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: 9RL52

Calculation Name: 2HNK-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine | sulfate ion | di(hydroxyethyl)ether

Ligand 3-letter code: SAH | SO4 | PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HNK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8F8Y3

Base Structure: X-ray

Registration Date: 2025-10-05

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2896747.879159
FMO2-HF: Nuclear repulsion 2806901.848018
FMO2-HF: Total energy -89846.031141
FMO2-MP2: Total energy -90112.134734


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:3:ARG)


Summations of interaction energy for fragment #1(A:3:ARG)
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.
-237.745-234.3636.259-5.258-4.383-0.064
Interaction energy analysis for fragmet #1(A:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.796 / q_NPA : 1.889
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].
3A5ASN00.0980.0673.43011.54613.4510.001-0.778-1.128-0.001
4A6ILE00.0240.0041.897-50.169-48.8696.259-4.450-3.109-0.063
5A7SER0-0.026-0.0174.265-6.531-6.354-0.001-0.030-0.1460.000
6A8LEU00.0260.0235.5104.0224.0220.0000.0000.0000.000
7A9THR00.0280.0039.0760.9190.9190.0000.0000.0000.000
8A10GLU-1-0.803-0.89812.337-30.012-30.0120.0000.0000.0000.000
9A11SER0-0.046-0.01815.2051.3501.3500.0000.0000.0000.000
10A12LEU0-0.046-0.02710.0550.7000.7000.0000.0000.0000.000
11A13GLU-1-0.890-0.95113.129-37.220-37.2200.0000.0000.0000.000
12A14GLU-1-0.843-0.92315.422-23.881-23.8810.0000.0000.0000.000
13A15TYR0-0.072-0.03916.1031.5861.5860.0000.0000.0000.000
14A16ILE00.0150.00512.5080.9160.9160.0000.0000.0000.000
15A17PHE00.0340.03417.1571.3521.3520.0000.0000.0000.000
16A18ARG10.9190.96019.89626.99426.9940.0000.0000.0000.000
17A19ASN0-0.119-0.05619.2961.4921.4920.0000.0000.0000.000
18A20SER0-0.081-0.05319.7750.0440.0440.0000.0000.0000.000
19A21VAL0-0.0390.00821.4780.8770.8770.0000.0000.0000.000
20A22ARG10.9160.95323.99521.65721.6570.0000.0000.0000.000
21A23GLU-1-0.711-0.81126.991-20.575-20.5750.0000.0000.0000.000
22A24PRO00.0100.01028.7620.3410.3410.0000.0000.0000.000
23A25ASP-1-0.869-0.93532.362-16.861-16.8610.0000.0000.0000.000
24A26SER0-0.036-0.04334.473-0.118-0.1180.0000.0000.0000.000
25A27PHE00.0280.00129.617-0.015-0.0150.0000.0000.0000.000
26A28LEU00.0110.01028.813-0.217-0.2170.0000.0000.0000.000
27A29LYS10.7480.85030.99815.48815.4880.0000.0000.0000.000
28A30LEU00.0420.03431.7630.0550.0550.0000.0000.0000.000
29A31ARG10.8410.89425.08621.82021.8200.0000.0000.0000.000
30A32LYS10.9220.96129.95117.62617.6260.0000.0000.0000.000
31A33GLU-1-0.772-0.84532.002-15.544-15.5440.0000.0000.0000.000
32A34THR00.0070.01130.3850.3110.3110.0000.0000.0000.000
33A35GLY0-0.017-0.01530.134-0.072-0.0720.0000.0000.0000.000
34A36THR0-0.126-0.06430.7870.1570.1570.0000.0000.0000.000
35A37LEU0-0.025-0.00334.2100.3230.3230.0000.0000.0000.000
36A38ALA00.0030.01132.9400.2530.2530.0000.0000.0000.000
37A39GLN00.0230.00226.813-0.666-0.6660.0000.0000.0000.000
38A40ALA00.0220.02026.737-0.168-0.1680.0000.0000.0000.000
39A41ASN0-0.039-0.02920.151-0.632-0.6320.0000.0000.0000.000
40A42MET0-0.0090.00223.442-0.735-0.7350.0000.0000.0000.000
41A43GLN0-0.005-0.00424.8991.4121.4120.0000.0000.0000.000
42A44ILE00.0010.01722.657-0.751-0.7510.0000.0000.0000.000
43A45SER0-0.012-0.02319.6490.5650.5650.0000.0000.0000.000
44A46PRO00.0230.01022.0610.1810.1810.0000.0000.0000.000
45A47GLU-1-0.805-0.90717.865-27.180-27.1800.0000.0000.0000.000
46A48GLU0-0.036-0.05419.515-0.306-0.3060.0000.0000.0000.000
47A49GLY00.0530.01120.7970.5400.5400.0000.0000.0000.000
48A50GLN0-0.035-0.04222.6801.4511.4510.0000.0000.0000.000
49A51PHE00.0030.00717.8560.2130.2130.0000.0000.0000.000
50A52LEU00.0460.02321.6720.3090.3090.0000.0000.0000.000
51A53ASN0-0.0220.01624.6570.6790.6790.0000.0000.0000.000
52A54ILE00.004-0.01122.3800.6560.6560.0000.0000.0000.000
53A55LEU00.0140.01020.8660.3950.3950.0000.0000.0000.000
54A56THR00.000-0.00824.9730.6330.6330.0000.0000.0000.000
55A57LYS10.8420.92928.53419.83219.8320.0000.0000.0000.000
56A58ILE0-0.045-0.02023.8230.3920.3920.0000.0000.0000.000
57A59SER0-0.052-0.03527.9180.3340.3340.0000.0000.0000.000
58A60GLY0-0.0030.00629.5220.4430.4430.0000.0000.0000.000
59A61ALA0-0.043-0.01031.9570.6240.6240.0000.0000.0000.000
60A62LYS10.8220.86933.70115.53015.5300.0000.0000.0000.000
61A63ARG10.7840.88936.36515.42115.4210.0000.0000.0000.000
62A64ILE00.0430.02531.177-0.299-0.2990.0000.0000.0000.000
63A65ILE00.001-0.00133.2720.6110.6110.0000.0000.0000.000
64A66GLU-1-0.746-0.83530.386-19.913-19.9130.0000.0000.0000.000
65A67ILE0-0.029-0.01430.5650.7340.7340.0000.0000.0000.000
66A68GLY00.0180.01029.988-0.700-0.7000.0000.0000.0000.000
67A69THR0-0.052-0.05530.474-0.181-0.1810.0000.0000.0000.000
68A70PHE00.016-0.00129.760-0.072-0.0720.0000.0000.0000.000
69A71THR0-0.013-0.02932.1930.4000.4000.0000.0000.0000.000
70A72GLY00.0410.00832.7200.2960.2960.0000.0000.0000.000
71A73TYR0-0.052-0.04125.998-0.205-0.2050.0000.0000.0000.000
72A74SER00.034-0.00627.168-0.109-0.1090.0000.0000.0000.000
73A75SER00.008-0.00328.7620.3190.3190.0000.0000.0000.000
74A76LEU0-0.0160.00631.9240.3810.3810.0000.0000.0000.000
75A77CYS0-0.0280.01527.8560.0160.0160.0000.0000.0000.000
76A78PHE00.0280.00927.055-0.012-0.0120.0000.0000.0000.000
77A79ALA00.0070.00231.3040.2730.2730.0000.0000.0000.000
78A80SER0-0.042-0.03532.3990.2790.2790.0000.0000.0000.000
79A81ALA0-0.087-0.03030.064-0.017-0.0170.0000.0000.0000.000
80A82LEU0-0.0170.00331.9870.1170.1170.0000.0000.0000.000
81A83PRO00.0210.02034.7800.2740.2740.0000.0000.0000.000
82A84GLU-1-0.935-0.97537.733-13.782-13.7820.0000.0000.0000.000
83A85ASP-1-0.805-0.88440.921-14.782-14.7820.0000.0000.0000.000
84A86GLY0-0.041-0.01337.8820.0040.0040.0000.0000.0000.000
85A87LYS10.8240.90738.48413.92513.9250.0000.0000.0000.000
86A88ILE00.010-0.00432.855-0.361-0.3610.0000.0000.0000.000
87A89LEU0-0.0230.00436.7100.4500.4500.0000.0000.0000.000
88A90CYS0-0.0010.00635.372-0.581-0.5810.0000.0000.0000.000
89A91CYS0-0.020-0.00835.1620.6850.6850.0000.0000.0000.000
90A92ASP-1-0.735-0.86134.194-17.911-17.9110.0000.0000.0000.000
91A93VAL00.023-0.00235.5720.4950.4950.0000.0000.0000.000
92A94SER0-0.0110.00337.1040.5670.5670.0000.0000.0000.000
93A95GLU-1-0.860-0.90938.930-13.721-13.7210.0000.0000.0000.000
94A96GLU-1-0.903-0.94539.442-15.071-15.0710.0000.0000.0000.000
95A97TRP00.006-0.00935.369-0.132-0.1320.0000.0000.0000.000
96A98THR00.016-0.02436.942-0.006-0.0060.0000.0000.0000.000
97A99ASN0-0.048-0.02438.6360.1360.1360.0000.0000.0000.000
98A100VAL0-0.032-0.01136.2690.1290.1290.0000.0000.0000.000
99A101ALA00.0220.02036.059-0.047-0.0470.0000.0000.0000.000
100A102ARG10.8970.92537.13414.14814.1480.0000.0000.0000.000
101A103LYS10.8180.90139.52115.24315.2430.0000.0000.0000.000
102A104TYR00.005-0.01236.1120.1560.1560.0000.0000.0000.000
103A105TRP0-0.010-0.01235.5170.3280.3280.0000.0000.0000.000
104A106LYS10.8210.89839.26913.43313.4330.0000.0000.0000.000
105A107GLU-1-0.823-0.86238.744-15.166-15.1660.0000.0000.0000.000
106A108ASN0-0.058-0.05536.727-0.150-0.1500.0000.0000.0000.000
107A109GLY00.0010.01239.620-0.022-0.0220.0000.0000.0000.000
108A110LEU0-0.004-0.00836.1990.0850.0850.0000.0000.0000.000
109A111GLU-1-0.766-0.86740.420-13.690-13.6900.0000.0000.0000.000
110A112ASN0-0.019-0.00142.456-0.120-0.1200.0000.0000.0000.000
111A113LYS10.7980.90737.29716.05616.0560.0000.0000.0000.000
112A114ILE0-0.033-0.01037.336-0.364-0.3640.0000.0000.0000.000
113A115PHE0-0.019-0.00439.9070.3720.3720.0000.0000.0000.000
114A116LEU00.000-0.01138.734-0.397-0.3970.0000.0000.0000.000
115A117LYS10.8400.93240.04814.62214.6220.0000.0000.0000.000
116A118LEU00.0250.02439.718-0.333-0.3330.0000.0000.0000.000
117A119GLY00.004-0.00240.2960.4250.4250.0000.0000.0000.000
118A120SER00.0430.02438.732-0.558-0.5580.0000.0000.0000.000
119A121ALA00.0790.03835.0420.2720.2720.0000.0000.0000.000
120A122LEU00.0150.01333.9340.0800.0800.0000.0000.0000.000
121A123GLU-1-0.951-0.97337.326-13.815-13.8150.0000.0000.0000.000
122A124THR0-0.040-0.02939.1050.3450.3450.0000.0000.0000.000
123A125LEU00.0170.00034.1500.1900.1900.0000.0000.0000.000
124A126GLN0-0.028-0.02638.859-0.235-0.2350.0000.0000.0000.000
125A127VAL00.0120.00241.2950.2940.2940.0000.0000.0000.000
126A128LEU0-0.0350.00639.4080.3210.3210.0000.0000.0000.000
127A129ILE0-0.037-0.01038.0530.0480.0480.0000.0000.0000.000
128A130ASP-1-0.846-0.91642.405-13.837-13.8370.0000.0000.0000.000
129A131SER0-0.097-0.06345.6220.4510.4510.0000.0000.0000.000
130A132LYS10.9390.95647.51911.72811.7280.0000.0000.0000.000
131A133SER0-0.007-0.00650.1670.2110.2110.0000.0000.0000.000
132A134ALA00.0100.01947.381-0.099-0.0990.0000.0000.0000.000
133A135PRO00.0270.03145.6620.3160.3160.0000.0000.0000.000
134A136SER00.014-0.01247.725-0.211-0.2110.0000.0000.0000.000
135A137TRP00.025-0.00341.858-0.019-0.0190.0000.0000.0000.000
136A138ALA00.0230.00543.244-0.357-0.3570.0000.0000.0000.000
137A139SER0-0.0140.00144.661-0.019-0.0190.0000.0000.0000.000
138A140ASP-1-0.895-0.96246.807-13.011-13.0110.0000.0000.0000.000
139A141PHE0-0.0170.01537.527-0.160-0.1600.0000.0000.0000.000
140A142ALA0-0.023-0.01140.608-0.016-0.0160.0000.0000.0000.000
141A143PHE0-0.001-0.01442.6800.0380.0380.0000.0000.0000.000
142A144GLY00.0660.05343.3780.0830.0830.0000.0000.0000.000
143A145PRO0-0.038-0.02940.221-0.373-0.3730.0000.0000.0000.000
144A146SER0-0.032-0.01238.0600.1410.1410.0000.0000.0000.000
145A147SER0-0.035-0.01639.1430.0330.0330.0000.0000.0000.000
146A148ILE0-0.044-0.02534.1820.1100.1100.0000.0000.0000.000
147A149ASP-1-0.760-0.85133.548-17.159-17.1590.0000.0000.0000.000
148A150LEU0-0.006-0.01127.461-0.553-0.5530.0000.0000.0000.000
149A151PHE00.0510.00029.3190.7150.7150.0000.0000.0000.000
150A152PHE00.009-0.00123.579-0.804-0.8040.0000.0000.0000.000
151A153LEU0-0.035-0.01526.0740.8910.8910.0000.0000.0000.000
152A154ASP-1-0.809-0.91525.249-24.016-24.0160.0000.0000.0000.000
153A155ALA0-0.0220.00326.7150.3850.3850.0000.0000.0000.000
154A156ASP-1-0.784-0.87027.999-19.230-19.2300.0000.0000.0000.000
155A157LYS10.8280.93024.14523.27023.2700.0000.0000.0000.000
156A158GLU-1-0.874-0.95526.900-20.535-20.5350.0000.0000.0000.000
157A159ASN0-0.031-0.01929.0280.2620.2620.0000.0000.0000.000
158A160TYR00.000-0.00422.8960.7440.7440.0000.0000.0000.000
159A161PRO0-0.051-0.03127.2580.1100.1100.0000.0000.0000.000
160A162ASN0-0.041-0.03129.1940.3310.3310.0000.0000.0000.000
161A163TYR0-0.024-0.05529.9980.7080.7080.0000.0000.0000.000
162A164TYR0-0.041-0.04026.8430.1050.1050.0000.0000.0000.000
163A165PRO00.0190.01030.1690.1490.1490.0000.0000.0000.000
164A166LEU0-0.026-0.01033.4780.4470.4470.0000.0000.0000.000
165A167ILE00.0260.00929.0450.3180.3180.0000.0000.0000.000
166A168LEU00.0150.00929.2390.2880.2880.0000.0000.0000.000
167A169LYS10.8950.96833.07316.05516.0550.0000.0000.0000.000
168A170LEU00.0240.00535.7300.4020.4020.0000.0000.0000.000
169A171LEU0-0.0410.00029.8590.2630.2630.0000.0000.0000.000
170A172LYS10.8460.91834.47616.57816.5780.0000.0000.0000.000
171A173PRO00.0220.01033.782-0.659-0.6590.0000.0000.0000.000
172A174GLY0-0.055-0.01831.1010.2700.2700.0000.0000.0000.000
173A175GLY00.0220.01730.376-0.455-0.4550.0000.0000.0000.000
174A176LEU0-0.043-0.02823.925-0.608-0.6080.0000.0000.0000.000
175A177LEU00.0210.01325.3110.6800.6800.0000.0000.0000.000
176A178ILE0-0.022-0.00822.214-1.140-1.1400.0000.0000.0000.000
177A179ALA00.008-0.00122.3320.9540.9540.0000.0000.0000.000
178A180ASP-1-0.773-0.85920.754-28.714-28.7140.0000.0000.0000.000
179A181ASN0-0.028-0.03419.2301.4041.4040.0000.0000.0000.000
180A182VAL0-0.037-0.00816.537-0.193-0.1930.0000.0000.0000.000
181A183LEU0-0.026-0.02911.619-1.608-1.6080.0000.0000.0000.000
182A184TRP00.0000.00615.678-0.156-0.1560.0000.0000.0000.000
183A185ASP-1-0.898-0.93716.051-31.657-31.6570.0000.0000.0000.000
184A186GLY0-0.0220.00013.853-1.146-1.1460.0000.0000.0000.000
185A187SER0-0.056-0.04914.457-0.200-0.2000.0000.0000.0000.000
186A188VAL00.011-0.00215.4570.8920.8920.0000.0000.0000.000
187A189ALA0-0.030-0.00613.7260.3900.3900.0000.0000.0000.000
188A190ASP-1-0.848-0.91415.733-30.715-30.7150.0000.0000.0000.000
189A191LEU00.011-0.01317.8381.5871.5870.0000.0000.0000.000
190A192SER0-0.023-0.00721.0201.7841.7840.0000.0000.0000.000
191A193HIS10.7780.90219.81528.94128.9410.0000.0000.0000.000
192A194GLN00.000-0.01623.010-0.165-0.1650.0000.0000.0000.000
193A195GLU-1-0.768-0.84124.067-24.009-24.0090.0000.0000.0000.000
194A196PRO00.023-0.00426.389-0.571-0.5710.0000.0000.0000.000
195A197SER00.0570.03025.393-0.290-0.2900.0000.0000.0000.000
196A198THR00.017-0.01420.879-0.545-0.5450.0000.0000.0000.000
197A199VAL0-0.034-0.01022.870-0.822-0.8220.0000.0000.0000.000
198A200GLY00.0230.01825.364-0.158-0.1580.0000.0000.0000.000
199A201ILE00.0160.01420.008-0.128-0.1280.0000.0000.0000.000
200A202ARG10.7630.86419.77827.55827.5580.0000.0000.0000.000
201A203LYS10.8720.93821.87122.02222.0220.0000.0000.0000.000
202A204PHE00.003-0.00522.0620.3590.3590.0000.0000.0000.000
203A205ASN00.008-0.01018.2060.5040.5040.0000.0000.0000.000
204A206GLU-1-0.898-0.94121.201-24.586-24.5860.0000.0000.0000.000
205A207LEU0-0.036-0.01822.7850.3070.3070.0000.0000.0000.000
206A208VAL00.0180.00221.6620.1870.1870.0000.0000.0000.000
207A209TYR0-0.076-0.02817.609-1.030-1.0300.0000.0000.0000.000
208A210ASN0-0.076-0.05221.784-0.232-0.2320.0000.0000.0000.000
209A211ASP-1-0.795-0.85624.937-20.319-20.3190.0000.0000.0000.000
210A212SER0-0.005-0.00626.898-0.317-0.3170.0000.0000.0000.000
211A213LEU0-0.016-0.00528.5750.3640.3640.0000.0000.0000.000
212A214VAL0-0.031-0.01525.1480.3440.3440.0000.0000.0000.000
213A215ASP-1-0.871-0.90423.210-24.986-24.9860.0000.0000.0000.000
214A216VAL0-0.010-0.01818.6180.2800.2800.0000.0000.0000.000
215A217SER0-0.053-0.02216.194-2.115-2.1150.0000.0000.0000.000
216A218LEU00.0240.01913.1861.1291.1290.0000.0000.0000.000
217A219VAL00.003-0.00113.134-3.447-3.4470.0000.0000.0000.000
218A220PRO0-0.043-0.0169.0741.2681.2680.0000.0000.0000.000
219A221ILE0-0.008-0.01111.401-1.576-1.5760.0000.0000.0000.000
220A222ALA00.0590.02214.2341.0911.0910.0000.0000.0000.000
221A223ASP-1-0.764-0.85914.570-33.359-33.3590.0000.0000.0000.000
222A224GLY0-0.013-0.00514.513-0.149-0.1490.0000.0000.0000.000
223A225VAL00.001-0.00215.3012.0442.0440.0000.0000.0000.000
224A226SER0-0.017-0.00917.205-2.140-2.1400.0000.0000.0000.000
225A227LEU0-0.038-0.00819.0461.6451.6450.0000.0000.0000.000
226A228VAL00.0360.00120.917-0.961-0.9610.0000.0000.0000.000
227A229ARG10.8940.96023.54822.84922.8490.0000.0000.0000.000
228A230LYS10.8970.96426.25917.62617.6260.0000.0000.0000.000
229A231ARG10.8220.90326.40022.78622.7860.0000.0000.0000.000
230A232LEU0-0.043-0.03830.4470.5180.5180.0000.0000.0000.000
231A233GLU-1-0.912-0.97433.576-17.380-17.3800.0000.0000.0000.000
232A234HIS-1-0.966-0.96532.844-17.268-17.2680.0000.0000.0000.000