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: K3GV3

Calculation Name: 1UZH-ABCI-Xray434

Preferred Name:

Target Type:

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

ligand 3-letter code: CAP

PDB ID: 1UZH

Chain ID: ABCI

ChEMBL ID:

UniProt ID: P00877

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 1177
LigandResidueName CAP
LigandFragmentNumber 1176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -41876652.818895
FMO2-HF: Nuclear repulsion 41402096.419067
FMO2-HF: Total energy -474556.399828
FMO2-MP2: Total energy -475911.154999


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.
-754.277-787.934222.723-103.133-85.934-0.713


Interactive mode: IFIE and PIEDA for fragment #1176(A:477:CAP)


Summations of interaction energy for fragment #1176(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.
-754.277-787.934222.723-103.133-85.9340.713
Interaction energy analysis for fragmet #1176(A:477:CAP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -4 / q_Mulliken : -3.107 / q_NPA : -3.480
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].
162A172CYS0-0.062-0.0295.1864.0814.231-0.001-0.004-0.1450.000
163A173THR00.1040.0472.048-16.549-14.3175.993-3.904-4.321-0.018
164A174ILE00.0090.0004.0558.2038.452-0.001-0.067-0.1810.000
165A175LYS10.8320.9132.003-233.220-232.33910.218-4.780-6.3190.067
167A177LYS10.7490.8894.357-162.725-162.408-0.001-0.090-0.2270.000
191A201KCX-1-0.495-0.7851.587176.699167.13029.413-11.940-7.904-0.102
193A203ASP00.2060.0614.4445.9686.112-0.001-0.030-0.1130.000
194A204GLU00.186-0.0214.052-17.030-16.669-0.001-0.089-0.2710.000
285A294HIS00.0970.0262.031-4.342-4.1976.253-2.374-4.0240.011
286A295ARG10.7510.8331.668-284.811-293.09135.326-16.562-10.4840.202
287A296ALA00.0340.0105.060-0.837-0.770-0.001-0.009-0.0570.000
289A298HIS10.8440.8993.408-175.658-173.7450.058-0.978-0.9930.009
318A327HIS00.1970.1941.749-57.347-57.86216.178-8.310-7.3530.092
319A328SER00.013-0.0094.749-7.431-7.292-0.001-0.019-0.1190.000
320A329GLY00.0270.0183.476-12.213-11.0080.039-0.622-0.6220.004
321A330THR00.0270.0084.444-20.221-20.0130.000-0.036-0.1720.000
325A334LYS10.7580.8671.947-272.856-271.4619.071-5.478-4.9880.076
326A335LEU0-0.012-0.0022.779-20.759-17.0521.388-2.121-2.9740.021
327A336GLU-1-0.793-0.8865.49583.44883.506-0.001-0.001-0.0550.000
369A378ALA00.0280.0364.77320.53420.741-0.001-0.007-0.1990.000
370A379SER0-0.002-0.0411.828-30.695-29.71711.692-6.429-6.2410.030
371A380GLY00.0700.0312.0569.27810.6119.939-5.988-5.2830.026
372A381GLY0-0.028-0.0371.724-47.313-56.90815.604-1.699-4.3100.065
373A382ILE0-0.065-0.0103.737-31.440-30.5030.035-0.446-0.5270.005
392A401GLN00.0310.0013.814-24.228-23.972-0.001-0.036-0.2200.000
393A402PHE00.0290.0083.68817.60418.3590.016-0.270-0.5010.001
394A403GLY00.0760.0461.923-39.166-39.2278.542-4.819-3.6610.063
395A404GLY00.0460.0111.953-52.685-55.1106.745-1.101-3.2190.047
396A405GLY0-0.028-0.0143.818-28.888-28.2370.024-0.325-0.3510.003
522B65THR0-0.053-0.0941.405-11.224-38.31251.870-20.777-4.0050.087
523B66TRP00.0270.0202.441-50.149-47.0102.605-2.471-3.2740.032
580B123ASN00.0930.0232.5806.7709.1161.725-1.346-2.725-0.008
581B124VAL00.0170.0094.9473.8033.906-0.001-0.005-0.0960.000
1A11ALA0-0.017-0.01951.360-0.110-0.1100.0000.0000.0000.000
2A12GLY00.0190.01252.3280.1260.1260.0000.0000.0000.000
3A13PHE0-0.0190.00147.4380.3330.3330.0000.0000.0000.000
4A14LYS10.9410.96749.655-23.453-23.4530.0000.0000.0000.000
5A15ALA00.0220.01948.5150.4350.4350.0000.0000.0000.000
6A16GLY00.0440.01447.253-0.400-0.4000.0000.0000.0000.000
7A17VAL00.0010.00042.1800.2800.2800.0000.0000.0000.000
8A18LYS10.8810.95043.282-26.979-26.9790.0000.0000.0000.000
9A19ASP-1-0.872-0.92641.10028.25428.2540.0000.0000.0000.000
10A20TYR0-0.036-0.05335.491-0.333-0.3330.0000.0000.0000.000
11A21ARG10.9430.95138.419-28.946-28.9460.0000.0000.0000.000
12A22LEU0-0.051-0.02239.308-0.289-0.2890.0000.0000.0000.000
13A23THR0-0.053-0.01839.755-0.694-0.6940.0000.0000.0000.000
14A24TYR00.0070.00335.222-0.329-0.3290.0000.0000.0000.000
15A25TYR00.0130.02435.5780.5420.5420.0000.0000.0000.000
16A26THR0-0.076-0.05236.804-0.843-0.8430.0000.0000.0000.000
17A27PRO00.0380.01937.2310.5210.5210.0000.0000.0000.000
18A28ASP-1-0.893-0.93038.30827.88527.8850.0000.0000.0000.000
19A29TYR0-0.169-0.09934.186-0.798-0.7980.0000.0000.0000.000
20A30VAL00.0130.01237.1280.4990.4990.0000.0000.0000.000
21A31VAL0-0.025-0.01331.715-0.149-0.1490.0000.0000.0000.000
22A32ARG10.9470.97234.186-30.916-30.9160.0000.0000.0000.000
23A33ASP-1-0.873-0.94432.29535.06535.0650.0000.0000.0000.000
24A34THR0-0.050-0.04031.1230.6330.6330.0000.0000.0000.000
25A35ASP-1-0.822-0.88730.57734.73634.7360.0000.0000.0000.000
26A36ILE00.0060.00524.3470.8520.8520.0000.0000.0000.000
27A37LEU0-0.040-0.00925.746-1.144-1.1440.0000.0000.0000.000
28A38ALA00.0300.02623.3272.0172.0170.0000.0000.0000.000
29A39ALA00.0150.02122.485-1.828-1.8280.0000.0000.0000.000
30A40PHE00.004-0.00921.9842.7092.7090.0000.0000.0000.000
31A41ARG10.8360.92119.248-54.551-54.5510.0000.0000.0000.000
32A42MET00.006-0.00123.3740.9360.9360.0000.0000.0000.000
33A43THR0-0.013-0.00225.171-0.617-0.6170.0000.0000.0000.000
34A44PRO00.0430.01727.6160.2940.2940.0000.0000.0000.000
35A45GLN0-0.016-0.00531.107-0.050-0.0500.0000.0000.0000.000
36A46PRO00.0330.00033.085-0.503-0.5030.0000.0000.0000.000
37A47GLY0-0.019-0.00136.130-0.368-0.3680.0000.0000.0000.000
38A48VAL0-0.034-0.00534.641-0.732-0.7320.0000.0000.0000.000
39A49PRO0-0.018-0.00635.7050.6260.6260.0000.0000.0000.000
40A50PRO00.0950.04033.2800.4610.4610.0000.0000.0000.000
41A51GLU-1-0.890-0.95633.70731.67731.6770.0000.0000.0000.000
42A52GLU-1-0.757-0.88135.74930.44830.4480.0000.0000.0000.000
43A53CYS0-0.024-0.00830.3480.5420.5420.0000.0000.0000.000
44A54GLY00.0560.01430.6740.9300.9300.0000.0000.0000.000
45A55ALA0-0.046-0.01331.6330.4260.4260.0000.0000.0000.000
46A56ALA00.0130.00832.540-0.016-0.0160.0000.0000.0000.000
47A57VAL00.0100.01426.8030.3530.3530.0000.0000.0000.000
48A58ALA00.0180.02829.4510.5440.5440.0000.0000.0000.000
49A59ALA0-0.0110.01031.043-0.053-0.0530.0000.0000.0000.000
50A60GLU-1-0.750-0.86530.88733.82433.8240.0000.0000.0000.000
51A61SER0-0.040-0.01326.9410.8400.8400.0000.0000.0000.000
52A62SER0-0.039-0.05328.754-0.028-0.0280.0000.0000.0000.000
53A63THR00.000-0.00931.518-0.132-0.1320.0000.0000.0000.000
54A64GLY00.0050.01934.539-0.919-0.9190.0000.0000.0000.000
55A65THR0-0.037-0.07334.7930.9450.9450.0000.0000.0000.000
56A66TRP00.0130.01636.899-0.606-0.6060.0000.0000.0000.000
57A67THR0-0.0040.00438.554-0.771-0.7710.0000.0000.0000.000
58A68THR0-0.046-0.01541.6400.4710.4710.0000.0000.0000.000
59A69VAL00.0280.01141.374-0.403-0.4030.0000.0000.0000.000
60A70TRP0-0.029-0.02844.292-0.137-0.1370.0000.0000.0000.000
61A71THR0-0.049-0.07542.616-0.385-0.3850.0000.0000.0000.000
62A72ASP-1-0.838-0.92241.78428.11728.1170.0000.0000.0000.000
63A73GLY0-0.052-0.02243.884-0.017-0.0170.0000.0000.0000.000
64A74LEU0-0.097-0.04345.772-0.407-0.4070.0000.0000.0000.000
65A75THR0-0.060-0.04041.168-0.007-0.0070.0000.0000.0000.000
66A76SER0-0.0010.00142.698-0.241-0.2410.0000.0000.0000.000
67A77LEU00.0880.02339.3840.6060.6060.0000.0000.0000.000
68A78ASP-1-0.937-0.95439.36127.75627.7560.0000.0000.0000.000
69A79ARG10.8680.94738.995-28.271-28.2710.0000.0000.0000.000
70A80TYR0-0.017-0.02036.0920.5620.5620.0000.0000.0000.000
71A81LYS10.8320.91134.785-28.331-28.3310.0000.0000.0000.000
72A82GLY00.0710.03331.9760.2310.2310.0000.0000.0000.000
73A83ARG10.8300.91432.427-31.450-31.4500.0000.0000.0000.000
74A84CYS0-0.0010.01231.3470.8150.8150.0000.0000.0000.000
75A85TYR0-0.006-0.02229.470-0.643-0.6430.0000.0000.0000.000
76A86ASP-1-0.859-0.93531.82534.24934.2490.0000.0000.0000.000
77A87ILE0-0.067-0.02731.1551.1221.1220.0000.0000.0000.000
78A88GLU-1-0.820-0.90727.90639.37239.3720.0000.0000.0000.000
79A89PRO0-0.011-0.00329.5991.1111.1110.0000.0000.0000.000
80A90VAL00.0000.00224.5910.5950.5950.0000.0000.0000.000
81A91PRO0-0.020-0.02126.524-0.729-0.7290.0000.0000.0000.000
82A92GLY0-0.020-0.01226.8641.4081.4080.0000.0000.0000.000
83A93GLU-1-0.911-0.95224.64545.63645.6360.0000.0000.0000.000
84A94ASP-1-0.915-0.94828.68834.73734.7370.0000.0000.0000.000
85A95ASN0-0.098-0.06429.946-1.530-1.5300.0000.0000.0000.000
86A96GLN00.0660.02623.0651.5171.5170.0000.0000.0000.000
87A97TYR00.003-0.00227.518-1.088-1.0880.0000.0000.0000.000
88A98ILE0-0.0100.00723.4581.7331.7330.0000.0000.0000.000
89A99ALA00.0010.00026.810-1.683-1.6830.0000.0000.0000.000
90A100TYR0-0.026-0.01426.1332.3942.3940.0000.0000.0000.000
91A101VAL0-0.003-0.00527.541-1.626-1.6260.0000.0000.0000.000
92A102ALA0-0.0100.00328.0621.2371.2370.0000.0000.0000.000
93A103TYR0-0.015-0.04126.087-0.646-0.6460.0000.0000.0000.000
94A104HYP00.0060.00830.2340.2060.2060.0000.0000.0000.000
95A105ILE00.0500.01329.6900.4250.4250.0000.0000.0000.000
96A106ASP-1-0.905-0.95830.95732.24132.2410.0000.0000.0000.000
97A107LEU0-0.091-0.04830.165-0.360-0.3600.0000.0000.0000.000
98A108PHE0-0.026-0.00225.5210.6160.6160.0000.0000.0000.000
99A109GLU-1-0.788-0.87627.19838.07638.0760.0000.0000.0000.000
100A110GLU-1-0.785-0.88526.57637.34437.3440.0000.0000.0000.000
101A111GLY00.0320.02324.448-0.137-0.1370.0000.0000.0000.000
102A112SER0-0.014-0.00222.8572.3372.3370.0000.0000.0000.000
103A113VAL00.0430.01816.653-0.913-0.9130.0000.0000.0000.000
104A114THR0-0.0060.00020.0610.7670.7670.0000.0000.0000.000
105A115ASN00.0030.00720.901-0.863-0.8630.0000.0000.0000.000
106A116MET0-0.0070.01519.278-1.236-1.2360.0000.0000.0000.000
107A117PHE00.000-0.02615.005-0.200-0.2000.0000.0000.0000.000
108A118THR0-0.0150.01420.6280.3120.3120.0000.0000.0000.000
109A119SER00.0290.01823.470-1.478-1.4780.0000.0000.0000.000
110A120ILE0-0.049-0.01122.201-0.568-0.5680.0000.0000.0000.000
111A121VAL0-0.011-0.02318.436-0.060-0.0600.0000.0000.0000.000
112A122GLY00.0130.02921.8000.8470.8470.0000.0000.0000.000
113A123ASN00.1010.02623.8501.5231.5230.0000.0000.0000.000
114A124VAL00.0230.01024.591-0.161-0.1610.0000.0000.0000.000
115A125PHE00.0310.01719.761-0.773-0.7730.0000.0000.0000.000
116A126GLY00.0340.01424.0790.5470.5470.0000.0000.0000.000
117A127PHE0-0.0150.00426.448-1.354-1.3540.0000.0000.0000.000
118A128LYS10.8210.91129.453-32.425-32.4250.0000.0000.0000.000
119A129ALA0-0.0100.01131.8210.0680.0680.0000.0000.0000.000
120A130LEU0-0.031-0.02026.143-0.330-0.3300.0000.0000.0000.000
121A131ARG10.8170.89327.856-38.302-38.3020.0000.0000.0000.000
122A132ALA00.005-0.00122.7311.3441.3440.0000.0000.0000.000
123A133LEU0-0.021-0.00422.550-1.838-1.8380.0000.0000.0000.000
124A134ARG10.8360.91813.346-66.674-66.6740.0000.0000.0000.000
125A135LEU0-0.0220.00518.177-1.979-1.9790.0000.0000.0000.000
126A136GLU-1-0.799-0.89917.29863.65563.6550.0000.0000.0000.000
127A137ASP-1-0.797-0.91317.51958.35158.3510.0000.0000.0000.000
128A138LEU00.008-0.01218.727-2.082-2.0820.0000.0000.0000.000
129A139ARG10.8690.96220.983-38.666-38.6660.0000.0000.0000.000
130A140ILE00.022-0.01420.322-1.807-1.8070.0000.0000.0000.000
131A141PRO0-0.0040.02223.5830.1720.1720.0000.0000.0000.000
132A142PRO00.1350.05226.5860.4280.4280.0000.0000.0000.000
133A143ALA0-0.014-0.01627.8710.0490.0490.0000.0000.0000.000
134A144TYR00.003-0.01323.4290.0230.0230.0000.0000.0000.000
135A145VAL00.0400.03222.8140.5010.5010.0000.0000.0000.000
136A146LYS10.9220.95324.805-38.940-38.9400.0000.0000.0000.000
137A147THR0-0.100-0.05126.447-0.515-0.5150.0000.0000.0000.000
138A148PHE0-0.014-0.00621.4320.2430.2430.0000.0000.0000.000
139A149VAL0-0.0030.00222.715-0.725-0.7250.0000.0000.0000.000
140A150GLY00.0070.01219.833-0.301-0.3010.0000.0000.0000.000
141A151HYP0-0.041-0.03716.4931.5151.5150.0000.0000.0000.000
142A152PRO0-0.0210.01117.319-2.965-2.9650.0000.0000.0000.000
143A153HIS0-0.051-0.02419.009-5.332-5.3320.0000.0000.0000.000
144A154GLY00.0340.01317.722-1.980-1.9800.0000.0000.0000.000
145A155ILE0-0.036-0.01615.292-1.066-1.0660.0000.0000.0000.000
146A156GLN0-0.063-0.02918.1260.4270.4270.0000.0000.0000.000
147A157VAL00.0900.04621.824-0.500-0.5000.0000.0000.0000.000
148A158GLU-1-0.799-0.87815.32273.81573.8150.0000.0000.0000.000
149A159ARG10.7960.87217.475-63.014-63.0140.0000.0000.0000.000
150A160ASP-1-0.811-0.89120.90945.99845.9980.0000.0000.0000.000
151A161LYS10.7830.89920.956-52.875-52.8750.0000.0000.0000.000
152A162LEU0-0.049-0.02616.776-0.124-0.1240.0000.0000.0000.000
153A163ASN00.0030.00921.222-0.636-0.6360.0000.0000.0000.000
154A164LYS10.7470.87817.941-61.699-61.6990.0000.0000.0000.000
155A165TYR0-0.026-0.04921.4541.1151.1150.0000.0000.0000.000
156A166GLY00.0120.01322.224-0.395-0.3950.0000.0000.0000.000
157A167ARG10.7720.86415.776-65.609-65.6090.0000.0000.0000.000
158A168GLY00.0420.03915.2310.3690.3690.0000.0000.0000.000
159A169LEU0-0.015-0.01013.359-1.870-1.8700.0000.0000.0000.000
160A170LEU0-0.0070.00110.2466.1216.1210.0000.0000.0000.000
161A171GLY00.0590.0118.630-5.838-5.8380.0000.0000.0000.000
166A176PRO00.0610.0437.033-8.902-8.9020.0000.0000.0000.000
168A178LEU0-0.021-0.0037.395-5.732-5.7320.0000.0000.0000.000
169A179GLY00.0480.01310.9360.0950.0950.0000.0000.0000.000
170A180LEU0-0.0460.00311.300-5.685-5.6850.0000.0000.0000.000
171A181SER00.0620.02314.478-0.172-0.1720.0000.0000.0000.000
172A182ALA00.0780.03516.0042.6712.6710.0000.0000.0000.000
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1160I107ARG10.9510.98227.455-39.437-39.4370.0000.0000.0000.000
1161I108PRO00.0810.05734.989-0.803-0.8030.0000.0000.0000.000
1162I109LYS10.9750.97436.970-30.380-30.3800.0000.0000.0000.000
1163I110THR0-0.031-0.01639.2300.2500.2500.0000.0000.0000.000
1164I111ALA00.0160.02634.332-0.092-0.0920.0000.0000.0000.000
1165I112ARG10.8990.93734.797-30.818-30.8180.0000.0000.0000.000
1166I113ASP-1-0.882-0.94731.19937.72137.7210.0000.0000.0000.000
1167I114PHE00.0120.01528.4061.4261.4260.0000.0000.0000.000
1168I115GLN0-0.012-0.01127.152-1.791-1.7910.0000.0000.0000.000
1169I116PRO0-0.012-0.01028.3090.7520.7520.0000.0000.0000.000
1170I117ALA00.0740.02426.0510.6010.6010.0000.0000.0000.000
1171I118ASN0-0.028-0.01525.8221.1991.1990.0000.0000.0000.000
1172I119LYS10.9130.95928.114-35.895-35.8950.0000.0000.0000.000
1173I120ARG10.8840.97522.820-47.582-47.5820.0000.0000.0000.000
1174I121SER00.000-0.01522.3000.5590.5590.0000.0000.0000.000
1175I122VAL0-0.059-0.00724.360-1.976-1.9760.0000.0000.0000.000
1177B477CAP-4-3.187-3.58128.369140.413140.4130.0000.0000.0000.000