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: 8N51Y

Calculation Name: 1D3U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D3U

Chain ID: A

ChEMBL ID:

UniProt ID: P62001

Base Structure: X-ray

Registration Date: 2023-09-27

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1736954.892643
FMO2-HF: Nuclear repulsion 1666369.403349
FMO2-HF: Total energy -70585.489294
FMO2-MP2: Total energy -70790.967552


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.
-0.6720.686-0.012-0.439-0.9090.001
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 : -0.013 / q_NPA : -0.030
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].
3A3ASP-1-0.896-0.9623.832-2.237-1.024-0.010-0.421-0.7830.001
4A4MET0-0.032-0.0194.2180.9291.070-0.001-0.011-0.1300.000
5A5SER0-0.066-0.0197.9000.3660.3660.0000.0000.0000.000
6A6LYS10.9960.99210.2440.8490.8490.0000.0000.0000.000
7A7VAL0-0.0280.01110.3060.1140.1140.0000.0000.0000.000
8A8LYS10.9310.96713.0930.2370.2370.0000.0000.0000.000
9A9LEU0-0.011-0.01416.1180.0320.0320.0000.0000.0000.000
10A10ARG10.9400.98018.6640.0970.0970.0000.0000.0000.000
11A11ILE00.0280.02222.3800.0140.0140.0000.0000.0000.000
12A12GLU-1-0.875-0.93124.579-0.063-0.0630.0000.0000.0000.000
13A13ASN0-0.007-0.01227.440-0.002-0.0020.0000.0000.0000.000
14A14ILE0-0.0100.02727.7010.0050.0050.0000.0000.0000.000
15A15VAL00.009-0.00629.959-0.002-0.0020.0000.0000.0000.000
16A16ALA00.0030.00231.6730.0050.0050.0000.0000.0000.000
17A17SER00.0080.02934.1630.0000.0000.0000.0000.0000.000
18A18VAL0-0.010-0.01636.9790.0000.0000.0000.0000.0000.000
19A19ASP-1-0.869-0.93739.6540.0250.0250.0000.0000.0000.000
20A20LEU00.005-0.00942.570-0.002-0.0020.0000.0000.0000.000
21A21PHE0-0.053-0.02242.651-0.001-0.0010.0000.0000.0000.000
22A22ALA0-0.018-0.04247.552-0.002-0.0020.0000.0000.0000.000
23A23GLN00.0210.02950.2660.0000.0000.0000.0000.0000.000
24A24LEU0-0.043-0.03048.832-0.002-0.0020.0000.0000.0000.000
25A25ASP-1-0.854-0.91753.1100.0100.0100.0000.0000.0000.000
26A26LEU0-0.010-0.03350.228-0.001-0.0010.0000.0000.0000.000
27A27GLU-1-0.857-0.93153.8270.0090.0090.0000.0000.0000.000
28A28LYS10.8750.95057.019-0.004-0.0040.0000.0000.0000.000
29A29VAL0-0.062-0.03550.691-0.001-0.0010.0000.0000.0000.000
30A30LEU0-0.014-0.01552.472-0.001-0.0010.0000.0000.0000.000
31A31ASP-1-0.860-0.90253.933-0.002-0.0020.0000.0000.0000.000
32A32LEU0-0.137-0.06951.587-0.002-0.0020.0000.0000.0000.000
33A33CYS0-0.087-0.04944.976-0.004-0.0040.0000.0000.0000.000
34A34PRO00.0160.01949.8970.0010.0010.0000.0000.0000.000
35A35ASN00.0520.02147.7310.0020.0020.0000.0000.0000.000
36A36SER00.005-0.00348.3740.0010.0010.0000.0000.0000.000
37A37LYS10.9620.97946.568-0.006-0.0060.0000.0000.0000.000
38A38TYR0-0.012-0.01649.6490.0010.0010.0000.0000.0000.000
39A39ASN00.005-0.01151.526-0.001-0.0010.0000.0000.0000.000
40A40PRO0-0.001-0.00352.0620.0010.0010.0000.0000.0000.000
41A41GLU-1-0.963-0.96652.5270.0160.0160.0000.0000.0000.000
42A42GLU-1-0.907-0.92549.2510.0130.0130.0000.0000.0000.000
43A43PHE0-0.025-0.03842.8320.0030.0030.0000.0000.0000.000
44A44PRO00.0140.00447.018-0.002-0.0020.0000.0000.0000.000
45A45GLY0-0.023-0.01946.8800.0000.0000.0000.0000.0000.000
46A46ILE0-0.049-0.01547.925-0.001-0.0010.0000.0000.0000.000
47A47ILE0-0.020-0.00643.9490.0000.0000.0000.0000.0000.000
48A49HIS00.0060.00242.131-0.001-0.0010.0000.0000.0000.000
49A50LEU0-0.043-0.01241.686-0.001-0.0010.0000.0000.0000.000
50A51ASP-1-0.849-0.93442.578-0.021-0.0210.0000.0000.0000.000
51A52ASP-1-0.887-0.92441.736-0.033-0.0330.0000.0000.0000.000
52A53PRO0-0.057-0.02138.006-0.002-0.0020.0000.0000.0000.000
53A54LYS10.8930.95733.7580.0340.0340.0000.0000.0000.000
54A55VAL0-0.082-0.04836.2060.0000.0000.0000.0000.0000.000
55A56ALA00.0600.03438.4310.0000.0000.0000.0000.0000.000
56A57LEU0-0.048-0.05439.4720.0020.0020.0000.0000.0000.000
57A58LEU0-0.0110.00940.6900.0000.0000.0000.0000.0000.000
58A59ILE00.009-0.00343.3780.0010.0010.0000.0000.0000.000
59A60PHE00.0510.03942.5510.0000.0000.0000.0000.0000.000
60A61SER00.0610.03347.7720.0000.0000.0000.0000.0000.000
61A62SER0-0.022-0.01446.604-0.001-0.0010.0000.0000.0000.000
62A63GLY00.0360.02147.9390.0010.0010.0000.0000.0000.000
63A64LYS10.9110.96042.538-0.033-0.0330.0000.0000.0000.000
64A65LEU00.008-0.01441.470-0.002-0.0020.0000.0000.0000.000
65A66VAL0-0.0200.00436.9960.0040.0040.0000.0000.0000.000
66A67VAL0-0.0120.00536.564-0.003-0.0030.0000.0000.0000.000
67A68THR0-0.010-0.00634.4360.0030.0030.0000.0000.0000.000
68A69GLY00.0520.02633.655-0.002-0.0020.0000.0000.0000.000
69A70ALA0-0.059-0.01632.789-0.006-0.0060.0000.0000.0000.000
70A71LYS10.9080.93929.3000.0430.0430.0000.0000.0000.000
71A72SER00.0600.01028.826-0.004-0.0040.0000.0000.0000.000
72A73VAL00.0730.02928.7770.0030.0030.0000.0000.0000.000
73A74GLN00.0720.04631.4290.0050.0050.0000.0000.0000.000
74A75ASP-1-0.822-0.92233.600-0.034-0.0340.0000.0000.0000.000
75A76ILE0-0.011-0.00932.6330.0020.0020.0000.0000.0000.000
76A77GLU-1-0.898-0.94634.953-0.011-0.0110.0000.0000.0000.000
77A78ARG10.7660.86037.0040.0340.0340.0000.0000.0000.000
78A79ALA00.0260.01439.1380.0010.0010.0000.0000.0000.000
79A80VAL00.0240.01138.8300.0020.0020.0000.0000.0000.000
80A81ALA0-0.034-0.00641.7980.0010.0010.0000.0000.0000.000
81A82LYS10.9140.95342.3640.0200.0200.0000.0000.0000.000
82A83LEU00.0740.04144.9990.0000.0000.0000.0000.0000.000
83A84ALA00.0580.02345.9080.0010.0010.0000.0000.0000.000
84A85GLN0-0.088-0.05047.6550.0020.0020.0000.0000.0000.000
85A86LYS10.9480.95649.1500.0100.0100.0000.0000.0000.000
86A87LEU00.0660.05448.6810.0010.0010.0000.0000.0000.000
87A88LYS10.9340.96950.0270.0040.0040.0000.0000.0000.000
88A89SER0-0.105-0.04354.0070.0000.0000.0000.0000.0000.000
89A90ILE00.0220.01955.4420.0000.0000.0000.0000.0000.000
90A91GLY0-0.023-0.00857.5430.0010.0010.0000.0000.0000.000
91A92VAL0-0.0010.01852.4530.0010.0010.0000.0000.0000.000
92A93LYS10.9510.95254.018-0.005-0.0050.0000.0000.0000.000
93A94PHE00.0220.01548.8100.0010.0010.0000.0000.0000.000
94A95LYS10.9320.97749.922-0.018-0.0180.0000.0000.0000.000
95A96ARG10.9090.95344.947-0.020-0.0200.0000.0000.0000.000
96A97ALA00.0180.02543.530-0.001-0.0010.0000.0000.0000.000
97A98PRO00.012-0.00941.7390.0020.0020.0000.0000.0000.000
98A99GLN0-0.0240.00437.684-0.002-0.0020.0000.0000.0000.000
99A100ILE0-0.013-0.01034.7260.0010.0010.0000.0000.0000.000
100A101ASP-1-0.838-0.91133.3220.0370.0370.0000.0000.0000.000
101A102VAL00.0050.00627.905-0.002-0.0020.0000.0000.0000.000
102A103GLN0-0.031-0.05729.9850.0130.0130.0000.0000.0000.000
103A104ASN0-0.018-0.01327.1880.0160.0160.0000.0000.0000.000
104A105MET0-0.0160.02524.474-0.014-0.0140.0000.0000.0000.000
105A106VAL00.0130.01124.8620.0110.0110.0000.0000.0000.000
106A107PHE00.0300.01120.823-0.011-0.0110.0000.0000.0000.000
107A108SER0-0.018-0.01922.4220.0090.0090.0000.0000.0000.000
108A109GLY00.007-0.02218.720-0.012-0.0120.0000.0000.0000.000
109A110ASP-1-0.965-0.98617.630-0.194-0.1940.0000.0000.0000.000
110A111ILE00.0480.01812.481-0.028-0.0280.0000.0000.0000.000
111A112GLY0-0.0080.00013.778-0.088-0.0880.0000.0000.0000.000
112A113ARG10.8500.92911.8540.1580.1580.0000.0000.0000.000
113A114GLU-1-0.902-0.93616.468-0.099-0.0990.0000.0000.0000.000
114A115PHE0-0.024-0.03213.524-0.010-0.0100.0000.0000.0000.000
115A116ASN00.0490.03518.7450.0140.0140.0000.0000.0000.000
116A117LEU00.022-0.01520.1220.0220.0220.0000.0000.0000.000
117A118ASP-1-0.828-0.89821.7910.0890.0890.0000.0000.0000.000
118A119VAL0-0.066-0.03917.5410.0200.0200.0000.0000.0000.000
119A120VAL0-0.040-0.02316.0890.0330.0330.0000.0000.0000.000
120A121ALA00.005-0.02118.1560.0440.0440.0000.0000.0000.000
121A122LEU0-0.0180.01119.7930.0110.0110.0000.0000.0000.000
122A123THR0-0.025-0.01815.2130.0000.0000.0000.0000.0000.000
123A124LEU0-0.0320.00414.9470.0600.0600.0000.0000.0000.000
124A125PRO00.0350.02615.658-0.050-0.0500.0000.0000.0000.000
125A126ASN0-0.082-0.06718.705-0.028-0.0280.0000.0000.0000.000
126A127CYS0-0.033-0.01020.034-0.019-0.0190.0000.0000.0000.000
127A128GLU-1-0.826-0.89122.1050.1290.1290.0000.0000.0000.000
128A129TYR00.001-0.02223.966-0.005-0.0050.0000.0000.0000.000
129A130GLU-1-0.873-0.92725.9530.0800.0800.0000.0000.0000.000
130A131PRO00.0170.00828.154-0.007-0.0070.0000.0000.0000.000
131A132GLU-1-0.914-0.93330.3540.0250.0250.0000.0000.0000.000
132A133GLN0-0.096-0.05732.615-0.002-0.0020.0000.0000.0000.000
133A134PHE0-0.064-0.05226.708-0.007-0.0070.0000.0000.0000.000
134A135PRO00.0160.01128.1980.0050.0050.0000.0000.0000.000
135A136GLY0-0.0170.00424.689-0.005-0.0050.0000.0000.0000.000
136A137VAL00.0180.00820.0670.0090.0090.0000.0000.0000.000
137A138ILE0-0.024-0.01522.646-0.007-0.0070.0000.0000.0000.000
138A139TYR00.0340.01515.2020.0290.0290.0000.0000.0000.000
139A140ARG10.8720.92320.800-0.151-0.1510.0000.0000.0000.000
140A141VAL00.0050.01416.9510.0470.0470.0000.0000.0000.000
141A142LYS10.8260.89319.676-0.297-0.2970.0000.0000.0000.000
142A143GLU-1-0.947-0.95219.3810.2100.2100.0000.0000.0000.000
143A144PRO00.0970.04216.9380.0440.0440.0000.0000.0000.000
144A145LYS10.9490.96820.137-0.134-0.1340.0000.0000.0000.000
145A146SER0-0.075-0.03319.946-0.020-0.0200.0000.0000.0000.000
146A147VAL0-0.017-0.01221.8600.0210.0210.0000.0000.0000.000
147A148ILE00.006-0.00216.341-0.020-0.0200.0000.0000.0000.000
148A149LEU0-0.0200.00220.4190.0130.0130.0000.0000.0000.000
149A150LEU00.0110.00417.091-0.019-0.0190.0000.0000.0000.000
150A151PHE00.0200.00620.4340.0080.0080.0000.0000.0000.000
151A152SER00.0790.04020.945-0.009-0.0090.0000.0000.0000.000
152A153SER00.0390.02221.446-0.015-0.0150.0000.0000.0000.000
153A154GLY00.0500.02518.317-0.030-0.0300.0000.0000.0000.000
154A155LYS10.8570.94018.0390.1080.1080.0000.0000.0000.000
155A156ILE00.0080.00515.9260.0250.0250.0000.0000.0000.000
156A157VAL00.0130.00320.109-0.021-0.0210.0000.0000.0000.000
157A158CYS0-0.0480.00219.0710.0250.0250.0000.0000.0000.000
158A159SER00.000-0.00621.203-0.023-0.0230.0000.0000.0000.000
159A160GLY00.0240.00223.4760.0190.0190.0000.0000.0000.000
160A161ALA00.0270.02820.8550.0070.0070.0000.0000.0000.000
161A162LYS10.9090.94222.908-0.089-0.0890.0000.0000.0000.000
162A163SER00.0300.00421.561-0.013-0.0130.0000.0000.0000.000
163A164GLU-1-0.792-0.91218.573-0.069-0.0690.0000.0000.0000.000
164A165ALA0-0.039-0.01517.2480.0020.0020.0000.0000.0000.000
165A166ASP-1-0.825-0.91616.3990.1480.1480.0000.0000.0000.000
166A167ALA0-0.042-0.02217.0180.0370.0370.0000.0000.0000.000
167A168TRP0-0.050-0.04112.1120.0250.0250.0000.0000.0000.000
168A169GLU-1-0.977-0.97812.5860.3420.3420.0000.0000.0000.000
169A170ALA0-0.015-0.01012.9140.0970.0970.0000.0000.0000.000
170A171VAL00.031-0.00211.9340.0590.0590.0000.0000.0000.000
171A172ARG10.9510.9907.810-0.181-0.1810.0000.0000.0000.000
172A173LYS10.9300.9579.169-0.277-0.2770.0000.0000.0000.000
173A174LEU00.0210.02311.4540.1090.1090.0000.0000.0000.000
174A175LEU0-0.007-0.0138.1350.0210.0210.0000.0000.0000.000
175A176ARG10.9450.9606.241-1.487-1.4870.0000.0000.0000.000
176A177GLU-1-0.953-0.9808.1840.9250.9250.0000.0000.0000.000
177A178LEU0-0.059-0.03210.918-0.048-0.0480.0000.0000.0000.000
178A179ASP-1-0.868-0.9354.7260.4480.452-0.001-0.0070.0040.000
179A180LYS10.8270.9367.948-1.061-1.0610.0000.0000.0000.000
180A181TYR0-0.0100.0057.764-0.048-0.0480.0000.0000.0000.000