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: 4JLKN

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2090422.839049
FMO2-HF: Nuclear repulsion 2016012.853367
FMO2-HF: Total energy -74409.985682
FMO2-MP2: Total energy -74627.453293


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.
-6.055-3.7080.006-0.954-1.3990.001
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 : 0.008 / 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].
3A68TYR0-0.025-0.0043.427-4.621-2.5800.005-0.890-1.1560.001
4A69LYS10.8440.9124.0060.9461.2520.001-0.064-0.2430.000
5A70HIS10.8290.8836.675-0.887-0.8870.0000.0000.0000.000
6A71PRO00.0300.01710.131-0.199-0.1990.0000.0000.0000.000
7A72LEU0-0.0180.00112.9180.0340.0340.0000.0000.0000.000
8A73MET0-0.031-0.00616.1200.0120.0120.0000.0000.0000.000
9A74ASN0-0.054-0.04219.712-0.018-0.0180.0000.0000.0000.000
10A75VAL00.0030.00417.967-0.014-0.0140.0000.0000.0000.000
11A76TRP00.0160.00318.3140.0000.0000.0000.0000.0000.000
12A77THR0-0.016-0.02318.913-0.047-0.0470.0000.0000.0000.000
13A78LEU0-0.027-0.00118.9490.0420.0420.0000.0000.0000.000
14A79TRP00.0370.00121.326-0.031-0.0310.0000.0000.0000.000
15A80TYR0-0.039-0.04024.4880.0010.0010.0000.0000.0000.000
16A81LEU0-0.0010.02626.270-0.001-0.0010.0000.0000.0000.000
17A82GLU-1-0.798-0.91828.982-0.308-0.3080.0000.0000.0000.000
18A83ASN0-0.055-0.04930.9590.0110.0110.0000.0000.0000.000
19A84ASP-1-0.783-0.84734.639-0.154-0.1540.0000.0000.0000.000
20A85ARG10.7860.88336.7860.1640.1640.0000.0000.0000.000
21A86SER0-0.0030.00238.007-0.003-0.0030.0000.0000.0000.000
22A87LYS10.8080.89240.1500.1790.1790.0000.0000.0000.000
23A88SER00.011-0.00841.146-0.008-0.0080.0000.0000.0000.000
24A89TRP00.0140.00840.8270.0060.0060.0000.0000.0000.000
25A90GLU-1-0.818-0.89937.940-0.188-0.1880.0000.0000.0000.000
26A91ASP-1-0.831-0.90932.949-0.223-0.2230.0000.0000.0000.000
27A92MET0-0.029-0.01432.657-0.007-0.0070.0000.0000.0000.000
28A93GLN0-0.021-0.01328.799-0.029-0.0290.0000.0000.0000.000
29A94ASN00.0270.02425.5600.0000.0000.0000.0000.0000.000
30A95GLU-1-0.788-0.89221.615-0.398-0.3980.0000.0000.0000.000
31A96ILE0-0.056-0.02818.418-0.023-0.0230.0000.0000.0000.000
32A97THR00.008-0.00615.420-0.043-0.0430.0000.0000.0000.000
33A98SER00.004-0.00717.3660.1070.1070.0000.0000.0000.000
34A99PHE0-0.032-0.00613.348-0.105-0.1050.0000.0000.0000.000
35A100ASP-1-0.846-0.93113.059-0.214-0.2140.0000.0000.0000.000
36A101THR0-0.011-0.0299.6070.1340.1340.0000.0000.0000.000
37A102VAL00.0440.01610.574-0.137-0.1370.0000.0000.0000.000
38A103GLU-1-0.779-0.8705.1530.5100.5100.0000.0000.0000.000
39A104ASP-1-0.774-0.8388.149-1.794-1.7940.0000.0000.0000.000
40A105PHE00.0200.0249.786-0.064-0.0640.0000.0000.0000.000
41A106TRP00.015-0.0059.919-0.045-0.0450.0000.0000.0000.000
42A107SER0-0.057-0.0397.778-0.254-0.2540.0000.0000.0000.000
43A108LEU0-0.0190.00710.089-0.044-0.0440.0000.0000.0000.000
44A109TYR00.014-0.01013.5870.0490.0490.0000.0000.0000.000
45A110ASN0-0.025-0.02411.1160.1680.1680.0000.0000.0000.000
46A111HIS0-0.084-0.0419.810-0.059-0.0590.0000.0000.0000.000
47A112ILE0-0.0340.00215.2080.0240.0240.0000.0000.0000.000
48A113LYS10.8210.89918.7320.4010.4010.0000.0000.0000.000
49A114PRO00.0830.06321.8560.0090.0090.0000.0000.0000.000
50A115PRO00.0460.01623.3240.0050.0050.0000.0000.0000.000
51A116SER0-0.096-0.07526.4310.0060.0060.0000.0000.0000.000
52A117GLU-1-0.917-0.95925.244-0.325-0.3250.0000.0000.0000.000
53A118ILE0-0.0010.03225.621-0.025-0.0250.0000.0000.0000.000
54A119LYS10.8120.89828.1790.3000.3000.0000.0000.0000.000
55A120LEU0-0.002-0.01331.5200.0080.0080.0000.0000.0000.000
56A121GLY0-0.016-0.01534.4700.0020.0020.0000.0000.0000.000
57A122SER0-0.0070.01329.737-0.006-0.0060.0000.0000.0000.000
58A123ASP-1-0.778-0.87230.076-0.164-0.1640.0000.0000.0000.000
59A124TYR0-0.012-0.01322.709-0.024-0.0240.0000.0000.0000.000
60A125SER0-0.043-0.04925.3460.0420.0420.0000.0000.0000.000
61A126LEU0-0.0070.01819.605-0.039-0.0390.0000.0000.0000.000
62A127PHE00.0260.00623.5990.0360.0360.0000.0000.0000.000
63A128LYS10.9010.96023.079-0.011-0.0110.0000.0000.0000.000
64A129LYS10.8410.92021.7420.3350.3350.0000.0000.0000.000
65A130ASN0-0.055-0.04623.7730.0040.0040.0000.0000.0000.000
66A131ILE0-0.0020.03026.9330.0140.0140.0000.0000.0000.000
67A132ARG10.8670.92227.6620.1330.1330.0000.0000.0000.000
68A133PRO00.0190.02828.1360.0210.0210.0000.0000.0000.000
69A134MET0-0.028-0.03130.5320.0030.0030.0000.0000.0000.000
70A135TRP00.039-0.00134.2600.0100.0100.0000.0000.0000.000
71A136GLU-1-0.831-0.90936.980-0.085-0.0850.0000.0000.0000.000
72A137ASP-1-0.839-0.90133.145-0.125-0.1250.0000.0000.0000.000
73A138ALA00.0370.01635.6590.0090.0090.0000.0000.0000.000
74A139ALA00.0090.01632.1230.0100.0100.0000.0000.0000.000
75A140ASN00.011-0.01831.9450.0120.0120.0000.0000.0000.000
76A141LYS10.8060.91535.6730.0870.0870.0000.0000.0000.000
77A142GLN00.0410.00439.3240.0000.0000.0000.0000.0000.000
78A143GLY00.0180.04037.6280.0050.0050.0000.0000.0000.000
79A144GLY00.000-0.02537.025-0.003-0.0030.0000.0000.0000.000
80A145ARG10.8600.95334.8740.0780.0780.0000.0000.0000.000
81A146TRP00.0380.03033.8840.0010.0010.0000.0000.0000.000
82A147VAL0-0.076-0.03134.426-0.012-0.0120.0000.0000.0000.000
83A148ILE00.0760.03431.6720.0100.0100.0000.0000.0000.000
84A149THR0-0.023-0.01834.903-0.014-0.0140.0000.0000.0000.000
85A150LEU00.0100.00431.9360.0070.0070.0000.0000.0000.000
86A151ASN00.0170.00136.253-0.014-0.0140.0000.0000.0000.000
87A152LYS10.9210.94738.7860.0920.0920.0000.0000.0000.000
88A153SER00.0360.04432.7010.0060.0060.0000.0000.0000.000
89A154SER0-0.061-0.05632.274-0.014-0.0140.0000.0000.0000.000
90A155LYS10.9020.91828.4020.2260.2260.0000.0000.0000.000
91A156THR00.0850.03726.722-0.007-0.0070.0000.0000.0000.000
92A157ASP-1-0.858-0.88227.325-0.075-0.0750.0000.0000.0000.000
93A158LEU0-0.038-0.01928.9110.0050.0050.0000.0000.0000.000
94A159ASP-1-0.776-0.87324.160-0.229-0.2290.0000.0000.0000.000
95A160ASN00.0000.00623.929-0.023-0.0230.0000.0000.0000.000
96A161LEU00.0400.02124.5680.0060.0060.0000.0000.0000.000
97A162TRP0-0.008-0.01123.0620.0200.0200.0000.0000.0000.000
98A163LEU0-0.0070.01117.815-0.006-0.0060.0000.0000.0000.000
99A164ASP-1-0.844-0.93321.193-0.024-0.0240.0000.0000.0000.000
100A165VAL0-0.025-0.01223.3650.0220.0220.0000.0000.0000.000
101A166LEU0-0.037-0.01919.6820.0050.0050.0000.0000.0000.000
102A167LEU00.000-0.00416.8190.0100.0100.0000.0000.0000.000
103A168CYS0-0.060-0.03619.9870.0430.0430.0000.0000.0000.000
104A169LEU0-0.062-0.01922.0990.0190.0190.0000.0000.0000.000
105A170ILE0-0.017-0.00715.5160.0200.0200.0000.0000.0000.000
106A171GLY0-0.016-0.00518.2740.0400.0400.0000.0000.0000.000
107A172GLU-1-0.862-0.93219.4260.0680.0680.0000.0000.0000.000
108A173ALA0-0.0190.00522.7010.0210.0210.0000.0000.0000.000
109A174PHE0-0.053-0.05524.737-0.010-0.0100.0000.0000.0000.000
110A175ASP-1-0.816-0.90427.6460.1170.1170.0000.0000.0000.000
111A176HIS0-0.031-0.02630.1110.0040.0040.0000.0000.0000.000
112A177SER00.0020.00425.506-0.021-0.0210.0000.0000.0000.000
113A178ASP-1-0.841-0.91627.4030.0230.0230.0000.0000.0000.000
114A179GLN0-0.053-0.03129.293-0.023-0.0230.0000.0000.0000.000
115A180ILE0-0.0190.01026.529-0.017-0.0170.0000.0000.0000.000
116A181CYS0-0.027-0.00828.4370.0020.0020.0000.0000.0000.000
117A182GLY00.0480.00926.145-0.018-0.0180.0000.0000.0000.000
118A183ALA0-0.0290.00226.1020.0220.0220.0000.0000.0000.000
119A184VAL0-0.0080.00327.173-0.024-0.0240.0000.0000.0000.000
120A185ILE00.0110.00426.7040.0190.0190.0000.0000.0000.000
121A186ASN0-0.046-0.01229.754-0.001-0.0010.0000.0000.0000.000
122A187ILE00.0130.01328.7060.0150.0150.0000.0000.0000.000
123A188ARG10.7710.83732.8120.1670.1670.0000.0000.0000.000
124A189GLY00.0230.03235.4510.0050.0050.0000.0000.0000.000
125A190LYS10.8540.92936.8900.0970.0970.0000.0000.0000.000
126A191SER0-0.035-0.05238.8480.0100.0100.0000.0000.0000.000
127A192ASN00.0730.05233.144-0.010-0.0100.0000.0000.0000.000
128A193LYS10.9070.94733.8190.1270.1270.0000.0000.0000.000
129A194ILE00.0770.04828.363-0.015-0.0150.0000.0000.0000.000
130A195SER0-0.079-0.04930.9150.0140.0140.0000.0000.0000.000
131A196ILE00.0400.02328.152-0.016-0.0160.0000.0000.0000.000
132A197TRP0-0.055-0.02430.4270.0090.0090.0000.0000.0000.000
133A198THR00.0180.01031.2000.0010.0010.0000.0000.0000.000
134A199ALA00.0830.03033.379-0.006-0.0060.0000.0000.0000.000
135A200ASP-1-0.803-0.90235.023-0.015-0.0150.0000.0000.0000.000
136A201GLY00.0120.00537.6880.0000.0000.0000.0000.0000.000
137A202ASN0-0.120-0.06840.3630.0030.0030.0000.0000.0000.000
138A203ASN00.0020.00237.0250.0080.0080.0000.0000.0000.000
139A204GLU-1-0.908-0.95639.2150.0160.0160.0000.0000.0000.000
140A205GLU-1-0.941-0.96138.1770.0580.0580.0000.0000.0000.000
141A206ALA00.0410.02034.7690.0030.0030.0000.0000.0000.000
142A207ALA0-0.0080.00335.174-0.002-0.0020.0000.0000.0000.000
143A208LEU00.009-0.00836.565-0.004-0.0040.0000.0000.0000.000
144A209GLU-1-0.751-0.83431.4230.0630.0630.0000.0000.0000.000
145A210ILE00.0100.00330.9790.0000.0000.0000.0000.0000.000
146A211GLY00.008-0.00232.551-0.005-0.0050.0000.0000.0000.000
147A212HIS00.020-0.01034.809-0.004-0.0040.0000.0000.0000.000
148A213LYS10.7880.88428.785-0.090-0.0900.0000.0000.0000.000
149A214LEU0-0.003-0.00329.024-0.003-0.0030.0000.0000.0000.000
150A215ARG10.7780.85931.255-0.039-0.0390.0000.0000.0000.000
151A216ASP-1-0.852-0.90332.2540.0450.0450.0000.0000.0000.000
152A217ALA0-0.007-0.00326.9250.0040.0040.0000.0000.0000.000
153A218LEU0-0.017-0.00527.241-0.007-0.0070.0000.0000.0000.000
154A219ARG10.8960.95030.030-0.041-0.0410.0000.0000.0000.000
155A220LEU0-0.0290.00132.854-0.006-0.0060.0000.0000.0000.000
156A221GLY00.0460.02535.4940.0070.0070.0000.0000.0000.000
157A222ARG10.8730.90838.981-0.009-0.0090.0000.0000.0000.000
158A223ASN0-0.032-0.01038.1800.0040.0040.0000.0000.0000.000
159A224ASN0-0.0040.00735.072-0.006-0.0060.0000.0000.0000.000
160A225SER00.0080.00737.9930.0050.0050.0000.0000.0000.000
161A226LEU00.0320.04134.355-0.008-0.0080.0000.0000.0000.000
162A227GLN00.0180.02938.4140.0080.0080.0000.0000.0000.000
163A228TYR00.0400.01636.485-0.007-0.0070.0000.0000.0000.000
164A229GLN00.0240.00939.352-0.004-0.0040.0000.0000.0000.000
165A230LEU00.0520.03139.646-0.004-0.0040.0000.0000.0000.000
166A231HIS0-0.0090.00135.425-0.005-0.0050.0000.0000.0000.000
167A232LYS10.7980.89640.6290.0480.0480.0000.0000.0000.000
168A233ASP-1-0.780-0.89744.317-0.043-0.0430.0000.0000.0000.000
169A234THR0-0.043-0.04040.040-0.002-0.0020.0000.0000.0000.000
170A235MET0-0.0590.00241.637-0.008-0.0080.0000.0000.0000.000
171A236VAL0-0.004-0.00445.4820.0030.0030.0000.0000.0000.000
172A237LYS10.9030.95846.0140.0820.0820.0000.0000.0000.000
173A238GLN00.0410.00246.935-0.007-0.0070.0000.0000.0000.000
174A239GLY0-0.0190.00548.9710.0030.0030.0000.0000.0000.000
175A240SER00.0040.00350.8770.0040.0040.0000.0000.0000.000
176A241ASN0-0.028-0.01247.285-0.003-0.0030.0000.0000.0000.000
177A242VAL00.0030.00643.2200.0010.0010.0000.0000.0000.000
178A243LYS10.8980.94345.6470.0320.0320.0000.0000.0000.000
179A244SER0-0.021-0.03243.933-0.005-0.0050.0000.0000.0000.000
180A245ILE0-0.078-0.03243.2280.0010.0010.0000.0000.0000.000
181A246TYR00.0420.01440.5980.0060.0060.0000.0000.0000.000
182A247THR0-0.034-0.03242.076-0.006-0.0060.0000.0000.0000.000
183A248LEU0-0.022-0.00137.6880.0080.0080.0000.0000.0000.000