Manual

About

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: 6NJ6Z

Calculation Name: 4F3P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F3P

Chain ID: A

ChEMBL ID:

UniProt ID: Q3JIF9

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2724829.415778
FMO2-HF: Nuclear repulsion 2638386.993677
FMO2-HF: Total energy -86442.422101
FMO2-MP2: Total energy -86697.060169


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:26:LYS)


Summations of interaction energy for fragment #1(A:26: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.
-73.819-75.8527.805-13.396-12.378-0.146
Interaction energy analysis for fragmet #1(A:26:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.919
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].
3A28LEU0-0.039-0.0182.417-18.392-13.5452.195-2.708-4.335-0.010
4A29VAL00.005-0.0052.79213.95514.8200.043-0.205-0.703-0.002
5A30VAL0-0.001-0.0064.680-0.334-0.265-0.001-0.002-0.0660.000
6A31GLY00.0600.0357.7952.9642.9640.0000.0000.0000.000
7A32THR0-0.028-0.01710.3510.6810.6810.0000.0000.0000.000
8A33ASP-1-0.738-0.87713.710-15.443-15.4430.0000.0000.0000.000
9A34THR0-0.040-0.03117.276-0.185-0.1850.0000.0000.0000.000
10A35SER0-0.071-0.04419.2960.2970.2970.0000.0000.0000.000
11A36PHE0-0.027-0.00420.9510.5140.5140.0000.0000.0000.000
12A37MET00.0190.04922.837-0.153-0.1530.0000.0000.0000.000
13A38PRO0-0.008-0.00425.1700.1890.1890.0000.0000.0000.000
14A39PHE00.0260.00420.385-0.094-0.0940.0000.0000.0000.000
15A40GLH00.005-0.04416.631-0.567-0.5670.0000.0000.0000.000
16A41PHE0-0.0080.00319.9250.3930.3930.0000.0000.0000.000
17A42LYS10.8810.93522.08613.24213.2420.0000.0000.0000.000
18A43GLN00.012-0.00123.0950.4820.4820.0000.0000.0000.000
19A44GLY00.0320.01725.174-0.136-0.1360.0000.0000.0000.000
20A45ASP-1-0.832-0.93123.473-13.140-13.1400.0000.0000.0000.000
21A46LYS10.9070.96520.72513.00113.0010.0000.0000.0000.000
22A47TYR0-0.035-0.01917.7430.3880.3880.0000.0000.0000.000
23A48VAL0-0.025-0.01619.508-0.417-0.4170.0000.0000.0000.000
24A49GLY00.0650.01321.090-0.022-0.0220.0000.0000.0000.000
25A50PHE00.0050.00620.503-0.558-0.5580.0000.0000.0000.000
26A51ASP-1-0.738-0.83416.625-17.584-17.5840.0000.0000.0000.000
27A52LEU0-0.0150.00914.910-1.147-1.1470.0000.0000.0000.000
28A53ASP-1-0.792-0.86616.562-15.313-15.3130.0000.0000.0000.000
29A54LEU0-0.028-0.01917.937-0.086-0.0860.0000.0000.0000.000
30A55TRP00.0400.0098.236-0.352-0.3520.0000.0000.0000.000
31A56ALA00.0090.01113.518-1.208-1.2080.0000.0000.0000.000
32A57GLU-1-0.820-0.88414.216-15.961-15.9610.0000.0000.0000.000
33A58ILE00.023-0.00812.3280.1270.1270.0000.0000.0000.000
34A59ALA0-0.0270.0029.890-0.400-0.4000.0000.0000.0000.000
35A60LYS10.8570.90810.18415.49515.4950.0000.0000.0000.000
36A61GLY0-0.0150.00312.2380.2750.2750.0000.0000.0000.000
37A62ALA0-0.104-0.0669.3490.7420.7420.0000.0000.0000.000
38A63GLY00.0160.0318.768-0.110-0.1100.0000.0000.0000.000
39A64TRP0-0.073-0.0355.296-2.763-2.7630.0000.0000.0000.000
40A65THR00.0590.0235.1391.3611.3610.0000.0000.0000.000
41A66TYR0-0.023-0.0285.691-5.746-5.7460.0000.0000.0000.000
42A67LYS10.8860.9435.11151.47951.4790.0000.0000.0000.000
43A68ILE0-0.013-0.0168.007-2.883-2.8830.0000.0000.0000.000
44A69GLN0-0.016-0.0049.592-0.169-0.1690.0000.0000.0000.000
45A70PRO0-0.025-0.02111.346-0.061-0.0610.0000.0000.0000.000
46A71MET0-0.0270.00412.429-1.079-1.0790.0000.0000.0000.000
47A72ASP-1-0.755-0.84615.928-14.925-14.9250.0000.0000.0000.000
48A73PHE0-0.001-0.00517.565-0.728-0.7280.0000.0000.0000.000
49A74ALA0-0.033-0.01817.907-0.607-0.6070.0000.0000.0000.000
50A75GLY00.0260.01616.1230.0630.0630.0000.0000.0000.000
51A76LEU0-0.004-0.00612.715-1.515-1.5150.0000.0000.0000.000
52A77ILE00.0220.00112.987-1.620-1.6200.0000.0000.0000.000
53A78PRO00.0260.00514.060-1.018-1.0180.0000.0000.0000.000
54A79ALA00.0330.02510.137-0.651-0.6510.0000.0000.0000.000
55A80LEU0-0.052-0.0189.049-3.096-3.0960.0000.0000.0000.000
56A81GLN0-0.025-0.02410.219-1.051-1.0510.0000.0000.0000.000
57A82THR0-0.038-0.02210.9960.2170.2170.0000.0000.0000.000
58A83GLN0-0.050-0.0186.428-2.703-2.7030.0000.0000.0000.000
59A84ASN0-0.0270.0005.703-2.563-2.5630.0000.0000.0000.000
60A85ILE0-0.039-0.0085.548-1.627-1.6270.0000.0000.0000.000
61A86ASP-1-0.780-0.8771.827-147.750-155.61325.569-10.475-7.231-0.134
62A87VAL0-0.041-0.0284.9895.9656.016-0.001-0.006-0.0430.000
63A88ALA00.0160.0198.200-0.251-0.2510.0000.0000.0000.000
64A89LEU0-0.038-0.01711.4691.3691.3690.0000.0000.0000.000
65A90SER00.032-0.01814.144-0.061-0.0610.0000.0000.0000.000
66A91GLY00.083-0.03317.4440.8480.8480.0000.0000.0000.000
67A92MET0-0.0300.00215.0420.5680.5680.0000.0000.0000.000
68A93THR00.016-0.02819.3430.0840.0840.0000.0000.0000.000
69A94ILE0-0.058-0.03120.213-0.331-0.3310.0000.0000.0000.000
70A95LYS10.7980.88021.84112.73512.7350.0000.0000.0000.000
71A96GLU-1-0.779-0.86722.400-13.807-13.8070.0000.0000.0000.000
72A97GLU-1-0.806-0.89623.475-12.566-12.5660.0000.0000.0000.000
73A98ARG10.8630.91319.23314.45414.4540.0000.0000.0000.000
74A99ARG10.8780.91718.81413.39413.3940.0000.0000.0000.000
75A100LYS10.7960.90219.12811.88411.8840.0000.0000.0000.000
76A101ALA0-0.024-0.00417.150-0.210-0.2100.0000.0000.0000.000
77A102ILE0-0.020-0.00813.455-1.275-1.2750.0000.0000.0000.000
78A103ASP-1-0.777-0.87313.106-18.704-18.7040.0000.0000.0000.000
79A104PHE0-0.022-0.03214.107-0.928-0.9280.0000.0000.0000.000
80A105SER0-0.013-0.00415.337-0.073-0.0730.0000.0000.0000.000
81A106ASP-1-0.921-0.96016.647-14.531-14.5310.0000.0000.0000.000
82A107PRO0-0.014-0.00319.819-0.493-0.4930.0000.0000.0000.000
83A108TYR0-0.009-0.05017.7590.2630.2630.0000.0000.0000.000
84A109TYR00.0380.04022.2970.2160.2160.0000.0000.0000.000
85A110ASP-1-0.892-0.93924.878-11.653-11.6530.0000.0000.0000.000
86A111SER00.1220.04626.5530.2780.2780.0000.0000.0000.000
87A112GLY0-0.021-0.04428.6150.2870.2870.0000.0000.0000.000
88A113LEU0-0.0540.00028.930-0.287-0.2870.0000.0000.0000.000
89A114ALA00.0120.00432.0630.3620.3620.0000.0000.0000.000
90A115ALA00.0260.02134.217-0.209-0.2090.0000.0000.0000.000
91A116MET0-0.0270.00633.5450.1540.1540.0000.0000.0000.000
92A117VAL00.0400.01037.6640.0360.0360.0000.0000.0000.000
93A118GLN00.0480.01540.9040.1340.1340.0000.0000.0000.000
94A119ALA0-0.002-0.01642.7760.1220.1220.0000.0000.0000.000
95A120ASN0-0.002-0.01544.7850.2380.2380.0000.0000.0000.000
96A121ASN00.0270.04645.0110.2310.2310.0000.0000.0000.000
97A122THR00.0460.01847.240-0.053-0.0530.0000.0000.0000.000
98A123THR00.012-0.00348.3120.0530.0530.0000.0000.0000.000
99A124ILE0-0.0170.00642.6950.0270.0270.0000.0000.0000.000
100A125LYS10.8640.93245.3876.3946.3940.0000.0000.0000.000
101A126SER0-0.035-0.03243.776-0.109-0.1090.0000.0000.0000.000
102A127ILE00.045-0.00337.130-0.028-0.0280.0000.0000.0000.000
103A128ASP-1-0.863-0.92541.157-7.323-7.3230.0000.0000.0000.000
104A129ASP-1-0.809-0.88943.881-6.846-6.8460.0000.0000.0000.000
105A130LEU0-0.008-0.01238.6310.0500.0500.0000.0000.0000.000
106A131ASN0-0.0070.00042.314-0.207-0.2070.0000.0000.0000.000
107A132GLY0-0.010-0.01843.9900.1500.1500.0000.0000.0000.000
108A133LYS10.8230.92042.2677.1727.1720.0000.0000.0000.000
109A134VAL0-0.034-0.02339.229-0.147-0.1470.0000.0000.0000.000
110A135ILE00.003-0.00235.3460.0160.0160.0000.0000.0000.000
111A136ALA0-0.026-0.00533.839-0.139-0.1390.0000.0000.0000.000
112A137ALA00.0460.00630.603-0.007-0.0070.0000.0000.0000.000
113A138LYS10.8270.92021.41714.46714.4670.0000.0000.0000.000
114A139THR00.025-0.00224.799-0.066-0.0660.0000.0000.0000.000
115A140GLY00.0010.00022.999-0.502-0.5020.0000.0000.0000.000
116A141THR0-0.068-0.02322.774-0.317-0.3170.0000.0000.0000.000
117A142ALA00.0390.00024.4450.3500.3500.0000.0000.0000.000
118A143THR00.004-0.00526.2160.3800.3800.0000.0000.0000.000
119A144ILE0-0.021-0.00128.1400.5610.5610.0000.0000.0000.000
120A145ASP-1-0.877-0.95126.610-11.659-11.6590.0000.0000.0000.000
121A146TRP00.0050.00830.2320.4340.4340.0000.0000.0000.000
122A147ILE00.020-0.00832.3530.3750.3750.0000.0000.0000.000
123A148LYS10.9230.96331.55510.13710.1370.0000.0000.0000.000
124A149ALA0-0.038-0.00233.7960.2380.2380.0000.0000.0000.000
125A150HIS10.8390.91734.4909.2689.2680.0000.0000.0000.000
126A151LEU00.0030.02437.5070.1790.1790.0000.0000.0000.000
127A152LYS10.9570.97839.7297.2387.2380.0000.0000.0000.000
128A153PRO0-0.0210.00137.9290.2070.2070.0000.0000.0000.000
129A154LYS10.9580.98541.2417.1527.1520.0000.0000.0000.000
130A155GLU-1-0.826-0.88937.953-8.327-8.3270.0000.0000.0000.000
131A156ILE0-0.0020.00332.899-0.042-0.0420.0000.0000.0000.000
132A157ARG10.7950.86834.7918.2658.2650.0000.0000.0000.000
133A158GLN0-0.019-0.01928.839-0.499-0.4990.0000.0000.0000.000
134A159PHE00.006-0.00129.1860.2110.2110.0000.0000.0000.000
135A160PRO00.0350.01424.200-0.155-0.1550.0000.0000.0000.000
136A161ASN0-0.008-0.01722.076-0.806-0.8060.0000.0000.0000.000
137A162ILE00.0050.01125.5000.4720.4720.0000.0000.0000.000
138A163ASP-1-0.787-0.88726.253-11.787-11.7870.0000.0000.0000.000
139A164GLN00.016-0.00526.7710.3690.3690.0000.0000.0000.000
140A165ALA0-0.0030.01130.5640.3980.3980.0000.0000.0000.000
141A166TYR00.000-0.03129.7210.4850.4850.0000.0000.0000.000
142A167LEU00.0410.02933.5160.3410.3410.0000.0000.0000.000
143A168ALA0-0.031-0.02135.0250.3320.3320.0000.0000.0000.000
144A169LEU0-0.0310.00136.6430.3010.3010.0000.0000.0000.000
145A170GLU-1-0.839-0.91837.356-8.215-8.2150.0000.0000.0000.000
146A171ALA0-0.057-0.01839.5240.2350.2350.0000.0000.0000.000
147A172GLY0-0.021-0.01041.3870.1900.1900.0000.0000.0000.000
148A173ARG10.8860.94139.5827.6687.6680.0000.0000.0000.000
149A174VAL0-0.028-0.00937.277-0.041-0.0410.0000.0000.0000.000
150A175ASP-1-0.838-0.90740.460-7.325-7.3250.0000.0000.0000.000
151A176ALA0-0.015-0.01939.0200.0860.0860.0000.0000.0000.000
152A177ALA0-0.0090.01033.663-0.131-0.1310.0000.0000.0000.000
153A178MET0-0.023-0.00633.3650.2340.2340.0000.0000.0000.000
154A179HIS00.0130.00324.9840.1260.1260.0000.0000.0000.000
155A180ASP-1-0.754-0.85525.089-12.339-12.3390.0000.0000.0000.000
156A181THR00.017-0.03028.6520.2400.2400.0000.0000.0000.000
157A182PRO00.0270.01527.2160.2910.2910.0000.0000.0000.000
158A183ASN0-0.0140.01126.2990.3770.3770.0000.0000.0000.000
159A184VAL00.0130.01428.6560.2300.2300.0000.0000.0000.000
160A185LEU00.000-0.01932.2140.2890.2890.0000.0000.0000.000
161A186PHE00.0200.01229.5420.2320.2320.0000.0000.0000.000
162A187PHE00.0800.03331.5050.1940.1940.0000.0000.0000.000
163A188VAL0-0.030-0.00932.9440.2660.2660.0000.0000.0000.000
164A189ASN0-0.102-0.07335.3820.5600.5600.0000.0000.0000.000
165A190ASN0-0.0060.00732.6200.3280.3280.0000.0000.0000.000
166A191GLU-1-0.867-0.94031.504-9.981-9.9810.0000.0000.0000.000
167A192GLY00.002-0.00235.1420.2400.2400.0000.0000.0000.000
168A193LYS10.9050.96337.2678.3908.3900.0000.0000.0000.000
169A194GLY0-0.045-0.02139.9660.1250.1250.0000.0000.0000.000
170A195ARG10.8790.93939.4018.2488.2480.0000.0000.0000.000
171A196VAL0-0.024-0.01236.9670.0960.0960.0000.0000.0000.000
172A197LYS10.8130.90240.2127.1327.1320.0000.0000.0000.000
173A198VAL00.0150.00637.117-0.116-0.1160.0000.0000.0000.000
174A199ALA0-0.0250.00239.5630.2350.2350.0000.0000.0000.000
175A200GLY00.0170.00540.615-0.145-0.1450.0000.0000.0000.000
176A201ALA0-0.054-0.02440.528-0.037-0.0370.0000.0000.0000.000
177A202PRO00.003-0.01134.944-0.029-0.0290.0000.0000.0000.000
178A203VAL0-0.0060.01834.0130.1940.1940.0000.0000.0000.000
179A204SER0-0.011-0.01432.990-0.317-0.3170.0000.0000.0000.000
180A205GLY00.0280.00332.0300.1340.1340.0000.0000.0000.000
181A206ASP-1-0.811-0.87327.056-11.772-11.7720.0000.0000.0000.000
182A207LYS10.9050.92924.83411.43811.4380.0000.0000.0000.000
183A208TYR0-0.0020.19420.422-0.302-0.3020.0000.0000.0000.000
184A209GLY0-0.030-0.03718.6260.3850.3850.0000.0000.0000.000
185A210ILE0-0.034-0.01112.342-0.096-0.0960.0000.0000.0000.000
186A211GLY00.0210.02213.3640.6620.6620.0000.0000.0000.000
187A212PHE00.006-0.0268.665-2.389-2.3890.0000.0000.0000.000
188A213PRO00.0560.0286.7082.8082.8080.0000.0000.0000.000
189A214LYS10.7980.88810.02018.79618.7960.0000.0000.0000.000
190A215GLY0-0.006-0.00411.832-0.922-0.9220.0000.0000.0000.000
191A216SER0-0.034-0.0047.826-1.249-1.2490.0000.0000.0000.000
192A217PRO00.0300.0067.5682.2022.2020.0000.0000.0000.000
193A218LEU0-0.027-0.0105.2851.6891.6890.0000.0000.0000.000
194A219VAL00.0530.0239.3041.8101.8100.0000.0000.0000.000
195A220ALA00.0270.02112.8701.3311.3310.0000.0000.0000.000
196A221LYS10.8730.92410.74921.14021.1400.0000.0000.0000.000
197A222VAL00.0250.01611.4050.9340.9340.0000.0000.0000.000
198A223ASN00.0530.02013.9260.4300.4300.0000.0000.0000.000
199A224ALA0-0.021-0.00315.9381.0841.0840.0000.0000.0000.000
200A225GLU-1-0.831-0.90513.592-16.421-16.4210.0000.0000.0000.000
201A226LEU00.0200.01916.6490.9390.9390.0000.0000.0000.000
202A227ALA0-0.019-0.01319.1570.8670.8670.0000.0000.0000.000
203A228ARG10.9080.93516.29716.17816.1780.0000.0000.0000.000
204A229MET0-0.0090.01318.3870.3160.3160.0000.0000.0000.000
205A230LYS10.8280.90421.78514.21614.2160.0000.0000.0000.000
206A231ALA0-0.023-0.00324.5430.4990.4990.0000.0000.0000.000
207A232ASP-1-0.773-0.86322.443-12.656-12.6560.0000.0000.0000.000
208A233GLY00.0220.00626.0270.2410.2410.0000.0000.0000.000
209A234ARG10.7230.82417.70814.77014.7700.0000.0000.0000.000
210A235TYR0-0.021-0.02722.8380.1660.1660.0000.0000.0000.000
211A236ALA00.009-0.00324.3320.0960.0960.0000.0000.0000.000
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