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

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FMODB ID: XRYV8

Calculation Name: 3IV4-A-Xray33

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IV4

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1223265.232289
FMO2-HF: Nuclear repulsion 1170189.682993
FMO2-HF: Total energy -53075.549296
FMO2-MP2: Total energy -53228.625594


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:-5:ASN)


Summations of interaction energy for fragment #1(A:-5: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.
-4.803-1.3910.168-1.446-2.1340.001
Interaction energy analysis for fragmet #1(A:-5:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.035
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].
3A-3TYR00.027-0.0053.658-2.755-1.4270.023-0.686-0.6650.001
4A-2PHE0-0.019-0.0082.842-0.6020.6790.139-0.402-1.0170.003
5A-1GLN00.0130.0188.093-0.140-0.1400.0000.0000.0000.000
6A0GLY0-0.0100.0179.7970.0000.0000.0000.0000.0000.000
7A1VAL00.0590.0459.8960.0190.0190.0000.0000.0000.000
8A2ALA0-0.0110.00810.4370.0960.0960.0000.0000.0000.000
9A3ILE00.0450.02412.240-0.334-0.3340.0000.0000.0000.000
10A4LYS10.8710.94214.8501.1381.1380.0000.0000.0000.000
11A5LEU00.0290.01916.3540.0510.0510.0000.0000.0000.000
12A6SER0-0.077-0.04320.008-0.038-0.0380.0000.0000.0000.000
13A7SER00.016-0.03222.0730.0220.0220.0000.0000.0000.000
14A8ILE00.0410.01525.4660.0040.0040.0000.0000.0000.000
15A9ASP-1-0.785-0.85827.873-0.216-0.2160.0000.0000.0000.000
16A10GLN00.0160.00122.502-0.012-0.0120.0000.0000.0000.000
17A11PHE00.0020.00623.0010.0130.0130.0000.0000.0000.000
18A12GLU-1-0.740-0.83124.985-0.082-0.0820.0000.0000.0000.000
19A13GLN0-0.0110.01626.8710.0240.0240.0000.0000.0000.000
20A14VAL00.0090.00721.5190.0190.0190.0000.0000.0000.000
21A15ILE0-0.065-0.01824.2090.0340.0340.0000.0000.0000.000
22A16GLU-1-0.911-0.95026.126-0.022-0.0220.0000.0000.0000.000
23A17GLU-1-0.948-0.98026.652-0.145-0.1450.0000.0000.0000.000
24A18ASN0-0.072-0.02123.3720.0280.0280.0000.0000.0000.000
25A19LYS10.8900.94925.720-0.107-0.1070.0000.0000.0000.000
26A20TYR00.004-0.00122.760-0.001-0.0010.0000.0000.0000.000
27A21VAL00.0410.02220.680-0.007-0.0070.0000.0000.0000.000
28A22PHE00.0020.01316.8830.0060.0060.0000.0000.0000.000
29A23VAL0-0.002-0.00917.793-0.069-0.0690.0000.0000.0000.000
30A24LEU0-0.026-0.01312.0370.0440.0440.0000.0000.0000.000
31A25LYS10.8120.91216.1900.0780.0780.0000.0000.0000.000
32A26HIS00.0950.04810.9300.2790.2790.0000.0000.0000.000
33A27SER0-0.049-0.03914.9450.0110.0110.0000.0000.0000.000
34A28GLU-1-0.856-0.93613.541-1.070-1.0700.0000.0000.0000.000
35A29THR0-0.022-0.00513.777-0.111-0.1110.0000.0000.0000.000
36A30CYS0-0.0290.12814.3900.1440.1440.0000.0000.0000.000
37A31PRO00.0820.03911.860-0.087-0.0870.0000.0000.0000.000
38A32ILE00.0890.02911.6320.0770.0770.0000.0000.0000.000
39A33SER00.037-0.02412.7060.1550.1550.0000.0000.0000.000
40A34ALA00.0030.0128.188-0.003-0.0030.0000.0000.0000.000
41A35ASN00.0010.0097.735-0.061-0.0610.0000.0000.0000.000
42A36ALA00.0470.0188.9010.2990.2990.0000.0000.0000.000
43A37TYR0-0.014-0.0026.6140.1020.1020.0000.0000.0000.000
44A38ASP-1-0.894-0.9543.3991.8982.5540.007-0.355-0.309-0.003
45A39GLN0-0.042-0.0095.9480.8080.8080.0000.0000.0000.000
46A40PHE00.0110.0119.0120.1880.1880.0000.0000.0000.000
47A41ASN00.0520.0236.106-0.013-0.0130.0000.0000.0000.000
48A42LYS10.8970.9634.930-6.300-6.153-0.001-0.003-0.1430.000
49A43PHE0-0.0020.0008.225-0.012-0.0120.0000.0000.0000.000
50A44LEU00.0110.00711.405-0.032-0.0320.0000.0000.0000.000
51A45TYR0-0.0310.0048.848-0.181-0.1810.0000.0000.0000.000
52A46GLU-1-0.860-0.88111.2731.9151.9150.0000.0000.0000.000
53A47ARG10.8340.92112.977-0.957-0.9570.0000.0000.0000.000
54A48ASP-1-0.894-0.90314.6830.2830.2830.0000.0000.0000.000
55A49MET0-0.016-0.00215.319-0.109-0.1090.0000.0000.0000.000
56A50ASP-1-0.779-0.86315.128-0.132-0.1320.0000.0000.0000.000
57A51GLY00.0310.01615.0030.0860.0860.0000.0000.0000.000
58A52TYR00.0220.02215.553-0.142-0.1420.0000.0000.0000.000
59A53TYR0-0.024-0.01612.274-0.001-0.0010.0000.0000.0000.000
60A54LEU00.0250.02115.740-0.031-0.0310.0000.0000.0000.000
61A55ILE00.004-0.00514.152-0.006-0.0060.0000.0000.0000.000
62A56VAL0-0.030-0.04517.4960.0760.0760.0000.0000.0000.000
63A57GLN0-0.007-0.01218.2820.0010.0010.0000.0000.0000.000
64A58GLN0-0.012-0.00918.7670.0750.0750.0000.0000.0000.000
65A59GLU-1-0.782-0.83020.818-0.516-0.5160.0000.0000.0000.000
66A60ARG10.9540.97822.9710.3770.3770.0000.0000.0000.000
67A61ASP-1-0.839-0.90525.820-0.241-0.2410.0000.0000.0000.000
68A62LEU00.0200.02122.2260.0330.0330.0000.0000.0000.000
69A63SER0-0.019-0.03222.9660.0330.0330.0000.0000.0000.000
70A64ASP-1-0.803-0.83624.399-0.126-0.1260.0000.0000.0000.000
71A65TYR0-0.027-0.04827.6160.0260.0260.0000.0000.0000.000
72A66ILE00.0510.02222.2800.0260.0260.0000.0000.0000.000
73A67ALA0-0.0010.01826.3030.0300.0300.0000.0000.0000.000
74A68LYS10.8000.87627.8400.1430.1430.0000.0000.0000.000
75A69LYS10.8480.94227.9490.0860.0860.0000.0000.0000.000
76A70THR00.0380.00625.8430.0210.0210.0000.0000.0000.000
77A71ASN00.0200.02529.2700.0090.0090.0000.0000.0000.000
78A72VAL00.0310.04625.4500.0140.0140.0000.0000.0000.000
79A73LYS10.8520.90227.5120.0250.0250.0000.0000.0000.000
80A74HIS00.0390.01421.6710.0260.0260.0000.0000.0000.000
81A75GLU-1-0.821-0.88121.727-0.034-0.0340.0000.0000.0000.000
82A76SER0-0.076-0.00217.729-0.063-0.0630.0000.0000.0000.000
83A77PRO0-0.0130.01114.4860.0020.0020.0000.0000.0000.000
84A78GLN00.050-0.00516.6210.0340.0340.0000.0000.0000.000
85A79ALA0-0.0020.01116.112-0.061-0.0610.0000.0000.0000.000
86A80PHE0-0.018-0.01518.1250.0330.0330.0000.0000.0000.000
87A81TYR00.0270.02019.962-0.007-0.0070.0000.0000.0000.000
88A82PHE0-0.019-0.02122.051-0.013-0.0130.0000.0000.0000.000
89A83VAL00.0820.04124.6320.0120.0120.0000.0000.0000.000
90A84ASN00.0280.05727.2200.0120.0120.0000.0000.0000.000
91A85GLY00.0720.05528.054-0.008-0.0080.0000.0000.0000.000
92A86GLU-1-0.849-0.84129.1800.0350.0350.0000.0000.0000.000
93A87MET0-0.076-0.03225.3170.0110.0110.0000.0000.0000.000
94A88VAL00.0170.01525.4700.0030.0030.0000.0000.0000.000
95A89TRP0-0.017-0.01917.6780.0010.0010.0000.0000.0000.000
96A90ASN00.018-0.00221.847-0.030-0.0300.0000.0000.0000.000
97A91ARG10.9300.98619.085-0.255-0.2550.0000.0000.0000.000
98A92ASP-1-0.642-0.74818.7960.0390.0390.0000.0000.0000.000
99A93HIS10.7570.84217.0040.0450.0450.0000.0000.0000.000
100A94GLY00.0610.03015.5290.0320.0320.0000.0000.0000.000
101A95ASP-1-0.759-0.85016.4590.4740.4740.0000.0000.0000.000
102A96ILE0-0.0500.02513.2800.0190.0190.0000.0000.0000.000
103A97ASN00.0400.00712.7290.0730.0730.0000.0000.0000.000
104A98VAL00.0570.02210.857-0.108-0.1080.0000.0000.0000.000
105A99SER0-0.0220.00913.555-0.083-0.0830.0000.0000.0000.000
106A100SER0-0.013-0.03416.931-0.069-0.0690.0000.0000.0000.000
107A101LEU00.000-0.00613.330-0.085-0.0850.0000.0000.0000.000
108A102ALA0-0.003-0.00417.295-0.057-0.0570.0000.0000.0000.000
109A103GLN00.0840.08518.888-0.096-0.0960.0000.0000.0000.000
110A104ALA0-0.064-0.01620.686-0.047-0.0470.0000.0000.0000.000
111A105GLU-1-0.850-0.91319.8440.4770.4770.0000.0000.0000.000
112A106GLU-2-1.741-1.81723.1870.7560.7560.0000.0000.0000.000
113A107HOH0-0.025-0.01918.281-0.039-0.0390.0000.0000.0000.000
114A108HOH0-0.017-0.02230.7430.0050.0050.0000.0000.0000.000
115A109HOH00.0190.02634.281-0.002-0.0020.0000.0000.0000.000
116A111HOH0-0.042-0.04330.6560.0070.0070.0000.0000.0000.000
117A112HOH0-0.050-0.02519.375-0.004-0.0040.0000.0000.0000.000
118A113HOH0-0.005-0.01616.3990.0510.0510.0000.0000.0000.000
119A115HOH00.0420.03325.305-0.016-0.0160.0000.0000.0000.000
120A116HOH00.006-0.00810.988-0.164-0.1640.0000.0000.0000.000
121A117HOH0-0.061-0.05115.359-0.036-0.0360.0000.0000.0000.000
122A118HOH0-0.029-0.03520.6950.0260.0260.0000.0000.0000.000
123A119HOH0-0.042-0.03632.5500.0000.0000.0000.0000.0000.000
124A120HOH0-0.055-0.04123.2180.0000.0000.0000.0000.0000.000
125A122HOH0-0.023-0.02215.2170.0370.0370.0000.0000.0000.000
126A123HOH0-0.015-0.00422.0660.0330.0330.0000.0000.0000.000
127A124HOH0-0.023-0.03025.156-0.013-0.0130.0000.0000.0000.000
128A125HOH0-0.019-0.01424.7480.0120.0120.0000.0000.0000.000
129A126HOH0-0.026-0.0245.277-0.085-0.0850.0000.0000.0000.000
130A128HOH0-0.047-0.06231.4020.0040.0040.0000.0000.0000.000
131A129HOH0-0.023-0.02120.0680.0200.0200.0000.0000.0000.000
132A130HOH0-0.009-0.00522.100-0.003-0.0030.0000.0000.0000.000
133A134HOH0-0.046-0.03325.062-0.002-0.0020.0000.0000.0000.000
134A135HOH0-0.033-0.01829.938-0.003-0.0030.0000.0000.0000.000
135A136HOH00.0030.00625.9420.0000.0000.0000.0000.0000.000
136A137HOH0-0.045-0.0259.379-0.120-0.1200.0000.0000.0000.000
137A139HOH0-0.008-0.02224.340-0.013-0.0130.0000.0000.0000.000
138A140HOH0-0.017-0.03217.920-0.012-0.0120.0000.0000.0000.000
139A141HOH0-0.070-0.07423.3940.0120.0120.0000.0000.0000.000
140A142HOH0-0.057-0.05932.0610.0010.0010.0000.0000.0000.000
141A143HOH00.0140.00925.5560.0070.0070.0000.0000.0000.000
142A144HOH0-0.043-0.0388.7840.3880.3880.0000.0000.0000.000
143A147HOH0-0.044-0.02619.507-0.019-0.0190.0000.0000.0000.000
144A148HOH0-0.019-0.01218.454-0.022-0.0220.0000.0000.0000.000
145A149HOH0-0.041-0.02422.3520.0070.0070.0000.0000.0000.000
146A150HOH0-0.037-0.0209.630-0.102-0.1020.0000.0000.0000.000
147A151HOH0-0.009-0.00928.6570.0070.0070.0000.0000.0000.000
148A152HOH0-0.026-0.01730.0280.0080.0080.0000.0000.0000.000
149A153HOH00.0020.01130.1010.0020.0020.0000.0000.0000.000
150A154HOH0-0.024-0.02131.9360.0000.0000.0000.0000.0000.000
151A158HOH0-0.006-0.0138.800-0.025-0.0250.0000.0000.0000.000
152A161HOH0-0.032-0.01518.976-0.004-0.0040.0000.0000.0000.000
153A162HOH0-0.043-0.13016.729-0.015-0.0150.0000.0000.0000.000
154A164HOH0-0.034-0.02423.199-0.002-0.0020.0000.0000.0000.000
155A165HOH0-0.055-0.03623.1300.0000.0000.0000.0000.0000.000
156A166HOH0-0.031-0.02235.488-0.003-0.0030.0000.0000.0000.000
157A167HOH0-0.037-0.02630.7310.0060.0060.0000.0000.0000.000
158A168HOH0-0.084-0.06434.5780.0020.0020.0000.0000.0000.000
159A170HOH0-0.065-0.04721.102-0.020-0.0200.0000.0000.0000.000
160A172HOH0-0.071-0.08132.2610.0070.0070.0000.0000.0000.000
161A175HOH0-0.018-0.02024.9150.0110.0110.0000.0000.0000.000
162A176HOH0-0.006-0.01523.110-0.015-0.0150.0000.0000.0000.000
163A177HOH0-0.018-0.01528.634-0.007-0.0070.0000.0000.0000.000
164A179HOH0-0.094-0.09227.0700.0030.0030.0000.0000.0000.000
165A183HOH0-0.007-0.00519.160-0.028-0.0280.0000.0000.0000.000
166A184HOH00.0220.01729.8970.0010.0010.0000.0000.0000.000
167A185HOH0-0.034-0.02511.914-0.117-0.1170.0000.0000.0000.000
168A186HOH00.0070.01322.343-0.010-0.0100.0000.0000.0000.000
169A187HOH00.002-0.00530.664-0.005-0.0050.0000.0000.0000.000
170A190HOH0-0.028-0.01731.235-0.002-0.0020.0000.0000.0000.000
171A195HOH0-0.047-0.04113.154-0.002-0.0020.0000.0000.0000.000
172A198HOH0-0.017-0.02828.1930.0020.0020.0000.0000.0000.000
173A199HOH0-0.012-0.01922.6390.0110.0110.0000.0000.0000.000
174A200HOH0-0.060-0.05015.560-0.034-0.0340.0000.0000.0000.000
175A201HOH0-0.056-0.04414.561-0.035-0.0350.0000.0000.0000.000
176A203HOH0-0.052-0.05027.9770.0000.0000.0000.0000.0000.000
177A204HOH00.0380.03136.6930.0010.0010.0000.0000.0000.000
178A206HOH00.0260.02529.959-0.006-0.0060.0000.0000.0000.000
179A207HOH0-0.023-0.01525.8660.0160.0160.0000.0000.0000.000
180A210HOH00.0030.00612.607-0.058-0.0580.0000.0000.0000.000
181A211HOH0-0.023-0.01328.6350.0100.0100.0000.0000.0000.000
182A212HOH0-0.058-0.05830.0330.0070.0070.0000.0000.0000.000
183A213HOH0-0.021-0.01224.6120.0080.0080.0000.0000.0000.000
184A215HOH00.0060.01933.718-0.001-0.0010.0000.0000.0000.000
185A216HOH00.0530.07429.025-0.013-0.0130.0000.0000.0000.000
186A217HOH0-0.031-0.02614.7220.0580.0580.0000.0000.0000.000
187A220HOH0-0.076-0.05824.0180.0110.0110.0000.0000.0000.000
188A221HOH0-0.037-0.04021.482-0.024-0.0240.0000.0000.0000.000
189A222HOH0-0.003-0.00524.7430.0140.0140.0000.0000.0000.000
190A223HOH0-0.042-0.02726.3190.0090.0090.0000.0000.0000.000
191A224HOH00.0140.01023.4890.0020.0020.0000.0000.0000.000
192A226HOH0-0.057-0.03626.768-0.004-0.0040.0000.0000.0000.000
193A227HOH00.0520.03021.1830.0030.0030.0000.0000.0000.000
194A228HOH0-0.018-0.02818.2710.0000.0000.0000.0000.0000.000
195A229HOH0-0.051-0.03618.4750.0090.0090.0000.0000.0000.000
196A231HOH00.0110.01021.4720.0070.0070.0000.0000.0000.000
197A232HOH00.0150.00321.360-0.024-0.0240.0000.0000.0000.000
198A235HOH00.0380.01718.599-0.009-0.0090.0000.0000.0000.000
199A236HOH0-0.049-0.02813.6380.0140.0140.0000.0000.0000.000
200A237HOH0-0.054-0.04324.597-0.013-0.0130.0000.0000.0000.000
201A238HOH0-0.025-0.04033.665-0.005-0.0050.0000.0000.0000.000
202A240HOH0-0.006-0.00410.1420.3140.3140.0000.0000.0000.000
203A242HOH0-0.061-0.04612.442-0.062-0.0620.0000.0000.0000.000
204A244HOH0-0.014-0.01814.9560.0300.0300.0000.0000.0000.000
205A245HOH0-0.035-0.01721.0200.0090.0090.0000.0000.0000.000