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: KG7K3

Calculation Name: 2AH5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AH5

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2460396.361344
FMO2-HF: Nuclear repulsion 2378856.646492
FMO2-HF: Total energy -81539.714852
FMO2-MP2: Total energy -81780.092036


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-26.213-14.5127.359-6.573-12.488-0.056
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.003
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].
3A3SER0-0.041-0.0143.577-2.837-0.8260.003-0.862-1.1520.002
4A4ILE0-0.0400.0002.467-1.0870.0420.911-0.702-1.338-0.001
5A5THR0-0.001-0.0175.638-0.061-0.0610.0000.0000.0000.000
6A6ALA0-0.0030.0058.5610.1470.1470.0000.0000.0000.000
7A7ILE00.0040.0147.433-0.193-0.1930.0000.0000.0000.000
8A8PHE0-0.028-0.01710.0870.2270.2270.0000.0000.0000.000
9A9PHE00.0500.01512.479-0.106-0.1060.0000.0000.0000.000
10A10ASP-1-0.686-0.82515.056-0.392-0.3920.0000.0000.0000.000
11A11LEU0-0.051-0.03818.062-0.028-0.0280.0000.0000.0000.000
12A12ASP-1-0.783-0.86221.002-0.351-0.3510.0000.0000.0000.000
13A13GLY00.0190.02122.044-0.010-0.0100.0000.0000.0000.000
14A14THR0-0.022-0.02316.135-0.040-0.0400.0000.0000.0000.000
15A15LEU00.0150.00916.688-0.011-0.0110.0000.0000.0000.000
16A16VAL00.000-0.02419.8800.0280.0280.0000.0000.0000.000
17A17ASP-1-0.773-0.84923.597-0.297-0.2970.0000.0000.0000.000
18A18SER0-0.041-0.07325.9940.0220.0220.0000.0000.0000.000
19A19SER0-0.034-0.04928.3920.0290.0290.0000.0000.0000.000
20A20ILE0-0.008-0.00330.1630.0200.0200.0000.0000.0000.000
21A21GLY00.0600.03132.7620.0150.0150.0000.0000.0000.000
22A22ILE0-0.063-0.02528.5270.0150.0150.0000.0000.0000.000
23A23HIS00.0060.00433.0040.0100.0100.0000.0000.0000.000
24A24ASN0-0.028-0.04035.2220.0170.0170.0000.0000.0000.000
25A25ALA00.0080.01835.8000.0110.0110.0000.0000.0000.000
26A26PHE00.003-0.00532.8170.0100.0100.0000.0000.0000.000
27A27THR0-0.022-0.01038.2230.0110.0110.0000.0000.0000.000
28A28TYR0-0.085-0.06040.9000.0080.0080.0000.0000.0000.000
29A29THR0-0.001-0.01540.2800.0060.0060.0000.0000.0000.000
30A30PHE00.0340.00039.1680.0050.0050.0000.0000.0000.000
31A31LYS10.8460.92344.3270.1150.1150.0000.0000.0000.000
32A32GLU-1-0.856-0.89545.900-0.102-0.1020.0000.0000.0000.000
33A33LEU0-0.042-0.02244.0600.0040.0040.0000.0000.0000.000
34A34GLY0-0.0340.00648.0610.0050.0050.0000.0000.0000.000
35A35VAL0-0.044-0.02445.2150.0040.0040.0000.0000.0000.000
36A36PRO0-0.017-0.01946.325-0.004-0.0040.0000.0000.0000.000
37A37SER00.0130.00441.067-0.004-0.0040.0000.0000.0000.000
38A38PRO0-0.0150.00438.6980.0040.0040.0000.0000.0000.000
39A39ASP-1-0.803-0.88837.653-0.139-0.1390.0000.0000.0000.000
40A40ALA00.0400.00435.633-0.006-0.0060.0000.0000.0000.000
41A41LYS10.8850.94832.8030.1330.1330.0000.0000.0000.000
42A42THR00.005-0.02332.943-0.008-0.0080.0000.0000.0000.000
43A43ILE0-0.0040.00433.733-0.007-0.0070.0000.0000.0000.000
44A44ARG10.9610.97229.3430.1920.1920.0000.0000.0000.000
45A45GLY00.0090.02129.204-0.017-0.0170.0000.0000.0000.000
46A46PHE0-0.033-0.02729.6920.0010.0010.0000.0000.0000.000
47A47MET0-0.103-0.03327.642-0.006-0.0060.0000.0000.0000.000
48A48GLY00.0740.03225.075-0.023-0.0230.0000.0000.0000.000
49A49PRO0-0.044-0.00925.813-0.001-0.0010.0000.0000.0000.000
50A50PRO00.0270.01727.700-0.001-0.0010.0000.0000.0000.000
51A51LEU00.0230.01530.0290.0100.0100.0000.0000.0000.000
52A52GLU-1-0.884-0.95833.205-0.157-0.1570.0000.0000.0000.000
53A53SER0-0.012-0.00731.8880.0110.0110.0000.0000.0000.000
54A54SER00.0050.00732.1590.0070.0070.0000.0000.0000.000
55A55PHE00.0340.01634.5120.0080.0080.0000.0000.0000.000
56A56ALA0-0.015-0.00837.0630.0080.0080.0000.0000.0000.000
57A57THR0-0.108-0.06135.1950.0070.0070.0000.0000.0000.000
58A58CYS0-0.082-0.03838.3940.0040.0040.0000.0000.0000.000
59A59LEU00.0090.02141.3550.0030.0030.0000.0000.0000.000
60A60SER00.0270.02043.1110.0010.0010.0000.0000.0000.000
61A61LYS10.9890.98342.3840.0720.0720.0000.0000.0000.000
62A62ASP-1-0.952-0.98943.917-0.082-0.0820.0000.0000.0000.000
63A63GLN00.007-0.00845.5740.0010.0010.0000.0000.0000.000
64A64ILE0-0.0350.00938.853-0.005-0.0050.0000.0000.0000.000
65A65SER00.0280.00740.942-0.007-0.0070.0000.0000.0000.000
66A66GLU-1-0.902-0.93942.224-0.099-0.0990.0000.0000.0000.000
67A67ALA00.0440.01741.088-0.004-0.0040.0000.0000.0000.000
68A68VAL0-0.005-0.00636.915-0.007-0.0070.0000.0000.0000.000
69A69GLN0-0.035-0.01639.063-0.007-0.0070.0000.0000.0000.000
70A70ILE00.0130.01141.444-0.005-0.0050.0000.0000.0000.000
71A71TYR00.0600.04032.997-0.007-0.0070.0000.0000.0000.000
72A72ARG10.8680.90231.9850.1920.1920.0000.0000.0000.000
73A73SER0-0.100-0.05537.994-0.004-0.0040.0000.0000.0000.000
74A74TYR0-0.025-0.02137.6460.0050.0050.0000.0000.0000.000
75A75TYR00.0390.00430.244-0.010-0.0100.0000.0000.0000.000
76A76LYS10.8460.92333.1480.2140.2140.0000.0000.0000.000
77A77ALA0-0.0140.00236.860-0.004-0.0040.0000.0000.0000.000
78A78LYS10.8570.91638.4510.1650.1650.0000.0000.0000.000
79A79GLY00.0070.00435.482-0.006-0.0060.0000.0000.0000.000
80A80ILE0-0.038-0.01231.080-0.012-0.0120.0000.0000.0000.000
81A81TYR0-0.006-0.01131.711-0.018-0.0180.0000.0000.0000.000
82A82GLU-1-0.825-0.85833.909-0.181-0.1810.0000.0000.0000.000
83A83ALA0-0.002-0.01028.651-0.003-0.0030.0000.0000.0000.000
84A84GLN0-0.049-0.01027.8450.0190.0190.0000.0000.0000.000
85A85LEU00.0380.02222.659-0.012-0.0120.0000.0000.0000.000
86A86PHE00.0060.01521.2940.0340.0340.0000.0000.0000.000
87A87PRO00.010-0.01822.518-0.018-0.0180.0000.0000.0000.000
88A88GLN0-0.066-0.04318.4360.0110.0110.0000.0000.0000.000
89A89ILE00.0030.02217.735-0.079-0.0790.0000.0000.0000.000
90A90ILE0-0.0040.00317.976-0.061-0.0610.0000.0000.0000.000
91A91ASP-1-0.811-0.90816.917-0.710-0.7100.0000.0000.0000.000
92A92LEU0-0.024-0.00611.616-0.078-0.0780.0000.0000.0000.000
93A93LEU0-0.014-0.01213.572-0.150-0.1500.0000.0000.0000.000
94A94GLU-1-0.922-0.94515.043-0.635-0.6350.0000.0000.0000.000
95A95GLU-1-0.934-0.96611.266-1.101-1.1010.0000.0000.0000.000
96A96LEU0-0.024-0.0118.370-0.170-0.1700.0000.0000.0000.000
97A97SER0-0.014-0.03311.087-0.057-0.0570.0000.0000.0000.000
98A98SER0-0.087-0.03411.8720.0680.0680.0000.0000.0000.000
99A99SER0-0.073-0.0457.9300.0090.0090.0000.0000.0000.000
100A100TYR0-0.075-0.0354.144-0.721-0.562-0.001-0.014-0.1440.000
101A101PRO00.0080.04110.9440.1080.1080.0000.0000.0000.000
102A102LEU00.004-0.00511.993-0.165-0.1650.0000.0000.0000.000
103A103TYR0-0.054-0.02513.8770.1520.1520.0000.0000.0000.000
104A104ILE0-0.025-0.00215.719-0.055-0.0550.0000.0000.0000.000
105A105THR00.005-0.00516.5940.0250.0250.0000.0000.0000.000
106A106THR0-0.025-0.01918.8450.0040.0040.0000.0000.0000.000
107A107THR00.0520.02021.7520.0110.0110.0000.0000.0000.000
108A108LYS10.7560.86824.6480.3520.3520.0000.0000.0000.000
109A109ASP-1-0.741-0.83026.462-0.239-0.2390.0000.0000.0000.000
110A110THR00.0360.02026.019-0.018-0.0180.0000.0000.0000.000
111A111SER0-0.009-0.00827.568-0.015-0.0150.0000.0000.0000.000
112A112THR00.003-0.01929.8400.0020.0020.0000.0000.0000.000
113A113ALA00.0380.02224.374-0.006-0.0060.0000.0000.0000.000
114A114GLN0-0.0020.01025.775-0.020-0.0200.0000.0000.0000.000
115A115ASP-1-0.863-0.94027.218-0.251-0.2510.0000.0000.0000.000
116A116MET0-0.0170.00626.151-0.003-0.0030.0000.0000.0000.000
117A117ALA00.0340.01523.805-0.008-0.0080.0000.0000.0000.000
118A118LYS10.8570.91725.4490.3140.3140.0000.0000.0000.000
119A119ASN0-0.042-0.02928.2760.0110.0110.0000.0000.0000.000
120A120LEU0-0.039-0.01126.1340.0100.0100.0000.0000.0000.000
121A121GLU-1-0.964-0.97226.366-0.334-0.3340.0000.0000.0000.000
122A122ILE00.0380.01421.119-0.023-0.0230.0000.0000.0000.000
123A123HIS0-0.030-0.02521.792-0.038-0.0380.0000.0000.0000.000
124A124HIS0-0.031-0.02121.9530.0100.0100.0000.0000.0000.000
125A125PHE0-0.0030.01118.0350.0020.0020.0000.0000.0000.000
126A126PHE0-0.046-0.02516.218-0.076-0.0760.0000.0000.0000.000
127A127ASP-1-0.828-0.90917.469-0.614-0.6140.0000.0000.0000.000
128A128GLY0-0.046-0.03619.3450.0600.0600.0000.0000.0000.000
129A129ILE0-0.054-0.02919.630-0.045-0.0450.0000.0000.0000.000
130A130TYR0-0.031-0.03519.5280.0580.0580.0000.0000.0000.000
131A131GLY00.0400.00522.083-0.030-0.0300.0000.0000.0000.000
132A132SER0-0.024-0.02324.7350.0150.0150.0000.0000.0000.000
133A133SER0-0.055-0.04426.9030.0130.0130.0000.0000.0000.000
134A134PRO0-0.022-0.03129.4060.0020.0020.0000.0000.0000.000
135A135GLU-1-0.919-0.94725.942-0.216-0.2160.0000.0000.0000.000
136A136ALA00.0050.00024.1160.0000.0000.0000.0000.0000.000
137A137PRO0-0.0240.00026.079-0.014-0.0140.0000.0000.0000.000
138A138HIS0-0.025-0.01824.382-0.013-0.0130.0000.0000.0000.000
139A139LYS10.8230.88518.5140.4550.4550.0000.0000.0000.000
140A140ALA00.0450.02218.810-0.032-0.0320.0000.0000.0000.000
141A141ASP-1-0.847-0.91419.682-0.223-0.2230.0000.0000.0000.000
142A142VAL0-0.018-0.00120.041-0.007-0.0070.0000.0000.0000.000
143A143ILE0-0.0130.00214.810-0.023-0.0230.0000.0000.0000.000
144A144HIS00.018-0.00317.246-0.029-0.0290.0000.0000.0000.000
145A145GLN0-0.025-0.00719.100-0.014-0.0140.0000.0000.0000.000
146A146ALA00.0060.01617.0510.0090.0090.0000.0000.0000.000
147A147LEU0-0.012-0.01012.647-0.020-0.0200.0000.0000.0000.000
148A148GLN0-0.029-0.01816.5060.0380.0380.0000.0000.0000.000
149A149THR0-0.065-0.03319.8020.0320.0320.0000.0000.0000.000
150A150HIS0-0.0100.01617.1160.0240.0240.0000.0000.0000.000
151A151GLN0-0.099-0.03817.4490.0060.0060.0000.0000.0000.000
152A152LEU0-0.0240.00112.503-0.003-0.0030.0000.0000.0000.000
153A153ALA0-0.008-0.00812.4900.0360.0360.0000.0000.0000.000
154A154PRO00.0250.00811.609-0.110-0.1100.0000.0000.0000.000
155A155GLU-1-0.870-0.9538.360-0.147-0.1470.0000.0000.0000.000
156A156GLN0-0.036-0.0166.745-0.011-0.0110.0000.0000.0000.000
157A157ALA00.0280.0248.379-0.324-0.3240.0000.0000.0000.000
158A158ILE0-0.008-0.0025.072-0.096-0.0960.0000.0000.0000.000
159A159ILE0-0.0050.0078.1570.1040.1040.0000.0000.0000.000
160A160ILE0-0.023-0.0089.497-0.059-0.0590.0000.0000.0000.000
161A161GLY00.0350.00312.2650.1080.1080.0000.0000.0000.000
162A162ASP-1-0.749-0.86815.677-0.479-0.4790.0000.0000.0000.000
163A163THR0-0.002-0.02518.5860.0820.0820.0000.0000.0000.000
164A164LYS10.8580.89318.4900.1750.1750.0000.0000.0000.000
165A165PHE00.014-0.00619.5610.0160.0160.0000.0000.0000.000
166A166ASP-1-0.743-0.83515.879-0.512-0.5120.0000.0000.0000.000
167A167MET0-0.040-0.01113.490-0.030-0.0300.0000.0000.0000.000
168A168LEU0-0.055-0.03015.4930.0250.0250.0000.0000.0000.000
169A169GLY00.0650.04217.5120.0260.0260.0000.0000.0000.000
170A170ALA0-0.0050.00811.8210.0180.0180.0000.0000.0000.000
171A171ARG10.9240.96813.4380.1170.1170.0000.0000.0000.000
172A172GLU-1-0.985-1.01314.989-0.167-0.1670.0000.0000.0000.000
173A173THR0-0.050-0.04114.8600.0150.0150.0000.0000.0000.000
174A174GLY0-0.016-0.00112.8590.0250.0250.0000.0000.0000.000
175A175ILE0-0.0430.0159.6330.0310.0310.0000.0000.0000.000
176A176GLN00.0390.0202.646-2.129-1.1420.087-0.458-0.617-0.003
177A177LYS10.7990.8777.7010.4860.4860.0000.0000.0000.000
178A178LEU0-0.0130.0057.094-0.026-0.0260.0000.0000.0000.000
179A179ALA00.004-0.00310.1560.1090.1090.0000.0000.0000.000
180A180ILE0-0.012-0.00213.522-0.050-0.0500.0000.0000.0000.000
181A181THR00.002-0.02715.7960.0630.0630.0000.0000.0000.000
182A182TRP0-0.080-0.03014.6710.0350.0350.0000.0000.0000.000
183A183GLY00.0120.01120.7330.0190.0190.0000.0000.0000.000
184A184PHE0-0.080-0.04122.1050.0330.0330.0000.0000.0000.000
185A185GLY0-0.0190.01022.1400.0340.0340.0000.0000.0000.000
186A186GLU-1-0.939-0.96822.417-0.232-0.2320.0000.0000.0000.000
187A187GLN00.026-0.01018.347-0.021-0.0210.0000.0000.0000.000
188A188ALA0-0.023-0.01919.7280.0000.0000.0000.0000.0000.000
189A189ASP-1-0.820-0.89321.515-0.198-0.1980.0000.0000.0000.000
190A190LEU00.0000.00816.6880.0140.0140.0000.0000.0000.000
191A191LEU00.0280.00115.279-0.012-0.0120.0000.0000.0000.000
192A192ASN0-0.071-0.02317.2540.0530.0530.0000.0000.0000.000
193A193TYR0-0.021-0.00816.2620.0400.0400.0000.0000.0000.000
194A194GLN0-0.081-0.03413.374-0.008-0.0080.0000.0000.0000.000
195A195PRO00.0040.00811.1610.0080.0080.0000.0000.0000.000
196A196ASP-1-0.822-0.9055.895-0.532-0.5320.0000.0000.0000.000
197A197TYR0-0.034-0.0236.429-0.048-0.0480.0000.0000.0000.000
198A198ILE0-0.029-0.0188.4370.0890.0890.0000.0000.0000.000
199A199ALA00.0000.01311.987-0.012-0.0120.0000.0000.0000.000
200A200HIS0-0.006-0.01614.0640.0960.0960.0000.0000.0000.000
201A201LYS10.8560.90516.2150.4450.4450.0000.0000.0000.000
202A202PRO00.0500.02714.988-0.082-0.0820.0000.0000.0000.000
203A203LEU00.0410.01113.350-0.119-0.1190.0000.0000.0000.000
204A204GLU-1-0.839-0.89511.933-0.658-0.6580.0000.0000.0000.000
205A205VAL00.0020.0019.370-0.122-0.1220.0000.0000.0000.000
206A206LEU00.0220.0157.787-0.489-0.4890.0000.0000.0000.000
207A207ALA0-0.022-0.0116.457-0.600-0.6000.0000.0000.0000.000
208A208TYR0-0.051-0.0142.677-3.023-0.6550.891-1.090-2.170-0.009
209A209PHE00.018-0.0032.226-5.573-2.5582.190-2.237-2.968-0.021
210A210GLN0-0.057-0.0152.458-3.572-1.5403.278-1.210-4.099-0.024