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: YZ9J2

Calculation Name: 5Y0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5Y0W

Chain ID: A

ChEMBL ID:

UniProt ID: P03518

Base Structure: X-ray

Registration Date: 2023-06-22

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 307
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4505200.519268
FMO2-HF: Nuclear repulsion 4378509.829778
FMO2-HF: Total energy -126690.689489
FMO2-MP2: Total energy -127045.446957


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:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-103.553-97.25326.269-13.975-18.5940.058
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.838 / q_NPA : -0.925
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].
3A3PRO0-0.042-0.0152.958-13.792-10.7890.293-1.389-1.9070.011
4A4HIS00.0040.0012.334-13.283-10.9491.603-1.717-2.2190.016
5A5LEU00.0480.0432.409-8.644-7.3051.399-1.039-1.6990.006
6A6ARG10.7490.8535.115-25.969-25.846-0.001-0.004-0.1180.000
7A7ASN0-0.046-0.0206.087-4.940-4.9400.0000.0000.0000.000
8A8ARG10.7460.8386.627-25.524-25.5240.0000.0000.0000.000
9A9PRO00.0300.0318.545-0.858-0.8580.0000.0000.0000.000
10A10GLY0-0.012-0.02410.810-1.029-1.0290.0000.0000.0000.000
11A11LYS10.8340.91114.181-13.197-13.1970.0000.0000.0000.000
12A12GLY00.0500.03213.355-0.156-0.1560.0000.0000.0000.000
13A13HIS0-0.020-0.01013.9910.3080.3080.0000.0000.0000.000
14A14ASN0-0.034-0.02813.5290.0720.0720.0000.0000.0000.000
15A15TYR00.0570.00017.466-0.239-0.2390.0000.0000.0000.000
16A16ILE00.0590.02321.2190.0940.0940.0000.0000.0000.000
17A17ASP-1-0.773-0.88024.18310.93810.9380.0000.0000.0000.000
18A18GLY0-0.042-0.00427.215-0.242-0.2420.0000.0000.0000.000
19A19MET0-0.070-0.03826.178-0.226-0.2260.0000.0000.0000.000
20A20THR00.0930.04526.0970.3280.3280.0000.0000.0000.000
21A21GLN0-0.003-0.01026.5810.3250.3250.0000.0000.0000.000
22A22GLU-1-0.765-0.86621.80513.29813.2980.0000.0000.0000.000
23A23ASP-1-0.784-0.90122.14112.36912.3690.0000.0000.0000.000
24A24ALA0-0.036-0.02521.2060.4790.4790.0000.0000.0000.000
25A25THR0-0.013-0.02119.0570.2480.2480.0000.0000.0000.000
26A26CYS0-0.0640.00316.143-0.123-0.1230.0000.0000.0000.000
27A27LYS10.8020.93417.901-11.505-11.5050.0000.0000.0000.000
28A28PRO00.0090.01514.712-0.805-0.8050.0000.0000.0000.000
29A29VAL0-0.020-0.01511.770-0.445-0.4450.0000.0000.0000.000
30A30THR00.0240.00211.4180.6650.6650.0000.0000.0000.000
31A31TYR0-0.062-0.0526.653-1.573-1.5730.0000.0000.0000.000
32A32ALA0-0.052-0.01711.306-0.033-0.0330.0000.0000.0000.000
33A33GLY00.0440.03315.031-0.302-0.3020.0000.0000.0000.000
34A34ALA0-0.014-0.00115.9781.1101.1100.0000.0000.0000.000
35A36SER0-0.008-0.02517.2360.5680.5680.0000.0000.0000.000
36A37SER00.0030.01018.816-0.385-0.3850.0000.0000.0000.000
37A38PHE0-0.034-0.0159.212-0.035-0.0350.0000.0000.0000.000
38A39ASP-1-0.711-0.84613.31820.32620.3260.0000.0000.0000.000
39A40VAL0-0.030-0.01513.6370.9730.9730.0000.0000.0000.000
40A41LEU0-0.008-0.00311.645-0.208-0.2080.0000.0000.0000.000
41A42LEU00.0250.0187.6511.8491.8490.0000.0000.0000.000
42A43GLU-1-0.859-0.90110.81517.87317.8730.0000.0000.0000.000
43A44LYS10.9580.97310.094-22.257-22.2570.0000.0000.0000.000
44A45GLY0-0.0060.00311.456-1.704-1.7040.0000.0000.0000.000
45A46LYS10.7820.87913.748-17.875-17.8750.0000.0000.0000.000
46A47PHE0-0.038-0.02012.7611.2051.2050.0000.0000.0000.000
47A48PRO00.0270.03010.8101.7861.7860.0000.0000.0000.000
48A49LEU0-0.018-0.01610.0502.2732.2730.0000.0000.0000.000
49A50PHE0-0.019-0.0249.2361.7481.7480.0000.0000.0000.000
50A51GLN0-0.015-0.0357.1082.7112.7110.0000.0000.0000.000
51A52SER0-0.037-0.0165.5646.3056.403-0.0010.000-0.0970.000
52A53TYR0-0.027-0.0086.5010.5600.5600.0000.0000.0000.000
53A54ALA00.0460.0433.754-3.155-2.9180.002-0.034-0.2060.000
54A55HIS00.0210.0112.5730.8202.4273.985-1.974-3.618-0.017
55A56HIS0-0.052-0.0186.077-1.905-1.9050.0000.0000.0000.000
56A57ARG10.7060.8359.469-18.024-18.0240.0000.0000.0000.000
57A58THR00.023-0.00912.237-0.612-0.6120.0000.0000.0000.000
58A59LEU00.020-0.00913.947-0.674-0.6740.0000.0000.0000.000
59A60LEU0-0.037-0.00917.250-0.684-0.6840.0000.0000.0000.000
60A61GLU-1-0.669-0.79312.28321.47221.4720.0000.0000.0000.000
61A62ALA0-0.0060.00216.576-0.431-0.4310.0000.0000.0000.000
62A63VAL0-0.015-0.01218.260-0.642-0.6420.0000.0000.0000.000
63A64HIS0-0.058-0.02619.488-0.678-0.6780.0000.0000.0000.000
64A65ASP-1-0.789-0.88616.42815.66615.6660.0000.0000.0000.000
65A66THR0-0.092-0.04919.839-0.279-0.2790.0000.0000.0000.000
66A67ILE00.0010.01716.960-0.349-0.3490.0000.0000.0000.000
67A68ILE0-0.028-0.01520.482-0.175-0.1750.0000.0000.0000.000
68A69ALA00.0230.01922.978-0.108-0.1080.0000.0000.0000.000
69A70LYS10.8930.91626.073-10.294-10.2940.0000.0000.0000.000
70A71ALA0-0.031-0.02227.619-0.218-0.2180.0000.0000.0000.000
71A72ASP-1-0.906-0.95230.2838.3338.3330.0000.0000.0000.000
72A73PRO0-0.0020.01833.860-0.073-0.0730.0000.0000.0000.000
73A74PRO0-0.020-0.01629.6790.2450.2450.0000.0000.0000.000
74A75SER0-0.027-0.01529.1350.4190.4190.0000.0000.0000.000
75A76CYS0-0.0010.01331.286-0.269-0.2690.0000.0000.0000.000
76A77ASP-1-0.765-0.87433.1568.4288.4280.0000.0000.0000.000
77A78LEU0-0.008-0.01032.748-0.142-0.1420.0000.0000.0000.000
78A79GLN0-0.047-0.02736.703-0.022-0.0220.0000.0000.0000.000
79A80SER0-0.052-0.04539.696-0.267-0.2670.0000.0000.0000.000
80A81ALA0-0.027-0.01941.7130.0110.0110.0000.0000.0000.000
81A82HIS0-0.0020.00139.772-0.213-0.2130.0000.0000.0000.000
82A83GLY00.0940.05137.9530.1400.1400.0000.0000.0000.000
83A84ASN0-0.053-0.04336.8660.3390.3390.0000.0000.0000.000
84A85PRO0-0.010-0.00135.6030.1020.1020.0000.0000.0000.000
85A87MET00.0090.03332.8000.3010.3010.0000.0000.0000.000
86A88LYS10.9250.96534.895-8.462-8.4620.0000.0000.0000.000
87A89GLU-1-0.771-0.88630.30810.20810.2080.0000.0000.0000.000
88A90LYS10.8450.92328.070-10.265-10.2650.0000.0000.0000.000
89A91LEU00.0140.00731.0600.1520.1520.0000.0000.0000.000
90A92VAL0-0.084-0.02131.185-0.059-0.0590.0000.0000.0000.000
91A93MET0-0.0090.00724.6720.1690.1690.0000.0000.0000.000
92A94LYS10.9540.98127.392-10.394-10.3940.0000.0000.0000.000
93A95THR0-0.020-0.01424.3300.4580.4580.0000.0000.0000.000
94A96HIS00.0430.01323.605-0.565-0.5650.0000.0000.0000.000
95A97CYS0-0.097-0.03623.9390.9930.9930.0000.0000.0000.000
96A98PRO0-0.005-0.00422.190-0.323-0.3230.0000.0000.0000.000
97A99ASN00.0590.02625.4750.1480.1480.0000.0000.0000.000
98A100ASP-1-0.844-0.91926.97711.24011.2400.0000.0000.0000.000
99A101TYR0-0.046-0.02120.3130.0820.0820.0000.0000.0000.000
100A102GLN0-0.024-0.01427.114-0.118-0.1180.0000.0000.0000.000
101A103SER0-0.023-0.03125.874-0.458-0.4580.0000.0000.0000.000
102A104ALA00.0490.02924.1880.4360.4360.0000.0000.0000.000
103A105HIS00.0140.02118.722-1.054-1.0540.0000.0000.0000.000
104A106TYR0-0.048-0.04622.2850.5360.5360.0000.0000.0000.000
105A107LEU00.0310.01320.606-0.381-0.3810.0000.0000.0000.000
106A108ASN00.0660.02323.8560.0880.0880.0000.0000.0000.000
107A109ASN00.0250.00126.9610.3580.3580.0000.0000.0000.000
108A110ASP-1-0.854-0.90329.3819.4869.4860.0000.0000.0000.000
109A111GLY00.0190.01225.498-0.031-0.0310.0000.0000.0000.000
110A112LYS10.8250.90625.422-9.981-9.9810.0000.0000.0000.000
111A113MET0-0.0020.00922.5820.2630.2630.0000.0000.0000.000
112A114ALA00.0040.00624.977-0.440-0.4400.0000.0000.0000.000
113A115SER0-0.030-0.04125.7700.4510.4510.0000.0000.0000.000
114A116VAL0-0.0080.00527.632-0.417-0.4170.0000.0000.0000.000
115A117LYS10.9330.96328.922-9.637-9.6370.0000.0000.0000.000
116A118CYS00.0200.04831.2530.0910.0910.0000.0000.0000.000
117A119PRO00.0430.02733.8460.1490.1490.0000.0000.0000.000
118A120PRO00.017-0.01335.0340.1880.1880.0000.0000.0000.000
119A121LYS10.9520.96335.176-7.895-7.8950.0000.0000.0000.000
120A122TYR00.0030.00935.260-0.207-0.2070.0000.0000.0000.000
121A123GLU-1-0.747-0.84231.0349.9069.9060.0000.0000.0000.000
122A124LEU00.025-0.01027.675-0.290-0.2900.0000.0000.0000.000
123A125THR0-0.034-0.02831.2050.0060.0060.0000.0000.0000.000
124A126GLU-1-0.736-0.85029.21910.02910.0290.0000.0000.0000.000
125A127ASP-1-0.816-0.86928.4759.8679.8670.0000.0000.0000.000
126A129ASN0-0.026-0.02229.5530.1380.1380.0000.0000.0000.000
127A130PHE00.0080.00432.990-0.280-0.2800.0000.0000.0000.000
128A132ARG10.7570.84332.105-9.684-9.6840.0000.0000.0000.000
129A133GLN0-0.005-0.00436.2220.1570.1570.0000.0000.0000.000
130A134MET0-0.044-0.01234.1010.1140.1140.0000.0000.0000.000
131A135THR0-0.019-0.02634.192-0.162-0.1620.0000.0000.0000.000
132A136GLY00.0350.03433.611-0.102-0.1020.0000.0000.0000.000
133A137ALA0-0.044-0.03934.622-0.055-0.0550.0000.0000.0000.000
134A138SER0-0.014-0.01229.315-0.046-0.0460.0000.0000.0000.000
135A139LEU0-0.0170.00430.0600.1880.1880.0000.0000.0000.000
136A140LYS10.8010.88623.318-11.912-11.9120.0000.0000.0000.000
137A141LYS10.7800.88724.697-11.981-11.9810.0000.0000.0000.000
138A142GLY00.0550.04222.303-0.136-0.1360.0000.0000.0000.000
139A143SER0-0.043-0.04921.926-0.807-0.8070.0000.0000.0000.000
140A144TYR00.001-0.02919.9120.9600.9600.0000.0000.0000.000
141A145PRO0-0.0220.00316.738-0.595-0.5950.0000.0000.0000.000
142A146LEU0-0.007-0.01619.6280.2220.2220.0000.0000.0000.000
143A147GLN0-0.041-0.03619.450-0.038-0.0380.0000.0000.0000.000
144A148ASP-1-0.803-0.88513.80921.78821.7880.0000.0000.0000.000
145A149LEU0-0.009-0.01514.930-0.418-0.4180.0000.0000.0000.000
146A150PHE00.0370.02811.1891.0561.0560.0000.0000.0000.000
147A151CYS0-0.070-0.03313.130-0.988-0.9880.0000.0000.0000.000
148A152GLN0-0.007-0.02613.2971.9521.9520.0000.0000.0000.000
149A153SER00.0450.03215.257-0.982-0.9820.0000.0000.0000.000
150A154SER0-0.033-0.06418.0810.3280.3280.0000.0000.0000.000
151A155GLU-1-0.791-0.88320.80310.96810.9680.0000.0000.0000.000
152A156ASP-1-0.816-0.87923.43411.36011.3600.0000.0000.0000.000
153A157ASP-1-0.760-0.85425.1549.7029.7020.0000.0000.0000.000
154A158GLY00.0560.00627.2880.1280.1280.0000.0000.0000.000
155A159SER0-0.052-0.04228.189-0.165-0.1650.0000.0000.0000.000
156A160LYS10.8310.91331.345-9.224-9.2240.0000.0000.0000.000
157A161LEU0-0.0170.01526.145-0.082-0.0820.0000.0000.0000.000
158A162LYS10.9470.95830.144-8.705-8.7050.0000.0000.0000.000
159A163THR00.0180.00429.0400.2960.2960.0000.0000.0000.000
160A164LYS10.8830.94429.637-9.244-9.2440.0000.0000.0000.000
161A165MET00.0300.03127.6770.2490.2490.0000.0000.0000.000
162A166LYS10.8590.90331.078-10.244-10.2440.0000.0000.0000.000
163A167GLY00.0270.01934.0840.1430.1430.0000.0000.0000.000
164A168VAL0-0.028-0.00631.659-0.137-0.1370.0000.0000.0000.000
165A169CYS0-0.023-0.02235.116-0.039-0.0390.0000.0000.0000.000
166A170GLU-1-0.870-0.95235.5568.0828.0820.0000.0000.0000.000
167A171VAL00.0330.01128.8450.1480.1480.0000.0000.0000.000
168A172GLY00.0550.03430.2590.0810.0810.0000.0000.0000.000
169A173VAL0-0.056-0.02731.184-0.363-0.3630.0000.0000.0000.000
170A174GLN0-0.048-0.01529.478-0.411-0.4110.0000.0000.0000.000
171A175ALA00.0380.02534.1510.0790.0790.0000.0000.0000.000
172A176LEU0-0.060-0.03632.4200.0300.0300.0000.0000.0000.000
173A177LYS10.7770.86436.801-7.732-7.7320.0000.0000.0000.000
174A178LYS10.9430.98040.480-6.935-6.9350.0000.0000.0000.000
175A180ASP-1-0.894-0.92843.9426.7056.7050.0000.0000.0000.000
176A181GLY00.0240.02045.935-0.158-0.1580.0000.0000.0000.000
177A182GLN0-0.021-0.01845.2220.0670.0670.0000.0000.0000.000
178A183LEU0-0.002-0.00240.0760.1190.1190.0000.0000.0000.000
179A184SER0-0.033-0.00937.0970.0640.0640.0000.0000.0000.000
180A185THR00.005-0.02435.7440.0170.0170.0000.0000.0000.000
181A186ALA0-0.0050.00931.579-0.051-0.0510.0000.0000.0000.000
182A187HIS00.004-0.00928.6840.2320.2320.0000.0000.0000.000
183A188GLU-1-0.778-0.84126.90610.82510.8250.0000.0000.0000.000
184A189VAL0-0.011-0.02220.268-0.012-0.0120.0000.0000.0000.000
185A190VAL00.0070.01622.7150.2930.2930.0000.0000.0000.000
186A191PRO00.0200.02120.2330.3450.3450.0000.0000.0000.000
187A192PHE0-0.044-0.04120.481-0.832-0.8320.0000.0000.0000.000
188A193ALA00.0330.02119.9240.8590.8590.0000.0000.0000.000
189A194VAL0-0.0070.00621.098-0.742-0.7420.0000.0000.0000.000
190A195PHE00.0560.01621.6900.5810.5810.0000.0000.0000.000
191A196LYS10.8750.94724.092-10.936-10.9360.0000.0000.0000.000
192A197ASN0-0.040-0.03026.121-0.184-0.1840.0000.0000.0000.000
193A198SER0-0.047-0.02526.505-0.213-0.2130.0000.0000.0000.000
194A199LYS10.8910.93828.777-9.295-9.2950.0000.0000.0000.000
195A200LYS10.8310.91724.518-11.549-11.5490.0000.0000.0000.000
196A201VAL0-0.0110.00425.240-0.470-0.4700.0000.0000.0000.000
197A202TYR0-0.003-0.02724.5550.3910.3910.0000.0000.0000.000
198A203LEU00.0200.00122.160-0.435-0.4350.0000.0000.0000.000
199A204ASP-1-0.835-0.92325.68610.43410.4340.0000.0000.0000.000
200A205LYS10.8970.94922.913-11.722-11.7220.0000.0000.0000.000
201A206LEU00.0350.02515.705-0.332-0.3320.0000.0000.0000.000
202A207ASP-1-0.859-0.92718.94314.78214.7820.0000.0000.0000.000
203A208LEU00.007-0.01113.614-0.553-0.5530.0000.0000.0000.000
204A209LYS10.8750.96714.792-14.400-14.4000.0000.0000.0000.000
205A210THR00.033-0.0059.658-1.080-1.0800.0000.0000.0000.000
206A211GLU-1-0.894-0.92112.95216.87416.8740.0000.0000.0000.000
207A212GLU-1-0.862-0.9327.83832.44632.4460.0000.0000.0000.000
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