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: LNMG9

Calculation Name: 2DG7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DG7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RK42

Base Structure: X-ray

Registration Date: 2023-09-20

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1828766.477391
FMO2-HF: Nuclear repulsion 1758309.708833
FMO2-HF: Total energy -70456.768558
FMO2-MP2: Total energy -70664.916859


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-22.727-18.54624.585-9.669-19.095-0.025
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.003
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].
3A3ARG10.9250.9693.3710.6242.858-0.012-1.019-1.203-0.001
4A4TRP0-0.011-0.0132.442-5.786-2.3604.985-3.086-5.325-0.027
5A5ASP-1-0.777-0.8694.4040.4890.771-0.001-0.016-0.2640.000
6A6PRO00.0070.0066.0920.3940.3940.0000.0000.0000.000
7A7GLY00.0230.0218.4160.2640.2640.0000.0000.0000.000
8A8ALA0-0.033-0.0104.9620.2220.2220.0000.0000.0000.000
9A9GLU-1-0.873-0.9476.8581.5991.5990.0000.0000.0000.000
10A10GLN00.0640.0268.379-0.047-0.0470.0000.0000.0000.000
11A11ARG10.7630.8507.416-0.710-0.7100.0000.0000.0000.000
12A12LEU0-0.0160.0016.7760.0060.0060.0000.0000.0000.000
13A13LYS10.8170.90811.020-0.852-0.8520.0000.0000.0000.000
14A14ARG10.8380.91413.772-0.412-0.4120.0000.0000.0000.000
15A15ALA00.0370.02013.585-0.054-0.0540.0000.0000.0000.000
16A16ALA0-0.004-0.00915.060-0.052-0.0520.0000.0000.0000.000
17A17LEU0-0.0200.00816.715-0.062-0.0620.0000.0000.0000.000
18A18GLU-1-0.871-0.91218.3720.3790.3790.0000.0000.0000.000
19A19LEU00.0350.01617.114-0.036-0.0360.0000.0000.0000.000
20A20TYR0-0.057-0.05517.942-0.029-0.0290.0000.0000.0000.000
21A21SER0-0.025-0.02522.337-0.036-0.0360.0000.0000.0000.000
22A22GLU-1-0.867-0.89822.0820.3010.3010.0000.0000.0000.000
23A23HIS0-0.003-0.00422.391-0.007-0.0070.0000.0000.0000.000
24A24GLY00.0320.03424.901-0.019-0.0190.0000.0000.0000.000
25A25TYR0-0.031-0.05420.4790.0350.0350.0000.0000.0000.000
26A26ASP-1-0.886-0.94222.0400.2880.2880.0000.0000.0000.000
27A27ASN0-0.099-0.04822.845-0.003-0.0030.0000.0000.0000.000
28A28VAL00.0400.03917.9160.0060.0060.0000.0000.0000.000
29A29THR0-0.077-0.06515.5930.0110.0110.0000.0000.0000.000
30A30VAL00.029-0.00411.3180.0170.0170.0000.0000.0000.000
31A31THR0-0.027-0.00611.2330.1770.1770.0000.0000.0000.000
32A32ASP-1-0.783-0.85312.3040.5360.5360.0000.0000.0000.000
33A33ILE00.0210.01712.2830.0260.0260.0000.0000.0000.000
34A34ALA0-0.027-0.0268.3610.1010.1010.0000.0000.0000.000
35A35GLU-1-0.933-0.97310.1840.6180.6180.0000.0000.0000.000
36A36ARG10.7510.84712.068-0.463-0.4630.0000.0000.0000.000
37A37ALA00.0040.01110.056-0.075-0.0750.0000.0000.0000.000
38A38GLY00.0000.01010.167-0.003-0.0030.0000.0000.0000.000
39A39LEU0-0.093-0.0464.7890.2930.4750.001-0.029-0.1540.000
40A40THR00.0420.0083.891-1.048-0.905-0.001-0.041-0.1020.000
41A41ARG11.0280.9876.0320.0330.0330.0000.0000.0000.000
42A42ARG10.9290.9613.7410.7921.0360.002-0.030-0.2150.000
43A43SER00.015-0.0202.330-4.333-5.7599.465-3.994-4.044-0.011
44A44TYR00.0390.0103.3493.1341.057-0.0302.609-0.502-0.004
45A45PHE00.0040.0006.4710.0520.0520.0000.0000.0000.000
46A46ARG10.8030.9122.100-18.479-19.2409.301-3.035-5.5040.031
47A47TYR0-0.033-0.0212.636-0.9380.9960.875-1.028-1.782-0.013
48A48PHE00.0600.0277.496-0.333-0.3330.0000.0000.0000.000
49A49PRO00.0080.00810.4220.0150.0150.0000.0000.0000.000
50A50ASP-1-0.763-0.87612.4030.4810.4810.0000.0000.0000.000
51A51LYS10.8220.90614.304-0.275-0.2750.0000.0000.0000.000
52A52ARG10.8720.94316.323-0.424-0.4240.0000.0000.0000.000
53A53GLU-1-0.755-0.88714.2710.6200.6200.0000.0000.0000.000
54A54VAL0-0.0230.02112.6660.0270.0270.0000.0000.0000.000
55A55LEU00.0200.00814.288-0.023-0.0230.0000.0000.0000.000
56A56PHE0-0.064-0.02016.667-0.076-0.0760.0000.0000.0000.000
57A57GLY00.0630.03013.9030.0340.0340.0000.0000.0000.000
58A58GLY00.0050.01413.478-0.086-0.0860.0000.0000.0000.000
59A59SER0-0.092-0.06214.920-0.042-0.0420.0000.0000.0000.000
60A60GLU-1-0.760-0.87818.4490.4510.4510.0000.0000.0000.000
61A61LEU00.0170.02220.6210.0050.0050.0000.0000.0000.000
62A62LEU00.0500.01716.588-0.012-0.0120.0000.0000.0000.000
63A63PRO00.0750.03721.157-0.027-0.0270.0000.0000.0000.000
64A64PRO0-0.008-0.01721.232-0.023-0.0230.0000.0000.0000.000
65A65ALA0-0.062-0.02521.208-0.020-0.0200.0000.0000.0000.000
66A66VAL00.0720.03823.265-0.022-0.0220.0000.0000.0000.000
67A67ALA00.0270.01426.573-0.019-0.0190.0000.0000.0000.000
68A68ARG10.8950.94220.893-0.233-0.2330.0000.0000.0000.000
69A69ALA00.0310.02326.900-0.014-0.0140.0000.0000.0000.000
70A70VAL00.0200.00228.528-0.011-0.0110.0000.0000.0000.000
71A71LEU0-0.084-0.03829.567-0.011-0.0110.0000.0000.0000.000
72A72ALA0-0.037-0.01029.787-0.011-0.0110.0000.0000.0000.000
73A73ALA0-0.0030.01931.851-0.006-0.0060.0000.0000.0000.000
74A74ASP-1-0.854-0.92934.5300.0600.0600.0000.0000.0000.000
75A75PRO0-0.053-0.03938.1310.0020.0020.0000.0000.0000.000
76A76GLY0-0.0090.00940.368-0.001-0.0010.0000.0000.0000.000
77A77ALA0-0.024-0.00339.247-0.001-0.0010.0000.0000.0000.000
78A78ALA00.0190.00941.3700.0000.0000.0000.0000.0000.000
79A79PRO00.0400.01039.1290.0050.0050.0000.0000.0000.000
80A80LEU00.002-0.00837.7490.0070.0070.0000.0000.0000.000
81A81THR00.0210.01237.2110.0060.0060.0000.0000.0000.000
82A82ALA00.0530.03435.8130.0060.0060.0000.0000.0000.000
83A83VAL0-0.017-0.01232.7500.0090.0090.0000.0000.0000.000
84A84LEU00.0070.00632.2030.0130.0130.0000.0000.0000.000
85A85ASP-1-0.850-0.90932.1970.1190.1190.0000.0000.0000.000
86A86ALA0-0.053-0.02329.6670.0100.0100.0000.0000.0000.000
87A87MET0-0.060-0.04027.9140.0130.0130.0000.0000.0000.000
88A88SER00.013-0.00927.3310.0190.0190.0000.0000.0000.000
89A89GLN0-0.061-0.02926.4310.0110.0110.0000.0000.0000.000
90A90VAL0-0.062-0.03722.3690.0120.0120.0000.0000.0000.000
91A91GLY00.022-0.00222.7380.0300.0300.0000.0000.0000.000
92A92ALA0-0.0030.00824.3630.0060.0060.0000.0000.0000.000
93A93GLN0-0.026-0.02819.324-0.005-0.0050.0000.0000.0000.000
94A94LEU0-0.0280.00020.9130.0040.0040.0000.0000.0000.000
95A95VAL0-0.0020.00022.556-0.004-0.0040.0000.0000.0000.000
96A96ALA00.0000.02124.005-0.020-0.0200.0000.0000.0000.000
97A97GLN0-0.072-0.05622.821-0.018-0.0180.0000.0000.0000.000
98A98VAL00.0480.02923.9590.0230.0230.0000.0000.0000.000
99A99GLU-1-0.806-0.88520.6460.2980.2980.0000.0000.0000.000
100A100GLY0-0.0010.01320.9770.0250.0250.0000.0000.0000.000
101A101ALA00.000-0.00822.0510.0110.0110.0000.0000.0000.000
102A102ALA00.0670.02424.072-0.001-0.0010.0000.0000.0000.000
103A103GLN0-0.020-0.01622.3280.0010.0010.0000.0000.0000.000
104A104ARG10.8050.88720.351-0.382-0.3820.0000.0000.0000.000
105A105ARG10.7740.86223.042-0.246-0.2460.0000.0000.0000.000
106A106ALA00.0320.01826.646-0.007-0.0070.0000.0000.0000.000
107A107VAL0-0.003-0.01122.312-0.007-0.0070.0000.0000.0000.000
108A108ILE0-0.026-0.01622.136-0.002-0.0020.0000.0000.0000.000
109A109ASP-1-0.803-0.86925.7100.1990.1990.0000.0000.0000.000
110A110ALA0-0.0180.00628.129-0.016-0.0160.0000.0000.0000.000
111A111SER00.0170.01225.779-0.011-0.0110.0000.0000.0000.000
112A112PRO00.0130.01228.1340.0080.0080.0000.0000.0000.000
113A113GLU-1-0.741-0.84523.3270.3430.3430.0000.0000.0000.000
114A114LEU00.0100.00921.6670.0180.0180.0000.0000.0000.000
115A115GLN0-0.029-0.01425.107-0.003-0.0030.0000.0000.0000.000
116A116GLU-1-0.959-0.98828.1730.1960.1960.0000.0000.0000.000
117A117ARG0-0.022-0.00218.8700.0020.0020.0000.0000.0000.000
118A118GLU-1-0.708-0.84124.7830.3010.3010.0000.0000.0000.000
119A119ARG10.8720.94625.779-0.200-0.2000.0000.0000.0000.000
120A120THR0-0.022-0.01925.852-0.014-0.0140.0000.0000.0000.000
121A121LYS10.7390.84818.262-0.516-0.5160.0000.0000.0000.000
122A122SER0-0.032-0.02625.256-0.008-0.0080.0000.0000.0000.000
123A123ALA00.0020.00528.341-0.013-0.0130.0000.0000.0000.000
124A124ALA0-0.004-0.00325.860-0.011-0.0110.0000.0000.0000.000
125A125ILE0-0.025-0.01224.880-0.009-0.0090.0000.0000.0000.000
126A126SER00.0200.00027.948-0.015-0.0150.0000.0000.0000.000
127A127ARG10.8630.90330.381-0.136-0.1360.0000.0000.0000.000
128A128ALA00.0140.00827.574-0.009-0.0090.0000.0000.0000.000
129A129VAL0-0.010-0.00529.572-0.010-0.0100.0000.0000.0000.000
130A130GLN00.0550.04231.966-0.014-0.0140.0000.0000.0000.000
131A131ASP-1-0.806-0.89531.4350.1260.1260.0000.0000.0000.000
132A132ALA0-0.086-0.02631.227-0.008-0.0080.0000.0000.0000.000
133A133LEU00.0390.01333.264-0.008-0.0080.0000.0000.0000.000
134A134VAL00.0470.04336.795-0.007-0.0070.0000.0000.0000.000
135A135ARG10.8040.87929.521-0.129-0.1290.0000.0000.0000.000
136A136ARG10.8190.89234.094-0.088-0.0880.0000.0000.0000.000
137A137GLN0-0.056-0.02038.519-0.007-0.0070.0000.0000.0000.000
138A138VAL00.0050.01940.269-0.003-0.0030.0000.0000.0000.000
139A139ASP-1-0.818-0.88641.5470.0750.0750.0000.0000.0000.000
140A140ALA00.025-0.01240.7520.0050.0050.0000.0000.0000.000
141A141ASP-1-0.869-0.92241.0150.0810.0810.0000.0000.0000.000
142A142THR0-0.038-0.05542.7350.0040.0040.0000.0000.0000.000
143A143ALA0-0.040-0.02138.0430.0050.0050.0000.0000.0000.000
144A144GLU-1-0.972-0.98637.9790.1150.1150.0000.0000.0000.000
145A145LEU00.0070.00438.6430.0060.0060.0000.0000.0000.000
146A146VAL0-0.014-0.01137.7080.0040.0040.0000.0000.0000.000
147A147ALA00.0060.01434.3630.0050.0050.0000.0000.0000.000
148A148GLN00.0300.03934.9720.0190.0190.0000.0000.0000.000
149A149LEU0-0.0050.00536.5580.0050.0050.0000.0000.0000.000
150A150ALA00.0220.00334.5810.0020.0020.0000.0000.0000.000
151A151THR0-0.030-0.03030.9420.0110.0110.0000.0000.0000.000
152A152VAL0-0.010-0.00432.9420.0080.0080.0000.0000.0000.000
153A153ALA0-0.0060.00235.4700.0020.0020.0000.0000.0000.000
154A154PHE00.0600.01627.3960.0020.0020.0000.0000.0000.000
155A155GLY00.0160.00630.5560.0080.0080.0000.0000.0000.000
156A156SER0-0.041-0.03531.6110.0030.0030.0000.0000.0000.000
157A157ALA0-0.035-0.00733.113-0.003-0.0030.0000.0000.0000.000
158A158PHE0-0.0030.00224.4100.0020.0020.0000.0000.0000.000
159A159ARG10.8370.89430.194-0.181-0.1810.0000.0000.0000.000
160A160ARG10.9080.95531.811-0.120-0.1200.0000.0000.0000.000
161A161TRP0-0.008-0.00525.4790.0010.0010.0000.0000.0000.000
162A162ILE0-0.047-0.01826.8440.0020.0020.0000.0000.0000.000
163A163ASP-1-0.919-0.97330.4180.1560.1560.0000.0000.0000.000
164A164ALA0-0.060-0.02133.899-0.008-0.0080.0000.0000.0000.000
165A165GLU-1-0.917-0.96631.4780.1280.1280.0000.0000.0000.000
166A166GLY00.0080.00831.1610.0020.0020.0000.0000.0000.000
167A167HIS0-0.105-0.04231.965-0.011-0.0110.0000.0000.0000.000
168A168ALA0-0.026-0.01434.771-0.009-0.0090.0000.0000.0000.000
169A169ASP-1-0.789-0.85933.0120.1200.1200.0000.0000.0000.000
170A170PHE00.0470.00230.396-0.001-0.0010.0000.0000.0000.000
171A171GLY00.0260.02332.5290.0000.0000.0000.0000.0000.000
172A172SER00.035-0.01435.291-0.004-0.0040.0000.0000.0000.000
173A173CYS0-0.128-0.03934.352-0.003-0.0030.0000.0000.0000.000
174A174LEU00.0380.00333.551-0.001-0.0010.0000.0000.0000.000
175A175ASP-1-0.858-0.92236.5080.0950.0950.0000.0000.0000.000
176A176THR0-0.048-0.03939.955-0.005-0.0050.0000.0000.0000.000
177A177VAL0-0.039-0.00737.114-0.004-0.0040.0000.0000.0000.000
178A178THR0-0.036-0.02338.973-0.004-0.0040.0000.0000.0000.000
179A179ASP-1-0.815-0.89241.4740.0760.0760.0000.0000.0000.000
180A180ARG10.9100.95943.182-0.086-0.0860.0000.0000.0000.000
181A181LEU00.006-0.00539.650-0.003-0.0030.0000.0000.0000.000
182A182ARG10.8840.92544.107-0.083-0.0830.0000.0000.0000.000
183A183ALA00.0100.01846.878-0.003-0.0030.0000.0000.0000.000
184A184VAL0-0.033-0.02046.257-0.003-0.0030.0000.0000.0000.000
185A185LEU0-0.033-0.01745.902-0.002-0.0020.0000.0000.0000.000
186A186THR0-0.066-0.03649.393-0.003-0.0030.0000.0000.0000.000
187A187GLY0-0.085-0.02952.205-0.004-0.0040.0000.0000.0000.000