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: YVJ82

Calculation Name: 3RD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I1S1

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1955400.722339
FMO2-HF: Nuclear repulsion 1880565.32634
FMO2-HF: Total energy -74835.395998
FMO2-MP2: Total energy -75048.613446


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.
-57.049-53.4890.022-1.605-1.9750.006
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 : -0.853 / q_NPA : -0.927
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].
3A9ARG10.9951.0033.758-45.235-42.785-0.007-1.213-1.2300.005
4A10GLN00.012-0.0063.285-6.479-5.8670.031-0.169-0.4740.000
5A11HIS00.000-0.0074.190-4.769-4.354-0.001-0.220-0.1930.001
6A12LEU0-0.002-0.0105.984-5.195-5.1950.0000.0000.0000.000
7A13LEU0-0.0220.0057.686-2.991-2.9910.0000.0000.0000.000
8A14ASP-1-0.832-0.9138.10624.92424.9240.0000.0000.0000.000
9A15THR0-0.093-0.0629.751-2.574-2.5740.0000.0000.0000.000
10A16GLY0-0.005-0.01411.704-1.644-1.6440.0000.0000.0000.000
11A17TYR0-0.024-0.01313.013-1.619-1.6190.0000.0000.0000.000
12A18ARG10.9870.99111.115-22.070-22.0700.0000.0000.0000.000
13A19ILE00.0010.00915.774-0.944-0.9440.0000.0000.0000.000
14A20MET0-0.0080.01017.355-0.914-0.9140.0000.0000.0000.000
15A21ALA0-0.0020.00018.687-0.824-0.8240.0000.0000.0000.000
16A22VAL0-0.019-0.00920.581-0.696-0.6960.0000.0000.0000.000
17A23LYS10.9040.94121.938-13.776-13.7760.0000.0000.0000.000
18A24GLY00.0490.05822.499-0.386-0.3860.0000.0000.0000.000
19A25PHE0-0.031-0.03818.3170.7540.7540.0000.0000.0000.000
20A26SER0-0.024-0.01622.0790.3000.3000.0000.0000.0000.000
21A27GLY00.0450.04025.160-0.204-0.2040.0000.0000.0000.000
22A28VAL0-0.0060.01519.6680.0460.0460.0000.0000.0000.000
23A29GLY00.0050.01021.8580.2770.2770.0000.0000.0000.000
24A30LEU0-0.007-0.01416.0380.4070.4070.0000.0000.0000.000
25A31ASN0-0.001-0.01717.7610.8240.8240.0000.0000.0000.000
26A32GLU-1-0.839-0.91518.60713.93513.9350.0000.0000.0000.000
27A33ILE00.0250.00713.8150.6630.6630.0000.0000.0000.000
28A34LEU0-0.044-0.02914.0061.0671.0670.0000.0000.0000.000
29A35GLN00.001-0.01013.9080.9220.9220.0000.0000.0000.000
30A36SER0-0.0320.00615.183-0.364-0.3640.0000.0000.0000.000
31A37ALA0-0.047-0.0079.8770.5470.5470.0000.0000.0000.000
32A38GLY00.0280.03210.1491.8201.8200.0000.0000.0000.000
33A39VAL0-0.040-0.0128.0381.6551.6550.0000.0000.0000.000
34A40PRO00.0430.00910.664-2.378-2.3780.0000.0000.0000.000
35A41LYS11.0150.99512.595-15.325-15.3250.0000.0000.0000.000
36A42GLY0-0.022-0.01414.3760.2100.2100.0000.0000.0000.000
37A43SER00.0250.0058.759-0.352-0.3520.0000.0000.0000.000
38A44PHE00.0430.0299.6692.6152.6150.0000.0000.0000.000
39A45TYR0-0.038-0.03211.7720.2240.2240.0000.0000.0000.000
40A46HIS0-0.0180.0098.726-1.554-1.5540.0000.0000.0000.000
41A47TYR0-0.029-0.0144.9773.0903.173-0.001-0.003-0.0780.000
42A48PHE0-0.028-0.0099.543-1.358-1.3580.0000.0000.0000.000
43A49LYS10.9530.96813.343-18.505-18.5050.0000.0000.0000.000
44A50SER0-0.014-0.00116.577-0.951-0.9510.0000.0000.0000.000
45A51LYS10.9000.95316.837-13.040-13.0400.0000.0000.0000.000
46A52GLU-1-0.837-0.92618.52513.22313.2230.0000.0000.0000.000
47A53GLN00.0460.00114.564-0.755-0.7550.0000.0000.0000.000
48A54PHE0-0.038-0.01711.1400.2120.2120.0000.0000.0000.000
49A55GLY00.0660.03215.1230.5630.5630.0000.0000.0000.000
50A56GLN00.021-0.01217.871-0.687-0.6870.0000.0000.0000.000
51A57ALA0-0.0240.00212.878-0.004-0.0040.0000.0000.0000.000
52A58LEU00.0100.00513.2400.1930.1930.0000.0000.0000.000
53A59LEU00.0190.01714.792-0.272-0.2720.0000.0000.0000.000
54A60GLU-1-0.991-0.99115.33917.74317.7430.0000.0000.0000.000
55A61ASP-1-0.869-0.94611.14922.78522.7850.0000.0000.0000.000
56A62TYR0-0.046-0.01614.767-0.449-0.4490.0000.0000.0000.000
57A63PHE00.0300.00716.913-0.549-0.5490.0000.0000.0000.000
58A64ARG10.8870.95312.727-19.895-19.8950.0000.0000.0000.000
59A65VAL0-0.0020.00114.074-0.441-0.4410.0000.0000.0000.000
60A66TYR00.0130.02817.348-0.725-0.7250.0000.0000.0000.000
61A67LEU0-0.012-0.02120.618-0.546-0.5460.0000.0000.0000.000
62A68ALA00.0300.02719.582-0.419-0.4190.0000.0000.0000.000
63A69ASP-1-0.885-0.94620.89911.78811.7880.0000.0000.0000.000
64A70MET0-0.025-0.00822.367-0.634-0.6340.0000.0000.0000.000
65A71ASP-1-0.811-0.87124.81810.99210.9920.0000.0000.0000.000
66A72GLN0-0.061-0.01522.628-0.472-0.4720.0000.0000.0000.000
67A73ARG10.9100.94824.804-11.377-11.3770.0000.0000.0000.000
68A74PHE0-0.056-0.03628.149-0.383-0.3830.0000.0000.0000.000
69A75SER0-0.059-0.03328.395-0.298-0.2980.0000.0000.0000.000
70A76ALA00.0240.02229.767-0.084-0.0840.0000.0000.0000.000
71A77PRO00.0190.00530.954-0.337-0.3370.0000.0000.0000.000
72A78GLY0-0.024-0.02034.1010.0780.0780.0000.0000.0000.000
73A79LEU0-0.0420.00532.241-0.063-0.0630.0000.0000.0000.000
74A80ASN00.0110.02336.4480.1390.1390.0000.0000.0000.000
75A81ALA00.0500.01836.9730.1990.1990.0000.0000.0000.000
76A82ARG10.9040.94436.994-6.882-6.8820.0000.0000.0000.000
77A83GLU-1-0.875-0.94836.3037.9397.9390.0000.0000.0000.000
78A84ARG10.8320.91532.826-8.395-8.3950.0000.0000.0000.000
79A85LEU0-0.003-0.00732.1900.3220.3220.0000.0000.0000.000
80A86MET00.0120.00333.3730.1740.1740.0000.0000.0000.000
81A87SER0-0.041-0.01230.8930.2470.2470.0000.0000.0000.000
82A88TYR0-0.013-0.03026.6230.2570.2570.0000.0000.0000.000
83A89TRP00.0350.00729.3540.2900.2900.0000.0000.0000.000
84A90GLN00.0310.01231.010-0.003-0.0030.0000.0000.0000.000
85A91LYS10.9430.98022.305-12.013-12.0130.0000.0000.0000.000
86A92TRP0-0.051-0.03426.4650.3840.3840.0000.0000.0000.000
87A93LEU0-0.041-0.02828.0410.1270.1270.0000.0000.0000.000
88A94ASP-1-0.895-0.93927.5449.7609.7600.0000.0000.0000.000
89A95ASN0-0.086-0.04621.5410.6060.6060.0000.0000.0000.000
90A96ALA0-0.062-0.00523.8810.4370.4370.0000.0000.0000.000
91A97CYS0-0.0020.01323.7770.0120.0120.0000.0000.0000.000
92A98PRO00.006-0.00126.9800.2180.2180.0000.0000.0000.000
93A99PRO00.003-0.00828.7530.0200.0200.0000.0000.0000.000
94A101ASP-1-0.880-0.95124.26311.04511.0450.0000.0000.0000.000
95A102GLU-1-0.997-0.99818.84614.97514.9750.0000.0000.0000.000
96A103GLN0-0.041-0.01922.539-0.037-0.0370.0000.0000.0000.000
97A104ARG10.9860.98617.301-14.514-14.5140.0000.0000.0000.000
98A105CYS0-0.0090.01721.1610.3740.3740.0000.0000.0000.000
99A106LEU00.0520.01118.354-0.305-0.3050.0000.0000.0000.000
100A107VAL00.0830.06223.093-0.147-0.1470.0000.0000.0000.000
101A108VAL0-0.003-0.01226.314-0.280-0.2800.0000.0000.0000.000
102A109LYS10.8800.94123.122-11.965-11.9650.0000.0000.0000.000
103A110LEU0-0.017-0.01621.331-0.044-0.0440.0000.0000.0000.000
104A111SER0-0.011-0.01525.897-0.223-0.2230.0000.0000.0000.000
105A112ALA0-0.050-0.01629.219-0.346-0.3460.0000.0000.0000.000
106A113GLU-1-0.859-0.93825.78311.46111.4610.0000.0000.0000.000
107A114VAL0-0.013-0.01728.9020.0760.0760.0000.0000.0000.000
108A115ALA0-0.083-0.04529.9850.0290.0290.0000.0000.0000.000
109A116ASP-1-0.851-0.91929.5299.7399.7390.0000.0000.0000.000
110A117LEU0-0.105-0.03524.4070.5230.5230.0000.0000.0000.000
111A118SER00.0380.01624.701-0.379-0.3790.0000.0000.0000.000
112A119GLU-1-0.883-0.95827.7119.5689.5680.0000.0000.0000.000
113A120SER0-0.027-0.01624.370-0.196-0.1960.0000.0000.0000.000
114A121MET00.0080.02621.4390.3990.3990.0000.0000.0000.000
115A122ARG10.9861.00224.652-9.514-9.5140.0000.0000.0000.000
116A123ILE0-0.015-0.02927.126-0.196-0.1960.0000.0000.0000.000
117A124THR00.0220.01921.4580.0580.0580.0000.0000.0000.000
118A125LEU0-0.033-0.01224.0530.1160.1160.0000.0000.0000.000
119A126ARG10.9090.95625.766-9.444-9.4440.0000.0000.0000.000
120A127ASP-1-0.830-0.89826.41210.51510.5150.0000.0000.0000.000
121A128GLY0-0.019-0.02724.598-0.074-0.0740.0000.0000.0000.000
122A129SER0-0.039-0.02925.399-0.080-0.0800.0000.0000.0000.000
123A130ASP-1-0.914-0.96428.2659.0999.0990.0000.0000.0000.000
124A131GLY0-0.023-0.00627.652-0.210-0.2100.0000.0000.0000.000
125A132ILE0-0.017-0.02025.419-0.010-0.0100.0000.0000.0000.000
126A133ILE00.0130.01228.887-0.235-0.2350.0000.0000.0000.000
127A134GLU-1-0.927-0.96331.5898.4558.4550.0000.0000.0000.000
128A135ARG10.8210.87926.080-11.213-11.2130.0000.0000.0000.000
129A136LEU0-0.025-0.00631.722-0.209-0.2090.0000.0000.0000.000
130A137VAL0-0.0080.00033.919-0.295-0.2950.0000.0000.0000.000
131A138GLY0-0.0160.00235.218-0.221-0.2210.0000.0000.0000.000
132A139CYS0-0.052-0.02533.949-0.241-0.2410.0000.0000.0000.000
133A140LEU00.0140.00036.027-0.193-0.1930.0000.0000.0000.000
134A141GLY0-0.073-0.04339.211-0.224-0.2240.0000.0000.0000.000
135A142GLN00.0450.01635.038-0.072-0.0720.0000.0000.0000.000
136A143GLY00.0610.01540.047-0.059-0.0590.0000.0000.0000.000
137A144ARG10.7870.89941.630-7.122-7.1220.0000.0000.0000.000
138A145ASP-1-0.910-0.94242.9356.8306.8300.0000.0000.0000.000
139A146ASP-1-0.814-0.85541.1577.2507.2500.0000.0000.0000.000
140A147GLY0-0.030-0.01244.481-0.060-0.0600.0000.0000.0000.000
141A148SER0-0.080-0.08641.759-0.047-0.0470.0000.0000.0000.000
142A149LEU0-0.074-0.05139.3950.0570.0570.0000.0000.0000.000
143A150ALA00.0290.02344.108-0.099-0.0990.0000.0000.0000.000
144A151PRO0-0.008-0.01545.9340.1270.1270.0000.0000.0000.000
145A152CYS00.0170.01443.8660.0310.0310.0000.0000.0000.000
146A153ASP-1-0.864-0.92344.7796.8346.8340.0000.0000.0000.000
147A154ALA00.047-0.00240.5490.0770.0770.0000.0000.0000.000
148A155ARG10.9831.00639.662-7.096-7.0960.0000.0000.0000.000
149A156HIS00.0210.00739.8390.2210.2210.0000.0000.0000.000
150A157MET00.0390.01840.1750.1150.1150.0000.0000.0000.000
151A158ALA00.0130.01336.0090.1250.1250.0000.0000.0000.000
152A159SER00.0050.00236.3830.2620.2620.0000.0000.0000.000
153A160ALA0-0.043-0.01237.4330.1000.1000.0000.0000.0000.000
154A161LEU00.024-0.00236.5610.0550.0550.0000.0000.0000.000
155A162TYR00.0530.01428.8300.2480.2480.0000.0000.0000.000
156A163GLN0-0.048-0.02433.5920.2220.2220.0000.0000.0000.000
157A164LEU0-0.0170.00635.7810.0760.0760.0000.0000.0000.000
158A165TRP00.0320.01231.8320.1090.1090.0000.0000.0000.000
159A166LEU0-0.007-0.01129.3600.2220.2220.0000.0000.0000.000
160A167GLY0-0.0050.00232.1280.1260.1260.0000.0000.0000.000
161A168ALA00.0340.01734.192-0.040-0.0400.0000.0000.0000.000
162A169SER0-0.0110.00128.9910.2280.2280.0000.0000.0000.000
163A170LEU0-0.022-0.01930.9230.1590.1590.0000.0000.0000.000
164A171LEU00.019-0.00232.1660.0180.0180.0000.0000.0000.000
165A172SER0-0.016-0.02731.447-0.138-0.1380.0000.0000.0000.000
166A173LYS10.7890.89425.739-11.053-11.0530.0000.0000.0000.000
167A174LEU0-0.062-0.00930.8430.0120.0120.0000.0000.0000.000
168A175HIS00.008-0.01333.949-0.047-0.0470.0000.0000.0000.000
169A176ARG10.9380.99331.014-9.497-9.4970.0000.0000.0000.000
170A177SER00.0200.01132.893-0.049-0.0490.0000.0000.0000.000
171A178PRO00.0650.02333.5470.1800.1800.0000.0000.0000.000
172A179GLY00.0440.03334.507-0.023-0.0230.0000.0000.0000.000
173A180PRO0-0.017-0.02535.590-0.110-0.1100.0000.0000.0000.000
174A181LEU00.0180.01430.571-0.013-0.0130.0000.0000.0000.000
175A182GLU-1-0.917-0.95734.8157.8427.8420.0000.0000.0000.000
176A183THR00.0100.01337.554-0.209-0.2090.0000.0000.0000.000
177A184ALA00.0190.03935.651-0.149-0.1490.0000.0000.0000.000
178A185MET0-0.0200.00335.928-0.036-0.0360.0000.0000.0000.000
179A186GLN0-0.022-0.02037.658-0.055-0.0550.0000.0000.0000.000
180A187THR0-0.004-0.02440.755-0.199-0.1990.0000.0000.0000.000
181A188THR0-0.015-0.02136.953-0.055-0.0550.0000.0000.0000.000
182A189ARG10.9290.95237.045-7.817-7.8170.0000.0000.0000.000
183A190SER0-0.036-0.00641.981-0.113-0.1130.0000.0000.0000.000
184A191LEU0-0.037-0.01241.878-0.117-0.1170.0000.0000.0000.000
185A192LEU0-0.0360.00238.936-0.022-0.0220.0000.0000.0000.000
186A193GLU-1-0.903-0.94742.6706.9276.9270.0000.0000.0000.000