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: 6YGQZ

Calculation Name: 2YVU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YCR6

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1946500.648503
FMO2-HF: Nuclear repulsion 1876438.416957
FMO2-HF: Total energy -70062.231546
FMO2-MP2: Total energy -70270.292753


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:8:LYS)


Summations of interaction energy for fragment #1(A:8:LYS)
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.
-163.989-162.1342.61-19.498-24.973-0.215
Interaction energy analysis for fragmet #1(A:8:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.878 / 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].
3A10ILE00.0420.0303.158-6.224-2.2390.096-2.034-2.047-0.001
4A11GLU-1-0.848-0.9175.288-18.762-18.732-0.001-0.001-0.0280.000
5A12LYS10.8250.9118.91022.81122.8110.0000.0000.0000.000
6A13GLY00.0090.0228.788-3.169-3.1690.0000.0000.0000.000
7A14ILE0-0.007-0.0119.7291.9231.9230.0000.0000.0000.000
8A15VAL00.0080.00512.280-0.287-0.2870.0000.0000.0000.000
9A16VAL0-0.0050.00212.0640.6220.6220.0000.0000.0000.000
10A17TRP00.010-0.00615.2720.2710.2710.0000.0000.0000.000
11A18LEU0-0.0020.00416.6630.6240.6240.0000.0000.0000.000
12A19THR00.002-0.00320.2430.7800.7800.0000.0000.0000.000
13A20GLY00.0610.02423.989-0.104-0.1040.0000.0000.0000.000
14A21LEU00.0150.02826.8090.0290.0290.0000.0000.0000.000
15A22PRO00.003-0.00727.947-0.493-0.4930.0000.0000.0000.000
16A23GLY00.0400.01528.4400.2210.2210.0000.0000.0000.000
17A24SER0-0.053-0.02325.865-0.077-0.0770.0000.0000.0000.000
18A25GLY00.0710.03224.024-0.182-0.1820.0000.0000.0000.000
19A26LYS10.8000.90121.11711.90511.9050.0000.0000.0000.000
20A27THR00.1320.05819.612-0.817-0.8170.0000.0000.0000.000
21A28THR0-0.0040.02519.010-0.660-0.6600.0000.0000.0000.000
22A29ILE00.005-0.00216.715-0.815-0.8150.0000.0000.0000.000
23A30ALA00.0260.00815.207-1.307-1.3070.0000.0000.0000.000
24A31THR0-0.002-0.00914.054-1.544-1.5440.0000.0000.0000.000
25A32ARG10.8340.89213.98815.87615.8760.0000.0000.0000.000
26A33LEU00.0270.02310.034-1.230-1.2300.0000.0000.0000.000
27A34ALA00.0330.0099.749-3.432-3.4320.0000.0000.0000.000
28A35ASP-1-0.831-0.8949.299-27.469-27.4690.0000.0000.0000.000
29A36LEU0-0.0020.0028.695-2.100-2.1000.0000.0000.0000.000
30A37LEU00.0120.0025.218-5.441-5.4410.0000.0000.0000.000
31A38GLN0-0.033-0.0204.480-10.655-10.554-0.001-0.010-0.0900.000
32A39LYS10.8120.8976.35523.05023.0500.0000.0000.0000.000
33A40GLU-1-0.797-0.8561.861-105.700-107.50910.840-4.743-4.289-0.053
34A41GLY00.0370.0211.759-44.985-47.29113.830-6.177-5.347-0.080
35A42TYR0-0.013-0.0112.094-27.951-26.86317.831-6.583-12.336-0.081
36A43ARG10.9150.9623.41946.33846.9180.0150.110-0.7060.000
37A44VAL0-0.028-0.0145.7630.0460.0460.0000.0000.0000.000
38A45GLU-1-0.877-0.9378.921-20.321-20.3210.0000.0000.0000.000
39A46VAL0-0.039-0.02212.587-0.347-0.3470.0000.0000.0000.000
40A47LEU00.0100.02215.5881.0731.0730.0000.0000.0000.000
41A48ASP-1-0.822-0.92718.926-14.382-14.3820.0000.0000.0000.000
42A49GLY00.001-0.01621.9410.3600.3600.0000.0000.0000.000
43A50ASP-1-0.832-0.88725.191-10.877-10.8770.0000.0000.0000.000
44A51TRP00.0550.02020.0490.3270.3270.0000.0000.0000.000
45A52ALA0-0.019-0.00123.8260.2770.2770.0000.0000.0000.000
46A53ARG10.7750.85825.44611.13611.1360.0000.0000.0000.000
47A54THR00.0180.01426.1820.3440.3440.0000.0000.0000.000
48A55THR00.010-0.01322.799-0.297-0.2970.0000.0000.0000.000
49A56VAL0-0.045-0.01322.8790.4060.4060.0000.0000.0000.000
50A57SER0-0.051-0.06426.0700.2180.2180.0000.0000.0000.000
51A58GLU-1-0.930-0.93729.144-9.846-9.8460.0000.0000.0000.000
52A59GLY00.0040.00930.9980.2370.2370.0000.0000.0000.000
53A60ALA0-0.064-0.01632.5510.2190.2190.0000.0000.0000.000
54A61GLY00.0300.01034.4620.0960.0960.0000.0000.0000.000
55A62PHE0-0.018-0.02933.866-0.272-0.2720.0000.0000.0000.000
56A63THR00.012-0.01036.778-0.014-0.0140.0000.0000.0000.000
57A64ARG10.9831.00435.8528.4938.4930.0000.0000.0000.000
58A65GLU-1-0.815-0.91135.204-8.472-8.4720.0000.0000.0000.000
59A66GLU-1-0.864-0.91034.691-9.136-9.1360.0000.0000.0000.000
60A67ARG10.8670.92031.9468.8138.8130.0000.0000.0000.000
61A68LEU0-0.015-0.00530.654-0.447-0.4470.0000.0000.0000.000
62A69ARG10.9060.96330.6108.4138.4130.0000.0000.0000.000
63A70HIS00.0160.04425.865-0.089-0.0890.0000.0000.0000.000
64A71LEU0-0.004-0.01025.897-0.462-0.4620.0000.0000.0000.000
65A72LYS10.9880.99025.6599.7069.7060.0000.0000.0000.000
66A73ARG10.8790.92325.62610.58910.5890.0000.0000.0000.000
67A74ILE0-0.011-0.00121.361-0.446-0.4460.0000.0000.0000.000
68A75ALA00.0020.00621.234-0.739-0.7390.0000.0000.0000.000
69A76TRP00.0210.00621.010-0.656-0.6560.0000.0000.0000.000
70A77ILE0-0.0020.01018.460-0.422-0.4220.0000.0000.0000.000
71A78ALA00.0240.00316.802-0.857-0.8570.0000.0000.0000.000
72A79ARG10.7160.83316.09212.25712.2570.0000.0000.0000.000
73A80LEU0-0.031-0.02516.825-0.535-0.5350.0000.0000.0000.000
74A81LEU00.0050.01413.254-0.526-0.5260.0000.0000.0000.000
75A82ALA00.0500.02311.975-1.304-1.3040.0000.0000.0000.000
76A83ARG10.8480.90712.22813.90413.9040.0000.0000.0000.000
77A84ASN0-0.080-0.04511.9950.6900.6900.0000.0000.0000.000
78A85GLY00.0470.0348.079-0.959-0.9590.0000.0000.0000.000
79A86VAL0-0.074-0.0347.135-4.328-4.3280.0000.0000.0000.000
80A87ILE00.0210.0025.3112.2772.2770.0000.0000.0000.000
81A88VAL00.002-0.0019.5870.4700.4700.0000.0000.0000.000
82A89ILE00.0040.01010.6471.3401.3400.0000.0000.0000.000
83A90CYS0-0.037-0.00714.3561.0231.0230.0000.0000.0000.000
84A91SER0-0.027-0.03018.1920.3030.3030.0000.0000.0000.000
85A92PHE00.0840.02520.6880.6830.6830.0000.0000.0000.000
86A93VAL0-0.0210.00124.4550.0570.0570.0000.0000.0000.000
87A94SER00.0100.00325.9530.0830.0830.0000.0000.0000.000
88A95PRO00.0340.01928.210-0.268-0.2680.0000.0000.0000.000
89A96TYR0-0.032-0.05630.8960.0270.0270.0000.0000.0000.000
90A97LYS10.8650.91729.7009.3019.3010.0000.0000.0000.000
91A98GLN0-0.010-0.00429.962-0.253-0.2530.0000.0000.0000.000
92A99ALA00.003-0.00130.070-0.113-0.1130.0000.0000.0000.000
93A100ARG10.7770.88024.96411.31311.3130.0000.0000.0000.000
94A101ASN00.0570.01725.718-0.740-0.7400.0000.0000.0000.000
95A102MET0-0.113-0.04027.650-0.085-0.0850.0000.0000.0000.000
96A103VAL00.005-0.01022.450-0.108-0.1080.0000.0000.0000.000
97A104ARG10.7810.87321.39213.61013.6100.0000.0000.0000.000
98A105ARG10.9530.97922.69810.42110.4210.0000.0000.0000.000
99A106ILE0-0.0280.00122.768-0.053-0.0530.0000.0000.0000.000
100A107VAL00.0130.00417.700-0.243-0.2430.0000.0000.0000.000
101A108GLU-1-0.806-0.91419.750-14.193-14.1930.0000.0000.0000.000
102A109GLU-1-0.895-0.91321.280-11.984-11.9840.0000.0000.0000.000
103A110GLU-1-0.836-0.88918.524-14.320-14.3200.0000.0000.0000.000
104A111GLY00.0180.00818.668-0.599-0.5990.0000.0000.0000.000
105A112ILE0-0.074-0.01814.232-0.874-0.8740.0000.0000.0000.000
106A113PRO00.0300.00513.7330.9380.9380.0000.0000.0000.000
107A114PHE00.0170.01115.623-0.842-0.8420.0000.0000.0000.000
108A115LEU0-0.004-0.01013.4600.8010.8010.0000.0000.0000.000
109A116GLU-1-0.794-0.88117.538-12.985-12.9850.0000.0000.0000.000
110A117ILE0-0.008-0.01016.6720.1510.1510.0000.0000.0000.000
111A118TYR00.012-0.00320.3370.4180.4180.0000.0000.0000.000
112A119VAL0-0.0020.00021.051-0.095-0.0950.0000.0000.0000.000
113A120LYS10.8440.90623.67611.09511.0950.0000.0000.0000.000
114A121ALA00.0070.01127.196-0.157-0.1570.0000.0000.0000.000
115A122SER0-0.014-0.02129.9250.1380.1380.0000.0000.0000.000
116A123LEU00.000-0.02333.634-0.113-0.1130.0000.0000.0000.000
117A124GLU-1-0.855-0.91535.765-8.031-8.0310.0000.0000.0000.000
118A125GLU-1-0.773-0.85532.147-9.574-9.5740.0000.0000.0000.000
119A126VAL0-0.041-0.03230.642-0.083-0.0830.0000.0000.0000.000
120A127ILE0-0.038-0.01333.234-0.005-0.0050.0000.0000.0000.000
121A128ARG10.7980.87936.1288.7758.7750.0000.0000.0000.000
122A129ARG10.7740.85828.19310.86010.8600.0000.0000.0000.000
123A130ASP-1-0.842-0.91733.232-9.443-9.4430.0000.0000.0000.000
124A131PRO00.0610.02635.2680.1020.1020.0000.0000.0000.000
125A132LYS10.9330.97737.1378.7058.7050.0000.0000.0000.000
126A133GLY00.006-0.00435.3220.1300.1300.0000.0000.0000.000
127A134LEU0-0.0070.00736.3440.0840.0840.0000.0000.0000.000
128A135TYR00.0270.00438.5170.1280.1280.0000.0000.0000.000
129A136LYS10.9260.96935.9928.9728.9720.0000.0000.0000.000
130A137LYS10.8250.88533.3699.5729.5720.0000.0000.0000.000
131A138ALA00.0090.00639.1500.1030.1030.0000.0000.0000.000
132A139LEU0-0.023-0.01142.5740.1450.1450.0000.0000.0000.000
133A140LYS10.8130.90038.3878.4658.4650.0000.0000.0000.000
134A141GLY00.0270.02342.612-0.038-0.0380.0000.0000.0000.000
135A142GLU-1-0.844-0.88635.833-9.080-9.0800.0000.0000.0000.000
136A143LEU00.0600.04037.873-0.297-0.2970.0000.0000.0000.000
137A144GLU-1-0.846-0.92738.476-7.976-7.9760.0000.0000.0000.000
138A145ASN0-0.083-0.05133.352-0.399-0.3990.0000.0000.0000.000
139A146PHE00.0180.01233.603-0.356-0.3560.0000.0000.0000.000
140A147THR00.007-0.01732.2040.1240.1240.0000.0000.0000.000
141A148GLY0-0.034-0.01334.5930.0780.0780.0000.0000.0000.000
142A149ILE0-0.017-0.00835.5940.1350.1350.0000.0000.0000.000
143A150THR0-0.009-0.02137.6400.1190.1190.0000.0000.0000.000
144A151ASP-1-0.864-0.88235.408-8.718-8.7180.0000.0000.0000.000
145A152PRO00.0140.00635.224-0.318-0.3180.0000.0000.0000.000
146A153TYR0-0.027-0.03126.887-0.044-0.0440.0000.0000.0000.000
147A154GLU-1-0.831-0.90832.335-9.158-9.1580.0000.0000.0000.000
148A155PRO00.013-0.00729.653-0.392-0.3920.0000.0000.0000.000
149A156PRO0-0.017-0.01225.4140.2430.2430.0000.0000.0000.000
150A157GLU-1-0.781-0.86828.164-9.704-9.7040.0000.0000.0000.000
151A158ASN0-0.057-0.04326.502-0.068-0.0680.0000.0000.0000.000
152A159PRO0-0.0400.00822.952-0.336-0.3360.0000.0000.0000.000
153A160GLN00.0670.03818.418-0.090-0.0900.0000.0000.0000.000
154A161LEU00.0020.01216.882-0.569-0.5690.0000.0000.0000.000
155A162VAL0-0.010-0.00620.4480.4090.4090.0000.0000.0000.000
156A163LEU0-0.031-0.01017.970-0.203-0.2030.0000.0000.0000.000
157A164ASP-1-0.724-0.85222.427-10.860-10.8600.0000.0000.0000.000
158A165THR0-0.010-0.01123.923-0.066-0.0660.0000.0000.0000.000
159A166GLU-1-0.813-0.87426.379-9.894-9.8940.0000.0000.0000.000
160A167SER0-0.029-0.00528.4290.4020.4020.0000.0000.0000.000
161A168ASN0-0.034-0.01623.9840.3130.3130.0000.0000.0000.000
162A169THR00.008-0.01222.822-0.122-0.1220.0000.0000.0000.000
163A170ILE00.011-0.00619.331-0.478-0.4780.0000.0000.0000.000
164A171GLU-1-0.779-0.85818.444-15.761-15.7610.0000.0000.0000.000
165A172HIS00.0020.00417.873-0.911-0.9110.0000.0000.0000.000
166A173ASN00.009-0.01118.345-0.936-0.9360.0000.0000.0000.000
167A174VAL00.0110.00613.859-0.520-0.5200.0000.0000.0000.000
168A175SER00.0120.01813.800-2.158-2.1580.0000.0000.0000.000
169A176TYR00.0060.01213.964-1.258-1.2580.0000.0000.0000.000
170A177LEU00.014-0.00813.360-0.346-0.3460.0000.0000.0000.000
171A178TYR0-0.024-0.0265.6221.9181.9180.0000.0000.0000.000
172A179SER0-0.024-0.01810.178-2.309-2.3090.0000.0000.0000.000
173A180LEU0-0.031-0.00311.971-0.579-0.5790.0000.0000.0000.000
174A181VAL00.009-0.0178.076-0.133-0.1330.0000.0000.0000.000
175A182LYS10.8410.8883.54862.95863.1480.000-0.060-0.1300.000
176A183ALA0-0.0220.0048.443-0.909-0.9090.0000.0000.0000.000
177A184VAL0-0.046-0.01711.4930.9730.9730.0000.0000.0000.000
178A185ILE0-0.046-0.0105.1500.3240.3240.0000.0000.0000.000
179A186GLU-1-1.016-1.0026.268-35.244-35.2440.0000.0000.0000.000