FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 98LK2

Calculation Name: 3MGK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MGK

Chain ID: A

ChEMBL ID:

UniProt ID: Q97FB4

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371071.885287
FMO2-HF: Nuclear repulsion 2292810.810312
FMO2-HF: Total energy -78261.074974
FMO2-MP2: Total energy -78493.078883


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-7.529-5.0456.155-3.705-4.933-0.03
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.009
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].
3A4ARG10.9130.9623.8260.0901.974-0.024-1.021-0.8390.002
4A5ILE0-0.047-0.0267.087-0.237-0.2370.0000.0000.0000.000
5A6ASP-1-0.775-0.8909.530-0.018-0.0180.0000.0000.0000.000
6A7VAL0-0.026-0.01813.008-0.023-0.0230.0000.0000.0000.000
7A8LEU0-0.011-0.00315.4070.0270.0270.0000.0000.0000.000
8A9LEU0-0.023-0.00518.719-0.004-0.0040.0000.0000.0000.000
9A10PHE0-0.023-0.02421.7850.0100.0100.0000.0000.0000.000
10A11ASN00.018-0.00725.352-0.002-0.0020.0000.0000.0000.000
11A12LYS10.9320.95228.7160.0410.0410.0000.0000.0000.000
12A13PHE00.0450.03923.310-0.001-0.0010.0000.0000.0000.000
13A14GLU-1-0.844-0.93525.328-0.065-0.0650.0000.0000.0000.000
14A15THR0-0.001-0.04624.021-0.006-0.0060.0000.0000.0000.000
15A16LEU0-0.018-0.00622.483-0.006-0.0060.0000.0000.0000.000
16A17ASP-1-0.807-0.92021.688-0.117-0.1170.0000.0000.0000.000
17A18VAL00.0030.00118.378-0.018-0.0180.0000.0000.0000.000
18A19PHE00.007-0.03418.088-0.014-0.0140.0000.0000.0000.000
19A20GLY00.0230.02618.964-0.006-0.0060.0000.0000.0000.000
20A21PRO00.006-0.00415.154-0.015-0.0150.0000.0000.0000.000
21A22VAL0-0.021-0.00614.184-0.039-0.0390.0000.0000.0000.000
22A23GLU-1-0.920-0.94014.155-0.199-0.1990.0000.0000.0000.000
23A24ILE0-0.010-0.01612.662-0.022-0.0220.0000.0000.0000.000
24A25PHE00.0300.0048.900-0.034-0.0340.0000.0000.0000.000
25A26GLY0-0.0070.0099.554-0.059-0.0590.0000.0000.0000.000
26A27ASN0-0.044-0.03011.8550.0580.0580.0000.0000.0000.000
27A28LEU0-0.050-0.0227.182-0.003-0.0030.0000.0000.0000.000
28A29GLN0-0.057-0.0436.657-0.196-0.1960.0000.0000.0000.000
29A30ASP-1-0.910-0.9335.950-0.034-0.0340.0000.0000.0000.000
30A31ASP-1-1.005-0.9952.370-6.761-5.5310.765-0.842-1.152-0.005
31A32PHE0-0.036-0.0472.225-0.668-1.8035.403-1.727-2.541-0.027
32A33GLU-1-0.914-0.9384.9360.7920.877-0.001-0.007-0.0770.000
33A34LEU0-0.049-0.0387.531-0.261-0.2610.0000.0000.0000.000
34A35ASN00.006-0.00610.8200.0690.0690.0000.0000.0000.000
35A36PHE0-0.0070.00813.038-0.047-0.0470.0000.0000.0000.000
36A37ILE00.0280.01115.8320.0170.0170.0000.0000.0000.000
37A38SER0-0.031-0.03918.544-0.011-0.0110.0000.0000.0000.000
38A39SER0-0.029-0.02421.9830.0020.0020.0000.0000.0000.000
39A40ASP-1-0.929-0.95624.330-0.015-0.0150.0000.0000.0000.000
40A41GLY0-0.0210.00322.7360.0060.0060.0000.0000.0000.000
41A42GLY00.0260.01023.362-0.002-0.0020.0000.0000.0000.000
42A43LEU0-0.041-0.02224.324-0.005-0.0050.0000.0000.0000.000
43A44VAL00.0080.01924.278-0.001-0.0010.0000.0000.0000.000
44A45GLU-1-0.901-0.96526.282-0.036-0.0360.0000.0000.0000.000
45A46SER00.0010.01826.4410.0010.0010.0000.0000.0000.000
46A47SER0-0.041-0.03828.0690.0070.0070.0000.0000.0000.000
47A48GLN0-0.070-0.01828.8790.0010.0010.0000.0000.0000.000
48A49LYS10.9130.95931.0720.0370.0370.0000.0000.0000.000
49A50VAL00.0270.03725.2490.0030.0030.0000.0000.0000.000
50A51ARG10.9000.95127.4460.0250.0250.0000.0000.0000.000
51A52VAL00.0430.03420.9050.0010.0010.0000.0000.0000.000
52A53GLU-1-0.938-0.97421.6640.0080.0080.0000.0000.0000.000
53A54THR0-0.059-0.01619.766-0.003-0.0030.0000.0000.0000.000
54A55SER00.0380.01517.3360.0080.0080.0000.0000.0000.000
55A56LEU00.0150.00319.609-0.010-0.0100.0000.0000.0000.000
56A57TYR0-0.0040.00114.3010.0060.0060.0000.0000.0000.000
57A58THR00.000-0.00514.4240.0030.0030.0000.0000.0000.000
58A59ARG10.9460.96713.8330.0060.0060.0000.0000.0000.000
59A60ASP-1-0.782-0.8908.8100.0910.0910.0000.0000.0000.000
60A61GLU-1-1.007-1.01311.013-0.038-0.0380.0000.0000.0000.000
61A62ASN0-0.110-0.0487.8780.0340.0340.0000.0000.0000.000
62A63ILE00.0200.0273.382-0.601-0.1810.012-0.108-0.3240.000
63A64GLU-1-0.879-0.9395.0090.3530.3530.0000.0000.0000.000
64A65LYS10.8720.9446.137-0.042-0.0420.0000.0000.0000.000
65A66ILE00.0110.0126.3130.0340.0340.0000.0000.0000.000
66A67LEU00.0180.0299.7450.0580.0580.0000.0000.0000.000
67A68PHE00.001-0.00513.348-0.002-0.0020.0000.0000.0000.000
68A69VAL00.005-0.01914.9810.0300.0300.0000.0000.0000.000
69A70PRO00.0170.01618.759-0.002-0.0020.0000.0000.0000.000
70A71GLY00.0320.00421.1900.0090.0090.0000.0000.0000.000
71A72GLY00.0770.03524.8660.0010.0010.0000.0000.0000.000
72A73SER0-0.070-0.05627.9200.0030.0030.0000.0000.0000.000
73A74GLY00.0180.01829.1910.0030.0030.0000.0000.0000.000
74A75THR0-0.0010.00726.3100.0030.0030.0000.0000.0000.000
75A76ARG10.8610.93428.9780.0520.0520.0000.0000.0000.000
76A77GLU-1-0.918-0.96932.653-0.031-0.0310.0000.0000.0000.000
77A78LYS10.9380.98127.1280.0440.0440.0000.0000.0000.000
78A79VAL0-0.010-0.00629.074-0.001-0.0010.0000.0000.0000.000
79A80ASN0-0.030-0.02430.3970.0010.0010.0000.0000.0000.000
80A81ASP-1-0.807-0.85429.695-0.029-0.0290.0000.0000.0000.000
81A82ASP-1-0.836-0.93129.615-0.029-0.0290.0000.0000.0000.000
82A83ASN0-0.002-0.02029.0360.0000.0000.0000.0000.0000.000
83A84PHE0-0.091-0.04023.894-0.004-0.0040.0000.0000.0000.000
84A85ILE00.010-0.00624.993-0.006-0.0060.0000.0000.0000.000
85A86ASN0-0.001-0.00724.886-0.004-0.0040.0000.0000.0000.000
86A87PHE0-0.0250.00620.452-0.002-0.0020.0000.0000.0000.000
87A88ILE00.0210.00720.260-0.006-0.0060.0000.0000.0000.000
88A89GLY00.0410.02520.050-0.010-0.0100.0000.0000.0000.000
89A90ASN0-0.077-0.04920.7520.0000.0000.0000.0000.0000.000
90A91MET00.0180.00816.754-0.003-0.0030.0000.0000.0000.000
91A92VAL0-0.046-0.01116.200-0.020-0.0200.0000.0000.0000.000
92A93LYS10.8720.92816.5130.0240.0240.0000.0000.0000.000
93A94GLU-1-0.937-0.95914.394-0.037-0.0370.0000.0000.0000.000
94A95SER0-0.073-0.03812.036-0.037-0.0370.0000.0000.0000.000
95A96LYS10.8920.9667.374-0.006-0.0060.0000.0000.0000.000
96A97TYR0-0.014-0.0247.6260.0740.0740.0000.0000.0000.000
97A98ILE0-0.0100.00611.606-0.004-0.0040.0000.0000.0000.000
98A99ILE00.0430.01811.3290.0120.0120.0000.0000.0000.000
99A100SER00.0130.01215.4290.0160.0160.0000.0000.0000.000
100A101VAL00.0140.02018.513-0.006-0.0060.0000.0000.0000.000
101A102CYS0-0.0260.01321.0100.0150.0150.0000.0000.0000.000
102A103THR0-0.038-0.05524.670-0.001-0.0010.0000.0000.0000.000
103A104GLY00.0520.05822.2400.0060.0060.0000.0000.0000.000
104A105SER0-0.028-0.03922.8430.0030.0030.0000.0000.0000.000
105A106ALA00.002-0.01223.8160.0060.0060.0000.0000.0000.000
106A107LEU0-0.023-0.00723.6600.0070.0070.0000.0000.0000.000
107A108LEU00.0240.01619.0010.0040.0040.0000.0000.0000.000
108A109SER0-0.019-0.01022.9280.0060.0060.0000.0000.0000.000
109A110LYS10.9871.01426.1120.0450.0450.0000.0000.0000.000
110A111ALA0-0.003-0.00223.5630.0050.0050.0000.0000.0000.000
111A112GLY0-0.023-0.02025.4450.0010.0010.0000.0000.0000.000
112A113ILE0-0.019-0.00819.8780.0020.0020.0000.0000.0000.000
113A114LEU0-0.062-0.03121.617-0.004-0.0040.0000.0000.0000.000
114A115ASN00.0490.03624.405-0.001-0.0010.0000.0000.0000.000
115A116GLY0-0.0170.00026.4740.0010.0010.0000.0000.0000.000
116A117LYS10.9130.95521.1370.0600.0600.0000.0000.0000.000
117A118ARG10.8800.95522.2390.0780.0780.0000.0000.0000.000
118A119ALA00.0130.00923.179-0.010-0.0100.0000.0000.0000.000
119A120THR0-0.008-0.01723.6950.0090.0090.0000.0000.0000.000
120A121THR00.0490.03624.858-0.002-0.0020.0000.0000.0000.000
121A122ASN00.0200.00026.504-0.001-0.0010.0000.0000.0000.000
122A123LYS10.7920.89227.8850.0890.0890.0000.0000.0000.000
123A124ARG10.9160.95231.6020.0600.0600.0000.0000.0000.000
124A125SER0-0.031-0.01730.6820.0050.0050.0000.0000.0000.000
125A126PHE00.0750.04729.7490.0010.0010.0000.0000.0000.000
126A127LYS10.9361.01232.5350.0360.0360.0000.0000.0000.000
127A128TRP00.0230.01230.1270.0000.0000.0000.0000.0000.000
128A129VAL00.0170.00028.1440.0010.0010.0000.0000.0000.000
129A130THR0-0.069-0.08030.9450.0020.0020.0000.0000.0000.000
130A131GLU-1-0.885-0.95032.655-0.036-0.0360.0000.0000.0000.000
131A132GLN0-0.092-0.03431.9960.0020.0020.0000.0000.0000.000
132A133ASN0-0.031-0.02529.1380.0050.0050.0000.0000.0000.000
133A134GLU-1-0.932-0.96232.363-0.034-0.0340.0000.0000.0000.000
134A135ASP-1-0.920-0.94931.623-0.033-0.0330.0000.0000.0000.000
135A136VAL0-0.056-0.01726.722-0.002-0.0020.0000.0000.0000.000
136A137LEU0-0.013-0.00428.1860.0030.0030.0000.0000.0000.000
137A138TRP0-0.027-0.02226.102-0.009-0.0090.0000.0000.0000.000
138A139VAL0-0.0010.00126.8620.0040.0040.0000.0000.0000.000
139A140LYS10.8740.93228.8210.0490.0490.0000.0000.0000.000
140A141GLU-1-0.901-0.97530.849-0.057-0.0570.0000.0000.0000.000
141A142ALA00.0340.05725.359-0.002-0.0020.0000.0000.0000.000
142A143ARG10.7700.90323.6900.1280.1280.0000.0000.0000.000
143A144TRP00.032-0.00618.257-0.002-0.0020.0000.0000.0000.000
144A145VAL0-0.0140.00421.1080.0080.0080.0000.0000.0000.000
145A146LYS10.8960.96814.8850.1440.1440.0000.0000.0000.000
146A147ASP-1-0.882-0.96018.864-0.055-0.0550.0000.0000.0000.000
147A148GLY00.0320.02317.6880.0000.0000.0000.0000.0000.000
148A149ASN0-0.034-0.02013.0020.0000.0000.0000.0000.0000.000
149A150ILE00.0340.01514.166-0.034-0.0340.0000.0000.0000.000
150A151TYR0-0.080-0.08913.5250.0120.0120.0000.0000.0000.000
151A152THR00.0050.01017.0200.0020.0020.0000.0000.0000.000
152A153SER00.0840.01619.7410.0030.0030.0000.0000.0000.000
153A154SER0-0.041-0.01421.7230.0120.0120.0000.0000.0000.000
154A155GLY0-0.018-0.02224.6990.0000.0000.0000.0000.0000.000
155A156VAL00.0570.02123.881-0.007-0.0070.0000.0000.0000.000
156A157SER00.0430.02323.001-0.006-0.0060.0000.0000.0000.000
157A158ALA0-0.030-0.00622.556-0.009-0.0090.0000.0000.0000.000
158A159GLY00.0190.01320.002-0.013-0.0130.0000.0000.0000.000
159A160ILE00.0450.03418.274-0.022-0.0220.0000.0000.0000.000
160A161ASP-1-0.700-0.83217.847-0.182-0.1820.0000.0000.0000.000
161A162MET00.0040.00615.666-0.003-0.0030.0000.0000.0000.000
162A163THR0-0.062-0.02312.739-0.023-0.0230.0000.0000.0000.000
163A164LEU00.0330.01813.199-0.065-0.0650.0000.0000.0000.000
164A165GLY00.0200.01514.312-0.027-0.0270.0000.0000.0000.000
165A166PHE0-0.013-0.0108.0670.0120.0120.0000.0000.0000.000
166A167ILE00.0060.0018.737-0.053-0.0530.0000.0000.0000.000
167A168GLU-1-0.908-0.96310.450-0.280-0.2800.0000.0000.0000.000
168A169ASP-1-0.854-0.88212.295-0.214-0.2140.0000.0000.0000.000
169A170LEU0-0.092-0.0375.4960.0640.0640.0000.0000.0000.000
170A171ILE0-0.008-0.0104.8340.0260.0260.0000.0000.0000.000
171A172GLY0-0.0180.0108.2250.0650.0650.0000.0000.0000.000
172A173LYS10.8870.93411.7980.1260.1260.0000.0000.0000.000
173A174GLU-1-0.933-0.97414.420-0.231-0.2310.0000.0000.0000.000
174A175LYS11.0421.0248.2360.8950.8950.0000.0000.0000.000
175A176ALA00.0100.02012.5920.0020.0020.0000.0000.0000.000
176A177LEU0-0.036-0.03414.4480.0360.0360.0000.0000.0000.000
177A178GLU-1-0.947-0.97613.585-0.364-0.3640.0000.0000.0000.000
178A179ILE00.0440.03911.7660.0340.0340.0000.0000.0000.000
179A180SER0-0.077-0.02516.0050.0470.0470.0000.0000.0000.000
180A181ARG10.9180.94618.9920.2260.2260.0000.0000.0000.000
181A182SER0-0.038-0.02217.7530.0140.0140.0000.0000.0000.000
182A183ILE0-0.025-0.00717.6380.0180.0180.0000.0000.0000.000
183A184GLU-1-1.007-0.99320.640-0.097-0.0970.0000.0000.0000.000
184A185TYR0-0.089-0.05120.5570.0170.0170.0000.0000.0000.000
185A186PHE0-0.067-0.04422.659-0.007-0.0070.0000.0000.0000.000
186A187TRP00.0310.01417.397-0.001-0.0010.0000.0000.0000.000
187A188ASN0-0.124-0.07222.5560.0160.0160.0000.0000.0000.000
188A189GLU-1-0.833-0.94221.075-0.164-0.1640.0000.0000.0000.000
189A190ASP-1-0.860-0.92122.458-0.095-0.0950.0000.0000.0000.000
190A191SER00.0290.01821.754-0.001-0.0010.0000.0000.0000.000
191A192ASN0-0.040-0.03523.7150.0030.0030.0000.0000.0000.000
192A193TYR0-0.020-0.00127.1710.0060.0060.0000.0000.0000.000
193A194ASP-1-0.815-0.93228.349-0.090-0.0900.0000.0000.0000.000
194A195PRO0-0.017-0.00229.8180.0070.0070.0000.0000.0000.000
195A196PHE00.006-0.01929.7560.0060.0060.0000.0000.0000.000
196A197SER0-0.036-0.03531.9590.0030.0030.0000.0000.0000.000
197A198LYS10.9110.95733.9760.0620.0620.0000.0000.0000.000
198A199ILE0-0.0110.01035.5550.0030.0030.0000.0000.0000.000
199A200TYR00.0400.04834.4670.0040.0040.0000.0000.0000.000