FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: YYVR2

Calculation Name: 5HAN-AB-Xray434

Preferred Name:

Target Type:

Ligand Name: 2-carboxyarabinitol-1,5-diphosphate

ligand 3-letter code: CAP

PDB ID: 5HAN

Chain ID: AB

ChEMBL ID:

UniProt ID: Q6N0W9

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: M. Fujii, S. Tanaka, Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand, Int. J. Mol. Sci. 2022, 23(19), 11347.

DOI: 10.3390/ijms231911347

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Manual
Number of fragment 915
LigandResidueName CAP
LigandFragmentNumber 914
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -27455767.57809
FMO2-HF: Nuclear repulsion 27097923.935126
FMO2-HF: Total energy -357843.642964
FMO2-MP2: Total energy -358876.495053


3D Structure
Snapshot
 
Ligand structure

CAP

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.
-858.603-847.567165.412-88.911-87.527-0.678


Interactive mode: IFIE and PIEDA for fragment #914(A:500:CAP)


Summations of interaction energy for fragment #914(A:500:CAP)
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.
-858.603-847.567165.412-88.911-87.5270.678
Interaction energy analysis for fragmet #914(A:500:CAP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -4 / q_Mulliken : -3.195 / q_NPA : -3.603
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].
165A165ILE00.0100.0042.270-10.542-8.8596.289-2.950-5.0220.014
166A166ILE00.0050.0045.1681.9392.065-0.001-0.003-0.1210.000
167A167LYS10.8790.9382.130-238.803-236.4918.118-4.397-6.0320.064
169A169LYS10.7940.8794.039-165.058-163.4970.001-0.926-0.6360.003
192A192KCX-1-0.518-0.8161.805173.192169.56321.306-8.687-8.990-0.094
194A194ASP00.1810.0274.0935.9406.102-0.001-0.053-0.1070.000
195A195GLU00.098-0.0623.841-15.073-14.725-0.001-0.082-0.2650.000
289A288HIS00.2810.1651.8596.7563.75713.882-5.937-4.946-0.051
290A289ARG10.8170.8781.784-284.038-281.63419.465-12.631-9.2370.175
291A290ALA00.0160.0184.6280.7740.865-0.001-0.014-0.0760.000
293A292HIS00.0280.0443.478-34.204-32.7200.042-0.742-0.7840.006
323A322HIS00.0370.0451.811-63.278-61.37613.194-8.143-6.9530.106
324A323THR0-0.014-0.0124.594-4.723-4.532-0.001-0.029-0.1610.000
325A324GLY00.0320.0263.160-11.726-9.8370.154-1.003-1.0400.009
326A325THR0-0.019-0.0164.074-26.222-25.9020.006-0.125-0.2010.001
331A330LYS10.7280.8521.863-279.695-279.95612.238-6.631-5.3450.079
332A331MET0-0.028-0.0042.449-23.897-20.3981.667-1.804-3.3620.019
333A332GLU-1-0.834-0.8735.77483.61583.672-0.001-0.002-0.0530.000
369A368ILE0-0.027-0.0165.05217.43817.656-0.001-0.005-0.2120.000
370A369SER00.0550.0032.031-26.647-21.9237.091-5.691-6.1230.033
371A370GLY00.0590.0332.2428.99812.7294.189-3.495-4.4240.014
372A371GLY0-0.026-0.0161.845-53.649-56.44110.487-3.225-4.4700.068
373A372MET0-0.032-0.0043.577-35.619-34.7630.045-0.293-0.6070.007
374A373ASN00.034-0.0094.8383.6403.787-0.001-0.005-0.1410.000
393A392THR0-0.043-0.0143.896-14.102-13.879-0.001-0.029-0.1930.000
394A393ALA00.0150.0062.94115.74317.8600.262-1.146-1.2330.010
395A394GLY00.0130.0201.893-46.945-47.2099.770-5.672-3.8350.078
396A395GLY00.030-0.0091.844-53.587-56.4269.906-3.590-3.4780.053
397A396GLY0-0.034-0.0173.730-31.375-30.5820.031-0.362-0.4610.004
506B49GLU-1-0.775-0.8915.560180.535180.547-0.001-0.0160.0050.000
511B54THR0-0.038-0.0481.655-16.057-22.76819.063-8.402-3.9500.069
512B55ASN0-0.012-0.0164.236-5.261-4.7400.003-0.157-0.3670.000
513B56VAL0-0.0190.0004.937-14.107-13.998-0.001-0.002-0.1050.000
569B112ASN00.099-0.0042.006-8.901-9.9408.215-2.654-4.5220.011
570B113ASN0-0.014-0.0194.7734.0454.135-0.001-0.008-0.0800.000
1A1MET0-0.003-0.01440.334-0.055-0.0550.0000.0000.0000.000
2A2ASP-1-0.833-0.87739.90129.28129.2810.0000.0000.0000.000
3A3GLN0-0.001-0.02037.236-0.759-0.7590.0000.0000.0000.000
4A4SER0-0.013-0.05238.4310.2770.2770.0000.0000.0000.000
5A5ASN0-0.017-0.01639.4620.3330.3330.0000.0000.0000.000
6A6ARG10.7770.89339.262-29.743-29.7430.0000.0000.0000.000
7A7TYR0-0.005-0.01535.088-0.112-0.1120.0000.0000.0000.000
8A8ALA0-0.0090.00635.3971.1401.1400.0000.0000.0000.000
9A9ASN0-0.004-0.01236.673-1.119-1.1190.0000.0000.0000.000
10A10LEU00.0170.00735.2270.4060.4060.0000.0000.0000.000
11A11ASN0-0.045-0.00937.723-0.200-0.2000.0000.0000.0000.000
12A12LEU0-0.041-0.00436.058-0.359-0.3590.0000.0000.0000.000
13A13LYS10.9971.00036.477-28.064-28.0640.0000.0000.0000.000
14A14GLU-1-0.714-0.86229.06839.57439.5740.0000.0000.0000.000
15A15SER00.014-0.00232.7650.3990.3990.0000.0000.0000.000
16A16GLU-1-0.958-0.98534.39829.11329.1130.0000.0000.0000.000
17A17LEU0-0.0170.00032.551-0.186-0.1860.0000.0000.0000.000
18A18ILE0-0.027-0.00729.2120.2560.2560.0000.0000.0000.000
19A19ALA0-0.046-0.02231.9090.0500.0500.0000.0000.0000.000
20A20GLY0-0.0110.00235.070-0.355-0.3550.0000.0000.0000.000
21A21GLY0-0.010-0.00432.116-0.315-0.3150.0000.0000.0000.000
22A22ARG10.8250.90132.625-32.190-32.1900.0000.0000.0000.000
23A23HIS00.0610.02130.761-0.006-0.0060.0000.0000.0000.000
24A24VAL00.0020.01024.3620.5820.5820.0000.0000.0000.000
25A25LEU0-0.0420.00425.974-1.020-1.0200.0000.0000.0000.000
26A26CYS0-0.031-0.00322.8932.0512.0510.0000.0000.0000.000
27A27ALA00.0420.03722.409-1.861-1.8610.0000.0000.0000.000
28A28TYR00.000-0.03221.6112.2962.2960.0000.0000.0000.000
29A29ILE0-0.0070.01021.097-1.478-1.4780.0000.0000.0000.000
30A30MET0-0.041-0.02922.7201.3001.3000.0000.0000.0000.000
31A31LYS10.9370.97925.495-41.013-41.0130.0000.0000.0000.000
32A32PRO00.0370.01927.8130.6410.6410.0000.0000.0000.000
33A33LYS10.8330.93729.501-38.105-38.1050.0000.0000.0000.000
34A34ALA00.000-0.01831.744-0.928-0.9280.0000.0000.0000.000
35A35GLY0-0.014-0.01034.9480.0540.0540.0000.0000.0000.000
36A36PHE00.0000.00434.551-0.532-0.5320.0000.0000.0000.000
37A37GLY00.0230.02636.549-0.745-0.7450.0000.0000.0000.000
38A38ASN00.0370.01636.1241.1241.1240.0000.0000.0000.000
39A39PHE00.0680.03228.8530.2130.2130.0000.0000.0000.000
40A40ILE00.0320.01233.5060.6770.6770.0000.0000.0000.000
41A41GLN0-0.008-0.00635.6920.5570.5570.0000.0000.0000.000
42A42THR00.0050.00030.9970.0830.0830.0000.0000.0000.000
43A43ALA00.004-0.00830.9230.7940.7940.0000.0000.0000.000
44A44ALA0-0.027-0.00531.8620.5010.5010.0000.0000.0000.000
45A45HIS10.7650.87133.707-34.133-34.1330.0000.0000.0000.000
46A46PHE00.0510.00824.1030.1500.1500.0000.0000.0000.000
47A47ALA00.0140.01129.6170.8100.8100.0000.0000.0000.000
48A48ALA00.0080.02331.1510.1340.1340.0000.0000.0000.000
49A49GLU-1-0.771-0.88730.08834.48834.4880.0000.0000.0000.000
50A50SER0-0.0320.00327.2061.5251.5250.0000.0000.0000.000
51A51SER0-0.044-0.04628.7380.0380.0380.0000.0000.0000.000
52A52THR0-0.012-0.02931.4760.0430.0430.0000.0000.0000.000
53A53GLY0-0.012-0.00234.454-1.002-1.0020.0000.0000.0000.000
54A54THR0-0.028-0.04234.6480.8720.8720.0000.0000.0000.000
55A55ASN0-0.020-0.01636.025-0.125-0.1250.0000.0000.0000.000
56A56VAL0-0.031-0.00437.476-0.439-0.4390.0000.0000.0000.000
57A57GLU-1-0.939-0.96540.79025.67125.6710.0000.0000.0000.000
58A58VAL0-0.007-0.01241.112-0.134-0.1340.0000.0000.0000.000
59A59PHE00.016-0.00343.836-0.013-0.0130.0000.0000.0000.000
60A60THR0-0.026-0.04142.818-0.439-0.4390.0000.0000.0000.000
61A61THR0-0.070-0.02742.0330.5400.5400.0000.0000.0000.000
62A62ASP-1-0.828-0.90543.65426.17826.1780.0000.0000.0000.000
63A63ASP-1-0.865-0.96243.81925.44525.4450.0000.0000.0000.000
64A64PHE0-0.100-0.04839.5910.1980.1980.0000.0000.0000.000
65A65THR0-0.012-0.02838.8410.8180.8180.0000.0000.0000.000
66A66ARG10.9330.97138.973-25.710-25.7100.0000.0000.0000.000
67A67GLY0-0.0230.00739.6120.3710.3710.0000.0000.0000.000
68A68VAL0-0.049-0.02135.5000.4440.4440.0000.0000.0000.000
69A69ASP-1-0.715-0.81834.65531.28531.2850.0000.0000.0000.000
70A70ALA0-0.003-0.00730.5090.1710.1710.0000.0000.0000.000
71A71LEU0-0.045-0.02232.545-0.687-0.6870.0000.0000.0000.000
72A72VAL00.007-0.00231.5470.9810.9810.0000.0000.0000.000
73A73TYR0-0.038-0.03828.820-0.820-0.8200.0000.0000.0000.000
74A74GLU-1-0.870-0.94530.49436.69236.6920.0000.0000.0000.000
75A75VAL0-0.041-0.02730.9240.9720.9720.0000.0000.0000.000
76A76ASP-1-0.834-0.91529.74336.10936.1090.0000.0000.0000.000
77A77GLU-1-0.931-0.96630.04934.31934.3190.0000.0000.0000.000
78A78ALA0-0.033-0.00730.8920.6330.6330.0000.0000.0000.000
79A79ASN0-0.060-0.03326.8341.2141.2140.0000.0000.0000.000
80A80SER0-0.068-0.03225.7581.8771.8770.0000.0000.0000.000
81A81LEU0-0.0160.00824.7601.5121.5120.0000.0000.0000.000
82A82MET00.0040.01326.251-2.326-2.3260.0000.0000.0000.000
83A83LYS10.8240.91726.339-38.637-38.6370.0000.0000.0000.000
84A84ILE0-0.003-0.00627.234-1.478-1.4780.0000.0000.0000.000
85A85ALA0-0.0110.00027.8891.2661.2660.0000.0000.0000.000
86A86TYR00.019-0.03125.662-1.287-1.2870.0000.0000.0000.000
87A87PRO00.0310.03029.8510.6810.6810.0000.0000.0000.000
88A88ILE00.013-0.00928.9570.5740.5740.0000.0000.0000.000
89A89GLU-1-0.922-0.96530.67433.14833.1480.0000.0000.0000.000
90A90LEU0-0.031-0.00430.183-0.276-0.2760.0000.0000.0000.000
91A91PHE0-0.027-0.00125.2070.4150.4150.0000.0000.0000.000
92A92ASP-1-0.726-0.88127.48036.57636.5760.0000.0000.0000.000
93A93ARG10.8220.91027.619-35.638-35.6380.0000.0000.0000.000
94A94ASN0-0.027-0.01426.122-0.500-0.5000.0000.0000.0000.000
95A95VAL0-0.049-0.04629.913-0.996-0.9960.0000.0000.0000.000
96A96ILE0-0.070-0.02428.877-1.029-1.0290.0000.0000.0000.000
97A97ASP-1-0.766-0.88728.46639.46739.4670.0000.0000.0000.000
98A98GLY0-0.019-0.00231.663-0.016-0.0160.0000.0000.0000.000
99A99ARG10.8270.92226.545-38.400-38.4000.0000.0000.0000.000
100A100ALA0-0.013-0.01224.628-0.695-0.6950.0000.0000.0000.000
101A101MET0-0.0220.01822.6570.9370.9370.0000.0000.0000.000
102A102ILE0-0.002-0.01916.938-0.846-0.8460.0000.0000.0000.000
103A103ALA00.0120.00520.1450.2590.2590.0000.0000.0000.000
104A104SER00.0250.04121.071-0.985-0.9850.0000.0000.0000.000
105A105PHE00.004-0.01118.383-0.974-0.9740.0000.0000.0000.000
106A106LEU00.0090.00316.220-0.119-0.1190.0000.0000.0000.000
107A107THR0-0.0060.00420.3050.3900.3900.0000.0000.0000.000
108A108LEU0-0.021-0.00723.365-0.869-0.8690.0000.0000.0000.000
109A109THR0-0.012-0.01221.5290.2660.2660.0000.0000.0000.000
110A110ILE0-0.053-0.01417.9410.3800.3800.0000.0000.0000.000
111A111GLY00.1020.05020.4121.8121.8120.0000.0000.0000.000
112A112ASN00.0740.00022.8621.8761.8760.0000.0000.0000.000
113A113ASN0-0.027-0.02623.5611.2351.2350.0000.0000.0000.000
114A114GLN00.0180.00620.0182.0332.0330.0000.0000.0000.000
115A115GLY00.0090.00123.2851.1111.1110.0000.0000.0000.000
116A116MET0-0.041-0.00325.981-1.076-1.0760.0000.0000.0000.000
117A117GLY00.0450.02928.7760.6980.6980.0000.0000.0000.000
118A118ASP-1-0.830-0.91231.27535.10235.1020.0000.0000.0000.000
119A119VAL0-0.027-0.01226.292-0.217-0.2170.0000.0000.0000.000
120A120GLU-1-0.917-0.96426.39941.34841.3480.0000.0000.0000.000
121A121TYR0-0.040-0.03922.1001.5361.5360.0000.0000.0000.000
122A122ALA00.0500.01422.259-1.710-1.7100.0000.0000.0000.000
123A123LYS10.8100.95113.235-70.282-70.2820.0000.0000.0000.000
124A124MET00.0030.00318.077-1.127-1.1270.0000.0000.0000.000
125A125TYR0-0.031-0.04117.0264.0204.0200.0000.0000.0000.000
126A126ASP-1-0.763-0.89317.43656.29756.2970.0000.0000.0000.000
127A127PHE00.008-0.00916.484-1.639-1.6390.0000.0000.0000.000
128A128TYR00.0110.02921.3161.0791.0790.0000.0000.0000.000
129A129VAL00.0130.00421.977-0.949-0.9490.0000.0000.0000.000
130A130PRO00.0330.03424.686-0.082-0.0820.0000.0000.0000.000
131A131PRO00.0790.02027.6730.5250.5250.0000.0000.0000.000
132A132ALA0-0.051-0.03429.1780.2360.2360.0000.0000.0000.000
133A133TYR00.0250.01024.0710.0080.0080.0000.0000.0000.000
134A134LEU00.0380.02122.7290.6660.6660.0000.0000.0000.000
135A135LYS10.9420.96624.835-34.950-34.9500.0000.0000.0000.000
136A136LEU0-0.099-0.03827.018-0.711-0.7110.0000.0000.0000.000
137A137PHE00.0170.00521.0940.0840.0840.0000.0000.0000.000
138A138ASP-1-0.816-0.88620.89147.35647.3560.0000.0000.0000.000
139A139GLY00.0150.01619.681-1.103-1.1030.0000.0000.0000.000
140A140PRO0-0.0180.00016.884-0.706-0.7060.0000.0000.0000.000
141A141SER0-0.033-0.02519.077-1.970-1.9700.0000.0000.0000.000
142A142THR0-0.059-0.01018.573-2.017-2.0170.0000.0000.0000.000
143A143THR00.010-0.00417.2472.3632.3630.0000.0000.0000.000
144A144ILE00.1020.03814.428-0.521-0.5210.0000.0000.0000.000
145A145LYS10.9340.97617.227-48.596-48.5960.0000.0000.0000.000
146A146ASP-1-0.832-0.91120.28650.19150.1910.0000.0000.0000.000
147A147LEU00.0330.02714.788-0.817-0.8170.0000.0000.0000.000
148A148TRP0-0.032-0.01817.917-2.625-2.6250.0000.0000.0000.000
149A149ARG10.8610.91721.135-48.852-48.8520.0000.0000.0000.000
150A150VAL0-0.0150.00820.277-1.689-1.6890.0000.0000.0000.000
151A151LEU0-0.050-0.02617.157-0.595-0.5950.0000.0000.0000.000
152A152GLY0-0.0060.01921.640-0.838-0.8380.0000.0000.0000.000
153A153ARG10.7940.90417.500-62.865-62.8650.0000.0000.0000.000
154A154PRO0-0.010-0.00924.437-0.862-0.8620.0000.0000.0000.000
155A155VAL00.024-0.00323.7551.6941.6940.0000.0000.0000.000
156A156ILE00.003-0.00523.5021.0301.0300.0000.0000.0000.000
157A157ASN0-0.041-0.02221.4490.8200.8200.0000.0000.0000.000
158A158GLY00.0650.02721.512-0.964-0.9640.0000.0000.0000.000
159A159GLY0-0.0060.00519.4210.0090.0090.0000.0000.0000.000
160A160PHE00.0590.01910.9361.3571.3570.0000.0000.0000.000
161A161ILE0-0.039-0.00713.083-3.452-3.4520.0000.0000.0000.000
162A162VAL0-0.0170.00311.3366.4026.4020.0000.0000.0000.000
163A163GLY00.0650.0189.433-5.348-5.3480.0000.0000.0000.000
164A164THR0-0.042-0.0406.0897.5537.5530.0000.0000.0000.000
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