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: Z6R3N

Calculation Name: 4UID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UID

Chain ID: A

ChEMBL ID:

UniProt ID: O68840

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1706040.224786
FMO2-HF: Nuclear repulsion 1634157.209566
FMO2-HF: Total energy -71883.01522
FMO2-MP2: Total energy -72097.72551


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:447:ALA)


Summations of interaction energy for fragment #1(A:447:ALA)
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.
-2.4481.6286.495-4.522-6.05-0.026
Interaction energy analysis for fragmet #1(A:447:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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].
3A449VAL0-0.033-0.0173.9960.3281.854-0.002-0.858-0.6640.003
4A450SER0-0.004-0.0026.1980.1710.1710.0000.0000.0000.000
5A451GLU-1-0.929-0.9758.488-0.113-0.1130.0000.0000.0000.000
6A452LEU0-0.023-0.01810.357-0.023-0.0230.0000.0000.0000.000
7A453LYS10.9270.98812.9050.2400.2400.0000.0000.0000.000
8A454LEU00.0470.03616.3710.0160.0160.0000.0000.0000.000
9A455THR0-0.046-0.04518.2590.0020.0020.0000.0000.0000.000
10A456LYS10.9420.97520.6800.0520.0520.0000.0000.0000.000
11A457ASP-1-0.911-0.97023.301-0.035-0.0350.0000.0000.0000.000
12A458ASN0-0.029-0.01220.327-0.003-0.0030.0000.0000.0000.000
13A459LYS10.9380.98921.5030.0470.0470.0000.0000.0000.000
14A460GLU-1-0.892-0.97119.678-0.213-0.2130.0000.0000.0000.000
15A461VAL0-0.037-0.01522.1040.0110.0110.0000.0000.0000.000
16A462VAL0-0.0050.00623.752-0.016-0.0160.0000.0000.0000.000
17A463THR0-0.059-0.02726.305-0.002-0.0020.0000.0000.0000.000
18A464LEU00.0470.01625.3500.0060.0060.0000.0000.0000.000
19A465TYR0-0.052-0.00728.807-0.003-0.0030.0000.0000.0000.000
20A466ALA00.044-0.00130.7680.0000.0000.0000.0000.0000.000
21A467ASN0-0.038-0.00832.1760.0000.0000.0000.0000.0000.000
22A468GLY00.0370.01629.5800.0050.0050.0000.0000.0000.000
23A469ASN0-0.046-0.01029.5720.0010.0010.0000.0000.0000.000
24A470ALA00.0380.00727.064-0.007-0.0070.0000.0000.0000.000
25A471PHE0-0.039-0.01628.6280.0080.0080.0000.0000.0000.000
26A472ASP-1-0.757-0.88027.075-0.091-0.0910.0000.0000.0000.000
27A473LYS10.8550.90422.9030.1470.1470.0000.0000.0000.000
28A474ASP-1-0.935-0.95229.057-0.083-0.0830.0000.0000.0000.000
29A475GLY0-0.040-0.00731.6480.0040.0040.0000.0000.0000.000
30A476ASN0-0.031-0.01532.5530.0100.0100.0000.0000.0000.000
31A477GLN0-0.036-0.02231.452-0.004-0.0040.0000.0000.0000.000
32A478ILE0-0.0160.00125.9280.0050.0050.0000.0000.0000.000
33A479SER0-0.025-0.02529.9960.0000.0000.0000.0000.0000.000
34A480SER00.0050.01328.5660.0060.0060.0000.0000.0000.000
35A481GLY00.0270.01325.581-0.007-0.0070.0000.0000.0000.000
36A482THR0-0.009-0.00223.177-0.002-0.0020.0000.0000.0000.000
37A483LEU0-0.027-0.01923.093-0.004-0.0040.0000.0000.0000.000
38A484THR00.0380.01417.4330.0130.0130.0000.0000.0000.000
39A485LEU00.0210.01915.510-0.025-0.0250.0000.0000.0000.000
40A486THR0-0.051-0.01713.3780.0440.0440.0000.0000.0000.000
41A487ALA00.034-0.0059.216-0.057-0.0570.0000.0000.0000.000
42A488LYS10.9541.0008.2740.2650.2650.0000.0000.0000.000
43A489PHE00.019-0.0032.835-0.558-0.1350.102-0.106-0.4200.000
44A490LYS10.9370.9823.9071.0981.3370.000-0.058-0.1820.000
45A491ASP-1-0.759-0.8952.003-2.517-1.7905.239-3.609-2.357-0.027
46A492GLN0-0.009-0.0163.0390.122-0.4350.0080.891-0.342-0.001
47A493TYR0-0.067-0.0274.834-0.058-0.012-0.001-0.007-0.0370.000
48A494GLY0-0.0150.0066.1730.0310.0310.0000.0000.0000.000
49A495ASN0-0.043-0.0256.732-0.111-0.1110.0000.0000.0000.000
50A496GLU-1-0.955-0.9946.514-0.125-0.1250.0000.0000.0000.000
51A497LEU0-0.025-0.0062.553-0.284-0.1070.906-0.290-0.793-0.001
52A498THR00.0110.0056.948-0.130-0.1300.0000.0000.0000.000
53A499GLY0-0.029-0.02310.3890.1090.1090.0000.0000.0000.000
54A500LYS10.8790.9546.442-1.088-1.0880.0000.0000.0000.000
55A501VAL00.002-0.01210.636-0.103-0.1030.0000.0000.0000.000
56A502ALA00.0000.00411.9770.0360.0360.0000.0000.0000.000
57A503GLY00.0090.00012.645-0.019-0.0190.0000.0000.0000.000
58A504THR0-0.080-0.04013.056-0.009-0.0090.0000.0000.0000.000
59A505ASP-1-0.864-0.9237.7590.7710.7710.0000.0000.0000.000
60A506TYR0-0.039-0.0237.2170.0130.0130.0000.0000.0000.000
61A507THR00.0110.0249.151-0.011-0.0110.0000.0000.0000.000
62A508PHE0-0.047-0.03311.490-0.100-0.1000.0000.0000.0000.000
63A509GLU-1-0.893-0.95114.056-0.061-0.0610.0000.0000.0000.000
64A510SER0-0.045-0.03716.535-0.036-0.0360.0000.0000.0000.000
65A511LEU0-0.026-0.01916.9920.0090.0090.0000.0000.0000.000
66A512ASN00.0100.00020.681-0.012-0.0120.0000.0000.0000.000
67A513PRO00.0650.02823.7590.0030.0030.0000.0000.0000.000
68A514GLU-1-0.929-0.95825.066-0.062-0.0620.0000.0000.0000.000
69A515VAL0-0.074-0.02226.4120.0030.0030.0000.0000.0000.000
70A516LEU00.003-0.01921.8820.0020.0020.0000.0000.0000.000
71A517VAL00.0210.03223.828-0.005-0.0050.0000.0000.0000.000
72A518VAL0-0.019-0.02017.504-0.004-0.0040.0000.0000.0000.000
73A519ALA0-0.0050.01119.9370.0030.0030.0000.0000.0000.000
74A520PRO00.0570.02216.457-0.011-0.0110.0000.0000.0000.000
75A521ASP-1-0.837-0.94814.9310.0300.0300.0000.0000.0000.000
76A522GLY0-0.0180.00016.077-0.003-0.0030.0000.0000.0000.000
77A523SER00.0140.00616.716-0.022-0.0220.0000.0000.0000.000
78A524VAL0-0.051-0.01620.101-0.010-0.0100.0000.0000.0000.000
79A525THR0-0.005-0.00822.5440.0100.0100.0000.0000.0000.000
80A526PRO0-0.027-0.00826.185-0.005-0.0050.0000.0000.0000.000
81A527ILE0-0.0060.01927.8180.0090.0090.0000.0000.0000.000
82A528VAL0-0.015-0.00830.5690.0050.0050.0000.0000.0000.000
83A529PRO0-0.052-0.04430.664-0.006-0.0060.0000.0000.0000.000
84A530GLY00.0380.03030.1880.0030.0030.0000.0000.0000.000
85A531THR0-0.054-0.03024.837-0.005-0.0050.0000.0000.0000.000
86A532ALA00.0150.01122.8820.0040.0040.0000.0000.0000.000
87A533LEU0-0.033-0.01619.170-0.020-0.0200.0000.0000.0000.000
88A534VAL00.0330.01716.0400.0160.0160.0000.0000.0000.000
89A535LYS10.9510.96712.1320.3450.3450.0000.0000.0000.000
90A536VAL00.0150.0288.4450.0570.0570.0000.0000.0000.000
91A537LYS10.9470.9528.323-0.117-0.1170.0000.0000.0000.000
92A538TYR00.0590.0263.620-0.1730.3710.014-0.107-0.4510.000
93A539GLY0-0.0020.0054.534-0.306-0.249-0.001-0.007-0.0490.000
94A540GLU-1-0.919-0.9715.785-0.280-0.2800.0000.0000.0000.000
95A541VAL0-0.054-0.0072.625-0.963-0.0690.230-0.371-0.7550.000
96A542THR0-0.025-0.0195.6430.5380.5380.0000.0000.0000.000
97A543LYS10.9450.9798.4690.6490.6490.0000.0000.0000.000
98A544THR00.0160.00510.6700.0990.0990.0000.0000.0000.000
99A545ILE0-0.035-0.01114.459-0.037-0.0370.0000.0000.0000.000
100A546PRO00.0170.00917.0810.0270.0270.0000.0000.0000.000
101A547VAL00.0210.01720.271-0.001-0.0010.0000.0000.0000.000
102A548THR0-0.023-0.00822.7260.0070.0070.0000.0000.0000.000
103A549VAL00.0120.03326.4930.0040.0040.0000.0000.0000.000
104A550LYS10.9230.95428.9210.1020.1020.0000.0000.0000.000
105A551ALA00.0740.02132.3420.0050.0050.0000.0000.0000.000
106A552ASN00.0440.02535.369-0.004-0.0040.0000.0000.0000.000
107A553PRO0-0.0010.00536.6510.0000.0000.0000.0000.0000.000
108A554VAL0-0.0190.00239.7870.0030.0030.0000.0000.0000.000
109A555LEU0-0.025-0.00543.334-0.001-0.0010.0000.0000.0000.000
110A556GLU-1-0.947-0.97045.131-0.052-0.0520.0000.0000.0000.000
111A557THR0-0.071-0.04747.1660.0010.0010.0000.0000.0000.000
112A558ILE00.0060.00749.4150.0000.0000.0000.0000.0000.000
113A559ALA0-0.022-0.01550.6230.0000.0000.0000.0000.0000.000
114A560VAL0-0.007-0.01552.4990.0010.0010.0000.0000.0000.000
115A561ASP-1-0.892-0.94655.921-0.031-0.0310.0000.0000.0000.000
116A562SER0-0.018-0.00756.8780.0010.0010.0000.0000.0000.000
117A563THR00.0210.00760.050-0.001-0.0010.0000.0000.0000.000
118A564GLY0-0.018-0.01362.5200.0000.0000.0000.0000.0000.000
119A565VAL0-0.045-0.00664.7990.0000.0000.0000.0000.0000.000
120A566SER00.0060.00167.2470.0010.0010.0000.0000.0000.000
121A567VAL0-0.0210.00369.8970.0000.0000.0000.0000.0000.000
122A568ALA00.0260.02871.7170.0000.0000.0000.0000.0000.000
123A569LYS10.9750.96174.5950.0130.0130.0000.0000.0000.000
124A570GLY0-0.039-0.01876.0770.0000.0000.0000.0000.0000.000
125A571GLN0-0.0310.00772.1530.0000.0000.0000.0000.0000.000
126A572LYS10.9770.98765.5980.0160.0160.0000.0000.0000.000
127A573ALA0-0.019-0.00966.3840.0000.0000.0000.0000.0000.000
128A574THR0-0.003-0.00860.4060.0000.0000.0000.0000.0000.000
129A575PHE00.0030.01858.7250.0000.0000.0000.0000.0000.000
130A576LYS10.9490.97554.1990.0270.0270.0000.0000.0000.000
131A577VAL00.0180.01253.465-0.001-0.0010.0000.0000.0000.000
132A578THR0-0.018-0.01648.0040.0000.0000.0000.0000.0000.000
133A579LEU0-0.0230.00848.067-0.001-0.0010.0000.0000.0000.000
134A580LYS10.9550.96844.9960.0470.0470.0000.0000.0000.000
135A581ASP-1-0.762-0.87740.233-0.058-0.0580.0000.0000.0000.000
136A582GLN00.0800.02239.3780.0020.0020.0000.0000.0000.000
137A583TYR0-0.117-0.08636.174-0.006-0.0060.0000.0000.0000.000
138A584GLY0-0.0110.01339.877-0.002-0.0020.0000.0000.0000.000
139A585ASN0-0.028-0.01837.4580.0010.0010.0000.0000.0000.000
140A586LYS10.9040.94941.4330.0450.0450.0000.0000.0000.000
141A587PHE00.0280.02142.022-0.001-0.0010.0000.0000.0000.000
142A588THR0-0.011-0.01343.6960.0010.0010.0000.0000.0000.000
143A589GLY00.0220.01245.582-0.001-0.0010.0000.0000.0000.000
144A590ASN0-0.018-0.00348.4740.0010.0010.0000.0000.0000.000
145A591VAL00.0060.01052.128-0.001-0.0010.0000.0000.0000.000
146A592ASN0-0.039-0.01955.0940.0030.0030.0000.0000.0000.000
147A593VAL00.0100.01858.846-0.001-0.0010.0000.0000.0000.000
148A594THR0-0.029-0.01261.7090.0010.0010.0000.0000.0000.000
149A595SER0-0.024-0.04065.317-0.001-0.0010.0000.0000.0000.000
150A596ASP-1-0.870-0.93068.348-0.020-0.0200.0000.0000.0000.000
151A597LYS10.9250.96370.8360.0170.0170.0000.0000.0000.000
152A598THR00.0090.01071.1110.0000.0000.0000.0000.0000.000
153A599GLU-1-0.890-0.95473.593-0.014-0.0140.0000.0000.0000.000
154A600THR0-0.052-0.01074.6240.0000.0000.0000.0000.0000.000
155A601ALA00.0330.00570.9520.0000.0000.0000.0000.0000.000
156A602THR00.0270.04969.8900.0000.0000.0000.0000.0000.000
157A603VAL0-0.008-0.00363.6880.0000.0000.0000.0000.0000.000
158A604SER0-0.016-0.00963.5440.0000.0000.0000.0000.0000.000
159A605VAL00.0400.02357.104-0.001-0.0010.0000.0000.0000.000
160A606SER00.0170.01855.7990.0010.0010.0000.0000.0000.000
161A607ASN00.011-0.03052.702-0.002-0.0020.0000.0000.0000.000
162A608SER00.0320.02455.1360.0000.0000.0000.0000.0000.000
163A609GLY00.0050.01855.3330.0000.0000.0000.0000.0000.000
164A610ILE0-0.018-0.00851.349-0.001-0.0010.0000.0000.0000.000
165A611GLY00.0230.01348.3140.0010.0010.0000.0000.0000.000
166A612GLN00.0070.00547.555-0.001-0.0010.0000.0000.0000.000
167A613SER00.013-0.00145.1910.0000.0000.0000.0000.0000.000
168A614GLU-1-0.923-0.96747.504-0.037-0.0370.0000.0000.0000.000
169A615TYR0-0.0270.00050.4800.0020.0020.0000.0000.0000.000
170A616THR0-0.014-0.02854.067-0.001-0.0010.0000.0000.0000.000
171A617VAL0-0.020-0.00557.3750.0010.0010.0000.0000.0000.000
172A618THR0-0.007-0.00360.4060.0000.0000.0000.0000.0000.000
173A619VAL0-0.010-0.01763.8780.0000.0000.0000.0000.0000.000
174A620ASN0-0.011-0.03266.9870.0000.0000.0000.0000.0000.000
175A621GLY00.0460.01170.3730.0000.0000.0000.0000.0000.000
176A622VAL0-0.053-0.01273.4170.0010.0010.0000.0000.0000.000
177A623ALA0-0.039-0.03476.0940.0010.0010.0000.0000.0000.000
178A624GLU-1-0.923-0.96077.502-0.015-0.0150.0000.0000.0000.000
179A625GLY00.0000.01078.0450.0000.0000.0000.0000.0000.000
180A626SER0-0.042-0.02273.8370.0000.0000.0000.0000.0000.000
181A627THR00.007-0.00670.6890.0000.0000.0000.0000.0000.000
182A628THR00.0190.01066.395-0.001-0.0010.0000.0000.0000.000
183A629ILE0-0.0100.01363.2390.0010.0010.0000.0000.0000.000
184A630THR0-0.007-0.00262.665-0.001-0.0010.0000.0000.0000.000
185A631ILE00.0090.00156.6740.0010.0010.0000.0000.0000.000
186A632LYS10.9660.97357.5520.0220.0220.0000.0000.0000.000
187A633SER00.009-0.01751.9940.0000.0000.0000.0000.0000.000
188A634GLY00.0190.01251.709-0.001-0.0010.0000.0000.0000.000
189A635THR0-0.024-0.01452.0530.0010.0010.0000.0000.0000.000
190A636LYS10.9370.98249.5830.0430.0430.0000.0000.0000.000
191A637GLU-1-0.880-0.96954.683-0.025-0.0250.0000.0000.0000.000
192A638VAL0-0.0150.01456.216-0.001-0.0010.0000.0000.0000.000
193A639LYS10.9120.95358.9500.0270.0270.0000.0000.0000.000
194A640VAL00.0000.00061.370-0.001-0.0010.0000.0000.0000.000
195A641PRO00.0340.04064.1120.0010.0010.0000.0000.0000.000
196A642VAL00.003-0.01767.1790.0000.0000.0000.0000.0000.000
197A643ASN0-0.013-0.01969.6980.0010.0010.0000.0000.0000.000
198A644VAL0-0.023-0.00472.9640.0000.0000.0000.0000.0000.000
199A645VAL00.0240.01175.0050.0000.0000.0000.0000.0000.000
200A646ALA00.0410.01977.3910.0000.0000.0000.0000.0000.000