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: GVK21

Calculation Name: 5ZW3-B-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine | magnesium ion

Ligand 3-letter code: SAH | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5ZW3

Chain ID: B

ChEMBL ID:

UniProt ID: O32036

Base Structure: X-ray

Registration Date: 2025-10-06

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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2277390.094186
FMO2-HF: Nuclear repulsion 2199897.358943
FMO2-HF: Total energy -77492.735243
FMO2-MP2: Total energy -77720.885686


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:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
-27.286-24.32115.641-7.935-10.6720.075
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.004
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].
3A5TYR00.000-0.0061.944-15.982-13.6198.545-5.116-5.7930.049
4A6GLU-1-0.836-0.9192.013-12.898-13.0377.079-2.657-4.2840.025
5A7GLN00.0150.0213.590-3.371-2.7570.018-0.155-0.4770.001
6A8ILE0-0.054-0.0335.1630.0200.147-0.001-0.007-0.1180.000
7A9ASN00.0270.0146.765-0.284-0.2840.0000.0000.0000.000
8A10ASP-1-0.856-0.9306.422-5.465-5.4650.0000.0000.0000.000
9A11TYR0-0.103-0.0559.212-0.011-0.0110.0000.0000.0000.000
10A12ILE00.003-0.00511.1090.0600.0600.0000.0000.0000.000
11A13GLU-1-0.796-0.89612.0420.2620.2620.0000.0000.0000.000
12A14ALA0-0.068-0.03013.247-0.065-0.0650.0000.0000.0000.000
13A15LEU0-0.065-0.02914.949-0.010-0.0100.0000.0000.0000.000
14A16LEU0-0.0250.00815.9890.0930.0930.0000.0000.0000.000
15A17LYS10.9550.98518.941-0.254-0.2540.0000.0000.0000.000
16A18PRO0-0.020-0.00621.9570.0560.0560.0000.0000.0000.000
17A19ARG10.8470.88919.110-0.142-0.1420.0000.0000.0000.000
18A20PRO00.026-0.00524.782-0.064-0.0640.0000.0000.0000.000
19A21ASP-1-0.861-0.94626.926-0.102-0.1020.0000.0000.0000.000
20A22ASN0-0.015-0.00328.084-0.021-0.0210.0000.0000.0000.000
21A23VAL00.0380.02223.7440.0170.0170.0000.0000.0000.000
22A24LYS10.8700.94722.7690.1320.1320.0000.0000.0000.000
23A25ARG10.9360.97423.828-0.016-0.0160.0000.0000.0000.000
24A26LEU00.0090.02224.867-0.004-0.0040.0000.0000.0000.000
25A27GLU-1-0.733-0.82719.8520.2540.2540.0000.0000.0000.000
26A28ALA00.0320.01220.613-0.001-0.0010.0000.0000.0000.000
27A29TYR00.0000.00522.255-0.023-0.0230.0000.0000.0000.000
28A30ALA0-0.012-0.01920.5250.0010.0010.0000.0000.0000.000
29A31GLU-1-0.940-0.96016.810-0.388-0.3880.0000.0000.0000.000
30A32GLU-1-0.930-0.95719.308-0.283-0.2830.0000.0000.0000.000
31A33HIS0-0.118-0.05922.211-0.029-0.0290.0000.0000.0000.000
32A34HIS0-0.089-0.04319.1300.0260.0260.0000.0000.0000.000
33A35VAL0-0.066-0.03420.3530.0980.0980.0000.0000.0000.000
34A36PRO0-0.0070.00317.676-0.028-0.0280.0000.0000.0000.000
35A37ILE0-0.029-0.02018.4230.0030.0030.0000.0000.0000.000
36A38MET00.0220.02117.1930.0940.0940.0000.0000.0000.000
37A39GLU-1-0.819-0.90811.7011.3251.3250.0000.0000.0000.000
38A40LYS10.8530.92514.272-0.145-0.1450.0000.0000.0000.000
39A41ALA00.0250.00312.189-0.091-0.0910.0000.0000.0000.000
40A42GLY00.0350.01514.2740.0560.0560.0000.0000.0000.000
41A43MET0-0.018-0.00215.683-0.158-0.1580.0000.0000.0000.000
42A44GLU-1-0.846-0.91317.8630.5020.5020.0000.0000.0000.000
43A45VAL0-0.021-0.00416.258-0.083-0.0830.0000.0000.0000.000
44A46LEU00.0100.00819.208-0.084-0.0840.0000.0000.0000.000
45A47LEU00.000-0.00421.555-0.098-0.0980.0000.0000.0000.000
46A48GLN00.0240.01422.336-0.095-0.0950.0000.0000.0000.000
47A49ILE0-0.034-0.02320.783-0.056-0.0560.0000.0000.0000.000
48A50LEU0-0.010-0.01424.803-0.068-0.0680.0000.0000.0000.000
49A51SER0-0.017-0.02727.127-0.066-0.0660.0000.0000.0000.000
50A52VAL0-0.067-0.02127.179-0.051-0.0510.0000.0000.0000.000
51A53LYS10.8230.91229.059-0.649-0.6490.0000.0000.0000.000
52A54GLN0-0.082-0.04430.745-0.056-0.0560.0000.0000.0000.000
53A55PRO0-0.027-0.00230.506-0.025-0.0250.0000.0000.0000.000
54A56LYS10.9410.95433.743-0.378-0.3780.0000.0000.0000.000
55A57LYS10.8310.92035.963-0.427-0.4270.0000.0000.0000.000
56A58ILE00.0020.00029.2300.0290.0290.0000.0000.0000.000
57A59LEU0-0.0030.01031.651-0.040-0.0400.0000.0000.0000.000
58A60GLU-1-0.753-0.83326.4510.7270.7270.0000.0000.0000.000
59A61ILE0-0.027-0.01727.619-0.060-0.0600.0000.0000.0000.000
60A62GLY00.0300.01125.5990.0820.0820.0000.0000.0000.000
61A63THR0-0.022-0.02525.5670.0140.0140.0000.0000.0000.000
62A64ALA00.0160.00824.100-0.018-0.0180.0000.0000.0000.000
63A65ILE0-0.015-0.00724.072-0.048-0.0480.0000.0000.0000.000
64A66GLY00.0540.01427.230-0.051-0.0510.0000.0000.0000.000
65A67TYR0-0.051-0.03620.2390.0110.0110.0000.0000.0000.000
66A68SER00.046-0.00422.957-0.024-0.0240.0000.0000.0000.000
67A69ALA00.0240.01324.522-0.017-0.0170.0000.0000.0000.000
68A70ILE00.0100.00427.823-0.024-0.0240.0000.0000.0000.000
69A71ARG10.7850.86420.708-0.585-0.5850.0000.0000.0000.000
70A72MET0-0.0010.00025.7410.0060.0060.0000.0000.0000.000
71A73ALA00.0150.01127.894-0.019-0.0190.0000.0000.0000.000
72A74LEU0-0.064-0.02728.597-0.046-0.0460.0000.0000.0000.000
73A75GLU-1-0.889-0.91727.2140.4640.4640.0000.0000.0000.000
74A76LEU0-0.018-0.00429.584-0.013-0.0130.0000.0000.0000.000
75A77PRO0-0.011-0.01332.582-0.011-0.0110.0000.0000.0000.000
76A78SER0-0.052-0.03135.676-0.023-0.0230.0000.0000.0000.000
77A79ALA0-0.0260.01033.776-0.004-0.0040.0000.0000.0000.000
78A80GLU-1-0.807-0.86735.8320.3040.3040.0000.0000.0000.000
79A81ILE0-0.038-0.02130.0030.0370.0370.0000.0000.0000.000
80A82TYR0-0.037-0.03633.654-0.035-0.0350.0000.0000.0000.000
81A83THR0-0.025-0.04229.3450.0410.0410.0000.0000.0000.000
82A84ILE00.0200.02530.822-0.042-0.0420.0000.0000.0000.000
83A85GLU-1-0.804-0.89327.6930.6010.6010.0000.0000.0000.000
84A86ARG10.9050.93328.001-0.622-0.6220.0000.0000.0000.000
85A87ASN0-0.057-0.03329.517-0.049-0.0490.0000.0000.0000.000
86A88GLU-1-0.878-0.94031.4900.2200.2200.0000.0000.0000.000
87A89LYS10.8370.90630.680-0.155-0.1550.0000.0000.0000.000
88A90ARG10.9440.97823.469-0.533-0.5330.0000.0000.0000.000
89A91HIS00.0740.03330.0020.0080.0080.0000.0000.0000.000
90A92GLU-1-0.918-0.95332.8790.1440.1440.0000.0000.0000.000
91A93GLU-1-0.862-0.92629.6080.1310.1310.0000.0000.0000.000
92A94ALA0-0.0200.00330.066-0.008-0.0080.0000.0000.0000.000
93A95VAL00.0120.00031.299-0.009-0.0090.0000.0000.0000.000
94A96ASN0-0.074-0.04134.468-0.026-0.0260.0000.0000.0000.000
95A97ASN00.0270.00729.231-0.046-0.0460.0000.0000.0000.000
96A98ILE0-0.004-0.00631.754-0.006-0.0060.0000.0000.0000.000
97A99LYS10.9680.99833.765-0.138-0.1380.0000.0000.0000.000
98A100GLU-1-1.005-1.00433.9780.0630.0630.0000.0000.0000.000
99A101PHE0-0.086-0.06628.622-0.018-0.0180.0000.0000.0000.000
100A102GLN0-0.086-0.03234.494-0.003-0.0030.0000.0000.0000.000
101A103LEU00.0190.01532.3720.0080.0080.0000.0000.0000.000
102A104ASP-1-0.881-0.94536.3090.2220.2220.0000.0000.0000.000
103A105ASP-1-0.934-0.97338.2540.2450.2450.0000.0000.0000.000
104A106ARG10.7920.89034.527-0.307-0.3070.0000.0000.0000.000
105A107ILE0-0.020-0.00231.5040.0310.0310.0000.0000.0000.000
106A108HIS10.7680.87435.284-0.338-0.3380.0000.0000.0000.000
107A109VAL00.0270.01233.0870.0300.0300.0000.0000.0000.000
108A110PHE0-0.020-0.00534.988-0.028-0.0280.0000.0000.0000.000
109A111TYR0-0.016-0.00734.6870.0290.0290.0000.0000.0000.000
110A112GLY00.0340.00334.838-0.018-0.0180.0000.0000.0000.000
111A113ASP-1-0.799-0.90432.5620.5990.5990.0000.0000.0000.000
112A114ALA00.0340.02831.216-0.017-0.0170.0000.0000.0000.000
113A115LEU0-0.043-0.03131.6090.0010.0010.0000.0000.0000.000
114A116GLU-1-0.985-0.98834.8100.3780.3780.0000.0000.0000.000
115A117LEU0-0.031-0.00935.360-0.025-0.0250.0000.0000.0000.000
116A118ALA00.0360.02837.802-0.008-0.0080.0000.0000.0000.000
117A119ASP-1-0.893-0.95938.6900.3680.3680.0000.0000.0000.000
118A120ALA0-0.044-0.03040.640-0.011-0.0110.0000.0000.0000.000
119A121VAL00.0120.01935.648-0.007-0.0070.0000.0000.0000.000
120A122HIS00.0480.01938.9550.0190.0190.0000.0000.0000.000
121A123VAL0-0.067-0.02541.111-0.010-0.0100.0000.0000.0000.000
122A124THR0-0.011-0.00739.220-0.019-0.0190.0000.0000.0000.000
123A125ALA00.0300.05039.0640.0170.0170.0000.0000.0000.000
124A126PRO0-0.086-0.05338.390-0.028-0.0280.0000.0000.0000.000
125A127TYR0-0.010-0.01533.893-0.018-0.0180.0000.0000.0000.000
126A128ASP-1-0.829-0.89834.0260.5170.5170.0000.0000.0000.000
127A129VAL0-0.008-0.01927.5100.0340.0340.0000.0000.0000.000
128A130ILE00.0030.01628.689-0.048-0.0480.0000.0000.0000.000
129A131PHE0-0.011-0.01021.0590.0660.0660.0000.0000.0000.000
130A132ILE0-0.034-0.02224.087-0.087-0.0870.0000.0000.0000.000
131A133ASP-1-0.846-0.92820.1521.4411.4410.0000.0000.0000.000
132A134ALA00.0730.02422.431-0.126-0.1260.0000.0000.0000.000
133A135ALA0-0.050-0.03122.3090.0870.0870.0000.0000.0000.000
134A136LYS10.8780.92516.144-2.150-2.1500.0000.0000.0000.000
135A137GLY0-0.051-0.02021.9040.0390.0390.0000.0000.0000.000
136A138GLN0-0.017-0.01224.419-0.082-0.0820.0000.0000.0000.000
137A139TYR00.004-0.00420.031-0.142-0.1420.0000.0000.0000.000
138A140GLN0-0.005-0.00225.602-0.080-0.0800.0000.0000.0000.000
139A141ASN0-0.029-0.01727.945-0.050-0.0500.0000.0000.0000.000
140A142PHE00.009-0.00426.179-0.048-0.0480.0000.0000.0000.000
141A143PHE00.0420.01426.720-0.043-0.0430.0000.0000.0000.000
142A144HIS0-0.031-0.02129.653-0.021-0.0210.0000.0000.0000.000
143A145LEU0-0.045-0.00632.905-0.039-0.0390.0000.0000.0000.000
144A146TYR0-0.006-0.04132.005-0.044-0.0440.0000.0000.0000.000
145A147GLU-1-0.859-0.90331.7460.6310.6310.0000.0000.0000.000
146A148PRO0-0.0100.00033.496-0.021-0.0210.0000.0000.0000.000
147A149MET0-0.065-0.00636.022-0.035-0.0350.0000.0000.0000.000
148A150LEU0-0.0340.00131.385-0.011-0.0110.0000.0000.0000.000
149A151SER0-0.027-0.04535.112-0.026-0.0260.0000.0000.0000.000
150A152PRO0-0.015-0.01535.6350.0330.0330.0000.0000.0000.000
151A153ASP-1-0.845-0.91634.6330.5830.5830.0000.0000.0000.000
152A154GLY0-0.019-0.00432.8900.0100.0100.0000.0000.0000.000
153A155VAL0-0.066-0.03826.3370.0210.0210.0000.0000.0000.000
154A156ILE00.0110.01225.882-0.030-0.0300.0000.0000.0000.000
155A157ILE0-0.011-0.01021.4980.0730.0730.0000.0000.0000.000
156A158THR0-0.020-0.00320.610-0.124-0.1240.0000.0000.0000.000
157A159ASP-1-0.774-0.88516.2122.4012.4010.0000.0000.0000.000
158A160ASN0-0.073-0.01515.620-0.143-0.1430.0000.0000.0000.000
159A161VAL0-0.036-0.02515.664-0.178-0.1780.0000.0000.0000.000
160A162LEU0-0.084-0.03410.3950.0430.0430.0000.0000.0000.000
161A163PHE-1-0.797-0.8756.9003.2913.2910.0000.0000.0000.000
162A186ILE00.0360.00816.527-0.072-0.0720.0000.0000.0000.000
163A187ASP-1-0.866-0.93517.5012.1122.1120.0000.0000.0000.000
164A188GLU-1-0.910-0.95019.4660.9580.9580.0000.0000.0000.000
165A189TYR0-0.008-0.01321.249-0.124-0.1240.0000.0000.0000.000
166A190ASN00.019-0.00616.668-0.192-0.1920.0000.0000.0000.000
167A191HIS0-0.064-0.03219.956-0.125-0.1250.0000.0000.0000.000
168A192TRP0-0.0040.00323.232-0.067-0.0670.0000.0000.0000.000
169A193LEU0-0.021-0.00722.210-0.072-0.0720.0000.0000.0000.000
170A194MET0-0.051-0.02321.039-0.011-0.0110.0000.0000.0000.000
171A195ASN0-0.109-0.06024.318-0.099-0.0990.0000.0000.0000.000
172A196HIS00.0740.06027.755-0.077-0.0770.0000.0000.0000.000
173A197PRO0-0.017-0.01029.8720.0010.0010.0000.0000.0000.000
174A198ASP-1-0.904-0.95533.1990.6240.6240.0000.0000.0000.000
175A199TYR0-0.023-0.04328.640-0.008-0.0080.0000.0000.0000.000
176A200GLN0-0.041-0.00527.530-0.011-0.0110.0000.0000.0000.000
177A201THR00.0380.01121.521-0.043-0.0430.0000.0000.0000.000
178A202ALA0-0.0250.00320.3420.0160.0160.0000.0000.0000.000
179A203ILE00.0410.00514.803-0.048-0.0480.0000.0000.0000.000
180A204ILE0-0.026-0.00914.2820.0900.0900.0000.0000.0000.000
181A205PRO0-0.028-0.0169.5420.0190.0190.0000.0000.0000.000
182A206VAL00.002-0.00910.3460.5050.5050.0000.0000.0000.000
183A207GLY00.0430.03110.648-0.455-0.4550.0000.0000.0000.000
184A208ASP-1-0.808-0.89310.3274.4174.4170.0000.0000.0000.000
185A209GLY0-0.027-0.01312.621-0.018-0.0180.0000.0000.0000.000
186A210LEU00.0330.01213.538-0.450-0.4500.0000.0000.0000.000
187A211ALA0-0.0040.00316.9840.0800.0800.0000.0000.0000.000
188A212ILE0-0.023-0.01419.636-0.159-0.1590.0000.0000.0000.000
189A213SER00.040-0.00722.4160.0380.0380.0000.0000.0000.000
190A214LYS10.8730.94525.686-0.747-0.7470.0000.0000.0000.000
191A215LYS10.9330.97429.245-0.602-0.6020.0000.0000.0000.000
192A216LYS10.7490.84730.624-0.842-0.8420.0000.0000.0000.000
193A217ARG0-0.0040.02532.819-0.016-0.0160.0000.0000.0000.000