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: 17N5Z

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 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 477
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8560596.453126
FMO2-HF: Nuclear repulsion 8378891.473817
FMO2-HF: Total energy -181704.979309
FMO2-MP2: Total energy -182237.151287


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.
-124.044-118.4031.152-2.444-4.346-0.012
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 : 0.949 / 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].
3A27VAL0-0.0100.0053.0480.3883.2820.030-1.081-1.842-0.002
4A28ASN0-0.007-0.0242.9335.3035.9840.039-0.130-0.5900.000
5A29THR0-0.066-0.0402.613-2.350-0.2471.084-1.214-1.972-0.010
6A30GLY00.0290.0064.695-0.743-0.780-0.001-0.0190.0580.000
7A31THR0-0.0040.0186.622-0.161-0.1610.0000.0000.0000.000
8A32VAL0-0.010-0.0019.0130.5890.5890.0000.0000.0000.000
9A33LEU0-0.026-0.00812.7090.3200.3200.0000.0000.0000.000
10A34GLN00.006-0.01014.8730.9530.9530.0000.0000.0000.000
11A35VAL00.001-0.00217.936-0.414-0.4140.0000.0000.0000.000
12A36GLY00.0050.01020.2320.4640.4640.0000.0000.0000.000
13A37ASP-1-0.917-0.96023.661-10.211-10.2110.0000.0000.0000.000
14A38GLY00.0110.00424.3510.1700.1700.0000.0000.0000.000
15A39ILE0-0.064-0.03021.173-0.303-0.3030.0000.0000.0000.000
16A40ALA00.003-0.00616.843-0.007-0.0070.0000.0000.0000.000
17A41ARG10.8190.89916.77913.68713.6870.0000.0000.0000.000
18A42ILE00.0210.01210.703-0.079-0.0790.0000.0000.0000.000
19A43HIS00.0400.0208.9991.3651.3650.0000.0000.0000.000
20A44GLY0-0.015-0.0227.677-1.939-1.9390.0000.0000.0000.000
21A45LEU0-0.063-0.0366.4041.4551.4550.0000.0000.0000.000
22A46ASP-1-0.879-0.9427.940-24.823-24.8230.0000.0000.0000.000
23A47GLU-1-0.920-0.9657.900-33.605-33.6050.0000.0000.0000.000
24A48VAL0-0.067-0.0049.9211.5231.5230.0000.0000.0000.000
25A49MET00.002-0.00111.8781.3861.3860.0000.0000.0000.000
26A50ALA0-0.040-0.02815.5470.2070.2070.0000.0000.0000.000
27A51GLY0-0.0040.00018.6990.4790.4790.0000.0000.0000.000
28A52GLU-1-0.853-0.93912.330-22.682-22.6820.0000.0000.0000.000
29A53LEU0-0.061-0.03515.6530.0330.0330.0000.0000.0000.000
30A54VAL00.0060.02411.915-1.403-1.4030.0000.0000.0000.000
31A55GLU-1-0.902-0.95011.975-22.403-22.4030.0000.0000.0000.000
32A56PHE00.016-0.00811.865-1.339-1.3390.0000.0000.0000.000
33A57GLU-1-0.771-0.85910.764-22.824-22.8240.0000.0000.0000.000
34A58GLU-1-0.923-0.95613.633-14.055-14.0550.0000.0000.0000.000
35A59GLY00.0000.00215.9900.7940.7940.0000.0000.0000.000
36A60THR0-0.035-0.01216.9710.9810.9810.0000.0000.0000.000
37A61ILE0-0.022-0.02316.860-0.877-0.8770.0000.0000.0000.000
38A62GLY00.0770.01417.5320.6960.6960.0000.0000.0000.000
39A63ILE00.0210.01817.125-0.817-0.8170.0000.0000.0000.000
40A64ALA00.0420.03115.5810.0910.0910.0000.0000.0000.000
41A65LEU0-0.013-0.02217.6840.4660.4660.0000.0000.0000.000
42A66ASN0-0.042-0.02819.2450.7790.7790.0000.0000.0000.000
43A67LEU00.0180.02715.015-0.296-0.2960.0000.0000.0000.000
44A68GLU-1-0.789-0.86917.269-13.314-13.3140.0000.0000.0000.000
45A69SER0-0.018-0.02416.392-0.512-0.5120.0000.0000.0000.000
46A70ASN0-0.020-0.00313.988-0.622-0.6220.0000.0000.0000.000
47A71ASN0-0.055-0.03113.099-0.715-0.7150.0000.0000.0000.000
48A72VAL00.0650.04812.0680.9150.9150.0000.0000.0000.000
49A73GLY00.009-0.00214.9940.2590.2590.0000.0000.0000.000
50A74VAL0-0.029-0.01714.7810.3060.3060.0000.0000.0000.000
51A75VAL00.0110.00818.0270.4550.4550.0000.0000.0000.000
52A76LEU00.0000.01218.440-0.299-0.2990.0000.0000.0000.000
53A77MET0-0.0200.00521.2610.3590.3590.0000.0000.0000.000
54A78GLY00.0150.00223.169-0.057-0.0570.0000.0000.0000.000
55A79ASP-1-0.918-0.95724.747-10.716-10.7160.0000.0000.0000.000
56A80GLY00.014-0.01121.964-0.431-0.4310.0000.0000.0000.000
57A81LEU0-0.070-0.04422.024-0.288-0.2880.0000.0000.0000.000
58A82MET0-0.0180.00620.5560.0720.0720.0000.0000.0000.000
59A83ILE0-0.024-0.00316.098-0.423-0.4230.0000.0000.0000.000
60A84GLN00.003-0.00116.6560.7940.7940.0000.0000.0000.000
61A85GLU-1-0.982-0.98615.130-14.855-14.8550.0000.0000.0000.000
62A86GLY00.0410.01412.1890.3940.3940.0000.0000.0000.000
63A87SER0-0.072-0.02110.859-1.112-1.1120.0000.0000.0000.000
64A88SER0-0.102-0.1007.203-0.936-0.9360.0000.0000.0000.000
65A89VAL0-0.045-0.0268.1201.8061.8060.0000.0000.0000.000
66A90LYS10.8650.9287.42422.75922.7590.0000.0000.0000.000
67A91ALA00.0660.0367.8932.8972.8970.0000.0000.0000.000
68A92THR0-0.071-0.0459.669-0.353-0.3530.0000.0000.0000.000
69A93GLY00.0380.02912.3670.1700.1700.0000.0000.0000.000
70A94ARG10.8790.93713.13120.42120.4210.0000.0000.0000.000
71A95ILE00.0350.01816.703-0.027-0.0270.0000.0000.0000.000
72A96ALA00.010-0.00519.3800.7540.7540.0000.0000.0000.000
73A97GLN0-0.020-0.00821.1010.7080.7080.0000.0000.0000.000
74A98ILE0-0.013-0.00523.538-0.161-0.1610.0000.0000.0000.000
75A99PRO00.0300.01625.7670.1900.1900.0000.0000.0000.000
76A100VAL0-0.0070.00128.1840.2960.2960.0000.0000.0000.000
77A101SER0-0.036-0.01631.775-0.059-0.0590.0000.0000.0000.000
78A102GLU-1-0.716-0.82934.777-7.818-7.8180.0000.0000.0000.000
79A103ALA0-0.041-0.02635.0240.1670.1670.0000.0000.0000.000
80A104TYR0-0.072-0.04231.0270.0190.0190.0000.0000.0000.000
81A105LEU0-0.020-0.02337.4930.1110.1110.0000.0000.0000.000
82A106GLY00.1370.08740.5360.1690.1690.0000.0000.0000.000
83A107ARG10.6700.81735.3458.7648.7640.0000.0000.0000.000
84A108VAL00.015-0.00237.762-0.078-0.0780.0000.0000.0000.000
85A109ILE0-0.0370.00932.118-0.220-0.2200.0000.0000.0000.000
86A110ASN00.007-0.00530.3670.0670.0670.0000.0000.0000.000
87A111ALA00.0760.04828.5250.1210.1210.0000.0000.0000.000
88A112LEU0-0.064-0.04823.420-0.242-0.2420.0000.0000.0000.000
89A113ALA0-0.010-0.01126.934-0.235-0.2350.0000.0000.0000.000
90A114LYS10.9880.98523.78612.37112.3710.0000.0000.0000.000
91A115PRO0-0.029-0.00729.8190.1360.1360.0000.0000.0000.000
92A116ILE00.0110.00332.780-0.222-0.2220.0000.0000.0000.000
93A117ASP-1-0.770-0.86935.130-8.283-8.2830.0000.0000.0000.000
94A118GLY0-0.025-0.01136.3880.1830.1830.0000.0000.0000.000
95A119ARG10.9030.95437.1717.6567.6560.0000.0000.0000.000
96A120GLY00.0200.02434.6960.0480.0480.0000.0000.0000.000
97A121GLU-1-0.933-0.96628.186-11.188-11.1880.0000.0000.0000.000
98A122ILE0-0.027-0.01229.7840.3620.3620.0000.0000.0000.000
99A123THR00.0210.00031.037-0.361-0.3610.0000.0000.0000.000
100A124ALA00.0090.01828.7500.2650.2650.0000.0000.0000.000
101A125SER00.0060.01529.608-0.168-0.1680.0000.0000.0000.000
102A126GLU-1-0.830-0.90928.698-10.108-10.1080.0000.0000.0000.000
103A127SER0-0.031-0.04325.601-0.146-0.1460.0000.0000.0000.000
104A128ARG10.8820.97226.8849.6449.6440.0000.0000.0000.000
105A129LEU00.0130.00723.632-0.105-0.1050.0000.0000.0000.000
106A130ILE00.0490.04125.0290.4910.4910.0000.0000.0000.000
107A131GLU-1-0.815-0.89226.287-10.796-10.7960.0000.0000.0000.000
108A132SER00.0110.00127.267-0.346-0.3460.0000.0000.0000.000
109A133PRO0-0.039-0.02029.7470.2610.2610.0000.0000.0000.000
110A134ALA00.0410.03232.5490.0210.0210.0000.0000.0000.000
111A135PRO0-0.004-0.00136.1510.0090.0090.0000.0000.0000.000
112A136GLY00.0460.03839.1440.0950.0950.0000.0000.0000.000
113A137ILE00.0340.00440.4170.1050.1050.0000.0000.0000.000
114A138MET00.0180.01041.8630.1720.1720.0000.0000.0000.000
115A139SER0-0.016-0.00141.4030.0700.0700.0000.0000.0000.000
116A140ARG10.7770.87640.4537.5207.5200.0000.0000.0000.000
117A141ARG10.9290.96045.8476.4956.4950.0000.0000.0000.000
118A142SER0-0.005-0.00149.374-0.087-0.0870.0000.0000.0000.000
119A143VAL00.0190.03149.786-0.006-0.0060.0000.0000.0000.000
120A144TYR0-0.024-0.00852.3180.1500.1500.0000.0000.0000.000
121A145GLU-1-0.839-0.92450.520-6.317-6.3170.0000.0000.0000.000
122A146PRO0-0.004-0.01053.689-0.062-0.0620.0000.0000.0000.000
123A147LEU00.002-0.00549.233-0.106-0.1060.0000.0000.0000.000
124A148GLN0-0.057-0.01453.8140.0180.0180.0000.0000.0000.000
125A149THR00.025-0.03953.057-0.076-0.0760.0000.0000.0000.000
126A150GLY00.0070.01355.181-0.035-0.0350.0000.0000.0000.000
127A151LEU0-0.077-0.04255.4200.1020.1020.0000.0000.0000.000
128A152ILE00.020-0.01159.3800.0040.0040.0000.0000.0000.000
129A153ALA0-0.021-0.01760.7030.0330.0330.0000.0000.0000.000
130A154ILE00.0500.03255.130-0.006-0.0060.0000.0000.0000.000
131A155ASP-1-0.673-0.78957.005-5.617-5.6170.0000.0000.0000.000
132A156ALA0-0.033-0.04059.1340.0680.0680.0000.0000.0000.000
133A157MET0-0.069-0.05161.0590.1090.1090.0000.0000.0000.000
134A158ILE0-0.0420.01155.3390.0060.0060.0000.0000.0000.000
135A159PRO0-0.068-0.02556.709-0.051-0.0510.0000.0000.0000.000
136A160VAL00.0950.06750.801-0.065-0.0650.0000.0000.0000.000
137A161GLY00.026-0.00952.3490.0660.0660.0000.0000.0000.000
138A162ARG10.8040.87648.7576.1766.1760.0000.0000.0000.000
139A163GLY00.002-0.00845.7650.0450.0450.0000.0000.0000.000
140A164GLN0-0.047-0.00546.003-0.064-0.0640.0000.0000.0000.000
141A165ARG10.7130.81142.8477.0337.0330.0000.0000.0000.000
142A166GLU-1-0.820-0.92646.426-6.003-6.0030.0000.0000.0000.000
143A167LEU0-0.0210.00545.592-0.102-0.1020.0000.0000.0000.000
144A168ILE00.000-0.00547.8170.1730.1730.0000.0000.0000.000
145A169ILE0-0.010-0.02048.452-0.119-0.1190.0000.0000.0000.000
146A170GLY00.0630.01850.4270.1310.1310.0000.0000.0000.000
147A171ASP-1-0.748-0.82450.367-5.997-5.9970.0000.0000.0000.000
148A172ARG10.9681.00250.1205.8135.8130.0000.0000.0000.000
149A173GLN0-0.047-0.03051.2720.0900.0900.0000.0000.0000.000
150A174THR00.026-0.02452.6570.1500.1500.0000.0000.0000.000
151A175GLY00.0090.00054.3410.0110.0110.0000.0000.0000.000
152A176LYS10.8560.94048.3816.4106.4100.0000.0000.0000.000
153A177THR00.0200.00847.0670.0420.0420.0000.0000.0000.000
154A178ALA0-0.0150.01549.433-0.040-0.0400.0000.0000.0000.000
155A179VAL00.0420.03051.9100.0190.0190.0000.0000.0000.000
156A180ALA0-0.0020.01247.5020.0070.0070.0000.0000.0000.000
157A181THR0-0.047-0.04249.630-0.057-0.0570.0000.0000.0000.000
158A182ASP-1-0.843-0.93550.697-5.735-5.7350.0000.0000.0000.000
159A183THR00.004-0.01150.4450.0070.0070.0000.0000.0000.000
160A184ILE0-0.0070.00345.6840.0000.0000.0000.0000.0000.000
161A185LEU00.0150.01849.807-0.006-0.0060.0000.0000.0000.000
162A186ASN0-0.060-0.02852.4030.1260.1260.0000.0000.0000.000
163A187GLN0-0.078-0.06149.474-0.033-0.0330.0000.0000.0000.000
164A188GLN00.0310.02152.453-0.059-0.0590.0000.0000.0000.000
165A189GLY00.0840.03851.436-0.123-0.1230.0000.0000.0000.000
166A190GLN0-0.062-0.04349.3590.1090.1090.0000.0000.0000.000
167A191ASN0-0.0310.00650.405-0.029-0.0290.0000.0000.0000.000
168A192VAL00.0060.00146.799-0.043-0.0430.0000.0000.0000.000
169A193ILE0-0.0030.02341.5450.0210.0210.0000.0000.0000.000
170A194CYS0-0.0200.00844.0540.0250.0250.0000.0000.0000.000
171A195VAL0-0.008-0.00537.662-0.142-0.1420.0000.0000.0000.000
172A196TYR0-0.026-0.02341.0310.0820.0820.0000.0000.0000.000
173A197VAL00.0220.00336.026-0.181-0.1810.0000.0000.0000.000
174A198ALA0-0.0150.00438.6360.1650.1650.0000.0000.0000.000
175A199ILE00.0060.00335.072-0.285-0.2850.0000.0000.0000.000
176A200GLY00.0390.02037.3090.1550.1550.0000.0000.0000.000
177A201GLN0-0.044-0.01238.6000.2060.2060.0000.0000.0000.000
178A202LYS10.9990.98840.0736.7956.7950.0000.0000.0000.000
179A203ALA00.0660.04039.3850.0610.0610.0000.0000.0000.000
180A204SER00.0170.00041.1480.0140.0140.0000.0000.0000.000
181A205SER0-0.001-0.01544.7050.0630.0630.0000.0000.0000.000
182A206VAL00.0560.02340.6240.0990.0990.0000.0000.0000.000
183A207ALA00.0270.02743.8370.0180.0180.0000.0000.0000.000
184A208GLN0-0.024-0.01645.2660.0300.0300.0000.0000.0000.000
185A209VAL00.0150.02245.9990.1520.1520.0000.0000.0000.000
186A210VAL00.006-0.01342.3590.0580.0580.0000.0000.0000.000
187A211THR0-0.032-0.00945.673-0.019-0.0190.0000.0000.0000.000
188A212ASN0-0.008-0.00448.8000.1820.1820.0000.0000.0000.000
189A213PHE00.0580.03046.9550.0960.0960.0000.0000.0000.000
190A214GLN0-0.033-0.03345.723-0.005-0.0050.0000.0000.0000.000
191A215GLU-1-0.947-0.96349.699-5.885-5.8850.0000.0000.0000.000
192A216ARG10.8460.90652.5605.9315.9310.0000.0000.0000.000
193A217GLY00.0160.00951.0380.0210.0210.0000.0000.0000.000
194A218ALA00.0420.02749.839-0.049-0.0490.0000.0000.0000.000
195A219MET0-0.123-0.05743.822-0.134-0.1340.0000.0000.0000.000
196A220GLU-1-0.907-0.94144.739-6.711-6.7110.0000.0000.0000.000
197A221TYR0-0.032-0.03244.275-0.099-0.0990.0000.0000.0000.000
198A222THR0-0.003-0.00743.223-0.047-0.0470.0000.0000.0000.000
199A223ILE0-0.050-0.01936.495-0.074-0.0740.0000.0000.0000.000
200A224VAL0-0.003-0.01338.8520.1350.1350.0000.0000.0000.000
201A225VAL0-0.0250.01633.374-0.158-0.1580.0000.0000.0000.000
202A226ALA0-0.003-0.00435.6170.2240.2240.0000.0000.0000.000
203A227GLU-1-0.811-0.93031.307-9.874-9.8740.0000.0000.0000.000
204A228THR0-0.045-0.03234.7150.1440.1440.0000.0000.0000.000
205A229ALA0-0.0080.00735.313-0.207-0.2070.0000.0000.0000.000
206A230ASP-1-0.912-0.95934.976-8.307-8.3070.0000.0000.0000.000
207A231SER0-0.067-0.02131.219-0.306-0.3060.0000.0000.0000.000
208A232PRO00.0710.04326.9880.1560.1560.0000.0000.0000.000
209A233ALA00.0770.01229.1820.0280.0280.0000.0000.0000.000
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