FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 52L8Z

Calculation Name: 5DUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUD

Chain ID: A

ChEMBL ID:

UniProt ID: P0AAV4

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 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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4368103.029184
FMO2-HF: Nuclear repulsion 4248260.246759
FMO2-HF: Total energy -119842.782425
FMO2-MP2: Total energy -120187.250949


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.
-9.093-1.40411.789-6.678-12.8-0.011
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 : 0.015 / q_NPA : 0.008
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].
3A3LYS10.9930.9943.8970.9752.219-0.014-0.571-0.6590.001
4A4ILE00.0160.0085.6780.2120.2120.0000.0000.0000.000
5A5ILE0-0.090-0.0399.108-0.018-0.0180.0000.0000.0000.000
6A6ARG10.9320.97412.3560.0440.0440.0000.0000.0000.000
7A7ALA00.0590.02613.4830.0040.0040.0000.0000.0000.000
8A8GLY00.0260.03514.6410.0230.0230.0000.0000.0000.000
9A9MET0-0.019-0.00718.400-0.002-0.0020.0000.0000.0000.000
10A10TYR00.005-0.02020.1210.0030.0030.0000.0000.0000.000
11A11THR00.006-0.01114.1010.0000.0000.0000.0000.0000.000
12A12THR0-0.0060.00715.1760.0090.0090.0000.0000.0000.000
13A13VAL00.0490.03911.290-0.003-0.0030.0000.0000.0000.000
14A14GLN0-0.027-0.01914.172-0.051-0.0510.0000.0000.0000.000
15A15ASP-1-0.807-0.91715.6530.4690.4690.0000.0000.0000.000
16A16GLY00.0280.00617.563-0.038-0.0380.0000.0000.0000.000
17A17GLY0-0.053-0.02720.781-0.025-0.0250.0000.0000.0000.000
18A18ARG10.7990.88519.392-0.290-0.2900.0000.0000.0000.000
19A19HIS00.012-0.00923.660-0.028-0.0280.0000.0000.0000.000
20A20GLY00.0250.01226.8510.0030.0030.0000.0000.0000.000
21A21PHE00.0240.01625.228-0.010-0.0100.0000.0000.0000.000
22A22ARG10.9710.98830.198-0.125-0.1250.0000.0000.0000.000
23A23GLN0-0.016-0.02032.362-0.003-0.0030.0000.0000.0000.000
24A24SER0-0.023-0.01832.127-0.007-0.0070.0000.0000.0000.000
25A25GLY0-0.042-0.00732.9840.0010.0010.0000.0000.0000.000
26A26ILE0-0.0030.00926.5850.0030.0030.0000.0000.0000.000
27A27SER0-0.017-0.01527.310-0.004-0.0040.0000.0000.0000.000
28A28HIS00.0270.01925.6850.0040.0040.0000.0000.0000.000
29A29CYS0-0.0120.01122.7400.0220.0220.0000.0000.0000.000
30A30GLY00.0790.04820.506-0.012-0.0120.0000.0000.0000.000
31A31ALA0-0.014-0.00619.746-0.011-0.0110.0000.0000.0000.000
32A32LEU0-0.031-0.02221.476-0.017-0.0170.0000.0000.0000.000
33A33ASP-1-0.784-0.89323.3970.1160.1160.0000.0000.0000.000
34A34MET0-0.0170.00121.6430.0150.0150.0000.0000.0000.000
35A35PRO0-0.011-0.02222.6150.0110.0110.0000.0000.0000.000
36A36ALA00.0290.03021.5480.0000.0000.0000.0000.0000.000
37A37LEU0-0.0080.01216.472-0.003-0.0030.0000.0000.0000.000
38A38ARG10.9070.96718.036-0.155-0.1550.0000.0000.0000.000
39A39ILE00.0170.01219.8230.0010.0010.0000.0000.0000.000
40A40ALA0-0.019-0.00115.935-0.007-0.0070.0000.0000.0000.000
41A41ASN00.007-0.02614.0930.0430.0430.0000.0000.0000.000
42A42LEU00.0060.00416.010-0.006-0.0060.0000.0000.0000.000
43A43LEU0-0.060-0.01617.684-0.012-0.0120.0000.0000.0000.000
44A44VAL0-0.061-0.02112.418-0.022-0.0220.0000.0000.0000.000
45A45GLY0-0.0140.00714.2060.0020.0020.0000.0000.0000.000
46A46ASN0-0.062-0.02310.988-0.027-0.0270.0000.0000.0000.000
47A47ASP-1-0.845-0.92714.9840.1970.1970.0000.0000.0000.000
48A48ALA00.0340.00316.9740.0310.0310.0000.0000.0000.000
49A49ASN0-0.038-0.04018.8800.0000.0000.0000.0000.0000.000
50A50ALA00.0280.03413.2940.0200.0200.0000.0000.0000.000
51A51PRO00.0210.01411.506-0.028-0.0280.0000.0000.0000.000
52A52ALA0-0.024-0.01611.5580.0930.0930.0000.0000.0000.000
53A53LEU0-0.019-0.0069.870-0.018-0.0180.0000.0000.0000.000
54A54GLU-1-0.777-0.88913.5840.1510.1510.0000.0000.0000.000
55A55ILE0-0.002-0.00515.1940.0080.0080.0000.0000.0000.000
56A56THR0-0.024-0.01218.355-0.016-0.0160.0000.0000.0000.000
57A57LEU0-0.032-0.03721.772-0.009-0.0090.0000.0000.0000.000
58A58GLY00.0380.01819.937-0.009-0.0090.0000.0000.0000.000
59A59GLN0-0.111-0.05219.5500.0080.0080.0000.0000.0000.000
60A60LEU00.0650.04112.8440.0070.0070.0000.0000.0000.000
61A61THR0-0.032-0.01013.2740.0040.0040.0000.0000.0000.000
62A62VAL00.0020.0068.8350.0180.0180.0000.0000.0000.000
63A63GLU-1-0.898-0.9427.825-0.419-0.4190.0000.0000.0000.000
64A64PHE00.0100.0055.550-0.572-0.5720.0000.0000.0000.000
65A65GLU-1-0.840-0.9132.487-5.051-1.3532.338-2.587-3.449-0.023
66A66THR0-0.004-0.0102.333-0.977-0.7464.633-1.407-3.4570.001
67A67ASP-1-0.862-0.9294.268-0.739-0.6560.021-0.035-0.0690.001
68A68GLY0-0.059-0.0407.4160.0270.0270.0000.0000.0000.000
69A69TRP00.0050.0028.986-0.042-0.0420.0000.0000.0000.000
70A70PHE0-0.001-0.0229.9710.0530.0530.0000.0000.0000.000
71A71ALA00.0450.03011.841-0.029-0.0290.0000.0000.0000.000
72A72LEU00.0150.00814.7120.0260.0260.0000.0000.0000.000
73A73THR0-0.010-0.01317.260-0.013-0.0130.0000.0000.0000.000
74A74GLY00.0120.00920.2920.0050.0050.0000.0000.0000.000
75A75ALA0-0.010-0.00522.796-0.011-0.0110.0000.0000.0000.000
76A76GLY00.0220.00822.8600.0040.0040.0000.0000.0000.000
77A77CYS0-0.038-0.01321.110-0.002-0.0020.0000.0000.0000.000
78A78GLU-1-0.906-0.96123.0470.0230.0230.0000.0000.0000.000
79A79ALA00.0000.01217.724-0.008-0.0080.0000.0000.0000.000
80A80ARG10.9660.98019.0740.0260.0260.0000.0000.0000.000
81A81LEU0-0.028-0.00312.671-0.008-0.0080.0000.0000.0000.000
82A82ASP-1-0.824-0.92115.217-0.144-0.1440.0000.0000.0000.000
83A83ASP-1-0.962-0.96817.460-0.049-0.0490.0000.0000.0000.000
84A84ASN0-0.011-0.00819.0540.0130.0130.0000.0000.0000.000
85A85ALA0-0.047-0.02620.141-0.003-0.0030.0000.0000.0000.000
86A86VAL0-0.0080.00716.7790.0030.0030.0000.0000.0000.000
87A87TRP00.014-0.00520.0390.0030.0030.0000.0000.0000.000
88A88THR0-0.049-0.02620.2380.0030.0030.0000.0000.0000.000
89A89GLY00.000-0.00620.330-0.007-0.0070.0000.0000.0000.000
90A90TRP00.0280.00119.557-0.008-0.0080.0000.0000.0000.000
91A91ARG10.8190.92215.554-0.087-0.0870.0000.0000.0000.000
92A92LEU0-0.011-0.00215.060-0.018-0.0180.0000.0000.0000.000
93A93PRO00.0160.01213.3390.0180.0180.0000.0000.0000.000
94A94MET0-0.074-0.0295.561-0.030-0.0300.0000.0000.0000.000
95A95LYS10.9690.98510.0330.0680.0680.0000.0000.0000.000
96A96ALA00.0030.0127.388-0.076-0.0760.0000.0000.0000.000
97A97GLY0-0.021-0.0218.301-0.011-0.0110.0000.0000.0000.000
98A98GLN0-0.0040.0059.8070.0460.0460.0000.0000.0000.000
99A99ARG10.9010.93910.4010.1740.1740.0000.0000.0000.000
100A100LEU00.0110.01712.4590.0480.0480.0000.0000.0000.000
101A101THR0-0.054-0.05414.0430.0080.0080.0000.0000.0000.000
102A102LEU00.0370.02416.0540.0080.0080.0000.0000.0000.000
103A103LYS10.8510.91018.989-0.022-0.0220.0000.0000.0000.000
104A104ARG11.0110.99622.442-0.040-0.0400.0000.0000.0000.000
105A105PRO00.0040.01723.836-0.006-0.0060.0000.0000.0000.000
106A106GLN0-0.029-0.01526.529-0.001-0.0010.0000.0000.0000.000
107A107HIS00.0090.00229.5030.0020.0020.0000.0000.0000.000
108A108GLY00.0000.00927.8180.0030.0030.0000.0000.0000.000
109A109MET0-0.041-0.01226.556-0.006-0.0060.0000.0000.0000.000
110A110ARG10.9270.96222.300-0.131-0.1310.0000.0000.0000.000
111A111SER0-0.0230.00219.600-0.008-0.0080.0000.0000.0000.000
112A112TYR00.006-0.01416.9420.0090.0090.0000.0000.0000.000
113A113LEU00.0030.00511.081-0.041-0.0410.0000.0000.0000.000
114A114ALA00.0130.01911.6100.0970.0970.0000.0000.0000.000
115A115VAL00.0510.0106.126-0.079-0.0790.0000.0000.0000.000
116A116ALA00.0300.0149.4270.0630.0630.0000.0000.0000.000
117A117GLY0-0.049-0.0307.9270.0410.0410.0000.0000.0000.000
118A118GLY00.0150.0228.785-0.020-0.0200.0000.0000.0000.000
119A119ILE0-0.034-0.0256.6560.2440.2440.0000.0000.0000.000
120A120ASP-1-0.904-0.9616.4110.4510.4510.0000.0000.0000.000
121A121VAL0-0.010-0.0127.9300.3920.3920.0000.0000.0000.000
122A122PRO00.023-0.00310.625-0.144-0.1440.0000.0000.0000.000
123A123PRO00.0240.01613.964-0.020-0.0200.0000.0000.0000.000
124A124VAL0-0.0150.00116.515-0.057-0.0570.0000.0000.0000.000
125A125MET0-0.032-0.01619.518-0.019-0.0190.0000.0000.0000.000
126A126GLY00.0410.01720.552-0.009-0.0090.0000.0000.0000.000
127A127SER00.0340.02018.6640.0010.0010.0000.0000.0000.000
128A128CYS00.0190.01513.162-0.022-0.0220.0000.0000.0000.000
129A129SER00.0020.01015.8610.0340.0340.0000.0000.0000.000
130A130THR0-0.037-0.01916.3740.0000.0000.0000.0000.0000.000
131A131ASP-1-0.827-0.92718.5120.1630.1630.0000.0000.0000.000
132A132LEU0-0.018-0.02119.381-0.002-0.0020.0000.0000.0000.000
133A133LYS10.9240.97422.520-0.124-0.1240.0000.0000.0000.000
134A134VAL0-0.052-0.02124.562-0.012-0.0120.0000.0000.0000.000
135A135GLY00.0170.03221.493-0.008-0.0080.0000.0000.0000.000
136A136ILE0-0.022-0.01519.8080.0080.0080.0000.0000.0000.000
137A137GLY00.0220.00417.166-0.002-0.0020.0000.0000.0000.000
138A138GLY00.0130.00413.706-0.025-0.0250.0000.0000.0000.000
139A139LEU0-0.010-0.0119.0030.1110.1110.0000.0000.0000.000
140A140GLU-1-0.924-0.98012.5630.2420.2420.0000.0000.0000.000
141A141GLY0-0.0040.02815.628-0.052-0.0520.0000.0000.0000.000
142A142ARG10.8410.92012.226-0.373-0.3730.0000.0000.0000.000
143A143LEU0-0.032-0.01416.0600.0450.0450.0000.0000.0000.000
144A144LEU0-0.028-0.01310.5850.0040.0040.0000.0000.0000.000
145A145LYS10.9610.98212.914-0.180-0.1800.0000.0000.0000.000
146A146ASP-1-0.888-0.96512.3410.0270.0270.0000.0000.0000.000
147A147GLY0-0.045-0.01910.7730.0110.0110.0000.0000.0000.000
148A148ASP-1-0.857-0.9238.7000.1850.1850.0000.0000.0000.000
149A149ARG10.8680.9123.0310.6451.0990.028-0.095-0.3870.000
150A150LEU0-0.0070.0034.319-0.1300.070-0.001-0.030-0.1690.000
151A151PRO00.0190.0082.6692.7044.0561.911-1.568-1.6950.011
152A152ILE0-0.0020.0171.991-5.208-4.9122.874-0.454-2.716-0.002
153A153GLY00.0130.0203.674-0.888-0.757-0.0010.069-0.1990.000
154A154LYS10.8830.9316.285-0.594-0.5940.0000.0000.0000.000
155A155SER00.0760.0418.079-0.008-0.0080.0000.0000.0000.000
156A156LYS10.8800.92310.690-0.037-0.0370.0000.0000.0000.000
157A157ARG10.9220.96810.218-0.038-0.0380.0000.0000.0000.000
158A158ASP-1-0.778-0.86716.4380.0200.0200.0000.0000.0000.000
159A159SER0-0.126-0.09215.7750.0180.0180.0000.0000.0000.000
160A160MET00.0570.03617.962-0.004-0.0040.0000.0000.0000.000
161A161GLU-1-0.836-0.90719.8530.0400.0400.0000.0000.0000.000
162A162ALA0-0.010-0.02019.0840.0090.0090.0000.0000.0000.000
163A163GLN0-0.060-0.02220.243-0.004-0.0040.0000.0000.0000.000
164A164GLY00.0230.02821.8140.0100.0100.0000.0000.0000.000
165A165VAL0-0.033-0.02222.767-0.004-0.0040.0000.0000.0000.000
166A166LYS10.9350.96225.086-0.052-0.0520.0000.0000.0000.000
167A167GLN00.0470.01423.6740.0170.0170.0000.0000.0000.000
168A168LEU00.0100.00726.830-0.007-0.0070.0000.0000.0000.000
169A169LEU00.0110.00629.1530.0010.0010.0000.0000.0000.000
170A170TRP0-0.022-0.00325.635-0.003-0.0030.0000.0000.0000.000
171A171GLY0-0.009-0.01432.135-0.006-0.0060.0000.0000.0000.000
172A172ASN00.0340.01635.0350.0020.0020.0000.0000.0000.000
173A173ARG10.9180.96937.582-0.045-0.0450.0000.0000.0000.000
174A174ILE00.0310.02935.2680.0020.0020.0000.0000.0000.000
175A175ARG10.8660.92737.166-0.066-0.0660.0000.0000.0000.000
176A176ALA0-0.012-0.00839.3410.0040.0040.0000.0000.0000.000
177A177LEU0-0.001-0.00741.485-0.003-0.0030.0000.0000.0000.000
178A178PRO00.0120.00543.7370.0020.0020.0000.0000.0000.000
179A179GLY0-0.024-0.00446.5130.0000.0000.0000.0000.0000.000
180A180PRO0-0.030-0.02944.5490.0030.0030.0000.0000.0000.000
181A181GLU-1-0.774-0.88246.7590.0510.0510.0000.0000.0000.000
182A182TYR00.0620.03348.596-0.001-0.0010.0000.0000.0000.000
183A183HIS0-0.006-0.01350.187-0.002-0.0020.0000.0000.0000.000
184A184GLU-1-0.808-0.88752.3140.0400.0400.0000.0000.0000.000
185A185PHE0-0.0160.01148.415-0.001-0.0010.0000.0000.0000.000
186A186ASP-1-0.768-0.87453.7210.0320.0320.0000.0000.0000.000
187A187ARG10.8610.88755.207-0.031-0.0310.0000.0000.0000.000
188A188ALA00.0020.00855.9340.0000.0000.0000.0000.0000.000
189A189SER0-0.017-0.02351.6580.0010.0010.0000.0000.0000.000
190A190GLN0-0.016-0.01350.7880.0010.0010.0000.0000.0000.000
191A191ASP-1-0.777-0.84950.7380.0330.0330.0000.0000.0000.000
192A192ALA0-0.0080.00650.5530.0010.0010.0000.0000.0000.000
193A193PHE00.0060.00342.4630.0010.0010.0000.0000.0000.000
194A194TRP0-0.027-0.02044.2400.0020.0020.0000.0000.0000.000
195A195ARG10.8230.88847.368-0.032-0.0320.0000.0000.0000.000
196A196SER0-0.013-0.00348.426-0.001-0.0010.0000.0000.0000.000
197A197PRO0-0.044-0.00444.3500.0020.0020.0000.0000.0000.000
198A198TRP00.0240.00341.5450.0000.0000.0000.0000.0000.000
199A199GLN00.0000.00239.6550.0010.0010.0000.0000.0000.000
200A200LEU0-0.0090.01732.5480.0010.0010.0000.0000.0000.000
201A201SER00.0430.02036.886-0.003-0.0030.0000.0000.0000.000
202A202SER00.005-0.01133.7370.0050.0050.0000.0000.0000.000
203A203GLN0-0.027-0.01732.7020.0040.0040.0000.0000.0000.000
204A204SER0-0.044-0.00632.4710.0050.0050.0000.0000.0000.000
205A205ASN00.0310.01427.719-0.001-0.0010.0000.0000.0000.000
206A206ARG10.8090.88421.924-0.218-0.2180.0000.0000.0000.000
207A207MET0-0.0430.00426.8550.0010.0010.0000.0000.0000.000
208A208GLY00.0550.00929.653-0.001-0.0010.0000.0000.0000.000
209A209TYR0-0.024-0.01429.5320.0010.0010.0000.0000.0000.000
210A210ARG10.9410.97134.265-0.073-0.0730.0000.0000.0000.000
211A211LEU0-0.009-0.00837.5100.0000.0000.0000.0000.0000.000
212A212GLN00.0200.00539.975-0.001-0.0010.0000.0000.0000.000
213A213GLY00.0320.00242.6020.0000.0000.0000.0000.0000.000
214A214GLN0-0.031-0.00545.914-0.002-0.0020.0000.0000.0000.000
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