216.1790.0010.0010.0000.0000.0000.000
112A112ALA0-0.012-0.00420.633-0.003-0.0030.0000.0000.0000.000
113A113ALA00.0320.01319.376-0.005-0.0050.0000.0000.0000.000
114A114SER0-0.0020.01821.0510.0030.0030.0000.0000.0000.000
115A115THR0-0.026-0.03723.069-0.007-0.0070.0000.0000.0000.000
116A116VAL0-0.0100.01125.3450.0080.0080.0000.0000.0000.000
117A117PRO00.024-0.00729.191-0.001-0.0010.0000.0000.0000.000
118A118MET00.0000.03025.443-0.006-0.0060.0000.0000.0000.000
119A119THR0-0.010-0.00122.4330.0060.0060.0000.0000.0000.000
120A120PRO00.000-0.00722.959-0.001-0.0010.0000.0000.0000.000
121A121LEU0-0.021-0.01417.880-0.009-0.0090.0000.0000.0000.000
122A122TRP0-0.049-0.01619.6610.0150.0150.0000.0000.0000.000
123A123VAL00.0210.01114.457-0.015-0.0150.0000.0000.0000.000
124A124SER00.0400.02112.7320.0100.0100.0000.0000.0000.000
125A125PRO00.0520.02314.8190.0070.0070.0000.0000.0000.000
126A126GLN0-0.016-0.01513.187-0.040-0.0400.0000.0000.0000.000
127A127LEU0-0.035-0.00610.4040.0820.0820.0000.0000.0000.000
128A128HIS10.8570.9218.888-0.713-0.7130.0000.0000.0000.000
129A129ARG10.7960.8764.819-0.493-0.4930.0000.0000.0000.000
130A130VAL00.0380.0408.1340.0440.0440.0000.0000.0000.000
131A131GLY00.0320.0156.0880.0110.0110.0000.0000.0000.000
132A132ILE0-0.016-0.0136.9700.0550.0550.0000.0000.0000.000
133A133PHE0-0.007-0.0129.067-0.133-0.1330.0000.0000.0000.000
134A134LEU00.0000.01811.1370.0850.0850.0000.0000.0000.000
135A135ASP-1-0.812-0.91214.754-0.416-0.4160.0000.0000.0000.000
136A136VAL00.0120.00517.0630.0340.0340.0000.0000.0000.000
137A137GLY0-0.024-0.00420.1600.0280.0280.0000.0000.0000.000
138A138MET0-0.037-0.02719.0700.0290.0290.0000.0000.0000.000
139A139ARG10.9340.98521.1860.1620.1620.0000.0000.0000.000
140A140SER00.017-0.00418.2270.0070.0070.0000.0000.0000.000
141A141ILE0-0.037-0.01614.563-0.026-0.0260.0000.0000.0000.000
142A142ALA00.0100.02312.7700.0420.0420.0000.0000.0000.000
143A143PHE00.0070.00111.113-0.062-0.0620.0000.0000.0000.000
144A144TYR00.0110.0057.568-0.011-0.0110.0000.0000.0000.000
145A145ASN00.0310.0188.3210.1590.1590.0000.0000.0000.000
146A146VAL0-0.018-0.0132.273-0.010-0.5152.460-1.160-0.795-0.002
147A147SER0-0.102-0.0663.6990.1260.4750.007-0.192-0.164-0.001
148A148ASP-1-0.821-0.9106.3090.3430.3430.0000.0000.0000.000
149A149GLY00.0080.0186.381-0.190-0.1900.0000.0000.0000.000
150A150CYS0-0.074-0.0297.068-0.086-0.0860.0000.0000.0000.000
151A151HIS00.0120.02010.457-0.017-0.0170.0000.0000.0000.000
152A152ILE0-0.069-0.02511.3350.0640.0640.0000.0000.0000.000
153A153TYR00.022-0.01114.2310.0250.0250.0000.0000.0000.000
154A154THR00.017-0.02315.060-0.067-0.0670.0000.0000.0000.000
155A155PHE0-0.0140.01317.2690.0250.0250.0000.0000.0000.000
156A156ILE00.017-0.01519.401-0.033-0.0330.0000.0000.0000.000
157A157GLU-1-0.947-0.97122.104-0.115-0.1150.0000.0000.0000.000
158A158ILE0-0.0110.01220.1510.0120.0120.0000.0000.0000.000
159A159PRO00.003-0.00324.319-0.002-0.0020.0000.0000.0000.000
160A160VAL0-0.032-0.01923.145-0.005-0.0050.0000.0000.0000.000
161A161CYS0-0.019-0.01725.7510.0020.0020.0000.0000.0000.000
162A162GLU-1-0.764-0.84026.518-0.101-0.1010.0000.0000.0000.000
163A163PRO0-0.034-0.02824.102-0.012-0.0120.0000.0000.0000.000
164A164TRP00.0000.00320.1820.0090.0090.0000.0000.0000.000
165A165ARG10.7300.82320.5560.1180.1180.0000.0000.0000.000
166A166PRO0-0.004-0.00115.5810.0030.0030.0000.0000.0000.000
167A167PHE00.0220.00417.3930.0220.0220.0000.0000.0000.000
168A168PHE00.001-0.00913.812-0.010-0.0100.0000.0000.0000.000
169A169ALA00.0430.01818.7920.0040.0040.0000.0000.0000.000
170A170HIS00.0150.01219.868-0.004-0.0040.0000.0000.0000.000
171A171LYS10.9540.97121.944-0.024-0.0240.0000.0000.0000.000
172A172ARG10.7060.84424.219-0.037-0.0370.0000.0000.0000.000
173A173GLY0-0.016-0.00525.317-0.006-0.0060.0000.0000.0000.000
174A174SER0-0.038-0.05126.888-0.002-0.0020.0000.0000.0000.000
175A175GLN0-0.012-0.02428.8800.0000.0000.0000.0000.0000.000
176A176ASP-1-0.804-0.87829.3900.0640.0640.0000.0000.0000.000
177A177ASP-1-0.826-0.88123.4680.0970.0970.0000.0000.0000.000
178A178GLN0-0.018-0.00623.047-0.009-0.0090.0000.0000.0000.000
179A179SER0-0.067-0.02719.7620.0030.0030.0000.0000.0000.000
180A180ILE0-0.006-0.01916.126-0.017-0.0170.0000.0000.0000.000
181A181LEU0-0.032-0.00115.2390.0160.0160.0000.0000.0000.000
182A182SER0-0.028-0.01512.8870.0000.0000.0000.0000.0000.000
183A183ILE00.0220.01111.5760.0060.0060.0000.0000.0000.000
184A184CYS0-0.072-0.0336.6000.1150.1150.0000.0000.0000.000
185A185SER0-0.044-0.0147.538-0.180-0.1800.0000.0000.0000.000
186A186VAL00.0360.0189.051-0.050-0.0500.0000.0000.0000.000
187A187ILE0-0.017-0.0087.701-0.170-0.1700.0000.0000.0000.000
188A188ASN0-0.0020.0119.4850.1090.1090.0000.0000.0000.000