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: NNV8Q

Calculation Name: 2DG8-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2DG8

Chain ID: A

ChEMBL ID:
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UniProt ID: Q93J02

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1788335.740718
FMO2-HF: Nuclear repulsion 1719581.413983
FMO2-HF: Total energy -68754.326735
FMO2-MP2: Total energy -68958.821326


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:7:ASP)


Summations of interaction energy for fragment #1(A:7: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.
-200.823-212.71148.82-19.996-16.9370.231
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.752 / q_NPA : -0.856
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].
3A9GLN00.020-0.0063.2620.4582.2960.020-0.715-1.1440.001
4A10ARG10.8390.9141.704-121.477-125.00322.120-9.685-8.9100.111
5A11ARG10.7520.8413.702-34.793-34.2050.069-0.250-0.4060.003
6A12GLU-1-0.765-0.8676.96926.34126.3410.0000.0000.0000.000
7A13ARG10.8430.9181.737-115.639-126.42726.611-9.346-6.4770.116
8A14ILE0-0.021-0.0037.303-3.864-3.8640.0000.0000.0000.000
9A15LEU0-0.0040.0149.759-2.862-2.8620.0000.0000.0000.000
10A16ALA00.004-0.00110.307-2.021-2.0210.0000.0000.0000.000
11A17ALA00.0600.03111.051-1.968-1.9680.0000.0000.0000.000
12A18THR0-0.051-0.04612.767-1.962-1.9620.0000.0000.0000.000
13A19LEU0-0.0110.00115.141-1.217-1.2170.0000.0000.0000.000
14A20ASP-1-0.810-0.88713.70920.39820.3980.0000.0000.0000.000
15A21LEU0-0.073-0.02716.736-0.951-0.9510.0000.0000.0000.000
16A22ILE0-0.027-0.02618.622-0.923-0.9230.0000.0000.0000.000
17A23ALA00.0140.00820.383-0.795-0.7950.0000.0000.0000.000
18A24GLU-1-0.835-0.88018.74316.03216.0320.0000.0000.0000.000
19A25GLU-1-0.851-0.91220.39014.81214.8120.0000.0000.0000.000
20A26GLY00.0630.04823.626-0.494-0.4940.0000.0000.0000.000
21A27ILE0-0.008-0.03023.2110.5400.5400.0000.0000.0000.000
22A28ALA0-0.034-0.01624.3720.2640.2640.0000.0000.0000.000
23A29ARG10.8010.89222.836-13.360-13.3600.0000.0000.0000.000
24A30VAL00.0560.03919.3790.8260.8260.0000.0000.0000.000
25A31SER0-0.037-0.03119.203-0.513-0.5130.0000.0000.0000.000
26A32HIS00.0770.02516.2530.8170.8170.0000.0000.0000.000
27A33ARG10.9510.96615.481-13.640-13.6400.0000.0000.0000.000
28A34ARG10.8960.95616.356-13.601-13.6010.0000.0000.0000.000
29A35ILE00.0630.03612.7770.5680.5680.0000.0000.0000.000
30A36ALA00.010-0.01011.5141.9101.9100.0000.0000.0000.000
31A37GLN0-0.059-0.02911.2821.3271.3270.0000.0000.0000.000
32A38ARG10.7550.85012.736-16.867-16.8670.0000.0000.0000.000
33A39ALA00.0080.0118.1860.7710.7710.0000.0000.0000.000
34A40GLY0-0.0080.0107.3925.5875.5870.0000.0000.0000.000
35A41VAL0-0.051-0.0305.8476.2196.2190.0000.0000.0000.000
36A42PRO00.0290.0207.693-4.422-4.4220.0000.0000.0000.000
37A43LEU00.0530.01510.8870.9250.9250.0000.0000.0000.000
38A44GLY00.0260.01713.508-0.354-0.3540.0000.0000.0000.000
39A45SER0-0.012-0.0298.7061.1861.1860.0000.0000.0000.000
40A46MET0-0.0370.00110.553-0.247-0.2470.0000.0000.0000.000
41A47THR00.004-0.00813.316-0.770-0.7700.0000.0000.0000.000
42A48TYR0-0.066-0.0179.566-0.832-0.8320.0000.0000.0000.000
43A49HIS00.0040.0057.148-2.382-2.3820.0000.0000.0000.000
44A50PHE00.001-0.00111.274-0.564-0.5640.0000.0000.0000.000
45A51THR00.000-0.01315.792-0.570-0.5700.0000.0000.0000.000
46A52GLY00.0250.00619.229-0.782-0.7820.0000.0000.0000.000
47A53ILE0-0.032-0.02318.6870.6290.6290.0000.0000.0000.000
48A54GLU-1-0.833-0.90520.53112.82112.8210.0000.0000.0000.000
49A55GLN00.0340.03317.005-0.308-0.3080.0000.0000.0000.000
50A56LEU0-0.032-0.01214.2730.2530.2530.0000.0000.0000.000
51A57LEU00.0260.00817.1780.4300.4300.0000.0000.0000.000
52A58ARG10.7930.87619.839-12.729-12.7290.0000.0000.0000.000
53A59GLU-1-0.742-0.83315.01020.86220.8620.0000.0000.0000.000
54A60ALA0-0.047-0.01516.1380.3880.3880.0000.0000.0000.000
55A61PHE00.037-0.00217.044-0.116-0.1160.0000.0000.0000.000
56A62GLY00.0200.02320.155-0.473-0.4730.0000.0000.0000.000
57A63ARG10.8610.90711.378-24.349-24.3490.0000.0000.0000.000
58A64PHE0-0.012-0.00217.8200.0660.0660.0000.0000.0000.000
59A65THR00.0140.00720.248-0.449-0.4490.0000.0000.0000.000
60A66ASP-1-0.868-0.92719.73614.45914.4590.0000.0000.0000.000
61A67HIS0-0.093-0.04719.1700.2270.2270.0000.0000.0000.000
62A68ILE00.0450.02521.084-0.411-0.4110.0000.0000.0000.000
63A69VAL0-0.030-0.02124.478-0.522-0.5220.0000.0000.0000.000
64A70ALA0-0.031-0.01622.027-0.395-0.3950.0000.0000.0000.000
65A71VAL00.0620.04524.099-0.312-0.3120.0000.0000.0000.000
66A72PHE0-0.005-0.01626.265-0.501-0.5010.0000.0000.0000.000
67A73ASP-1-0.835-0.91726.86810.34010.3400.0000.0000.0000.000
68A74GLU-1-0.981-0.97425.12311.79511.7950.0000.0000.0000.000
69A75HIS0-0.013-0.01528.136-0.631-0.6310.0000.0000.0000.000
70A76LEU0-0.065-0.04231.571-0.369-0.3690.0000.0000.0000.000
71A77GLY0-0.048-0.02831.088-0.303-0.3030.0000.0000.0000.000
72A78ALA0-0.036-0.01131.808-0.127-0.1270.0000.0000.0000.000
73A79ALA0-0.0080.02033.331-0.231-0.2310.0000.0000.0000.000
74A80ALA00.0060.00836.9020.0430.0430.0000.0000.0000.000
75A81ASP-1-0.880-0.94139.3707.1157.1150.0000.0000.0000.000
76A82ARG10.8810.89340.877-6.486-6.4860.0000.0000.0000.000
77A83ASP-1-0.834-0.88042.7156.8046.8040.0000.0000.0000.000
78A84GLU-1-0.830-0.91239.4887.9177.9170.0000.0000.0000.000
79A85ALA0-0.0160.00038.1190.1870.1870.0000.0000.0000.000
80A86ARG10.7650.84638.765-6.788-6.7880.0000.0000.0000.000
81A87GLU-1-0.815-0.90140.4687.5477.5470.0000.0000.0000.000
82A88ALA00.0470.02335.1800.0910.0910.0000.0000.0000.000
83A89VAL0-0.002-0.01235.6240.2240.2240.0000.0000.0000.000
84A90ALA0-0.036-0.02637.0030.0550.0550.0000.0000.0000.000
85A91ASP-1-0.816-0.86534.3528.6078.6070.0000.0000.0000.000
86A92LEU00.0040.01430.9310.1340.1340.0000.0000.0000.000
87A93VAL0-0.032-0.01832.7920.1660.1660.0000.0000.0000.000
88A94HIS0-0.062-0.02934.9360.0220.0220.0000.0000.0000.000
89A95GLU-1-0.794-0.88328.68810.92310.9230.0000.0000.0000.000
90A96LEU0-0.043-0.02927.8200.2930.2930.0000.0000.0000.000
91A97SER0-0.085-0.06430.568-0.034-0.0340.0000.0000.0000.000
92A98GLU-1-0.914-0.93332.1428.6438.6430.0000.0000.0000.000
93A99ASP-1-0.868-0.91827.95810.60110.6010.0000.0000.0000.000
94A100SER0-0.056-0.06323.7600.4760.4760.0000.0000.0000.000
95A101GLN00.0280.00926.7130.0670.0670.0000.0000.0000.000
96A102ARG10.8520.90016.110-17.496-17.4960.0000.0000.0000.000
97A103ASP-1-0.777-0.85922.96113.89113.8910.0000.0000.0000.000
98A104LEU00.0610.05324.676-0.117-0.1170.0000.0000.0000.000
99A105VAL0-0.011-0.00925.062-0.200-0.2000.0000.0000.0000.000
100A106LEU0-0.059-0.02820.0530.0140.0140.0000.0000.0000.000
101A107THR00.013-0.00324.2710.0410.0410.0000.0000.0000.000
102A108GLN00.0420.01727.162-0.345-0.3450.0000.0000.0000.000
103A109GLU-1-0.843-0.90825.50511.64411.6440.0000.0000.0000.000
104A110LEU0-0.036-0.00324.417-0.098-0.0980.0000.0000.0000.000
105A111TYR0-0.034-0.05026.746-0.086-0.0860.0000.0000.0000.000
106A112THR0-0.028-0.01829.917-0.499-0.4990.0000.0000.0000.000
107A113LEU0-0.064-0.03525.252-0.287-0.2870.0000.0000.0000.000
108A114ALA00.0350.01729.230-0.193-0.1930.0000.0000.0000.000
109A115ALA0-0.0150.00830.825-0.354-0.3540.0000.0000.0000.000
110A116ARG10.9010.95031.645-9.867-9.8670.0000.0000.0000.000
111A117GLN0-0.009-0.00628.5880.0380.0380.0000.0000.0000.000
112A118PRO00.004-0.01631.0770.2650.2650.0000.0000.0000.000
113A119ALA00.0520.04328.898-0.024-0.0240.0000.0000.0000.000
114A120TYR00.0560.01223.4700.4250.4250.0000.0000.0000.000
115A121ARG10.8440.90828.376-9.063-9.0630.0000.0000.0000.000
116A122GLU-1-0.851-0.90128.20711.31411.3140.0000.0000.0000.000
117A123LEU00.0000.00422.890-0.020-0.0200.0000.0000.0000.000
118A124THR00.0560.02727.008-0.014-0.0140.0000.0000.0000.000
119A125HIS0-0.044-0.01129.795-0.291-0.2910.0000.0000.0000.000
120A126GLU-1-0.812-0.91226.75610.92810.9280.0000.0000.0000.000
121A127TRP00.0090.00226.9480.1020.1020.0000.0000.0000.000
122A128MET00.0520.02028.580-0.229-0.2290.0000.0000.0000.000
123A129ARG10.7960.89528.680-11.050-11.0500.0000.0000.0000.000
124A130ARG10.8120.88222.771-13.082-13.0820.0000.0000.0000.000
125A131SER00.0570.03329.4070.1560.1560.0000.0000.0000.000
126A132ARG10.8420.92030.988-9.075-9.0750.0000.0000.0000.000
127A133VAL0-0.053-0.00931.043-0.217-0.2170.0000.0000.0000.000
128A134HIS00.0460.01227.354-0.488-0.4880.0000.0000.0000.000
129A135LEU00.0060.01132.870-0.212-0.2120.0000.0000.0000.000
130A136GLU-1-0.816-0.92536.2918.2638.2630.0000.0000.0000.000
131A137LYS10.7180.87129.718-10.330-10.3300.0000.0000.0000.000
132A138HIS10.7790.88735.217-8.660-8.6600.0000.0000.0000.000
133A139PHE0-0.0060.00738.987-0.216-0.2160.0000.0000.0000.000
134A140ASP-1-0.774-0.84241.2227.1927.1920.0000.0000.0000.000
135A141PRO00.025-0.01240.6510.0480.0480.0000.0000.0000.000
136A142GLY0-0.046-0.00741.6820.0990.0990.0000.0000.0000.000
137A143THR0-0.014-0.05043.8950.1040.1040.0000.0000.0000.000
138A144ALA00.0350.02838.5690.0900.0900.0000.0000.0000.000
139A145ARG10.9290.95739.203-7.859-7.8590.0000.0000.0000.000
140A146GLN0-0.048-0.03740.183-0.023-0.0230.0000.0000.0000.000
141A147LEU00.0290.02138.8260.0030.0030.0000.0000.0000.000
142A148ASP-1-0.867-0.95234.4659.4639.4630.0000.0000.0000.000
143A149ALA0-0.027-0.01136.7070.1310.1310.0000.0000.0000.000
144A150LEU0-0.026-0.00838.969-0.018-0.0180.0000.0000.0000.000
145A151ILE00.0330.02034.065-0.021-0.0210.0000.0000.0000.000
146A152GLU-1-0.848-0.87932.9069.8489.8480.0000.0000.0000.000
147A153GLY0-0.007-0.00735.7950.0070.0070.0000.0000.0000.000
148A154LEU0-0.046-0.03539.118-0.110-0.1100.0000.0000.0000.000
149A155THR00.025-0.00132.449-0.026-0.0260.0000.0000.0000.000
150A156LEU0-0.021-0.00934.5740.0740.0740.0000.0000.0000.000
151A157HIS0-0.019-0.02936.1730.0220.0220.0000.0000.0000.000
152A158ARG10.7320.84536.356-8.622-8.6220.0000.0000.0000.000
153A159ALA00.0440.01833.379-0.023-0.0230.0000.0000.0000.000
154A160LEU0-0.098-0.04034.2990.1340.1340.0000.0000.0000.000
155A161ALA0-0.0170.01637.544-0.225-0.2250.0000.0000.0000.000
156A162ARG10.8580.93439.849-7.364-7.3640.0000.0000.0000.000
157A163GLU-1-0.916-0.97642.2156.9206.9200.0000.0000.0000.000
158A164PRO00.0040.01838.850-0.147-0.1470.0000.0000.0000.000
159A165HIS0-0.0040.00641.040-0.210-0.2100.0000.0000.0000.000
160A166GLY00.0540.02041.8370.1770.1770.0000.0000.0000.000
161A167ARG10.7580.81838.122-8.133-8.1330.0000.0000.0000.000
162A168ALA00.0050.00242.743-0.007-0.0070.0000.0000.0000.000
163A169LEU00.0060.01044.735-0.062-0.0620.0000.0000.0000.000
164A170THR00.0180.01539.6860.0450.0450.0000.0000.0000.000
165A171LEU00.0600.04142.7950.0040.0040.0000.0000.0000.000
166A172GLU-1-0.885-0.92144.2356.2896.2890.0000.0000.0000.000
167A173ALA00.0150.00244.567-0.077-0.0770.0000.0000.0000.000
168A174ILE00.0200.01539.951-0.041-0.0410.0000.0000.0000.000
169A175ALA00.0120.01643.866-0.013-0.0130.0000.0000.0000.000
170A176ARG10.8240.90846.832-6.362-6.3620.0000.0000.0000.000
171A177ILE0-0.038-0.01343.186-0.083-0.0830.0000.0000.0000.000
172A178THR0-0.006-0.00842.8950.0210.0210.0000.0000.0000.000
173A179THR0-0.055-0.02646.172-0.091-0.0910.0000.0000.0000.000
174A180THR0-0.046-0.03148.4860.0400.0400.0000.0000.0000.000
175A181ASP-1-0.980-0.97551.4885.6535.6530.0000.0000.0000.000