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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: 22NGR

Calculation Name: 5IU0-ABIJ-Xray434

Preferred Name:

Target Type:

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

ligand 3-letter code: CAP

PDB ID: 5IU0

Chain ID: ABIJ

ChEMBL ID:

UniProt ID: O03042

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


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 1175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -41915686.310602
FMO2-HF: Nuclear repulsion 41448786.021256
FMO2-HF: Total energy -466900.289346
FMO2-MP2: Total energy -468257.988917


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.
-815.099-817.168179.290-92.248-84.976-0.670


Interactive mode: IFIE and PIEDA for fragment #1174(A:502:CAP)


Summations of interaction energy for fragment #1174(A:502: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.
-815.099-817.168179.29-92.248-84.9760.67
Interaction energy analysis for fragmet #1174(A:502:CAP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -4 / q_Mulliken : -3.118 / q_NPA : -3.510
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].
160A172CYS0-0.059-0.0275.1642.2972.445-0.001-0.003-0.1430.000
161A173THR00.1360.0441.854-19.790-21.23314.223-7.041-5.739-0.028
162A174ILE0-0.024-0.0103.9347.3177.677-0.001-0.135-0.2240.000
163A175LYS10.8400.9192.311-225.793-221.5375.169-3.946-5.4790.057
165A177LYS10.7490.8834.515-160.272-159.887-0.001-0.130-0.2550.000
189A201KCX-1-0.500-0.8011.551176.561163.60834.447-13.412-8.081-0.107
191A203ASP00.2100.0494.3496.0436.183-0.001-0.039-0.1000.000
192A204GLU00.187-0.0094.122-16.825-16.498-0.001-0.074-0.2530.000
283A294HIS00.5940.4971.969-6.741-7.4717.260-2.546-3.9840.012
284A295ARG10.7690.8521.792-277.877-277.85122.700-13.334-9.3930.182
285A296ALA00.0340.0125.1680.7890.852-0.001-0.008-0.0540.000
287A298HIS10.8490.8963.440-172.719-171.1390.047-0.776-0.8510.007
316A327HIS00.1890.1941.753-58.577-58.62316.785-8.947-7.7930.100
317A328ALA0-0.001-0.0134.762-7.672-7.523-0.001-0.020-0.1280.000
318A329GLY00.0300.0173.536-13.083-11.9840.029-0.565-0.5640.004
319A330THR00.0430.0244.528-20.672-20.4680.000-0.030-0.1730.000
323A334LYS10.7920.8841.995-268.356-265.4227.057-5.331-4.6600.071
324A335LEU0-0.012-0.0032.786-20.390-16.9551.094-1.897-2.6330.019
325A336GLU-1-0.833-0.9285.59682.91482.971-0.001-0.001-0.0550.000
367A378ALA00.0140.0204.87119.38619.573-0.001-0.006-0.1800.000
368A379SER0-0.009-0.0401.874-32.180-29.50910.619-6.647-6.6430.036
369A380GLY00.0750.0352.2429.21612.6046.184-4.514-5.0580.023
370A381GLY0-0.037-0.0191.982-44.932-46.3025.686-1.014-3.3020.051
371A382ILE0-0.063-0.0133.980-28.417-27.8460.014-0.253-0.3320.002
390A401GLN00.002-0.0043.900-22.313-22.050-0.001-0.027-0.2360.000
391A402PHE00.0340.0033.70118.52419.3440.018-0.305-0.5330.001
392A403GLY00.0530.0231.924-41.757-41.7239.486-5.526-3.9940.070
393A404GLY00.022-0.0181.693-54.905-65.03318.329-4.143-4.0580.066
394A405GLY0-0.014-0.0123.650-30.802-29.9050.039-0.466-0.4700.006
517B65THR0-0.034-0.0431.708-14.925-19.70616.730-7.823-4.1260.073
518B66TRP00.0270.0102.411-47.911-45.1892.518-2.165-3.0740.030
575B123ASN00.0910.0092.7726.2588.8250.867-1.120-2.314-0.005
576B124VAL00.0280.0125.1154.1384.237-0.001-0.004-0.0940.000
1A13PHE0-0.036-0.02247.574-0.016-0.0160.0000.0000.0000.000
2A14LYS10.9400.98048.522-24.680-24.6800.0000.0000.0000.000
3A15ALA00.0310.01848.5770.4410.4410.0000.0000.0000.000
4A16GLY00.0690.03047.439-0.362-0.3620.0000.0000.0000.000
5A17VAL0-0.0010.00542.1600.2850.2850.0000.0000.0000.000
6A18LYS10.8810.94243.280-27.518-27.5180.0000.0000.0000.000
7A19GLU-1-0.856-0.92741.12228.29928.2990.0000.0000.0000.000
8A20TYR0-0.033-0.04335.661-0.443-0.4430.0000.0000.0000.000
9A21LYS10.9180.93138.530-28.640-28.6400.0000.0000.0000.000
10A22LEU0-0.070-0.02639.407-0.369-0.3690.0000.0000.0000.000
11A23THR0-0.059-0.02139.714-0.611-0.6110.0000.0000.0000.000
12A24TYR00.008-0.00935.325-0.199-0.1990.0000.0000.0000.000
13A25TYR00.0270.02735.6531.0921.0920.0000.0000.0000.000
14A26THR0-0.073-0.06336.966-0.784-0.7840.0000.0000.0000.000
15A27PRO00.0050.01937.1820.5110.5110.0000.0000.0000.000
16A28GLU-1-0.878-0.93538.25628.54728.5470.0000.0000.0000.000
17A29TYR0-0.159-0.08634.143-0.690-0.6900.0000.0000.0000.000
18A30GLU-1-0.904-0.95337.13729.00629.0060.0000.0000.0000.000
19A31THR0-0.070-0.03531.7050.2450.2450.0000.0000.0000.000
20A32LYS10.9570.98134.146-31.022-31.0220.0000.0000.0000.000
21A33ASP-1-0.877-0.94032.34034.92134.9210.0000.0000.0000.000
22A34THR0-0.049-0.03931.4600.5110.5110.0000.0000.0000.000
23A35ASP-1-0.817-0.89230.56635.02435.0240.0000.0000.0000.000
24A36ILE00.0030.01024.4460.9120.9120.0000.0000.0000.000
25A37LEU0-0.049-0.00925.879-1.062-1.0620.0000.0000.0000.000
26A38ALA00.0400.02523.4632.0902.0900.0000.0000.0000.000
27A39ALA00.0090.02022.644-1.901-1.9010.0000.0000.0000.000
28A40PHE00.011-0.00522.0912.6072.6070.0000.0000.0000.000
29A41ARG10.8480.92719.903-52.999-52.9990.0000.0000.0000.000
30A42VAL00.016-0.00223.5210.9900.9900.0000.0000.0000.000
31A43THR00.0310.01725.137-0.414-0.4140.0000.0000.0000.000
32A44PRO00.0140.00627.6360.3950.3950.0000.0000.0000.000
33A45GLN00.0090.00330.999-0.189-0.1890.0000.0000.0000.000
34A46PRO00.015-0.00832.831-0.649-0.6490.0000.0000.0000.000
35A47GLY00.0020.00735.742-0.457-0.4570.0000.0000.0000.000
36A48VAL0-0.059-0.01334.548-0.753-0.7530.0000.0000.0000.000
37A49PRO00.0110.00835.5890.5850.5850.0000.0000.0000.000
38A50PRO00.0840.03433.4770.5050.5050.0000.0000.0000.000
39A51GLU-1-0.885-0.95934.03831.30331.3030.0000.0000.0000.000
40A52GLU-1-0.773-0.89036.14030.43830.4380.0000.0000.0000.000
41A53ALA0-0.0060.00331.5860.3820.3820.0000.0000.0000.000
42A54GLY00.0250.00430.9210.9180.9180.0000.0000.0000.000
43A55ALA0-0.026-0.00631.8870.3820.3820.0000.0000.0000.000
44A56ALA0-0.008-0.00432.714-0.009-0.0090.0000.0000.0000.000
45A57VAL0-0.0060.00527.0150.3650.3650.0000.0000.0000.000
46A58ALA00.0290.01529.5050.4540.4540.0000.0000.0000.000
47A59ALA0-0.0180.01131.175-0.124-0.1240.0000.0000.0000.000
48A60GLU-1-0.787-0.88431.01933.69233.6920.0000.0000.0000.000
49A61SER00.0410.05327.0620.9050.9050.0000.0000.0000.000
50A62SER0-0.062-0.06828.8440.0670.0670.0000.0000.0000.000
51A63THR0-0.025-0.02031.590-0.361-0.3610.0000.0000.0000.000
52A64GLY0-0.0140.00534.679-0.890-0.8900.0000.0000.0000.000
53A65THR0-0.023-0.05934.9240.9140.9140.0000.0000.0000.000
54A66TRP00.0150.00336.963-0.629-0.6290.0000.0000.0000.000
55A67THR00.003-0.00738.682-0.767-0.7670.0000.0000.0000.000
56A68THR0-0.089-0.03141.8950.4260.4260.0000.0000.0000.000
57A69VAL00.0460.01841.523-0.434-0.4340.0000.0000.0000.000
58A70TRP0-0.027-0.02144.441-0.120-0.1200.0000.0000.0000.000
59A71THR0-0.044-0.07142.731-0.383-0.3830.0000.0000.0000.000
60A72ASP-1-0.830-0.92041.95228.13828.1380.0000.0000.0000.000
61A73GLY0-0.059-0.02544.109-0.004-0.0040.0000.0000.0000.000
62A74LEU0-0.091-0.03745.598-0.427-0.4270.0000.0000.0000.000
63A75THR0-0.043-0.01441.310-0.058-0.0580.0000.0000.0000.000
64A76SER0-0.004-0.00242.475-0.260-0.2600.0000.0000.0000.000
65A77LEU00.0610.01639.0050.6040.6040.0000.0000.0000.000
66A78ASP-1-0.936-0.95239.46127.60127.6010.0000.0000.0000.000
67A79ARG10.8960.93539.668-28.028-28.0280.0000.0000.0000.000
68A80TYR0-0.029-0.01036.3180.5470.5470.0000.0000.0000.000
69A81LYS10.8570.94234.950-28.344-28.3440.0000.0000.0000.000
70A82GLY00.0560.02032.0870.2240.2240.0000.0000.0000.000
71A83ARG10.8500.93232.628-31.365-31.3650.0000.0000.0000.000
72A84CYS00.0180.01531.9891.2021.2020.0000.0000.0000.000
73A85TYR00.005-0.00929.649-0.548-0.5480.0000.0000.0000.000
74A86HIS00.0260.01630.985-1.248-1.2480.0000.0000.0000.000
75A87ILE00.0220.01631.6351.1191.1190.0000.0000.0000.000
76A88GLU-1-0.854-0.92027.22640.64940.6490.0000.0000.0000.000
77A89PRO00.005-0.00529.2801.3061.3060.0000.0000.0000.000
78A90VAL0-0.0050.02325.3120.6130.6130.0000.0000.0000.000
79A91PRO0-0.017-0.02327.131-0.815-0.8150.0000.0000.0000.000
80A92GLY0-0.028-0.01527.8951.1251.1250.0000.0000.0000.000
81A93GLU-1-0.940-0.96326.25343.12443.1240.0000.0000.0000.000
82A94GLU-1-0.974-0.97129.39432.40532.4050.0000.0000.0000.000
83A95THR00.010-0.01431.185-0.338-0.3380.0000.0000.0000.000
84A96GLN0-0.0020.00523.6530.8200.8200.0000.0000.0000.000
85A97PHE0-0.020-0.02328.071-0.570-0.5700.0000.0000.0000.000
86A98ILE0-0.015-0.01123.6141.6181.6180.0000.0000.0000.000
87A99ALA00.0020.00726.834-1.763-1.7630.0000.0000.0000.000
88A100TYR0-0.043-0.02726.4212.1632.1630.0000.0000.0000.000
89A101VAL0-0.003-0.00527.664-1.648-1.6480.0000.0000.0000.000
90A102ALA0-0.016-0.00128.1581.1671.1670.0000.0000.0000.000
91A103TYR0-0.045-0.05726.279-0.725-0.7250.0000.0000.0000.000
92A104PRO00.0210.01130.3380.5620.5620.0000.0000.0000.000
93A105LEU00.0640.02329.7050.6870.6870.0000.0000.0000.000
94A106ASP-1-0.922-0.97331.02932.56532.5650.0000.0000.0000.000
95A107LEU0-0.077-0.03830.311-0.285-0.2850.0000.0000.0000.000
96A108PHE0-0.0080.00725.5490.6170.6170.0000.0000.0000.000
97A109GLU-1-0.801-0.88327.26037.93437.9340.0000.0000.0000.000
98A110GLU-1-0.794-0.89026.62337.60537.6050.0000.0000.0000.000
99A111GLY00.0410.03124.430-0.177-0.1770.0000.0000.0000.000
100A112SER0-0.018-0.00822.8862.3042.3040.0000.0000.0000.000
101A113VAL00.0470.02016.830-0.767-0.7670.0000.0000.0000.000
102A114THR0-0.0070.00320.1820.8900.8900.0000.0000.0000.000
103A115ASN0-0.003-0.00520.997-0.761-0.7610.0000.0000.0000.000
104A116MET0-0.0040.00619.313-1.110-1.1100.0000.0000.0000.000
105A117PHE0-0.026-0.03114.919-0.070-0.0700.0000.0000.0000.000
106A118THR00.0070.02420.7890.4140.4140.0000.0000.0000.000
107A119SER00.0130.01023.612-1.468-1.4680.0000.0000.0000.000
108A120ILE0-0.053-0.01022.357-0.561-0.5610.0000.0000.0000.000
109A121VAL0-0.010-0.02818.711-0.101-0.1010.0000.0000.0000.000
110A122GLY00.0070.02822.0080.8250.8250.0000.0000.0000.000
111A123ASN00.0860.00724.1001.4611.4610.0000.0000.0000.000
112A124VAL00.0180.00924.648-0.147-0.1470.0000.0000.0000.000
113A125PHE00.0270.01419.891-0.836-0.8360.0000.0000.0000.000
114A126GLY00.0270.01324.2820.5970.5970.0000.0000.0000.000
115A127PHE0-0.0140.00226.636-1.395-1.3950.0000.0000.0000.000
116A128LYS10.7960.89229.624-32.262-32.2620.0000.0000.0000.000
117A129ALA0-0.004-0.00132.1220.1050.1050.0000.0000.0000.000
118A130LEU0-0.030-0.01527.334-0.342-0.3420.0000.0000.0000.000
119A131ALA00.0070.00928.1750.0730.0730.0000.0000.0000.000
120A132ALA0-0.015-0.01122.8671.4211.4210.0000.0000.0000.000
121A133LEU0-0.021-0.00822.743-1.728-1.7280.0000.0000.0000.000
122A134ARG10.7720.88013.352-66.455-66.4550.0000.0000.0000.000
123A135LEU0-0.0220.00918.329-2.088-2.0880.0000.0000.0000.000
124A136GLU-1-0.782-0.90317.40963.32063.3200.0000.0000.0000.000
125A137ASP-1-0.796-0.91917.59258.79258.7920.0000.0000.0000.000
126A138LEU0-0.011-0.01418.922-1.958-1.9580.0000.0000.0000.000
127A139ARG10.8470.94621.055-38.513-38.5130.0000.0000.0000.000
128A140ILE00.025-0.00120.514-1.606-1.6060.0000.0000.0000.000
129A141PRO00.0070.02723.7800.0540.0540.0000.0000.0000.000
130A142PRO00.1160.03226.7480.5500.5500.0000.0000.0000.000
131A143ALA0-0.020-0.01528.2510.0010.0010.0000.0000.0000.000
132A144TYR0-0.005-0.01923.5100.0740.0740.0000.0000.0000.000
133A145THR00.0740.04222.8550.7390.7390.0000.0000.0000.000
134A146LYS10.9310.97024.904-38.777-38.7770.0000.0000.0000.000
135A147THR0-0.101-0.05426.349-0.557-0.5570.0000.0000.0000.000
136A148PHE00.0080.00221.3460.4190.4190.0000.0000.0000.000
137A149GLN0-0.035-0.02020.707-2.615-2.6150.0000.0000.0000.000
138A150GLY00.0410.02719.241-0.348-0.3480.0000.0000.0000.000
139A151PRO0-0.060-0.02516.6060.1630.1630.0000.0000.0000.000
140A152PRO0-0.023-0.00217.451-3.114-3.1140.0000.0000.0000.000
141A153HIS0-0.063-0.03519.048-5.582-5.5820.0000.0000.0000.000
142A154GLY00.0460.01817.981-2.130-2.1300.0000.0000.0000.000
143A155ILE0-0.051-0.02215.897-1.126-1.1260.0000.0000.0000.000
144A156GLN0-0.050-0.02818.4790.2230.2230.0000.0000.0000.000
145A157VAL00.0670.03322.038-0.565-0.5650.0000.0000.0000.000
146A158GLU-1-0.806-0.87515.21473.67873.6780.0000.0000.0000.000
147A159ARG10.8010.88017.709-62.865-62.8650.0000.0000.0000.000
148A160ASP-1-0.812-0.89021.02745.75345.7530.0000.0000.0000.000
149A161LYS10.8070.91521.504-50.592-50.5920.0000.0000.0000.000
150A162LEU0-0.032-0.03016.905-1.065-1.0650.0000.0000.0000.000
151A163ASN0-0.0070.00521.400-0.535-0.5350.0000.0000.0000.000
152A164LYS10.7580.88817.467-62.329-62.3290.0000.0000.0000.000
153A165TYR00.000-0.02821.4870.8430.8430.0000.0000.0000.000
154A166GLY00.0310.02922.213-0.011-0.0110.0000.0000.0000.000
155A167ARG10.7830.88015.516-67.184-67.1840.0000.0000.0000.000
156A168PRO0-0.0240.01413.776-0.248-0.2480.0000.0000.0000.000
157A169LEU0-0.019-0.00113.286-2.140-2.1400.0000.0000.0000.000
158A170LEU0-0.0060.00010.2865.9785.9780.0000.0000.0000.000
159A171GLY00.0350.0038.446-5.763-5.7630.0000.0000.0000.000
164A176PRO00.0530.0576.978-8.667-8.6670.0000.0000.0000.000
166A178LEU0-0.012-0.0057.457-6.067-6.0670.0000.0000.0000.000
167A179GLY00.0480.01910.994-0.072-0.0720.0000.0000.0000.000
168A180LEU0-0.042-0.00811.208-5.488-5.4880.0000.0000.0000.000
169A181SER00.0680.02914.392-0.349-0.3490.0000.0000.0000.000
170A182ALA00.0860.03316.0382.4472.4470.0000.0000.0000.000
171A183LYS10.9640.98717.028-46.892-46.8920.0000.0000.0000.000
172A184ASN0-0.014-0.02215.918-1.524-1.5240.0000.0000.0000.000
173A185TYR00.0920.0428.1802.0072.0070.0000.0000.0000.000
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