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: 89JQY

Calculation Name: 3MVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DWD0

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 OptH
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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2273021.369672
FMO2-HF: Nuclear repulsion 2191858.162478
FMO2-HF: Total energy -81163.207194
FMO2-MP2: Total energy -81405.851617


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:14:LYS)


Summations of interaction energy for fragment #1(A:14: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.
79.72483.5840.259-1.546-2.571-0.001
Interaction energy analysis for fragmet #1(A:14:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.022 / q_NPA : 1.007
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].
3A16ILE00.0890.0542.7249.15712.8530.261-1.531-2.425-0.001
4A17ARG10.9660.9784.86219.49719.523-0.001-0.009-0.0160.000
5A18LYS10.8890.9494.64448.25048.388-0.001-0.006-0.1300.000
6A19PRO00.0390.0187.769-1.272-1.2720.0000.0000.0000.000
7A20LYS10.9940.9776.88325.01425.0140.0000.0000.0000.000
8A21GLN0-0.0040.0137.737-1.480-1.4800.0000.0000.0000.000
9A22GLU-1-0.793-0.8955.596-45.316-45.3160.0000.0000.0000.000
10A23ARG10.9340.9488.90824.29024.2900.0000.0000.0000.000
11A24SER00.007-0.00610.7651.8161.8160.0000.0000.0000.000
12A25ILE00.0340.01511.9451.7861.7860.0000.0000.0000.000
13A26GLU-1-0.842-0.90513.345-20.769-20.7690.0000.0000.0000.000
14A27LYS10.9190.96215.09119.91819.9180.0000.0000.0000.000
15A28ARG10.9871.01016.57616.35016.3500.0000.0000.0000.000
16A29ASN00.0210.00317.4981.4571.4570.0000.0000.0000.000
17A30LYS10.9511.00019.28014.17814.1780.0000.0000.0000.000
18A31ILE0-0.004-0.01120.5280.7290.7290.0000.0000.0000.000
19A32LEU0-0.031-0.00721.4680.5380.5380.0000.0000.0000.000
20A33GLN0-0.0100.00023.7220.1700.1700.0000.0000.0000.000
21A34VAL0-0.018-0.02025.2480.4810.4810.0000.0000.0000.000
22A35ALA00.0230.00726.9560.4420.4420.0000.0000.0000.000
23A36LYS10.8790.95128.27311.15611.1560.0000.0000.0000.000
24A37ASP-1-0.850-0.92729.649-10.435-10.4350.0000.0000.0000.000
25A38LEU0-0.051-0.02630.4910.3090.3090.0000.0000.0000.000
26A39PHE0-0.027-0.03530.8620.2820.2820.0000.0000.0000.000
27A40SER0-0.025-0.02333.5960.3330.3330.0000.0000.0000.000
28A41ASP-1-0.963-0.95035.806-8.253-8.2530.0000.0000.0000.000
29A42LYS10.9090.93336.8218.8458.8450.0000.0000.0000.000
30A43THR0-0.020-0.00938.1670.2810.2810.0000.0000.0000.000
31A44TYR0-0.002-0.01933.198-0.182-0.1820.0000.0000.0000.000
32A45PHE0-0.006-0.01736.771-0.196-0.1960.0000.0000.0000.000
33A46ASN0-0.0180.01739.3860.1080.1080.0000.0000.0000.000
34A47VAL0-0.0060.02332.807-0.108-0.1080.0000.0000.0000.000
35A48THR00.000-0.00534.641-0.114-0.1140.0000.0000.0000.000
36A49THR00.0680.00829.273-0.165-0.1650.0000.0000.0000.000
37A50ASN0-0.003-0.00429.794-0.620-0.6200.0000.0000.0000.000
38A51GLU-1-0.854-0.91630.526-9.332-9.3320.0000.0000.0000.000
39A52ILE00.0310.01626.654-0.264-0.2640.0000.0000.0000.000
40A53ALA0-0.002-0.00325.762-0.416-0.4160.0000.0000.0000.000
41A54LYS10.9040.96125.92310.92810.9280.0000.0000.0000.000
42A55LYS10.9570.98127.50810.17610.1760.0000.0000.0000.000
43A56ALA0-0.036-0.01423.040-0.246-0.2460.0000.0000.0000.000
44A57ASP-1-0.946-0.96822.444-13.494-13.4940.0000.0000.0000.000
45A58VAL0-0.076-0.02720.155-0.939-0.9390.0000.0000.0000.000
46A59SER00.0360.01722.4800.5020.5020.0000.0000.0000.000
47A60VAL00.1020.03024.283-0.278-0.2780.0000.0000.0000.000
48A61GLY00.0140.00924.830-0.015-0.0150.0000.0000.0000.000
49A62THR0-0.025-0.02319.071-0.605-0.6050.0000.0000.0000.000
50A63LEU0-0.018-0.00221.348-0.448-0.4480.0000.0000.0000.000
51A64TYR00.012-0.00823.5950.0010.0010.0000.0000.0000.000
52A65ALA0-0.0440.00119.8970.0200.0200.0000.0000.0000.000
53A66TYR0-0.100-0.04215.651-1.043-1.0430.0000.0000.0000.000
54A67PHE0-0.025-0.03321.069-0.155-0.1550.0000.0000.0000.000
55A68ALA00.0740.05024.7480.1600.1600.0000.0000.0000.000
56A69SER00.0520.01327.4670.2660.2660.0000.0000.0000.000
57A70LYS10.8810.93329.0918.5948.5940.0000.0000.0000.000
58A71GLU-1-0.832-0.92630.853-9.244-9.2440.0000.0000.0000.000
59A72ASP-1-0.877-0.92626.978-10.995-10.9950.0000.0000.0000.000
60A73ILE0-0.084-0.04626.021-0.416-0.4160.0000.0000.0000.000
61A74LEU00.0250.01327.644-0.224-0.2240.0000.0000.0000.000
62A75THR00.002-0.00828.396-0.049-0.0490.0000.0000.0000.000
63A76ALA0-0.078-0.04124.561-0.129-0.1290.0000.0000.0000.000
64A77LEU0-0.036-0.01926.610-0.228-0.2280.0000.0000.0000.000
65A78LEU00.0280.02128.4150.0520.0520.0000.0000.0000.000
66A79LYS10.9310.96526.20611.75711.7570.0000.0000.0000.000
67A80ARG10.9100.94520.34614.07314.0730.0000.0000.0000.000
68A81TYR00.0340.02527.601-0.091-0.0910.0000.0000.0000.000
69A82ASN00.0330.02331.0750.5350.5350.0000.0000.0000.000
70A83ASP-1-0.889-0.93826.878-11.385-11.3850.0000.0000.0000.000
71A84PHE0-0.0110.00129.538-0.014-0.0140.0000.0000.0000.000
72A85PHE00.0200.01830.5490.2160.2160.0000.0000.0000.000
73A86LEU0-0.008-0.01431.7820.2250.2250.0000.0000.0000.000
74A87THR0-0.082-0.05328.3800.0830.0830.0000.0000.0000.000
75A88THR0-0.055-0.02830.9800.1340.1340.0000.0000.0000.000
76A89ILE00.0220.02833.4430.2290.2290.0000.0000.0000.000
77A90PHE0-0.046-0.03736.3850.2580.2580.0000.0000.0000.000
78A91ALA0-0.0020.00434.4410.2100.2100.0000.0000.0000.000
79A92ASP-1-0.881-0.93336.584-8.393-8.3930.0000.0000.0000.000
80A93ILE0-0.033-0.00939.1700.2490.2490.0000.0000.0000.000
81A94ASN0-0.013-0.00439.2380.4610.4610.0000.0000.0000.000
82A95SER00.0600.03840.535-0.106-0.1060.0000.0000.0000.000
83A96GLN0-0.022-0.03342.3450.0820.0820.0000.0000.0000.000
84A97ASP-1-0.869-0.92343.090-7.206-7.2060.0000.0000.0000.000
85A98SER0-0.121-0.09544.3940.1880.1880.0000.0000.0000.000
86A99LEU00.006-0.00546.4410.1580.1580.0000.0000.0000.000
87A100ASP-1-0.838-0.91248.372-6.415-6.4150.0000.0000.0000.000
88A101ARG10.8820.95144.9987.0807.0800.0000.0000.0000.000
89A102PHE00.014-0.01151.0300.1460.1460.0000.0000.0000.000
90A103LYS10.8440.92352.9615.9215.9210.0000.0000.0000.000
91A104LYS10.9070.97553.3746.0746.0740.0000.0000.0000.000
92A105ASN00.004-0.03855.3090.1970.1970.0000.0000.0000.000
93A106PRO00.0560.04754.938-0.110-0.1100.0000.0000.0000.000
94A107LYS10.8870.94254.6705.3305.3300.0000.0000.0000.000
95A108GLU-1-0.973-0.98751.399-6.265-6.2650.0000.0000.0000.000
96A109TRP0-0.017-0.01048.316-0.100-0.1000.0000.0000.0000.000
97A110LEU00.0240.01849.704-0.144-0.1440.0000.0000.0000.000
98A111ASN0-0.044-0.02250.306-0.120-0.1200.0000.0000.0000.000
99A112VAL0-0.020-0.00845.501-0.111-0.1110.0000.0000.0000.000
100A113LEU00.0380.02644.861-0.173-0.1730.0000.0000.0000.000
101A114ILE00.0220.00045.543-0.145-0.1450.0000.0000.0000.000
102A115ASN00.0250.01045.348-0.024-0.0240.0000.0000.0000.000
103A116GLN00.0200.00641.748-0.041-0.0410.0000.0000.0000.000
104A117LEU0-0.035-0.02041.223-0.204-0.2040.0000.0000.0000.000
105A118LEU0-0.022-0.00642.414-0.104-0.1040.0000.0000.0000.000
106A119ALA0-0.040-0.01439.779-0.078-0.0780.0000.0000.0000.000
107A120ALA0-0.0120.01837.873-0.278-0.2780.0000.0000.0000.000
108A121GLU-1-0.813-0.88634.069-8.752-8.7520.0000.0000.0000.000
109A122ASP-1-0.898-0.97732.418-9.926-9.9260.0000.0000.0000.000
110A123LYS10.9180.94235.0978.1938.1930.0000.0000.0000.000
111A124ILE00.0340.02235.5900.1110.1110.0000.0000.0000.000
112A125PHE00.002-0.01132.275-0.004-0.0040.0000.0000.0000.000
113A126HIS00.003-0.00335.713-0.219-0.2190.0000.0000.0000.000
114A127ALA00.0770.04737.8670.1290.1290.0000.0000.0000.000
115A128GLN00.0240.01536.2680.1420.1420.0000.0000.0000.000
116A129ILE0-0.051-0.03034.4930.0090.0090.0000.0000.0000.000
117A130GLU-1-0.834-0.92838.242-7.305-7.3050.0000.0000.0000.000
118A131MET0-0.050-0.01640.4800.1650.1650.0000.0000.0000.000
119A132LEU0-0.042-0.03436.2700.0700.0700.0000.0000.0000.000
120A133ALA00.0070.02040.4420.0090.0090.0000.0000.0000.000
121A134TYR0-0.025-0.00942.2330.1620.1620.0000.0000.0000.000
122A135ALA0-0.031-0.01941.8630.1090.1090.0000.0000.0000.000
123A136ILE0-0.042-0.01736.408-0.078-0.0780.0000.0000.0000.000
124A137PRO00.0470.01039.351-0.050-0.0500.0000.0000.0000.000
125A138GLN00.0100.00132.289-0.112-0.1120.0000.0000.0000.000
126A139ALA00.0150.02136.898-0.118-0.1180.0000.0000.0000.000
127A140LYS10.8660.91137.9827.1237.1230.0000.0000.0000.000
128A141ALA0-0.024-0.01238.3610.0740.0740.0000.0000.0000.000
129A142LEU0-0.021-0.00634.185-0.011-0.0110.0000.0000.0000.000
130A143LEU00.0270.01537.722-0.003-0.0030.0000.0000.0000.000
131A144GLU-1-0.789-0.86840.481-7.013-7.0130.0000.0000.0000.000
132A145GLU-1-0.911-0.94737.809-7.993-7.9930.0000.0000.0000.000
133A146HIS10.8640.91935.1688.8498.8490.0000.0000.0000.000
134A147ASN00.0560.03340.2430.1900.1900.0000.0000.0000.000
135A148ASN00.0350.00843.4060.2840.2840.0000.0000.0000.000
136A149ASN0-0.085-0.03839.136-0.072-0.0720.0000.0000.0000.000
137A150LEU00.0180.01741.7050.0690.0690.0000.0000.0000.000
138A151LYS10.8430.92944.4746.6996.6990.0000.0000.0000.000
139A152ASN0-0.036-0.01744.3080.2830.2830.0000.0000.0000.000
140A153LEU0-0.028-0.00344.0230.1170.1170.0000.0000.0000.000
141A154THR00.0240.00746.2000.1290.1290.0000.0000.0000.000
142A155TYR00.004-0.00649.5070.1690.1690.0000.0000.0000.000
143A156LYS10.9000.95243.5917.3467.3460.0000.0000.0000.000
144A157CYS0-0.0260.00748.6090.0420.0420.0000.0000.0000.000
145A158LEU00.0050.00551.2510.1090.1090.0000.0000.0000.000
146A159LEU0-0.066-0.02951.9250.1130.1130.0000.0000.0000.000
147A160TYR00.0350.01251.6710.1070.1070.0000.0000.0000.000
148A161TYR0-0.036-0.01253.8120.0620.0620.0000.0000.0000.000
149A162SER0-0.034-0.02956.7220.0580.0580.0000.0000.0000.000
150A163ASP-1-0.884-0.92656.024-5.677-5.6770.0000.0000.0000.000
151A164GLN0-0.0070.03056.9000.0050.0050.0000.0000.0000.000
152A165ALA00.0250.01054.582-0.107-0.1070.0000.0000.0000.000
153A166ALA0-0.031-0.03453.974-0.125-0.1250.0000.0000.0000.000
154A167ASN00.0440.01955.9870.1310.1310.0000.0000.0000.000
155A168PRO00.0370.00657.149-0.069-0.0690.0000.0000.0000.000
156A169SER0-0.004-0.01058.080-0.033-0.0330.0000.0000.0000.000
157A170PHE00.0700.02855.980-0.040-0.0400.0000.0000.0000.000
158A171LYS10.9360.98250.3416.2416.2410.0000.0000.0000.000
159A172THR00.0020.02754.294-0.087-0.0870.0000.0000.0000.000
160A173LEU00.0230.01956.357-0.038-0.0380.0000.0000.0000.000
161A174SER0-0.076-0.06651.437-0.083-0.0830.0000.0000.0000.000
162A175LEU0-0.025-0.01551.418-0.115-0.1150.0000.0000.0000.000
163A176VAL00.0560.03352.907-0.055-0.0550.0000.0000.0000.000
164A177VAL00.0080.00152.800-0.026-0.0260.0000.0000.0000.000
165A178PHE00.017-0.01245.209-0.067-0.0670.0000.0000.0000.000
166A179ASP-1-0.835-0.91150.163-6.392-6.3920.0000.0000.0000.000
167A180PHE0-0.042-0.02451.9570.0190.0190.0000.0000.0000.000
168A181ILE0-0.007-0.00748.600-0.010-0.0100.0000.0000.0000.000
169A182SER0-0.021-0.01747.455-0.107-0.1070.0000.0000.0000.000
170A183ALA00.0170.02148.873-0.060-0.0600.0000.0000.0000.000
171A184LEU0-0.045-0.01251.6540.0300.0300.0000.0000.0000.000
172A185VAL0-0.011-0.02745.186-0.021-0.0210.0000.0000.0000.000
173A186ASP-1-0.866-0.93546.538-7.000-7.0000.0000.0000.0000.000
174A187GLU-1-0.941-0.95248.404-6.013-6.0130.0000.0000.0000.000
175A188LEU0-0.051-0.04149.1710.0210.0210.0000.0000.0000.000
176A189LEU0-0.075-0.02842.943-0.088-0.0880.0000.0000.0000.000
177A190TYR0-0.093-0.05341.103-0.178-0.1780.0000.0000.0000.000
178A191HIS0-0.022-0.00147.1300.0810.0810.0000.0000.0000.000
179A192GLU-1-0.971-0.96950.169-6.501-6.5010.0000.0000.0000.000
180A193HIS0-0.013-0.02151.7010.2130.2130.0000.0000.0000.000
181A194THR00.0080.00152.500-0.087-0.0870.0000.0000.0000.000
182A195GLN00.015-0.00949.299-0.035-0.0350.0000.0000.0000.000
183A196GLU-1-0.908-0.96053.475-5.517-5.5170.0000.0000.0000.000
184A197GLU-1-0.901-0.94656.410-5.404-5.4040.0000.0000.0000.000
185A198ALA00.0580.02251.8250.0050.0050.0000.0000.0000.000
186A199HIS0-0.050-0.02153.958-0.112-0.1120.0000.0000.0000.000
187A200GLN00.0140.00655.2180.0730.0730.0000.0000.0000.000
188A201ILE00.0540.04954.7650.0660.0660.0000.0000.0000.000
189A202LYS10.9460.97950.0406.4116.4110.0000.0000.0000.000
190A203LYS10.8710.94554.5115.2815.2810.0000.0000.0000.000
191A204THR00.003-0.01657.5000.0920.0920.0000.0000.0000.000
192A205GLY00.0310.02856.0530.0580.0580.0000.0000.0000.000
193A206ILE0-0.015-0.00952.3230.0200.0200.0000.0000.0000.000
194A207ASP-1-0.857-0.93456.288-5.365-5.3650.0000.0000.0000.000
195A208SER0-0.045-0.03559.5730.1070.1070.0000.0000.0000.000
196A209LEU0-0.003-0.01253.9900.0370.0370.0000.0000.0000.000
197A210ASP-1-0.798-0.89257.961-5.452-5.4520.0000.0000.0000.000
198A211LEU0-0.0110.00159.0760.0470.0470.0000.0000.0000.000
199A212ILE00.0280.01059.5560.0520.0520.0000.0000.0000.000
200A213ILE0-0.0070.01955.1620.0300.0300.0000.0000.0000.000
201A214LYS10.8040.87059.4085.3655.3650.0000.0000.0000.000
202A215SER0-0.107-0.05062.1210.0790.0790.0000.0000.0000.000
203A216TYR0-0.013-0.00961.1140.0780.0780.0000.0000.0000.000
204A217LEU0-0.064-0.01257.9390.0250.0250.0000.0000.0000.000