FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: ZLYKN

Calculation Name: 3A27-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A27

Chain ID: A

ChEMBL ID:

UniProt ID: Q58952

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3083733.432093
FMO2-HF: Nuclear repulsion 2990062.102528
FMO2-HF: Total energy -93671.329565
FMO2-MP2: Total energy -93946.760027


3D Structure Molmil
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
158.875160.735-0.01-0.896-0.954-0.003
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.808 / q_NPA : 1.890
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].
3A6GLN00.006-0.0063.764-1.5500.310-0.010-0.896-0.954-0.003
4A7LYS10.8540.9306.18148.67248.6720.0000.0000.0000.000
5A8ILE0-0.0240.0109.0710.6380.6380.0000.0000.0000.000
6A9GLY00.0630.03212.0411.9551.9550.0000.0000.0000.000
7A10ASP-1-0.927-0.97714.115-36.088-36.0880.0000.0000.0000.000
8A11VAL00.0550.02412.8720.5650.5650.0000.0000.0000.000
9A12VAL0-0.067-0.0377.903-3.238-3.2380.0000.0000.0000.000
10A13ILE0-0.0040.0078.3673.6403.6400.0000.0000.0000.000
11A14VAL-1-0.830-0.9255.754-78.934-78.9340.0000.0000.0000.000
12A32CYS0-0.027-0.01613.926-2.326-2.3260.0000.0000.0000.000
13A33LYS10.8890.93210.45647.99747.9970.0000.0000.0000.000
14A34ALA00.0410.04215.3241.3981.3980.0000.0000.0000.000
15A35ILE00.0020.00415.8001.0071.0070.0000.0000.0000.000
16A36LEU0-0.047-0.02910.061-3.065-3.0650.0000.0000.0000.000
17A37LEU00.0230.01112.0763.1973.1970.0000.0000.0000.000
18A38TYR00.0440.0099.916-2.745-2.7450.0000.0000.0000.000
19A39THR0-0.021-0.0159.0424.6654.6650.0000.0000.0000.000
20A40THR0-0.010-0.01111.038-1.071-1.0710.0000.0000.0000.000
21A41GLN00.0270.02112.239-2.487-2.4870.0000.0000.0000.000
22A42ILE00.0180.00910.1910.1590.1590.0000.0000.0000.000
23A43THR0-0.055-0.0329.461-3.700-3.7000.0000.0000.0000.000
24A44GLY00.0120.0137.970-4.172-4.1720.0000.0000.0000.000
25A45GLU0-0.089-0.0768.584-0.660-0.6600.0000.0000.0000.000
26A46PHE00.0050.00311.3322.5092.5090.0000.0000.0000.000
27A47ARG10.9050.94613.31729.84429.8440.0000.0000.0000.000
28A48THR00.0850.02117.073-0.242-0.2420.0000.0000.0000.000
29A49PRO0-0.064-0.02919.210-0.074-0.0740.0000.0000.0000.000
30A50HIS00.0510.02615.529-0.694-0.6940.0000.0000.0000.000
31A51VAL00.0160.02715.443-2.595-2.5950.0000.0000.0000.000
32A52LYS10.9080.98313.33639.50039.5000.0000.0000.0000.000
33A53ILE00.016-0.00114.934-2.588-2.5880.0000.0000.0000.000
34A54LEU0-0.038-0.01711.4100.2430.2430.0000.0000.0000.000
35A55TYR00.0150.00915.6451.2091.2090.0000.0000.0000.000
36A56GLY00.0290.01817.785-0.799-0.7990.0000.0000.0000.000
37A57LYS10.8720.90320.74223.69723.6970.0000.0000.0000.000
38A58GLU-1-0.875-0.90821.052-24.261-24.2610.0000.0000.0000.000
39A59THR00.010-0.03017.934-1.018-1.0180.0000.0000.0000.000
40A60GLU-1-0.820-0.88418.500-26.243-26.2430.0000.0000.0000.000
41A61THR0-0.030-0.01017.046-0.817-0.8170.0000.0000.0000.000
42A62ILE00.0600.01819.4540.3000.3000.0000.0000.0000.000
43A63HIS00.0210.01612.229-0.385-0.3850.0000.0000.0000.000
44A64LYS10.9340.97014.19540.93440.9340.0000.0000.0000.000
45A65GLU-1-0.798-0.88312.517-45.475-45.4750.0000.0000.0000.000
46A66TYR00.0710.02012.7720.9230.9230.0000.0000.0000.000
47A67GLY00.0440.04417.2431.6251.6250.0000.0000.0000.000
48A68CYS0-0.0490.01019.2682.0332.0330.0000.0000.0000.000
49A69LEU0-0.024-0.01919.247-1.782-1.7820.0000.0000.0000.000
50A70PHE00.015-0.00817.8330.6640.6640.0000.0000.0000.000
51A71LYS10.8280.92519.13222.31822.3180.0000.0000.0000.000
52A72LEU0-0.019-0.02215.905-0.004-0.0040.0000.0000.0000.000
53A73ASP-1-0.739-0.84419.669-30.287-30.2870.0000.0000.0000.000
54A74VAL0-0.013-0.02014.430-0.450-0.4500.0000.0000.0000.000
55A75ALA00.0030.01015.876-1.672-1.6720.0000.0000.0000.000
56A76LYS0-0.044-0.02317.8730.3090.3090.0000.0000.0000.000
57A77ILE0-0.043-0.01718.1201.2181.2180.0000.0000.0000.000
58A78MET00.0190.04314.513-2.166-2.1660.0000.0000.0000.000
59A79TRP00.0540.03210.9882.4812.4810.0000.0000.0000.000
60A80SER0-0.0050.01011.430-4.123-4.1230.0000.0000.0000.000
61A81GLN00.0590.0275.1831.6231.6230.0000.0000.0000.000
62A82GLY00.013-0.0068.6040.8700.8700.0000.0000.0000.000
63A83ASN00.0340.0129.8822.7672.7670.0000.0000.0000.000
64A84ILE00.0150.0188.1852.1102.1100.0000.0000.0000.000
65A85GLU-1-0.802-0.88512.064-38.439-38.4390.0000.0000.0000.000
66A86GLU-1-0.735-0.84213.801-26.784-26.7840.0000.0000.0000.000
67A87ARG10.7490.85111.92742.72142.7210.0000.0000.0000.000
68A88LYS10.8040.88512.35441.28741.2870.0000.0000.0000.000
69A89ARG10.7360.81717.36027.62327.6230.0000.0000.0000.000
70A90MET0-0.026-0.01919.8201.5741.5740.0000.0000.0000.000
71A91ALA00.0040.00520.5111.0601.0600.0000.0000.0000.000
72A92PHE0-0.0090.00221.9200.8520.8520.0000.0000.0000.000
73A93ILE0-0.0320.00424.1650.5160.5160.0000.0000.0000.000
74A94SER0-0.034-0.05125.9730.6860.6860.0000.0000.0000.000
75A95ASN00.0240.00529.2660.3350.3350.0000.0000.0000.000
76A96GLU-1-0.838-0.92432.080-17.410-17.4100.0000.0000.0000.000
77A97ASN0-0.041-0.02534.8360.6490.6490.0000.0000.0000.000
78A98GLU-1-0.799-0.82331.826-18.555-18.5550.0000.0000.0000.000
79A99VAL0-0.043-0.01535.1570.0220.0220.0000.0000.0000.000
80A100VAL0-0.002-0.00528.940-0.075-0.0750.0000.0000.0000.000
81A101VAL00.0410.02331.2230.1360.1360.0000.0000.0000.000
82A102ASP-1-0.817-0.89824.824-24.943-24.9430.0000.0000.0000.000
83A103MET00.0010.00327.8770.2070.2070.0000.0000.0000.000
84A104PHE0-0.029-0.01224.6730.3390.3390.0000.0000.0000.000
85A105ALA00.0680.05023.773-1.213-1.2130.0000.0000.0000.000
86A106GLY0-0.006-0.00522.298-1.332-1.3320.0000.0000.0000.000
87A107ILE0-0.052-0.02318.4530.7300.7300.0000.0000.0000.000
88A108GLY00.0470.01522.7220.2280.2280.0000.0000.0000.000
89A109TYR0-0.087-0.05616.6690.2100.2100.0000.0000.0000.000
90A110PHE00.007-0.00617.768-1.109-1.1090.0000.0000.0000.000
91A111THR00.021-0.01721.6670.6490.6490.0000.0000.0000.000
92A112ILE0-0.0340.00422.3320.7080.7080.0000.0000.0000.000
93A113PRO00.005-0.01519.5270.6020.6020.0000.0000.0000.000
94A114LEU0-0.0090.02322.4850.6390.6390.0000.0000.0000.000
95A115ALA00.0240.00325.2680.7660.7660.0000.0000.0000.000
96A116LYS10.8520.92123.34525.59925.5990.0000.0000.0000.000
97A117TYR0-0.079-0.07021.2490.7810.7810.0000.0000.0000.000
98A118SER00.024-0.00226.0670.5280.5280.0000.0000.0000.000
99A119LYS10.8300.94428.23020.06320.0630.0000.0000.0000.000
100A120PRO00.0470.04530.0480.5620.5620.0000.0000.0000.000
101A121LYS10.8870.93632.98215.86815.8680.0000.0000.0000.000
102A122LEU0-0.021-0.01134.5980.1110.1110.0000.0000.0000.000
103A123VAL0-0.0150.00328.438-0.122-0.1220.0000.0000.0000.000
104A124TYR00.0660.02031.9100.0390.0390.0000.0000.0000.000
105A125ALA0-0.007-0.01128.004-0.475-0.4750.0000.0000.0000.000
106A126ILE00.0030.00829.6270.2500.2500.0000.0000.0000.000
107A127GLU-1-0.846-0.90625.724-24.951-24.9510.0000.0000.0000.000
108A128LYS10.9080.95028.39921.23421.2340.0000.0000.0000.000
109A129ASN0-0.037-0.03225.7520.0650.0650.0000.0000.0000.000
110A130PRO00.0730.02327.910-0.449-0.4490.0000.0000.0000.000
111A131THR00.0000.00924.1170.1560.1560.0000.0000.0000.000
112A132ALA0-0.005-0.01123.847-0.585-0.5850.0000.0000.0000.000
113A133TYR00.028-0.00824.881-0.233-0.2330.0000.0000.0000.000
114A134HIS0-0.0140.00426.6450.8580.8580.0000.0000.0000.000
115A135TYR0-0.025-0.05823.298-0.142-0.1420.0000.0000.0000.000
116A136LEU0-0.0030.01125.325-0.229-0.2290.0000.0000.0000.000
117A137CYS0-0.021-0.00626.3410.4470.4470.0000.0000.0000.000
118A138GLU-1-0.839-0.91526.280-21.857-21.8570.0000.0000.0000.000
119A139ASN0-0.016-0.00622.105-0.006-0.0060.0000.0000.0000.000
120A140ILE00.0410.03025.741-0.066-0.0660.0000.0000.0000.000
121A141LYS10.9550.99028.83718.59818.5980.0000.0000.0000.000
122A142LEU00.0170.01124.3860.1730.1730.0000.0000.0000.000
123A143ASN0-0.098-0.07523.468-0.525-0.5250.0000.0000.0000.000
124A144LYS10.8510.92626.97721.88321.8830.0000.0000.0000.000
125A145LEU0-0.0230.00426.5210.3620.3620.0000.0000.0000.000
126A146ASN00.005-0.01031.0850.0820.0820.0000.0000.0000.000
127A147ASN0-0.031-0.00730.8580.2020.2020.0000.0000.0000.000
128A148VAL00.007-0.00629.201-0.359-0.3590.0000.0000.0000.000
129A149ILE00.0190.02232.3810.3000.3000.0000.0000.0000.000
130A150PRO0-0.0200.00730.663-0.285-0.2850.0000.0000.0000.000
131A151ILE00.0130.00032.1670.5200.5200.0000.0000.0000.000
132A152LEU0-0.0010.00231.330-0.654-0.6540.0000.0000.0000.000
133A153ALA00.0440.01232.6650.6170.6170.0000.0000.0000.000
134A154ASP-1-0.777-0.86232.358-20.057-20.0570.0000.0000.0000.000
135A155ASN0-0.011-0.02129.8460.9800.9800.0000.0000.0000.000
136A156ARG10.8500.88333.52618.75918.7590.0000.0000.0000.000
137A157ASP-1-0.873-0.93636.416-16.325-16.3250.0000.0000.0000.000
138A158VAL0-0.049-0.01435.1050.3340.3340.0000.0000.0000.000
139A159GLU-1-0.909-0.96238.205-14.371-14.3710.0000.0000.0000.000
140A160LEU0-0.045-0.02136.0990.1760.1760.0000.0000.0000.000
141A161LYS10.8590.91339.41913.93413.9340.0000.0000.0000.000
142A162ASP-1-0.806-0.88041.125-14.019-14.0190.0000.0000.0000.000
143A163VAL0-0.014-0.00437.2750.0740.0740.0000.0000.0000.000
144A164ALA0-0.046-0.02034.486-0.090-0.0900.0000.0000.0000.000
145A165ASP-1-0.801-0.88935.023-15.912-15.9120.0000.0000.0000.000
146A166ARG10.7930.84928.21819.67719.6770.0000.0000.0000.000
147A167VAL00.0320.01630.288-0.092-0.0920.0000.0000.0000.000
148A168ILE0-0.014-0.00823.878-0.466-0.4660.0000.0000.0000.000
149A169MET0-0.0100.00226.0770.2450.2450.0000.0000.0000.000
150A170GLY00.0390.02322.051-0.465-0.4650.0000.0000.0000.000
151A171TYR0-0.028-0.02321.792-1.190-1.1900.0000.0000.0000.000
152A172VAL00.0540.02020.0960.3660.3660.0000.0000.0000.000
153A173HIS0-0.053-0.01322.034-0.136-0.1360.0000.0000.0000.000
154A174LYS10.9200.94825.96020.46120.4610.0000.0000.0000.000
155A175THR00.0500.02525.4320.8030.8030.0000.0000.0000.000
156A176HIS00.0700.03028.5180.7830.7830.0000.0000.0000.000
157A177LYS10.8840.94631.80318.12418.1240.0000.0000.0000.000
158A178PHE0-0.008-0.00929.7340.2480.2480.0000.0000.0000.000
159A179LEU0-0.025-0.01131.6240.0020.0020.0000.0000.0000.000
160A180ASP-1-0.753-0.85634.072-15.700-15.7000.0000.0000.0000.000
161A181LYS10.8080.93034.98816.20516.2050.0000.0000.0000.000
162A182THR0-0.035-0.01832.1530.2000.2000.0000.0000.0000.000
163A183PHE00.0210.00034.7660.0460.0460.0000.0000.0000.000
164A184GLU-1-0.855-0.90637.952-14.730-14.7300.0000.0000.0000.000
165A185PHE0-0.031-0.01933.4100.0310.0310.0000.0000.0000.000
166A186LEU0-0.070-0.01734.557-0.008-0.0080.0000.0000.0000.000
167A187LYS10.8750.93337.60315.85215.8520.0000.0000.0000.000
168A188ASP-1-0.801-0.88640.481-13.845-13.8450.0000.0000.0000.000
169A189ARG10.9280.95839.37215.07215.0720.0000.0000.0000.000
170A190GLY00.0270.02336.259-0.014-0.0140.0000.0000.0000.000
171A191VAL0-0.065-0.03430.0320.0320.0320.0000.0000.0000.000
172A192ILE00.0010.01929.347-0.322-0.3220.0000.0000.0000.000
173A193HIS00.000-0.00824.7400.1910.1910.0000.0000.0000.000
174A194TYR00.016-0.03126.021-0.337-0.3370.0000.0000.0000.000
175A195HIS0-0.0130.01319.323-1.357-1.3570.0000.0000.0000.000
176A196GLU-1-0.754-0.84522.814-20.833-20.8330.0000.0000.0000.000
177A197THR00.0130.02019.994-1.124-1.1240.0000.0000.0000.000
178A198VAL0-0.031-0.01322.4591.2211.2210.0000.0000.0000.000
179A199ALA00.0290.01722.915-1.104-1.1040.0000.0000.0000.000
180A200GLU-1-0.837-0.93721.466-27.384-27.3840.0000.0000.0000.000
181A201LYS10.9130.95124.23120.83620.8360.0000.0000.0000.000
182A202ILE00.0900.04927.5930.4290.4290.0000.0000.0000.000
183A203MET0-0.060-0.02020.991-0.011-0.0110.0000.0000.0000.000
184A204TYR00.013-0.00823.357-0.693-0.6930.0000.0000.0000.000
185A205GLU-1-0.904-0.93728.301-17.759-17.7590.0000.0000.0000.000
186A206ARG10.9050.92826.60021.94821.9480.0000.0000.0000.000
187A207PRO0-0.056-0.04026.7090.2860.2860.0000.0000.0000.000
188A208ILE0-0.0060.00729.5800.2620.2620.0000.0000.0000.000
189A209GLU-1-0.875-0.93232.380-17.189-17.1890.0000.0000.0000.000
190A210ARG10.8350.91029.10820.38520.3850.0000.0000.0000.000
191A211LEU00.015-0.00329.7730.3320.3320.0000.0000.0000.000
192A212LYS10.9640.98934.05216.72816.7280.0000.0000.0000.000
193A213PHE00.0280.02537.4570.3050.3050.0000.0000.0000.000
194A214TYR0-0.026-0.04235.2680.2790.2790.0000.0000.0000.000
195A215ALA00.0080.02537.5250.1680.1680.0000.0000.0000.000
196A216GLU-1-0.905-0.94439.069-13.783-13.7830.0000.0000.0000.000
197A217LYS10.8040.88740.35815.49815.4980.0000.0000.0000.000
198A218ASN0-0.111-0.08039.7200.3450.3450.0000.0000.0000.000
199A219GLY00.0220.02442.7890.0950.0950.0000.0000.0000.000
200A220TYR0-0.071-0.04739.8500.1270.1270.0000.0000.0000.000
201A221LYS10.9130.95340.84913.68213.6820.0000.0000.0000.000
202A222LEU0-0.066-0.04533.732-0.272-0.2720.0000.0000.0000.000
203A223ILE0-0.079-0.02937.1990.1960.1960.0000.0000.0000.000
204A224ASP-1-0.878-0.94834.213-17.463-17.4630.0000.0000.0000.000
205A225TYR0-0.040-0.04129.944-0.152-0.1520.0000.0000.0000.000
206A226GLU-1-0.797-0.86126.368-21.736-21.7360.0000.0000.0000.000
207A227VAL0-0.034-0.02424.031-0.435-0.4350.0000.0000.0000.000
208A228ARG10.7770.86520.34823.19523.1950.0000.0000.0000.000
209A229LYS10.9060.95317.20727.94727.9470.0000.0000.0000.000
210A230ILE0-0.0060.01414.249-0.726-0.7260.0000.0000.0000.000
211A231LYS10.8630.92412.11236.76936.7690.0000.0000.0000.000
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