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: G6581

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 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 477
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8563570.611763
FMO2-HF: Nuclear repulsion 8381861.909347
FMO2-HF: Total energy -181708.702416
FMO2-MP2: Total energy -182240.351488


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.
-122.061-117.5080.854-2.125-3.281-0.01
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 : 0.964 / q_NPA : 0.958
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].
3A27VAL00.0010.0053.333-0.0942.1520.021-1.002-1.264-0.002
4A28ASN0-0.010-0.0163.4675.6576.0620.003-0.055-0.3530.000
5A29THR0-0.063-0.0472.725-2.697-0.7550.831-1.054-1.719-0.008
6A30GLY00.0170.0044.888-0.665-0.705-0.001-0.0140.0550.000
7A31THR0-0.035-0.0107.155-0.955-0.9550.0000.0000.0000.000
8A32VAL0-0.0050.0059.4570.8450.8450.0000.0000.0000.000
9A33LEU0-0.023-0.00513.1110.3580.3580.0000.0000.0000.000
10A34GLN0-0.005-0.01015.2250.9680.9680.0000.0000.0000.000
11A35VAL00.0240.00518.357-0.531-0.5310.0000.0000.0000.000
12A36GLY0-0.0010.00420.7170.4350.4350.0000.0000.0000.000
13A37ASP-1-0.927-0.96524.359-10.244-10.2440.0000.0000.0000.000
14A38GLY00.0080.01124.4160.2120.2120.0000.0000.0000.000
15A39ILE0-0.065-0.03421.962-0.381-0.3810.0000.0000.0000.000
16A40ALA00.0320.01317.4810.0740.0740.0000.0000.0000.000
17A41ARG10.7780.87417.18913.20513.2050.0000.0000.0000.000
18A42ILE00.0130.00911.022-0.006-0.0060.0000.0000.0000.000
19A43HIS00.0370.0148.8030.9230.9230.0000.0000.0000.000
20A44GLY00.017-0.0057.634-1.934-1.9340.0000.0000.0000.000
21A45LEU0-0.053-0.0236.9491.6431.6430.0000.0000.0000.000
22A46ASP-1-0.868-0.9427.924-24.642-24.6420.0000.0000.0000.000
23A47GLU-1-0.907-0.9518.039-31.749-31.7490.0000.0000.0000.000
24A48VAL0-0.072-0.0169.9351.2821.2820.0000.0000.0000.000
25A49MET0-0.024-0.01212.0691.5881.5880.0000.0000.0000.000
26A50ALA0-0.013-0.01215.7580.1550.1550.0000.0000.0000.000
27A51GLY00.003-0.00518.8440.3910.3910.0000.0000.0000.000
28A52GLU-1-0.830-0.92012.464-22.281-22.2810.0000.0000.0000.000
29A53LEU0-0.026-0.01516.6180.4040.4040.0000.0000.0000.000
30A54VAL0-0.0050.01712.204-1.297-1.2970.0000.0000.0000.000
31A55GLU-1-0.812-0.89212.279-22.590-22.5900.0000.0000.0000.000
32A56PHE00.0320.00611.869-1.593-1.5930.0000.0000.0000.000
33A57GLU-1-0.794-0.86510.974-21.885-21.8850.0000.0000.0000.000
34A58GLU-1-0.876-0.92213.798-13.976-13.9760.0000.0000.0000.000
35A59GLY0-0.014-0.00816.5160.7970.7970.0000.0000.0000.000
36A60THR0-0.036-0.00617.2030.8880.8880.0000.0000.0000.000
37A61ILE0-0.009-0.01516.682-0.959-0.9590.0000.0000.0000.000
38A62GLY00.0380.00617.3430.8420.8420.0000.0000.0000.000
39A63ILE0-0.0140.00017.476-0.714-0.7140.0000.0000.0000.000
40A64ALA00.0380.03115.2500.3930.3930.0000.0000.0000.000
41A65LEU0-0.016-0.02117.3690.4740.4740.0000.0000.0000.000
42A66ASN0-0.054-0.03919.3560.8760.8760.0000.0000.0000.000
43A67LEU00.0270.03315.241-0.281-0.2810.0000.0000.0000.000
44A68GLU-1-0.756-0.83917.800-12.847-12.8470.0000.0000.0000.000
45A69SER0-0.004-0.02616.602-0.517-0.5170.0000.0000.0000.000
46A70ASN0-0.069-0.02114.387-0.495-0.4950.0000.0000.0000.000
47A71ASN0-0.049-0.03613.494-0.703-0.7030.0000.0000.0000.000
48A72VAL00.0500.03912.3590.8670.8670.0000.0000.0000.000
49A73GLY00.0210.00615.1870.0670.0670.0000.0000.0000.000
50A74VAL0-0.020-0.01814.9270.0280.0280.0000.0000.0000.000
51A75VAL00.002-0.00418.3040.5060.5060.0000.0000.0000.000
52A76LEU00.0280.02718.290-0.372-0.3720.0000.0000.0000.000
53A77MET0-0.067-0.02721.3130.4800.4800.0000.0000.0000.000
54A78GLY00.0240.00223.2830.1210.1210.0000.0000.0000.000
55A79ASP-1-0.914-0.95424.407-10.795-10.7950.0000.0000.0000.000
56A80GLY00.005-0.01521.904-0.332-0.3320.0000.0000.0000.000
57A81LEU0-0.039-0.02322.102-0.245-0.2450.0000.0000.0000.000
58A82MET00.0040.01520.6810.0990.0990.0000.0000.0000.000
59A83ILE0-0.061-0.01716.345-0.698-0.6980.0000.0000.0000.000
60A84GLN0-0.013-0.01517.0680.6830.6830.0000.0000.0000.000
61A85GLU-1-0.967-0.98415.869-14.495-14.4950.0000.0000.0000.000
62A86GLY0-0.009-0.01012.6180.2010.2010.0000.0000.0000.000
63A87SER0-0.0290.00011.504-0.924-0.9240.0000.0000.0000.000
64A88SER0-0.110-0.0977.306-1.000-1.0000.0000.0000.0000.000
65A89VAL0-0.018-0.0148.1441.8921.8920.0000.0000.0000.000
66A90LYS10.7870.8627.46922.63022.6300.0000.0000.0000.000
67A91ALA00.0640.0407.7342.9372.9370.0000.0000.0000.000
68A92THR0-0.062-0.0569.633-0.671-0.6710.0000.0000.0000.000
69A93GLY0-0.007-0.00612.2510.2080.2080.0000.0000.0000.000
70A94ARG10.8650.93313.34720.88120.8810.0000.0000.0000.000
71A95ILE00.0430.03116.8760.1600.1600.0000.0000.0000.000
72A96ALA00.021-0.00219.3900.2280.2280.0000.0000.0000.000
73A97GLN0-0.024-0.00321.1450.7250.7250.0000.0000.0000.000
74A98ILE0-0.023-0.01223.660-0.154-0.1540.0000.0000.0000.000
75A99PRO00.0330.01525.4700.2070.2070.0000.0000.0000.000
76A100VAL0-0.0170.00227.9760.3230.3230.0000.0000.0000.000
77A101SER0-0.002-0.01831.644-0.084-0.0840.0000.0000.0000.000
78A102GLU-1-0.720-0.83534.684-7.912-7.9120.0000.0000.0000.000
79A103ALA0-0.044-0.01535.0410.1910.1910.0000.0000.0000.000
80A104TYR0-0.015-0.04130.672-0.033-0.0330.0000.0000.0000.000
81A105LEU0-0.050-0.01437.4340.0750.0750.0000.0000.0000.000
82A106GLY00.0850.05441.1320.1690.1690.0000.0000.0000.000
83A107ARG10.6610.79135.4398.7338.7330.0000.0000.0000.000
84A108VAL0-0.001-0.00137.8960.0090.0090.0000.0000.0000.000
85A109ILE0-0.053-0.01932.011-0.193-0.1930.0000.0000.0000.000
86A110ASN00.0300.01329.183-0.151-0.1510.0000.0000.0000.000
87A111ALA00.0480.01828.656-0.131-0.1310.0000.0000.0000.000
88A112LEU0-0.066-0.03623.608-0.233-0.2330.0000.0000.0000.000
89A113ALA00.004-0.00526.892-0.307-0.3070.0000.0000.0000.000
90A114LYS10.9560.98823.72112.47812.4780.0000.0000.0000.000
91A115PRO00.0130.00829.8040.1860.1860.0000.0000.0000.000
92A116ILE0-0.013-0.02132.873-0.170-0.1700.0000.0000.0000.000
93A117ASP-1-0.732-0.84035.420-8.259-8.2590.0000.0000.0000.000
94A118GLY00.0010.00136.5930.1990.1990.0000.0000.0000.000
95A119ARG10.8040.90737.5577.5127.5120.0000.0000.0000.000
96A120GLY00.0290.02034.8840.0040.0040.0000.0000.0000.000
97A121GLU-1-0.929-0.95828.146-11.171-11.1710.0000.0000.0000.000
98A122ILE00.0100.00429.6930.3800.3800.0000.0000.0000.000
99A123THR00.0230.01431.077-0.354-0.3540.0000.0000.0000.000
100A124ALA0-0.0150.01628.9810.2620.2620.0000.0000.0000.000
101A125SER0-0.025-0.01229.986-0.160-0.1600.0000.0000.0000.000
102A126GLU-1-0.782-0.85828.646-9.949-9.9490.0000.0000.0000.000
103A127SER0-0.027-0.03525.586-0.289-0.2890.0000.0000.0000.000
104A128ARG10.8400.93827.5319.8069.8060.0000.0000.0000.000
105A129LEU00.0150.00923.458-0.154-0.1540.0000.0000.0000.000
106A130ILE00.0450.02924.9690.4650.4650.0000.0000.0000.000
107A131GLU-1-0.832-0.89526.656-10.548-10.5480.0000.0000.0000.000
108A132SER00.0180.00527.396-0.391-0.3910.0000.0000.0000.000
109A133PRO0-0.040-0.02229.8920.2180.2180.0000.0000.0000.000
110A134ALA00.0290.02132.6650.0340.0340.0000.0000.0000.000
111A135PRO00.0220.01736.294-0.038-0.0380.0000.0000.0000.000
112A136GLY00.0610.03939.0490.1260.1260.0000.0000.0000.000
113A137ILE00.012-0.00340.3730.0980.0980.0000.0000.0000.000
114A138MET00.002-0.00742.2930.1530.1530.0000.0000.0000.000
115A139SER0-0.033-0.01641.1790.0220.0220.0000.0000.0000.000
116A140ARG10.7990.88840.6587.4647.4640.0000.0000.0000.000
117A141ARG10.8480.91845.7276.4516.4510.0000.0000.0000.000
118A142SER00.0040.00049.179-0.098-0.0980.0000.0000.0000.000
119A143VAL00.0200.02949.6620.0120.0120.0000.0000.0000.000
120A144TYR0-0.011-0.01252.1920.1350.1350.0000.0000.0000.000
121A145GLU-1-0.843-0.90950.686-6.250-6.2500.0000.0000.0000.000
122A146PRO0-0.013-0.01053.491-0.088-0.0880.0000.0000.0000.000
123A147LEU0-0.033-0.01048.915-0.069-0.0690.0000.0000.0000.000
124A148GLN0-0.062-0.03253.4360.0300.0300.0000.0000.0000.000
125A149THR00.045-0.00852.980-0.053-0.0530.0000.0000.0000.000
126A150GLY00.0190.00554.936-0.032-0.0320.0000.0000.0000.000
127A151LEU0-0.0180.00555.4320.1040.1040.0000.0000.0000.000
128A152ILE00.019-0.00159.177-0.009-0.0090.0000.0000.0000.000
129A153ALA0-0.015-0.01860.5640.0200.0200.0000.0000.0000.000
130A154ILE0-0.0010.00955.1320.0130.0130.0000.0000.0000.000
131A155ASP-1-0.687-0.79857.288-5.583-5.5830.0000.0000.0000.000
132A156ALA0-0.0140.00759.4310.0410.0410.0000.0000.0000.000
133A157MET0-0.038-0.04261.3740.0730.0730.0000.0000.0000.000
134A158ILE0-0.0270.00755.5300.0150.0150.0000.0000.0000.000
135A159PRO0-0.0290.00356.471-0.076-0.0760.0000.0000.0000.000
136A160VAL00.0970.04550.842-0.077-0.0770.0000.0000.0000.000
137A161GLY00.033-0.00752.2490.0780.0780.0000.0000.0000.000
138A162ARG10.7610.85748.8896.1156.1150.0000.0000.0000.000
139A163GLY00.025-0.00345.6960.0340.0340.0000.0000.0000.000
140A164GLN0-0.081-0.03046.238-0.030-0.0300.0000.0000.0000.000
141A165ARG10.7330.81142.8926.9406.9400.0000.0000.0000.000
142A166GLU-1-0.812-0.92246.548-5.954-5.9540.0000.0000.0000.000
143A167LEU0-0.017-0.01645.805-0.095-0.0950.0000.0000.0000.000
144A168ILE00.0130.00648.0960.1710.1710.0000.0000.0000.000
145A169ILE0-0.021-0.01248.758-0.127-0.1270.0000.0000.0000.000
146A170GLY00.0860.03050.4400.1420.1420.0000.0000.0000.000
147A171ASP-1-0.766-0.84450.418-5.993-5.9930.0000.0000.0000.000
148A172ARG10.9610.99649.9395.8215.8210.0000.0000.0000.000
149A173GLN0-0.008-0.02150.9780.0650.0650.0000.0000.0000.000
150A174THR0-0.038-0.01652.7650.1360.1360.0000.0000.0000.000
151A175GLY00.022-0.00354.059-0.008-0.0080.0000.0000.0000.000
152A176LYS10.8140.90448.5796.3646.3640.0000.0000.0000.000
153A177THR00.015-0.00247.0130.0380.0380.0000.0000.0000.000
154A178ALA0-0.0270.00849.330-0.035-0.0350.0000.0000.0000.000
155A179VAL00.0260.01452.3970.0210.0210.0000.0000.0000.000
156A180ALA00.0190.01747.6310.0080.0080.0000.0000.0000.000
157A181THR0-0.026-0.01949.633-0.079-0.0790.0000.0000.0000.000
158A182ASP-1-0.804-0.91350.704-5.717-5.7170.0000.0000.0000.000
159A183THR0-0.009-0.01950.2240.0450.0450.0000.0000.0000.000
160A184ILE0-0.0170.00245.539-0.005-0.0050.0000.0000.0000.000
161A185LEU0-0.037-0.01349.9040.0080.0080.0000.0000.0000.000
162A186ASN0-0.023-0.01152.8310.1360.1360.0000.0000.0000.000
163A187GLN0-0.080-0.05749.134-0.014-0.0140.0000.0000.0000.000
164A188GLN00.0450.02252.019-0.081-0.0810.0000.0000.0000.000
165A189GLY00.0780.03751.310-0.110-0.1100.0000.0000.0000.000
166A190GLN0-0.047-0.03249.1370.1030.1030.0000.0000.0000.000
167A191ASN0-0.0370.00649.903-0.068-0.0680.0000.0000.0000.000
168A192VAL00.0030.00246.790-0.002-0.0020.0000.0000.0000.000
169A193ILE0-0.0150.01341.6340.0200.0200.0000.0000.0000.000
170A194CYS0-0.014-0.00244.1310.0370.0370.0000.0000.0000.000
171A195VAL0-0.009-0.00637.876-0.166-0.1660.0000.0000.0000.000
172A196TYR0-0.029-0.03340.9100.1340.1340.0000.0000.0000.000
173A197VAL00.0160.01236.255-0.169-0.1690.0000.0000.0000.000
174A198ALA0-0.023-0.01238.4050.2190.2190.0000.0000.0000.000
175A199ILE0-0.010-0.00635.331-0.264-0.2640.0000.0000.0000.000
176A200GLY00.0170.00937.2750.1860.1860.0000.0000.0000.000
177A201GLN0-0.0110.00638.7400.2070.2070.0000.0000.0000.000
178A202LYS10.9870.98440.1746.8236.8230.0000.0000.0000.000
179A203ALA00.0740.03439.6360.0600.0600.0000.0000.0000.000
180A204SER0-0.0020.00341.4260.0070.0070.0000.0000.0000.000
181A205SER00.015-0.01044.6280.0690.0690.0000.0000.0000.000
182A206VAL00.0490.02240.4680.0930.0930.0000.0000.0000.000
183A207ALA00.0270.01743.7270.0500.0500.0000.0000.0000.000
184A208GLN0-0.023-0.00845.1260.0370.0370.0000.0000.0000.000
185A209VAL00.0120.02045.9810.1350.1350.0000.0000.0000.000
186A210VAL00.0330.00542.6210.0630.0630.0000.0000.0000.000
187A211THR0-0.054-0.01945.9590.0060.0060.0000.0000.0000.000
188A212ASN0-0.032-0.02549.0610.1780.1780.0000.0000.0000.000
189A213PHE00.018-0.00146.0900.0930.0930.0000.0000.0000.000
190A214GLN0-0.027-0.01945.970-0.086-0.0860.0000.0000.0000.000
191A215GLU-1-0.891-0.94849.722-5.876-5.8760.0000.0000.0000.000
192A216ARG10.8270.91552.6565.9255.9250.0000.0000.0000.000
193A217GLY00.0420.03251.2840.0270.0270.0000.0000.0000.000
194A218ALA00.0470.01949.634-0.119-0.1190.0000.0000.0000.000
195A219MET0-0.078-0.02443.751-0.154-0.1540.0000.0000.0000.000
196A220GLU-1-0.925-0.96044.771-6.672-6.6720.0000.0000.0000.000
197A221TYR0-0.043-0.02544.774-0.068-0.0680.0000.0000.0000.000
198A222THR0-0.028-0.03043.172-0.046-0.0460.0000.0000.0000.000
199A223ILE0-0.0290.00136.602-0.085-0.0850.0000.0000.0000.000
200A224VAL0-0.006-0.01039.0610.1280.1280.0000.0000.0000.000
201A225VAL0-0.0150.00733.563-0.177-0.1770.0000.0000.0000.000
202A226ALA00.002-0.00535.6240.1970.1970.0000.0000.0000.000
203A227GLU-1-0.767-0.88731.805-9.635-9.6350.0000.0000.0000.000
204A228THR0-0.023-0.02134.7530.1860.1860.0000.0000.0000.000
205A229ALA0-0.036-0.00235.488-0.230-0.2300.0000.0000.0000.000
206A230ASP-1-0.918-0.95935.486-8.214-8.2140.0000.0000.0000.000
207A231SER0-0.060-0.02731.427-0.309-0.3090.0000.0000.0000.000
208A232PRO00.0820.04327.3170.1740.1740.0000.0000.0000.000
209A233ALA00.0430.00829.446-0.085-0.0850.0000.0000.0000.000
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