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: 721GK

Calculation Name: 2C46-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C46

Chain ID: A

ChEMBL ID:

UniProt ID: O60942

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 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 205
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2539748.636146
FMO2-HF: Nuclear repulsion 2455126.779933
FMO2-HF: Total energy -84621.856213
FMO2-MP2: Total energy -84864.363138


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:-5:ASN)


Summations of interaction energy for fragment #1(A:-5:ASN)
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.
-32.527-24.35513.276-9.191-12.257-0.032
Interaction energy analysis for fragmet #1(A:-5:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.017
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].
3A-3TYR0-0.0050.0312.744-6.959-2.8850.563-1.953-2.6830.014
4A-2PHE00.001-0.0032.320-2.762-1.2791.998-0.861-2.6210.003
5A-1GLN0-0.0140.0074.148-2.071-1.9350.000-0.057-0.0780.000
6A0SER00.0200.0007.4090.5540.5540.0000.0000.0000.000
7A1MET00.0200.03110.4000.2820.2820.0000.0000.0000.000
8A2ALA0-0.025-0.00512.3450.0620.0620.0000.0000.0000.000
9A3HIS00.0840.04614.2450.0140.0140.0000.0000.0000.000
10A4ASN0-0.044-0.0269.3910.0450.0450.0000.0000.0000.000
11A5LYS11.0021.00513.075-0.523-0.5230.0000.0000.0000.000
12A6ILE00.0090.00514.5100.1890.1890.0000.0000.0000.000
13A7PRO0-0.017-0.01714.271-0.088-0.0880.0000.0000.0000.000
14A8PRO00.0800.04917.177-0.032-0.0320.0000.0000.0000.000
15A9ARG10.8060.88320.628-0.325-0.3250.0000.0000.0000.000
16A10TRP0-0.039-0.01615.142-0.036-0.0360.0000.0000.0000.000
17A11LEU0-0.011-0.01319.7090.0130.0130.0000.0000.0000.000
18A12ASN00.0670.02821.2900.0220.0220.0000.0000.0000.000
19A13CYS0-0.0440.02920.904-0.010-0.0100.0000.0000.0000.000
20A14PRO00.0390.03121.8060.0270.0270.0000.0000.0000.000
21A15ARG10.8010.88419.231-0.385-0.3850.0000.0000.0000.000
22A16ARG10.8880.92519.242-0.233-0.2330.0000.0000.0000.000
23A17GLY00.0560.03321.464-0.025-0.0250.0000.0000.0000.000
24A18GLN0-0.025-0.00224.1470.0050.0050.0000.0000.0000.000
25A19PRO00.002-0.02024.6510.0200.0200.0000.0000.0000.000
26A20VAL00.0610.04825.751-0.025-0.0250.0000.0000.0000.000
27A21ALA00.0320.01627.2770.0030.0030.0000.0000.0000.000
28A22GLY0-0.031-0.00828.181-0.013-0.0130.0000.0000.0000.000
29A23ARG10.8340.91825.604-0.184-0.1840.0000.0000.0000.000
30A24PHE00.0710.01921.9140.0160.0160.0000.0000.0000.000
31A25LEU0-0.032-0.02419.317-0.025-0.0250.0000.0000.0000.000
32A26PRO00.0170.02519.6150.0670.0670.0000.0000.0000.000
33A27LEU0-0.033-0.03014.769-0.055-0.0550.0000.0000.0000.000
34A28LYS10.8400.94416.689-0.605-0.6050.0000.0000.0000.000
35A29THR0-0.047-0.02511.2240.1460.1460.0000.0000.0000.000
36A30MET00.0130.02710.736-0.209-0.2090.0000.0000.0000.000
37A31LEU0-0.007-0.00610.3870.3810.3810.0000.0000.0000.000
38A32GLY00.0360.0008.832-0.321-0.3210.0000.0000.0000.000
39A33PRO00.015-0.0179.8270.0250.0250.0000.0000.0000.000
40A34ARG10.8510.9278.256-0.759-0.7590.0000.0000.0000.000
41A35TYR0-0.026-0.0308.651-0.315-0.3150.0000.0000.0000.000
42A36ASP-1-0.767-0.86213.4740.4650.4650.0000.0000.0000.000
43A37SER0-0.027-0.00816.298-0.042-0.0420.0000.0000.0000.000
44A38GLN0-0.024-0.01614.820-0.028-0.0280.0000.0000.0000.000
45A39VAL0-0.0180.00516.3300.0040.0040.0000.0000.0000.000
46A40ALA00.0660.05119.117-0.018-0.0180.0000.0000.0000.000
47A41GLU-1-0.812-0.91120.5610.2970.2970.0000.0000.0000.000
48A42GLU-1-0.803-0.88821.5820.3230.3230.0000.0000.0000.000
49A43ASN0-0.043-0.03420.8250.0300.0300.0000.0000.0000.000
50A44ARG10.7540.87117.139-0.266-0.2660.0000.0000.0000.000
51A45PHE00.016-0.02115.580-0.073-0.0730.0000.0000.0000.000
52A46HIS10.8500.90912.345-0.369-0.3690.0000.0000.0000.000
53A47PRO00.0820.0338.337-0.088-0.0880.0000.0000.0000.000
54A48SER00.0240.01011.510-0.050-0.0500.0000.0000.0000.000
55A49MET0-0.0330.00513.894-0.039-0.0390.0000.0000.0000.000
56A50LEU00.0270.01913.683-0.044-0.0440.0000.0000.0000.000
57A51SER0-0.013-0.03314.095-0.025-0.0250.0000.0000.0000.000
58A52ASN00.0220.00616.161-0.081-0.0810.0000.0000.0000.000
59A53TYR00.0230.01919.110-0.014-0.0140.0000.0000.0000.000
60A54LEU00.0300.02516.857-0.021-0.0210.0000.0000.0000.000
61A55LYS10.8500.91516.494-0.009-0.0090.0000.0000.0000.000
62A56SER0-0.081-0.04922.086-0.008-0.0080.0000.0000.0000.000
63A57LEU0-0.029-0.01623.657-0.008-0.0080.0000.0000.0000.000
64A58LYS10.8750.93624.893-0.082-0.0820.0000.0000.0000.000
65A59VAL00.0120.01823.473-0.010-0.0100.0000.0000.0000.000
66A60LYS10.8210.90817.612-0.004-0.0040.0000.0000.0000.000
67A61MET00.0040.03516.2000.0510.0510.0000.0000.0000.000
68A62GLY00.0590.03017.528-0.048-0.0480.0000.0000.0000.000
69A63LEU0-0.054-0.01715.161-0.031-0.0310.0000.0000.0000.000
70A64LEU00.004-0.00210.757-0.021-0.0210.0000.0000.0000.000
71A65VAL0-0.004-0.00613.2360.0970.0970.0000.0000.0000.000
72A66ASP-1-0.729-0.8088.8102.8532.8530.0000.0000.0000.000
73A67LEU00.015-0.00312.3550.0260.0260.0000.0000.0000.000
74A68THR0-0.092-0.05510.4150.0180.0180.0000.0000.0000.000
75A69ASN00.0390.00110.9980.2310.2310.0000.0000.0000.000
76A70THR00.0170.0067.7810.0540.0540.0000.0000.0000.000
77A71SER00.0450.0192.720-1.991-0.8140.284-0.641-0.820-0.002
78A72ARG10.9100.9463.8242.6063.0550.013-0.159-0.303-0.001
79A73PHE00.0120.0286.249-0.460-0.4600.0000.0000.0000.000
80A74TYR0-0.006-0.0455.989-0.958-0.9580.0000.0000.0000.000
81A75ASP-1-0.760-0.8551.825-17.801-18.70910.188-4.911-4.369-0.049
82A76ARG10.8530.8992.931-4.514-3.0510.228-0.483-1.2090.003
83A77ASN00.003-0.0183.3091.0641.3620.002-0.126-0.1740.000
84A78ASP-1-0.887-0.9745.1450.7040.7040.0000.0000.0000.000
85A79ILE0-0.036-0.0177.2100.3250.3250.0000.0000.0000.000
86A80GLU-1-0.838-0.8997.027-0.624-0.6240.0000.0000.0000.000
87A81LYS10.8260.9379.0880.5980.5980.0000.0000.0000.000
88A82GLU-1-0.812-0.87010.985-0.096-0.0960.0000.0000.0000.000
89A83GLY00.0150.01213.1640.0860.0860.0000.0000.0000.000
90A84ILE0-0.075-0.02512.6770.0790.0790.0000.0000.0000.000
91A85LYS10.9750.97811.825-0.142-0.1420.0000.0000.0000.000
92A86TYR0-0.014-0.0327.2370.3700.3700.0000.0000.0000.000
93A87ILE0-0.040-0.03010.572-0.107-0.1070.0000.0000.0000.000
94A88LYS10.7460.8877.304-2.878-2.8780.0000.0000.0000.000
95A89LEU0-0.014-0.00911.055-0.138-0.1380.0000.0000.0000.000
96A90GLN00.0160.0009.9480.2100.2100.0000.0000.0000.000
97A91CYS0-0.031-0.00114.086-0.128-0.1280.0000.0000.0000.000
98A92LYS10.8320.90417.622-0.346-0.3460.0000.0000.0000.000
99A93GLY00.0270.01919.3000.0320.0320.0000.0000.0000.000
100A94HIS00.0360.00419.975-0.031-0.0310.0000.0000.0000.000
101A95GLY00.0250.01921.910-0.029-0.0290.0000.0000.0000.000
102A96GLU-1-0.801-0.87523.5590.3620.3620.0000.0000.0000.000
103A97CYS00.0000.02723.4680.0430.0430.0000.0000.0000.000
104A98PRO0-0.027-0.00721.3770.0090.0090.0000.0000.0000.000
105A99THR00.017-0.01123.069-0.022-0.0220.0000.0000.0000.000
106A100THR00.0470.00624.8630.0130.0130.0000.0000.0000.000
107A101GLU-1-0.781-0.85623.2610.3410.3410.0000.0000.0000.000
108A102ASN0-0.0150.01119.8580.0270.0270.0000.0000.0000.000
109A103THR00.0580.02821.6270.0310.0310.0000.0000.0000.000
110A104GLU-1-0.759-0.85524.2870.2460.2460.0000.0000.0000.000
111A105THR0-0.063-0.04818.511-0.002-0.0020.0000.0000.0000.000
112A106PHE00.001-0.01319.3130.0200.0200.0000.0000.0000.000
113A107ILE00.0610.03921.300-0.009-0.0090.0000.0000.0000.000
114A108ARG10.8120.87222.995-0.239-0.2390.0000.0000.0000.000
115A109LEU0-0.062-0.01516.411-0.025-0.0250.0000.0000.0000.000
116A110CYS00.0220.00720.663-0.017-0.0170.0000.0000.0000.000
117A111GLU-1-0.811-0.88922.3900.1690.1690.0000.0000.0000.000
118A112ARG10.8270.91319.191-0.266-0.2660.0000.0000.0000.000
119A113PHE0-0.032-0.02217.967-0.021-0.0210.0000.0000.0000.000
120A114ASN0-0.0030.01423.253-0.024-0.0240.0000.0000.0000.000
121A115GLU-1-0.833-0.93425.9550.1210.1210.0000.0000.0000.000
122A116ARG10.7910.90921.152-0.106-0.1060.0000.0000.0000.000
123A117ASN00.0210.00227.882-0.004-0.0040.0000.0000.0000.000
124A118PRO0-0.0140.00926.9360.0010.0010.0000.0000.0000.000
125A119PRO00.0170.01126.5440.0040.0040.0000.0000.0000.000
126A120GLU-1-0.828-0.91720.4440.0530.0530.0000.0000.0000.000
127A121LEU0-0.028-0.00721.0520.0230.0230.0000.0000.0000.000
128A122ILE00.0010.00018.824-0.002-0.0020.0000.0000.0000.000
129A123GLY00.011-0.00816.7330.0010.0010.0000.0000.0000.000
130A124VAL0-0.008-0.00816.9850.0490.0490.0000.0000.0000.000
131A125HIS00.0340.03611.1790.1360.1360.0000.0000.0000.000
132A126CYM-1-0.789-0.74914.9670.8820.8820.0000.0000.0000.000
133A127THR0-0.015-0.02014.8070.0960.0960.0000.0000.0000.000
134A128HIS00.025-0.01316.0750.0520.0520.0000.0000.0000.000
135A129GLY00.0570.01518.907-0.049-0.0490.0000.0000.0000.000
136A130PHE00.014-0.03119.861-0.055-0.0550.0000.0000.0000.000
137A131ASN00.0530.04222.818-0.044-0.0440.0000.0000.0000.000
138A132ARG10.9400.95518.292-0.671-0.6710.0000.0000.0000.000
139A133THR0-0.030-0.11119.3400.0010.0010.0000.0000.0000.000
140A134GLY00.0490.01520.848-0.027-0.0270.0000.0000.0000.000
141A135PHE00.0320.01023.814-0.027-0.0270.0000.0000.0000.000
142A136LEU00.001-0.00519.437-0.027-0.0270.0000.0000.0000.000
143A137ILE0-0.017-0.00222.127-0.030-0.0300.0000.0000.0000.000
144A138CYS0-0.037-0.02425.156-0.035-0.0350.0000.0000.0000.000
145A139ALA00.0560.03426.325-0.022-0.0220.0000.0000.0000.000
146A140PHE0-0.048-0.02625.284-0.021-0.0210.0000.0000.0000.000
147A141LEU0-0.041-0.03527.823-0.020-0.0200.0000.0000.0000.000
148A142VAL00.0310.03530.702-0.017-0.0170.0000.0000.0000.000
149A143GLU-1-0.862-0.91429.4220.2530.2530.0000.0000.0000.000
150A144LYS10.7910.88428.823-0.191-0.1910.0000.0000.0000.000
151A145MET0-0.116-0.05530.251-0.002-0.0020.0000.0000.0000.000
152A146ASP-1-0.893-0.92533.4800.1340.1340.0000.0000.0000.000
153A147TRP0-0.057-0.03032.9590.0010.0010.0000.0000.0000.000
154A148SER00.029-0.00835.8950.0050.0050.0000.0000.0000.000
155A149ILE00.0340.00731.6310.0120.0120.0000.0000.0000.000
156A150GLU-1-0.793-0.88434.5260.1900.1900.0000.0000.0000.000
157A151ALA00.0110.01736.2080.0070.0070.0000.0000.0000.000
158A152ALA0-0.0180.01031.2790.0080.0080.0000.0000.0000.000
159A153VAL00.024-0.00231.0910.0190.0190.0000.0000.0000.000
160A154ALA00.0100.01532.1150.0120.0120.0000.0000.0000.000
161A155THR0-0.027-0.02830.985-0.001-0.0010.0000.0000.0000.000
162A156PHE0-0.030-0.01123.8350.0150.0150.0000.0000.0000.000
163A157ALA00.010-0.01028.8380.0170.0170.0000.0000.0000.000
164A158GLN0-0.051-0.01931.102-0.007-0.0070.0000.0000.0000.000
165A159ALA0-0.042-0.01127.974-0.005-0.0050.0000.0000.0000.000
166A160ARG10.7480.85321.113-0.499-0.4990.0000.0000.0000.000
167A161PRO00.0670.06127.0030.0150.0150.0000.0000.0000.000
168A162PRO0-0.021-0.02427.6540.0200.0200.0000.0000.0000.000
169A163GLY00.0460.02228.407-0.021-0.0210.0000.0000.0000.000
170A164ILE0-0.088-0.04026.4320.0310.0310.0000.0000.0000.000
171A165TYR00.0520.00424.447-0.016-0.0160.0000.0000.0000.000
172A166LYS10.8330.93326.187-0.386-0.3860.0000.0000.0000.000
173A167GLY00.0600.02528.985-0.003-0.0030.0000.0000.0000.000
174A168ASP-1-0.781-0.90729.6730.3100.3100.0000.0000.0000.000
175A169TYR0-0.081-0.08422.8710.0250.0250.0000.0000.0000.000
176A170LEU0-0.0140.00029.093-0.003-0.0030.0000.0000.0000.000
177A171LYS10.9270.97332.016-0.211-0.2110.0000.0000.0000.000
178A172GLU-1-0.773-0.85428.9800.2650.2650.0000.0000.0000.000
179A173LEU0-0.051-0.02627.970-0.005-0.0050.0000.0000.0000.000
180A174PHE00.0550.01131.747-0.006-0.0060.0000.0000.0000.000
181A175ARG10.8310.90232.034-0.241-0.2410.0000.0000.0000.000
182A176ARG10.7110.84827.007-0.317-0.3170.0000.0000.0000.000
183A177TYR0-0.076-0.09029.5120.0030.0030.0000.0000.0000.000
184A178GLY00.0350.01835.805-0.004-0.0040.0000.0000.0000.000
185A179ASP-1-0.824-0.89538.9480.1460.1460.0000.0000.0000.000
186A180ILE0-0.059-0.04737.2220.0090.0090.0000.0000.0000.000
187A181GLU-1-0.933-0.98039.3790.1610.1610.0000.0000.0000.000
188A182GLU-1-0.971-0.97841.6590.1410.1410.0000.0000.0000.000
189A183ALA0-0.059-0.01036.3940.0060.0060.0000.0000.0000.000
190A184PRO0-0.026-0.00835.237-0.004-0.0040.0000.0000.0000.000
191A185PRO0-0.013-0.01036.7280.0070.0070.0000.0000.0000.000
192A186PRO00.000-0.02233.1130.0070.0070.0000.0000.0000.000
193A187PRO0-0.0330.01331.931-0.013-0.0130.0000.0000.0000.000
194A188LEU00.002-0.00934.0640.0070.0070.0000.0000.0000.000
195A189LEU0-0.0050.00529.8790.0080.0080.0000.0000.0000.000
196A190PRO0-0.018-0.01128.972-0.014-0.0140.0000.0000.0000.000
197A191ASP-1-0.869-0.95330.0860.2930.2930.0000.0000.0000.000
198A192TRP00.0360.01523.4450.0240.0240.0000.0000.0000.000
199A193CYS0-0.137-0.06026.0370.0330.0330.0000.0000.0000.000
200A194PHE00.0500.02127.801-0.016-0.0160.0000.0000.0000.000
201A195GLU-1-0.950-0.98427.7730.3420.3420.0000.0000.0000.000
202A196ASP-1-0.818-0.91829.0000.2510.2510.0000.0000.0000.000
203A197ASP-1-0.908-0.94727.1920.3580.3580.0000.0000.0000.000
204A198GLU-1-0.998-0.99028.4060.2260.2260.0000.0000.0000.000
205A199ASP-1-1.018-0.98426.9480.3670.3670.0000.0000.0000.000