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: V5QV1

Calculation Name: 1FX0-A-Xray372

Preferred Name: Chloroplast coupling factor 1

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 1FX0

Chain ID: A

ChEMBL ID: CHEMBL2366567

UniProt ID: P06450

Base Structure: X-ray

Registration Date: 2023-06-22

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 477
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8563521.026703
FMO2-HF: Nuclear repulsion 8381820.20263
FMO2-HF: Total energy -181700.824072
FMO2-MP2: Total energy -182233.562247


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:25:LYS)


Summations of interaction energy for fragment #1(A:25: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.
-118.603-111.9950.851-2.726-4.733-0.013
Interaction energy analysis for fragmet #1(A:25:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.957 / q_NPA : 0.955
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].
3A27VAL00.0040.0172.9920.2053.1040.036-1.052-1.883-0.002
4A28ASN00.0400.0002.8786.9807.7760.052-0.160-0.6880.000
5A29THR0-0.111-0.0682.787-1.4741.4640.764-1.497-2.205-0.011
6A30GLY00.0550.0164.570-1.079-1.104-0.001-0.0170.0430.000
7A31THR00.0010.0246.561-0.039-0.0390.0000.0000.0000.000
8A32VAL0-0.018-0.0048.9510.5520.5520.0000.0000.0000.000
9A33LEU0-0.038-0.01812.5300.3950.3950.0000.0000.0000.000
10A34GLN00.010-0.01114.7931.0921.0920.0000.0000.0000.000
11A35VAL00.0000.00517.911-0.446-0.4460.0000.0000.0000.000
12A36GLY0-0.0010.00720.1740.4840.4840.0000.0000.0000.000
13A37ASP-1-0.907-0.95823.597-10.313-10.3130.0000.0000.0000.000
14A38GLY00.0180.00724.2810.1700.1700.0000.0000.0000.000
15A39ILE0-0.048-0.02121.070-0.342-0.3420.0000.0000.0000.000
16A40ALA0-0.002-0.00616.689-0.007-0.0070.0000.0000.0000.000
17A41ARG10.8600.93316.69913.94313.9430.0000.0000.0000.000
18A42ILE00.0380.02010.581-0.040-0.0400.0000.0000.0000.000
19A43HIS00.0260.0099.2541.1631.1630.0000.0000.0000.000
20A44GLY0-0.010-0.0177.678-2.019-2.0190.0000.0000.0000.000
21A45LEU0-0.056-0.0346.4311.4681.4680.0000.0000.0000.000
22A46ASP-1-0.886-0.9467.892-25.861-25.8610.0000.0000.0000.000
23A47GLU-1-0.960-0.9957.352-35.254-35.2540.0000.0000.0000.000
24A48VAL0-0.0580.0019.8301.6751.6750.0000.0000.0000.000
25A49MET00.0160.00811.8051.3691.3690.0000.0000.0000.000
26A50ALA0-0.048-0.03015.4820.2370.2370.0000.0000.0000.000
27A51GLY0-0.016-0.00518.6210.5020.5020.0000.0000.0000.000
28A52GLU-1-0.862-0.95712.161-23.466-23.4660.0000.0000.0000.000
29A53LEU0-0.061-0.03215.5610.0530.0530.0000.0000.0000.000
30A54VAL00.0080.03211.849-1.492-1.4920.0000.0000.0000.000
31A55GLU-1-0.959-0.99611.872-21.379-21.3790.0000.0000.0000.000
32A56PHE0-0.005-0.01211.814-1.412-1.4120.0000.0000.0000.000
33A57GLU-1-0.780-0.87111.262-22.113-22.1130.0000.0000.0000.000
34A58GLU-1-0.924-0.97113.581-13.801-13.8010.0000.0000.0000.000
35A59GLY00.0070.01015.9500.8040.8040.0000.0000.0000.000
36A60THR0-0.055-0.01916.9210.9070.9070.0000.0000.0000.000
37A61ILE0-0.001-0.01916.810-0.874-0.8740.0000.0000.0000.000
38A62GLY00.0600.00717.4100.7210.7210.0000.0000.0000.000
39A63ILE00.0190.01817.019-0.859-0.8590.0000.0000.0000.000
40A64ALA00.0530.03615.4770.1010.1010.0000.0000.0000.000
41A65LEU0-0.028-0.02517.5790.5140.5140.0000.0000.0000.000
42A66ASN0-0.058-0.02119.1430.8010.8010.0000.0000.0000.000
43A67LEU00.0140.02614.764-0.319-0.3190.0000.0000.0000.000
44A68GLU-1-0.828-0.91917.175-13.556-13.5560.0000.0000.0000.000
45A69SER0-0.019-0.02616.392-0.557-0.5570.0000.0000.0000.000
46A70ASN0-0.0130.00113.987-0.733-0.7330.0000.0000.0000.000
47A71ASN0-0.033-0.01313.099-0.697-0.6970.0000.0000.0000.000
48A72VAL00.0750.05611.8500.8780.8780.0000.0000.0000.000
49A73GLY0-0.016-0.01814.8790.2850.2850.0000.0000.0000.000
50A74VAL0-0.014-0.01314.7160.3270.3270.0000.0000.0000.000
51A75VAL00.0120.01217.9050.4790.4790.0000.0000.0000.000
52A76LEU0-0.006-0.00118.394-0.323-0.3230.0000.0000.0000.000
53A77MET0-0.0110.01421.1380.3820.3820.0000.0000.0000.000
54A78GLY00.015-0.00723.054-0.039-0.0390.0000.0000.0000.000
55A79ASP-1-0.913-0.95624.686-10.794-10.7940.0000.0000.0000.000
56A80GLY00.014-0.01221.900-0.427-0.4270.0000.0000.0000.000
57A81LEU0-0.084-0.04721.997-0.287-0.2870.0000.0000.0000.000
58A82MET0-0.0310.00720.6470.1360.1360.0000.0000.0000.000
59A83ILE0-0.0090.01416.049-0.422-0.4220.0000.0000.0000.000
60A84GLN00.0320.01016.6450.6800.6800.0000.0000.0000.000
61A85GLU-1-0.999-0.99815.100-15.287-15.2870.0000.0000.0000.000
62A86GLY00.0550.02212.1440.3920.3920.0000.0000.0000.000
63A87SER0-0.084-0.03110.833-1.166-1.1660.0000.0000.0000.000
64A88SER0-0.081-0.0837.207-0.921-0.9210.0000.0000.0000.000
65A89VAL0-0.025-0.0208.0711.7671.7670.0000.0000.0000.000
66A90LYS10.9140.9646.97027.67027.6700.0000.0000.0000.000
67A91ALA00.0800.0427.8022.8842.8840.0000.0000.0000.000
68A92THR0-0.077-0.0529.589-0.427-0.4270.0000.0000.0000.000
69A93GLY00.0390.03212.2820.2220.2220.0000.0000.0000.000
70A94ARG10.8760.93612.98320.36620.3660.0000.0000.0000.000
71A95ILE00.0270.01516.542-0.058-0.0580.0000.0000.0000.000
72A96ALA00.016-0.00119.3190.7820.7820.0000.0000.0000.000
73A97GLN0-0.033-0.01421.3810.8980.8980.0000.0000.0000.000
74A98ILE00.0100.00523.358-0.170-0.1700.0000.0000.0000.000
75A99PRO00.0130.01325.6080.1920.1920.0000.0000.0000.000
76A100VAL0-0.008-0.02528.0060.2930.2930.0000.0000.0000.000
77A101SER0-0.007-0.01131.605-0.038-0.0380.0000.0000.0000.000
78A102GLU-1-0.776-0.89534.619-7.814-7.8140.0000.0000.0000.000
79A103ALA0-0.048-0.02434.8560.1680.1680.0000.0000.0000.000
80A104TYR0-0.112-0.03430.925-0.028-0.0280.0000.0000.0000.000
81A105LEU0-0.023-0.02037.2970.1190.1190.0000.0000.0000.000
82A106GLY00.1180.07840.3420.1730.1730.0000.0000.0000.000
83A107ARG10.7140.85935.0638.7818.7810.0000.0000.0000.000
84A108VAL00.005-0.00737.271-0.080-0.0800.0000.0000.0000.000
85A109ILE0-0.0430.02331.847-0.227-0.2270.0000.0000.0000.000
86A110ASN00.008-0.01129.6370.2660.2660.0000.0000.0000.000
87A111ALA00.0880.04928.4550.1130.1130.0000.0000.0000.000
88A112LEU0-0.079-0.04423.453-0.260-0.2600.0000.0000.0000.000
89A113ALA0-0.001-0.01926.703-0.217-0.2170.0000.0000.0000.000
90A114LYS10.9610.97423.74612.35612.3560.0000.0000.0000.000
91A115PRO0-0.032-0.01129.5830.1340.1340.0000.0000.0000.000
92A116ILE00.0180.01632.531-0.197-0.1970.0000.0000.0000.000
93A117ASP-1-0.800-0.90334.874-8.274-8.2740.0000.0000.0000.000
94A118GLY0-0.037-0.01436.1480.1840.1840.0000.0000.0000.000
95A119ARG10.9630.97936.9257.6827.6820.0000.0000.0000.000
96A120GLY00.0220.02234.4830.0550.0550.0000.0000.0000.000
97A121GLU-1-0.930-0.96328.186-11.209-11.2090.0000.0000.0000.000
98A122ILE0-0.023-0.01329.6140.3540.3540.0000.0000.0000.000
99A123THR00.0240.00130.858-0.362-0.3620.0000.0000.0000.000
100A124ALA00.0070.01528.5710.2650.2650.0000.0000.0000.000
101A125SER0-0.0020.01129.470-0.191-0.1910.0000.0000.0000.000
102A126GLU-1-0.875-0.93928.464-10.349-10.3490.0000.0000.0000.000
103A127SER0-0.052-0.05925.406-0.171-0.1710.0000.0000.0000.000
104A128ARG10.8920.96926.6979.8759.8750.0000.0000.0000.000
105A129LEU0-0.012-0.00323.393-0.093-0.0930.0000.0000.0000.000
106A130ILE00.0730.05224.8380.5030.5030.0000.0000.0000.000
107A131GLU-1-0.891-0.95726.261-10.894-10.8940.0000.0000.0000.000
108A132SER0-0.068-0.03527.205-0.273-0.2730.0000.0000.0000.000
109A133PRO0-0.035-0.01829.6890.2650.2650.0000.0000.0000.000
110A134ALA00.0640.04632.4950.0390.0390.0000.0000.0000.000
111A135PRO0-0.033-0.01736.0940.0370.0370.0000.0000.0000.000
112A136GLY00.0570.04639.0940.0900.0900.0000.0000.0000.000
113A137ILE00.0490.01340.3680.1030.1030.0000.0000.0000.000
114A138MET00.0260.01240.8160.1680.1680.0000.0000.0000.000
115A139SER0-0.026-0.00240.9470.0650.0650.0000.0000.0000.000
116A140ARG10.8140.88239.8607.6947.6940.0000.0000.0000.000
117A141ARG10.9240.97945.6416.5726.5720.0000.0000.0000.000
118A142SER00.0180.00949.321-0.089-0.0890.0000.0000.0000.000
119A143VAL00.0320.03249.847-0.008-0.0080.0000.0000.0000.000
120A144TYR0-0.040-0.01552.2580.0990.0990.0000.0000.0000.000
121A145GLU-1-0.835-0.90950.382-6.349-6.3490.0000.0000.0000.000
122A146PRO00.002-0.00953.626-0.060-0.0600.0000.0000.0000.000
123A147LEU0-0.007-0.01049.140-0.109-0.1090.0000.0000.0000.000
124A148GLN0-0.0240.00353.7450.0040.0040.0000.0000.0000.000
125A149THR0-0.003-0.03752.933-0.077-0.0770.0000.0000.0000.000
126A150GLY00.0230.01155.102-0.038-0.0380.0000.0000.0000.000
127A151LEU0-0.065-0.03355.4490.1000.1000.0000.0000.0000.000
128A152ILE00.008-0.01359.2950.0090.0090.0000.0000.0000.000
129A153ALA0-0.024-0.02260.6190.0350.0350.0000.0000.0000.000
130A154ILE00.0440.02855.155-0.004-0.0040.0000.0000.0000.000
131A155ASP-1-0.727-0.83156.565-5.688-5.6880.0000.0000.0000.000
132A156ALA0-0.041-0.03459.0550.0710.0710.0000.0000.0000.000
133A157MET0-0.097-0.06560.9780.1070.1070.0000.0000.0000.000
134A158ILE0-0.0510.00755.3690.0070.0070.0000.0000.0000.000
135A159PRO0-0.096-0.03756.626-0.039-0.0390.0000.0000.0000.000
136A160VAL00.1190.08150.710-0.063-0.0630.0000.0000.0000.000
137A161GLY00.023-0.01552.2390.0690.0690.0000.0000.0000.000
138A162ARG10.8090.86348.6946.2486.2480.0000.0000.0000.000
139A163GLY00.004-0.00545.7010.0490.0490.0000.0000.0000.000
140A164GLN0-0.0100.01745.936-0.062-0.0620.0000.0000.0000.000
141A165ARG10.7290.86042.7227.1357.1350.0000.0000.0000.000
142A166GLU-1-0.839-0.93946.347-6.051-6.0510.0000.0000.0000.000
143A167LEU0-0.025-0.00245.475-0.110-0.1100.0000.0000.0000.000
144A168ILE0-0.013-0.00547.7220.1760.1760.0000.0000.0000.000
145A169ILE00.010-0.01348.351-0.120-0.1200.0000.0000.0000.000
146A170GLY00.0500.01150.3170.1340.1340.0000.0000.0000.000
147A171ASP-1-0.730-0.81850.257-6.058-6.0580.0000.0000.0000.000
148A172ARG10.9630.99750.1215.8455.8450.0000.0000.0000.000
149A173GLN0-0.040-0.02851.1750.1050.1050.0000.0000.0000.000
150A174THR00.032-0.04452.5470.1490.1490.0000.0000.0000.000
151A175GLY00.012-0.00254.2380.0090.0090.0000.0000.0000.000
152A176LYS10.8790.95448.4396.4286.4280.0000.0000.0000.000
153A177THR00.0560.02746.923-0.010-0.0100.0000.0000.0000.000
154A178ALA0-0.0220.01749.333-0.043-0.0430.0000.0000.0000.000
155A179VAL00.0350.03051.6680.0210.0210.0000.0000.0000.000
156A180ALA00.0010.00847.4130.0090.0090.0000.0000.0000.000
157A181THR0-0.055-0.05749.538-0.054-0.0540.0000.0000.0000.000
158A182ASP-1-0.869-0.95050.607-5.752-5.7520.0000.0000.0000.000
159A183THR00.004-0.00950.0630.0070.0070.0000.0000.0000.000
160A184ILE00.009-0.01345.5080.0050.0050.0000.0000.0000.000
161A185LEU0-0.0090.03949.6640.0060.0060.0000.0000.0000.000
162A186ASN0-0.051-0.02052.1830.1270.1270.0000.0000.0000.000
163A187GLN0-0.052-0.02648.590-0.045-0.0450.0000.0000.0000.000
164A188GLN00.0210.02052.256-0.057-0.0570.0000.0000.0000.000
165A189GLY00.0880.03951.253-0.123-0.1230.0000.0000.0000.000
166A190GLN0-0.055-0.03649.2110.1240.1240.0000.0000.0000.000
167A191ASN0-0.0110.00650.246-0.034-0.0340.0000.0000.0000.000
168A192VAL0-0.021-0.00746.457-0.038-0.0380.0000.0000.0000.000
169A193ILE0-0.0010.03441.2950.0330.0330.0000.0000.0000.000
170A194CYS00.0020.02043.8350.0170.0170.0000.0000.0000.000
171A195VAL0-0.025-0.00337.684-0.137-0.1370.0000.0000.0000.000
172A196TYR0-0.040-0.03240.8820.0930.0930.0000.0000.0000.000
173A197VAL00.017-0.00336.005-0.189-0.1890.0000.0000.0000.000
174A198ALA00.0350.01538.5390.1560.1560.0000.0000.0000.000
175A199ILE0-0.009-0.00434.957-0.295-0.2950.0000.0000.0000.000
176A200GLY00.0350.00937.1850.1610.1610.0000.0000.0000.000
177A201GLN0-0.010-0.01038.4870.1880.1880.0000.0000.0000.000
178A202LYS10.9840.97739.9626.8096.8090.0000.0000.0000.000
179A203ALA00.0660.03439.3720.0580.0580.0000.0000.0000.000
180A204SER00.0200.00341.0880.0070.0070.0000.0000.0000.000
181A205SER00.0120.00344.5220.0600.0600.0000.0000.0000.000
182A206VAL00.0540.02540.6370.1010.1010.0000.0000.0000.000
183A207ALA00.0260.02743.7370.0140.0140.0000.0000.0000.000
184A208GLN0-0.037-0.02445.1670.0390.0390.0000.0000.0000.000
185A209VAL00.0100.01745.2890.1530.1530.0000.0000.0000.000
186A210VAL00.008-0.01642.0600.0590.0590.0000.0000.0000.000
187A211THR0-0.014-0.00445.455-0.015-0.0150.0000.0000.0000.000
188A212ASN0-0.048-0.03148.5490.1530.1530.0000.0000.0000.000
189A213PHE00.0310.01347.4540.0850.0850.0000.0000.0000.000
190A214GLN0-0.058-0.04144.8440.1120.1120.0000.0000.0000.000
191A215GLU-1-0.943-0.96449.467-5.896-5.8960.0000.0000.0000.000
192A216ARG10.9030.95652.3325.9245.9240.0000.0000.0000.000
193A217GLY00.0160.01050.8220.0200.0200.0000.0000.0000.000
194A218ALA00.0410.02249.583-0.049-0.0490.0000.0000.0000.000
195A219MET0-0.116-0.04543.275-0.137-0.1370.0000.0000.0000.000
196A220GLU-1-0.910-0.94644.527-6.731-6.7310.0000.0000.0000.000
197A221TYR0-0.055-0.06344.117-0.096-0.0960.0000.0000.0000.000
198A222THR00.009-0.00542.880-0.045-0.0450.0000.0000.0000.000
199A223ILE0-0.043-0.01336.284-0.068-0.0680.0000.0000.0000.000
200A224VAL0-0.010-0.00938.6240.1340.1340.0000.0000.0000.000
201A225VAL0-0.0010.01433.196-0.160-0.1600.0000.0000.0000.000
202A226ALA0-0.006-0.00935.5420.2150.2150.0000.0000.0000.000
203A227GLU-1-0.789-0.92731.488-10.052-10.0520.0000.0000.0000.000
204A228THR0-0.017-0.01434.6100.1200.1200.0000.0000.0000.000
205A229ALA0-0.022-0.00335.199-0.213-0.2130.0000.0000.0000.000
206A230ASP-1-0.916-0.95934.689-8.454-8.4540.0000.0000.0000.000
207A231SER0-0.095-0.02931.050-0.295-0.2950.0000.0000.0000.000
208A232PRO00.0660.04326.9100.1350.1350.0000.0000.0000.000
209A233ALA00.0970.03428.9830.0180.0180.0000.0000.0000.000
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