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: G55R1

Calculation Name: 4R3O-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: M

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2448255.108588
FMO2-HF: Nuclear repulsion 2364768.973372
FMO2-HF: Total energy -83486.135217
FMO2-MP2: Total energy -83726.432167


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(M:1:ARG)


Summations of interaction energy for fragment #1(M:1:ARG)
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.
9.511.685-0.017-1.009-1.158-0.003
Interaction energy analysis for fragmet #1(M:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.970 / q_NPA : 0.966
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].
3M3SER00.0050.0053.745-3.018-0.833-0.017-1.009-1.158-0.003
4M4PRO0-0.0190.0015.4652.1502.1500.0000.0000.0000.000
5M5TYR0-0.038-0.0508.5691.7881.7880.0000.0000.0000.000
6M6VAL00.0330.0139.882-1.569-1.5690.0000.0000.0000.000
7M7PHE0-0.028-0.00412.6160.9820.9820.0000.0000.0000.000
8M8ASN00.0310.01615.770-0.184-0.1840.0000.0000.0000.000
9M9GLY00.0190.02018.8440.6370.6370.0000.0000.0000.000
10M10GLY0-0.012-0.00621.5110.0350.0350.0000.0000.0000.000
11M11THR0-0.064-0.06124.863-0.393-0.3930.0000.0000.0000.000
12M12ILE00.004-0.00326.7610.2440.2440.0000.0000.0000.000
13M13LEU0-0.0230.00229.671-0.046-0.0460.0000.0000.0000.000
14M14ALA0-0.010-0.00133.0000.1000.1000.0000.0000.0000.000
15M15ILE00.000-0.00235.405-0.006-0.0060.0000.0000.0000.000
16M16ALA0-0.018-0.00738.9360.0470.0470.0000.0000.0000.000
17M17GLY0-0.0020.00041.3270.0580.0580.0000.0000.0000.000
18M18GLU-1-0.915-0.97345.066-6.359-6.3590.0000.0000.0000.000
19M19ASP-1-0.920-0.96248.048-6.258-6.2580.0000.0000.0000.000
20M20PHE00.0080.00743.501-0.017-0.0170.0000.0000.0000.000
21M21ALA00.0180.01339.563-0.079-0.0790.0000.0000.0000.000
22M22ILE0-0.043-0.01738.0710.0310.0310.0000.0000.0000.000
23M23VAL00.0160.00833.281-0.163-0.1630.0000.0000.0000.000
24M24ALA0-0.008-0.01134.6400.0980.0980.0000.0000.0000.000
25M25SER0-0.001-0.01029.648-0.330-0.3300.0000.0000.0000.000
26M26ASP-1-0.740-0.87128.101-10.447-10.4470.0000.0000.0000.000
27M27THR0-0.110-0.08929.752-0.080-0.0800.0000.0000.0000.000
28M28ARG10.8400.94125.28810.54010.5400.0000.0000.0000.000
29M29LEU0-0.0050.01021.463-0.307-0.3070.0000.0000.0000.000
30M30SER00.0090.00621.2850.2930.2930.0000.0000.0000.000
31M31GLU-1-0.836-0.92314.019-18.174-18.1740.0000.0000.0000.000
32M32GLY0-0.0140.00215.9840.1340.1340.0000.0000.0000.000
33M33PHE0-0.013-0.01416.5180.3310.3310.0000.0000.0000.000
34M34SER0-0.0100.00418.9680.8210.8210.0000.0000.0000.000
35M35ILE0-0.027-0.02121.015-0.176-0.1760.0000.0000.0000.000
36M36HIS0-0.047-0.03517.4140.7270.7270.0000.0000.0000.000
37M37THR0-0.010-0.02122.7940.5180.5180.0000.0000.0000.000
38M38ARG10.8750.92826.3829.6159.6150.0000.0000.0000.000
39M39ASP-1-0.951-0.93429.378-8.747-8.7470.0000.0000.0000.000
40M40SER0-0.008-0.01026.353-0.160-0.1600.0000.0000.0000.000
41M41PRO0-0.032-0.01027.948-0.227-0.2270.0000.0000.0000.000
42M42LYS10.8880.95624.78011.10211.1020.0000.0000.0000.000
43M43CYS0-0.049-0.00628.324-0.115-0.1150.0000.0000.0000.000
44M44TYR00.0280.01326.443-0.070-0.0700.0000.0000.0000.000
45M45LYS10.8680.91732.1957.9197.9190.0000.0000.0000.000
46M46LEU0-0.0230.00331.542-0.062-0.0620.0000.0000.0000.000
47M47THR0-0.012-0.02135.5350.1410.1410.0000.0000.0000.000
48M48ASP-1-0.883-0.94139.209-7.099-7.0990.0000.0000.0000.000
49M49LYS10.8800.93741.2297.0337.0330.0000.0000.0000.000
50M50THR0-0.036-0.02035.574-0.014-0.0140.0000.0000.0000.000
51M51VAL00.0300.01434.049-0.051-0.0510.0000.0000.0000.000
52M52ILE0-0.010-0.00728.344-0.004-0.0040.0000.0000.0000.000
53M53GLY00.0310.01729.5120.0120.0120.0000.0000.0000.000
54M54CYS0-0.053-0.03324.316-0.099-0.0990.0000.0000.0000.000
55M55SER00.005-0.01523.439-0.159-0.1590.0000.0000.0000.000
56M56GLY00.0410.01719.469-0.183-0.1830.0000.0000.0000.000
57M57PHE00.0280.01414.186-0.116-0.1160.0000.0000.0000.000
58M58HIS00.0970.01917.1610.3170.3170.0000.0000.0000.000
59M59GLY0-0.0070.00817.2590.5840.5840.0000.0000.0000.000
60M60ASP-1-0.785-0.90215.936-16.454-16.4540.0000.0000.0000.000
61M61CYS0-0.050-0.01618.7220.6970.6970.0000.0000.0000.000
62M62LEU0-0.0050.00621.4950.6240.6240.0000.0000.0000.000
63M63THR0-0.036-0.02919.8390.5320.5320.0000.0000.0000.000
64M64LEU00.0070.00522.2820.4650.4650.0000.0000.0000.000
65M65THR00.0440.02023.8850.4240.4240.0000.0000.0000.000
66M66LYS10.9500.97125.67211.21211.2120.0000.0000.0000.000
67M67ILE0-0.034-0.00523.1390.4050.4050.0000.0000.0000.000
68M68ILE00.003-0.00227.3810.3840.3840.0000.0000.0000.000
69M69GLU-1-0.921-0.95729.789-8.915-8.9150.0000.0000.0000.000
70M70ALA0-0.051-0.02930.4230.3560.3560.0000.0000.0000.000
71M71ARG10.9800.95629.6949.9199.9190.0000.0000.0000.000
72M72LEU00.0160.01432.9200.2510.2510.0000.0000.0000.000
73M73LYS10.9330.96735.1488.6208.6200.0000.0000.0000.000
74M74MET0-0.0310.00032.5140.1280.1280.0000.0000.0000.000
75M75TYR00.0430.02537.0230.2150.2150.0000.0000.0000.000
76M76LYS10.9691.00338.6887.1977.1970.0000.0000.0000.000
77M77HIS0-0.048-0.03739.5550.2710.2710.0000.0000.0000.000
78M78SER0-0.0150.00740.2590.0930.0930.0000.0000.0000.000
79M79ASN0-0.070-0.05040.6140.1700.1700.0000.0000.0000.000
80M80ASN0-0.037-0.00544.2900.1650.1650.0000.0000.0000.000
81M81LYS10.9730.99444.0476.9526.9520.0000.0000.0000.000
82M82ALA00.0250.00541.679-0.154-0.1540.0000.0000.0000.000
83M83MET0-0.052-0.01235.0180.0270.0270.0000.0000.0000.000
84M84THR00.0580.03139.870-0.063-0.0630.0000.0000.0000.000
85M85THR00.0740.01937.243-0.231-0.2310.0000.0000.0000.000
86M86GLY00.0150.01136.622-0.229-0.2290.0000.0000.0000.000
87M87ALA0-0.013-0.00336.421-0.205-0.2050.0000.0000.0000.000
88M88ILE00.019-0.00232.851-0.233-0.2330.0000.0000.0000.000
89M89ALA00.0130.00832.427-0.327-0.3270.0000.0000.0000.000
90M90ALA00.0570.02531.514-0.331-0.3310.0000.0000.0000.000
91M91MET0-0.042-0.01530.891-0.243-0.2430.0000.0000.0000.000
92M92LEU00.0240.02126.339-0.348-0.3480.0000.0000.0000.000
93M93SER0-0.008-0.00727.086-0.446-0.4460.0000.0000.0000.000
94M94THR0-0.063-0.05026.835-0.378-0.3780.0000.0000.0000.000
95M95ILE0-0.029-0.02324.482-0.343-0.3430.0000.0000.0000.000
96M96LEU0-0.0130.01022.167-0.510-0.5100.0000.0000.0000.000
97M97TYR00.0330.01721.919-0.779-0.7790.0000.0000.0000.000
98M98SER0-0.098-0.05122.546-0.448-0.4480.0000.0000.0000.000
99M99ARG10.9000.93915.71015.88215.8820.0000.0000.0000.000
100M100ARG10.9390.98217.43714.24214.2420.0000.0000.0000.000
101M101PHE0-0.039-0.03115.300-0.371-0.3710.0000.0000.0000.000
102M102PHE0-0.036-0.00711.153-1.415-1.4150.0000.0000.0000.000
103M103PRO00.0440.04513.9150.7550.7550.0000.0000.0000.000
104M104TYR00.0370.05015.339-0.852-0.8520.0000.0000.0000.000
105M105TYR0-0.043-0.01414.3130.1640.1640.0000.0000.0000.000
106M106VAL0-0.010-0.02416.8320.1940.1940.0000.0000.0000.000
107M107TYR0-0.015-0.00119.712-0.048-0.0480.0000.0000.0000.000
108M108ASN00.0390.00823.4340.3650.3650.0000.0000.0000.000
109M109ILE00.010-0.00226.6110.0830.0830.0000.0000.0000.000
110M110ILE0-0.0190.00230.2120.0880.0880.0000.0000.0000.000
111M111GLY00.0450.01433.0290.0800.0800.0000.0000.0000.000
112M112GLY0-0.007-0.01736.439-0.026-0.0260.0000.0000.0000.000
113M113LEU0-0.0110.01539.6590.0960.0960.0000.0000.0000.000
114M114ASP-1-0.822-0.90642.371-6.959-6.9590.0000.0000.0000.000
115M115GLU-1-0.923-0.99443.796-6.735-6.7350.0000.0000.0000.000
116M116GLU-1-0.950-0.96646.816-6.159-6.1590.0000.0000.0000.000
117M117GLY0-0.042-0.01247.4700.1220.1220.0000.0000.0000.000
118M118LYS10.9660.99246.5256.2136.2130.0000.0000.0000.000
119M119GLY00.0090.02943.197-0.131-0.1310.0000.0000.0000.000
120M120ALA0-0.063-0.04939.786-0.009-0.0090.0000.0000.0000.000
121M121VAL00.0220.01334.707-0.104-0.1040.0000.0000.0000.000
122M122TYR0-0.018-0.01833.1990.1290.1290.0000.0000.0000.000
123M123SER0-0.022-0.03030.022-0.270-0.2700.0000.0000.0000.000
124M124PHE0-0.013-0.00726.3550.1310.1310.0000.0000.0000.000
125M125ASP-1-0.829-0.90923.522-12.654-12.6540.0000.0000.0000.000
126M126PRO0-0.001-0.01419.1300.1590.1590.0000.0000.0000.000
127M127VAL0-0.047-0.01719.516-0.331-0.3310.0000.0000.0000.000
128M128GLY00.0080.00322.1060.2790.2790.0000.0000.0000.000
129M129SER0-0.042-0.00225.5300.6880.6880.0000.0000.0000.000
130M130TYR0-0.002-0.01327.534-0.077-0.0770.0000.0000.0000.000
131M131GLN0-0.0010.00530.4100.1840.1840.0000.0000.0000.000
132M132ARG10.8660.93333.7207.4007.4000.0000.0000.0000.000
133M133ASP-1-0.822-0.88533.813-8.988-8.9880.0000.0000.0000.000
134M134SER00.0100.00037.2930.0990.0990.0000.0000.0000.000
135M135PHE0-0.013-0.02136.8170.1140.1140.0000.0000.0000.000
136M136LYS10.8980.96930.7249.2449.2440.0000.0000.0000.000
137M137ALA00.0410.03331.0530.0270.0270.0000.0000.0000.000
138M138GLY00.0020.00727.249-0.180-0.1800.0000.0000.0000.000
139M139GLY0-0.003-0.00823.8450.1980.1980.0000.0000.0000.000
140M140SER00.000-0.00622.847-0.079-0.0790.0000.0000.0000.000
141M141ALA00.0400.02024.2930.0260.0260.0000.0000.0000.000
142M142SER0-0.070-0.03726.9270.4420.4420.0000.0000.0000.000
143M143ALA00.0400.00027.9350.3350.3350.0000.0000.0000.000
144M144MET0-0.047-0.01828.6200.3340.3340.0000.0000.0000.000
145M145LEU0-0.002-0.00431.5270.3280.3280.0000.0000.0000.000
146M146GLN00.0480.00531.6330.2690.2690.0000.0000.0000.000
147M147PRO00.0310.03133.3390.2470.2470.0000.0000.0000.000
148M148LEU00.0320.02336.5290.2450.2450.0000.0000.0000.000
149M149LEU00.0030.00535.4250.2600.2600.0000.0000.0000.000
150M150ASP-1-0.862-0.94736.778-8.246-8.2460.0000.0000.0000.000
151M151ASN0-0.070-0.02639.7970.2260.2260.0000.0000.0000.000
152M152GLN0-0.016-0.03342.3070.2880.2880.0000.0000.0000.000
153M153VAL0-0.029-0.01741.4280.1740.1740.0000.0000.0000.000
154M154GLY00.0000.00742.7850.0850.0850.0000.0000.0000.000
155M155PHE00.0000.00343.8180.0810.0810.0000.0000.0000.000
156M156LYS10.9530.98439.0837.9597.9590.0000.0000.0000.000
157M157ASN0-0.058-0.04242.0870.0250.0250.0000.0000.0000.000
158M158MET0-0.0390.00946.1850.0650.0650.0000.0000.0000.000
159M159GLN00.0360.02449.199-0.061-0.0610.0000.0000.0000.000
160M160ASN0-0.086-0.06652.6500.0580.0580.0000.0000.0000.000
161M161VAL00.0410.03750.4800.0460.0460.0000.0000.0000.000
162M162GLU-1-0.904-0.94353.325-5.842-5.8420.0000.0000.0000.000
163M163HIS0-0.041-0.02650.450-0.149-0.1490.0000.0000.0000.000
164M164VAL0-0.0160.00251.5360.0360.0360.0000.0000.0000.000
165M165PRO00.0330.01249.431-0.134-0.1340.0000.0000.0000.000
166M166LEU0-0.018-0.01043.5290.0590.0590.0000.0000.0000.000
167M167SER00.0470.02047.790-0.033-0.0330.0000.0000.0000.000
168M168LEU00.0670.02344.950-0.118-0.1180.0000.0000.0000.000
169M169ASP-1-0.840-0.90646.248-6.313-6.3130.0000.0000.0000.000
170M170ARG10.9030.94746.5846.5216.5210.0000.0000.0000.000
171M171ALA00.0310.01542.928-0.129-0.1290.0000.0000.0000.000
172M172MET0-0.0200.00142.343-0.252-0.2520.0000.0000.0000.000
173M173ARG10.8830.92342.3956.2006.2000.0000.0000.0000.000
174M174LEU00.0610.03741.285-0.088-0.0880.0000.0000.0000.000
175M175VAL0-0.013-0.00337.115-0.203-0.2030.0000.0000.0000.000
176M176LYS10.8420.89337.9736.8376.8370.0000.0000.0000.000
177M177ASP-1-0.868-0.92339.180-7.292-7.2920.0000.0000.0000.000
178M178VAL0-0.053-0.03035.924-0.161-0.1610.0000.0000.0000.000
179M179PHE0-0.019-0.02831.325-0.293-0.2930.0000.0000.0000.000
180M180ILE0-0.0020.01034.765-0.201-0.2010.0000.0000.0000.000
181M181SER0-0.019-0.00636.620-0.027-0.0270.0000.0000.0000.000
182M182ALA0-0.014-0.01231.241-0.169-0.1690.0000.0000.0000.000
183M183ALA0-0.030-0.01731.507-0.288-0.2880.0000.0000.0000.000
184M184GLU-1-0.898-0.90632.418-8.389-8.3890.0000.0000.0000.000
185M185ARG10.8990.94231.6768.8308.8300.0000.0000.0000.000
186M186ASP-1-0.786-0.90025.966-11.952-11.9520.0000.0000.0000.000
187M187VAL00.0260.01623.7120.1940.1940.0000.0000.0000.000
188M188TYR0-0.053-0.04418.852-0.205-0.2050.0000.0000.0000.000
189M189THR0-0.0310.02425.2190.0870.0870.0000.0000.0000.000
190M190GLY00.0730.02728.6610.1890.1890.0000.0000.0000.000
191M191ASP-1-0.794-0.87829.093-10.033-10.0330.0000.0000.0000.000
192M192ALA0-0.039-0.02732.3780.4100.4100.0000.0000.0000.000
193M193LEU00.0430.03533.018-0.267-0.2670.0000.0000.0000.000
194M194ARG10.9520.98734.1748.7118.7110.0000.0000.0000.000
195M195ILE00.002-0.01235.298-0.178-0.1780.0000.0000.0000.000
196M196CYS0-0.0080.00436.2700.1170.1170.0000.0000.0000.000
197M197ILE0-0.010-0.01138.755-0.037-0.0370.0000.0000.0000.000
198M198VAL0-0.0010.01339.6120.0500.0500.0000.0000.0000.000
199M199THR00.0250.00242.767-0.022-0.0220.0000.0000.0000.000
200M200LYS10.8090.89546.3116.3276.3270.0000.0000.0000.000
201M201GLU-1-0.917-0.95848.856-6.084-6.0840.0000.0000.0000.000
202M202GLY00.0210.02545.5450.0190.0190.0000.0000.0000.000
203M203ILE0-0.023-0.02339.276-0.083-0.0830.0000.0000.0000.000
204M204ARG10.9300.97743.0226.7126.7120.0000.0000.0000.000
205M205GLU-1-0.826-0.90937.817-8.146-8.1460.0000.0000.0000.000
206M206GLU-1-0.875-0.91640.416-6.800-6.8000.0000.0000.0000.000
207M207THR0-0.026-0.02737.381-0.296-0.2960.0000.0000.0000.000
208M208VAL00.0080.00938.6060.2130.2130.0000.0000.0000.000
209M209SER00.002-0.00537.766-0.260-0.2600.0000.0000.0000.000
210M210LEU0-0.0080.01033.2830.0930.0930.0000.0000.0000.000
211M211ARG10.8050.85033.9048.7048.7040.0000.0000.0000.000
212M212LYS10.8550.91532.1958.2538.2530.0000.0000.0000.000
213M213ASP-1-0.763-0.84628.463-9.367-9.3670.0000.0000.0000.000