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

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FMODB ID: NNVJQ

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 OptAll
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 -2604087.046147
FMO2-HF: Nuclear repulsion 2520740.785169
FMO2-HF: Total energy -83346.260979
FMO2-MP2: Total energy -83595.567766


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.
-20.637-16.24821.537-9.244-16.684-0.034
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 : 0.002 / q_NPA : 0.003
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].
3A3LEU0-0.010-0.0022.580-2.3751.5860.705-1.597-3.070-0.001
4A4ARG10.7890.8715.0240.4700.491-0.001-0.005-0.0150.000
5A5VAL0-0.006-0.0078.5120.0540.0540.0000.0000.0000.000
6A6ILE0-0.019-0.0018.8640.2480.2480.0000.0000.0000.000
7A7LEU0-0.029-0.01211.074-0.103-0.1030.0000.0000.0000.000
8A8PHE00.0200.00213.0140.0790.0790.0000.0000.0000.000
9A9ASP-1-0.722-0.86915.7300.1280.1280.0000.0000.0000.000
10A10LEU0-0.042-0.02818.584-0.028-0.0280.0000.0000.0000.000
11A11ASP-1-0.762-0.84421.7530.0410.0410.0000.0000.0000.000
12A12GLY00.0030.00622.0150.0160.0160.0000.0000.0000.000
13A13THR0-0.013-0.00216.664-0.001-0.0010.0000.0000.0000.000
14A14LEU00.0090.00718.059-0.027-0.0270.0000.0000.0000.000
15A15ILE0-0.032-0.02920.935-0.027-0.0270.0000.0000.0000.000
16A16ASP-1-0.779-0.84924.7030.0180.0180.0000.0000.0000.000
17A17SER0-0.027-0.05426.812-0.004-0.0040.0000.0000.0000.000
18A18ALA00.001-0.01128.6420.0000.0000.0000.0000.0000.000
19A19LYS10.8410.89830.279-0.002-0.0020.0000.0000.0000.000
20A20ASP-1-0.660-0.78232.8460.0010.0010.0000.0000.0000.000
21A21ILE0-0.0110.00128.7960.0020.0020.0000.0000.0000.000
22A22ALA00.0040.00033.2610.0020.0020.0000.0000.0000.000
23A23LEU00.0100.01835.7510.0000.0000.0000.0000.0000.000
24A24ALA00.0130.00435.7030.0000.0000.0000.0000.0000.000
25A25LEU00.0040.01135.7320.0020.0020.0000.0000.0000.000
26A26GLU-1-0.896-0.95738.1640.0160.0160.0000.0000.0000.000
27A27LYS10.8320.90640.789-0.012-0.0120.0000.0000.0000.000
28A28THR0-0.046-0.04539.4400.0000.0000.0000.0000.0000.000
29A29LEU0-0.025-0.01240.5190.0010.0010.0000.0000.0000.000
30A30LYS10.9600.99543.541-0.015-0.0150.0000.0000.0000.000
31A31GLU-1-0.894-0.90645.2470.0230.0230.0000.0000.0000.000
32A32LEU0-0.057-0.03243.1000.0000.0000.0000.0000.0000.000
33A33GLY0-0.0350.01247.2230.0000.0000.0000.0000.0000.000
34A34LEU0-0.003-0.00444.3990.0010.0010.0000.0000.0000.000
35A35GLU-1-0.863-0.95744.6750.0240.0240.0000.0000.0000.000
36A36GLU-1-0.910-0.96044.5920.0300.0300.0000.0000.0000.000
37A37TYR0-0.075-0.03741.3400.0010.0010.0000.0000.0000.000
38A38TYR0-0.064-0.04338.2100.0030.0030.0000.0000.0000.000
39A39PRO0-0.056-0.01235.772-0.001-0.0010.0000.0000.0000.000
40A40ASP-1-0.899-0.95837.5470.0320.0320.0000.0000.0000.000
41A41ASN0-0.040-0.03030.691-0.005-0.0050.0000.0000.0000.000
42A42VAL00.0620.02332.1440.0060.0060.0000.0000.0000.000
43A43THR0-0.022-0.04127.9940.0070.0070.0000.0000.0000.000
44A44LYN0-0.0120.02027.7200.0070.0070.0000.0000.0000.000
45A45TYR0-0.061-0.02528.6570.0090.0090.0000.0000.0000.000
46A46ILE0-0.0120.00825.1980.0020.0020.0000.0000.0000.000
47A47GLY00.0680.04723.3410.0060.0060.0000.0000.0000.000
48A48GLY0-0.024-0.01723.8110.0120.0120.0000.0000.0000.000
49A49GLY00.0500.02025.580-0.001-0.0010.0000.0000.0000.000
50A50VAL0-0.035-0.01927.737-0.003-0.0030.0000.0000.0000.000
51A51ARG10.7640.84631.373-0.091-0.0910.0000.0000.0000.000
52A52ALA00.0550.03428.705-0.003-0.0030.0000.0000.0000.000
53A53LEU0-0.0150.00030.558-0.003-0.0030.0000.0000.0000.000
54A54LEU00.0260.00431.881-0.005-0.0050.0000.0000.0000.000
55A55GLU-1-0.843-0.90432.6810.0900.0900.0000.0000.0000.000
56A56LYS10.9220.96128.296-0.110-0.1100.0000.0000.0000.000
57A57VAL00.0080.01034.235-0.003-0.0030.0000.0000.0000.000
58A58LEU00.0400.01836.805-0.002-0.0020.0000.0000.0000.000
59A59LYS10.8430.92037.381-0.059-0.0590.0000.0000.0000.000
60A60ASP-1-0.835-0.89939.4250.0470.0470.0000.0000.0000.000
61A61LYS10.8220.89942.538-0.044-0.0440.0000.0000.0000.000
62A62PHE0-0.041-0.01436.694-0.001-0.0010.0000.0000.0000.000
63A63ARG10.8190.88940.578-0.045-0.0450.0000.0000.0000.000
64A64GLU-1-0.737-0.84137.0210.0750.0750.0000.0000.0000.000
65A65GLU-1-0.767-0.86939.0460.0470.0470.0000.0000.0000.000
66A66TYR00.006-0.01439.999-0.003-0.0030.0000.0000.0000.000
67A67VAL00.0180.00234.553-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.940-0.96236.9410.0410.0410.0000.0000.0000.000
69A69VAL0-0.051-0.01239.204-0.003-0.0030.0000.0000.0000.000
70A70PHE00.0390.01533.447-0.003-0.0030.0000.0000.0000.000
71A71ARG10.7940.84130.479-0.075-0.0750.0000.0000.0000.000
72A72LYS10.8660.92136.289-0.028-0.0280.0000.0000.0000.000
73A73HIS10.8180.87039.641-0.026-0.0260.0000.0000.0000.000
74A74TYR00.0020.01430.3950.0020.0020.0000.0000.0000.000
75A75LEU00.001-0.01134.608-0.004-0.0040.0000.0000.0000.000
76A76GLU-1-0.843-0.87836.9880.0110.0110.0000.0000.0000.000
77A77ASN0-0.071-0.04338.272-0.002-0.0020.0000.0000.0000.000
78A78PRO00.0170.02833.4770.0020.0020.0000.0000.0000.000
79A79VAL00.005-0.01031.6100.0020.0020.0000.0000.0000.000
80A80VAL0-0.058-0.02334.233-0.003-0.0030.0000.0000.0000.000
81A81TYR0-0.037-0.04134.667-0.007-0.0070.0000.0000.0000.000
82A82THR0-0.042-0.03928.800-0.002-0.0020.0000.0000.0000.000
83A83LYS10.8150.90328.8230.0180.0180.0000.0000.0000.000
84A84PRO00.0550.02523.9350.0110.0110.0000.0000.0000.000
85A85TYR00.0150.02722.032-0.004-0.0040.0000.0000.0000.000
86A86PRO00.011-0.01823.332-0.015-0.0150.0000.0000.0000.000
87A87GLU-1-0.756-0.84618.906-0.171-0.1710.0000.0000.0000.000
88A88ILE00.0020.03918.462-0.033-0.0330.0000.0000.0000.000
89A89PRO00.016-0.00319.354-0.020-0.0200.0000.0000.0000.000
90A90TYR0-0.0010.00516.703-0.013-0.0130.0000.0000.0000.000
91A91THR00.011-0.01114.280-0.051-0.0510.0000.0000.0000.000
92A92LEU0-0.013-0.00215.484-0.050-0.0500.0000.0000.0000.000
93A93GLU-1-0.856-0.90617.101-0.307-0.3070.0000.0000.0000.000
94A94ALA0-0.0080.01215.074-0.038-0.0380.0000.0000.0000.000
95A95LEU0-0.006-0.00710.514-0.099-0.0990.0000.0000.0000.000
96A96LYS10.8280.90713.5230.1470.1470.0000.0000.0000.000
97A97SER0-0.070-0.05016.246-0.035-0.0350.0000.0000.0000.000
98A98LYN0-0.025-0.0078.657-0.234-0.2340.0000.0000.0000.000
99A99GLY0-0.006-0.00313.209-0.109-0.1090.0000.0000.0000.000
100A100PHE0-0.045-0.0197.1370.0960.0960.0000.0000.0000.000
101A101LYS10.8230.89612.8050.2520.2520.0000.0000.0000.000
102A102LEU0-0.048-0.02913.0250.0220.0220.0000.0000.0000.000
103A103ALA0-0.018-0.01115.369-0.004-0.0040.0000.0000.0000.000
104A104VAL0-0.021-0.00516.6650.0310.0310.0000.0000.0000.000
105A105VAL00.006-0.01017.413-0.009-0.0090.0000.0000.0000.000
106A106SER0-0.0070.01019.1210.0130.0130.0000.0000.0000.000
107A107ASN0-0.032-0.01921.838-0.003-0.0030.0000.0000.0000.000
108A108LYS10.7540.86524.791-0.066-0.0660.0000.0000.0000.000
109A109LEU0-0.0020.00326.9850.0070.0070.0000.0000.0000.000
110A110GLU-1-0.754-0.85626.2690.0430.0430.0000.0000.0000.000
111A111GLU-1-0.917-0.95928.2800.0180.0180.0000.0000.0000.000
112A112LEU00.0020.00030.823-0.008-0.0080.0000.0000.0000.000
113A113SER00.006-0.01025.478-0.008-0.0080.0000.0000.0000.000
114A114LYS10.8530.92326.415-0.039-0.0390.0000.0000.0000.000
115A115LYS10.8220.91228.3560.0040.0040.0000.0000.0000.000
116A116ILE00.0240.00127.938-0.008-0.0080.0000.0000.0000.000
117A117LEU00.0240.00823.464-0.009-0.0090.0000.0000.0000.000
118A118ASP-1-0.808-0.87827.325-0.035-0.0350.0000.0000.0000.000
119A119ILE0-0.077-0.02730.201-0.008-0.0080.0000.0000.0000.000
120A120LEU0-0.055-0.02827.374-0.004-0.0040.0000.0000.0000.000
121A121ASN0-0.055-0.03127.864-0.006-0.0060.0000.0000.0000.000
122A122LEU00.0230.01322.658-0.012-0.0120.0000.0000.0000.000
123A123SER0-0.019-0.04423.642-0.006-0.0060.0000.0000.0000.000
124A124GLY0-0.0100.00424.1190.0010.0010.0000.0000.0000.000
125A125TYR0-0.062-0.05019.629-0.005-0.0050.0000.0000.0000.000
126A126PHE0-0.043-0.03017.774-0.020-0.0200.0000.0000.0000.000
127A127ASP-1-0.789-0.87717.647-0.164-0.1640.0000.0000.0000.000
128A128LEU0-0.024-0.01519.7930.0160.0160.0000.0000.0000.000
129A129ILE00.000-0.00520.5140.0060.0060.0000.0000.0000.000
130A130VAL0-0.017-0.00521.267-0.006-0.0060.0000.0000.0000.000
131A131GLY00.0280.01123.0900.0050.0050.0000.0000.0000.000
132A132GLY00.0170.00625.2670.0090.0090.0000.0000.0000.000
133A133ASP-1-0.855-0.93626.4300.0770.0770.0000.0000.0000.000
134A134THR0-0.017-0.02624.9930.0000.0000.0000.0000.0000.000
135A135PHE00.0340.01321.745-0.002-0.0020.0000.0000.0000.000
136A136GLY0-0.0080.00827.0770.0030.0030.0000.0000.0000.000
137A137GLU-1-0.776-0.85528.2580.0980.0980.0000.0000.0000.000
138A138LYS10.9270.96729.370-0.089-0.0890.0000.0000.0000.000
139A139LYS10.7950.88825.541-0.134-0.1340.0000.0000.0000.000
140A140PRO00.0120.02224.2380.0030.0030.0000.0000.0000.000
141A141SER00.0450.03419.2790.0210.0210.0000.0000.0000.000
142A142PRO00.0340.01116.700-0.021-0.0210.0000.0000.0000.000
143A143THR0-0.015-0.04018.4830.0000.0000.0000.0000.0000.000
144A144PRO00.0210.01020.310-0.005-0.0050.0000.0000.0000.000
145A145VAL00.0410.03613.830-0.023-0.0230.0000.0000.0000.000
146A146LEU0-0.020-0.00115.695-0.001-0.0010.0000.0000.0000.000
147A147LYN00.1130.07117.672-0.030-0.0300.0000.0000.0000.000
148A148THR0-0.014-0.02016.628-0.046-0.0460.0000.0000.0000.000
149A149LEU0-0.020-0.01012.285-0.029-0.0290.0000.0000.0000.000
150A150GLU-1-0.936-0.97615.9490.1610.1610.0000.0000.0000.000
151A151ILE0-0.057-0.02818.967-0.034-0.0340.0000.0000.0000.000
152A152LEU0-0.020-0.00615.634-0.032-0.0320.0000.0000.0000.000
153A153GLY0-0.0090.01717.096-0.052-0.0520.0000.0000.0000.000
154A154GLU-1-0.795-0.86111.890-0.276-0.2760.0000.0000.0000.000
155A155GLU-1-0.860-0.92010.4360.2640.2640.0000.0000.0000.000
156A156PRO00.010-0.0079.9730.0670.0670.0000.0000.0000.000
157A157GLU-1-0.865-0.9107.3191.1751.1750.0000.0000.0000.000
158A158LYS10.7960.8935.5671.1331.1330.0000.0000.0000.000
159A159ALA00.0210.0116.601-0.485-0.4850.0000.0000.0000.000
160A160LEU0-0.017-0.0085.7160.8291.022-0.001-0.009-0.1830.000
161A161ILE0-0.0120.0077.598-0.485-0.4850.0000.0000.0000.000
162A162VAL0-0.023-0.01210.1330.0930.0930.0000.0000.0000.000
163A163GLY00.0600.01412.517-0.048-0.0480.0000.0000.0000.000
164A164ASP-1-0.777-0.88314.7610.1340.1340.0000.0000.0000.000
165A165THR0-0.004-0.01517.304-0.006-0.0060.0000.0000.0000.000
166A166ASP-1-0.728-0.85516.1910.2680.2680.0000.0000.0000.000
167A167ALA0-0.001-0.00216.2050.0440.0440.0000.0000.0000.000
168A168ASP-1-0.818-0.88215.2760.2920.2920.0000.0000.0000.000
169A169ILE00.0070.00310.5810.0980.0980.0000.0000.0000.000
170A170GLU-1-0.853-0.91312.2080.4180.4180.0000.0000.0000.000
171A171ALA0-0.023-0.01714.7660.0310.0310.0000.0000.0000.000
172A172GLY00.0580.01811.2880.0020.0020.0000.0000.0000.000
173A173LYS10.8510.9109.822-0.471-0.4710.0000.0000.0000.000
174A174ARG10.7600.86211.652-0.345-0.3450.0000.0000.0000.000
175A175ALA0-0.025-0.00813.221-0.064-0.0640.0000.0000.0000.000
176A176GLY0-0.0180.00210.878-0.035-0.0350.0000.0000.0000.000
177A177THR0-0.064-0.0358.1380.1440.1440.0000.0000.0000.000
178A178LYS10.8710.9422.717-7.066-10.75910.088-2.036-4.3580.012
179A179THR0-0.064-0.0495.763-0.932-0.9320.0000.0000.0000.000
180A180ALA00.023-0.0076.774-0.071-0.0710.0000.0000.0000.000
181A181LEU00.0040.0129.240-0.049-0.0490.0000.0000.0000.000
182A182ALA00.007-0.00312.650-0.055-0.0550.0000.0000.0000.000
183A183LEU0-0.029-0.02515.314-0.006-0.0060.0000.0000.0000.000
184A184TRP0-0.046-0.02614.939-0.014-0.0140.0000.0000.0000.000
185A185GLY0-0.0030.01119.683-0.007-0.0070.0000.0000.0000.000
186A186TYR0-0.073-0.06621.333-0.013-0.0130.0000.0000.0000.000
187A187VAL0-0.040-0.01719.944-0.006-0.0060.0000.0000.0000.000
188A188LYS10.9280.96221.105-0.046-0.0460.0000.0000.0000.000
189A189LEU0-0.054-0.02621.173-0.009-0.0090.0000.0000.0000.000
190A190ASN0-0.035-0.02216.494-0.013-0.0130.0000.0000.0000.000
191A191SER0-0.097-0.06917.869-0.013-0.0130.0000.0000.0000.000
192A192GLN0-0.012-0.01113.7230.0470.0470.0000.0000.0000.000
193A193ILE00.0130.00710.1040.0090.0090.0000.0000.0000.000
194A194PRO0-0.0070.0208.5190.0720.0720.0000.0000.0000.000
195A195ASP-1-0.847-0.9003.0000.8941.6120.047-0.259-0.507-0.002
196A196PHE0-0.006-0.0112.466-2.483-1.4811.735-0.562-2.176-0.002
197A197THR0-0.015-0.0237.0800.1110.1110.0000.0000.0000.000
198A198LEU0-0.036-0.00310.003-0.082-0.0820.0000.0000.0000.000
199A199SER0-0.078-0.05213.2810.0320.0320.0000.0000.0000.000
200A200ARG10.8440.90516.3000.1640.1640.0000.0000.0000.000
201A201PRO00.0240.01615.589-0.023-0.0230.0000.0000.0000.000
202A202SER0-0.011-0.03914.367-0.045-0.0450.0000.0000.0000.000
203A203ASP-1-0.811-0.89112.567-0.284-0.2840.0000.0000.0000.000
204A204LEU00.005-0.0029.274-0.105-0.1050.0000.0000.0000.000
205A205VAL0-0.0130.0069.513-0.226-0.2260.0000.0000.0000.000
206A206LYS10.9881.00310.6770.2070.2070.0000.0000.0000.000
207A207LEU0-0.026-0.0216.640-0.049-0.0490.0000.0000.0000.000
208A208MET00.0100.0296.272-0.499-0.4990.0000.0000.0000.000
209A209ASP-1-0.881-0.9357.670-0.950-0.9500.0000.0000.0000.000
210A210ASN0-0.120-0.0738.2810.0670.0670.0000.0000.0000.000
211A211HIS10.8190.9085.3022.2012.2010.0000.0000.0000.000
212A212ILE0-0.0090.0113.356-1.979-0.5980.045-0.613-0.813-0.004
213A213VAL0-0.027-0.0031.993-7.290-6.9778.911-4.303-4.922-0.037
214A214GLU-1-0.907-0.9663.272-1.596-1.0760.0090.151-0.6800.000
215A215PHE00.0080.0035.324-0.211-0.238-0.001-0.0110.0400.000
216A216GLU-1-0.891-0.9596.857-0.970-0.9700.0000.0000.0000.000
217A217GLY0-0.038-0.0148.8160.4780.4780.0000.0000.0000.000