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: MMGYZ

Calculation Name: 1F6F-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F6F

Chain ID: A

ChEMBL ID:

UniProt ID: P16038

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2023734.426946
FMO2-HF: Nuclear repulsion 1948038.140344
FMO2-HF: Total energy -75696.286602
FMO2-MP2: Total energy -75916.459854


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:ALA )


Summations of interaction energy for fragment #1(A:1:ALA )
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.
-0.870.755-0.003-0.894-0.7290.001
Interaction energy analysis for fragmet #1(A:1:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.002
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].
3A3HIS 00.0170.0093.511-1.990-0.365-0.003-0.894-0.7290.001
4A4PRO 0-0.001-0.0056.2500.4170.4170.0000.0000.0000.000
5A5PRO 00.0430.0119.830-0.121-0.1210.0000.0000.0000.000
6A6TYR 00.0980.01712.663-0.023-0.0230.0000.0000.0000.000
7A14CYS 0-0.0110.0089.703-0.013-0.0130.0000.0000.0000.000
8A8ARG 10.9591.0019.9060.3170.3170.0000.0000.0000.000
9A9ASN 0-0.066-0.06412.5880.1120.1120.0000.0000.0000.000
10A10GLN 00.0470.01314.360-0.025-0.0250.0000.0000.0000.000
11A11PRO 0-0.0140.01314.992-0.020-0.0200.0000.0000.0000.000
12A12GLY 00.0670.02913.047-0.045-0.0450.0000.0000.0000.000
13A13LYS 10.9120.97111.6950.2330.2330.0000.0000.0000.000
14A15GLN 0-0.0220.00311.9150.0320.0320.0000.0000.0000.000
15A16ILE 0-0.027-0.00114.566-0.004-0.0040.0000.0000.0000.000
16A17PRO 00.0430.02116.0100.0110.0110.0000.0000.0000.000
17A18LEU 00.0750.02619.0380.0140.0140.0000.0000.0000.000
18A19GLN 00.0460.02422.4720.0080.0080.0000.0000.0000.000
19A20SER 00.0150.00118.3090.0130.0130.0000.0000.0000.000
20A21LEU 0-0.034-0.01319.5570.0160.0160.0000.0000.0000.000
21A22PHE 00.0880.03222.1890.0140.0140.0000.0000.0000.000
22A23ASP -1-0.888-0.93623.402-0.051-0.0510.0000.0000.0000.000
23A24ARG 10.9560.95716.2320.0740.0740.0000.0000.0000.000
24A25ALA 00.0410.03824.2230.0090.0090.0000.0000.0000.000
25A26THR 0-0.021-0.02527.0190.0060.0060.0000.0000.0000.000
26A27THR 0-0.057-0.02426.2300.0060.0060.0000.0000.0000.000
27A28VAL 00.0540.03626.0810.0060.0060.0000.0000.0000.000
28A29ALA 00.0260.00028.9220.0030.0030.0000.0000.0000.000
29A30ASN 0-0.033-0.01931.8250.0020.0020.0000.0000.0000.000
30A31TYR 0-0.037-0.01331.0580.0020.0020.0000.0000.0000.000
31A32ASN 00.0510.01332.0520.0050.0050.0000.0000.0000.000
32A33SER 00.0130.00334.8030.0010.0010.0000.0000.0000.000
33A34LYS 10.8960.95935.809-0.008-0.0080.0000.0000.0000.000
34A35LEU 00.0510.02534.0600.0010.0010.0000.0000.0000.000
35A36ALA 00.0230.01138.2110.0010.0010.0000.0000.0000.000
36A37GLY 00.0260.01440.6680.0000.0000.0000.0000.0000.000
37A38GLU -1-0.929-0.96239.1800.0230.0230.0000.0000.0000.000
38A39MET 0-0.083-0.04439.1530.0010.0010.0000.0000.0000.000
39A40VAL 00.0070.00144.1310.0000.0000.0000.0000.0000.000
40A41ASN 00.0200.01845.813-0.001-0.0010.0000.0000.0000.000
41A42ARG 10.8910.95044.786-0.021-0.0210.0000.0000.0000.000
42A43PHE 0-0.021-0.00648.3180.0000.0000.0000.0000.0000.000
43A44ASP -1-0.774-0.92350.0540.0060.0060.0000.0000.0000.000
44A45GLU -1-0.989-0.97651.7840.0100.0100.0000.0000.0000.000
45A46GLN 0-0.057-0.05751.0460.0030.0030.0000.0000.0000.000
46A47TYR 0-0.105-0.02951.5960.0010.0010.0000.0000.0000.000
47A48NME 0-0.0240.02154.280-0.001-0.0010.0000.0000.0000.000
48A56ACE 00.0290.00658.3590.0000.0000.0000.0000.0000.000
49A57VAL 0-0.025-0.02456.3460.0000.0000.0000.0000.0000.000
50A58ILE 0-0.0130.00650.3440.0000.0000.0000.0000.0000.000
51A59ASN 0-0.026-0.02452.489-0.001-0.0010.0000.0000.0000.000
52A175CYS 0-0.109-0.05346.224-0.001-0.0010.0000.0000.0000.000
53A61HIS 00.0840.04443.464-0.001-0.0010.0000.0000.0000.000
54A62THR 0-0.058-0.03842.793-0.001-0.0010.0000.0000.0000.000
55A63SER 0-0.079-0.03145.895-0.002-0.0020.0000.0000.0000.000
56A64SER 00.0190.01347.903-0.001-0.0010.0000.0000.0000.000
57A65ILE 00.0040.01741.852-0.001-0.0010.0000.0000.0000.000
58A66THR 0-0.006-0.01245.7730.0010.0010.0000.0000.0000.000
59A67THR 0-0.034-0.01643.051-0.001-0.0010.0000.0000.0000.000
60A68PRO 00.0140.03842.8550.0010.0010.0000.0000.0000.000
61A69ASN 00.0610.01544.9540.0000.0000.0000.0000.0000.000
62A70SER 00.0250.01847.4550.0010.0010.0000.0000.0000.000
63A71LYS 10.9960.97744.4410.0220.0220.0000.0000.0000.000
64A72ALA 0-0.0020.00045.245-0.002-0.0020.0000.0000.0000.000
65A73GLU -1-0.864-0.93546.349-0.024-0.0240.0000.0000.0000.000
66A74ALA 0-0.0020.01142.063-0.002-0.0020.0000.0000.0000.000
67A75ILE 0-0.058-0.04241.241-0.002-0.0020.0000.0000.0000.000
68A76ASN 00.0240.00241.669-0.004-0.0040.0000.0000.0000.000
69A77THR 0-0.053-0.00540.652-0.001-0.0010.0000.0000.0000.000
70A78GLU -1-0.851-0.93138.778-0.050-0.0500.0000.0000.0000.000
71A79ASP -1-0.834-0.92833.618-0.064-0.0640.0000.0000.0000.000
72A80LYS 10.9510.99035.0040.0630.0630.0000.0000.0000.000
73A81ILE 00.0270.00736.3470.0010.0010.0000.0000.0000.000
74A82LEU 0-0.017-0.00236.3650.0030.0030.0000.0000.0000.000
75A83PHE 00.023-0.00229.7370.0020.0020.0000.0000.0000.000
76A84LYS 10.9160.97334.3210.0480.0480.0000.0000.0000.000
77A85LEU 00.0130.01036.7180.0030.0030.0000.0000.0000.000
78A86VAL 0-0.032-0.01432.9550.0030.0030.0000.0000.0000.000
79A87ILE 00.0070.00131.1090.0030.0030.0000.0000.0000.000
80A88SER 00.0220.01334.4850.0030.0030.0000.0000.0000.000
81A89LEU 0-0.0200.00037.9300.0030.0030.0000.0000.0000.000
82A90LEU 0-0.027-0.02031.9270.0030.0030.0000.0000.0000.000
83A91HIS 00.0130.01232.2040.0060.0060.0000.0000.0000.000
84A92SER 0-0.026-0.02236.5360.0020.0020.0000.0000.0000.000
85A93TRP 0-0.070-0.05538.3780.0030.0030.0000.0000.0000.000
86A94ASP -1-0.873-0.93935.5160.0060.0060.0000.0000.0000.000
87A95GLU -1-0.852-0.94537.9650.0010.0010.0000.0000.0000.000
88A96PRO 00.0080.00641.2610.0020.0020.0000.0000.0000.000
89A97LEU 0-0.011-0.00537.6830.0020.0020.0000.0000.0000.000
90A98HIS 0-0.0010.00439.6170.0040.0040.0000.0000.0000.000
91A99HIS 0-0.020-0.01040.8910.0020.0020.0000.0000.0000.000
92A100ALA 0-0.0140.00243.2960.0010.0010.0000.0000.0000.000
93A101VAL 0-0.012-0.01739.2500.0020.0020.0000.0000.0000.000
94A102THR 0-0.026-0.00642.5750.0020.0020.0000.0000.0000.000
95A103GLU -1-0.822-0.88644.6370.0140.0140.0000.0000.0000.000
96A104LEU 0-0.021-0.01344.4280.0010.0010.0000.0000.0000.000
97A105ALA 0-0.0070.03643.4670.0020.0020.0000.0000.0000.000
98A106ASN 00.0720.08745.3910.0020.0020.0000.0000.0000.000
99A107SER 00.027-0.03147.7600.0000.0000.0000.0000.0000.000
100A108LYS 10.8450.91544.189-0.028-0.0280.0000.0000.0000.000
101A109GLY 00.0250.02148.8310.0000.0000.0000.0000.0000.000
102A110THR 0-0.050-0.03349.946-0.001-0.0010.0000.0000.0000.000
103A111SER 0-0.017-0.04045.0920.0000.0000.0000.0000.0000.000
104A112PRO 0-0.003-0.00145.1080.0020.0020.0000.0000.0000.000
105A113ALA 0-0.005-0.00942.9100.0010.0010.0000.0000.0000.000
106A114LEU 00.0300.00642.0670.0010.0010.0000.0000.0000.000
107A115LEU 00.0250.01841.1770.0000.0000.0000.0000.0000.000
108A116THR 00.0040.00937.4530.0010.0010.0000.0000.0000.000
109A117LYS 10.8830.93037.419-0.025-0.0250.0000.0000.0000.000
110A118ALA 00.0370.01837.637-0.001-0.0010.0000.0000.0000.000
111A119GLN 00.000-0.00735.8750.0000.0000.0000.0000.0000.000
112A120GLU -1-0.813-0.90331.5350.0410.0410.0000.0000.0000.000
113A121ILE 0-0.028-0.01132.973-0.002-0.0020.0000.0000.0000.000
114A122LYS 10.8870.96634.218-0.014-0.0140.0000.0000.0000.000
115A123GLU -1-0.959-0.98130.1650.0250.0250.0000.0000.0000.000
116A124LYS 10.8860.93727.002-0.042-0.0420.0000.0000.0000.000
117A125ALA 0-0.0030.00829.930-0.005-0.0050.0000.0000.0000.000
118A126LYS 10.9870.98729.552-0.017-0.0170.0000.0000.0000.000
119A127VAL 0-0.0190.00624.660-0.004-0.0040.0000.0000.0000.000
120A128LEU 0-0.039-0.02826.228-0.007-0.0070.0000.0000.0000.000
121A129VAL 0-0.005-0.00628.135-0.007-0.0070.0000.0000.0000.000
122A130ASP -1-0.881-0.92323.155-0.042-0.0420.0000.0000.0000.000
123A131GLY 0-0.013-0.00923.883-0.012-0.0120.0000.0000.0000.000
124A132VAL 0-0.037-0.03924.890-0.011-0.0110.0000.0000.0000.000
125A133GLU -1-0.904-0.95026.924-0.048-0.0480.0000.0000.0000.000
126A134VAL 0-0.039-0.01220.881-0.012-0.0120.0000.0000.0000.000
127A135ILE 0-0.069-0.04224.099-0.014-0.0140.0000.0000.0000.000
128A136GLN 00.0370.01625.444-0.007-0.0070.0000.0000.0000.000
129A137LYS 10.9360.96725.4220.0670.0670.0000.0000.0000.000
130A138ARG 10.8180.91718.4040.1780.1780.0000.0000.0000.000
131A139ILE 0-0.020-0.02024.752-0.008-0.0080.0000.0000.0000.000
132A140HIS 0-0.059-0.03927.861-0.001-0.0010.0000.0000.0000.000
133A141PRO 0-0.011-0.00426.8570.0050.0050.0000.0000.0000.000
134A142GLY 0-0.029-0.01229.0070.0040.0040.0000.0000.0000.000
135A143GLU -1-0.859-0.91831.344-0.053-0.0530.0000.0000.0000.000
136A144LYS 10.9020.93732.5770.0500.0500.0000.0000.0000.000
137A145ASN 0-0.002-0.02132.3650.0020.0020.0000.0000.0000.000
138A146GLU -1-0.902-0.94836.103-0.032-0.0320.0000.0000.0000.000
139A147PRO 0-0.040-0.00639.3280.0010.0010.0000.0000.0000.000
140A148TYR 00.0080.00137.7440.0000.0000.0000.0000.0000.000
141A149PRO 0-0.031-0.01042.0050.0010.0010.0000.0000.0000.000
142A150VAL 00.0670.02943.8140.0010.0010.0000.0000.0000.000
143A151TRP 0-0.025-0.01046.1360.0000.0000.0000.0000.0000.000
144A152SER 00.036-0.00148.2450.0010.0010.0000.0000.0000.000
145A153GLU -1-0.902-0.95750.884-0.001-0.0010.0000.0000.0000.000
146A154GLN 00.0230.03045.8690.0020.0020.0000.0000.0000.000
147A155SER 00.0390.02249.8820.0010.0010.0000.0000.0000.000
148A156SER 0-0.046-0.04551.9790.0010.0010.0000.0000.0000.000
149A157LEU 0-0.034-0.02147.2710.0010.0010.0000.0000.0000.000
150A158THR 0-0.015-0.00950.2540.0010.0010.0000.0000.0000.000
151A159SER 0-0.079-0.02752.7980.0000.0000.0000.0000.0000.000
152A160GLN 00.018-0.00356.4580.0010.0010.0000.0000.0000.000
153A161ASP -1-0.902-0.93358.9420.0060.0060.0000.0000.0000.000
154A162GLU -1-0.844-0.95858.5350.0100.0100.0000.0000.0000.000
155A163ASN 0-0.023-0.00758.1920.0010.0010.0000.0000.0000.000
156A164VAL 0-0.008-0.00757.2160.0000.0000.0000.0000.0000.000
157A165ARG 10.8880.94051.507-0.013-0.0130.0000.0000.0000.000
158A166ARG 10.9240.95553.726-0.009-0.0090.0000.0000.0000.000
159A167VAL 00.0170.00354.0700.0000.0000.0000.0000.0000.000
160A168ALA 00.0070.01851.885-0.001-0.0010.0000.0000.0000.000
161A169PHE 00.028-0.00446.8010.0000.0000.0000.0000.0000.000
162A170TYR 0-0.0030.02149.2690.0000.0000.0000.0000.0000.000
163A171ARG 10.8770.93350.1940.0000.0000.0000.0000.0000.000
164A172LEU 00.0120.01644.588-0.001-0.0010.0000.0000.0000.000
165A173PHE 00.0340.00443.8630.0000.0000.0000.0000.0000.000
166A174HIS 00.0370.02145.350-0.002-0.0020.0000.0000.0000.000
167A176LEU 00.0440.03939.983-0.001-0.0010.0000.0000.0000.000
168A177HIS 00.0020.00341.401-0.001-0.0010.0000.0000.0000.000
169A178ARG 10.9510.96642.4250.0060.0060.0000.0000.0000.000
170A179ASP -1-0.751-0.87240.611-0.012-0.0120.0000.0000.0000.000
171A180SER 0-0.0130.00137.938-0.002-0.0020.0000.0000.0000.000
172A181SER 0-0.015-0.00637.799-0.003-0.0030.0000.0000.0000.000
173A182LYS 10.8990.94539.6640.0130.0130.0000.0000.0000.000
174A183ILE 00.0280.02434.280-0.003-0.0030.0000.0000.0000.000
175A184TYR 00.0250.00933.250-0.004-0.0040.0000.0000.0000.000
176A185THR 0-0.046-0.04035.411-0.003-0.0030.0000.0000.0000.000
177A186TYR 00.006-0.01136.804-0.003-0.0030.0000.0000.0000.000
178A187LEU 00.0190.01430.111-0.004-0.0040.0000.0000.0000.000
179A188ARG 10.8960.96232.3720.0150.0150.0000.0000.0000.000
180A189ILE 0-0.0180.00234.158-0.003-0.0030.0000.0000.0000.000
181A190LEU 00.0130.00931.943-0.003-0.0030.0000.0000.0000.000
182A191LYS 10.9110.98327.9240.0380.0380.0000.0000.0000.000
183A197CYS 0-0.125-0.08629.7600.0010.0010.0000.0000.0000.000
184A193ARG 10.8590.94233.5300.0470.0470.0000.0000.0000.000
185A194LEU 0-0.008-0.00529.713-0.003-0.0030.0000.0000.0000.000
186A195THR 0-0.091-0.03226.184-0.009-0.0090.0000.0000.0000.000
187A196SER 00.0230.02327.9950.0030.0030.0000.0000.0000.000
188A0NME 00.0240.01731.715-0.002-0.0020.0000.0000.0000.000