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: 664QZ

Calculation Name: 4GHU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VCF0

Base Structure: X-ray

Registration Date: 2023-03-14

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1976894.671983
FMO2-HF: Nuclear repulsion 1900022.939967
FMO2-HF: Total energy -76871.732016
FMO2-MP2: Total energy -77091.573731


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:376:ASN)


Summations of interaction energy for fragment #1(A:376: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.
-15.61-9.8614.55-3.68-6.620.032
Interaction energy analysis for fragmet #1(A:376:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3A378GLY00.1110.0693.144-1.5700.8030.277-1.202-1.4490.004
4A379LEU0-0.018-0.0072.251-11.854-8.8934.266-2.342-4.8850.027
5A380LEU0-0.010-0.0034.128-2.812-2.3970.007-0.136-0.2860.001
6A381GLU-1-0.845-0.9246.2622.7992.7990.0000.0000.0000.000
7A382SER0-0.018-0.0206.487-0.888-0.8880.0000.0000.0000.000
8A383GLN0-0.041-0.0188.462-0.561-0.5610.0000.0000.0000.000
9A384LEU00.0360.02010.137-0.167-0.1670.0000.0000.0000.000
10A385SER00.0030.01811.536-0.121-0.1210.0000.0000.0000.000
11A386ARG10.9220.94612.630-0.380-0.3800.0000.0000.0000.000
12A387HIS0-0.032-0.02412.738-0.054-0.0540.0000.0000.0000.000
13A388ASP-1-0.885-0.93416.0420.3190.3190.0000.0000.0000.000
14A389GLN00.0250.02016.784-0.070-0.0700.0000.0000.0000.000
15A390MET0-0.054-0.02718.780-0.045-0.0450.0000.0000.0000.000
16A391LEU0-0.011-0.01319.619-0.034-0.0340.0000.0000.0000.000
17A392SER00.0320.01121.544-0.022-0.0220.0000.0000.0000.000
18A393VAL0-0.044-0.02323.328-0.018-0.0180.0000.0000.0000.000
19A394HIS0-0.030-0.03423.422-0.017-0.0170.0000.0000.0000.000
20A395ASP-1-0.909-0.94126.2850.0980.0980.0000.0000.0000.000
21A396ILE00.0160.01027.169-0.009-0.0090.0000.0000.0000.000
22A397ARG10.9040.95227.664-0.074-0.0740.0000.0000.0000.000
23A398LEU0-0.0030.00429.518-0.011-0.0110.0000.0000.0000.000
24A399ALA00.0550.03832.470-0.007-0.0070.0000.0000.0000.000
25A400ASP-1-0.910-0.96433.3020.0730.0730.0000.0000.0000.000
26A401MET0-0.108-0.06032.834-0.008-0.0080.0000.0000.0000.000
27A402ASP-1-0.846-0.91636.6800.0420.0420.0000.0000.0000.000
28A403LEU0-0.057-0.02338.347-0.004-0.0040.0000.0000.0000.000
29A404ARG10.9130.95638.408-0.036-0.0360.0000.0000.0000.000
30A405PHE0-0.016-0.00238.118-0.004-0.0040.0000.0000.0000.000
31A406GLN00.0270.01241.322-0.002-0.0020.0000.0000.0000.000
32A407VAL0-0.050-0.01744.229-0.002-0.0020.0000.0000.0000.000
33A408LEU0-0.042-0.01745.255-0.002-0.0020.0000.0000.0000.000
34A409GLU-1-0.932-0.97945.1990.0230.0230.0000.0000.0000.000
35A410THR0-0.088-0.05448.636-0.001-0.0010.0000.0000.0000.000
36A411ALA00.0030.02650.0460.0000.0000.0000.0000.0000.000
37A412SER0-0.059-0.04351.885-0.002-0.0020.0000.0000.0000.000
38A413TYR00.025-0.00250.6310.0010.0010.0000.0000.0000.000
39A414ASN00.0590.02557.2320.0000.0000.0000.0000.0000.000
40A415GLY00.0550.03459.8740.0000.0000.0000.0000.0000.000
41A416VAL0-0.065-0.02960.8200.0010.0010.0000.0000.0000.000
42A417LEU00.0120.03054.7380.0000.0000.0000.0000.0000.000
43A418ILE0-0.003-0.02457.1370.0000.0000.0000.0000.0000.000
44A419TRP00.0520.02851.8230.0000.0000.0000.0000.0000.000
45A420LYS10.9280.98053.969-0.027-0.0270.0000.0000.0000.000
46A421ILE0-0.0030.00552.3020.0020.0020.0000.0000.0000.000
47A422ARG10.9900.98749.768-0.037-0.0370.0000.0000.0000.000
48A423ASP-1-0.734-0.84549.1900.0490.0490.0000.0000.0000.000
49A424TYR0-0.007-0.03752.3080.0020.0020.0000.0000.0000.000
50A425LYS10.9090.94054.892-0.035-0.0350.0000.0000.0000.000
51A426ARG10.8080.88546.170-0.055-0.0550.0000.0000.0000.000
52A427ARG10.8680.91547.515-0.046-0.0460.0000.0000.0000.000
53A428LYS10.8330.91651.738-0.036-0.0360.0000.0000.0000.000
54A429GLN00.0370.00852.5590.0020.0020.0000.0000.0000.000
55A430GLU-1-0.849-0.90247.3610.0610.0610.0000.0000.0000.000
56A431ALA0-0.0090.00450.8920.0010.0010.0000.0000.0000.000
57A432VAL0-0.053-0.04053.3330.0000.0000.0000.0000.0000.000
58A433MET0-0.061-0.03251.2530.0000.0000.0000.0000.0000.000
59A434GLY00.006-0.00150.8450.0030.0030.0000.0000.0000.000
60A435LYS10.9070.97446.162-0.063-0.0630.0000.0000.0000.000
61A436THR00.000-0.02346.9290.0030.0030.0000.0000.0000.000
62A437LEU0-0.035-0.00548.949-0.003-0.0030.0000.0000.0000.000
63A438SER0-0.036-0.01250.860-0.003-0.0030.0000.0000.0000.000
64A439LEU0-0.0120.00149.1730.0030.0030.0000.0000.0000.000
65A440TYR00.064-0.00649.064-0.001-0.0010.0000.0000.0000.000
66A441SER0-0.053-0.02950.3120.0010.0010.0000.0000.0000.000
67A442GLN00.0280.00949.1290.0040.0040.0000.0000.0000.000
68A443PRO00.002-0.00448.017-0.001-0.0010.0000.0000.0000.000
69A444PHE0-0.045-0.01651.170-0.001-0.0010.0000.0000.0000.000
70A445TYR00.0310.00949.5070.0010.0010.0000.0000.0000.000
71A446THR0-0.034-0.02456.4030.0000.0000.0000.0000.0000.000
72A447GLY00.0640.03058.059-0.001-0.0010.0000.0000.0000.000
73A448TYR0-0.036-0.02654.5580.0010.0010.0000.0000.0000.000
74A449PHE0-0.014-0.00252.8710.0000.0000.0000.0000.0000.000
75A450GLY00.0140.02255.7770.0000.0000.0000.0000.0000.000
76A451TYR0-0.025-0.05455.8650.0010.0010.0000.0000.0000.000
77A452LYS10.8460.91847.208-0.029-0.0290.0000.0000.0000.000
78A453MET0-0.056-0.01254.1650.0000.0000.0000.0000.0000.000
79A454CYS00.0200.01051.1930.0000.0000.0000.0000.0000.000
80A455ALA00.0020.00854.245-0.001-0.0010.0000.0000.0000.000
81A456ARG10.9110.95652.094-0.041-0.0410.0000.0000.0000.000
82A457VAL0-0.006-0.00354.481-0.002-0.0020.0000.0000.0000.000
83A458TYR0-0.002-0.01154.6320.0030.0030.0000.0000.0000.000
84A459LEU0-0.002-0.00853.935-0.002-0.0020.0000.0000.0000.000
85A460ASN00.0430.02156.857-0.002-0.0020.0000.0000.0000.000
86A461GLY00.0470.02958.4610.0000.0000.0000.0000.0000.000
87A462ASP-1-0.808-0.92357.7220.0420.0420.0000.0000.0000.000
88A463GLY00.0010.00259.982-0.002-0.0020.0000.0000.0000.000
89A464MET0-0.004-0.01762.5550.0010.0010.0000.0000.0000.000
90A465GLY00.0470.03364.147-0.001-0.0010.0000.0000.0000.000
91A466LYS10.8130.92156.674-0.041-0.0410.0000.0000.0000.000
92A467GLY0-0.016-0.00760.891-0.001-0.0010.0000.0000.0000.000
93A468THR0-0.0020.01162.240-0.001-0.0010.0000.0000.0000.000
94A469HIS0-0.052-0.02563.937-0.002-0.0020.0000.0000.0000.000
95A470LEU0-0.0080.02059.2440.0020.0020.0000.0000.0000.000
96A471SER0-0.044-0.04159.975-0.001-0.0010.0000.0000.0000.000
97A472LEU0-0.027-0.00758.9140.0020.0020.0000.0000.0000.000
98A473PHE0-0.022-0.01157.944-0.001-0.0010.0000.0000.0000.000
99A474PHE00.0320.00858.2690.0010.0010.0000.0000.0000.000
100A475VAL0-0.002-0.01453.5450.0010.0010.0000.0000.0000.000
101A476ILE00.0080.02455.734-0.001-0.0010.0000.0000.0000.000
102A477MET00.003-0.01548.6320.0020.0020.0000.0000.0000.000
103A478ARG10.8250.90045.011-0.038-0.0380.0000.0000.0000.000
104A479GLY00.0410.01849.7830.0010.0010.0000.0000.0000.000
105A480GLU-1-0.839-0.91347.2260.0250.0250.0000.0000.0000.000
106A481TYR00.0360.02150.439-0.002-0.0020.0000.0000.0000.000
107A482ASP-1-0.785-0.89353.8210.0210.0210.0000.0000.0000.000
108A483ALA0-0.042-0.02054.9750.0000.0000.0000.0000.0000.000
109A484LEU0-0.0120.00256.405-0.001-0.0010.0000.0000.0000.000
110A485LEU0-0.0340.00357.346-0.001-0.0010.0000.0000.0000.000
111A486PRO00.0100.00560.8760.0000.0000.0000.0000.0000.000
112A487TRP0-0.020-0.00357.2520.0020.0020.0000.0000.0000.000
113A488PRO00.0240.01262.953-0.001-0.0010.0000.0000.0000.000
114A489PHE0-0.021-0.01360.911-0.001-0.0010.0000.0000.0000.000
115A490LYS10.8860.91463.218-0.012-0.0120.0000.0000.0000.000
116A491GLN0-0.025-0.00464.000-0.001-0.0010.0000.0000.0000.000
117A492LYS10.9700.98266.235-0.015-0.0150.0000.0000.0000.000
118A493VAL00.0270.02262.9500.0000.0000.0000.0000.0000.000
119A494THR0-0.043-0.03065.307-0.001-0.0010.0000.0000.0000.000
120A495LEU0-0.0090.00761.7340.0000.0000.0000.0000.0000.000
121A496MET00.015-0.01763.423-0.001-0.0010.0000.0000.0000.000
122A497LEU00.0010.01161.6440.0010.0010.0000.0000.0000.000
123A498MET0-0.013-0.01162.960-0.001-0.0010.0000.0000.0000.000
124A499ASP-1-0.756-0.84564.6890.0210.0210.0000.0000.0000.000
125A500GLN0-0.105-0.08460.552-0.001-0.0010.0000.0000.0000.000
126A501GLY00.0290.01565.6550.0000.0000.0000.0000.0000.000
127A502SER0-0.026-0.02969.0610.0000.0000.0000.0000.0000.000
128A503SER00.000-0.00271.979-0.001-0.0010.0000.0000.0000.000
129A504ARG10.8570.94165.945-0.018-0.0180.0000.0000.0000.000
130A505ARG10.9770.99671.239-0.018-0.0180.0000.0000.0000.000
131A506HIS00.0160.00267.7350.0020.0020.0000.0000.0000.000
132A507LEU00.0180.03067.431-0.001-0.0010.0000.0000.0000.000
133A508GLY0-0.007-0.03467.3900.0000.0000.0000.0000.0000.000
134A509ASP-1-0.860-0.90368.1360.0200.0200.0000.0000.0000.000
135A510ALA0-0.085-0.05868.1720.0000.0000.0000.0000.0000.000
136A511PHE00.0300.02563.4300.0000.0000.0000.0000.0000.000
137A512LYS10.9070.93468.863-0.015-0.0150.0000.0000.0000.000
138A513PRO0-0.051-0.01565.0670.0000.0000.0000.0000.0000.000
139A514ASP-1-0.775-0.87767.0320.0190.0190.0000.0000.0000.000
140A515PRO0-0.018-0.02466.5230.0010.0010.0000.0000.0000.000
141A516ASN0-0.040-0.02966.6960.0000.0000.0000.0000.0000.000
142A517SER00.0190.03763.4630.0010.0010.0000.0000.0000.000
143A518SER00.018-0.00659.2350.0000.0000.0000.0000.0000.000
144A519SER0-0.046-0.03658.9430.0010.0010.0000.0000.0000.000
145A520PHE0-0.025-0.02059.3450.0000.0000.0000.0000.0000.000
146A521LYS10.9410.99454.727-0.030-0.0300.0000.0000.0000.000
147A522LYS10.8810.94152.988-0.022-0.0220.0000.0000.0000.000
148A523PRO0-0.0080.01152.9550.0010.0010.0000.0000.0000.000
149A524THR00.0020.00851.965-0.001-0.0010.0000.0000.0000.000
150A525GLY00.0520.02648.7250.0010.0010.0000.0000.0000.000
151A526GLU-1-0.842-0.92744.1910.0430.0430.0000.0000.0000.000
152A527MET0-0.0140.00248.207-0.002-0.0020.0000.0000.0000.000
153A528ASN0-0.058-0.02651.6130.0020.0020.0000.0000.0000.000
154A529ILE00.005-0.00254.6830.0010.0010.0000.0000.0000.000
155A530ALA00.0030.01055.834-0.002-0.0020.0000.0000.0000.000
156A531SER00.0080.00557.6460.0000.0000.0000.0000.0000.000
157A532GLY00.0230.00661.4070.0000.0000.0000.0000.0000.000
158A533CYS00.0070.02063.365-0.001-0.0010.0000.0000.0000.000
159A534PRO00.043-0.00563.0130.0010.0010.0000.0000.0000.000
160A535VAL00.0250.03564.0980.0010.0010.0000.0000.0000.000
161A536PHE0-0.052-0.00863.990-0.001-0.0010.0000.0000.0000.000
162A537VAL00.0390.02064.416-0.001-0.0010.0000.0000.0000.000
163A538ALA00.0540.03565.5440.0010.0010.0000.0000.0000.000
164A539GLN00.010-0.01761.1530.0000.0000.0000.0000.0000.000
165A540THR00.0140.01165.1060.0000.0000.0000.0000.0000.000
166A541VAL00.0290.01468.0890.0000.0000.0000.0000.0000.000
167A542LEU0-0.023-0.00861.284-0.001-0.0010.0000.0000.0000.000
168A543GLU-1-0.831-0.89760.9320.0350.0350.0000.0000.0000.000
169A544ASN0-0.075-0.03064.8250.0000.0000.0000.0000.0000.000
170A545GLY00.0470.03467.326-0.001-0.0010.0000.0000.0000.000
171A546THR0-0.054-0.06066.6500.0010.0010.0000.0000.0000.000
172A547TYR0-0.019-0.01464.4660.0000.0000.0000.0000.0000.000
173A548ILE0-0.0380.00759.9090.0010.0010.0000.0000.0000.000
174A549LYS10.8610.91360.865-0.024-0.0240.0000.0000.0000.000
175A550ASP-1-0.807-0.88957.5460.0260.0260.0000.0000.0000.000
176A551ASP-1-0.813-0.88855.2410.0390.0390.0000.0000.0000.000
177A552THR0-0.058-0.03655.4380.0020.0020.0000.0000.0000.000
178A553ILE00.0390.02656.883-0.001-0.0010.0000.0000.0000.000
179A554PHE00.020-0.01257.4070.0010.0010.0000.0000.0000.000
180A555ILE00.0310.03057.062-0.001-0.0010.0000.0000.0000.000
181A556LYS10.9240.96059.157-0.018-0.0180.0000.0000.0000.000
182A557VAL0-0.0120.00159.7000.0000.0000.0000.0000.0000.000
183A558ILE0-0.029-0.01361.839-0.001-0.0010.0000.0000.0000.000
184A559VAL0-0.004-0.00560.8710.0000.0000.0000.0000.0000.000
185A560ASP-1-0.880-0.93263.9930.0120.0120.0000.0000.0000.000
186A561THR00.017-0.00362.9660.0000.0000.0000.0000.0000.000
187A562SER0-0.070-0.04166.020-0.001-0.0010.0000.0000.0000.000
188A563ASP-1-0.842-0.89968.4010.0120.0120.0000.0000.0000.000
189A564LEU0-0.0260.00263.7590.0000.0000.0000.0000.0000.000
190A565PRO00.0100.00864.1380.0000.0000.0000.0000.0000.000