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: Q1GMY

Calculation Name: 4C47-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C47

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZL65

Base Structure: X-ray

Registration Date: 2023-06-19

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1673460.334241
FMO2-HF: Nuclear repulsion 1597518.977628
FMO2-HF: Total energy -75941.356613
FMO2-MP2: Total energy -76165.236997


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:23:ASP)


Summations of interaction energy for fragment #1(A:23:ASP)
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.
-16.969-10.6482.656-3.984-4.9940.038
Interaction energy analysis for fragmet #1(A:23:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.873 / q_NPA : -0.943
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].
3A25PHE0-0.057-0.0262.024-27.713-22.1232.601-3.578-4.6130.041
4A26ALA0-0.0080.0003.3161.2401.9710.055-0.406-0.381-0.003
5A27ASP-1-0.821-0.9286.03031.21131.2110.0000.0000.0000.000
6A28LYS10.9470.9686.977-26.220-26.2200.0000.0000.0000.000
7A29HIS00.0070.00910.080-1.551-1.5510.0000.0000.0000.000
8A30LEU00.0360.02810.270-1.607-1.6070.0000.0000.0000.000
9A31VAL00.004-0.00610.640-1.535-1.5350.0000.0000.0000.000
10A32GLU-1-0.983-0.99312.84115.71515.7150.0000.0000.0000.000
11A33GLU-1-0.890-0.93915.30215.12115.1210.0000.0000.0000.000
12A34MET0-0.042-0.02314.240-0.627-0.6270.0000.0000.0000.000
13A35LYS10.9360.97116.982-15.805-15.8050.0000.0000.0000.000
14A36GLU-1-0.880-0.94618.84112.80012.8000.0000.0000.0000.000
15A37GLN00.0140.00720.115-0.326-0.3260.0000.0000.0000.000
16A38GLN0-0.029-0.01220.227-0.558-0.5580.0000.0000.0000.000
17A39LYS10.9370.96422.606-13.360-13.3600.0000.0000.0000.000
18A40GLU-1-0.940-0.96224.89610.89810.8980.0000.0000.0000.000
19A41GLN0-0.069-0.05223.345-0.375-0.3750.0000.0000.0000.000
20A42GLU-1-0.877-0.92726.77510.33910.3390.0000.0000.0000.000
21A43THR0-0.036-0.00828.581-0.557-0.5570.0000.0000.0000.000
22A44LYS10.9220.94528.238-10.715-10.7150.0000.0000.0000.000
23A45ILE00.0410.02728.604-0.357-0.3570.0000.0000.0000.000
24A46ASN00.0080.00431.996-0.568-0.5680.0000.0000.0000.000
25A47LEU0-0.093-0.03534.679-0.341-0.3410.0000.0000.0000.000
26A48LEU00.007-0.00733.359-0.294-0.2940.0000.0000.0000.000
27A49GLU-1-0.897-0.93735.0758.5498.5490.0000.0000.0000.000
28A50LYS10.9130.95538.280-7.823-7.8230.0000.0000.0000.000
29A51GLN00.001-0.02039.548-0.066-0.0660.0000.0000.0000.000
30A52GLN00.0290.02640.405-0.137-0.1370.0000.0000.0000.000
31A53LYS10.9800.98740.847-7.760-7.7600.0000.0000.0000.000
32A54GLU-1-0.967-0.98044.5166.6926.6920.0000.0000.0000.000
33A55GLN0-0.047-0.03643.727-0.196-0.1960.0000.0000.0000.000
34A56GLU-1-0.893-0.92846.3086.4476.4470.0000.0000.0000.000
35A57ALA0-0.018-0.01348.085-0.176-0.1760.0000.0000.0000.000
36A58LYS10.9130.94248.974-6.484-6.4840.0000.0000.0000.000
37A59ILE00.0550.03748.225-0.149-0.1490.0000.0000.0000.000
38A60ASN00.0270.01551.551-0.255-0.2550.0000.0000.0000.000
39A61LEU0-0.057-0.03154.219-0.155-0.1550.0000.0000.0000.000
40A62LEU0-0.006-0.00353.366-0.133-0.1330.0000.0000.0000.000
41A63GLU-1-0.887-0.93153.8415.7065.7060.0000.0000.0000.000
42A64LYS10.9180.95357.293-5.613-5.6130.0000.0000.0000.000
43A65GLN0-0.008-0.01759.724-0.108-0.1080.0000.0000.0000.000
44A66GLN00.0370.02858.840-0.087-0.0870.0000.0000.0000.000
45A67ALA00.0280.01861.927-0.097-0.0970.0000.0000.0000.000
46A68THR0-0.030-0.02163.883-0.124-0.1240.0000.0000.0000.000
47A69ILE00.0310.01863.156-0.108-0.1080.0000.0000.0000.000
48A70ILE00.0150.04663.241-0.105-0.1050.0000.0000.0000.000
49A71ASN0-0.012-0.00567.318-0.143-0.1430.0000.0000.0000.000
50A72THR0-0.005-0.01569.754-0.099-0.0990.0000.0000.0000.000
51A73THR00.010-0.02768.927-0.073-0.0730.0000.0000.0000.000
52A74LYS10.9731.00171.453-4.468-4.4680.0000.0000.0000.000
53A75LYS10.9010.95473.308-4.341-4.3410.0000.0000.0000.000
54A76VAL00.0330.02074.081-0.072-0.0720.0000.0000.0000.000
55A77THR0-0.047-0.03873.873-0.056-0.0560.0000.0000.0000.000
56A78GLU-1-0.917-0.96476.8503.8563.8560.0000.0000.0000.000
57A79VAL0-0.039-0.02079.372-0.070-0.0700.0000.0000.0000.000
58A80VAL00.0160.00378.423-0.061-0.0610.0000.0000.0000.000
59A81GLY00.0550.03780.932-0.043-0.0430.0000.0000.0000.000
60A82ARG10.8560.93082.502-3.868-3.8680.0000.0000.0000.000
61A83VAL0-0.001-0.00584.663-0.055-0.0550.0000.0000.0000.000
62A84GLU-1-0.781-0.88583.3493.7513.7510.0000.0000.0000.000
63A85ARG10.9140.94285.138-3.712-3.7120.0000.0000.0000.000
64A86LYS10.9260.95988.282-3.529-3.5290.0000.0000.0000.000
65A87GLN00.009-0.00488.431-0.029-0.0290.0000.0000.0000.000
66A88ARG10.8220.92984.850-3.701-3.7010.0000.0000.0000.000
67A89LEU0-0.084-0.03791.769-0.025-0.0250.0000.0000.0000.000
68A90PHE0-0.0190.00294.729-0.033-0.0330.0000.0000.0000.000
69A91ASP-1-0.889-0.92991.5493.4603.4600.0000.0000.0000.000
70A92TYR0-0.056-0.04590.5910.0060.0060.0000.0000.0000.000
71A93THR00.011-0.01496.5990.0170.0170.0000.0000.0000.000
72A94GLU-1-0.913-0.91092.7713.4493.4490.0000.0000.0000.000
73A95LEU0-0.0060.00697.332-0.009-0.0090.0000.0000.0000.000
74A96ASP-1-0.763-0.85299.2913.2013.2010.0000.0000.0000.000
75A97PRO00.0090.003100.678-0.023-0.0230.0000.0000.0000.000
76A98SER0-0.047-0.050102.493-0.030-0.0300.0000.0000.0000.000
77A99GLN0-0.068-0.034102.264-0.041-0.0410.0000.0000.0000.000
78A100THR0-0.013-0.004103.4670.0130.0130.0000.0000.0000.000
79A101HIS0-0.0110.014106.111-0.028-0.0280.0000.0000.0000.000
80A102TYR00.023-0.002108.818-0.007-0.0070.0000.0000.0000.000
81A103PHE0-0.019-0.008103.8250.0320.0320.0000.0000.0000.000
82A104ILE00.0160.004103.711-0.027-0.0270.0000.0000.0000.000
83A105ILE00.0160.036101.0400.0370.0370.0000.0000.0000.000
84A106ASN00.003-0.010101.103-0.014-0.0140.0000.0000.0000.000
85A107ASN00.1180.04898.3560.0080.0080.0000.0000.0000.000
86A108GLY0-0.0200.00198.4840.0290.0290.0000.0000.0000.000
87A109ASN0-0.121-0.061100.1570.0020.0020.0000.0000.0000.000
88A110ILE00.0720.033102.836-0.034-0.0340.0000.0000.0000.000
89A111GLY0-0.021-0.006103.9860.0300.0300.0000.0000.0000.000
90A112LEU00.0130.007105.871-0.034-0.0340.0000.0000.0000.000
91A113ALA00.0040.000106.6970.0290.0290.0000.0000.0000.000
92A114GLY00.0220.008108.501-0.016-0.0160.0000.0000.0000.000
93A115ARG10.8050.898109.304-2.742-2.7420.0000.0000.0000.000
94A116ILE0-0.014-0.010106.053-0.011-0.0110.0000.0000.0000.000
95A117LEU0-0.049-0.015110.687-0.011-0.0110.0000.0000.0000.000
96A118SER00.0070.000112.541-0.010-0.0100.0000.0000.0000.000
97A119ILE0-0.028-0.013106.7340.0220.0220.0000.0000.0000.000
98A120GLU-1-0.875-0.953109.9422.7992.7990.0000.0000.0000.000
99A121PRO0-0.037-0.012108.7530.0360.0360.0000.0000.0000.000
100A122ILE00.0020.001106.941-0.030-0.0300.0000.0000.0000.000
101A123ASP-1-0.884-0.950107.6762.9832.9830.0000.0000.0000.000
102A124ASN0-0.015-0.006100.7130.0290.0290.0000.0000.0000.000
103A125GLY0-0.0050.008103.0610.0400.0400.0000.0000.0000.000
104A126SER0-0.021-0.034104.267-0.029-0.0290.0000.0000.0000.000
105A127VAL0-0.024-0.014106.3960.0140.0140.0000.0000.0000.000
106A128ILE0-0.0110.009104.516-0.011-0.0110.0000.0000.0000.000
107A129HIS00.0430.032108.992-0.002-0.0020.0000.0000.0000.000
108A130LEU0-0.029-0.024108.0040.0090.0090.0000.0000.0000.000
109A131ASP-1-0.761-0.864111.9852.7402.7400.0000.0000.0000.000
110A132LEU0-0.014-0.020107.7420.0300.0300.0000.0000.0000.000
111A133VAL00.0110.013111.208-0.029-0.0290.0000.0000.0000.000
112A134ASN00.0250.012110.9060.0570.0570.0000.0000.0000.000
113A135LEU0-0.038-0.030107.696-0.023-0.0230.0000.0000.0000.000
114A136LEU0-0.032-0.008107.592-0.005-0.0050.0000.0000.0000.000
115A137SER0-0.003-0.011111.713-0.014-0.0140.0000.0000.0000.000
116A138ILE00.0060.007110.795-0.027-0.0270.0000.0000.0000.000
117A139PRO00.0210.007113.3350.0220.0220.0000.0000.0000.000
118A140VAL0-0.0180.009109.0510.0210.0210.0000.0000.0000.000
119A141SER00.0480.016110.789-0.024-0.0240.0000.0000.0000.000
120A142ASN0-0.024-0.015108.4070.0070.0070.0000.0000.0000.000
121A143LEU00.0300.030105.2560.0300.0300.0000.0000.0000.000
122A144ALA00.0590.041102.164-0.014-0.0140.0000.0000.0000.000
123A145PHE0-0.016-0.010101.9310.0240.0240.0000.0000.0000.000
124A146ASN0-0.0040.00496.305-0.005-0.0050.0000.0000.0000.000
125A147MET00.0140.00098.630-0.010-0.0100.0000.0000.0000.000
126A148THR0-0.032-0.02892.8910.0360.0360.0000.0000.0000.000
127A149TRP0-0.013-0.00196.293-0.011-0.0110.0000.0000.0000.000
128A150GLY00.0250.00595.5270.0250.0250.0000.0000.0000.000
129A151THR00.0530.02493.329-0.015-0.0150.0000.0000.0000.000
130A152LYS10.8640.92394.365-3.266-3.2660.0000.0000.0000.000
131A153LYS10.9540.98188.152-3.541-3.5410.0000.0000.0000.000
132A154PRO0-0.0110.01187.140-0.010-0.0100.0000.0000.0000.000
133A155SER00.0260.00187.6040.0040.0040.0000.0000.0000.000
134A156GLU-1-0.928-0.95081.4233.9013.9010.0000.0000.0000.000
135A157ALA00.024-0.00880.228-0.013-0.0130.0000.0000.0000.000
136A158LYS10.9380.96979.024-3.928-3.9280.0000.0000.0000.000
137A159ASP-1-0.874-0.94880.3653.7943.7940.0000.0000.0000.000
138A160LEU0-0.016-0.00982.683-0.040-0.0400.0000.0000.0000.000
139A161PRO0-0.029-0.02279.917-0.038-0.0380.0000.0000.0000.000
140A162ARG10.9900.98879.470-3.906-3.9060.0000.0000.0000.000
141A163TRP00.0350.02684.844-0.002-0.0020.0000.0000.0000.000
142A164LYS10.9430.96582.078-3.832-3.8320.0000.0000.0000.000
143A165GLN0-0.040-0.01881.858-0.038-0.0380.0000.0000.0000.000
144A166LEU0-0.021-0.00487.252-0.022-0.0220.0000.0000.0000.000
145A167LEU0-0.091-0.01890.316-0.045-0.0450.0000.0000.0000.000
146A168LEU00.0060.02092.4240.0120.0120.0000.0000.0000.000
147A169ASN0-0.024-0.03093.794-0.017-0.0170.0000.0000.0000.000
148A170THR0-0.022-0.00795.945-0.004-0.0040.0000.0000.0000.000
149A171LYS10.9410.97996.811-3.236-3.2360.0000.0000.0000.000
150A172MET0-0.044-0.012100.224-0.014-0.0140.0000.0000.0000.000
151A173ASP-1-0.860-0.928103.8803.0813.0810.0000.0000.0000.000
152A174SER0-0.093-0.046105.715-0.035-0.0350.0000.0000.0000.000
153A175THR00.015-0.003109.0430.0120.0120.0000.0000.0000.000
154A176ILE0-0.029-0.018111.554-0.026-0.0260.0000.0000.0000.000
155A177GLU-1-0.899-0.940112.3302.7472.7470.0000.0000.0000.000
156A178LEU0-0.056-0.027110.301-0.017-0.0170.0000.0000.0000.000
157A179LEU00.0640.014114.3240.0100.0100.0000.0000.0000.000
158A180PRO0-0.031-0.019115.3480.0100.0100.0000.0000.0000.000
159A181GLY0-0.0120.006115.567-0.026-0.0260.0000.0000.0000.000
160A182ALA0-0.026-0.010117.268-0.015-0.0150.0000.0000.0000.000
161A183TRP0-0.041-0.030112.2470.0270.0270.0000.0000.0000.000
162A184THR00.001-0.006114.698-0.031-0.0310.0000.0000.0000.000
163A185ASN00.0090.004114.3960.0420.0420.0000.0000.0000.000
164A186VAL0-0.0020.006109.2830.0040.0040.0000.0000.0000.000
165A187THR00.0000.001110.564-0.005-0.0050.0000.0000.0000.000
166A188LEU0-0.012-0.006104.5680.0180.0180.0000.0000.0000.000
167A189THR0-0.004-0.024105.756-0.005-0.0050.0000.0000.0000.000
168A190LEU0-0.0090.012101.7090.0270.0270.0000.0000.0000.000
169A191LYS10.9170.942101.880-3.032-3.0320.0000.0000.0000.000
170A192GLY00.007-0.01399.2650.0320.0320.0000.0000.0000.000
171A193VAL00.0080.00698.1130.0270.0270.0000.0000.0000.000
172A194SER00.0230.059100.853-0.017-0.0170.0000.0000.0000.000
173A195PRO00.1420.052102.9480.0300.0300.0000.0000.0000.000
174A196ASN0-0.025-0.010103.005-0.006-0.0060.0000.0000.0000.000
175A197ASN0-0.087-0.05898.9920.0430.0430.0000.0000.0000.000
176A198LEU0-0.025-0.00699.1310.0440.0440.0000.0000.0000.000
177A199LYS10.9240.96297.969-3.170-3.1700.0000.0000.0000.000
178A200TYR0-0.139-0.12393.0110.0240.0240.0000.0000.0000.000
179A201LEU00.0450.02197.557-0.007-0.0070.0000.0000.0000.000
180A202LYS10.9070.97690.820-3.462-3.4620.0000.0000.0000.000
181A203ILE00.010-0.00497.259-0.001-0.0010.0000.0000.0000.000
182A204GLY00.0450.01097.8700.0100.0100.0000.0000.0000.000
183A205ILE0-0.030-0.00698.913-0.020-0.0200.0000.0000.0000.000
184A206ASP-1-0.885-0.95198.2853.2733.2730.0000.0000.0000.000
185A207MET0-0.004-0.01699.537-0.046-0.0460.0000.0000.0000.000
186A208GLU-1-0.944-0.93798.4153.2213.2210.0000.0000.0000.000
187A209ASN0-0.032-0.027101.087-0.007-0.0070.0000.0000.0000.000
188A210VAL00.0100.011104.365-0.034-0.0340.0000.0000.0000.000
189A211ILE0-0.044-0.016106.3830.0030.0030.0000.0000.0000.000
190A212PHE0-0.019-0.024105.788-0.008-0.0080.0000.0000.0000.000
191A213ASP-1-0.943-0.962111.1222.7442.7440.0000.0000.0000.000