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: 9Y6M2

Calculation Name: 1DUS-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DUS

Chain ID: A

ChEMBL ID:

UniProt ID: Q58292

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 194
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2218872.52996
FMO2-HF: Nuclear repulsion 2143563.501594
FMO2-HF: Total energy -75309.028366
FMO2-MP2: Total energy -75532.807538


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:4:PHE )


Summations of interaction energy for fragment #1(A:4:PHE )
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.
-6.931-1.1010.734-3.025-3.539-0.007
Interaction energy analysis for fragmet #1(A:4:PHE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.037
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].
3A6GLU -1-0.876-0.9462.713-11.866-6.1170.733-3.003-3.479-0.007
4A7LYS 10.8780.9344.2691.4911.5720.001-0.022-0.0600.000
5A8PRO 00.0250.0157.8670.0550.0550.0000.0000.0000.000
6A9THR 00.0300.0168.8880.1990.1990.0000.0000.0000.000
7A10THR 0-0.0040.00011.1500.1610.1610.0000.0000.0000.000
8A11LYS 10.9560.98413.5690.4340.4340.0000.0000.0000.000
9A12SER 00.0240.00815.763-0.065-0.0650.0000.0000.0000.000
10A13ASP -1-0.861-0.88917.756-0.392-0.3920.0000.0000.0000.000
11A14VAL 0-0.022-0.03121.2610.0010.0010.0000.0000.0000.000
12A15LYS 10.9010.96323.3910.2510.2510.0000.0000.0000.000
13A16ILE 00.0210.01626.820-0.004-0.0040.0000.0000.0000.000
14A17VAL 0-0.047-0.01228.7270.0050.0050.0000.0000.0000.000
15A18GLU -1-0.893-0.94131.213-0.112-0.1120.0000.0000.0000.000
16A19ASP -1-0.868-0.94433.970-0.103-0.1030.0000.0000.0000.000
17A20ILE 0-0.053-0.02435.7800.0040.0040.0000.0000.0000.000
18A21LEU 0-0.037-0.02232.339-0.002-0.0020.0000.0000.0000.000
19A22ARG 10.7830.85635.6000.0290.0290.0000.0000.0000.000
20A23GLY 00.0000.00638.8900.0030.0030.0000.0000.0000.000
21A24LYS 10.7490.83035.7290.0380.0380.0000.0000.0000.000
22A25LYS 10.8910.94737.7510.0530.0530.0000.0000.0000.000
23A26LEU 00.0390.02732.6020.0000.0000.0000.0000.0000.000
24A27LYS 10.9680.97931.4080.1160.1160.0000.0000.0000.000
25A28PHE 00.000-0.00527.256-0.002-0.0020.0000.0000.0000.000
26A29LYS 10.8580.92722.3010.2790.2790.0000.0000.0000.000
27A30THR 0-0.045-0.02123.739-0.009-0.0090.0000.0000.0000.000
28A31ASP -1-0.745-0.89818.182-0.518-0.5180.0000.0000.0000.000
29A32SER 0-0.040-0.04019.5300.0030.0030.0000.0000.0000.000
30A33GLY 0-0.0070.00916.253-0.009-0.0090.0000.0000.0000.000
31A34VAL 0-0.079-0.04916.594-0.019-0.0190.0000.0000.0000.000
32A35PHE 00.0140.00419.1830.0110.0110.0000.0000.0000.000
33A36SER 0-0.041-0.04121.6050.0120.0120.0000.0000.0000.000
34A37TYR 00.0890.03622.7890.0140.0140.0000.0000.0000.000
35A38GLY 0-0.031-0.03024.7710.0120.0120.0000.0000.0000.000
36A39LYS 10.9570.97628.0450.1740.1740.0000.0000.0000.000
37A40VAL 00.0720.06728.832-0.008-0.0080.0000.0000.0000.000
38A41ASP -1-0.827-0.91627.790-0.111-0.1110.0000.0000.0000.000
39A42LYS 10.9730.96929.9020.1080.1080.0000.0000.0000.000
40A43GLY 00.0540.03230.9790.0090.0090.0000.0000.0000.000
41A44THR 00.025-0.01227.9150.0100.0100.0000.0000.0000.000
42A45LYS 10.8430.93230.1850.1060.1060.0000.0000.0000.000
43A46ILE 0-0.055-0.01233.5530.0070.0070.0000.0000.0000.000
44A47LEU 00.0060.00229.2760.0060.0060.0000.0000.0000.000
45A48VAL 00.0150.00431.1740.0060.0060.0000.0000.0000.000
46A49GLU -1-0.865-0.91333.644-0.048-0.0480.0000.0000.0000.000
47A50ASN 0-0.103-0.06936.6060.0080.0080.0000.0000.0000.000
48A51VAL 0-0.0070.02233.1690.0050.0050.0000.0000.0000.000
49A52VAL 00.0010.00836.084-0.003-0.0030.0000.0000.0000.000
50A53VAL 0-0.047-0.03334.0830.0050.0050.0000.0000.0000.000
51A54ASP -1-0.818-0.91637.2800.0170.0170.0000.0000.0000.000
52A55LYS 10.9110.95837.462-0.016-0.0160.0000.0000.0000.000
53A56ASP -1-0.924-0.96337.8740.0280.0280.0000.0000.0000.000
54A57ASP -1-0.878-0.94533.8280.0320.0320.0000.0000.0000.000
55A58ASP -1-0.783-0.85130.0600.0550.0550.0000.0000.0000.000
56A59ILE 0-0.024-0.03328.5940.0050.0050.0000.0000.0000.000
57A60LEU 0-0.019-0.01121.8030.0010.0010.0000.0000.0000.000
58A61ASP -1-0.833-0.92424.387-0.064-0.0640.0000.0000.0000.000
59A62LEU 00.000-0.01619.617-0.003-0.0030.0000.0000.0000.000
60A63GLY 0-0.035-0.00818.808-0.009-0.0090.0000.0000.0000.000
61A64CYS 0-0.0020.00819.870-0.016-0.0160.0000.0000.0000.000
62A65GLY 00.0240.01519.588-0.013-0.0130.0000.0000.0000.000
63A66TYR 0-0.102-0.07420.4740.0010.0010.0000.0000.0000.000
64A67GLY 00.0530.00822.4250.0060.0060.0000.0000.0000.000
65A68VAL 0-0.0360.00024.4790.0130.0130.0000.0000.0000.000
66A69ILE 00.0270.00826.1710.0070.0070.0000.0000.0000.000
67A70GLY 00.0430.00826.6380.0080.0080.0000.0000.0000.000
68A71ILE 0-0.039-0.02426.4020.0050.0050.0000.0000.0000.000
69A72ALA 0-0.020-0.01229.5370.0040.0040.0000.0000.0000.000
70A73LEU 00.000-0.00630.7560.0050.0050.0000.0000.0000.000
71A74ALA 00.0160.01530.3080.0070.0070.0000.0000.0000.000
72A75ASP -1-0.854-0.89532.209-0.028-0.0280.0000.0000.0000.000
73A76GLU -1-0.805-0.87235.405-0.022-0.0220.0000.0000.0000.000
74A77VAL 0-0.087-0.02832.1060.0050.0050.0000.0000.0000.000
75A78LYS 10.9090.98434.006-0.050-0.0500.0000.0000.0000.000
76A79SER 0-0.039-0.04929.6400.0020.0020.0000.0000.0000.000
77A80THR 00.0140.01126.544-0.002-0.0020.0000.0000.0000.000
78A81THR 0-0.0260.00622.1010.0070.0070.0000.0000.0000.000
79A82MET 0-0.0320.00221.797-0.011-0.0110.0000.0000.0000.000
80A83ALA 00.0340.01817.8830.0100.0100.0000.0000.0000.000
81A84ASP -1-0.794-0.90115.814-0.226-0.2260.0000.0000.0000.000
82A85ILE 00.1020.0619.899-0.001-0.0010.0000.0000.0000.000
83A86ASN 0-0.032-0.01511.013-0.184-0.1840.0000.0000.0000.000
84A87ARG 11.0360.9916.5130.8490.8490.0000.0000.0000.000
85A88ARG 10.8350.92412.5760.5460.5460.0000.0000.0000.000
86A89ALA 00.0230.00715.3160.0510.0510.0000.0000.0000.000
87A90ILE 00.0210.02514.5870.0360.0360.0000.0000.0000.000
88A91LYS 10.9090.94815.9100.4900.4900.0000.0000.0000.000
89A92LEU 0-0.003-0.01018.3730.0270.0270.0000.0000.0000.000
90A93ALA 00.0670.04420.5310.0240.0240.0000.0000.0000.000
91A94LYS 10.9430.96217.2170.1450.1450.0000.0000.0000.000
92A95GLU -1-0.924-0.95521.781-0.261-0.2610.0000.0000.0000.000
93A96ASN 00.0240.00224.5050.0100.0100.0000.0000.0000.000
94A97ILE 00.0360.04024.7700.0100.0100.0000.0000.0000.000
95A98LYS 10.9570.98324.8720.1290.1290.0000.0000.0000.000
96A99LEU 0-0.100-0.04727.9130.0040.0040.0000.0000.0000.000
97A100ASN 0-0.029-0.02729.9300.0070.0070.0000.0000.0000.000
98A101ASN 0-0.0170.00832.8090.0050.0050.0000.0000.0000.000
99A102LEU 00.0220.00530.4820.0070.0070.0000.0000.0000.000
100A103ASP -1-0.915-0.97829.918-0.062-0.0620.0000.0000.0000.000
101A104ASN 0-0.049-0.00931.7880.0040.0040.0000.0000.0000.000
102A105TYR 00.0080.01532.0880.0070.0070.0000.0000.0000.000
103A106ASP -1-0.909-0.94029.1470.0350.0350.0000.0000.0000.000
104A107ILE 00.0230.00525.6960.0010.0010.0000.0000.0000.000
105A108ARG 10.7630.86422.287-0.113-0.1130.0000.0000.0000.000
106A109VAL 0-0.032-0.01918.713-0.007-0.0070.0000.0000.0000.000
107A110VAL 0-0.039-0.02816.658-0.003-0.0030.0000.0000.0000.000
108A111HIS 0-0.101-0.0488.4310.0410.0410.0000.0000.0000.000
109A112SER 00.013-0.03113.6030.1100.1100.0000.0000.0000.000
110A113ASP -1-0.878-0.91011.1870.2450.2450.0000.0000.0000.000
111A114LEU 00.033-0.01213.1790.0340.0340.0000.0000.0000.000
112A115TYR 0-0.054-0.05316.895-0.023-0.0230.0000.0000.0000.000
113A116GLU -1-0.934-0.97012.7510.5940.5940.0000.0000.0000.000
114A117ASN 0-0.046-0.01914.4760.0660.0660.0000.0000.0000.000
115A118VAL 0-0.021-0.00116.581-0.035-0.0350.0000.0000.0000.000
116A119LYS 10.9640.98619.579-0.320-0.3200.0000.0000.0000.000
117A120ASP -1-0.791-0.86822.0960.1780.1780.0000.0000.0000.000
118A121ARG 10.9260.96423.689-0.106-0.1060.0000.0000.0000.000
119A122LYS 10.9690.99526.129-0.124-0.1240.0000.0000.0000.000
120A123TYR 0-0.012-0.02723.351-0.016-0.0160.0000.0000.0000.000
121A124ASN 00.0290.02829.7150.0050.0050.0000.0000.0000.000
122A125LYS 10.9120.96631.090-0.027-0.0270.0000.0000.0000.000
123A126ILE 00.0040.02625.4740.0020.0020.0000.0000.0000.000
124A127ILE 00.001-0.00527.197-0.004-0.0040.0000.0000.0000.000
125A128THR 0-0.003-0.01423.403-0.005-0.0050.0000.0000.0000.000
126A129ASN 00.006-0.00625.1050.0080.0080.0000.0000.0000.000
127A130PRO 0-0.032-0.00123.053-0.012-0.0120.0000.0000.0000.000
128A131PRO 00.0370.01619.149-0.015-0.0150.0000.0000.0000.000
129A132ILE 00.031-0.00522.0280.0180.0180.0000.0000.0000.000
130A133ARG 10.9350.94720.7000.2450.2450.0000.0000.0000.000
131A134ALA 00.0070.02218.738-0.004-0.0040.0000.0000.0000.000
132A135GLY 00.0660.04820.1160.0230.0230.0000.0000.0000.000
133A136LYS 10.9180.92523.0860.0030.0030.0000.0000.0000.000
134A137GLU -1-0.846-0.91621.7590.0560.0560.0000.0000.0000.000
135A138VAL 00.0360.02018.4870.0190.0190.0000.0000.0000.000
136A139LEU 0-0.025-0.01221.1100.0040.0040.0000.0000.0000.000
137A140HIS 10.8700.91724.341-0.054-0.0540.0000.0000.0000.000
138A141ARG 11.0031.03415.832-0.305-0.3050.0000.0000.0000.000
139A142ILE 00.0000.00721.1830.0070.0070.0000.0000.0000.000
140A143ILE 0-0.041-0.00323.5520.0000.0000.0000.0000.0000.000
141A144GLU -1-0.935-0.97525.9730.1420.1420.0000.0000.0000.000
142A145GLU -1-0.843-0.93320.5110.2570.2570.0000.0000.0000.000
143A146GLY 00.0230.00924.7460.0010.0010.0000.0000.0000.000
144A147LYS 10.9070.95526.326-0.093-0.0930.0000.0000.0000.000
145A148GLU -1-0.944-0.96925.3860.1910.1910.0000.0000.0000.000
146A149LEU 0-0.042-0.01322.7250.0050.0050.0000.0000.0000.000
147A150LEU 0-0.046-0.00827.370-0.009-0.0090.0000.0000.0000.000
148A151LYS 10.7910.87830.644-0.061-0.0610.0000.0000.0000.000
149A152ASP -1-0.844-0.92333.6040.0780.0780.0000.0000.0000.000
150A153ASN 0-0.064-0.04036.906-0.005-0.0050.0000.0000.0000.000
151A154GLY 00.0040.01333.876-0.006-0.0060.0000.0000.0000.000
152A155GLU -1-0.829-0.94233.5860.0200.0200.0000.0000.0000.000
153A156ILE 0-0.0180.00627.0360.0000.0000.0000.0000.0000.000
154A157TRP 0-0.011-0.01730.390-0.008-0.0080.0000.0000.0000.000
155A158VAL 00.0240.00428.319-0.003-0.0030.0000.0000.0000.000
156A159VAL 0-0.038-0.00129.198-0.001-0.0010.0000.0000.0000.000
157A160ILE 00.0210.00329.045-0.005-0.0050.0000.0000.0000.000
158A161GLN 0-0.031-0.01230.431-0.003-0.0030.0000.0000.0000.000
159A162THR 0-0.114-0.12132.9820.0070.0070.0000.0000.0000.000
160A163LYS 10.9740.98335.5960.0480.0480.0000.0000.0000.000
161A164GLN 00.0750.00136.3390.0080.0080.0000.0000.0000.000
162A165GLY 00.0300.04032.7080.0060.0060.0000.0000.0000.000
163A166ALA 00.0610.02532.7060.0070.0070.0000.0000.0000.000
164A167LYS 10.9370.97634.3180.0200.0200.0000.0000.0000.000
165A168SER 0-0.047-0.01932.8070.0060.0060.0000.0000.0000.000
166A169LEU 00.0350.02028.8770.0070.0070.0000.0000.0000.000
167A170ALA 00.0480.02132.1700.0070.0070.0000.0000.0000.000
168A171LYS 10.8980.94035.281-0.009-0.0090.0000.0000.0000.000
169A172TYR 00.0630.04528.0220.0000.0000.0000.0000.0000.000
170A173MET 00.000-0.00431.3540.0040.0040.0000.0000.0000.000
171A174LYS 10.9300.97233.316-0.026-0.0260.0000.0000.0000.000
172A175ASP -1-0.905-0.95334.1000.0530.0530.0000.0000.0000.000
173A176VAL 0-0.0210.00030.1940.0050.0050.0000.0000.0000.000
174A177PHE 0-0.030-0.04130.4150.0060.0060.0000.0000.0000.000
175A178GLY 00.0410.04635.431-0.001-0.0010.0000.0000.0000.000
176A179ASN 0-0.054-0.03937.848-0.010-0.0100.0000.0000.0000.000
177A180VAL 0-0.0240.00535.8670.0020.0020.0000.0000.0000.000
178A181GLU -1-0.889-0.93137.9340.0060.0060.0000.0000.0000.000
179A182THR 0-0.093-0.05838.082-0.003-0.0030.0000.0000.0000.000
180A183VAL 00.0370.02537.959-0.001-0.0010.0000.0000.0000.000
181A184THR 00.0310.01238.087-0.004-0.0040.0000.0000.0000.000
182A185ILE 0-0.026-0.02438.698-0.001-0.0010.0000.0000.0000.000
183A186LYS 11.0011.00538.8410.0470.0470.0000.0000.0000.000
184A187GLY 00.0450.01938.243-0.004-0.0040.0000.0000.0000.000
185A188GLY 00.0550.03437.611-0.005-0.0050.0000.0000.0000.000
186A189TYR 0-0.0120.05931.2980.0000.0000.0000.0000.0000.000
187A190ARG 10.9290.94534.6890.0260.0260.0000.0000.0000.000
188A191VAL 00.0510.03934.035-0.003-0.0030.0000.0000.0000.000
189A192LEU 0-0.073-0.03232.8680.0020.0020.0000.0000.0000.000
190A193LYS 10.9690.99433.650-0.015-0.0150.0000.0000.0000.000
191A194SER 0-0.004-0.02533.616-0.002-0.0020.0000.0000.0000.000
192A195LYS 10.8840.95434.620-0.035-0.0350.0000.0000.0000.000
193A196LYS 10.8350.92431.477-0.103-0.1030.0000.0000.0000.000
194A197LEU -1-0.914-0.94935.8260.0580.0580.0000.0000.0000.000