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: J2M49

Calculation Name: 1IXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IXV

Chain ID: A

ChEMBL ID:

UniProt ID: P50086

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2687695.470385
FMO2-HF: Nuclear repulsion 2598220.612205
FMO2-HF: Total energy -89474.85818
FMO2-MP2: Total energy -89738.355057


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-10.628-7.1550.041-1.358-2.1570.004
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.006
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].
3A5PRO0-0.010-0.0143.251-2.2490.5460.043-1.197-1.6420.005
4A6LEU00.0210.0135.192-1.069-0.988-0.001-0.005-0.0750.000
5A7HIS00.0430.0176.6770.2520.2520.0000.0000.0000.000
6A8GLN0-0.023-0.0185.1051.3461.518-0.001-0.004-0.1660.000
7A9ALA00.0130.0107.266-0.646-0.6460.0000.0000.0000.000
8A10CYS0-0.076-0.04410.241-0.466-0.4660.0000.0000.0000.000
9A11MET0-0.064-0.0206.694-0.327-0.3270.0000.0000.0000.000
10A12GLU-1-0.881-0.9269.7971.5211.5210.0000.0000.0000.000
11A13ASN0-0.048-0.02412.744-0.129-0.1290.0000.0000.0000.000
12A14GLU-1-0.799-0.87911.8831.8281.8280.0000.0000.0000.000
13A15PHE00.030-0.00714.4940.1600.1600.0000.0000.0000.000
14A16PHE00.0190.01116.1740.0130.0130.0000.0000.0000.000
15A17LYS10.8860.91410.588-2.157-2.1570.0000.0000.0000.000
16A18VAL0-0.0100.00212.6760.1610.1610.0000.0000.0000.000
17A19GLN0-0.054-0.02513.717-0.039-0.0390.0000.0000.0000.000
18A20GLU-1-0.909-0.95113.6901.2041.2040.0000.0000.0000.000
19A21LEU0-0.036-0.0318.6520.0670.0670.0000.0000.0000.000
20A22LEU0-0.026-0.00912.252-0.091-0.0910.0000.0000.0000.000
21A23HIS0-0.0120.00814.777-0.159-0.1590.0000.0000.0000.000
22A24SER0-0.035-0.01012.9140.0190.0190.0000.0000.0000.000
23A25LYS10.8980.9377.675-3.273-3.2730.0000.0000.0000.000
24A26PRO00.1100.05212.6920.0210.0210.0000.0000.0000.000
25A27SER0-0.062-0.02412.960-0.008-0.0080.0000.0000.0000.000
26A28LEU0-0.006-0.0127.366-0.088-0.0880.0000.0000.0000.000
27A29LEU0-0.020-0.00211.367-0.041-0.0410.0000.0000.0000.000
28A30LEU0-0.012-0.01014.238-0.056-0.0560.0000.0000.0000.000
29A31GLN0-0.0040.0056.9420.0710.0710.0000.0000.0000.000
30A32LYS10.9330.95810.6880.5900.5900.0000.0000.0000.000
31A33ASP-1-0.790-0.8786.471-2.292-2.2920.0000.0000.0000.000
32A34GLN0-0.069-0.0343.772-3.035-2.6100.000-0.152-0.274-0.001
33A35ASP-1-0.871-0.9377.713-1.664-1.6640.0000.0000.0000.000
34A36GLY00.010-0.00310.5900.3190.3190.0000.0000.0000.000
35A37ARG10.7750.88410.9690.7640.7640.0000.0000.0000.000
36A38ILE0-0.002-0.00510.998-0.070-0.0700.0000.0000.0000.000
37A39PRO00.020-0.00510.975-0.015-0.0150.0000.0000.0000.000
38A40LEU00.0340.01312.6260.0220.0220.0000.0000.0000.000
39A41HIS00.0360.01813.8580.0420.0420.0000.0000.0000.000
40A42TRP00.013-0.0148.9020.1440.1440.0000.0000.0000.000
41A43SER00.0070.02213.4890.0120.0120.0000.0000.0000.000
42A44VAL00.0110.01115.894-0.021-0.0210.0000.0000.0000.000
43A45SER0-0.043-0.02414.986-0.055-0.0550.0000.0000.0000.000
44A46PHE0-0.049-0.02612.271-0.038-0.0380.0000.0000.0000.000
45A47GLN00.0060.00917.1050.0400.0400.0000.0000.0000.000
46A48ALA00.0520.05217.1220.0090.0090.0000.0000.0000.000
47A49HIS0-0.035-0.04719.151-0.005-0.0050.0000.0000.0000.000
48A50GLU-1-0.877-0.93621.6740.4100.4100.0000.0000.0000.000
49A51ILE0-0.013-0.00215.4430.0180.0180.0000.0000.0000.000
50A52THR0-0.024-0.02218.899-0.002-0.0020.0000.0000.0000.000
51A53SER00.0440.01920.111-0.038-0.0380.0000.0000.0000.000
52A54PHE0-0.0050.00517.355-0.011-0.0110.0000.0000.0000.000
53A55LEU0-0.013-0.00615.339-0.005-0.0050.0000.0000.0000.000
54A56LEU00.0320.00619.466-0.038-0.0380.0000.0000.0000.000
55A57SER0-0.052-0.01622.678-0.022-0.0220.0000.0000.0000.000
56A58LYS10.8920.94819.457-0.541-0.5410.0000.0000.0000.000
57A59MET0-0.054-0.03219.2730.0010.0010.0000.0000.0000.000
58A60GLU-1-0.884-0.93622.6220.1490.1490.0000.0000.0000.000
59A61ASN0-0.077-0.03525.566-0.031-0.0310.0000.0000.0000.000
60A62VAL0-0.0200.00320.918-0.024-0.0240.0000.0000.0000.000
61A63ASN00.0800.04224.3160.0220.0220.0000.0000.0000.000
62A64LEU00.0310.00222.189-0.019-0.0190.0000.0000.0000.000
63A65ASP-1-0.852-0.92722.561-0.128-0.1280.0000.0000.0000.000
64A66ASP-1-0.889-0.94322.643-0.142-0.1420.0000.0000.0000.000
65A67TYR0-0.073-0.04316.649-0.044-0.0440.0000.0000.0000.000
66A68PRO0-0.051-0.03618.9530.0170.0170.0000.0000.0000.000
67A69ASP-1-0.808-0.87615.791-0.548-0.5480.0000.0000.0000.000
68A70ASP-1-0.811-0.90313.287-1.090-1.0900.0000.0000.0000.000
69A71SER0-0.076-0.05916.3060.0270.0270.0000.0000.0000.000
70A72GLY00.006-0.01218.8540.0650.0650.0000.0000.0000.000
71A73TRP0-0.049-0.03618.6260.0720.0720.0000.0000.0000.000
72A74THR00.0520.03718.861-0.025-0.0250.0000.0000.0000.000
73A75PRO00.0430.00418.285-0.002-0.0020.0000.0000.0000.000
74A76PHE00.0690.03020.0730.0230.0230.0000.0000.0000.000
75A77HIS00.0230.01021.927-0.006-0.0060.0000.0000.0000.000
76A78ILE0-0.023-0.00416.4660.0020.0020.0000.0000.0000.000
77A79ALA00.0310.02320.7700.0150.0150.0000.0000.0000.000
78A80CYS0-0.041-0.01623.1490.0120.0120.0000.0000.0000.000
79A81SER0-0.020-0.00822.2130.0020.0020.0000.0000.0000.000
80A82VAL0-0.035-0.02620.243-0.006-0.0060.0000.0000.0000.000
81A83GLY00.0090.00923.3490.0110.0110.0000.0000.0000.000
82A84ASN00.0000.00325.1100.0010.0010.0000.0000.0000.000
83A85LEU00.025-0.01427.0120.0010.0010.0000.0000.0000.000
84A86GLU-1-0.913-0.94628.0620.1910.1910.0000.0000.0000.000
85A87VAL00.0330.00522.6330.0050.0050.0000.0000.0000.000
86A88VAL0-0.032-0.01626.014-0.006-0.0060.0000.0000.0000.000
87A89LYS10.9430.96427.661-0.073-0.0730.0000.0000.0000.000
88A90SER0-0.0090.01326.178-0.002-0.0020.0000.0000.0000.000
89A91LEU0-0.035-0.02022.4150.0020.0020.0000.0000.0000.000
90A92TYR0-0.024-0.02326.585-0.016-0.0160.0000.0000.0000.000
91A93ASP-1-0.927-0.96130.1220.0640.0640.0000.0000.0000.000
92A94ARG10.8520.93425.577-0.086-0.0860.0000.0000.0000.000
93A95PRO00.016-0.00330.291-0.016-0.0160.0000.0000.0000.000
94A96LEU0-0.019-0.00728.060-0.015-0.0150.0000.0000.0000.000
95A97LYS10.8670.94829.285-0.042-0.0420.0000.0000.0000.000
96A98PRO0-0.0160.00427.126-0.010-0.0100.0000.0000.0000.000
97A99ASP-1-0.823-0.92629.155-0.093-0.0930.0000.0000.0000.000
98A100LEU0-0.045-0.02729.989-0.015-0.0150.0000.0000.0000.000
99A101ASN0-0.067-0.04331.452-0.009-0.0090.0000.0000.0000.000
100A102LYS10.9120.97824.4310.1870.1870.0000.0000.0000.000
101A103ILE0-0.036-0.01228.205-0.001-0.0010.0000.0000.0000.000
102A104THR0-0.030-0.00423.225-0.024-0.0240.0000.0000.0000.000
103A105ASN00.0490.01420.7260.0500.0500.0000.0000.0000.000
104A106GLN0-0.039-0.02623.4040.0130.0130.0000.0000.0000.000
105A107GLY00.0400.00926.6820.0200.0200.0000.0000.0000.000
106A108VAL0-0.068-0.01326.2820.0200.0200.0000.0000.0000.000
107A109THR00.0870.01427.856-0.004-0.0040.0000.0000.0000.000
108A110CYS00.0310.00027.225-0.013-0.0130.0000.0000.0000.000
109A111LEU00.0490.03528.4220.0050.0050.0000.0000.0000.000
110A112HIS0-0.0150.01329.6520.0040.0040.0000.0000.0000.000
111A113LEU0-0.061-0.02923.958-0.001-0.0010.0000.0000.0000.000
112A114ALA00.0240.01927.7020.0030.0030.0000.0000.0000.000
113A115VAL00.0160.00329.4870.0080.0080.0000.0000.0000.000
114A116GLY0-0.025-0.00830.1180.0040.0040.0000.0000.0000.000
115A117LYS10.8760.95022.7840.1330.1330.0000.0000.0000.000
116A118LYS10.8440.92229.2170.0800.0800.0000.0000.0000.000
117A119TRP00.0060.02426.1240.0190.0190.0000.0000.0000.000
118A120PHE0-0.002-0.01231.754-0.005-0.0050.0000.0000.0000.000
119A121GLU-1-0.825-0.92733.7670.0090.0090.0000.0000.0000.000
120A122VAL00.0230.01928.9280.0010.0010.0000.0000.0000.000
121A123SER0-0.011-0.02532.198-0.009-0.0090.0000.0000.0000.000
122A124GLN0-0.069-0.04034.164-0.004-0.0040.0000.0000.0000.000
123A125PHE00.0280.01731.9880.0010.0010.0000.0000.0000.000
124A126LEU00.004-0.00130.210-0.002-0.0020.0000.0000.0000.000
125A127ILE0-0.007-0.01334.494-0.003-0.0030.0000.0000.0000.000
126A128GLU-1-0.922-0.95337.9840.0100.0100.0000.0000.0000.000
127A129ASN0-0.061-0.03435.8240.0080.0080.0000.0000.0000.000
128A130GLY00.0170.01237.372-0.002-0.0020.0000.0000.0000.000
129A131ALA0-0.044-0.00534.462-0.008-0.0080.0000.0000.0000.000
130A132SER0-0.0020.00236.1950.0030.0030.0000.0000.0000.000
131A133VAL00.0350.00436.463-0.007-0.0070.0000.0000.0000.000
132A134ARG10.8600.91638.4800.0670.0670.0000.0000.0000.000
133A135ILE00.0450.03633.666-0.003-0.0030.0000.0000.0000.000
134A136LYS10.9200.96535.3850.1240.1240.0000.0000.0000.000
135A137ASP-1-0.771-0.87530.702-0.208-0.2080.0000.0000.0000.000
136A138LYS10.9150.96827.0060.3530.3530.0000.0000.0000.000
137A139PHE0-0.012-0.01628.907-0.005-0.0050.0000.0000.0000.000
138A140ASN0-0.041-0.02534.2280.0050.0050.0000.0000.0000.000
139A141GLN0-0.026-0.00534.2810.0090.0090.0000.0000.0000.000
140A142ILE0-0.0100.00335.131-0.007-0.0070.0000.0000.0000.000
141A143PRO00.012-0.00733.996-0.002-0.0020.0000.0000.0000.000
142A144LEU00.0390.02035.5820.0010.0010.0000.0000.0000.000
143A145HIS00.0400.02136.5510.0030.0030.0000.0000.0000.000
144A146ARG10.9210.95628.0320.1920.1920.0000.0000.0000.000
145A147ALA00.001-0.00234.9050.0030.0030.0000.0000.0000.000
146A148ALA00.0000.00037.0810.0060.0060.0000.0000.0000.000
147A149SER00.0030.02035.1540.0000.0000.0000.0000.0000.000
148A150VAL0-0.015-0.00732.6900.0020.0020.0000.0000.0000.000
149A151GLY00.0890.04835.9050.0090.0090.0000.0000.0000.000
150A152SER0-0.087-0.03737.1570.0110.0110.0000.0000.0000.000
151A153LEU00.1000.03739.243-0.001-0.0010.0000.0000.0000.000
152A154LYS10.9150.97238.8080.0020.0020.0000.0000.0000.000
153A155LEU00.0350.01035.5600.0020.0020.0000.0000.0000.000
154A156ILE00.0410.03139.221-0.003-0.0030.0000.0000.0000.000
155A157GLU-1-0.770-0.83741.875-0.030-0.0300.0000.0000.0000.000
156A158LEU0-0.060-0.01338.0080.0010.0010.0000.0000.0000.000
157A159LEU0-0.015-0.01937.1460.0000.0000.0000.0000.0000.000
158A160CYS0-0.026-0.01041.302-0.003-0.0030.0000.0000.0000.000
159A161GLY00.0550.03844.8970.0010.0010.0000.0000.0000.000
160A162LEU0-0.038-0.01541.8170.0000.0000.0000.0000.0000.000
161A163GLY00.0230.00142.0560.0010.0010.0000.0000.0000.000
162A164LYS10.8140.92142.9040.0280.0280.0000.0000.0000.000
163A165SER0-0.002-0.00841.924-0.006-0.0060.0000.0000.0000.000
164A166ALA0-0.062-0.01843.4900.0030.0030.0000.0000.0000.000
165A167VAL00.0620.00643.901-0.004-0.0040.0000.0000.0000.000
166A168ASN00.0180.01445.560-0.005-0.0050.0000.0000.0000.000
167A169TRP0-0.052-0.03140.872-0.005-0.0050.0000.0000.0000.000
168A170GLN0-0.009-0.01142.9030.0010.0010.0000.0000.0000.000
169A171ASP-1-0.781-0.87637.747-0.158-0.1580.0000.0000.0000.000
170A172LYS10.8570.90434.7800.2140.2140.0000.0000.0000.000
171A173GLN0-0.052-0.01436.707-0.012-0.0120.0000.0000.0000.000
172A174GLY00.0430.02540.9120.0050.0050.0000.0000.0000.000
173A175TRP0-0.028-0.01539.8140.0070.0070.0000.0000.0000.000
174A176THR00.0160.01441.717-0.005-0.0050.0000.0000.0000.000
175A177PRO00.000-0.02241.008-0.003-0.0030.0000.0000.0000.000
176A178LEU00.0120.02442.049-0.001-0.0010.0000.0000.0000.000
177A179PHE00.0160.00943.0880.0020.0020.0000.0000.0000.000
178A180HIS0-0.030-0.02437.0860.0000.0000.0000.0000.0000.000
179A181ALA0-0.0130.01040.3400.0000.0000.0000.0000.0000.000
180A182LEU00.0070.00442.1540.0020.0020.0000.0000.0000.000
181A183ALA00.0050.01240.7220.0010.0010.0000.0000.0000.000
182A184GLU-1-0.975-0.99036.467-0.138-0.1380.0000.0000.0000.000
183A185GLY0-0.020-0.00640.0090.0040.0040.0000.0000.0000.000
184A186HIS0-0.047-0.02237.8760.0150.0150.0000.0000.0000.000
185A187GLY00.0360.00543.3540.0000.0000.0000.0000.0000.000
186A188ASP-1-0.878-0.95146.124-0.043-0.0430.0000.0000.0000.000
187A189ALA0-0.037-0.02043.0240.0020.0020.0000.0000.0000.000
188A190ALA00.001-0.00544.9890.0000.0000.0000.0000.0000.000
189A191VAL00.0430.02046.9390.0000.0000.0000.0000.0000.000
190A192LEU0-0.050-0.00345.2530.0020.0020.0000.0000.0000.000
191A193LEU0-0.035-0.03843.5030.0010.0010.0000.0000.0000.000
192A194VAL0-0.006-0.00147.9100.0000.0000.0000.0000.0000.000
193A195GLU-1-0.824-0.90451.318-0.041-0.0410.0000.0000.0000.000
194A196LYS10.7690.87549.1290.0310.0310.0000.0000.0000.000
195A197TYR0-0.107-0.10747.3610.0020.0020.0000.0000.0000.000
196A198GLY00.0390.03450.402-0.003-0.0030.0000.0000.0000.000
197A199ALA0-0.030-0.01348.350-0.002-0.0020.0000.0000.0000.000
198A200GLU-1-0.896-0.94550.126-0.068-0.0680.0000.0000.0000.000
199A201TYR0-0.034-0.05050.413-0.006-0.0060.0000.0000.0000.000
200A202ASP-1-0.856-0.93651.982-0.070-0.0700.0000.0000.0000.000
201A203LEU0-0.031-0.00248.684-0.002-0.0020.0000.0000.0000.000
202A204VAL0-0.026-0.02050.1770.0000.0000.0000.0000.0000.000
203A205ASP-1-0.850-0.89944.951-0.134-0.1340.0000.0000.0000.000
204A206ASN0-0.048-0.02542.6760.0080.0080.0000.0000.0000.000
205A207LYS10.8620.90742.1030.1510.1510.0000.0000.0000.000
206A208GLY00.0000.00447.8190.0030.0030.0000.0000.0000.000
207A209ALA0-0.0090.00847.5350.0040.0040.0000.0000.0000.000
208A210LYS10.8750.93849.0920.0720.0720.0000.0000.0000.000
209A211ALA00.0390.01147.403-0.003-0.0030.0000.0000.0000.000
210A212GLU-1-0.827-0.91747.869-0.072-0.0720.0000.0000.0000.000
211A213ASP-1-0.905-0.96149.789-0.084-0.0840.0000.0000.0000.000
212A214VAL0-0.055-0.01944.147-0.003-0.0030.0000.0000.0000.000
213A215ALA0-0.045-0.01644.685-0.003-0.0030.0000.0000.0000.000
214A216LEU0-0.0010.02541.3180.0000.0000.0000.0000.0000.000
215A217ASN0-0.041-0.02644.6890.0010.0010.0000.0000.0000.000
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