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

tag_button

FMODB ID: 37NYL

Calculation Name: 2D8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D8N

Chain ID: A

ChEMBL ID:

UniProt ID: P35243

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2279786.39909
FMO2-HF: Nuclear repulsion 2199574.388433
FMO2-HF: Total energy -80212.010657
FMO2-MP2: Total energy -80445.903984


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.
-17.808-19.72117.378-7.743-7.7220.032
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 : 0.095 / q_NPA : 0.066
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].
3A3ASN0-0.0080.0023.599-2.877-0.068-0.012-1.428-1.3690.005
4A4SER00.011-0.0092.349-3.279-2.0761.460-0.933-1.730-0.008
5A5LYS10.8430.9112.229-11.003-16.92815.930-5.382-4.6230.035
6A6SER00.0820.0486.070-0.410-0.4100.0000.0000.0000.000
7A7GLY00.0400.0157.375-0.263-0.2630.0000.0000.0000.000
8A8ALA0-0.044-0.0148.725-0.057-0.0570.0000.0000.0000.000
9A9LEU00.0320.02410.311-0.080-0.0800.0000.0000.0000.000
10A10SER00.0490.01014.055-0.046-0.0460.0000.0000.0000.000
11A11LYS10.8500.90613.602-0.125-0.1250.0000.0000.0000.000
12A12GLU-1-0.883-0.91617.3310.0090.0090.0000.0000.0000.000
13A13ILE00.0250.00917.6320.0040.0040.0000.0000.0000.000
14A14LEU0-0.031-0.01716.3650.0040.0040.0000.0000.0000.000
15A15GLU-1-0.951-0.96119.7550.0250.0250.0000.0000.0000.000
16A16GLU-1-0.772-0.87822.6800.0560.0560.0000.0000.0000.000
17A17LEU0-0.011-0.01420.900-0.001-0.0010.0000.0000.0000.000
18A18GLN0-0.042-0.01921.2310.0030.0030.0000.0000.0000.000
19A19LEU0-0.0280.00225.256-0.005-0.0050.0000.0000.0000.000
20A20ASN0-0.119-0.06227.992-0.008-0.0080.0000.0000.0000.000
21A21THR0-0.040-0.01626.4110.0050.0050.0000.0000.0000.000
22A22LYS10.8600.91629.001-0.074-0.0740.0000.0000.0000.000
23A23PHE0-0.0020.01323.9510.0030.0030.0000.0000.0000.000
24A24SER00.000-0.03122.555-0.001-0.0010.0000.0000.0000.000
25A25GLU-1-0.803-0.92016.5930.1590.1590.0000.0000.0000.000
26A26GLU-1-0.943-0.97516.6580.2650.2650.0000.0000.0000.000
27A27GLU-1-0.822-0.87818.0940.1840.1840.0000.0000.0000.000
28A28LEU0-0.0010.00719.6800.0220.0220.0000.0000.0000.000
29A29CYS0-0.047-0.02114.2420.0330.0330.0000.0000.0000.000
30A30SER00.0250.00715.1650.0770.0770.0000.0000.0000.000
31A31TRP0-0.017-0.00916.7920.0170.0170.0000.0000.0000.000
32A32TYR0-0.017-0.01312.607-0.009-0.0090.0000.0000.0000.000
33A33GLN0-0.036-0.02510.1820.0870.0870.0000.0000.0000.000
34A34SER00.002-0.00414.2180.0130.0130.0000.0000.0000.000
35A35PHE00.0400.02417.052-0.021-0.0210.0000.0000.0000.000
36A36LEU0-0.023-0.01312.0410.0030.0030.0000.0000.0000.000
37A37LYS10.7650.89011.263-0.686-0.6860.0000.0000.0000.000
38A38ASP-1-0.880-0.92415.8590.1590.1590.0000.0000.0000.000
39A39CYS0-0.106-0.04318.230-0.042-0.0420.0000.0000.0000.000
40A40PRO00.0390.02215.0250.0180.0180.0000.0000.0000.000
41A41THR0-0.049-0.02114.9760.0270.0270.0000.0000.0000.000
42A42GLY0-0.012-0.01716.9310.0020.0020.0000.0000.0000.000
43A43ARG10.8300.91517.553-0.075-0.0750.0000.0000.0000.000
44A44ILE0-0.044-0.01321.3720.0020.0020.0000.0000.0000.000
45A45THR00.047-0.00724.102-0.013-0.0130.0000.0000.0000.000
46A46GLN00.0900.05127.3160.0080.0080.0000.0000.0000.000
47A47GLN0-0.018-0.00229.5640.0070.0070.0000.0000.0000.000
48A48GLN00.0800.04823.085-0.005-0.0050.0000.0000.0000.000
49A49PHE00.0430.02928.1900.0050.0050.0000.0000.0000.000
50A50GLN00.010-0.02329.670-0.001-0.0010.0000.0000.0000.000
51A51SER0-0.097-0.06130.154-0.004-0.0040.0000.0000.0000.000
52A52ILE0-0.039-0.00626.3850.0010.0010.0000.0000.0000.000
53A53TYR00.0540.01330.7450.0010.0010.0000.0000.0000.000
54A54ALA0-0.031-0.01934.215-0.003-0.0030.0000.0000.0000.000
55A55LYS10.8920.95328.388-0.110-0.1100.0000.0000.0000.000
56A56PHE0-0.037-0.02429.4700.0030.0030.0000.0000.0000.000
57A57PHE00.0010.01235.390-0.001-0.0010.0000.0000.0000.000
58A58PRO0-0.026-0.01038.807-0.002-0.0020.0000.0000.0000.000
59A59ASP-1-0.909-0.95040.7530.0470.0470.0000.0000.0000.000
60A60THR0-0.117-0.06242.573-0.002-0.0020.0000.0000.0000.000
61A61ASP-1-0.840-0.91941.2340.0430.0430.0000.0000.0000.000
62A62PRO00.0070.01337.692-0.002-0.0020.0000.0000.0000.000
63A63LYS10.9120.96534.844-0.054-0.0540.0000.0000.0000.000
64A64ALA00.0260.01537.9800.0000.0000.0000.0000.0000.000
65A65TYR00.038-0.00237.4560.0000.0000.0000.0000.0000.000
66A66ALA00.000-0.01034.2900.0000.0000.0000.0000.0000.000
67A67GLN0-0.036-0.01934.7450.0020.0020.0000.0000.0000.000
68A68HIS00.009-0.00736.0590.0000.0000.0000.0000.0000.000
69A69VAL00.0220.01933.140-0.001-0.0010.0000.0000.0000.000
70A70PHE0-0.055-0.00128.2200.0010.0010.0000.0000.0000.000
71A71ARG10.8550.91432.461-0.028-0.0280.0000.0000.0000.000
72A72SER0-0.060-0.03734.513-0.002-0.0020.0000.0000.0000.000
73A73PHE0-0.003-0.01729.748-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.802-0.89430.0150.0400.0400.0000.0000.0000.000
75A75SER00.0060.00029.914-0.007-0.0070.0000.0000.0000.000
76A76ASN0-0.134-0.06727.1760.0000.0000.0000.0000.0000.000
77A77LEU0-0.007-0.00731.232-0.004-0.0040.0000.0000.0000.000
78A78ASP-1-0.829-0.88626.5440.0250.0250.0000.0000.0000.000
79A79GLY0-0.031-0.01829.987-0.001-0.0010.0000.0000.0000.000
80A80THR0-0.148-0.10725.0420.0090.0090.0000.0000.0000.000
81A81LEU00.0610.05525.627-0.004-0.0040.0000.0000.0000.000
82A82ASP-1-0.824-0.93520.7170.1340.1340.0000.0000.0000.000
83A83PHE00.009-0.00418.9150.0040.0040.0000.0000.0000.000
84A84LYS10.8340.90220.947-0.069-0.0690.0000.0000.0000.000
85A85GLU-1-0.822-0.91022.8880.0590.0590.0000.0000.0000.000
86A86TYR0-0.017-0.00322.5720.0000.0000.0000.0000.0000.000
87A87VAL0-0.003-0.00522.517-0.004-0.0040.0000.0000.0000.000
88A88ILE0-0.003-0.00125.596-0.007-0.0070.0000.0000.0000.000
89A89ALA00.0160.02228.490-0.006-0.0060.0000.0000.0000.000
90A90LEU0-0.062-0.03926.572-0.004-0.0040.0000.0000.0000.000
91A91HIS0-0.071-0.05627.319-0.002-0.0020.0000.0000.0000.000
92A92MET0-0.062-0.00531.745-0.006-0.0060.0000.0000.0000.000
93A93THR0-0.0190.02133.741-0.003-0.0030.0000.0000.0000.000
94A94THR00.0250.00134.854-0.003-0.0030.0000.0000.0000.000
95A95ALA00.0380.01236.0180.0020.0020.0000.0000.0000.000
96A96GLY00.0130.03235.2560.0020.0020.0000.0000.0000.000
97A97LYS10.9130.92935.180-0.040-0.0400.0000.0000.0000.000
98A98THR00.0480.04437.5770.0000.0000.0000.0000.0000.000
99A99ASN0-0.007-0.01640.962-0.002-0.0020.0000.0000.0000.000
100A100GLN0-0.083-0.05036.905-0.003-0.0030.0000.0000.0000.000
101A101LYS10.8610.92832.672-0.035-0.0350.0000.0000.0000.000
102A102LEU00.0080.00437.7060.0010.0010.0000.0000.0000.000
103A103GLU-1-0.764-0.87634.2640.0310.0310.0000.0000.0000.000
104A104TRP00.0430.01934.935-0.001-0.0010.0000.0000.0000.000
105A105ALA00.0350.01537.2140.0000.0000.0000.0000.0000.000
106A106PHE0-0.002-0.00940.611-0.001-0.0010.0000.0000.0000.000
107A107SER00.0370.00837.190-0.002-0.0020.0000.0000.0000.000
108A108LEU0-0.052-0.00937.9240.0000.0000.0000.0000.0000.000
109A109TYR0-0.040-0.04439.705-0.001-0.0010.0000.0000.0000.000
110A110ASP-1-0.827-0.88741.9100.0120.0120.0000.0000.0000.000
111A111VAL0-0.049-0.04241.5830.0010.0010.0000.0000.0000.000
112A112ASP-1-0.949-0.98341.2460.0140.0140.0000.0000.0000.000
113A113GLY0-0.0170.01040.418-0.001-0.0010.0000.0000.0000.000
114A114ASN0-0.088-0.03041.297-0.003-0.0030.0000.0000.0000.000
115A115GLY00.0200.00243.438-0.002-0.0020.0000.0000.0000.000
116A116THR0-0.143-0.08844.354-0.001-0.0010.0000.0000.0000.000
117A117ILE00.0000.01044.8730.0010.0010.0000.0000.0000.000
118A118SER0-0.010-0.04348.047-0.001-0.0010.0000.0000.0000.000
119A119LYS10.8280.88450.220-0.012-0.0120.0000.0000.0000.000
120A120ASN00.004-0.01151.2680.0010.0010.0000.0000.0000.000
121A121GLU-1-0.736-0.83045.7960.0160.0160.0000.0000.0000.000
122A122VAL00.0010.00246.9700.0020.0020.0000.0000.0000.000
123A123LEU0-0.035-0.02348.3720.0020.0020.0000.0000.0000.000
124A124GLU-1-0.839-0.89644.7690.0270.0270.0000.0000.0000.000
125A125ILE00.0150.01241.9120.0020.0020.0000.0000.0000.000
126A126VAL0-0.036-0.02245.0650.0020.0020.0000.0000.0000.000
127A127MET0-0.017-0.01747.6400.0010.0010.0000.0000.0000.000
128A128ALA0-0.028-0.00742.4820.0010.0010.0000.0000.0000.000
129A129ILE00.006-0.00242.8530.0020.0020.0000.0000.0000.000
130A130PHE0-0.026-0.02544.6230.0010.0010.0000.0000.0000.000
131A131LYS10.8140.91744.551-0.034-0.0340.0000.0000.0000.000
132A132MET00.0230.02940.0920.0030.0030.0000.0000.0000.000
133A133ILE0-0.0200.01843.5630.0020.0020.0000.0000.0000.000
134A134THR0-0.005-0.03546.338-0.002-0.0020.0000.0000.0000.000
135A135PRO00.027-0.01149.091-0.001-0.0010.0000.0000.0000.000
136A136GLU-1-0.829-0.91152.1040.0280.0280.0000.0000.0000.000
137A137ASP-1-0.758-0.84247.9300.0390.0390.0000.0000.0000.000
138A138VAL00.0130.00351.137-0.001-0.0010.0000.0000.0000.000
139A139LYS10.7750.88253.244-0.029-0.0290.0000.0000.0000.000
140A140LEU0-0.031-0.01752.605-0.001-0.0010.0000.0000.0000.000
141A141LEU0-0.0250.00850.9280.0000.0000.0000.0000.0000.000
142A142PRO0-0.030-0.00754.924-0.001-0.0010.0000.0000.0000.000
143A143ASP-1-0.819-0.91957.7850.0200.0200.0000.0000.0000.000
144A144ASP-1-0.865-0.91459.2440.0190.0190.0000.0000.0000.000
145A145GLU-1-0.758-0.86553.9960.0230.0230.0000.0000.0000.000
146A146ASN0-0.027-0.01254.3320.0000.0000.0000.0000.0000.000
147A147THR00.015-0.01054.5200.0000.0000.0000.0000.0000.000
148A148PRO00.0470.03151.1400.0000.0000.0000.0000.0000.000
149A149GLU-1-0.784-0.89152.8630.0200.0200.0000.0000.0000.000
150A150LYS10.7720.89555.956-0.020-0.0200.0000.0000.0000.000
151A151ARG10.9040.95049.364-0.027-0.0270.0000.0000.0000.000
152A152ALA00.0400.02452.2880.0000.0000.0000.0000.0000.000
153A153GLU-1-0.850-0.89653.5560.0130.0130.0000.0000.0000.000
154A154LYS10.7350.84256.018-0.020-0.0200.0000.0000.0000.000
155A155ILE0-0.011-0.02649.972-0.001-0.0010.0000.0000.0000.000
156A156TRP00.003-0.00551.0700.0000.0000.0000.0000.0000.000
157A157LYS10.9600.98355.546-0.015-0.0150.0000.0000.0000.000
158A158TYR0-0.105-0.06355.479-0.001-0.0010.0000.0000.0000.000
159A159PHE0-0.025-0.00649.2600.0000.0000.0000.0000.0000.000
160A160GLY0-0.040-0.01755.246-0.001-0.0010.0000.0000.0000.000
161A161LYS10.7720.88054.189-0.009-0.0090.0000.0000.0000.000
162A162ASN0-0.056-0.04058.0930.0010.0010.0000.0000.0000.000
163A163ASP-1-0.802-0.91758.0950.0110.0110.0000.0000.0000.000
164A164ASP-1-0.905-0.94757.0760.0070.0070.0000.0000.0000.000
165A165ASP-1-0.885-0.90556.6420.0060.0060.0000.0000.0000.000
166A166LYS10.8580.92051.314-0.007-0.0070.0000.0000.0000.000
167A167LEU0-0.064-0.01149.449-0.001-0.0010.0000.0000.0000.000
168A168THR00.036-0.01148.4910.0000.0000.0000.0000.0000.000
169A169GLU-1-0.846-0.92941.3730.0150.0150.0000.0000.0000.000
170A170LYS10.7830.86646.090-0.005-0.0050.0000.0000.0000.000
171A171GLU-1-0.747-0.83348.1320.0090.0090.0000.0000.0000.000
172A172PHE00.0390.03143.6330.0010.0010.0000.0000.0000.000
173A173ILE00.0030.00743.1990.0010.0010.0000.0000.0000.000
174A174GLU-1-0.816-0.90247.0450.0080.0080.0000.0000.0000.000
175A175GLY00.0100.01950.5770.0000.0000.0000.0000.0000.000
176A176THR0-0.050-0.04746.7120.0010.0010.0000.0000.0000.000
177A177LEU0-0.037-0.01346.0190.0010.0010.0000.0000.0000.000
178A178ALA0-0.055-0.01749.8130.0000.0000.0000.0000.0000.000
179A179ASN00.026-0.00353.0920.0010.0010.0000.0000.0000.000
180A180LYS10.9590.97449.059-0.024-0.0240.0000.0000.0000.000
181A181GLU-1-0.796-0.88551.7180.0230.0230.0000.0000.0000.000
182A182ILE00.0210.01750.2350.0010.0010.0000.0000.0000.000
183A183LEU00.0070.01644.9100.0010.0010.0000.0000.0000.000
184A184ARG10.6100.75547.607-0.023-0.0230.0000.0000.0000.000
185A185LEU0-0.043-0.00848.6410.0010.0010.0000.0000.0000.000
186A186ILE00.0530.02445.1070.0010.0010.0000.0000.0000.000
187A187GLN00.0040.02542.9470.0020.0020.0000.0000.0000.000
188A188PHE0-0.041-0.04644.6350.0010.0010.0000.0000.0000.000
189A189GLU-1-0.751-0.86141.0130.0480.0480.0000.0000.0000.000
190A190PRO0-0.118-0.04244.3140.0020.0020.0000.0000.0000.000
191A191GLN00.047-0.00642.474-0.003-0.0030.0000.0000.0000.000
192A192LYS10.8790.94545.533-0.038-0.0380.0000.0000.0000.000
193A193VAL0-0.073-0.03046.687-0.001-0.0010.0000.0000.0000.000
194A194LYS10.8770.92149.414-0.029-0.0290.0000.0000.0000.000
195A195GLU-1-0.752-0.84649.1510.0290.0290.0000.0000.0000.000
196A196LYS10.8240.90351.726-0.022-0.0220.0000.0000.0000.000
197A197MET0-0.0180.00054.371-0.001-0.0010.0000.0000.0000.000