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: ZNVVN

Calculation Name: 1UEB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UEB

Chain ID: A

ChEMBL ID:

UniProt ID: Q76G20

Base Structure: X-ray

Registration Date: 2023-09-27

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1705659.795446
FMO2-HF: Nuclear repulsion 1634301.366553
FMO2-HF: Total energy -71358.428893
FMO2-MP2: Total energy -71565.127877


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.
-17.363-16.46518.433-5.738-13.591-0.08
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 : -0.036 / 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].
3A3SER0-0.050-0.0273.888-0.3871.546-0.007-1.034-0.8920.005
4A4VAL00.0250.0146.4700.2120.2120.0000.0000.0000.000
5A5THR0-0.049-0.0488.4740.2290.2290.0000.0000.0000.000
6A6ASP-1-0.812-0.8877.740-2.467-2.4670.0000.0000.0000.000
7A7LEU0-0.0280.0098.4980.0750.0750.0000.0000.0000.000
8A8ARG10.8340.90810.9441.1521.1520.0000.0000.0000.000
9A9PRO00.0320.00813.809-0.026-0.0260.0000.0000.0000.000
10A10GLY00.0350.03615.391-0.023-0.0230.0000.0000.0000.000
11A11THR0-0.035-0.0368.997-0.050-0.0500.0000.0000.0000.000
12A12LYS10.8760.9409.9120.4400.4400.0000.0000.0000.000
13A13VAL00.009-0.0056.439-0.355-0.3550.0000.0000.0000.000
14A14LYS10.8450.9187.196-2.773-2.7730.0000.0000.0000.000
15A15MET0-0.056-0.0346.7330.2340.2340.0000.0000.0000.000
16A16ASP-1-0.817-0.8998.6440.4250.4250.0000.0000.0000.000
17A17GLY00.0020.00910.450-0.114-0.1140.0000.0000.0000.000
18A18GLY00.0040.02012.206-0.028-0.0280.0000.0000.0000.000
19A19LEU00.0500.02511.4810.1520.1520.0000.0000.0000.000
20A20TRP0-0.045-0.03811.068-0.183-0.1830.0000.0000.0000.000
21A21GLU-1-0.778-0.88612.141-0.296-0.2960.0000.0000.0000.000
22A22CYS0-0.063-0.00712.3030.0330.0330.0000.0000.0000.000
23A23VAL0-0.002-0.01214.153-0.010-0.0100.0000.0000.0000.000
24A24GLU-1-0.854-0.91117.327-0.197-0.1970.0000.0000.0000.000
25A25TYR0-0.012-0.02113.3130.0050.0050.0000.0000.0000.000
26A26GLN00.0000.01716.6040.0400.0400.0000.0000.0000.000
27A27HIS00.0450.02215.746-0.032-0.0320.0000.0000.0000.000
28A28GLN00.006-0.00217.3640.0560.0560.0000.0000.0000.000
29A29LYS10.8820.92019.0060.2770.2770.0000.0000.0000.000
30A30LEU00.0610.05121.4580.0140.0140.0000.0000.0000.000
31A31GLY00.0280.01824.8000.0210.0210.0000.0000.0000.000
32A32ARG10.9440.94724.5430.1340.1340.0000.0000.0000.000
33A33GLY0-0.0140.01323.074-0.003-0.0030.0000.0000.0000.000
34A34GLY00.0300.01618.792-0.023-0.0230.0000.0000.0000.000
35A35ALA00.000-0.00616.5860.0190.0190.0000.0000.0000.000
36A36LYS10.8700.93515.1980.2240.2240.0000.0000.0000.000
37A37VAL00.0070.00911.963-0.012-0.0120.0000.0000.0000.000
38A38VAL0-0.017-0.00714.3460.0480.0480.0000.0000.0000.000
39A39ALA00.005-0.00613.213-0.049-0.0490.0000.0000.0000.000
40A40LYS10.8620.92315.3650.2190.2190.0000.0000.0000.000
41A41PHE00.024-0.00610.785-0.060-0.0600.0000.0000.0000.000
42A42LYS10.8950.95016.0850.2010.2010.0000.0000.0000.000
43A43ASN00.0460.01916.023-0.009-0.0090.0000.0000.0000.000
44A44LEU00.0120.00413.601-0.049-0.0490.0000.0000.0000.000
45A45GLU-1-0.811-0.86417.1090.3790.3790.0000.0000.0000.000
46A46THR0-0.040-0.02719.796-0.031-0.0310.0000.0000.0000.000
47A47GLY00.0310.00621.730-0.018-0.0180.0000.0000.0000.000
48A48ALA0-0.0300.00119.368-0.017-0.0170.0000.0000.0000.000
49A49THR0-0.001-0.01418.776-0.016-0.0160.0000.0000.0000.000
50A50VAL0-0.016-0.00114.1610.0240.0240.0000.0000.0000.000
51A51GLU-1-0.885-0.93116.532-0.196-0.1960.0000.0000.0000.000
52A52ARG10.8050.8919.586-0.173-0.1730.0000.0000.0000.000
53A53THR0-0.008-0.01114.229-0.059-0.0590.0000.0000.0000.000
54A54PHE00.0290.0258.6090.0220.0220.0000.0000.0000.000
55A55ASN0-0.048-0.04311.8380.0130.0130.0000.0000.0000.000
56A56SER00.008-0.01410.832-0.043-0.0430.0000.0000.0000.000
57A57GLY0-0.0060.00410.358-0.134-0.1340.0000.0000.0000.000
58A58GLU-1-0.821-0.8937.117-0.431-0.4310.0000.0000.0000.000
59A59LYS10.8590.9032.2731.0091.6631.267-0.447-1.4730.003
60A60LEU0-0.010-0.0072.906-0.8980.3680.815-0.433-1.648-0.004
61A61GLU-1-0.742-0.8572.4160.1221.8827.531-4.007-5.283-0.026
62A62ASP-1-0.873-0.9331.903-15.589-20.5138.8280.191-4.095-0.058
63A63ILE0-0.026-0.0084.7310.9661.175-0.001-0.008-0.2000.000
64A64TYR0-0.078-0.0577.396-0.342-0.3420.0000.0000.0000.000
65A65VAL0-0.032-0.0349.7820.1940.1940.0000.0000.0000.000
66A66GLU-1-0.823-0.86813.260-0.145-0.1450.0000.0000.0000.000
67A67THR0-0.039-0.03716.4050.0280.0280.0000.0000.0000.000
68A68ARG10.7600.86319.253-0.060-0.0600.0000.0000.0000.000
69A69GLU-1-0.916-0.96422.632-0.051-0.0510.0000.0000.0000.000
70A70LEU0-0.0050.00424.1150.0090.0090.0000.0000.0000.000
71A71GLN0-0.038-0.03027.953-0.003-0.0030.0000.0000.0000.000
72A72TYR0-0.014-0.00731.7530.0110.0110.0000.0000.0000.000
73A73LEU0-0.041-0.02633.144-0.007-0.0070.0000.0000.0000.000
74A74TYR0-0.038-0.03335.653-0.006-0.0060.0000.0000.0000.000
75A75PRO0-0.0250.00435.7140.0070.0070.0000.0000.0000.000
76A76GLU-1-0.874-0.94134.9530.0980.0980.0000.0000.0000.000
77A77GLY0-0.018-0.00235.7770.0090.0090.0000.0000.0000.000
78A78GLU-1-0.936-0.98233.4100.0920.0920.0000.0000.0000.000
79A79GLU-1-0.942-0.96929.9140.1670.1670.0000.0000.0000.000
80A80MET0-0.082-0.03031.386-0.011-0.0110.0000.0000.0000.000
81A81VAL00.0200.02330.8860.0080.0080.0000.0000.0000.000
82A82PHE00.008-0.01328.556-0.013-0.0130.0000.0000.0000.000
83A83MET0-0.0160.00430.0850.0110.0110.0000.0000.0000.000
84A84ASP-1-0.800-0.89224.2880.0120.0120.0000.0000.0000.000
85A85LEU0-0.023-0.01927.6780.0000.0000.0000.0000.0000.000
86A86GLU-1-0.960-0.95924.232-0.066-0.0660.0000.0000.0000.000
87A87THR0-0.079-0.09523.318-0.001-0.0010.0000.0000.0000.000
88A88TYR0-0.103-0.05126.7690.0100.0100.0000.0000.0000.000
89A89GLU-1-0.833-0.87023.2790.1110.1110.0000.0000.0000.000
90A90GLN0-0.015-0.01627.641-0.016-0.0160.0000.0000.0000.000
91A91PHE0-0.007-0.01423.4920.0160.0160.0000.0000.0000.000
92A92ALA00.0220.03027.815-0.015-0.0150.0000.0000.0000.000
93A93VAL00.005-0.00625.8250.0170.0170.0000.0000.0000.000
94A94PRO00.0350.01826.512-0.013-0.0130.0000.0000.0000.000
95A95ARG10.9560.96428.387-0.074-0.0740.0000.0000.0000.000
96A96SER0-0.045-0.01627.434-0.009-0.0090.0000.0000.0000.000
97A97ARG10.7740.85120.288-0.265-0.2650.0000.0000.0000.000
98A98VAL0-0.0130.00025.517-0.012-0.0120.0000.0000.0000.000
99A99VAL0-0.030-0.02326.267-0.003-0.0030.0000.0000.0000.000
100A100GLY00.0790.03029.054-0.007-0.0070.0000.0000.0000.000
101A101ALA00.000-0.00131.989-0.005-0.0050.0000.0000.0000.000
102A102GLU-1-0.946-0.96233.5410.0400.0400.0000.0000.0000.000
103A103PHE00.0200.01035.748-0.004-0.0040.0000.0000.0000.000
104A104PHE00.032-0.00830.001-0.005-0.0050.0000.0000.0000.000
105A105LYS10.8680.91236.0430.0000.0000.0000.0000.0000.000
106A106GLU-1-0.886-0.95937.4310.0390.0390.0000.0000.0000.000
107A107GLY0-0.0030.00236.983-0.005-0.0050.0000.0000.0000.000
108A108MET0-0.076-0.00134.236-0.006-0.0060.0000.0000.0000.000
109A109THR00.0120.01029.8270.0100.0100.0000.0000.0000.000
110A110ALA0-0.067-0.02728.506-0.004-0.0040.0000.0000.0000.000
111A111LEU00.0230.02123.746-0.001-0.0010.0000.0000.0000.000
112A112GLY00.0330.00623.2000.0140.0140.0000.0000.0000.000
113A113ASP-1-0.900-0.93218.129-0.046-0.0460.0000.0000.0000.000
114A114MET0-0.0050.01217.9070.0520.0520.0000.0000.0000.000
115A115TYR0-0.033-0.07010.551-0.001-0.0010.0000.0000.0000.000
116A116GLU-1-0.910-0.93412.8100.9660.9660.0000.0000.0000.000
117A117GLY00.0160.02115.095-0.006-0.0060.0000.0000.0000.000
118A118GLN0-0.026-0.01918.200-0.034-0.0340.0000.0000.0000.000
119A119PRO00.0620.02519.1160.0070.0070.0000.0000.0000.000
120A120ILE0-0.045-0.00315.7590.0210.0210.0000.0000.0000.000
121A121LYS10.8300.91419.970-0.090-0.0900.0000.0000.0000.000
122A122VAL00.0350.02422.308-0.011-0.0110.0000.0000.0000.000
123A123THR0-0.020-0.00623.6470.0070.0070.0000.0000.0000.000
124A124PRO00.0400.03826.541-0.013-0.0130.0000.0000.0000.000
125A125PRO00.0540.01029.338-0.008-0.0080.0000.0000.0000.000
126A126THR0-0.0030.00730.5870.0070.0070.0000.0000.0000.000
127A127VAL0-0.0060.01432.2240.0050.0050.0000.0000.0000.000
128A128VAL0-0.0050.01134.840-0.004-0.0040.0000.0000.0000.000
129A129GLU-1-0.818-0.92337.460-0.027-0.0270.0000.0000.0000.000
130A130LEU0-0.0080.01039.5940.0030.0030.0000.0000.0000.000
131A131LYS10.8620.91543.176-0.002-0.0020.0000.0000.0000.000
132A132VAL00.0230.02146.7540.0030.0030.0000.0000.0000.000
133A133VAL0-0.050-0.03448.452-0.001-0.0010.0000.0000.0000.000
134A134ASP-1-0.900-0.93750.8440.0150.0150.0000.0000.0000.000
135A135THR00.025-0.00351.600-0.001-0.0010.0000.0000.0000.000
136A136PRO0-0.0160.00053.9500.0000.0000.0000.0000.0000.000
137A137PRO0-0.0130.00057.376-0.001-0.0010.0000.0000.0000.000
138A138GLY00.0220.00059.1620.0000.0000.0000.0000.0000.000
139A139VAL0-0.020-0.02258.6360.0000.0000.0000.0000.0000.000
140A140ARG10.8860.95259.507-0.007-0.0070.0000.0000.0000.000
141A141GLY00.0590.02756.4200.0010.0010.0000.0000.0000.000
142A142ASP-1-0.840-0.90053.0340.0070.0070.0000.0000.0000.000
143A143THR0-0.031-0.03455.0540.0000.0000.0000.0000.0000.000
144A144VAL0-0.024-0.02257.713-0.001-0.0010.0000.0000.0000.000
145A145SER0-0.047-0.02759.067-0.001-0.0010.0000.0000.0000.000
146A146GLY00.0310.04655.322-0.001-0.0010.0000.0000.0000.000
147A147GLY0-0.014-0.01754.0330.0000.0000.0000.0000.0000.000
148A148SER0-0.032-0.02850.820-0.002-0.0020.0000.0000.0000.000
149A149LYS10.8060.90652.2010.0010.0010.0000.0000.0000.000
150A150PRO00.0450.03250.023-0.001-0.0010.0000.0000.0000.000
151A151ALA0-0.023-0.00648.559-0.001-0.0010.0000.0000.0000.000
152A152THR00.0140.00947.5870.0020.0020.0000.0000.0000.000
153A153LEU0-0.006-0.01242.600-0.003-0.0030.0000.0000.0000.000
154A154GLU-1-0.806-0.90543.5920.0080.0080.0000.0000.0000.000
155A155THR0-0.030-0.02039.7070.0000.0000.0000.0000.0000.000
156A156GLY0-0.022-0.00342.2670.0050.0050.0000.0000.0000.000
157A157ALA00.0090.02040.8340.0010.0010.0000.0000.0000.000
158A158VAL0-0.031-0.02242.893-0.003-0.0030.0000.0000.0000.000
159A159VAL00.0130.01642.3600.0000.0000.0000.0000.0000.000
160A160GLN0-0.034-0.02945.2730.0010.0010.0000.0000.0000.000
161A161VAL00.005-0.00346.786-0.003-0.0030.0000.0000.0000.000
162A162PRO00.0170.00348.7860.0010.0010.0000.0000.0000.000
163A163LEU00.0000.00151.9890.0010.0010.0000.0000.0000.000
164A164PHE0-0.069-0.03451.3410.0010.0010.0000.0000.0000.000
165A165VAL0-0.0170.00249.853-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.799-0.89153.1980.0010.0010.0000.0000.0000.000
167A167PRO0-0.013-0.01353.1930.0000.0000.0000.0000.0000.000
168A168GLY0-0.0040.01152.393-0.001-0.0010.0000.0000.0000.000
169A169GLU-1-0.834-0.90350.604-0.012-0.0120.0000.0000.0000.000
170A170VAL0-0.009-0.01245.1300.0020.0020.0000.0000.0000.000
171A171ILE0-0.024-0.00544.269-0.004-0.0040.0000.0000.0000.000
172A172LYS10.8090.89241.1740.0320.0320.0000.0000.0000.000
173A173VAL00.011-0.00238.7940.0010.0010.0000.0000.0000.000
174A174ASP-1-0.792-0.89534.918-0.028-0.0280.0000.0000.0000.000
175A175THR0-0.056-0.05732.2810.0060.0060.0000.0000.0000.000
176A176ARG10.7840.88728.6060.0380.0380.0000.0000.0000.000
177A177THR0-0.073-0.06932.5420.0060.0060.0000.0000.0000.000
178A178GLY00.0380.02235.7880.0050.0050.0000.0000.0000.000
179A179GLU-1-0.909-0.92038.043-0.007-0.0070.0000.0000.0000.000
180A180TYR00.013-0.00540.676-0.004-0.0040.0000.0000.0000.000
181A181VAL0-0.010-0.01339.493-0.002-0.0020.0000.0000.0000.000
182A182GLY0-0.013-0.00842.723-0.004-0.0040.0000.0000.0000.000
183A183ARG10.8410.92545.3700.0190.0190.0000.0000.0000.000
184A184ALA0-0.0020.01844.850-0.005-0.0050.0000.0000.0000.000