Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QVN4Y

Calculation Name: 4AXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AXG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VMA3

Base Structure: X-ray

Registration Date: 2023-09-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2084994.350644
FMO2-HF: Nuclear repulsion 2010585.910017
FMO2-HF: Total energy -74408.440626
FMO2-MP2: Total energy -74625.821317


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:66:HIS)


Summations of interaction energy for fragment #1(A:66:HIS)
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.
-5.994-4.002-0.011-0.767-1.2150.001
Interaction energy analysis for fragmet #1(A:66:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.013
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].
3A68TYR0-0.020-0.0083.807-4.745-2.963-0.010-0.742-1.0310.001
4A69LYS10.8620.9244.4070.1710.381-0.001-0.025-0.1840.000
5A70HIS10.8030.8637.026-0.857-0.8570.0000.0000.0000.000
6A71PRO00.0340.02410.275-0.180-0.1800.0000.0000.0000.000
7A72LEU0-0.0070.00213.175-0.002-0.0020.0000.0000.0000.000
8A73MET0-0.0240.00316.1740.0160.0160.0000.0000.0000.000
9A74ASN0-0.062-0.04719.678-0.016-0.0160.0000.0000.0000.000
10A75VAL0-0.0010.00818.156-0.011-0.0110.0000.0000.0000.000
11A76TRP00.0240.01018.425-0.018-0.0180.0000.0000.0000.000
12A77THR0-0.007-0.01819.186-0.027-0.0270.0000.0000.0000.000
13A78LEU0-0.032-0.00719.3900.0260.0260.0000.0000.0000.000
14A79TRP00.0210.00821.704-0.021-0.0210.0000.0000.0000.000
15A80TYR0-0.019-0.02124.986-0.003-0.0030.0000.0000.0000.000
16A81LEU0-0.0130.01926.7420.0070.0070.0000.0000.0000.000
17A82GLU-1-0.906-0.95530.034-0.279-0.2790.0000.0000.0000.000
18A83ASN0-0.003-0.01631.6940.0110.0110.0000.0000.0000.000
19A84ASP-1-0.853-0.92035.239-0.149-0.1490.0000.0000.0000.000
20A85ARG10.8460.92837.0790.1540.1540.0000.0000.0000.000
21A86SER00.0020.00038.614-0.006-0.0060.0000.0000.0000.000
22A87LYS10.8970.93640.7030.1450.1450.0000.0000.0000.000
23A88SER0-0.006-0.01141.755-0.006-0.0060.0000.0000.0000.000
24A89TRP00.0160.00541.3880.0070.0070.0000.0000.0000.000
25A90GLU-1-0.904-0.94138.429-0.163-0.1630.0000.0000.0000.000
26A91ASP-1-0.904-0.95132.829-0.184-0.1840.0000.0000.0000.000
27A92MET0-0.048-0.01733.490-0.010-0.0100.0000.0000.0000.000
28A93GLN00.003-0.00129.346-0.025-0.0250.0000.0000.0000.000
29A94ASN00.0510.02126.6520.0150.0150.0000.0000.0000.000
30A95GLU-1-0.914-0.96123.660-0.263-0.2630.0000.0000.0000.000
31A96ILE0-0.078-0.02719.110-0.028-0.0280.0000.0000.0000.000
32A97THR00.034-0.00516.069-0.027-0.0270.0000.0000.0000.000
33A98SER0-0.029-0.01717.6750.0800.0800.0000.0000.0000.000
34A99PHE0-0.012-0.00513.716-0.073-0.0730.0000.0000.0000.000
35A100ASP-1-0.840-0.92912.6720.0770.0770.0000.0000.0000.000
36A101THR00.003-0.0119.8510.0750.0750.0000.0000.0000.000
37A102VAL00.0100.00110.663-0.138-0.1380.0000.0000.0000.000
38A103GLU-1-0.761-0.8625.6220.4400.4400.0000.0000.0000.000
39A104ASP-1-0.777-0.8558.328-1.060-1.0600.0000.0000.0000.000
40A105PHE0-0.0050.0079.988-0.096-0.0960.0000.0000.0000.000
41A106TRP00.019-0.00310.156-0.075-0.0750.0000.0000.0000.000
42A107SER0-0.030-0.0127.796-0.244-0.2440.0000.0000.0000.000
43A108LEU0-0.0290.00610.520-0.039-0.0390.0000.0000.0000.000
44A109TYR00.003-0.00713.9460.0340.0340.0000.0000.0000.000
45A110ASN0-0.009-0.01311.0730.1680.1680.0000.0000.0000.000
46A111HIS0-0.085-0.04910.020-0.153-0.1530.0000.0000.0000.000
47A112ILE0-0.047-0.00515.3380.0450.0450.0000.0000.0000.000
48A113LYS10.9400.97618.8370.4450.4450.0000.0000.0000.000
49A114PRO00.1020.06921.7030.0190.0190.0000.0000.0000.000
50A115PRO00.0380.00423.4340.0060.0060.0000.0000.0000.000
51A116SER0-0.093-0.08626.7650.0110.0110.0000.0000.0000.000
52A117GLU-1-0.998-1.01524.406-0.381-0.3810.0000.0000.0000.000
53A118ILE0-0.0540.00525.834-0.014-0.0140.0000.0000.0000.000
54A119LYS10.8580.91428.2910.2770.2770.0000.0000.0000.000
55A120LEU0-0.023-0.01631.6930.0080.0080.0000.0000.0000.000
56A121GLY0-0.028-0.01934.7230.0010.0010.0000.0000.0000.000
57A122SER00.0000.00629.850-0.007-0.0070.0000.0000.0000.000
58A123ASP-1-0.803-0.90530.189-0.153-0.1530.0000.0000.0000.000
59A124TYR0-0.024-0.01322.884-0.022-0.0220.0000.0000.0000.000
60A125SER0-0.022-0.02925.5910.0350.0350.0000.0000.0000.000
61A126LEU00.0130.02719.997-0.027-0.0270.0000.0000.0000.000
62A127PHE00.023-0.00123.8040.0280.0280.0000.0000.0000.000
63A128LYS10.9290.98723.459-0.049-0.0490.0000.0000.0000.000
64A129LYS10.9690.97520.9540.1740.1740.0000.0000.0000.000
65A130ASN0-0.066-0.04324.1780.0030.0030.0000.0000.0000.000
66A131ILE00.0020.03327.2700.0120.0120.0000.0000.0000.000
67A132ARG10.9170.92028.0420.0900.0900.0000.0000.0000.000
68A133PRO00.0200.03428.6470.0160.0160.0000.0000.0000.000
69A134MET0-0.0120.00530.8730.0020.0020.0000.0000.0000.000
70A135TRP00.0660.01234.5990.0110.0110.0000.0000.0000.000
71A136GLU-1-0.888-0.94637.191-0.058-0.0580.0000.0000.0000.000
72A137ASP-1-0.825-0.90132.673-0.062-0.0620.0000.0000.0000.000
73A138ALA00.0400.01235.9030.0050.0050.0000.0000.0000.000
74A139ALA0-0.0020.00532.5290.0070.0070.0000.0000.0000.000
75A140ASN0-0.002-0.01532.2700.0100.0100.0000.0000.0000.000
76A141LYS10.8440.95135.8530.0530.0530.0000.0000.0000.000
77A142GLN0-0.018-0.02639.404-0.003-0.0030.0000.0000.0000.000
78A143GLY00.0780.06337.3640.0060.0060.0000.0000.0000.000
79A144GLY0-0.013-0.02836.946-0.003-0.0030.0000.0000.0000.000
80A145ARG10.8940.97034.9570.0740.0740.0000.0000.0000.000
81A146TRP00.0290.02633.981-0.003-0.0030.0000.0000.0000.000
82A147VAL0-0.074-0.02934.362-0.010-0.0100.0000.0000.0000.000
83A148ILE00.0750.03932.0070.0080.0080.0000.0000.0000.000
84A149THR0-0.035-0.03235.393-0.012-0.0120.0000.0000.0000.000
85A150LEU00.0170.01232.1560.0060.0060.0000.0000.0000.000
86A151ASN00.0160.01936.611-0.012-0.0120.0000.0000.0000.000
87A152LYS10.9440.96939.3010.1060.1060.0000.0000.0000.000
88A153SER00.0520.04533.2400.0070.0070.0000.0000.0000.000
89A154SER0-0.034-0.01432.733-0.014-0.0140.0000.0000.0000.000
90A155LYS10.9490.95229.3710.2570.2570.0000.0000.0000.000
91A156THR00.0790.03827.411-0.013-0.0130.0000.0000.0000.000
92A157ASP-1-0.868-0.93127.412-0.113-0.1130.0000.0000.0000.000
93A158LEU0-0.066-0.02529.0510.0080.0080.0000.0000.0000.000
94A159ASP-1-0.764-0.86824.151-0.263-0.2630.0000.0000.0000.000
95A160ASN00.0190.00724.132-0.018-0.0180.0000.0000.0000.000
96A161LEU00.0180.02225.0080.0130.0130.0000.0000.0000.000
97A162TRP0-0.002-0.01523.0850.0220.0220.0000.0000.0000.000
98A163LEU0-0.007-0.00118.2200.0030.0030.0000.0000.0000.000
99A164ASP-1-0.827-0.92121.563-0.061-0.0610.0000.0000.0000.000
100A165VAL0-0.050-0.02623.6640.0270.0270.0000.0000.0000.000
101A166LEU0-0.046-0.02719.9460.0150.0150.0000.0000.0000.000
102A167LEU0-0.007-0.00317.4850.0170.0170.0000.0000.0000.000
103A168CYS0-0.054-0.02020.5110.0430.0430.0000.0000.0000.000
104A169LEU0-0.076-0.03422.3580.0230.0230.0000.0000.0000.000
105A170ILE0-0.018-0.01215.9220.0230.0230.0000.0000.0000.000
106A171GLY0-0.021-0.00418.8220.0400.0400.0000.0000.0000.000
107A172GLU-1-0.887-0.94419.7770.1330.1330.0000.0000.0000.000
108A173ALA0-0.022-0.01022.9880.0190.0190.0000.0000.0000.000
109A174PHE0-0.072-0.04725.116-0.007-0.0070.0000.0000.0000.000
110A175ASP-1-0.860-0.93227.7690.1310.1310.0000.0000.0000.000
111A176HIS0-0.063-0.05230.1280.0060.0060.0000.0000.0000.000
112A177SER00.0590.02326.194-0.020-0.0200.0000.0000.0000.000
113A178ASP-1-0.969-0.98228.2510.0610.0610.0000.0000.0000.000
114A179GLN00.004-0.00729.938-0.019-0.0190.0000.0000.0000.000
115A180ILE0-0.029-0.00226.833-0.018-0.0180.0000.0000.0000.000
116A181CYS0-0.055-0.02528.6450.0070.0070.0000.0000.0000.000
117A182GLY00.0620.00926.478-0.009-0.0090.0000.0000.0000.000
118A183ALA0-0.0220.00726.2700.0140.0140.0000.0000.0000.000
119A184VAL0-0.040-0.01427.224-0.020-0.0200.0000.0000.0000.000
120A185ILE00.0010.00726.9640.0150.0150.0000.0000.0000.000
121A186ASN0-0.068-0.03029.8470.0000.0000.0000.0000.0000.000
122A187ILE00.0300.01829.1960.0150.0150.0000.0000.0000.000
123A188ARG10.8410.90233.1670.1590.1590.0000.0000.0000.000
124A189GLY00.0150.02535.6340.0060.0060.0000.0000.0000.000
125A190LYS10.8620.94236.9900.1010.1010.0000.0000.0000.000
126A191SER0-0.066-0.08638.6730.0050.0050.0000.0000.0000.000
127A192ASN00.0630.04733.349-0.004-0.0040.0000.0000.0000.000
128A193LYS10.9190.95134.0510.1130.1130.0000.0000.0000.000
129A194ILE00.0810.05028.538-0.014-0.0140.0000.0000.0000.000
130A195SER0-0.059-0.03831.3070.0150.0150.0000.0000.0000.000
131A196ILE00.0590.03528.507-0.013-0.0130.0000.0000.0000.000
132A197TRP0-0.051-0.02830.6930.0070.0070.0000.0000.0000.000
133A198THR00.0450.04631.3740.0010.0010.0000.0000.0000.000
134A199ALA00.0760.02133.587-0.007-0.0070.0000.0000.0000.000
135A200ASP-1-0.904-0.95635.2540.0080.0080.0000.0000.0000.000
136A201GLY0-0.041-0.02338.7510.0030.0030.0000.0000.0000.000
137A202ASN0-0.053-0.04140.9510.0000.0000.0000.0000.0000.000
138A203ASN0-0.0040.01538.0450.0060.0060.0000.0000.0000.000
139A204GLU-1-0.925-0.97139.6670.0250.0250.0000.0000.0000.000
140A205GLU-1-0.924-0.95738.3700.0650.0650.0000.0000.0000.000
141A206ALA00.0480.02235.2380.0010.0010.0000.0000.0000.000
142A207ALA0-0.0090.00435.518-0.002-0.0020.0000.0000.0000.000
143A208LEU00.017-0.00436.799-0.005-0.0050.0000.0000.0000.000
144A209GLU-1-0.784-0.85031.7830.0720.0720.0000.0000.0000.000
145A210ILE00.014-0.00331.226-0.002-0.0020.0000.0000.0000.000
146A211GLY0-0.005-0.00432.805-0.006-0.0060.0000.0000.0000.000
147A212HIS0-0.007-0.03035.012-0.007-0.0070.0000.0000.0000.000
148A213LYS10.9350.98029.699-0.085-0.0850.0000.0000.0000.000
149A214LEU0-0.0050.00029.454-0.006-0.0060.0000.0000.0000.000
150A215ARG10.8940.94031.556-0.019-0.0190.0000.0000.0000.000
151A216ASP-1-0.906-0.95531.8450.0370.0370.0000.0000.0000.000
152A217ALA0-0.053-0.02227.219-0.002-0.0020.0000.0000.0000.000
153A218LEU0-0.015-0.00427.731-0.013-0.0130.0000.0000.0000.000
154A219ARG10.9120.96330.340-0.001-0.0010.0000.0000.0000.000
155A220LEU0-0.0180.01233.217-0.008-0.0080.0000.0000.0000.000
156A221GLY00.0370.01335.8190.0090.0090.0000.0000.0000.000
157A222ARG10.8650.91639.4700.0050.0050.0000.0000.0000.000
158A223ASN0-0.0130.00138.1950.0040.0040.0000.0000.0000.000
159A224ASN00.0240.01435.860-0.005-0.0050.0000.0000.0000.000
160A225SER00.0160.00538.8300.0070.0070.0000.0000.0000.000
161A226LEU00.0040.02334.592-0.007-0.0070.0000.0000.0000.000
162A227GLN0-0.0070.00938.6750.0060.0060.0000.0000.0000.000
163A228TYR00.0350.00236.551-0.005-0.0050.0000.0000.0000.000
164A229GLN00.004-0.00639.596-0.003-0.0030.0000.0000.0000.000
165A230LEU00.0540.02939.956-0.002-0.0020.0000.0000.0000.000
166A231HIS00.008-0.00435.737-0.007-0.0070.0000.0000.0000.000
167A232LYS10.8150.90440.9340.0250.0250.0000.0000.0000.000
168A233ASP-1-0.812-0.89944.473-0.030-0.0300.0000.0000.0000.000
169A234THR0-0.047-0.02540.706-0.003-0.0030.0000.0000.0000.000
170A235MET0-0.050-0.00641.956-0.008-0.0080.0000.0000.0000.000
171A236VAL00.0260.01745.7590.0030.0030.0000.0000.0000.000
172A237LYS10.8860.95246.3550.0730.0730.0000.0000.0000.000
173A238GLN00.003-0.02147.390-0.006-0.0060.0000.0000.0000.000
174A239GLY00.0080.00849.1320.0030.0030.0000.0000.0000.000
175A240SER00.0130.01050.4900.0020.0020.0000.0000.0000.000
176A241ASN0-0.042-0.02147.168-0.002-0.0020.0000.0000.0000.000
177A242VAL00.0200.01544.0860.0010.0010.0000.0000.0000.000
178A243LYS10.8870.94646.4480.0220.0220.0000.0000.0000.000
179A244SER0-0.036-0.06244.144-0.004-0.0040.0000.0000.0000.000
180A245ILE0-0.034-0.00343.4380.0020.0020.0000.0000.0000.000
181A246TYR00.0890.04741.1080.0040.0040.0000.0000.0000.000
182A247THR0-0.050-0.03542.556-0.007-0.0070.0000.0000.0000.000
183A248LEU0-0.0440.00138.1380.0050.0050.0000.0000.0000.000