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: ZG24N

Calculation Name: 2V3K-A-Xray549

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2V3K

Chain ID: A

ChEMBL ID:

UniProt ID: Q06287

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2767753.303318
FMO2-HF: Nuclear repulsion 2678372.739906
FMO2-HF: Total energy -89380.563412
FMO2-MP2: Total energy -89637.925306


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:25:PRO)


Summations of interaction energy for fragment #1(A:25:PRO)
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.
-11.467-8.189-0.021-1.323-1.935-0.005
Interaction energy analysis for fragmet #1(A:25:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.911
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].
3A27ALA00.0280.0283.7366.5739.418-0.019-1.281-1.545-0.005
4A28PRO00.0100.0244.282-2.029-1.637-0.001-0.038-0.3540.000
5A29PRO00.000-0.0024.9283.9704.011-0.001-0.004-0.0360.000
6A30VAL00.007-0.0048.2970.2280.2280.0000.0000.0000.000
7A31LEU00.0100.02310.8491.4721.4720.0000.0000.0000.000
8A32THR0-0.025-0.03613.0611.3361.3360.0000.0000.0000.000
9A33SER0-0.013-0.03916.705-0.241-0.2410.0000.0000.0000.000
10A34LYS10.8200.92218.19614.88614.8860.0000.0000.0000.000
11A35ASP-1-0.778-0.84112.987-20.333-20.3330.0000.0000.0000.000
12A36LYS10.8300.91316.48213.33613.3360.0000.0000.0000.000
13A37ILE00.0090.00414.8810.5980.5980.0000.0000.0000.000
14A38THR0-0.056-0.05510.177-0.744-0.7440.0000.0000.0000.000
15A39LYS10.8460.93312.90318.25218.2520.0000.0000.0000.000
16A40ARG10.7440.85912.47516.57916.5790.0000.0000.0000.000
17A41MET00.0600.04514.5771.1021.1020.0000.0000.0000.000
18A42ILE0-0.060-0.04016.742-0.475-0.4750.0000.0000.0000.000
19A43VAL00.0330.01919.5280.5390.5390.0000.0000.0000.000
20A44VAL0-0.019-0.01422.284-0.130-0.1300.0000.0000.0000.000
21A45LEU0-0.022-0.01325.1790.3880.3880.0000.0000.0000.000
22A46ALA00.0760.03927.7380.1610.1610.0000.0000.0000.000
23A47MET00.014-0.00331.0500.1240.1240.0000.0000.0000.000
24A48ALA00.0260.03230.7500.1760.1760.0000.0000.0000.000
25A49SER00.0200.01132.8930.2570.2570.0000.0000.0000.000
26A50LEU0-0.067-0.03530.008-0.025-0.0250.0000.0000.0000.000
27A51GLU-1-0.749-0.84534.761-7.479-7.4790.0000.0000.0000.000
28A52THR0-0.0110.00037.101-0.050-0.0500.0000.0000.0000.000
29A53HIS00.0630.03139.5870.0980.0980.0000.0000.0000.000
30A54LYS10.8640.91742.6277.1917.1910.0000.0000.0000.000
31A55ILE00.0140.01145.3790.0920.0920.0000.0000.0000.000
32A56SER00.012-0.01147.5640.0700.0700.0000.0000.0000.000
33A57SER0-0.025-0.00443.2780.0390.0390.0000.0000.0000.000
34A58ASN0-0.007-0.01745.217-0.100-0.1000.0000.0000.0000.000
35A59GLY00.0220.02046.7150.0260.0260.0000.0000.0000.000
36A60PRO00.000-0.00147.053-0.051-0.0510.0000.0000.0000.000
37A61GLY00.0370.03443.254-0.077-0.0770.0000.0000.0000.000
38A62GLY00.0090.01542.821-0.142-0.1420.0000.0000.0000.000
39A63ASP-1-0.871-0.95039.331-8.028-8.0280.0000.0000.0000.000
40A64LYS10.8390.91141.3757.2037.2030.0000.0000.0000.000
41A65TYR-1-0.857-0.93539.168-7.441-7.4410.0000.0000.0000.000
42A66VAL0-0.0330.00238.404-0.148-0.1480.0000.0000.0000.000
43A67LEU00.0050.00133.0470.0680.0680.0000.0000.0000.000
44A68LEU0-0.028-0.01337.7770.1100.1100.0000.0000.0000.000
45A69ASN0-0.049-0.05238.586-0.115-0.1150.0000.0000.0000.000
46A70CYS00.008-0.00740.4210.1360.1360.0000.0000.0000.000
47A71ASP-1-0.919-0.93840.274-7.668-7.6680.0000.0000.0000.000
48A72ASP-1-0.861-0.91841.083-7.586-7.5860.0000.0000.0000.000
49A73HIS0-0.014-0.01241.0710.1770.1770.0000.0000.0000.000
50A74GLN00.0070.01545.7130.2770.2770.0000.0000.0000.000
51A75GLY00.008-0.00547.9770.1000.1000.0000.0000.0000.000
52A76LEU0-0.029-0.01846.0460.1270.1270.0000.0000.0000.000
53A77LEU00.0370.00143.7000.0700.0700.0000.0000.0000.000
54A78LYS10.9590.98347.8656.2156.2150.0000.0000.0000.000
55A79LYS10.9080.95751.3435.9165.9160.0000.0000.0000.000
56A80MET0-0.056-0.01445.2910.0450.0450.0000.0000.0000.000
57A81GLY00.0040.01749.908-0.038-0.0380.0000.0000.0000.000
58A82ARG10.8050.88442.9397.0867.0860.0000.0000.0000.000
59A83ASP-1-0.776-0.84545.368-6.877-6.8770.0000.0000.0000.000
60A84ILE0-0.016-0.02944.875-0.147-0.1470.0000.0000.0000.000
61A85SER0-0.094-0.08243.074-0.186-0.1860.0000.0000.0000.000
62A86GLU-1-0.883-0.95340.742-7.473-7.4730.0000.0000.0000.000
63A87ALA0-0.0150.00239.396-0.225-0.2250.0000.0000.0000.000
64A88ARG10.8760.88436.3668.5258.5250.0000.0000.0000.000
65A89PRO00.0080.00933.818-0.299-0.2990.0000.0000.0000.000
66A90ASP-1-0.785-0.87132.198-9.386-9.3860.0000.0000.0000.000
67A91ILE00.0340.03431.366-0.378-0.3780.0000.0000.0000.000
68A92THR00.0470.02028.431-0.390-0.3900.0000.0000.0000.000
69A93HIS0-0.106-0.05027.565-0.268-0.2680.0000.0000.0000.000
70A94GLN00.0460.01026.822-0.743-0.7430.0000.0000.0000.000
71A95CYS0-0.0350.00525.846-0.433-0.4330.0000.0000.0000.000
72A96LEU00.007-0.00223.133-0.602-0.6020.0000.0000.0000.000
73A97LEU0-0.065-0.03121.892-0.714-0.7140.0000.0000.0000.000
74A98THR0-0.015-0.02321.562-0.545-0.5450.0000.0000.0000.000
75A99LEU00.0170.00919.863-0.644-0.6440.0000.0000.0000.000
76A100LEU0-0.0140.00617.343-0.970-0.9700.0000.0000.0000.000
77A101ASP-1-0.823-0.90116.744-16.687-16.6870.0000.0000.0000.000
78A102SER0-0.0070.00616.385-1.003-1.0030.0000.0000.0000.000
79A103PRO00.0490.02112.609-1.049-1.0490.0000.0000.0000.000
80A104ILE00.0430.02111.401-2.328-2.3280.0000.0000.0000.000
81A105ASN0-0.096-0.06311.930-1.230-1.2300.0000.0000.0000.000
82A106LYS10.7750.89111.15218.67218.6720.0000.0000.0000.000
83A107ALA00.0290.0287.419-3.035-3.0350.0000.0000.0000.000
84A108GLY0-0.062-0.0227.124-3.134-3.1340.0000.0000.0000.000
85A109LYS10.9320.9537.39832.23132.2310.0000.0000.0000.000
86A110LEU00.0140.02311.1961.7781.7780.0000.0000.0000.000
87A111GLN0-0.0040.00414.177-0.554-0.5540.0000.0000.0000.000
88A112VAL0-0.011-0.00316.9660.5230.5230.0000.0000.0000.000
89A113TYR00.0280.00519.8520.1410.1410.0000.0000.0000.000
90A114ILE0-0.035-0.01523.7020.1420.1420.0000.0000.0000.000
91A115GLN00.0470.02127.276-0.040-0.0400.0000.0000.0000.000
92A116THR00.0100.00030.5970.1660.1660.0000.0000.0000.000
93A117SER00.0160.01533.4850.0850.0850.0000.0000.0000.000
94A118ARG10.8410.90436.5117.9297.9290.0000.0000.0000.000
95A119GLY00.0490.03435.3090.0970.0970.0000.0000.0000.000
96A120ILE0-0.052-0.02331.684-0.145-0.1450.0000.0000.0000.000
97A121LEU00.0190.02527.059-0.176-0.1760.0000.0000.0000.000
98A122ILE0-0.032-0.02825.0940.0640.0640.0000.0000.0000.000
99A123GLU-1-0.736-0.83919.626-14.662-14.6620.0000.0000.0000.000
100A124VAL0-0.050-0.03719.9900.3580.3580.0000.0000.0000.000
101A125ASN00.0100.02616.020-1.501-1.5010.0000.0000.0000.000
102A126PRO00.0680.02813.2100.4800.4800.0000.0000.0000.000
103A127THR0-0.010-0.01012.925-0.085-0.0850.0000.0000.0000.000
104A128VAL0-0.043-0.00515.3870.5700.5700.0000.0000.0000.000
105A129ARG10.9880.99219.21213.15413.1540.0000.0000.0000.000
106A130ILE00.0230.01321.0770.8250.8250.0000.0000.0000.000
107A131PRO0-0.074-0.04423.896-0.091-0.0910.0000.0000.0000.000
108A132ARG10.9140.93221.91513.88113.8810.0000.0000.0000.000
109A133THR00.0110.01027.9530.2000.2000.0000.0000.0000.000
110A134PHE00.1300.05531.495-0.168-0.1680.0000.0000.0000.000
111A135LYS10.9360.97633.1618.2368.2360.0000.0000.0000.000
112A136ARG10.9490.96430.6349.9919.9910.0000.0000.0000.000
113A137PHE00.0270.01927.536-0.149-0.1490.0000.0000.0000.000
114A138SER00.0410.01130.3660.0080.0080.0000.0000.0000.000
115A139GLY00.0080.00533.6930.0950.0950.0000.0000.0000.000
116A140LEU0-0.011-0.00325.5740.0470.0470.0000.0000.0000.000
117A141MET00.0080.00626.886-0.109-0.1090.0000.0000.0000.000
118A142VAL00.0130.00931.2180.1290.1290.0000.0000.0000.000
119A143GLN0-0.042-0.01730.755-0.065-0.0650.0000.0000.0000.000
120A144LEU0-0.017-0.00727.2560.0380.0380.0000.0000.0000.000
121A145LEU0-0.009-0.01130.5400.0230.0230.0000.0000.0000.000
122A146HIS00.0340.02333.5670.0450.0450.0000.0000.0000.000
123A147LYS10.8800.94031.9408.9098.9090.0000.0000.0000.000
124A148LEU00.0210.02131.441-0.161-0.1610.0000.0000.0000.000
125A149SER0-0.051-0.04126.553-0.400-0.4000.0000.0000.0000.000
126A150ILE0-0.0150.00825.2000.3660.3660.0000.0000.0000.000
127A151ARG10.8380.90124.04010.32510.3250.0000.0000.0000.000
128A152SER0-0.019-0.01219.8700.0950.0950.0000.0000.0000.000
129A153VAL0-0.008-0.01322.1990.1610.1610.0000.0000.0000.000
130A154ASN00.002-0.00422.2750.8380.8380.0000.0000.0000.000
131A155SER0-0.037-0.03519.7120.1240.1240.0000.0000.0000.000
132A156GLU-1-0.820-0.89421.916-11.305-11.3050.0000.0000.0000.000
133A157GLU-1-0.804-0.85217.960-15.533-15.5330.0000.0000.0000.000
134A158LYS10.8620.91221.30511.54711.5470.0000.0000.0000.000
135A159LEU00.0150.01118.837-0.590-0.5900.0000.0000.0000.000
136A160LEU00.0230.00721.080-0.184-0.1840.0000.0000.0000.000
137A161LYS10.9150.95423.77711.90511.9050.0000.0000.0000.000
138A162VAL00.0410.03625.790-0.155-0.1550.0000.0000.0000.000
139A163ILE0-0.067-0.04024.963-0.012-0.0120.0000.0000.0000.000
140A164LYS10.9630.97828.8699.0769.0760.0000.0000.0000.000
141A165ASN00.0180.02829.885-0.514-0.5140.0000.0000.0000.000
142A166PRO00.0390.02730.9930.2180.2180.0000.0000.0000.000
143A167ILE00.031-0.00424.395-0.231-0.2310.0000.0000.0000.000
144A168THR00.0260.00026.073-0.415-0.4150.0000.0000.0000.000
145A169ASP-1-0.878-0.91926.507-10.360-10.3600.0000.0000.0000.000
146A170HIS0-0.120-0.07823.258-0.734-0.7340.0000.0000.0000.000
147A171LEU00.004-0.00621.543-0.681-0.6810.0000.0000.0000.000
148A172PRO00.0250.00317.9960.2770.2770.0000.0000.0000.000
149A173THR0-0.008-0.00220.3430.3900.3900.0000.0000.0000.000
150A174LYS10.7890.89320.49314.12114.1210.0000.0000.0000.000
151A175CYS0-0.054-0.02320.482-0.929-0.9290.0000.0000.0000.000
152A176ARG10.9050.95722.41812.94112.9410.0000.0000.0000.000
153A177LYS10.8770.92924.04811.09111.0910.0000.0000.0000.000
154A178VAL00.0690.04526.1240.3780.3780.0000.0000.0000.000
155A179THR0-0.020-0.00527.872-0.361-0.3610.0000.0000.0000.000
156A180LEU0-0.029-0.01525.8840.0840.0840.0000.0000.0000.000
157A181SER0-0.057-0.06930.1190.2680.2680.0000.0000.0000.000
158A182PHE0-0.045-0.03133.697-0.112-0.1120.0000.0000.0000.000
159A183ASP-1-0.933-0.95835.888-7.892-7.8920.0000.0000.0000.000
160A184ALA0-0.0310.00133.9790.1260.1260.0000.0000.0000.000
161A185PRO00.0050.00234.050-0.018-0.0180.0000.0000.0000.000
162A186VAL0-0.021-0.01431.499-0.319-0.3190.0000.0000.0000.000
163A187ILE0-0.0160.00025.9900.0770.0770.0000.0000.0000.000
164A188ARG10.8560.93522.48012.94012.9400.0000.0000.0000.000
165A189VAL0-0.015-0.01020.977-0.006-0.0060.0000.0000.0000.000
166A190GLN0-0.036-0.03320.0320.3460.3460.0000.0000.0000.000
167A191ASP-1-0.801-0.90421.426-12.270-12.2700.0000.0000.0000.000
168A192TYR0-0.102-0.08322.942-0.134-0.1340.0000.0000.0000.000
169A193ILE0-0.014-0.01317.231-0.068-0.0680.0000.0000.0000.000
170A194GLU-1-0.934-0.97419.056-15.243-15.2430.0000.0000.0000.000
171A195LYS10.8650.93520.46212.29312.2930.0000.0000.0000.000
172A196LEU0-0.0280.00418.9680.4610.4610.0000.0000.0000.000
173A197ASP-1-0.773-0.86919.318-13.610-13.6100.0000.0000.0000.000
174A198ASP-1-0.920-0.95215.149-18.191-18.1910.0000.0000.0000.000
175A199ASP-1-0.887-0.93814.886-15.836-15.8360.0000.0000.0000.000
176A200GLU-1-0.840-0.90217.079-12.632-12.6320.0000.0000.0000.000
177A201SER00.005-0.00717.163-1.069-1.0690.0000.0000.0000.000
178A202ILE00.0060.00718.4440.8110.8110.0000.0000.0000.000
179A203CYS0-0.069-0.03220.246-0.419-0.4190.0000.0000.0000.000
180A204VAL00.0340.02522.5450.5320.5320.0000.0000.0000.000
181A205PHE00.018-0.00324.784-0.149-0.1490.0000.0000.0000.000
182A206VAL00.019-0.00626.3770.1910.1910.0000.0000.0000.000
183A207GLY00.0610.04129.1780.0080.0080.0000.0000.0000.000
184A208ALA0-0.061-0.03729.961-0.040-0.0400.0000.0000.0000.000
185A209MET0-0.042-0.02331.9180.1270.1270.0000.0000.0000.000
186A210ALA00.005-0.00835.690-0.072-0.0720.0000.0000.0000.000
187A211ARG10.9000.95038.1917.3377.3370.0000.0000.0000.000
188A212GLY00.0230.01039.5720.0090.0090.0000.0000.0000.000
189A213LYS10.9740.99640.0237.1297.1290.0000.0000.0000.000
190A214ASP-1-0.739-0.84034.918-9.009-9.0090.0000.0000.0000.000
191A215ASN0-0.033-0.03236.117-0.131-0.1310.0000.0000.0000.000
192A216PHE0-0.049-0.02531.4070.0700.0700.0000.0000.0000.000
193A217ALA00.0200.00931.254-0.162-0.1620.0000.0000.0000.000
194A218ASP-1-0.773-0.86633.070-8.768-8.7680.0000.0000.0000.000
195A219GLU-1-0.889-0.94734.181-8.746-8.7460.0000.0000.0000.000
196A220TYR0-0.107-0.06529.821-0.179-0.1790.0000.0000.0000.000
197A221VAL0-0.068-0.03329.328-0.375-0.3750.0000.0000.0000.000
198A222ASP-1-0.898-0.93730.519-9.816-9.8160.0000.0000.0000.000
199A223GLU-1-0.844-0.88928.441-10.672-10.6720.0000.0000.0000.000
200A224LYS10.7830.84131.4468.5888.5880.0000.0000.0000.000
201A225VAL00.0060.01227.6320.1070.1070.0000.0000.0000.000
202A226GLY00.0730.04330.864-0.062-0.0620.0000.0000.0000.000
203A227LEU0-0.027-0.02425.874-0.243-0.2430.0000.0000.0000.000
204A228SER0-0.068-0.05929.558-0.149-0.1490.0000.0000.0000.000
205A229ASN00.0570.03432.5350.0920.0920.0000.0000.0000.000
206A230TYR0-0.026-0.00134.6850.2170.2170.0000.0000.0000.000
207A231PRO00.0440.02634.936-0.301-0.3010.0000.0000.0000.000
208A232LEU0-0.013-0.00329.601-0.115-0.1150.0000.0000.0000.000
209A233SER00.0090.00831.8500.1740.1740.0000.0000.0000.000
210A234ALA00.0750.03129.620-0.303-0.3030.0000.0000.0000.000
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212A236VAL00.0070.00025.823-0.507-0.5070.0000.0000.0000.000
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