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

tag_button

FMODB ID: G5LZ1

Calculation Name: 2NYV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYV

Chain ID: A

ChEMBL ID:

UniProt ID: O67359

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2597804.959478
FMO2-HF: Nuclear repulsion 2514460.992046
FMO2-HF: Total energy -83343.967431
FMO2-MP2: Total energy -83593.305117


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.
-14.929-11.115.867-6.504-13.193-0.013
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 : -0.023 / q_NPA : -0.016
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].
3A3LEU0-0.0120.0043.058-1.0861.0340.039-0.708-1.4520.001
4A4ARG10.8170.8765.5840.2740.2740.0000.0000.0000.000
5A5VAL0-0.0100.0078.8170.0410.0410.0000.0000.0000.000
6A6ILE0-0.0110.0009.0920.1370.1370.0000.0000.0000.000
7A7LEU0-0.032-0.02011.133-0.072-0.0720.0000.0000.0000.000
8A8PHE0-0.006-0.01013.3640.0770.0770.0000.0000.0000.000
9A9ASP-1-0.718-0.85215.8220.1520.1520.0000.0000.0000.000
10A10LEU0-0.067-0.06518.339-0.031-0.0310.0000.0000.0000.000
11A11ASP-1-0.805-0.88221.6400.0480.0480.0000.0000.0000.000
12A12GLY00.0080.00722.2650.0130.0130.0000.0000.0000.000
13A13THR0-0.0020.00216.5030.0060.0060.0000.0000.0000.000
14A14LEU00.0170.01418.133-0.031-0.0310.0000.0000.0000.000
15A15ILE0-0.059-0.04520.869-0.023-0.0230.0000.0000.0000.000
16A16ASP-1-0.839-0.88124.4920.0050.0050.0000.0000.0000.000
17A17SER00.009-0.02626.705-0.005-0.0050.0000.0000.0000.000
18A18ALA00.008-0.00728.9540.0010.0010.0000.0000.0000.000
19A19LYS10.9290.95930.5830.0080.0080.0000.0000.0000.000
20A20ASP-1-0.650-0.78732.7100.0070.0070.0000.0000.0000.000
21A21ILE00.0010.00628.9880.0020.0020.0000.0000.0000.000
22A22ALA0-0.022-0.01533.4400.0010.0010.0000.0000.0000.000
23A23LEU00.0160.01136.0730.0000.0000.0000.0000.0000.000
24A24ALA00.0000.00336.1780.0000.0000.0000.0000.0000.000
25A25LEU00.0020.00136.0530.0010.0010.0000.0000.0000.000
26A26GLU-1-0.933-0.96638.4670.0130.0130.0000.0000.0000.000
27A27LYS10.9060.96041.164-0.015-0.0150.0000.0000.0000.000
28A28THR0-0.041-0.03339.8010.0010.0010.0000.0000.0000.000
29A29LEU0-0.024-0.00840.6370.0010.0010.0000.0000.0000.000
30A30LYS11.0121.03044.034-0.014-0.0140.0000.0000.0000.000
31A31GLU-1-0.935-0.95645.4590.0270.0270.0000.0000.0000.000
32A32LEU0-0.052-0.03743.1110.0000.0000.0000.0000.0000.000
33A33GLY0-0.0290.01147.2430.0010.0010.0000.0000.0000.000
34A34LEU0-0.037-0.02844.1940.0010.0010.0000.0000.0000.000
35A35GLU-1-0.848-0.94044.8990.0180.0180.0000.0000.0000.000
36A36GLU-1-0.935-0.97345.0110.0190.0190.0000.0000.0000.000
37A37TYR0-0.056-0.04041.6530.0000.0000.0000.0000.0000.000
38A38TYR0-0.018-0.00838.0730.0030.0030.0000.0000.0000.000
39A39PRO0-0.040-0.00535.931-0.001-0.0010.0000.0000.0000.000
40A40ASP-1-0.890-0.95838.2280.0090.0090.0000.0000.0000.000
41A41ASN0-0.043-0.03630.773-0.003-0.0030.0000.0000.0000.000
42A42VAL00.0370.00832.6090.0050.0050.0000.0000.0000.000
43A43THR0-0.026-0.01528.2710.0060.0060.0000.0000.0000.000
44A44LYN00.0200.02027.9550.0050.0050.0000.0000.0000.000
45A45TYR0-0.060-0.02928.5730.0060.0060.0000.0000.0000.000
46A46ILE0-0.0210.00025.7310.0040.0040.0000.0000.0000.000
47A47GLY00.0690.03823.9420.0010.0010.0000.0000.0000.000
48A48GLY0-0.0010.00623.8020.0150.0150.0000.0000.0000.000
49A49GLY00.0210.01125.9210.0030.0030.0000.0000.0000.000
50A50VAL0-0.003-0.00628.148-0.005-0.0050.0000.0000.0000.000
51A51ARG10.8340.89131.618-0.084-0.0840.0000.0000.0000.000
52A52ALA00.0450.03929.153-0.004-0.0040.0000.0000.0000.000
53A53LEU0-0.016-0.00831.195-0.006-0.0060.0000.0000.0000.000
54A54LEU00.008-0.01232.374-0.005-0.0050.0000.0000.0000.000
55A55GLU-1-0.878-0.93233.6640.0740.0740.0000.0000.0000.000
56A56LYS10.9080.95328.272-0.085-0.0850.0000.0000.0000.000
57A57VAL0-0.020-0.00534.840-0.004-0.0040.0000.0000.0000.000
58A58LEU00.000-0.01337.200-0.004-0.0040.0000.0000.0000.000
59A59LYS10.8330.93838.005-0.040-0.0400.0000.0000.0000.000
60A60ASP-1-0.908-0.95239.7900.0360.0360.0000.0000.0000.000
61A61LYS10.9160.95842.993-0.029-0.0290.0000.0000.0000.000
62A62PHE0-0.017-0.00437.001-0.001-0.0010.0000.0000.0000.000
63A63ARG10.8900.94741.368-0.039-0.0390.0000.0000.0000.000
64A64GLU-1-0.755-0.85437.4130.0690.0690.0000.0000.0000.000
65A65GLU-1-0.826-0.91239.5460.0440.0440.0000.0000.0000.000
66A66TYR0-0.007-0.01940.270-0.002-0.0020.0000.0000.0000.000
67A67VAL00.0070.00134.723-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.920-0.96637.5050.0440.0440.0000.0000.0000.000
69A69VAL0-0.040-0.00239.332-0.002-0.0020.0000.0000.0000.000
70A70PHE00.0270.00733.589-0.002-0.0020.0000.0000.0000.000
71A71ARG10.8870.93630.759-0.076-0.0760.0000.0000.0000.000
72A72LYS10.9200.96836.687-0.030-0.0300.0000.0000.0000.000
73A73HIS10.8040.87339.939-0.028-0.0280.0000.0000.0000.000
74A74TYR00.0090.00330.6700.0010.0010.0000.0000.0000.000
75A75LEU00.0150.00434.653-0.002-0.0020.0000.0000.0000.000
76A76GLU-1-0.929-0.92637.3700.0180.0180.0000.0000.0000.000
77A77ASN0-0.090-0.06538.321-0.003-0.0030.0000.0000.0000.000
78A78PRO00.0110.01633.5870.0000.0000.0000.0000.0000.000
79A79VAL00.007-0.00331.8080.0010.0010.0000.0000.0000.000
80A80VAL0-0.090-0.03634.413-0.002-0.0020.0000.0000.0000.000
81A81TYR0-0.065-0.06634.302-0.006-0.0060.0000.0000.0000.000
82A82THR0-0.050-0.03728.706-0.003-0.0030.0000.0000.0000.000
83A83LYS10.9090.95628.9120.0250.0250.0000.0000.0000.000
84A84PRO00.0320.02723.9530.0060.0060.0000.0000.0000.000
85A85TYR00.0670.04821.843-0.005-0.0050.0000.0000.0000.000
86A86PRO00.024-0.00623.047-0.009-0.0090.0000.0000.0000.000
87A87GLU-1-0.845-0.94019.277-0.197-0.1970.0000.0000.0000.000
88A88ILE0-0.0010.02718.246-0.021-0.0210.0000.0000.0000.000
89A89PRO00.000-0.00419.468-0.010-0.0100.0000.0000.0000.000
90A90TYR0-0.0100.00416.7860.0030.0030.0000.0000.0000.000
91A91THR00.015-0.01714.340-0.036-0.0360.0000.0000.0000.000
92A92LEU0-0.0080.00315.616-0.028-0.0280.0000.0000.0000.000
93A93GLU-1-0.914-0.95917.219-0.153-0.1530.0000.0000.0000.000
94A94ALA0-0.017-0.00814.871-0.011-0.0110.0000.0000.0000.000
95A95LEU0-0.019-0.01310.733-0.045-0.0450.0000.0000.0000.000
96A96LYS10.9650.98413.6790.0610.0610.0000.0000.0000.000
97A97SER0-0.074-0.02216.311-0.001-0.0010.0000.0000.0000.000
98A98LYN00.0080.0088.199-0.085-0.0850.0000.0000.0000.000
99A99GLY0-0.038-0.03112.719-0.023-0.0230.0000.0000.0000.000
100A100PHE0-0.066-0.0267.4230.0550.0550.0000.0000.0000.000
101A101LYS10.7970.88312.7130.0080.0080.0000.0000.0000.000
102A102LEU0-0.032-0.01413.2210.0100.0100.0000.0000.0000.000
103A103ALA00.002-0.00215.503-0.002-0.0020.0000.0000.0000.000
104A104VAL0-0.033-0.00316.7680.0190.0190.0000.0000.0000.000
105A105VAL00.0210.00417.464-0.003-0.0030.0000.0000.0000.000
106A106SER00.0250.02219.2610.0060.0060.0000.0000.0000.000
107A107ASN00.0150.00221.8850.0010.0010.0000.0000.0000.000
108A108LYS10.7410.87324.983-0.075-0.0750.0000.0000.0000.000
109A109LEU00.0190.00427.0110.0060.0060.0000.0000.0000.000
110A110GLU-1-0.737-0.85027.0390.0740.0740.0000.0000.0000.000
111A111GLU-1-0.949-0.97428.6270.0380.0380.0000.0000.0000.000
112A112LEU00.000-0.00730.689-0.006-0.0060.0000.0000.0000.000
113A113SER0-0.027-0.02825.749-0.004-0.0040.0000.0000.0000.000
114A114LYS10.8730.92726.964-0.068-0.0680.0000.0000.0000.000
115A115LYS10.9190.98828.763-0.027-0.0270.0000.0000.0000.000
116A116ILE00.025-0.01027.910-0.007-0.0070.0000.0000.0000.000
117A117LEU00.0090.00923.823-0.008-0.0080.0000.0000.0000.000
118A118ASP-1-0.844-0.89327.5960.0070.0070.0000.0000.0000.000
119A119ILE0-0.082-0.03230.393-0.006-0.0060.0000.0000.0000.000
120A120LEU0-0.078-0.04527.590-0.006-0.0060.0000.0000.0000.000
121A121ASN0-0.041-0.01928.237-0.002-0.0020.0000.0000.0000.000
122A122LEU0-0.007-0.01323.023-0.009-0.0090.0000.0000.0000.000
123A123SER0-0.006-0.02623.5580.0000.0000.0000.0000.0000.000
124A124GLY00.000-0.00324.0630.0040.0040.0000.0000.0000.000
125A125TYR0-0.056-0.02619.554-0.003-0.0030.0000.0000.0000.000
126A126PHE0-0.056-0.03817.661-0.009-0.0090.0000.0000.0000.000
127A127ASP-1-0.855-0.92618.119-0.014-0.0140.0000.0000.0000.000
128A128LEU0-0.026-0.01919.8050.0090.0090.0000.0000.0000.000
129A129ILE0-0.038-0.01420.4400.0060.0060.0000.0000.0000.000
130A130VAL0-0.010-0.00421.163-0.006-0.0060.0000.0000.0000.000
131A131GLY00.0190.00223.0620.0040.0040.0000.0000.0000.000
132A132GLY00.015-0.00125.4770.0080.0080.0000.0000.0000.000
133A133ASP-1-0.869-0.94426.6600.0930.0930.0000.0000.0000.000
134A134THR0-0.015-0.00125.1870.0000.0000.0000.0000.0000.000
135A135PHE00.0290.01722.044-0.002-0.0020.0000.0000.0000.000
136A136GLY0-0.0120.00327.0550.0020.0020.0000.0000.0000.000
137A137GLU-1-0.854-0.93827.9940.1020.1020.0000.0000.0000.000
138A138LYS10.9200.95729.141-0.095-0.0950.0000.0000.0000.000
139A139LYS10.7620.89225.978-0.141-0.1410.0000.0000.0000.000
140A140PRO00.0600.04424.6820.0010.0010.0000.0000.0000.000
141A141SER00.0260.03519.5580.0230.0230.0000.0000.0000.000
142A142PRO00.0340.01217.032-0.019-0.0190.0000.0000.0000.000
143A143THR00.000-0.04618.8270.0060.0060.0000.0000.0000.000
144A144PRO00.0370.02420.249-0.001-0.0010.0000.0000.0000.000
145A145VAL00.0450.04613.987-0.016-0.0160.0000.0000.0000.000
146A146LEU00.0010.00315.7290.0050.0050.0000.0000.0000.000
147A147LYN00.0460.01817.612-0.022-0.0220.0000.0000.0000.000
148A148THR0-0.012-0.03517.292-0.035-0.0350.0000.0000.0000.000
149A149LEU0-0.012-0.00812.373-0.021-0.0210.0000.0000.0000.000
150A150GLU-1-0.926-0.97215.9280.2140.2140.0000.0000.0000.000
151A151ILE0-0.060-0.02918.754-0.025-0.0250.0000.0000.0000.000
152A152LEU0-0.047-0.01215.464-0.023-0.0230.0000.0000.0000.000
153A153GLY00.0040.01617.141-0.028-0.0280.0000.0000.0000.000
154A154GLU-1-0.808-0.87411.9550.0240.0240.0000.0000.0000.000
155A155GLU-1-0.837-0.93010.4550.4120.4120.0000.0000.0000.000
156A156PRO00.010-0.00410.1190.0080.0080.0000.0000.0000.000
157A157GLU-1-0.917-0.9487.3851.0131.0130.0000.0000.0000.000
158A158LYS10.8010.9125.4250.0210.0210.0000.0000.0000.000
159A159ALA00.0310.0096.794-0.350-0.3500.0000.0000.0000.000
160A160LEU0-0.030-0.0165.4470.5780.729-0.001-0.009-0.1410.000
161A161ILE00.0080.0097.889-0.403-0.4030.0000.0000.0000.000
162A162VAL0-0.029-0.02110.2750.1000.1000.0000.0000.0000.000
163A163GLY00.0410.01212.376-0.055-0.0550.0000.0000.0000.000
164A164ASP-1-0.791-0.89814.8300.1240.1240.0000.0000.0000.000
165A165THR00.0070.01117.510-0.012-0.0120.0000.0000.0000.000
166A166ASP-1-0.722-0.86216.4190.2040.2040.0000.0000.0000.000
167A167ALA0-0.005-0.00516.7850.0430.0430.0000.0000.0000.000
168A168ASP-1-0.802-0.90115.3680.2860.2860.0000.0000.0000.000
169A169ILE0-0.018-0.01011.1020.0940.0940.0000.0000.0000.000
170A170GLU-1-0.957-0.98913.1440.3750.3750.0000.0000.0000.000
171A171ALA0-0.033-0.02315.6550.0250.0250.0000.0000.0000.000
172A172GLY00.0590.02711.5570.0050.0050.0000.0000.0000.000
173A173LYS10.8560.92510.120-0.480-0.4800.0000.0000.0000.000
174A174ARG10.8370.93512.487-0.332-0.3320.0000.0000.0000.000
175A175ALA0-0.027-0.01713.490-0.037-0.0370.0000.0000.0000.000
176A176GLY0-0.0060.01211.163-0.038-0.0380.0000.0000.0000.000
177A177THR0-0.048-0.0218.5330.0220.0220.0000.0000.0000.000
178A178LYS10.9050.9572.640-7.307-10.0628.533-1.941-3.8370.017
179A179THR0-0.073-0.0365.784-1.196-1.190-0.001-0.0100.0060.000
180A180ALA00.028-0.0116.9130.0640.0640.0000.0000.0000.000
181A181LEU00.0030.0129.231-0.060-0.0600.0000.0000.0000.000
182A182ALA0-0.0070.00712.471-0.074-0.0740.0000.0000.0000.000
183A183LEU0-0.016-0.03314.841-0.006-0.0060.0000.0000.0000.000
184A184TRP0-0.080-0.03715.001-0.012-0.0120.0000.0000.0000.000
185A185GLY00.0250.03019.609-0.002-0.0020.0000.0000.0000.000
186A186TYR0-0.088-0.08621.356-0.011-0.0110.0000.0000.0000.000
187A187VAL0-0.047-0.00920.187-0.007-0.0070.0000.0000.0000.000
188A188LYS10.9510.97521.369-0.008-0.0080.0000.0000.0000.000
189A189LEU0-0.051-0.03021.159-0.013-0.0130.0000.0000.0000.000
190A190ASN0-0.017-0.00416.451-0.018-0.0180.0000.0000.0000.000
191A191SER0-0.097-0.07118.054-0.016-0.0160.0000.0000.0000.000
192A192GLN0-0.019-0.01113.6510.0580.0580.0000.0000.0000.000
193A193ILE0-0.007-0.0059.547-0.030-0.0300.0000.0000.0000.000
194A194PRO0-0.0070.0168.5430.0970.0970.0000.0000.0000.000
195A195ASP-1-0.866-0.9332.9731.8872.3630.047-0.113-0.410-0.001
196A196PHE0-0.005-0.0102.397-2.650-1.7542.084-0.601-2.380-0.002
197A197THR00.017-0.0026.8660.1940.1940.0000.0000.0000.000
198A198LEU0-0.042-0.0159.590-0.120-0.1200.0000.0000.0000.000
199A199SER0-0.043-0.00812.8180.0500.0500.0000.0000.0000.000
200A200ARG10.9190.96015.9970.2290.2290.0000.0000.0000.000
201A201PRO00.0050.01015.500-0.035-0.0350.0000.0000.0000.000
202A202SER00.0070.00114.444-0.049-0.0490.0000.0000.0000.000
203A203ASP-1-0.824-0.93112.616-0.410-0.4100.0000.0000.0000.000
204A204LEU0-0.016-0.0188.919-0.123-0.1230.0000.0000.0000.000
205A205VAL00.0080.0049.615-0.196-0.1960.0000.0000.0000.000
206A206LYS10.9820.99511.0100.4060.4060.0000.0000.0000.000
207A207LEU0-0.0110.0046.270-0.098-0.0980.0000.0000.0000.000
208A208MET00.0280.0286.539-0.514-0.5140.0000.0000.0000.000
209A209ASP-1-0.928-0.9577.949-0.619-0.6190.0000.0000.0000.000
210A210ASN0-0.117-0.0678.5640.2190.2190.0000.0000.0000.000
211A211HIS10.8470.9315.5710.8130.8130.0000.0000.0000.000
212A212ILE0-0.0030.0143.771-1.010-0.0980.007-0.332-0.587-0.002
213A213VAL0-0.033-0.0122.173-7.788-6.6545.108-2.645-3.597-0.026
214A214GLU-1-0.931-0.9713.0953.1164.0880.052-0.131-0.8930.000
215A215PHE0-0.0060.0005.026-0.515-0.598-0.001-0.0140.0980.000
216A216GLU-1-0.902-0.9577.4320.1710.1710.0000.0000.0000.000
217A217GLY0-0.0140.0099.0110.0840.0840.0000.0000.0000.000