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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: 1JQYZ

Calculation Name: 4GHU-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 191
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1978207.829059
FMO2-HF: Nuclear repulsion 1901318.009772
FMO2-HF: Total energy -76889.819286
FMO2-MP2: Total energy -77109.714928


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.
-17.247-11.7844.606-3.461-6.6080.023
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 : 0.011 / q_NPA : -0.010
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].
3A378GLY 00.0960.0733.017-3.808-1.4100.193-1.115-1.4760.003
4A379LEU 0-0.010-0.0132.355-10.867-8.5174.402-2.126-4.6260.020
5A380LEU 0-0.018-0.0123.558-2.800-2.0850.011-0.220-0.5060.000
6A381GLU -1-0.915-0.9616.0952.6672.6670.0000.0000.0000.000
7A382SER 0-0.016-0.0096.955-0.937-0.9370.0000.0000.0000.000
8A383GLN 0-0.052-0.0338.071-0.631-0.6310.0000.0000.0000.000
9A384LEU 00.0420.02510.124-0.199-0.1990.0000.0000.0000.000
10A385SER 00.0150.02211.626-0.218-0.2180.0000.0000.0000.000
11A386ARG 10.9270.96312.493-0.460-0.4600.0000.0000.0000.000
12A387HIS 0-0.048-0.03113.362-0.069-0.0690.0000.0000.0000.000
13A388ASP -1-0.900-0.93516.0340.5010.5010.0000.0000.0000.000
14A389GLN 00.0180.00116.887-0.056-0.0560.0000.0000.0000.000
15A390MET 0-0.058-0.03018.926-0.065-0.0650.0000.0000.0000.000
16A391LEU 0-0.004-0.01219.166-0.046-0.0460.0000.0000.0000.000
17A392SER 00.0400.03021.971-0.029-0.0290.0000.0000.0000.000
18A393VAL 0-0.048-0.02323.461-0.031-0.0310.0000.0000.0000.000
19A394HIS 0-0.033-0.03923.721-0.017-0.0170.0000.0000.0000.000
20A395ASP -1-0.887-0.93426.2500.1900.1900.0000.0000.0000.000
21A396ILE 00.0040.01027.615-0.012-0.0120.0000.0000.0000.000
22A397ARG 10.8930.94327.737-0.113-0.1130.0000.0000.0000.000
23A398LEU 00.000-0.00929.125-0.016-0.0160.0000.0000.0000.000
24A399ALA 00.0660.04932.284-0.010-0.0100.0000.0000.0000.000
25A400ASP -1-0.909-0.96334.1240.1220.1220.0000.0000.0000.000
26A401MET 0-0.121-0.07433.117-0.014-0.0140.0000.0000.0000.000
27A402ASP -1-0.859-0.91036.2930.0940.0940.0000.0000.0000.000
28A403LEU 0-0.044-0.02538.094-0.007-0.0070.0000.0000.0000.000
29A404ARG 10.9080.95338.152-0.065-0.0650.0000.0000.0000.000
30A405PHE 00.0320.00938.148-0.008-0.0080.0000.0000.0000.000
31A406GLN 00.0250.02642.523-0.004-0.0040.0000.0000.0000.000
32A407VAL 0-0.037-0.01644.527-0.004-0.0040.0000.0000.0000.000
33A408LEU 0-0.045-0.02644.168-0.004-0.0040.0000.0000.0000.000
34A409GLU -1-0.956-0.97645.1190.0520.0520.0000.0000.0000.000
35A410THR 0-0.125-0.06048.519-0.002-0.0020.0000.0000.0000.000
36A411ALA 00.0130.01950.2050.0000.0000.0000.0000.0000.000
37A412SER 0-0.057-0.05151.988-0.003-0.0030.0000.0000.0000.000
38A413TYR 00.029-0.00950.6020.0010.0010.0000.0000.0000.000
39A414ASN 00.0480.02657.257-0.001-0.0010.0000.0000.0000.000
40A415GLY 00.0510.02459.773-0.001-0.0010.0000.0000.0000.000
41A416VAL 0-0.045-0.01160.5200.0010.0010.0000.0000.0000.000
42A417LEU 00.0110.04054.8970.0000.0000.0000.0000.0000.000
43A418ILE 0-0.015-0.02557.360-0.001-0.0010.0000.0000.0000.000
44A419TRP 00.0420.01451.9650.0000.0000.0000.0000.0000.000
45A420LYS 10.9470.98253.239-0.061-0.0610.0000.0000.0000.000
46A421ILE 0-0.0080.00053.0600.0030.0030.0000.0000.0000.000
47A422ARG 11.0070.98950.304-0.077-0.0770.0000.0000.0000.000
48A423ASP -1-0.821-0.88549.1340.0940.0940.0000.0000.0000.000
49A424TYR 0-0.037-0.05152.5960.0020.0020.0000.0000.0000.000
50A425LYS 10.9410.96755.078-0.072-0.0720.0000.0000.0000.000
51A426ARG 10.8990.93046.740-0.105-0.1050.0000.0000.0000.000
52A427ARG 10.9530.97946.987-0.090-0.0900.0000.0000.0000.000
53A428LYS 10.8680.94652.133-0.069-0.0690.0000.0000.0000.000
54A429GLN 00.026-0.00953.0250.0030.0030.0000.0000.0000.000
55A430GLU -1-0.876-0.93347.3780.1140.1140.0000.0000.0000.000
56A431ALA 00.0020.01551.0650.0020.0020.0000.0000.0000.000
57A432VAL 0-0.061-0.03053.437-0.001-0.0010.0000.0000.0000.000
58A433MET 0-0.077-0.03751.1820.0000.0000.0000.0000.0000.000
59A434GLY 0-0.005-0.00351.4870.0030.0030.0000.0000.0000.000
60A435LYS 10.8900.96246.473-0.116-0.1160.0000.0000.0000.000
61A436THR 00.016-0.00347.2430.0040.0040.0000.0000.0000.000
62A437LEU 0-0.034-0.00449.052-0.005-0.0050.0000.0000.0000.000
63A438SER 0-0.025-0.00951.040-0.005-0.0050.0000.0000.0000.000
64A439LEU 0-0.020-0.01149.3540.0050.0050.0000.0000.0000.000
65A440TYR 00.0610.00648.999-0.003-0.0030.0000.0000.0000.000
66A441SER 0-0.048-0.02350.2510.0020.0020.0000.0000.0000.000
67A442GLN 00.0310.01849.2390.0050.0050.0000.0000.0000.000
68A443PRO 0-0.009-0.01748.545-0.002-0.0020.0000.0000.0000.000
69A444PHE 0-0.037-0.00851.599-0.001-0.0010.0000.0000.0000.000
70A445TYR 00.0390.01049.6880.0010.0010.0000.0000.0000.000
71A446THR 0-0.002-0.00956.4510.0000.0000.0000.0000.0000.000
72A447GLY 00.0660.02358.048-0.002-0.0020.0000.0000.0000.000
73A448TYR 0-0.039-0.01954.4400.0010.0010.0000.0000.0000.000
74A449PHE 0-0.0100.00252.1360.0010.0010.0000.0000.0000.000
75A450GLY 0-0.0090.01055.578-0.001-0.0010.0000.0000.0000.000
76A451TYR 0-0.001-0.04855.9120.0010.0010.0000.0000.0000.000
77A452LYS 10.9610.98847.358-0.052-0.0520.0000.0000.0000.000
78A453MET 0-0.063-0.00954.3590.0000.0000.0000.0000.0000.000
79A454CYS 0-0.0020.00751.3340.0010.0010.0000.0000.0000.000
80A455ALA 00.0050.01954.482-0.002-0.0020.0000.0000.0000.000
81A456ARG 10.9360.96751.274-0.071-0.0710.0000.0000.0000.000
82A457VAL 0-0.0060.00254.674-0.003-0.0030.0000.0000.0000.000
83A458TYR 00.0450.01854.9590.0040.0040.0000.0000.0000.000
84A459LEU 0-0.001-0.00554.148-0.003-0.0030.0000.0000.0000.000
85A460ASN 00.0410.01357.278-0.003-0.0030.0000.0000.0000.000
86A461GLY 00.0340.03658.943-0.001-0.0010.0000.0000.0000.000
87A462ASP -1-0.922-1.00158.5440.0670.0670.0000.0000.0000.000
88A463GLY 00.0260.01860.307-0.003-0.0030.0000.0000.0000.000
89A464MET 0-0.015-0.02362.7520.0010.0010.0000.0000.0000.000
90A465GLY 00.0390.02764.432-0.001-0.0010.0000.0000.0000.000
91A466LYS 10.9010.96057.595-0.071-0.0710.0000.0000.0000.000
92A467GLY 0-0.040-0.01961.413-0.001-0.0010.0000.0000.0000.000
93A468THR 00.0300.02562.670-0.001-0.0010.0000.0000.0000.000
94A469HIS 0-0.042-0.03364.228-0.003-0.0030.0000.0000.0000.000
95A470LEU 0-0.0080.02459.8560.0030.0030.0000.0000.0000.000
96A471SER 0-0.050-0.04360.165-0.002-0.0020.0000.0000.0000.000
97A472LEU 0-0.017-0.01359.2090.0030.0030.0000.0000.0000.000
98A473PHE 0-0.027-0.00758.144-0.002-0.0020.0000.0000.0000.000
99A474PHE 00.0390.00258.5960.0010.0010.0000.0000.0000.000
100A475VAL 00.013-0.00853.4680.0010.0010.0000.0000.0000.000
101A476ILE 00.0190.02656.081-0.001-0.0010.0000.0000.0000.000
102A477MET 0-0.025-0.02948.6600.0030.0030.0000.0000.0000.000
103A478ARG 10.9410.97145.739-0.056-0.0560.0000.0000.0000.000
104A479GLY 0-0.017-0.01850.3290.0020.0020.0000.0000.0000.000
105A480GLU -1-0.938-0.97946.5470.0350.0350.0000.0000.0000.000
106A481TYR 00.0330.01050.409-0.002-0.0020.0000.0000.0000.000
107A482ASP -1-0.786-0.89253.9880.0340.0340.0000.0000.0000.000
108A483ALA 0-0.087-0.04055.271-0.001-0.0010.0000.0000.0000.000
109A484LEU 00.0010.00056.989-0.002-0.0020.0000.0000.0000.000
110A485LEU 0-0.049-0.00157.370-0.001-0.0010.0000.0000.0000.000
111A486PRO 00.0040.00660.8640.0000.0000.0000.0000.0000.000
112A487TRP 0-0.0350.00757.3330.0040.0040.0000.0000.0000.000
113A488PRO 00.039-0.00262.993-0.001-0.0010.0000.0000.0000.000
114A489PHE 0-0.031-0.00561.176-0.001-0.0010.0000.0000.0000.000
115A490LYS 10.9740.97963.446-0.022-0.0220.0000.0000.0000.000
116A491GLN 00.000-0.01564.252-0.001-0.0010.0000.0000.0000.000
117A492LYS 10.9760.98666.333-0.027-0.0270.0000.0000.0000.000
118A493VAL 00.0310.02763.1390.0000.0000.0000.0000.0000.000
119A494THR 0-0.045-0.02165.639-0.001-0.0010.0000.0000.0000.000
120A495LEU 0-0.022-0.01062.0320.0010.0010.0000.0000.0000.000
121A496MET 00.027-0.01263.837-0.001-0.0010.0000.0000.0000.000
122A497LEU 00.0030.01162.2470.0020.0020.0000.0000.0000.000
123A498MET 0-0.062-0.03563.156-0.002-0.0020.0000.0000.0000.000
124A499ASP -1-0.732-0.83164.9490.0440.0440.0000.0000.0000.000
125A500GLN 0-0.105-0.07960.975-0.002-0.0020.0000.0000.0000.000
126A501GLY 00.0230.00966.0490.0000.0000.0000.0000.0000.000
127A502SER 0-0.043-0.03369.371-0.001-0.0010.0000.0000.0000.000
128A503SER 0-0.010-0.00971.783-0.001-0.0010.0000.0000.0000.000
129A504ARG 10.8710.95665.785-0.040-0.0400.0000.0000.0000.000
130A505ARG 10.9790.97871.384-0.037-0.0370.0000.0000.0000.000
131A506HIS 00.0170.00068.1390.0030.0030.0000.0000.0000.000
132A507LEU 00.0020.01867.804-0.001-0.0010.0000.0000.0000.000
133A508GLY 00.004-0.01967.6890.0010.0010.0000.0000.0000.000
134A509ASP -1-0.838-0.89968.3420.0350.0350.0000.0000.0000.000
135A510ALA 0-0.075-0.03968.2680.0010.0010.0000.0000.0000.000
136A511PHE 00.0160.01363.7350.0000.0000.0000.0000.0000.000
137A512LYS 10.8850.93068.726-0.027-0.0270.0000.0000.0000.000
138A513PRO 0-0.040-0.01165.3340.0000.0000.0000.0000.0000.000
139A514ASP -1-0.823-0.91967.4050.0320.0320.0000.0000.0000.000
140A515PRO 0-0.024-0.02166.8280.0010.0010.0000.0000.0000.000
141A516ASN 00.0070.00466.845-0.001-0.0010.0000.0000.0000.000
142A517SER 00.0130.02863.8560.0020.0020.0000.0000.0000.000
143A518SER 00.011-0.01159.9180.0000.0000.0000.0000.0000.000
144A519SER 0-0.033-0.03859.4310.0010.0010.0000.0000.0000.000
145A520PHE 0-0.026-0.01059.6300.0010.0010.0000.0000.0000.000
146A521LYS 10.9701.01155.268-0.048-0.0480.0000.0000.0000.000
147A522LYS 10.9920.99954.825-0.029-0.0290.0000.0000.0000.000
148A523PRO 0-0.0110.01453.3640.0010.0010.0000.0000.0000.000
149A524THR 0-0.027-0.01252.606-0.001-0.0010.0000.0000.0000.000
150A525GLY 00.0050.00249.1870.0010.0010.0000.0000.0000.000
151A526GLU -1-0.930-0.97543.7330.0730.0730.0000.0000.0000.000
152A527MET 0-0.023-0.00448.249-0.003-0.0030.0000.0000.0000.000
153A528ASN 0-0.039-0.02051.5500.0020.0020.0000.0000.0000.000
154A529ILE 00.0080.00254.6090.0030.0030.0000.0000.0000.000
155A530ALA 0-0.0100.01256.076-0.003-0.0030.0000.0000.0000.000
156A531SER 00.0170.00757.777-0.001-0.0010.0000.0000.0000.000
157A532GLY 00.0210.00261.4960.0000.0000.0000.0000.0000.000
158A533CYS 0-0.0090.01063.409-0.001-0.0010.0000.0000.0000.000
159A534PRO 00.0650.01963.2240.0020.0020.0000.0000.0000.000
160A535VAL 00.0280.02864.3020.0020.0020.0000.0000.0000.000
161A536PHE 0-0.060-0.00564.606-0.001-0.0010.0000.0000.0000.000
162A537VAL 00.0500.01965.008-0.002-0.0020.0000.0000.0000.000
163A538ALA 00.0340.02165.9630.0020.0020.0000.0000.0000.000
164A539GLN 00.007-0.01861.6680.0010.0010.0000.0000.0000.000
165A540THR 00.0220.01765.4090.0000.0000.0000.0000.0000.000
166A541VAL 00.0320.01368.2600.0000.0000.0000.0000.0000.000
167A542LEU 0-0.032-0.01461.719-0.001-0.0010.0000.0000.0000.000
168A543GLU -1-0.875-0.93761.7430.0650.0650.0000.0000.0000.000
169A544ASN 0-0.048-0.01165.3660.0010.0010.0000.0000.0000.000
170A545GLY 00.0080.02968.058-0.002-0.0020.0000.0000.0000.000
171A546THR 0-0.043-0.04667.4880.0010.0010.0000.0000.0000.000
172A547TYR 0-0.008-0.00764.7350.0000.0000.0000.0000.0000.000
173A548ILE 0-0.0170.00860.1650.0010.0010.0000.0000.0000.000
174A549LYS 10.9480.97361.202-0.049-0.0490.0000.0000.0000.000
175A550ASP -1-0.878-0.94557.5080.0590.0590.0000.0000.0000.000
176A551ASP -1-0.858-0.93054.9200.0790.0790.0000.0000.0000.000
177A552THR 0-0.062-0.02955.7330.0040.0040.0000.0000.0000.000
178A553ILE 0-0.0030.00057.219-0.003-0.0030.0000.0000.0000.000
179A554PHE 00.012-0.00657.2770.0020.0020.0000.0000.0000.000
180A555ILE 00.0180.01557.639-0.002-0.0020.0000.0000.0000.000
181A556LYS 10.9160.96459.501-0.036-0.0360.0000.0000.0000.000
182A557VAL 00.0080.01259.5380.0000.0000.0000.0000.0000.000
183A558ILE 0-0.026-0.01461.948-0.001-0.0010.0000.0000.0000.000
184A559VAL 0-0.006-0.00661.0940.0000.0000.0000.0000.0000.000
185A560ASP -1-0.881-0.93964.2380.0230.0230.0000.0000.0000.000
186A561THR 00.011-0.00562.9280.0000.0000.0000.0000.0000.000
187A562SER 0-0.059-0.02966.086-0.001-0.0010.0000.0000.0000.000
188A563ASP -1-0.941-0.96468.4620.0200.0200.0000.0000.0000.000
189A564LEU 0-0.0420.05764.001-0.001-0.0010.0000.0000.0000.000
190A565PRO 0-0.044-0.06864.0200.0000.0000.0000.0000.0000.000
191A1NME 00.0480.01666.0230.0000.0000.0000.0000.0000.000