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: Z6MYN

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2727390.04516
FMO2-HF: Nuclear repulsion 2640945.609385
FMO2-HF: Total energy -86444.435776
FMO2-MP2: Total energy -86698.890048


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.
-71.156-77.73932.576-14.534-11.456-0.149
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 : 0.869 / q_NPA : 0.909
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].
3A28LEU0-0.022-0.0072.602-9.999-6.4800.808-1.561-2.766-0.002
4A29VAL0-0.005-0.0063.00012.05612.9940.032-0.285-0.685-0.001
5A30VAL0-0.004-0.0054.810-1.261-1.196-0.001-0.001-0.0620.000
6A31GLY00.0650.0327.9073.0413.0410.0000.0000.0000.000
7A32THR0-0.040-0.03010.5270.6770.6770.0000.0000.0000.000
8A33ASP-1-0.756-0.89513.966-15.369-15.3690.0000.0000.0000.000
9A34THR0-0.045-0.02917.466-0.151-0.1510.0000.0000.0000.000
10A35SER0-0.068-0.05219.4850.3760.3760.0000.0000.0000.000
11A36PHE0-0.003-0.00320.7840.3590.3590.0000.0000.0000.000
12A37MET00.0390.05822.945-0.201-0.2010.0000.0000.0000.000
13A38PRO0-0.0160.00825.2760.2020.2020.0000.0000.0000.000
14A39PHE00.0130.00320.785-0.050-0.0500.0000.0000.0000.000
15A40GLH0-0.001-0.05016.834-0.639-0.6390.0000.0000.0000.000
16A41PHE00.0160.00620.0890.4810.4810.0000.0000.0000.000
17A42LYS10.8830.93122.18013.04313.0430.0000.0000.0000.000
18A43GLN00.0260.02323.1480.4860.4860.0000.0000.0000.000
19A44GLY00.0310.01425.762-0.053-0.0530.0000.0000.0000.000
20A45ASP-1-0.889-0.94724.293-13.294-13.2940.0000.0000.0000.000
21A46LYS10.9360.97420.92713.08613.0860.0000.0000.0000.000
22A47TYR0-0.040-0.03117.8290.3920.3920.0000.0000.0000.000
23A48VAL0-0.035-0.02119.429-0.494-0.4940.0000.0000.0000.000
24A49GLY00.0890.02421.2940.0960.0960.0000.0000.0000.000
25A50PHE00.0070.00820.789-0.674-0.6740.0000.0000.0000.000
26A51ASP-1-0.756-0.84417.006-17.361-17.3610.0000.0000.0000.000
27A52LEU0-0.0180.00615.121-1.236-1.2360.0000.0000.0000.000
28A53ASP-1-0.776-0.85816.880-14.974-14.9740.0000.0000.0000.000
29A54LEU0-0.029-0.01218.151-0.187-0.1870.0000.0000.0000.000
30A55TRP00.0480.0078.401-0.310-0.3100.0000.0000.0000.000
31A56ALA00.0090.01613.759-1.131-1.1310.0000.0000.0000.000
32A57GLU-1-0.798-0.87414.308-15.701-15.7010.0000.0000.0000.000
33A58ILE00.020-0.00412.5430.1510.1510.0000.0000.0000.000
34A59ALA0-0.0130.0019.877-0.344-0.3440.0000.0000.0000.000
35A60LYS10.8310.90310.22915.17215.1720.0000.0000.0000.000
36A61GLY00.0080.00712.6790.4810.4810.0000.0000.0000.000
37A62ALA0-0.074-0.0369.3280.7580.7580.0000.0000.0000.000
38A63GLY0-0.0090.0208.882-0.107-0.1070.0000.0000.0000.000
39A64TRP0-0.051-0.0355.336-2.553-2.5530.0000.0000.0000.000
40A65THR00.0590.0255.2380.7490.7490.0000.0000.0000.000
41A66TYR0-0.014-0.0206.104-5.110-5.1100.0000.0000.0000.000
42A67LYS10.8490.9195.10651.36751.3670.0000.0000.0000.000
43A68ILE0-0.006-0.0058.239-2.885-2.8850.0000.0000.0000.000
44A69GLN0-0.010-0.0109.892-0.434-0.4340.0000.0000.0000.000
45A70PRO0-0.019-0.01011.6630.1720.1720.0000.0000.0000.000
46A71MET0-0.0030.01612.378-1.024-1.0240.0000.0000.0000.000
47A72ASP-1-0.757-0.85416.090-14.987-14.9870.0000.0000.0000.000
48A73PHE00.0190.00017.616-0.750-0.7500.0000.0000.0000.000
49A74ALA0-0.034-0.02317.908-0.633-0.6330.0000.0000.0000.000
50A75GLY00.0190.01816.3820.0920.0920.0000.0000.0000.000
51A76LEU0-0.011-0.00512.612-1.537-1.5370.0000.0000.0000.000
52A77ILE00.0190.00312.914-1.561-1.5610.0000.0000.0000.000
53A78PRO00.0260.00613.877-1.077-1.0770.0000.0000.0000.000
54A79ALA00.0330.02310.059-0.812-0.8120.0000.0000.0000.000
55A80LEU0-0.031-0.0019.057-3.523-3.5230.0000.0000.0000.000
56A81GLN0-0.018-0.02110.073-1.155-1.1550.0000.0000.0000.000
57A82THR0-0.045-0.03210.7020.0480.0480.0000.0000.0000.000
58A83GLN0-0.037-0.0166.062-2.512-2.5120.0000.0000.0000.000
59A84ASN0-0.042-0.0035.083-4.837-4.794-0.0010.001-0.0420.000
60A85ILE0-0.037-0.0085.287-1.880-1.8800.0000.0000.0000.000
61A86ASP-1-0.771-0.8571.761-151.389-162.61831.739-12.667-7.843-0.146
62A87VAL0-0.024-0.0214.6876.8616.942-0.001-0.021-0.0580.000
63A88ALA0-0.0030.0058.210-0.409-0.4090.0000.0000.0000.000
64A89LEU0-0.028-0.01011.3761.5531.5530.0000.0000.0000.000
65A90SER00.038-0.00514.246-0.078-0.0780.0000.0000.0000.000
66A91GLY00.0580.01117.4490.8450.8450.0000.0000.0000.000
67A92MET0-0.034-0.00914.7320.7230.7230.0000.0000.0000.000
68A93THR00.0330.02218.995-0.124-0.1240.0000.0000.0000.000
69A94ILE0-0.038-0.01120.070-0.209-0.2090.0000.0000.0000.000
70A95LYS10.7940.87021.73512.75912.7590.0000.0000.0000.000
71A96GLU-1-0.766-0.85222.255-14.054-14.0540.0000.0000.0000.000
72A97GLU-1-0.820-0.90123.055-12.727-12.7270.0000.0000.0000.000
73A98ARG10.8740.93419.14514.15114.1510.0000.0000.0000.000
74A99ARG10.8600.90018.61413.62113.6210.0000.0000.0000.000
75A100LYS10.8140.90319.02912.07112.0710.0000.0000.0000.000
76A101ALA0-0.016-0.00317.346-0.283-0.2830.0000.0000.0000.000
77A102ILE0-0.024-0.00513.434-1.316-1.3160.0000.0000.0000.000
78A103ASP-1-0.804-0.89012.932-19.318-19.3180.0000.0000.0000.000
79A104PHE0-0.014-0.02914.141-0.733-0.7330.0000.0000.0000.000
80A105SER0-0.024-0.00915.506-0.084-0.0840.0000.0000.0000.000
81A106ASP-1-0.862-0.92516.615-14.426-14.4260.0000.0000.0000.000
82A107PRO0-0.0130.01019.966-0.510-0.5100.0000.0000.0000.000
83A108TYR0-0.021-0.04518.0830.4740.4740.0000.0000.0000.000
84A109TYR00.0220.04122.3230.4520.4520.0000.0000.0000.000
85A110ASP-1-0.841-0.90225.123-11.877-11.8770.0000.0000.0000.000
86A111SER00.0740.02926.3800.4340.4340.0000.0000.0000.000
87A112GLY00.033-0.00829.0320.3290.3290.0000.0000.0000.000
88A113LEU0-0.0760.01128.598-0.267-0.2670.0000.0000.0000.000
89A114ALA00.0340.00732.0790.3680.3680.0000.0000.0000.000
90A115ALA00.0360.02334.420-0.188-0.1880.0000.0000.0000.000
91A116MET0-0.0390.00533.8370.1180.1180.0000.0000.0000.000
92A117VAL00.0240.00037.8790.0390.0390.0000.0000.0000.000
93A118GLN00.0640.02141.0500.1230.1230.0000.0000.0000.000
94A119ALA00.001-0.00742.8930.1090.1090.0000.0000.0000.000
95A120ASN00.001-0.00744.9700.2520.2520.0000.0000.0000.000
96A121ASN00.0200.03144.7210.2470.2470.0000.0000.0000.000
97A122THR00.0610.02647.217-0.048-0.0480.0000.0000.0000.000
98A123THR0-0.017-0.00748.7680.0510.0510.0000.0000.0000.000
99A124ILE0-0.0100.00542.9300.0380.0380.0000.0000.0000.000
100A125LYS10.8690.92846.0546.4256.4250.0000.0000.0000.000
101A126SER0-0.055-0.04643.427-0.100-0.1000.0000.0000.0000.000
102A127ILE00.0590.01036.926-0.021-0.0210.0000.0000.0000.000
103A128ASP-1-0.849-0.92540.860-7.399-7.3990.0000.0000.0000.000
104A129ASP-1-0.807-0.88043.484-6.877-6.8770.0000.0000.0000.000
105A130LEU0-0.021-0.01638.7020.0640.0640.0000.0000.0000.000
106A131ASN00.0020.00742.270-0.225-0.2250.0000.0000.0000.000
107A132GLY0-0.003-0.01644.0610.1720.1720.0000.0000.0000.000
108A133LYS10.7770.89742.3107.1777.1770.0000.0000.0000.000
109A134VAL0-0.038-0.02439.080-0.146-0.1460.0000.0000.0000.000
110A135ILE00.0070.00035.1250.0210.0210.0000.0000.0000.000
111A136ALA0-0.0100.00033.900-0.173-0.1730.0000.0000.0000.000
112A137ALA00.0260.00330.3200.0070.0070.0000.0000.0000.000
113A138LYS10.8350.92521.63314.49114.4910.0000.0000.0000.000
114A139THR00.030-0.00224.530-0.012-0.0120.0000.0000.0000.000
115A140GLY0-0.009-0.00123.269-0.534-0.5340.0000.0000.0000.000
116A141THR0-0.023-0.00322.805-0.299-0.2990.0000.0000.0000.000
117A142ALA00.008-0.00424.3800.3680.3680.0000.0000.0000.000
118A143THR00.015-0.01426.2110.4310.4310.0000.0000.0000.000
119A144ILE0-0.037-0.00927.7850.5460.5460.0000.0000.0000.000
120A145ASP-1-0.845-0.93226.006-12.065-12.0650.0000.0000.0000.000
121A146TRP00.003-0.00429.6610.4120.4120.0000.0000.0000.000
122A147ILE00.012-0.00732.0840.3590.3590.0000.0000.0000.000
123A148LYS10.9250.96231.03310.29210.2920.0000.0000.0000.000
124A149ALA0-0.0050.01733.5060.2100.2100.0000.0000.0000.000
125A150HIS10.8030.89934.1799.3149.3140.0000.0000.0000.000
126A151LEU00.0250.03837.5080.1550.1550.0000.0000.0000.000
127A152LYS10.9570.98039.6757.2127.2120.0000.0000.0000.000
128A153PRO0-0.0040.01637.8440.2170.2170.0000.0000.0000.000
129A154LYS10.9540.97941.1397.2317.2310.0000.0000.0000.000
130A155GLU-1-0.830-0.88837.818-8.381-8.3810.0000.0000.0000.000
131A156ILE00.0030.00132.885-0.035-0.0350.0000.0000.0000.000
132A157ARG10.7780.85734.1488.2588.2580.0000.0000.0000.000
133A158GLN00.002-0.01628.425-0.488-0.4880.0000.0000.0000.000
134A159PHE00.0130.00928.9010.2650.2650.0000.0000.0000.000
135A160PRO00.0230.01523.824-0.153-0.1530.0000.0000.0000.000
136A161ASN0-0.032-0.03522.085-0.914-0.9140.0000.0000.0000.000
137A162ILE00.0190.01625.3740.4090.4090.0000.0000.0000.000
138A163ASP-1-0.788-0.86726.473-11.708-11.7080.0000.0000.0000.000
139A164GLN00.0340.00026.7770.3800.3800.0000.0000.0000.000
140A165ALA0-0.0150.00730.7380.3820.3820.0000.0000.0000.000
141A166TYR00.009-0.03629.9890.4590.4590.0000.0000.0000.000
142A167LEU00.0350.02533.6660.3400.3400.0000.0000.0000.000
143A168ALA0-0.016-0.01235.1390.3250.3250.0000.0000.0000.000
144A169LEU0-0.0200.01436.8850.2850.2850.0000.0000.0000.000
145A170GLU-1-0.829-0.90537.698-8.148-8.1480.0000.0000.0000.000
146A171ALA0-0.050-0.02039.5120.2460.2460.0000.0000.0000.000
147A172GLY0-0.013-0.00741.2900.1560.1560.0000.0000.0000.000
148A173ARG10.8750.94039.7287.6557.6550.0000.0000.0000.000
149A174VAL0-0.016-0.00637.389-0.062-0.0620.0000.0000.0000.000
150A175ASP-1-0.839-0.90440.675-7.317-7.3170.0000.0000.0000.000
151A176ALA0-0.009-0.01539.3060.0940.0940.0000.0000.0000.000
152A177ALA0-0.0070.01134.069-0.139-0.1390.0000.0000.0000.000
153A178MET0-0.031-0.01633.4920.2490.2490.0000.0000.0000.000
154A179HIS00.0370.01425.2970.1090.1090.0000.0000.0000.000
155A180ASP-1-0.742-0.81625.571-12.222-12.2220.0000.0000.0000.000
156A181THR00.025-0.00528.9860.2560.2560.0000.0000.0000.000
157A182PRO00.0400.00627.8060.2720.2720.0000.0000.0000.000
158A183ASN0-0.0080.01526.8310.3530.3530.0000.0000.0000.000
159A184VAL00.0230.01429.1820.2150.2150.0000.0000.0000.000
160A185LEU00.012-0.01232.7080.2760.2760.0000.0000.0000.000
161A186PHE00.0130.01329.9230.2190.2190.0000.0000.0000.000
162A187PHE00.0860.04431.8840.2440.2440.0000.0000.0000.000
163A188VAL0-0.027-0.01033.4070.2690.2690.0000.0000.0000.000
164A189ASN0-0.079-0.05535.6110.6040.6040.0000.0000.0000.000
165A190ASN0-0.0170.00833.1840.2290.2290.0000.0000.0000.000
166A191GLU-1-0.858-0.94131.878-9.866-9.8660.0000.0000.0000.000
167A192GLY00.0230.00535.4660.2160.2160.0000.0000.0000.000
168A193LYS10.8180.90037.5178.3998.3990.0000.0000.0000.000
169A194GLY0-0.017-0.00340.2620.1160.1160.0000.0000.0000.000
170A195ARG10.8580.92939.2408.2828.2820.0000.0000.0000.000
171A196VAL0-0.018-0.01637.2150.1060.1060.0000.0000.0000.000
172A197LYS10.7980.89740.3927.1227.1220.0000.0000.0000.000
173A198VAL00.0390.01337.542-0.121-0.1210.0000.0000.0000.000
174A199ALA0-0.045-0.01939.6080.2390.2390.0000.0000.0000.000
175A200GLY00.0470.02541.056-0.069-0.0690.0000.0000.0000.000
176A201ALA0-0.038-0.02240.839-0.121-0.1210.0000.0000.0000.000
177A202PRO0-0.012-0.01435.220-0.027-0.0270.0000.0000.0000.000
178A203VAL0-0.0120.00634.4860.1980.1980.0000.0000.0000.000
179A204SER0-0.006-0.01732.796-0.282-0.2820.0000.0000.0000.000
180A205GLY00.0060.00231.7620.2450.2450.0000.0000.0000.000
181A206ASP-1-0.816-0.87226.950-11.856-11.8560.0000.0000.0000.000
182A207LYS10.8760.91824.70011.49011.4900.0000.0000.0000.000
183A208TYR00.1560.19620.290-0.256-0.2560.0000.0000.0000.000
184A209GLY0-0.007-0.01218.5000.4620.4620.0000.0000.0000.000
185A210ILE0-0.035-0.01112.451-0.142-0.1420.0000.0000.0000.000
186A211GLY00.0410.02613.3140.3740.3740.0000.0000.0000.000
187A212PHE00.011-0.0258.636-2.496-2.4960.0000.0000.0000.000
188A213PRO00.0460.0266.3753.1213.1210.0000.0000.0000.000
189A214LYS10.7820.8869.69519.25419.2540.0000.0000.0000.000
190A215GLY00.0120.00911.551-0.818-0.8180.0000.0000.0000.000
191A216SER0-0.026-0.0037.318-1.326-1.3260.0000.0000.0000.000
192A217PRO00.0260.0037.7192.2332.2330.0000.0000.0000.000
193A218LEU0-0.033-0.0125.1842.1982.1980.0000.0000.0000.000
194A219VAL00.0480.0229.3261.9741.9740.0000.0000.0000.000
195A220ALA00.0310.02312.9021.4571.4570.0000.0000.0000.000
196A221LYS10.8180.88210.48620.82220.8220.0000.0000.0000.000
197A222VAL00.0290.01411.3661.0461.0460.0000.0000.0000.000
198A223ASN00.0280.00313.9500.2840.2840.0000.0000.0000.000
199A224ALA0-0.0020.01015.8821.1211.1210.0000.0000.0000.000
200A225GLU-1-0.823-0.89213.988-16.033-16.0330.0000.0000.0000.000
201A226LEU00.0070.00816.9130.9360.9360.0000.0000.0000.000
202A227ALA0-0.016-0.01219.3260.8540.8540.0000.0000.0000.000
203A228ARG10.8820.92916.66415.94515.9450.0000.0000.0000.000
204A229MET0-0.0200.00118.4900.3500.3500.0000.0000.0000.000
205A230LYS10.8610.92921.94313.83613.8360.0000.0000.0000.000
206A231ALA0-0.0160.01424.6200.5130.5130.0000.0000.0000.000
207A232ASP-1-0.773-0.87122.363-12.696-12.6960.0000.0000.0000.000
208A233GLY00.0610.02325.9540.2530.2530.0000.0000.0000.000
209A234ARG10.7420.83017.67814.77214.7720.0000.0000.0000.000
210A235TYR0-0.015-0.02623.2050.1060.1060.0000.0000.0000.000
211A236ALA00.0390.01924.3130.0800.0800.0000.0000.0000.000
212A237LYS10.8570.93526.25111.48011.4800.0000.0000.0000.000
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