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: N9K5Q

Calculation Name: 4F8T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F8T

Chain ID: A

ChEMBL ID:

UniProt ID: O00478

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptHSide
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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2076258.993713
FMO2-HF: Nuclear repulsion 1995533.445081
FMO2-HF: Total energy -80725.548632
FMO2-MP2: Total energy -80958.881692


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-6.33-1.2820.429-2.628-2.85-0.005
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.002
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].
3A3SER00.004-0.0033.687-0.8842.070-0.035-1.529-1.3910.007
4A4VAL0-0.020-0.0036.031-0.289-0.2890.0000.0000.0000.000
5A5LEU0-0.023-0.0049.7420.2990.2990.0000.0000.0000.000
6A6GLY00.0850.04612.610-0.117-0.1170.0000.0000.0000.000
7A7PRO0-0.050-0.03216.2550.0250.0250.0000.0000.0000.000
8A8SER0-0.002-0.01019.1910.0260.0260.0000.0000.0000.000
9A9GLY00.0270.01120.8150.0330.0330.0000.0000.0000.000
10A10PRO0-0.101-0.03923.087-0.018-0.0180.0000.0000.0000.000
11A11ILE00.0140.00923.5390.0010.0010.0000.0000.0000.000
12A12LEU0-0.019-0.01026.8020.0010.0010.0000.0000.0000.000
13A13ALA00.0220.01930.559-0.006-0.0060.0000.0000.0000.000
14A14MET0-0.004-0.00432.3690.0080.0080.0000.0000.0000.000
15A15VAL0-0.024-0.03535.503-0.007-0.0070.0000.0000.0000.000
16A16GLY0-0.024-0.00236.6240.0020.0020.0000.0000.0000.000
17A17GLU-1-0.907-0.93434.384-0.049-0.0490.0000.0000.0000.000
18A18ASP-1-0.831-0.92030.828-0.107-0.1070.0000.0000.0000.000
19A19ALA0-0.016-0.00928.2640.0080.0080.0000.0000.0000.000
20A20ASP-1-0.784-0.84524.525-0.168-0.1680.0000.0000.0000.000
21A21LEU0-0.031-0.02921.9460.0220.0220.0000.0000.0000.000
22A22PRO0-0.037-0.02319.352-0.038-0.0380.0000.0000.0000.000
23A23CYS0-0.070-0.02614.3300.0410.0410.0000.0000.0000.000
24A24HIS0-0.016-0.01313.503-0.088-0.0880.0000.0000.0000.000
25A25LEU00.0100.0267.0590.1400.1400.0000.0000.0000.000
26A26PHE0-0.0310.0207.2540.1860.1860.0000.0000.0000.000
27A27PRO00.020-0.0146.220-0.274-0.2740.0000.0000.0000.000
28A28THR00.010-0.0188.763-0.401-0.4010.0000.0000.0000.000
29A29MET0-0.0130.0064.496-0.406-0.310-0.001-0.028-0.0670.000
30A30SER00.0050.0019.5290.1350.1350.0000.0000.0000.000
31A31ALA00.0520.0058.794-0.341-0.3410.0000.0000.0000.000
32A32GLU-1-1.000-0.99710.536-0.490-0.4900.0000.0000.0000.000
33A33THR0-0.010-0.0149.6510.1020.1020.0000.0000.0000.000
34A34MET0-0.0460.0165.9910.1130.1130.0000.0000.0000.000
35A35GLU-1-0.763-0.84310.989-0.319-0.3190.0000.0000.0000.000
36A36LEU0-0.048-0.02612.495-0.080-0.0800.0000.0000.0000.000
37A37ARG10.8040.88412.7420.5920.5920.0000.0000.0000.000
38A38TRP00.0730.04016.486-0.024-0.0240.0000.0000.0000.000
39A39VAL0-0.026-0.01518.8090.0150.0150.0000.0000.0000.000
40A40SER00.0660.03921.0210.0200.0200.0000.0000.0000.000
41A41SER0-0.011-0.01321.7420.0090.0090.0000.0000.0000.000
42A42SER0-0.007-0.01823.7620.0110.0110.0000.0000.0000.000
43A43LEU00.0290.02327.3660.0060.0060.0000.0000.0000.000
44A44ARG10.8390.92325.0330.0110.0110.0000.0000.0000.000
45A45GLN00.0440.03825.574-0.013-0.0130.0000.0000.0000.000
46A46VAL00.0030.00321.033-0.004-0.0040.0000.0000.0000.000
47A47VAL0-0.0040.00222.6880.0100.0100.0000.0000.0000.000
48A48ASN0-0.011-0.02822.138-0.004-0.0040.0000.0000.0000.000
49A49VAL0-0.020-0.01517.859-0.021-0.0210.0000.0000.0000.000
50A50TYR00.0230.02315.6100.0510.0510.0000.0000.0000.000
51A51ALA00.0630.02016.618-0.068-0.0680.0000.0000.0000.000
52A52ASP-1-0.897-0.94516.801-0.412-0.4120.0000.0000.0000.000
53A53GLY0-0.017-0.01618.3950.0410.0410.0000.0000.0000.000
54A54LYS10.8470.93020.3240.3450.3450.0000.0000.0000.000
55A55GLU-1-0.762-0.87021.004-0.294-0.2940.0000.0000.0000.000
56A56VAL0-0.062-0.03421.7350.0210.0210.0000.0000.0000.000
57A57GLU-1-0.799-0.90624.478-0.142-0.1420.0000.0000.0000.000
58A58ASP-1-0.859-0.93126.403-0.176-0.1760.0000.0000.0000.000
59A59ARG10.7300.84117.5020.3580.3580.0000.0000.0000.000
60A60GLN00.0040.00924.4130.0160.0160.0000.0000.0000.000
61A61SER0-0.021-0.02326.5930.0140.0140.0000.0000.0000.000
62A62ALA00.0460.02028.5990.0000.0000.0000.0000.0000.000
63A63PRO0-0.030-0.01130.0800.0010.0010.0000.0000.0000.000
64A64TYR00.011-0.01527.4380.0030.0030.0000.0000.0000.000
65A65ARG10.8000.90429.4980.1330.1330.0000.0000.0000.000
66A66GLY00.0000.01229.9980.0100.0100.0000.0000.0000.000
67A67ARG10.7640.85730.5610.0950.0950.0000.0000.0000.000
68A68THR0-0.014-0.02125.873-0.004-0.0040.0000.0000.0000.000
69A69SER0-0.0120.00825.2710.0010.0010.0000.0000.0000.000
70A70ILE0-0.038-0.01718.478-0.005-0.0050.0000.0000.0000.000
71A71LEU0-0.0180.00421.341-0.006-0.0060.0000.0000.0000.000
72A72ARG10.9280.94815.5100.5180.5180.0000.0000.0000.000
73A73ASP-1-0.860-0.92819.000-0.310-0.3100.0000.0000.0000.000
74A74GLY0-0.038-0.02018.5030.0070.0070.0000.0000.0000.000
75A75ILE00.0290.01513.763-0.045-0.0450.0000.0000.0000.000
76A76THR00.0120.00713.430-0.137-0.1370.0000.0000.0000.000
77A77ALA0-0.036-0.02013.669-0.057-0.0570.0000.0000.0000.000
78A78GLY00.0460.02711.549-0.021-0.0210.0000.0000.0000.000
79A79LYS10.8780.93912.2380.3280.3280.0000.0000.0000.000
80A80ALA00.0360.01815.444-0.007-0.0070.0000.0000.0000.000
81A81ALA0-0.031-0.01717.0190.0380.0380.0000.0000.0000.000
82A82LEU0-0.0160.02420.117-0.013-0.0130.0000.0000.0000.000
83A83ARG10.8780.90522.3140.1760.1760.0000.0000.0000.000
84A84ILE0-0.036-0.02525.896-0.006-0.0060.0000.0000.0000.000
85A85HIS0-0.028-0.03428.453-0.002-0.0020.0000.0000.0000.000
86A86ASN0-0.063-0.03531.9070.0070.0070.0000.0000.0000.000
87A87VAL0-0.0020.01130.9150.0020.0020.0000.0000.0000.000
88A88THR00.026-0.00733.4720.0090.0090.0000.0000.0000.000
89A89ALA00.0690.01933.7850.0000.0000.0000.0000.0000.000
90A90SER0-0.023-0.00833.4950.0050.0050.0000.0000.0000.000
91A91ASP-1-0.755-0.81529.782-0.083-0.0830.0000.0000.0000.000
92A92SER0-0.0200.01228.8980.0010.0010.0000.0000.0000.000
93A93GLY0-0.007-0.00127.7610.0000.0000.0000.0000.0000.000
94A94LYS10.9080.96122.610-0.094-0.0940.0000.0000.0000.000
95A95TYR00.001-0.02621.125-0.017-0.0170.0000.0000.0000.000
96A96LEU0-0.046-0.02016.1470.0230.0230.0000.0000.0000.000
97A98TYR00.009-0.01112.1670.0190.0190.0000.0000.0000.000
98A99PHE00.0270.0099.0480.0370.0370.0000.0000.0000.000
99A100GLN00.000-0.0108.598-0.116-0.1160.0000.0000.0000.000
100A101ASP-1-0.907-0.9615.514-1.945-1.9450.0000.0000.0000.000
101A102GLY00.0410.0307.0460.0800.0800.0000.0000.0000.000
102A103ASP-1-0.901-0.9529.140-0.432-0.4320.0000.0000.0000.000
103A104PHE0-0.051-0.0153.248-2.154-0.1560.465-1.071-1.392-0.012
104A105TYR00.008-0.0166.679-0.082-0.0820.0000.0000.0000.000
105A106GLU-1-0.854-0.8966.2310.2040.2040.0000.0000.0000.000
106A107LYS10.8530.9068.145-0.089-0.0890.0000.0000.0000.000
107A108ALA00.0160.00811.7200.1510.1510.0000.0000.0000.000
108A109LEU0-0.033-0.01813.901-0.043-0.0430.0000.0000.0000.000
109A110VAL00.0240.00517.5510.0200.0200.0000.0000.0000.000
110A111GLU-1-0.931-0.99020.2650.0620.0620.0000.0000.0000.000
111A112LEU00.0330.03623.875-0.001-0.0010.0000.0000.0000.000
112A113LYS10.8690.93326.963-0.048-0.0480.0000.0000.0000.000
113A114VAL00.0350.01630.203-0.003-0.0030.0000.0000.0000.000
114A115ALA0-0.014-0.00633.3530.0070.0070.0000.0000.0000.000
115A116ALA00.003-0.00836.669-0.006-0.0060.0000.0000.0000.000
116A117LEU0-0.005-0.01540.1070.0050.0050.0000.0000.0000.000
117A118GLY00.0520.02643.065-0.003-0.0030.0000.0000.0000.000
118A119SER00.0190.00546.2100.0000.0000.0000.0000.0000.000
119A120ASP-1-0.882-0.93249.684-0.004-0.0040.0000.0000.0000.000
120A121LEU0-0.027-0.01251.131-0.001-0.0010.0000.0000.0000.000
121A122HIS0-0.031-0.00154.463-0.001-0.0010.0000.0000.0000.000
122A123ILE0-0.009-0.01757.3100.0020.0020.0000.0000.0000.000
123A124GLU-1-0.903-0.94459.9230.0000.0000.0000.0000.0000.000
124A125VAL00.004-0.01462.4070.0010.0010.0000.0000.0000.000
125A126LYS10.7870.87860.658-0.008-0.0080.0000.0000.0000.000
126A127GLY00.0300.01066.002-0.001-0.0010.0000.0000.0000.000
127A128TYR0-0.081-0.04068.1480.0000.0000.0000.0000.0000.000
128A129GLU-1-0.870-0.94164.8000.0120.0120.0000.0000.0000.000
129A130ASP-1-0.859-0.91067.2520.0180.0180.0000.0000.0000.000
130A131GLY0-0.017-0.00269.5730.0010.0010.0000.0000.0000.000
131A132GLY0-0.045-0.01968.5110.0000.0000.0000.0000.0000.000
132A133ILE00.0060.01166.428-0.001-0.0010.0000.0000.0000.000
133A134HIS00.0080.00061.9950.0000.0000.0000.0000.0000.000
134A135LEU0-0.019-0.01461.312-0.002-0.0020.0000.0000.0000.000
135A136GLU-1-0.739-0.84457.3970.0070.0070.0000.0000.0000.000
136A137CYS0-0.089-0.01353.8250.0000.0000.0000.0000.0000.000
137A138ARG10.8650.91753.723-0.001-0.0010.0000.0000.0000.000
138A139SER0-0.017-0.00549.850-0.001-0.0010.0000.0000.0000.000
139A140THR0-0.016-0.01948.7370.0000.0000.0000.0000.0000.000
140A141GLY00.0840.02545.1230.0000.0000.0000.0000.0000.000
141A142TRP00.0200.01643.217-0.001-0.0010.0000.0000.0000.000
142A143TYR0-0.0300.01534.2520.0020.0020.0000.0000.0000.000
143A144PRO00.0240.01036.142-0.002-0.0020.0000.0000.0000.000
144A145GLN00.015-0.01638.5100.0020.0020.0000.0000.0000.000
145A146PRO0-0.0490.00040.7060.0040.0040.0000.0000.0000.000
146A147GLN00.008-0.00143.1670.0000.0000.0000.0000.0000.000
147A148ILE00.015-0.00145.121-0.002-0.0020.0000.0000.0000.000
148A149LYS10.8720.93648.923-0.028-0.0280.0000.0000.0000.000
149A150TRP00.0360.00551.557-0.002-0.0020.0000.0000.0000.000
150A151SER0-0.0030.00454.3550.0030.0030.0000.0000.0000.000
151A152ASP-1-0.751-0.87556.1810.0230.0230.0000.0000.0000.000
152A153THR0-0.0040.00358.2950.0010.0010.0000.0000.0000.000
153A154LYS10.8230.90759.634-0.026-0.0260.0000.0000.0000.000
154A155GLY00.0060.00756.0310.0020.0020.0000.0000.0000.000
155A156GLU-1-0.936-0.94554.7100.0380.0380.0000.0000.0000.000
156A157ASN0-0.030-0.02850.444-0.003-0.0030.0000.0000.0000.000
157A158ILE00.0100.00555.0030.0000.0000.0000.0000.0000.000
158A159PRO0-0.065-0.04555.3670.0000.0000.0000.0000.0000.000
159A160ALA0-0.001-0.00254.115-0.002-0.0020.0000.0000.0000.000
160A161VAL0-0.0210.00254.8570.0020.0020.0000.0000.0000.000
161A162GLU-1-0.925-0.96047.9820.0210.0210.0000.0000.0000.000
162A163ALA0-0.022-0.00752.5950.0000.0000.0000.0000.0000.000
163A164PRO0-0.013-0.02049.5880.0010.0010.0000.0000.0000.000
164A165VAL00.0150.01544.151-0.002-0.0020.0000.0000.0000.000
165A166VAL0-0.008-0.00647.165-0.001-0.0010.0000.0000.0000.000
166A167ALA0-0.020-0.00242.6340.0000.0000.0000.0000.0000.000
167A168ASP-1-0.821-0.92043.737-0.022-0.0220.0000.0000.0000.000
168A169GLY0-0.015-0.01243.616-0.001-0.0010.0000.0000.0000.000
169A170VAL0-0.041-0.02940.603-0.003-0.0030.0000.0000.0000.000
170A171GLY0-0.0160.00039.534-0.002-0.0020.0000.0000.0000.000
171A172LEU0-0.080-0.02940.1000.0050.0050.0000.0000.0000.000
172A173TYR00.0250.00839.2060.0020.0020.0000.0000.0000.000
173A174ALA0-0.054-0.01344.5890.0000.0000.0000.0000.0000.000
174A175VAL0-0.006-0.01046.6740.0010.0010.0000.0000.0000.000
175A176ALA00.024-0.00349.494-0.001-0.0010.0000.0000.0000.000
176A177ALA00.0300.02652.5060.0020.0020.0000.0000.0000.000
177A178SER00.0040.01054.406-0.001-0.0010.0000.0000.0000.000
178A179VAL00.0070.01057.2850.0020.0020.0000.0000.0000.000
179A180ILE0-0.022-0.00559.826-0.001-0.0010.0000.0000.0000.000
180A181MET0-0.038-0.00563.4610.0010.0010.0000.0000.0000.000
181A182ARG10.8920.91063.820-0.019-0.0190.0000.0000.0000.000
182A183GLY00.0160.02267.6530.0010.0010.0000.0000.0000.000
183A184SER00.001-0.01368.4680.0000.0000.0000.0000.0000.000
184A185SER0-0.029-0.02865.9300.0010.0010.0000.0000.0000.000
185A186GLY00.0350.02367.6780.0000.0000.0000.0000.0000.000
186A187GLY00.0220.02364.233-0.001-0.0010.0000.0000.0000.000
187A188GLY0-0.0090.01863.8530.0010.0010.0000.0000.0000.000
188A189VAL00.0020.00459.6970.0010.0010.0000.0000.0000.000
189A190SER0-0.015-0.03155.913-0.001-0.0010.0000.0000.0000.000
190A192ILE0-0.007-0.02549.042-0.001-0.0010.0000.0000.0000.000
191A193ILE00.0360.00946.7310.0020.0020.0000.0000.0000.000
192A194ARG10.8690.92441.833-0.032-0.0320.0000.0000.0000.000
193A195ASN00.0350.01638.9110.0050.0050.0000.0000.0000.000
194A196SER0-0.008-0.02538.524-0.001-0.0010.0000.0000.0000.000
195A197LEU0-0.040-0.00932.3030.0050.0050.0000.0000.0000.000
196A198LEU00.0340.00835.8160.0010.0010.0000.0000.0000.000
197A199GLY0-0.027-0.00538.1890.0000.0000.0000.0000.0000.000
198A200LEU0-0.040-0.01640.475-0.001-0.0010.0000.0000.0000.000
199A201GLU-1-0.857-0.92843.3000.0250.0250.0000.0000.0000.000
200A202LYS10.8240.92046.5180.0040.0040.0000.0000.0000.000
201A203THR0-0.027-0.02049.5910.0010.0010.0000.0000.0000.000
202A204ALA00.0280.03252.898-0.002-0.0020.0000.0000.0000.000
203A205SER00.0120.01056.5370.0020.0020.0000.0000.0000.000
204A206ILE0-0.0030.01659.508-0.001-0.0010.0000.0000.0000.000
205A207SER0-0.016-0.03862.8770.0010.0010.0000.0000.0000.000
206A208ILE0-0.020-0.01366.049-0.001-0.0010.0000.0000.0000.000
207A209ALA00.0090.00969.0720.0010.0010.0000.0000.0000.000
208A210ASP-1-0.833-0.94172.7670.0110.0110.0000.0000.0000.000
209A211PRO0-0.039-0.03174.7940.0000.0000.0000.0000.0000.000
210A212PHE0-0.0260.00472.5970.0000.0000.0000.0000.0000.000
211A213PHE0-0.0050.02268.2040.0000.0000.0000.0000.0000.000