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: 49MYN

Calculation Name: 4XH3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XH3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NQW6

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2323380.690304
FMO2-HF: Nuclear repulsion 2239715.147749
FMO2-HF: Total energy -83665.542555
FMO2-MP2: Total energy -83906.734759


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:-2:GLY)


Summations of interaction energy for fragment #1(A:-2:GLY)
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.
0.4031.556-0.017-0.606-0.530.001
Interaction energy analysis for fragmet #1(A:-2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / 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].
3A0MET00.0000.0023.8620.2231.376-0.017-0.606-0.5300.001
4A1CYS0-0.009-0.0037.0810.1490.1490.0000.0000.0000.000
5A2GLN00.0330.0229.940-0.109-0.1090.0000.0000.0000.000
6A3VAL00.0290.00713.3930.0440.0440.0000.0000.0000.000
7A4ASN0-0.020-0.02115.4320.0210.0210.0000.0000.0000.000
8A5ILE00.0830.03318.142-0.010-0.0100.0000.0000.0000.000
9A6LYS10.9700.99220.2810.0290.0290.0000.0000.0000.000
10A7GLN0-0.014-0.00716.1970.0060.0060.0000.0000.0000.000
11A8LYS10.9160.94715.803-0.078-0.0780.0000.0000.0000.000
12A9MET0-0.020-0.00818.652-0.008-0.0080.0000.0000.0000.000
13A10GLN0-0.025-0.01921.7310.0050.0050.0000.0000.0000.000
14A11GLU-1-0.914-0.96215.701-0.144-0.1440.0000.0000.0000.000
15A12LEU00.0010.00619.933-0.008-0.0080.0000.0000.0000.000
16A13ASN0-0.020-0.01121.8640.0040.0040.0000.0000.0000.000
17A14ASN0-0.011-0.00422.0630.0100.0100.0000.0000.0000.000
18A15GLU-1-0.738-0.85120.828-0.086-0.0860.0000.0000.0000.000
19A16ILE0-0.019-0.00222.9740.0040.0040.0000.0000.0000.000
20A17ASN0-0.044-0.03626.0770.0060.0060.0000.0000.0000.000
21A18MET0-0.0040.01923.759-0.002-0.0020.0000.0000.0000.000
22A19GLN0-0.014-0.03323.7070.0080.0080.0000.0000.0000.000
23A20GLN00.0240.02027.3410.0090.0090.0000.0000.0000.000
24A21THR0-0.035-0.01129.5440.0020.0020.0000.0000.0000.000
25A22VAL00.0140.00727.2500.0020.0020.0000.0000.0000.000
26A23ILE00.0010.00830.3010.0030.0030.0000.0000.0000.000
27A24TYR0-0.0020.01232.8600.0020.0020.0000.0000.0000.000
28A25GLN00.004-0.00831.6090.0000.0000.0000.0000.0000.000
29A26ALA00.0170.01633.3030.0010.0010.0000.0000.0000.000
30A27SER00.003-0.01535.3150.0040.0040.0000.0000.0000.000
31A28GLN00.0150.00338.2490.0040.0040.0000.0000.0000.000
32A29ALA00.0180.01537.7120.0010.0010.0000.0000.0000.000
33A30LEU00.007-0.00837.1840.0010.0010.0000.0000.0000.000
34A31ASN0-0.067-0.03540.9010.0040.0040.0000.0000.0000.000
35A32CYS0-0.047-0.01842.9610.0010.0010.0000.0000.0000.000
36A33CYS0-0.0550.00842.3190.0000.0000.0000.0000.0000.000
37A34VAL0-0.036-0.02845.1280.0020.0020.0000.0000.0000.000
38A35ASP-1-0.823-0.92748.786-0.020-0.0200.0000.0000.0000.000
39A36GLU-1-0.795-0.86048.461-0.017-0.0170.0000.0000.0000.000
40A37GLU-1-0.909-0.92648.922-0.025-0.0250.0000.0000.0000.000
41A38HIS10.7620.86547.3310.0240.0240.0000.0000.0000.000
42A39GLY00.0960.05844.092-0.001-0.0010.0000.0000.0000.000
43A40LYS10.8920.95843.9480.0150.0150.0000.0000.0000.000
44A41GLY0-0.045-0.02844.4750.0000.0000.0000.0000.0000.000
45A42SER0-0.006-0.00441.980-0.001-0.0010.0000.0000.0000.000
46A43LEU00.031-0.00136.5120.0010.0010.0000.0000.0000.000
47A44GLU-1-0.924-0.95737.275-0.043-0.0430.0000.0000.0000.000
48A45GLU-1-0.784-0.88037.345-0.021-0.0210.0000.0000.0000.000
49A46ALA00.0130.00237.8640.0010.0010.0000.0000.0000.000
50A47GLU-1-0.788-0.90631.674-0.039-0.0390.0000.0000.0000.000
51A48ALA0-0.0030.01733.246-0.001-0.0010.0000.0000.0000.000
52A49GLU-1-0.717-0.85434.619-0.018-0.0180.0000.0000.0000.000
53A50ARG10.8000.89226.9730.0420.0420.0000.0000.0000.000
54A51LEU0-0.036-0.02628.4410.0010.0010.0000.0000.0000.000
55A52LEU0-0.0110.01230.265-0.001-0.0010.0000.0000.0000.000
56A53LEU0-0.0170.00831.4150.0020.0020.0000.0000.0000.000
57A54ILE0-0.013-0.01125.7130.0040.0040.0000.0000.0000.000
58A55ALA00.0120.01527.0250.0030.0030.0000.0000.0000.000
59A56THR0-0.023-0.03528.0640.0020.0020.0000.0000.0000.000
60A57GLY00.0010.00728.2460.0050.0050.0000.0000.0000.000
61A58LYS10.9020.93320.8090.0720.0720.0000.0000.0000.000
62A59ARG10.8940.93424.8780.0160.0160.0000.0000.0000.000
63A60THR0-0.035-0.02227.1000.0020.0020.0000.0000.0000.000
64A61LEU00.0230.01623.2920.0050.0050.0000.0000.0000.000
65A62LEU00.0100.00520.4050.0080.0080.0000.0000.0000.000
66A63ILE0-0.016-0.00823.8550.0020.0020.0000.0000.0000.000
67A64ASP-1-0.852-0.92726.8820.0380.0380.0000.0000.0000.000
68A65GLU-1-0.835-0.91219.0810.0900.0900.0000.0000.0000.000
69A66LEU0-0.023-0.00623.6320.0060.0060.0000.0000.0000.000
70A67ASN0-0.045-0.03525.241-0.003-0.0030.0000.0000.0000.000
71A68LYS10.8870.94322.319-0.127-0.1270.0000.0000.0000.000
72A69LEU00.0340.00520.2170.0000.0000.0000.0000.0000.000
73A70LYS10.8090.90924.331-0.024-0.0240.0000.0000.0000.000
74A71ASN0-0.074-0.04227.477-0.008-0.0080.0000.0000.0000.000
75A72GLU-1-0.867-0.90322.2780.1380.1380.0000.0000.0000.000
76A73GLY0-0.0030.00226.294-0.009-0.0090.0000.0000.0000.000
77A74PRO0-0.034-0.03225.6190.0030.0030.0000.0000.0000.000
78A75GLN00.0080.01918.3190.0010.0010.0000.0000.0000.000
79A90LYS10.8350.8888.864-1.113-1.1130.0000.0000.0000.000
80A91GLY00.022-0.00214.801-0.055-0.0550.0000.0000.0000.000
81A92SER0-0.074-0.01914.4200.0390.0390.0000.0000.0000.000
82A93VAL00.0580.02916.270-0.026-0.0260.0000.0000.0000.000
83A94THR0-0.029-0.01517.937-0.007-0.0070.0000.0000.0000.000
84A95LEU00.0200.03820.181-0.003-0.0030.0000.0000.0000.000
85A96SER00.021-0.00622.768-0.009-0.0090.0000.0000.0000.000
86A97GLU-1-0.801-0.89425.0520.0230.0230.0000.0000.0000.000
87A98ILE00.0360.02925.5980.0020.0020.0000.0000.0000.000
88A99ARG10.9230.95729.689-0.017-0.0170.0000.0000.0000.000
89A100LEU00.0160.01233.4820.0040.0040.0000.0000.0000.000
90A101PRO0-0.0120.01336.022-0.003-0.0030.0000.0000.0000.000
91A102LEU0-0.001-0.00239.6790.0000.0000.0000.0000.0000.000
92A103LYS10.8540.91642.662-0.009-0.0090.0000.0000.0000.000
93A104ALA00.0460.00846.427-0.001-0.0010.0000.0000.0000.000
94A105ASP-1-0.850-0.92448.5740.0030.0030.0000.0000.0000.000
95A106PHE00.0160.01943.755-0.001-0.0010.0000.0000.0000.000
96A107VAL00.0270.01044.743-0.001-0.0010.0000.0000.0000.000
97A108CYS0-0.024-0.00847.464-0.002-0.0020.0000.0000.0000.000
98A109SER0-0.032-0.03050.705-0.001-0.0010.0000.0000.0000.000
99A110THR0-0.094-0.05946.018-0.001-0.0010.0000.0000.0000.000
100A111VAL00.0010.00549.061-0.001-0.0010.0000.0000.0000.000
101A112GLN0-0.015-0.01351.0350.0000.0000.0000.0000.0000.000
102A113LYS10.9000.95352.8600.0030.0030.0000.0000.0000.000
103A114PRO00.0380.03350.1870.0000.0000.0000.0000.0000.000
104A115ASP-1-0.888-0.94849.918-0.013-0.0130.0000.0000.0000.000
105A116ALA0-0.069-0.02151.8880.0000.0000.0000.0000.0000.000
106A117ALA0-0.050-0.05547.3210.0000.0000.0000.0000.0000.000
107A118ASN00.0050.03743.1650.0010.0010.0000.0000.0000.000
108A119TYR0-0.023-0.03242.7250.0020.0020.0000.0000.0000.000
109A120TYR00.0070.01137.322-0.001-0.0010.0000.0000.0000.000
110A121TYR00.0170.00836.0300.0030.0030.0000.0000.0000.000
111A122LEU0-0.0060.00330.372-0.004-0.0040.0000.0000.0000.000
112A123ILE00.0030.00228.5610.0050.0050.0000.0000.0000.000
113A124ILE0-0.010-0.00226.457-0.006-0.0060.0000.0000.0000.000
114A125LEU0-0.013-0.00723.4400.0060.0060.0000.0000.0000.000
115A126LYS10.8630.91022.760-0.039-0.0390.0000.0000.0000.000
116A127ALA00.0300.01819.3520.0050.0050.0000.0000.0000.000
117A128GLY00.0490.03418.780-0.001-0.0010.0000.0000.0000.000
118A129ALA0-0.009-0.00819.790-0.017-0.0170.0000.0000.0000.000
119A130GLU-1-0.859-0.91715.6590.0250.0250.0000.0000.0000.000
120A131ASN0-0.102-0.05414.9510.0180.0180.0000.0000.0000.000
121A132MET00.0230.02418.2920.0080.0080.0000.0000.0000.000
122A133VAL0-0.032-0.01020.394-0.016-0.0160.0000.0000.0000.000
123A134ALA00.0230.00322.3470.0090.0090.0000.0000.0000.000
124A135THR0-0.0220.00025.340-0.006-0.0060.0000.0000.0000.000
125A136PRO00.0130.00126.745-0.002-0.0020.0000.0000.0000.000
126A137LEU00.0010.02429.4970.0060.0060.0000.0000.0000.000
127A138ALA0-0.0070.01033.232-0.002-0.0020.0000.0000.0000.000
128A139SER00.006-0.01635.1910.0010.0010.0000.0000.0000.000
129A140THR00.049-0.00538.998-0.001-0.0010.0000.0000.0000.000
130A141SER0-0.0010.00741.7350.0000.0000.0000.0000.0000.000
131A142ASN00.0110.01535.5400.0010.0010.0000.0000.0000.000
132A143SER00.0020.00535.259-0.002-0.0020.0000.0000.0000.000
133A144LEU0-0.0230.00036.7610.0020.0020.0000.0000.0000.000
134A145ASN0-0.041-0.02535.987-0.002-0.0020.0000.0000.0000.000
135A146GLY0-0.013-0.00439.3710.0020.0020.0000.0000.0000.000
136A147ASP-1-0.821-0.92440.6640.0090.0090.0000.0000.0000.000
137A148ALA0-0.009-0.00137.3390.0000.0000.0000.0000.0000.000
138A149LEU0-0.0200.01336.165-0.002-0.0020.0000.0000.0000.000
139A150THR00.0080.00331.9690.0040.0040.0000.0000.0000.000
140A151PHE00.020-0.00328.948-0.004-0.0040.0000.0000.0000.000
141A152THR0-0.001-0.00826.1530.0020.0020.0000.0000.0000.000
142A153THR0-0.0050.00323.150-0.005-0.0050.0000.0000.0000.000
143A154THR0-0.033-0.01819.9110.0080.0080.0000.0000.0000.000
144A155PHE0-0.015-0.00818.568-0.012-0.0120.0000.0000.0000.000
145A156THR0-0.012-0.01314.3790.0030.0030.0000.0000.0000.000
146A157LEU00.0020.00915.088-0.009-0.0090.0000.0000.0000.000
147A158GLN00.004-0.0249.132-0.025-0.0250.0000.0000.0000.000
148A159ASP-1-0.798-0.8759.6631.1801.1800.0000.0000.0000.000
149A160VAL0-0.0210.01012.511-0.011-0.0110.0000.0000.0000.000
150A161SER00.0290.01416.1770.0180.0180.0000.0000.0000.000
151A162ASN0-0.021-0.02319.100-0.006-0.0060.0000.0000.0000.000
152A163ASP-1-0.913-0.96722.4010.1860.1860.0000.0000.0000.000
153A164PHE0-0.039-0.00720.737-0.013-0.0130.0000.0000.0000.000
154A165GLU-1-0.826-0.92722.5660.0780.0780.0000.0000.0000.000
155A166ILE0-0.112-0.06320.9030.0080.0080.0000.0000.0000.000
156A167ASN0-0.0140.00724.264-0.014-0.0140.0000.0000.0000.000
157A168ILE0-0.009-0.00326.713-0.006-0.0060.0000.0000.0000.000
158A169GLU-1-0.829-0.89228.7500.0270.0270.0000.0000.0000.000
159A170VAL00.0100.01230.890-0.004-0.0040.0000.0000.0000.000
160A171TYR0-0.008-0.03131.145-0.001-0.0010.0000.0000.0000.000
161A172SER0-0.068-0.04535.381-0.001-0.0010.0000.0000.0000.000
162A173LEU00.0230.02738.2610.0000.0000.0000.0000.0000.000
163A174VAL0-0.016-0.02040.1050.0000.0000.0000.0000.0000.000
164A175GLN0-0.038-0.01841.4830.0010.0010.0000.0000.0000.000
165A176LYS10.9390.96845.0900.0050.0050.0000.0000.0000.000
166A177LYS10.8230.87448.8990.0140.0140.0000.0000.0000.000
167A222ALA0-0.013-0.01942.5410.0000.0000.0000.0000.0000.000
168A223VAL00.012-0.00136.591-0.001-0.0010.0000.0000.0000.000
169A224ARG10.8220.91538.6510.0220.0220.0000.0000.0000.000
170A225THR00.007-0.00737.630-0.001-0.0010.0000.0000.0000.000
171A226SER0-0.006-0.00935.2300.0000.0000.0000.0000.0000.000
172A227ASN0-0.065-0.05737.3590.0040.0040.0000.0000.0000.000
173A228PHE0-0.036-0.02335.5780.0010.0010.0000.0000.0000.000
174A229ALA00.0340.03037.1250.0020.0020.0000.0000.0000.000
175A230LEU0-0.028-0.01734.1980.0000.0000.0000.0000.0000.000
176A231VAL0-0.036-0.04337.1320.0000.0000.0000.0000.0000.000
177A232GLY00.0700.02036.7680.0000.0000.0000.0000.0000.000
178A233SER0-0.068-0.01733.048-0.001-0.0010.0000.0000.0000.000
179A234TYR00.0420.01631.1530.0010.0010.0000.0000.0000.000
180A235THR00.0270.01728.519-0.002-0.0020.0000.0000.0000.000
181A236LEU0-0.0280.00326.3990.0020.0020.0000.0000.0000.000
182A237SER00.0790.03825.7420.0070.0070.0000.0000.0000.000
183A238LEU00.0130.00724.219-0.005-0.0050.0000.0000.0000.000
184A239SER0-0.049-0.03026.248-0.007-0.0070.0000.0000.0000.000
185A240SER00.0370.02028.282-0.006-0.0060.0000.0000.0000.000
186A241VAL0-0.008-0.00724.851-0.007-0.0070.0000.0000.0000.000
187A242GLY0-0.0100.00327.773-0.001-0.0010.0000.0000.0000.000
188A243ASN0-0.062-0.01929.986-0.010-0.0100.0000.0000.0000.000
189A244THR0-0.010-0.02330.7450.0010.0010.0000.0000.0000.000
190A245LYS10.8150.90832.805-0.027-0.0270.0000.0000.0000.000
191A246PHE00.0160.00930.6240.0030.0030.0000.0000.0000.000
192A247VAL00.0280.01035.402-0.003-0.0030.0000.0000.0000.000
193A248LEU0-0.054-0.01334.2230.0020.0020.0000.0000.0000.000
194A249ASP-1-0.842-0.92335.4760.0390.0390.0000.0000.0000.000
195A250LYS10.8610.89534.974-0.033-0.0330.0000.0000.0000.000
196A251VAL00.0160.02739.558-0.002-0.0020.0000.0000.0000.000
197A252PRO0-0.0160.01140.8740.0000.0000.0000.0000.0000.000
198A253PHE00.0420.01544.0900.0000.0000.0000.0000.0000.000
199A254LEU0-0.047-0.02347.674-0.001-0.0010.0000.0000.0000.000
200A255SER00.0020.00943.260-0.001-0.0010.0000.0000.0000.000
201A256SER00.003-0.01042.6550.0010.0010.0000.0000.0000.000
202A257LEU00.0330.02738.412-0.001-0.0010.0000.0000.0000.000
203A258GLU-1-0.830-0.89341.3670.0190.0190.0000.0000.0000.000
204A259GLY00.0150.00941.1460.0000.0000.0000.0000.0000.000
205A260HIS0-0.043-0.03537.6820.0040.0040.0000.0000.0000.000
206A261ILE00.0020.00131.156-0.003-0.0030.0000.0000.0000.000
207A262TYR0-0.044-0.03733.6920.0040.0040.0000.0000.0000.000
208A263LEU0-0.0090.00427.514-0.003-0.0030.0000.0000.0000.000
209A264LYS10.8170.88926.347-0.024-0.0240.0000.0000.0000.000
210A265ILE00.0190.01424.2360.0000.0000.0000.0000.0000.000
211A266LYS10.9310.96821.637-0.049-0.0490.0000.0000.0000.000
212A267CYS0-0.017-0.02420.4150.0070.0070.0000.0000.0000.000
213A268GLN0-0.0100.01116.053-0.027-0.0270.0000.0000.0000.000
214A269VAL00.0390.02417.8960.0400.0400.0000.0000.0000.000