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: R9878

Calculation Name: 2DG6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DG6

Chain ID: A

ChEMBL ID:

UniProt ID: O86531

Base Structure: X-ray

Registration Date: 2023-06-22

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2149727.821523
FMO2-HF: Nuclear repulsion 2068915.298235
FMO2-HF: Total energy -80812.523288
FMO2-MP2: Total energy -81049.279513


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.
-37.733-36.13735.581-15.34-21.834-0.034
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 : 0.042 / q_NPA : 0.074
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].
3A3LEU00.0860.0342.690-2.1180.4770.738-1.537-1.796-0.005
4A4ALA00.0300.0165.4920.6650.6650.0000.0000.0000.000
5A5ASP-1-0.851-0.9252.0221.1492.7012.499-1.657-2.395-0.009
6A6LEU00.0490.0313.1350.3512.3510.939-0.773-2.166-0.001
7A7SER0-0.048-0.0284.168-1.030-1.3790.0300.568-0.2490.000
8A8LYS10.9510.9637.277-1.781-1.7810.0000.0000.0000.000
9A9ARG10.7830.8242.164-12.053-23.42223.073-6.689-5.0150.040
10A10SER0-0.034-0.0336.864-0.898-0.8980.0000.0000.0000.000
11A11GLY0-0.0120.0108.396-0.365-0.3650.0000.0000.0000.000
12A12VAL0-0.0130.00610.211-0.251-0.2510.0000.0000.0000.000
13A13SER00.0470.05310.8840.1160.1160.0000.0000.0000.000
14A14THR00.0750.00010.662-0.057-0.0570.0000.0000.0000.000
15A15ALA0-0.0400.00411.591-0.123-0.1230.0000.0000.0000.000
16A16THR00.011-0.03514.242-0.089-0.0890.0000.0000.0000.000
17A17ILE00.0330.0338.013-0.069-0.0690.0000.0000.0000.000
18A18LYN00.0370.03611.796-0.146-0.1460.0000.0000.0000.000
19A19TYR0-0.027-0.03313.433-0.045-0.0450.0000.0000.0000.000
20A20TYR00.0750.02011.9990.0290.0290.0000.0000.0000.000
21A21LEU0-0.052-0.0189.592-0.028-0.0280.0000.0000.0000.000
22A22ARG10.8850.94913.3590.1940.1940.0000.0000.0000.000
23A23GLU-1-0.940-0.97016.700-0.234-0.2340.0000.0000.0000.000
24A24GLY0-0.002-0.00216.1960.0280.0280.0000.0000.0000.000
25A25LEU0-0.035-0.01014.446-0.043-0.0430.0000.0000.0000.000
26A26LEU0-0.036-0.0137.291-0.044-0.0440.0000.0000.0000.000
27A27PRO00.0850.0439.6290.0740.0740.0000.0000.0000.000
28A28PRO00.0230.0059.631-0.231-0.2310.0000.0000.0000.000
29A29GLY0-0.0120.0007.929-0.247-0.2470.0000.0000.0000.000
30A39TYR0-0.074-0.0532.4170.1371.3530.874-0.514-1.5750.000
31A40ASP-1-0.768-0.8842.512-15.537-12.4302.984-2.617-3.473-0.033
32A41GLU-1-0.839-0.9342.488-5.540-3.9693.632-1.938-3.265-0.024
33A42ASP-1-0.806-0.8963.497-0.837-0.9040.0050.240-0.1770.000
34A43HIS00.0020.0153.326-0.580-0.2690.009-0.053-0.2670.000
35A44LEU0-0.070-0.0372.3360.8031.7290.798-0.347-1.376-0.002
36A45ARG10.8930.9464.2852.8842.9870.000-0.023-0.0800.000
37A46ARG10.7860.8857.2761.4561.4560.0000.0000.0000.000
38A47LEU00.002-0.0107.4190.3950.3950.0000.0000.0000.000
39A48ARG10.9170.9447.471-0.239-0.2390.0000.0000.0000.000
40A49LEU00.0430.04610.2420.1240.1240.0000.0000.0000.000
41A50VAL00.0270.00912.2120.0950.0950.0000.0000.0000.000
42A51ARG10.8120.88212.130-0.017-0.0170.0000.0000.0000.000
43A52ALA00.0240.02314.4800.0480.0480.0000.0000.0000.000
44A53LEU00.0520.02016.4060.0260.0260.0000.0000.0000.000
45A54ILE0-0.026-0.00617.2340.0280.0280.0000.0000.0000.000
46A55GLN0-0.058-0.02116.9730.0590.0590.0000.0000.0000.000
47A56VAL0-0.0200.00019.0050.0170.0170.0000.0000.0000.000
48A57GLY00.0330.01820.6190.0010.0010.0000.0000.0000.000
49A58LYS10.8530.94022.3520.0580.0580.0000.0000.0000.000
50A59VAL00.0160.01221.264-0.001-0.0010.0000.0000.0000.000
51A60PRO00.0040.00022.1770.0010.0010.0000.0000.0000.000
52A61VAL00.0400.00919.506-0.020-0.0200.0000.0000.0000.000
53A62ALA0-0.020-0.02221.190-0.034-0.0340.0000.0000.0000.000
54A63THR00.0490.02823.553-0.011-0.0110.0000.0000.0000.000
55A64ALA00.0110.00218.484-0.020-0.0200.0000.0000.0000.000
56A65ARG10.8830.95419.0160.2430.2430.0000.0000.0000.000
57A66GLU-1-0.888-0.93320.087-0.293-0.2930.0000.0000.0000.000
58A67VAL0-0.0030.00419.280-0.024-0.0240.0000.0000.0000.000
59A68LEU0-0.029-0.03514.555-0.025-0.0250.0000.0000.0000.000
60A69GLY00.0180.02217.689-0.060-0.0600.0000.0000.0000.000
61A70HIS0-0.008-0.00819.945-0.031-0.0310.0000.0000.0000.000
62A71VAL0-0.090-0.05215.603-0.001-0.0010.0000.0000.0000.000
63A72ASP-1-0.835-0.89714.859-1.016-1.0160.0000.0000.0000.000
64A73ASP-1-0.848-0.88617.590-0.414-0.4140.0000.0000.0000.000
65A74ASP-1-0.962-0.98919.932-0.567-0.5670.0000.0000.0000.000
66A75SER0-0.092-0.05821.7770.0360.0360.0000.0000.0000.000
67A76LEU00.0020.00224.5890.0410.0410.0000.0000.0000.000
68A77GLY00.0120.01224.343-0.038-0.0380.0000.0000.0000.000
69A78ARG10.9860.97819.6880.4820.4820.0000.0000.0000.000
70A79THR0-0.038-0.02023.479-0.003-0.0030.0000.0000.0000.000
71A80VAL00.0480.03026.3230.0140.0140.0000.0000.0000.000
72A81ARG10.9080.96619.3270.5660.5660.0000.0000.0000.000
73A82LEU0-0.0010.00421.145-0.005-0.0050.0000.0000.0000.000
74A83GLY00.0140.01223.3300.0140.0140.0000.0000.0000.000
75A84ALA00.0150.00525.2490.0150.0150.0000.0000.0000.000
76A85ALA00.010-0.00120.8960.0090.0090.0000.0000.0000.000
77A86LEU0-0.020-0.02422.8330.0150.0150.0000.0000.0000.000
78A87TRP0-0.023-0.02224.4230.0200.0200.0000.0000.0000.000
79A88ALA00.0380.05124.2570.0150.0150.0000.0000.0000.000
80A89LEU0-0.087-0.04321.3180.0070.0070.0000.0000.0000.000
81A90PRO0-0.053-0.04024.7960.0100.0100.0000.0000.0000.000
82A91GLN00.0100.00727.9710.0100.0100.0000.0000.0000.000
83A92ASP-1-0.910-0.94131.186-0.083-0.0830.0000.0000.0000.000
84A93ALA0-0.056-0.04134.699-0.006-0.0060.0000.0000.0000.000
85A94GLU-1-0.915-0.97037.900-0.114-0.1140.0000.0000.0000.000
86A95PRO0-0.031-0.01239.9210.0050.0050.0000.0000.0000.000
87A96ASP-1-0.850-0.92043.160-0.065-0.0650.0000.0000.0000.000
88A97GLU-1-0.800-0.88844.096-0.082-0.0820.0000.0000.0000.000
89A98ALA0-0.048-0.01147.5520.0010.0010.0000.0000.0000.000
90A99ASP-1-0.846-0.91549.008-0.049-0.0490.0000.0000.0000.000
91A100PRO00.006-0.00950.434-0.002-0.0020.0000.0000.0000.000
92A101ALA0-0.008-0.01949.689-0.001-0.0010.0000.0000.0000.000
93A102VAL0-0.012-0.00445.134-0.001-0.0010.0000.0000.0000.000
94A103ALA00.0150.01546.904-0.003-0.0030.0000.0000.0000.000
95A104ALA0-0.022-0.02048.902-0.002-0.0020.0000.0000.0000.000
96A105ALA00.0190.01144.794-0.001-0.0010.0000.0000.0000.000
97A106ARG10.8080.86541.1680.0880.0880.0000.0000.0000.000
98A107VAL0-0.038-0.00745.116-0.003-0.0030.0000.0000.0000.000
99A108GLU-1-0.856-0.93246.428-0.058-0.0580.0000.0000.0000.000
100A109VAL0-0.007-0.00740.266-0.001-0.0010.0000.0000.0000.000
101A110ASP-1-0.928-0.96942.236-0.094-0.0940.0000.0000.0000.000
102A111ARG10.9920.99543.7940.0610.0610.0000.0000.0000.000
103A112LEU00.0050.00740.0860.0000.0000.0000.0000.0000.000
104A113LEU0-0.050-0.03037.658-0.003-0.0030.0000.0000.0000.000
105A114GLU-1-0.953-0.96540.719-0.081-0.0810.0000.0000.0000.000
106A115LEU0-0.078-0.04143.5740.0000.0000.0000.0000.0000.000
107A116LEU0-0.052-0.02238.0660.0010.0010.0000.0000.0000.000
108A117GLY00.0300.03439.257-0.003-0.0030.0000.0000.0000.000
109A118TRP0-0.090-0.03734.842-0.011-0.0110.0000.0000.0000.000
110A119GLU-1-0.797-0.93737.229-0.109-0.1090.0000.0000.0000.000
111A120THR00.0190.01231.936-0.002-0.0020.0000.0000.0000.000
112A121SER0-0.023-0.02434.198-0.009-0.0090.0000.0000.0000.000
113A122ARG10.8530.93735.4180.0990.0990.0000.0000.0000.000
114A123GLU-1-0.962-0.97336.422-0.148-0.1480.0000.0000.0000.000
115A124LEU0-0.073-0.03631.159-0.005-0.0050.0000.0000.0000.000
116A125ALA00.0020.00435.268-0.002-0.0020.0000.0000.0000.000
117A126PRO0-0.059-0.02237.7190.0030.0030.0000.0000.0000.000
118A127LEU0-0.006-0.01034.6070.0010.0010.0000.0000.0000.000
119A128SER0-0.0030.02132.805-0.004-0.0040.0000.0000.0000.000
120A129PRO00.0340.02030.7560.0110.0110.0000.0000.0000.000
121A130VAL00.0410.01529.5060.0100.0100.0000.0000.0000.000
122A131HIS00.0120.00532.7310.0090.0090.0000.0000.0000.000
123A132ARG10.9190.96335.0220.1290.1290.0000.0000.0000.000
124A133SER00.0160.00534.2070.0090.0090.0000.0000.0000.000
125A134LEU0-0.0120.01436.5600.0080.0080.0000.0000.0000.000
126A135VAL0-0.002-0.00638.1040.0070.0070.0000.0000.0000.000
127A136VAL00.010-0.00539.3080.0060.0060.0000.0000.0000.000
128A137ALA0-0.036-0.01838.7540.0060.0060.0000.0000.0000.000
129A138VAL00.0200.00140.8540.0060.0060.0000.0000.0000.000
130A139ALA00.0210.00443.5780.0040.0040.0000.0000.0000.000
131A140ALA0-0.052-0.02143.7940.0040.0040.0000.0000.0000.000
132A141LEU00.0000.00643.2270.0040.0040.0000.0000.0000.000
133A142ARG10.9440.97746.7440.0520.0520.0000.0000.0000.000
134A143ARG10.8960.96446.2250.0500.0500.0000.0000.0000.000
135A144LEU0-0.099-0.04547.6940.0020.0020.0000.0000.0000.000
136A145ASP-1-0.918-0.95551.203-0.029-0.0290.0000.0000.0000.000
137A146TYR0-0.045-0.01348.7620.0020.0020.0000.0000.0000.000
138A147PRO0-0.038-0.02149.809-0.003-0.0030.0000.0000.0000.000
139A148TRP0-0.002-0.02241.574-0.001-0.0010.0000.0000.0000.000
140A149ASP-1-0.860-0.93947.449-0.048-0.0480.0000.0000.0000.000
141A150ALA00.003-0.00345.227-0.001-0.0010.0000.0000.0000.000
142A151GLU-1-0.889-0.96045.361-0.054-0.0540.0000.0000.0000.000
143A152LEU0-0.089-0.02545.0470.0010.0010.0000.0000.0000.000
144A153MET0-0.036-0.02441.9450.0000.0000.0000.0000.0000.000
145A154ALA00.0490.02341.419-0.003-0.0030.0000.0000.0000.000
146A155PRO00.000-0.00340.988-0.003-0.0030.0000.0000.0000.000
147A156TYR0-0.010-0.00438.9950.0020.0020.0000.0000.0000.000
148A157GLY00.0210.01437.081-0.003-0.0030.0000.0000.0000.000
149A158GLU-1-0.890-0.94835.979-0.082-0.0820.0000.0000.0000.000
150A159LEU0-0.046-0.01935.662-0.002-0.0020.0000.0000.0000.000
151A160MET0-0.034-0.02932.9860.0000.0000.0000.0000.0000.000
152A161MET00.0080.01931.477-0.011-0.0110.0000.0000.0000.000
153A162GLU-1-0.926-0.96030.952-0.059-0.0590.0000.0000.0000.000
154A163VAL0-0.058-0.03328.3960.0010.0010.0000.0000.0000.000
155A164ALA00.0460.03127.205-0.005-0.0050.0000.0000.0000.000
156A165ARG10.9320.95426.0690.0920.0920.0000.0000.0000.000
157A166ARG10.9060.96325.8690.0410.0410.0000.0000.0000.000
158A167ASP-1-0.902-0.94523.043-0.097-0.0970.0000.0000.0000.000
159A168LEU0-0.023-0.03521.471-0.016-0.0160.0000.0000.0000.000
160A169ASP-1-0.850-0.90521.082-0.159-0.1590.0000.0000.0000.000
161A170PHE0-0.064-0.03417.6250.0000.0000.0000.0000.0000.000
162A171MET0-0.072-0.04315.3250.0090.0090.0000.0000.0000.000
163A172GLU-1-0.939-0.98816.305-0.313-0.3130.0000.0000.0000.000
164A173THR0-0.063-0.02417.640-0.014-0.0140.0000.0000.0000.000
165A174HIS0-0.044-0.02013.252-0.010-0.0100.0000.0000.0000.000
166A175ALA0-0.074-0.04112.1830.0030.0030.0000.0000.0000.000
167A176SER00.0070.00613.110-0.081-0.0810.0000.0000.0000.000
168A177GLU-1-0.966-0.97910.104-0.742-0.7420.0000.0000.0000.000
169A178ALA0-0.061-0.03310.803-0.225-0.2250.0000.0000.0000.000
170A179GLU-1-0.773-0.88911.766-0.634-0.6340.0000.0000.0000.000
171A180LYS10.9480.95113.8540.5320.5320.0000.0000.0000.000
172A181VAL0-0.009-0.00317.3600.0670.0670.0000.0000.0000.000
173A182GLU-1-0.813-0.89411.138-1.170-1.1700.0000.0000.0000.000
174A183MET0-0.078-0.02115.2530.0810.0810.0000.0000.0000.000
175A184ALA00.012-0.00216.1970.0650.0650.0000.0000.0000.000
176A185VAL00.0170.00217.8390.0470.0470.0000.0000.0000.000
177A186ALA0-0.009-0.01515.6040.0450.0450.0000.0000.0000.000
178A187ALA00.0070.00217.6700.0530.0530.0000.0000.0000.000
179A188ALA00.0050.02320.3430.0320.0320.0000.0000.0000.000
180A189VAL0-0.032-0.01819.9060.0250.0250.0000.0000.0000.000
181A190LEU0-0.072-0.02616.9910.0320.0320.0000.0000.0000.000
182A191PHE00.0690.02219.4620.0320.0320.0000.0000.0000.000
183A192GLN00.0400.01923.7110.0230.0230.0000.0000.0000.000
184A193PRO0-0.025-0.02424.4340.0110.0110.0000.0000.0000.000
185A194VAL00.0120.00924.5050.0100.0100.0000.0000.0000.000
186A195LEU00.0900.04126.5440.0090.0090.0000.0000.0000.000
187A196ARG10.9540.99229.2480.0140.0140.0000.0000.0000.000
188A197ALA0-0.069-0.04029.9970.0030.0030.0000.0000.0000.000
189A198LEU00.0300.01229.0230.0040.0040.0000.0000.0000.000
190A199HIS00.0430.03632.5510.0020.0020.0000.0000.0000.000
191A200ARG10.9020.93534.595-0.007-0.0070.0000.0000.0000.000
192A201LEU00.0270.02034.3830.0020.0020.0000.0000.0000.000
193A202ALA00.0200.01936.6630.0020.0020.0000.0000.0000.000
194A203GLN0-0.020-0.01838.352-0.004-0.0040.0000.0000.0000.000
195A204GLU-1-0.965-0.96840.1760.0260.0260.0000.0000.0000.000
196A205GLU-1-0.794-0.89540.3210.0260.0260.0000.0000.0000.000
197A206GLU-1-0.839-0.91942.1570.0020.0020.0000.0000.0000.000
198A207SER0-0.064-0.04944.287-0.002-0.0020.0000.0000.0000.000
199A208ALA0-0.0150.00045.2760.0000.0000.0000.0000.0000.000
200A209ARG10.7710.88142.628-0.016-0.0160.0000.0000.0000.000
201A210ARG10.8150.90047.3000.0050.0050.0000.0000.0000.000
202A211TYR0-0.055-0.03548.345-0.002-0.0020.0000.0000.0000.000
203A212GLY00.0120.03550.1160.0000.0000.0000.0000.0000.000
204A213ILE0-0.034-0.02645.541-0.001-0.0010.0000.0000.0000.000
205A214GLU-1-0.966-0.97648.4580.0280.0280.0000.0000.0000.000
206A215LEU0-0.053-0.02344.6220.0000.0000.0000.0000.0000.000
207A216GLU-1-0.969-0.98348.6920.0310.0310.0000.0000.0000.000