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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 7G64K

Calculation Name: 5MAC-CD-Xray434

Preferred Name:

Target Type:

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

ligand 3-letter code: CAP

PDB ID: 5MAC

Chain ID: CD

ChEMBL ID:

UniProt ID: Q12TQ0

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 949
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -29933532.061353
FMO2-HF: Nuclear repulsion 29554356.118186
FMO2-HF: Total energy -379175.943167
FMO2-MP2: Total energy -380260.553087


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.
191.362220.960127.702-74.295-82.995-0.688


Interactive mode: IFIE and PIEDA for fragment #948(C:501:CAP)


Summations of interaction energy for fragment #948(C:501: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.
191.362220.96127.702-74.295-82.9950.688
Interaction energy analysis for fragmet #948(C:501:CAP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -4 / q_Mulliken : -3.180 / q_NPA : -3.624
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].
165C165ILE00.0290.0211.930-11.372-8.6253.682-2.467-3.9620.015
166C166VAL00.0070.0185.1333.4663.563-0.001-0.003-0.0930.000
167C167LYS10.8740.9352.242-249.551-244.4905.008-4.440-5.6300.060
169C169LYS10.8530.9644.329-164.031-163.388-0.001-0.288-0.3540.001
193C193KCX-1-0.581-0.8512.313191.790194.0719.465-4.694-7.052-0.056
195C195ASP00.1880.0304.4526.0956.256-0.001-0.035-0.1240.000
196C196GLU00.108-0.0683.783-16.601-16.245-0.001-0.077-0.2780.000
289C288HIS00.1750.0832.04812.24312.2997.553-3.482-4.127-0.035
290C289ARG10.8100.8801.750-265.777-264.94720.781-12.409-9.2020.168
291C290ALA00.0230.0204.6860.9831.105-0.001-0.014-0.1070.000
293C292HIS00.0210.0223.748-31.389-30.5370.018-0.352-0.5180.003
323C322HIS00.0200.0251.899-53.148-50.0998.459-5.726-5.7810.076
324C323THR0-0.005-0.0204.990-4.601-4.435-0.001-0.018-0.1470.000
325C324GLY00.0270.0283.373-8.958-7.7870.076-0.590-0.6570.004
326C325THR0-0.006-0.0014.248-25.419-25.1530.004-0.090-0.1790.001
331C330LYS10.7460.8411.763-281.922-283.94215.193-7.270-5.9020.086
332C331MET0-0.0140.0122.433-30.439-26.6653.027-2.522-4.2790.036
333C332LYS10.9050.9505.558-91.494-91.450-0.0010.000-0.0420.000
399C398VAL0-0.018-0.0184.90718.86019.047-0.001-0.005-0.1800.000
400C399SER00.020-0.0082.023-27.430-22.4816.563-5.443-6.0680.035
401C400GLY00.0640.0342.1324.9548.6584.418-3.561-4.5610.018
402C401GLY0-0.035-0.0191.769-54.157-59.66914.575-4.287-4.7770.073
403C402LEU0-0.048-0.0313.434-39.660-38.8850.0670.039-0.8810.011
404C403ASN00.0810.0065.3360.1830.253-0.001-0.003-0.0660.000
423C422THR0-0.029-0.0104.427-14.670-14.507-0.001-0.017-0.1440.000
424C423MET0-0.0150.0023.04614.61316.6120.188-1.001-1.1860.008
425C424GLY00.0460.0432.106-43.455-40.6375.466-4.562-3.7210.065
426C425SER0-0.022-0.0321.891-54.478-56.37710.365-4.032-4.4340.055
427C426GLY0-0.0180.0043.800-30.617-30.0250.028-0.319-0.3010.004
530D57GLU-1-0.826-0.9225.491178.670178.737-0.001-0.013-0.0520.000
535D62THR0-0.056-0.0332.016-7.021-4.9574.811-3.824-3.0500.053
536D63ASN00.1120.0584.218-2.869-2.4480.004-0.096-0.3280.000
588D115ASN00.0710.0022.188-5.080-5.6477.963-2.679-4.7180.007
589D116ILE0-0.007-0.0064.6625.9706.081-0.001-0.015-0.0940.000
1C1MET0-0.0020.00741.5080.0000.0000.0000.0000.0000.000
2C2SER0-0.025-0.03040.9920.4380.4380.0000.0000.0000.000
3C3LEU00.0270.01843.4510.0870.0870.0000.0000.0000.000
4C4ILE00.0180.01838.014-0.086-0.0860.0000.0000.0000.000
5C5TYR00.0530.01835.4410.3060.3060.0000.0000.0000.000
6C6GLU-1-0.911-0.97440.30025.54425.5440.0000.0000.0000.000
7C7ASP-1-0.926-0.96943.43925.70825.7080.0000.0000.0000.000
8C8LEU0-0.006-0.00236.0900.0100.0100.0000.0000.0000.000
9C9VAL00.0040.01040.2620.1840.1840.0000.0000.0000.000
10C10LYS10.8890.93241.634-24.777-24.7770.0000.0000.0000.000
11C11SER0-0.059-0.01740.736-0.178-0.1780.0000.0000.0000.000
12C12LEU0-0.0220.01237.9500.1790.1790.0000.0000.0000.000
13C13ASP-1-0.809-0.89840.75028.19828.1980.0000.0000.0000.000
14C14SER0-0.016-0.03742.1590.4320.4320.0000.0000.0000.000
15C15LYS10.7460.88036.365-31.127-31.1270.0000.0000.0000.000
16C16GLN00.0910.03036.808-0.053-0.0530.0000.0000.0000.000
17C17GLN0-0.046-0.02837.8810.1230.1230.0000.0000.0000.000
18C18ALA0-0.055-0.01238.972-0.010-0.0100.0000.0000.0000.000
19C19TYR0-0.0460.00233.832-0.038-0.0380.0000.0000.0000.000
20C20VAL0-0.019-0.01334.4720.9930.9930.0000.0000.0000.000
21C21ASP-1-0.880-0.94836.16528.72728.7270.0000.0000.0000.000
22C22LEU0-0.028-0.01335.4140.4750.4750.0000.0000.0000.000
23C23LYS10.8480.93537.595-26.691-26.6910.0000.0000.0000.000
24C24LEU00.0400.04133.772-0.555-0.5550.0000.0000.0000.000
25C25PRO0-0.074-0.03337.5530.2130.2130.0000.0000.0000.000
26C26ASP-1-0.848-0.94535.71832.36632.3660.0000.0000.0000.000
27C27PRO00.0000.00231.6070.1190.1190.0000.0000.0000.000
28C28THR0-0.013-0.00929.9520.9930.9930.0000.0000.0000.000
29C29ASN0-0.045-0.02532.1410.9060.9060.0000.0000.0000.000
30C30GLY00.0180.00531.531-0.483-0.4830.0000.0000.0000.000
31C31GLU-1-0.917-0.94431.53231.78831.7880.0000.0000.0000.000
32C32PHE0-0.048-0.03429.9690.2520.2520.0000.0000.0000.000
33C33LEU00.0070.02122.2400.3510.3510.0000.0000.0000.000
34C34LEU0-0.042-0.02325.961-0.398-0.3980.0000.0000.0000.000
35C35ALA00.0420.01322.9042.0012.0010.0000.0000.0000.000
36C36VAL00.0020.00121.809-1.794-1.7940.0000.0000.0000.000
37C37PHE00.0250.00621.3352.5162.5160.0000.0000.0000.000
38C38HIS0-0.0270.00620.645-0.434-0.4340.0000.0000.0000.000
39C39MET0-0.071-0.03122.4630.6980.6980.0000.0000.0000.000
40C40ILE00.0220.02524.724-0.952-0.9520.0000.0000.0000.000
41C41PRO00.011-0.01527.4100.5180.5180.0000.0000.0000.000
42C42GLY0-0.016-0.00730.2400.5190.5190.0000.0000.0000.000
43C43GLY0-0.038-0.00131.228-0.425-0.4250.0000.0000.0000.000
44C44ASP-1-0.889-0.93134.74030.63730.6370.0000.0000.0000.000
45C45LEU0-0.040-0.02234.323-0.688-0.6880.0000.0000.0000.000
46C46ASN0-0.039-0.03435.2511.0871.0870.0000.0000.0000.000
47C47VAL00.054-0.00331.0000.4160.4160.0000.0000.0000.000
48C48LEU00.002-0.00532.5500.7950.7950.0000.0000.0000.000
49C49GLN00.0160.01034.9770.4460.4460.0000.0000.0000.000
50C50ALA00.0740.04630.7770.1310.1310.0000.0000.0000.000
51C51ALA0-0.006-0.00429.9620.6760.6760.0000.0000.0000.000
52C52ALA0-0.019-0.00930.9400.5350.5350.0000.0000.0000.000
53C53GLU-1-0.797-0.89132.21132.15832.1580.0000.0000.0000.000
54C54ILE00.0350.01526.2230.4520.4520.0000.0000.0000.000
55C55ALA0-0.0040.01528.9170.5380.5380.0000.0000.0000.000
56C56ALA0-0.030-0.00630.2820.0820.0820.0000.0000.0000.000
57C57GLU-1-0.780-0.89529.20235.24035.2400.0000.0000.0000.000
58C58SER0-0.082-0.04625.9921.3941.3940.0000.0000.0000.000
59C59SER0-0.025-0.03527.5520.0510.0510.0000.0000.0000.000
60C60THR0-0.002-0.01730.3560.2430.2430.0000.0000.0000.000
61C61GLY0-0.011-0.00433.457-0.936-0.9360.0000.0000.0000.000
62C62THR0-0.068-0.04133.6400.6230.6230.0000.0000.0000.000
63C63ASN00.0680.03935.272-0.092-0.0920.0000.0000.0000.000
64C64ILE0-0.027-0.00736.663-0.434-0.4340.0000.0000.0000.000
65C65LYS10.9340.96140.265-26.641-26.6410.0000.0000.0000.000
66C66VAL00.011-0.00840.280-0.324-0.3240.0000.0000.0000.000
67C67SER0-0.045-0.03942.865-0.204-0.2040.0000.0000.0000.000
68C68THR00.010-0.00541.663-0.375-0.3750.0000.0000.0000.000
69C69GLU-1-0.862-0.92241.14827.88227.8820.0000.0000.0000.000
70C70THR00.0410.02642.230-0.539-0.5390.0000.0000.0000.000
71C71ALA0-0.037-0.03742.6620.4330.4330.0000.0000.0000.000
72C72PHE00.0020.00139.6540.2200.2200.0000.0000.0000.000
73C73SER00.0510.03438.4140.6510.6510.0000.0000.0000.000
74C74ARG10.9230.96537.696-25.958-25.9580.0000.0000.0000.000
75C75THR0-0.119-0.06838.4400.5040.5040.0000.0000.0000.000
76C76MET00.0130.00433.8500.6090.6090.0000.0000.0000.000
77C77ASN00.0060.02633.2331.0541.0540.0000.0000.0000.000
78C78ALA00.0170.01429.851-0.067-0.0670.0000.0000.0000.000
79C79ARG10.8740.92831.748-32.651-32.6510.0000.0000.0000.000
80C80VAL00.0240.01430.8130.8800.8800.0000.0000.0000.000
81C81TYR00.026-0.01129.028-0.791-0.7910.0000.0000.0000.000
82C82GLN0-0.004-0.01030.436-0.739-0.7390.0000.0000.0000.000
83C83LEU0-0.022-0.01630.6820.6460.6460.0000.0000.0000.000
84C84ASP-1-0.869-0.92728.41637.51537.5150.0000.0000.0000.000
85C85LEU0-0.016-0.02829.3400.7990.7990.0000.0000.0000.000
86C86GLU-1-0.965-0.96530.75135.85635.8560.0000.0000.0000.000
87C87ARG10.8940.95122.639-44.539-44.5390.0000.0000.0000.000
88C88GLU-1-0.892-0.94125.49443.40843.4080.0000.0000.0000.000
89C89LEU0-0.030-0.01223.0851.5861.5860.0000.0000.0000.000
90C90VAL0-0.014-0.01925.924-1.986-1.9860.0000.0000.0000.000
91C91TRP0-0.0030.00526.2121.3741.3740.0000.0000.0000.000
92C92ILE0-0.008-0.00826.737-1.769-1.7690.0000.0000.0000.000
93C93ALA00.0010.00927.2811.2241.2240.0000.0000.0000.000
94C94TYR00.032-0.01625.353-0.813-0.8130.0000.0000.0000.000
95C95PRO00.0020.00928.7270.6240.6240.0000.0000.0000.000
96C96TRP00.0270.00827.8380.2510.2510.0000.0000.0000.000
97C97ARG10.7870.87529.096-30.585-30.5850.0000.0000.0000.000
98C98LEU0-0.037-0.01029.094-0.584-0.5840.0000.0000.0000.000
99C99PHE00.0250.00825.3400.2340.2340.0000.0000.0000.000
100C100ASP-1-0.776-0.87826.46338.43738.4370.0000.0000.0000.000
101C101ARG10.8820.94727.178-34.241-34.2410.0000.0000.0000.000
102C102GLY00.0200.01428.1990.2680.2680.0000.0000.0000.000
103C103GLY00.0670.04224.8561.1021.1020.0000.0000.0000.000
104C104ASN0-0.032-0.02522.6383.8023.8020.0000.0000.0000.000
105C105VAL00.024-0.00116.938-0.794-0.7940.0000.0000.0000.000
106C106GLN00.0520.02818.797-0.302-0.3020.0000.0000.0000.000
107C107ASN0-0.0200.00119.777-0.840-0.8400.0000.0000.0000.000
108C108ILE00.0190.00920.539-0.699-0.6990.0000.0000.0000.000
109C109LEU0-0.010-0.01015.394-0.523-0.5230.0000.0000.0000.000
110C110THR0-0.0190.00419.4541.2441.2440.0000.0000.0000.000
111C111TYR0-0.045-0.01122.162-1.414-1.4140.0000.0000.0000.000
112C112ILE0-0.021-0.01819.405-0.473-0.4730.0000.0000.0000.000
113C113ILE0-0.028-0.01016.1051.1141.1140.0000.0000.0000.000
114C114GLY00.0850.03819.0921.8831.8830.0000.0000.0000.000
115C115ASN00.045-0.01021.755-0.386-0.3860.0000.0000.0000.000
116C116ILE00.0290.01122.821-0.253-0.2530.0000.0000.0000.000
117C117LEU0-0.0030.01018.010-0.158-0.1580.0000.0000.0000.000
118C118GLY0-0.017-0.00622.2480.7840.7840.0000.0000.0000.000
119C119MET00.0030.01224.649-1.223-1.2230.0000.0000.0000.000
120C120LYS10.8650.91227.461-32.814-32.8140.0000.0000.0000.000
121C121GLU-1-0.896-0.94430.19034.14034.1400.0000.0000.0000.000
122C122ILE0-0.074-0.02924.240-0.131-0.1310.0000.0000.0000.000
123C123GLN0-0.039-0.01926.1860.9560.9560.0000.0000.0000.000
124C124ALA00.0200.00722.0731.8131.8130.0000.0000.0000.000
125C125LEU00.026-0.00821.311-2.019-2.0190.0000.0000.0000.000
126C126LYS10.8370.93513.818-68.259-68.2590.0000.0000.0000.000
127C127LEU0-0.020-0.00617.482-1.615-1.6150.0000.0000.0000.000
128C128MET00.000-0.00715.9064.1254.1250.0000.0000.0000.000
129C129ASP-1-0.720-0.87216.97558.68258.6820.0000.0000.0000.000
130C130ILE0-0.025-0.01918.003-1.652-1.6520.0000.0000.0000.000
131C131TRP00.0250.01320.8030.6190.6190.0000.0000.0000.000
132C132PHE00.017-0.00318.616-1.130-1.1300.0000.0000.0000.000
133C133PRO00.0230.03024.187-0.131-0.1310.0000.0000.0000.000
134C134PRO00.0550.01227.2870.5240.5240.0000.0000.0000.000
135C135SER0-0.055-0.03128.8990.4640.4640.0000.0000.0000.000
136C136MET00.0210.03123.342-0.368-0.3680.0000.0000.0000.000
137C137LEU00.012-0.00622.4450.8020.8020.0000.0000.0000.000
138C138GLU-1-0.910-0.95625.38139.22839.2280.0000.0000.0000.000
139C139GLN0-0.135-0.05727.111-1.259-1.2590.0000.0000.0000.000
140C140TYR0-0.057-0.02522.102-0.035-0.0350.0000.0000.0000.000
141C141ASP-1-0.842-0.90721.38147.06047.0600.0000.0000.0000.000
142C142GLY00.0220.00620.067-1.138-1.1380.0000.0000.0000.000
143C143PRO0-0.034-0.01617.284-0.825-0.8250.0000.0000.0000.000
144C144SER0-0.079-0.04719.557-1.794-1.7940.0000.0000.0000.000
145C145TYR00.0430.04018.462-0.231-0.2310.0000.0000.0000.000
146C146THR0-0.018-0.02717.9072.8812.8810.0000.0000.0000.000
147C147VAL00.0810.01615.1320.0500.0500.0000.0000.0000.000
148C148ASP-1-0.852-0.92217.36154.51754.5170.0000.0000.0000.000
149C149ASP-1-0.896-0.94920.92349.13549.1350.0000.0000.0000.000
150C150MET0-0.033-0.00814.3250.4690.4690.0000.0000.0000.000
151C151ARG10.8630.92116.333-65.949-65.9490.0000.0000.0000.000
152C152LYS10.9631.00320.808-44.573-44.5730.0000.0000.0000.000
153C153TYR0-0.092-0.04019.952-1.249-1.2490.0000.0000.0000.000
154C154LEU0-0.050-0.04516.438-0.687-0.6870.0000.0000.0000.000
155C155ASP-1-0.959-0.96221.14145.65145.6510.0000.0000.0000.000
156C156VAL0-0.058-0.01717.7570.2800.2800.0000.0000.0000.000
157C157TYR0-0.001-0.02521.2190.9620.9620.0000.0000.0000.000
158C158ASP-1-0.931-0.96322.14849.49449.4940.0000.0000.0000.000
159C159ARG10.8650.92416.168-65.457-65.4570.0000.0000.0000.000
160C160PRO00.0050.01113.513-0.801-0.8010.0000.0000.0000.000
161C161ILE00.0100.01812.697-1.711-1.7110.0000.0000.0000.000
162C162LEU0-0.027-0.01910.9817.4127.4120.0000.0000.0000.000
163C163GLY00.055-0.0029.273-6.441-6.4410.0000.0000.0000.000
164C164THR0-0.050-0.0356.0557.6787.6780.0000.0000.0000.000
168C168PRO00.0200.0067.062-7.083-7.0830.0000.0000.0000.000
170C170MET0-0.030-0.0077.658-7.832-7.8320.0000.0000.0000.000
171C171GLY0-0.006-0.01811.3080.5870.5870.0000.0000.0000.000
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173C173THR00.005-0.00614.986-0.464-0.4640.0000.0000.0000.000
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924D450GLN0-0.072-0.02452.013-0.665-0.6650.0000.0000.0000.000
925D451GLY0-0.048-0.01953.872-0.384-0.3840.0000.0000.0000.000
926D452MET0-0.054-0.01854.510-0.372-0.3720.0000.0000.0000.000
927D453ASP-1-0.918-0.94753.33623.00823.0080.0000.0000.0000.000
928D454ILE00.034-0.00349.116-0.255-0.2550.0000.0000.0000.000
929D455GLU-1-0.888-0.95953.08722.75522.7550.0000.0000.0000.000
930D456GLU-1-0.920-0.94155.74919.67919.6790.0000.0000.0000.000
931D457TYR00.0590.00854.938-0.424-0.4240.0000.0000.0000.000
932D458ALA0-0.026-0.01255.063-0.212-0.2120.0000.0000.0000.000
933D459LYS10.7820.89156.959-20.124-20.1240.0000.0000.0000.000
934D460ASP-1-0.946-0.96460.27719.72419.7240.0000.0000.0000.000
935D461HIS10.8310.91756.059-21.055-21.0550.0000.0000.0000.000
936D462LYS10.9600.98856.447-20.592-20.5920.0000.0000.0000.000
937D463GLU-1-0.816-0.89952.27121.83221.8320.0000.0000.0000.000
938D464LEU00.0600.03650.5690.3960.3960.0000.0000.0000.000
939D465ALA0-0.028-0.01252.3720.1990.1990.0000.0000.0000.000
940D466GLU-1-0.960-1.00353.23221.90521.9050.0000.0000.0000.000
941D467ALA0-0.0050.00848.5050.3110.3110.0000.0000.0000.000
942D468ILE00.004-0.00449.1560.3970.3970.0000.0000.0000.000
943D469GLU-1-0.929-0.96150.66422.25422.2540.0000.0000.0000.000
944D470PHE0-0.059-0.03445.2600.0840.0840.0000.0000.0000.000
945D471TYR0-0.045-0.04243.6730.2130.2130.0000.0000.0000.000
946D472LEU0-0.051-0.00345.5560.5570.5570.0000.0000.0000.000
947D473ASN0-0.078-0.02347.8770.4000.4000.0000.0000.0000.000
949D501CAP-4-3.361-3.82126.960146.267146.2670.0000.0000.0000.000