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: GN5V1

Calculation Name: 3ZXW-ABEF-Xray434

Preferred Name:

Target Type:

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

ligand 3-letter code: CAP

PDB ID: 3ZXW

Chain ID: ABEF

ChEMBL ID:

UniProt ID: Q8DIS5

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 1115
LigandResidueName CAP
LigandFragmentNumber 558
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -38639837.872432
FMO2-HF: Nuclear repulsion 38190097.860426
FMO2-HF: Total energy -449740.012007
FMO2-MP2: Total energy -451031.408331


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.
-313.556-329.158183.997-84.954-83.445-0.722


Interactive mode: IFIE and PIEDA for fragment #558(A:477:CAP)


Summations of interaction energy for fragment #558(A:477: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.
-313.556-329.158183.997-84.954-83.4450.722
Interaction energy analysis for fragmet #558(A:477:CAP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -4 / q_Mulliken : -3.262 / q_NPA : -3.619
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].
162A173THR00.0800.0032.029-13.718-10.6311.405-1.950-2.543-0.003
163A174ILE0-0.034-0.0184.6716.9277.081-0.001-0.008-0.1450.000
164A175LYS10.8480.9192.110-223.360-219.8566.031-4.011-5.5240.061
166A177LYS10.7760.8924.323-158.887-158.541-0.001-0.111-0.2350.000
189A201KCX-1-0.527-0.8251.636179.021167.36530.175-10.731-7.788-0.093
191A203ASP00.2190.0544.6306.0736.172-0.002-0.022-0.0750.000
192A204GLU00.144-0.0314.276-15.906-15.634-0.001-0.042-0.2290.000
283A294HIS00.0890.0151.944-6.300-6.7187.187-2.751-4.0190.016
284A295ARG10.7570.8411.650-280.455-286.25831.170-15.404-9.9630.191
285A296ALA00.0390.0144.9621.3901.487-0.001-0.012-0.0840.000
287A298HIS10.8450.8943.377-175.902-173.9290.063-0.990-1.0450.009
316A327HIS00.0530.0671.874-55.357-51.9879.885-6.732-6.5230.088
317A328THR0-0.003-0.0154.740-7.722-7.562-0.001-0.018-0.1410.000
318A329GLY00.0450.0243.422-11.521-10.2900.046-0.651-0.6270.005
319A330THR00.0110.0074.407-19.881-19.6620.000-0.042-0.1780.000
323A334LYS10.7880.8811.853-269.079-270.14513.094-6.566-5.4610.084
324A335LEU0-0.0140.0002.635-19.802-16.1991.213-1.802-3.0140.015
325A336GLU-1-0.813-0.9065.54785.75685.825-0.001-0.002-0.0670.000
326A337GLY00.0310.0035.56814.73014.859-0.001-0.003-0.1250.000
367A378ALA00.0260.0255.12716.77516.928-0.001-0.004-0.1480.000
368A379SER0-0.002-0.0292.084-26.644-21.6845.613-4.985-5.5880.025
369A380GLY00.0720.0332.15910.36312.5858.532-5.182-5.5720.021
370A381GLY0-0.026-0.0231.806-45.058-51.53811.463-1.034-3.9490.058
371A382ILE0-0.070-0.0113.773-31.266-30.4940.032-0.369-0.4350.004
390A401GLN00.0430.0074.301-23.216-23.064-0.001-0.011-0.1400.000
391A402PHE00.001-0.0083.56917.63018.6060.029-0.402-0.6040.002
392A403GLY00.0350.0261.783-41.175-45.90515.640-6.757-4.1540.077
393A404GLY00.050-0.0031.737-52.026-62.58516.019-1.552-3.9080.059
394A405GLY0-0.042-0.0213.647-31.524-30.7120.039-0.388-0.4630.006
607E60GLU-1-0.794-0.8995.098177.349177.382-0.001-0.017-0.0150.000
612E65THR0-0.037-0.0511.632-10.665-19.34621.137-8.471-3.9840.071
613E66TRP00.0070.0012.453-50.752-47.9162.904-2.378-3.3620.033
670E123ASN00.0840.0152.5426.3938.8522.333-1.548-3.244-0.007
671E124VAL00.0230.0174.8044.4844.587-0.001-0.008-0.0930.000
1A12GLY00.002-0.01653.162-0.196-0.1960.0000.0000.0000.000
2A13TYR0-0.042-0.02547.6900.4760.4760.0000.0000.0000.000
3A14GLN0-0.040-0.02050.197-0.533-0.5330.0000.0000.0000.000
4A15ALA00.0210.02048.7310.4390.4390.0000.0000.0000.000
5A16GLY00.0380.02047.621-0.311-0.3110.0000.0000.0000.000
6A17VAL00.003-0.00342.4280.2870.2870.0000.0000.0000.000
7A18LYS10.8960.95343.515-26.926-26.9260.0000.0000.0000.000
8A19ASP-1-0.900-0.94041.36828.19128.1910.0000.0000.0000.000
9A20TYR0-0.019-0.02435.787-0.325-0.3250.0000.0000.0000.000
10A21ARG10.9430.94938.631-28.832-28.8320.0000.0000.0000.000
11A22LEU0-0.064-0.02939.520-0.298-0.2980.0000.0000.0000.000
12A23THR0-0.039-0.01240.053-0.622-0.6220.0000.0000.0000.000
13A24TYR00.026-0.00135.369-0.125-0.1250.0000.0000.0000.000
14A25TYR0-0.0120.00435.7120.5820.5820.0000.0000.0000.000
15A26THR0-0.017-0.02737.042-0.796-0.7960.0000.0000.0000.000
16A27PRO00.0110.01637.4600.5070.5070.0000.0000.0000.000
17A28ASP-1-0.904-0.93938.54527.63527.6350.0000.0000.0000.000
18A29TYR0-0.123-0.07834.350-0.796-0.7960.0000.0000.0000.000
19A30THR0-0.014-0.01336.8680.4130.4130.0000.0000.0000.000
20A31PRO0-0.026-0.01232.077-0.334-0.3340.0000.0000.0000.000
21A32LYS10.9430.97934.191-31.471-31.4710.0000.0000.0000.000
22A33ASP-1-0.879-0.94432.05635.23635.2360.0000.0000.0000.000
23A34THR0-0.059-0.04731.1020.6470.6470.0000.0000.0000.000
24A35ASP-1-0.803-0.87530.84434.57034.5700.0000.0000.0000.000
25A36ILE0-0.0050.00024.5320.9730.9730.0000.0000.0000.000
26A37LEU0-0.046-0.01026.012-1.030-1.0300.0000.0000.0000.000
27A38ALA00.0270.02423.5762.1172.1170.0000.0000.0000.000
28A39ALA00.0150.02122.516-1.805-1.8050.0000.0000.0000.000
29A40PHE00.010-0.00822.1482.6522.6520.0000.0000.0000.000
30A41ARG10.8550.92019.347-53.820-53.8200.0000.0000.0000.000
31A42VAL00.008-0.00823.5010.9730.9730.0000.0000.0000.000
32A43THR00.0050.00825.549-0.016-0.0160.0000.0000.0000.000
33A44PRO00.0250.02027.5040.3140.3140.0000.0000.0000.000
34A45GLN0-0.018-0.01030.881-0.275-0.2750.0000.0000.0000.000
35A46PRO00.011-0.00933.025-0.572-0.5720.0000.0000.0000.000
36A47GLY0-0.020-0.00235.861-0.420-0.4200.0000.0000.0000.000
37A48VAL0-0.022-0.00135.014-0.798-0.7980.0000.0000.0000.000
38A49PRO0-0.011-0.00235.8730.5600.5600.0000.0000.0000.000
39A50PHE00.0720.02032.5460.5290.5290.0000.0000.0000.000
40A51GLU-1-0.895-0.95534.06131.30131.3010.0000.0000.0000.000
41A52GLU-1-0.768-0.89136.17330.37230.3720.0000.0000.0000.000
42A53ALA0-0.0160.00131.5420.3560.3560.0000.0000.0000.000
43A54ALA00.021-0.00630.9880.8870.8870.0000.0000.0000.000
44A55ALA0-0.0170.00331.8390.4830.4830.0000.0000.0000.000
45A56ALA00.0190.01332.830-0.041-0.0410.0000.0000.0000.000
46A57VAL00.0020.01027.0200.3320.3320.0000.0000.0000.000
47A58ALA00.0180.02629.5070.6220.6220.0000.0000.0000.000
48A59ALA00.0020.01931.233-0.067-0.0670.0000.0000.0000.000
49A60GLU-1-0.811-0.91530.82733.73633.7360.0000.0000.0000.000
50A61SER0-0.040-0.00727.0950.6360.6360.0000.0000.0000.000
51A62SER0-0.028-0.04228.9480.0520.0520.0000.0000.0000.000
52A63THR0-0.027-0.01631.701-0.290-0.2900.0000.0000.0000.000
53A64GLY0-0.0030.00734.772-0.851-0.8510.0000.0000.0000.000
54A65THR0-0.045-0.06535.0370.9040.9040.0000.0000.0000.000
55A66TRP00.009-0.00137.160-0.623-0.6230.0000.0000.0000.000
56A67THR0-0.009-0.00338.816-0.742-0.7420.0000.0000.0000.000
57A68THR0-0.046-0.01841.9810.4800.4800.0000.0000.0000.000
58A69VAL00.0330.01541.788-0.424-0.4240.0000.0000.0000.000
59A70TRP0-0.025-0.03444.702-0.169-0.1690.0000.0000.0000.000
60A71THR0-0.068-0.08642.908-0.331-0.3310.0000.0000.0000.000
61A72ASP-1-0.789-0.90941.83628.13428.1340.0000.0000.0000.000
62A73LEU0-0.063-0.03544.138-0.055-0.0550.0000.0000.0000.000
63A74LEU0-0.113-0.04146.048-0.461-0.4610.0000.0000.0000.000
64A75THR0-0.075-0.04241.624-0.102-0.1020.0000.0000.0000.000
65A76ASP-1-0.878-0.94043.23526.17326.1730.0000.0000.0000.000
66A77LEU00.0230.00039.2680.6280.6280.0000.0000.0000.000
67A78ASP-1-0.858-0.93239.69027.93427.9340.0000.0000.0000.000
68A79ARG10.8320.92039.638-27.453-27.4530.0000.0000.0000.000
69A80TYR0-0.040-0.01836.4450.2540.2540.0000.0000.0000.000
70A81LYS10.8390.93935.070-28.041-28.0410.0000.0000.0000.000
71A82GLY00.0530.02532.1250.2630.2630.0000.0000.0000.000
72A83CYS0-0.102-0.05132.786-0.632-0.6320.0000.0000.0000.000
73A84CYS0-0.0110.00631.7510.8040.8040.0000.0000.0000.000
74A85TYR00.011-0.01229.714-0.621-0.6210.0000.0000.0000.000
75A86ASP-1-0.888-0.94531.61634.52734.5270.0000.0000.0000.000
76A87ILE0-0.026-0.01331.5041.0261.0260.0000.0000.0000.000
77A88GLU-1-0.775-0.85827.81840.34340.3430.0000.0000.0000.000
78A89PRO0-0.022-0.02129.3631.2211.2210.0000.0000.0000.000
79A90LEU0-0.0030.00124.8720.3820.3820.0000.0000.0000.000
80A91PRO0-0.003-0.00428.9070.2230.2230.0000.0000.0000.000
81A92GLY0-0.051-0.02028.064-0.499-0.4990.0000.0000.0000.000
82A93GLU-1-0.940-0.96723.51448.73648.7360.0000.0000.0000.000
83A94ASP-1-0.948-0.96926.88536.78936.7890.0000.0000.0000.000
84A95ASN0-0.037-0.02128.194-0.100-0.1000.0000.0000.0000.000
85A96GLN00.0580.01722.8471.0391.0390.0000.0000.0000.000
86A97PHE0-0.024-0.01627.676-1.116-1.1160.0000.0000.0000.000
87A98ILE0-0.0070.00523.5331.5681.5680.0000.0000.0000.000
88A99ALA00.0050.00626.906-1.715-1.7150.0000.0000.0000.000
89A100TYR0-0.030-0.02526.1022.4452.4450.0000.0000.0000.000
90A101ILE0-0.016-0.01327.736-1.632-1.6320.0000.0000.0000.000
91A102ALA0-0.0060.00228.3761.1951.1950.0000.0000.0000.000
92A103TYR0-0.032-0.04426.495-0.476-0.4760.0000.0000.0000.000
93A104PRO00.0490.02830.5440.6040.6040.0000.0000.0000.000
94A105LEU00.028-0.00129.8870.6350.6350.0000.0000.0000.000
95A106ASP-1-0.930-0.97131.27832.38032.3800.0000.0000.0000.000
96A107LEU0-0.068-0.03330.569-0.383-0.3830.0000.0000.0000.000
97A108PHE0-0.0170.00025.9020.7320.7320.0000.0000.0000.000
98A109GLU-1-0.794-0.87627.37737.97637.9760.0000.0000.0000.000
99A110GLU-1-0.798-0.89226.83937.30037.3000.0000.0000.0000.000
100A111GLY00.0080.01124.704-0.055-0.0550.0000.0000.0000.000
101A112SER0-0.024-0.00723.1972.2912.2910.0000.0000.0000.000
102A113VAL00.0510.01816.904-0.732-0.7320.0000.0000.0000.000
103A114THR00.0020.00320.3061.1571.1570.0000.0000.0000.000
104A115ASN00.0010.01021.152-0.634-0.6340.0000.0000.0000.000
105A116MET0-0.0140.00419.683-1.136-1.1360.0000.0000.0000.000
106A117LEU0-0.006-0.01416.429-0.484-0.4840.0000.0000.0000.000
107A118THR0-0.0100.01020.8840.4090.4090.0000.0000.0000.000
108A119SER00.0170.00723.585-1.361-1.3610.0000.0000.0000.000
109A120ILE0-0.033-0.00122.493-0.585-0.5850.0000.0000.0000.000
110A121VAL0-0.011-0.02918.739-0.115-0.1150.0000.0000.0000.000
111A122GLY00.0140.02921.9900.8750.8750.0000.0000.0000.000
112A123ASN00.0870.01724.0431.4231.4230.0000.0000.0000.000
113A124VAL00.0250.01624.557-0.249-0.2490.0000.0000.0000.000
114A125PHE00.0220.01319.919-0.770-0.7700.0000.0000.0000.000
115A126GLY00.0200.01524.1780.5210.5210.0000.0000.0000.000
116A127PHE00.0040.00726.555-1.371-1.3710.0000.0000.0000.000
117A128LYS10.8350.91129.675-32.381-32.3810.0000.0000.0000.000
118A129ALA0-0.0090.00532.0690.0960.0960.0000.0000.0000.000
119A130LEU0-0.041-0.02027.299-0.320-0.3200.0000.0000.0000.000
120A131LYS10.9540.98127.723-39.314-39.3140.0000.0000.0000.000
121A132ALA0-0.021-0.01722.7631.3701.3700.0000.0000.0000.000
122A133LEU0-0.0090.00722.667-1.620-1.6200.0000.0000.0000.000
123A134ARG10.8450.92513.462-65.284-65.2840.0000.0000.0000.000
124A135LEU0-0.0330.01518.399-1.819-1.8190.0000.0000.0000.000
125A136GLU-1-0.782-0.88817.51962.70262.7020.0000.0000.0000.000
126A137ASP-1-0.809-0.92617.51558.27558.2750.0000.0000.0000.000
127A138LEU00.007-0.00819.209-1.901-1.9010.0000.0000.0000.000
128A139ARG10.8430.94221.087-38.475-38.4750.0000.0000.0000.000
129A140ILE00.029-0.00920.367-1.737-1.7370.0000.0000.0000.000
130A141PRO00.0160.03823.8620.1000.1000.0000.0000.0000.000
131A142VAL00.1030.02826.7810.4900.4900.0000.0000.0000.000
132A143ALA0-0.026-0.02528.2740.1610.1610.0000.0000.0000.000
133A144TYR00.019-0.01323.7620.1470.1470.0000.0000.0000.000
134A145LEU00.0540.04121.8490.5700.5700.0000.0000.0000.000
135A146LYS10.9060.95925.239-38.384-38.3840.0000.0000.0000.000
136A147THR0-0.089-0.05026.877-0.429-0.4290.0000.0000.0000.000
137A148PHE0-0.010-0.00621.5090.3720.3720.0000.0000.0000.000
138A149GLN0-0.070-0.04220.899-3.273-3.2730.0000.0000.0000.000
139A150GLY00.0430.02619.733-0.641-0.6410.0000.0000.0000.000
140A151PRO0-0.031-0.01716.9270.0290.0290.0000.0000.0000.000
141A152PRO0-0.0200.00917.687-3.176-3.1760.0000.0000.0000.000
142A153HIS0-0.047-0.01819.449-5.323-5.3230.0000.0000.0000.000
143A154GLY00.0410.01817.932-2.074-2.0740.0000.0000.0000.000
144A155ILE0-0.031-0.01815.804-1.194-1.1940.0000.0000.0000.000
145A156GLN0-0.043-0.02218.430-0.082-0.0820.0000.0000.0000.000
146A157VAL00.0670.03422.121-0.651-0.6510.0000.0000.0000.000
147A158GLU-1-0.786-0.87415.76472.58372.5830.0000.0000.0000.000
148A159ARG10.8010.89017.539-62.878-62.8780.0000.0000.0000.000
149A160ASP-1-0.815-0.88721.22945.38145.3810.0000.0000.0000.000
150A161LYS10.7980.90821.483-52.285-52.2850.0000.0000.0000.000
151A162LEU0-0.019-0.00817.184-0.990-0.9900.0000.0000.0000.000
152A163ASN0-0.048-0.01421.687-0.201-0.2010.0000.0000.0000.000
153A164LYS10.7900.90217.938-61.825-61.8250.0000.0000.0000.000
154A165TYR0-0.024-0.04621.4281.2471.2470.0000.0000.0000.000
155A166GLY00.000-0.00122.396-0.014-0.0140.0000.0000.0000.000
156A167ARG10.8080.89615.828-66.348-66.3480.0000.0000.0000.000
157A168PRO00.0040.02213.948-0.100-0.1000.0000.0000.0000.000
158A169LEU0-0.042-0.01813.667-2.663-2.6630.0000.0000.0000.000
159A170LEU0-0.0030.00210.1865.5195.5190.0000.0000.0000.000
160A171GLY00.0520.0168.885-6.150-6.1500.0000.0000.0000.000
161A172CYS0-0.086-0.0195.7496.8516.8510.0000.0000.0000.000
165A176PRO00.0530.0597.035-8.684-8.6840.0000.0000.0000.000
167A178LEU0-0.012-0.0097.587-5.933-5.9330.0000.0000.0000.000
168A179GLY00.0670.02811.189-0.160-0.1600.0000.0000.0000.000
169A180LEU0-0.0290.00411.421-5.456-5.4560.0000.0000.0000.000
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