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: RK9Y8

Calculation Name: 3DCM-X-Xray549

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DCM

Chain ID: X

ChEMBL ID:

UniProt ID: Q9X1Q6

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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2139333.208995
FMO2-HF: Nuclear repulsion 2065138.381894
FMO2-HF: Total energy -74194.827101
FMO2-MP2: Total energy -74415.182254


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(X:1:MET)


Summations of interaction energy for fragment #1(X:1:MET)
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.
-261.18-252.11212.922-10.322-11.669-0.111
Interaction energy analysis for fragmet #1(X:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.927
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].
3X3GLU-1-0.929-0.9513.093-30.636-28.2990.028-0.886-1.4780.000
4X4LYS10.8220.9063.72057.78058.2960.001-0.082-0.4350.000
129X129ILE00.000-0.0063.470-9.217-8.4740.004-0.304-0.444-0.002
130X130ILE0-0.044-0.0201.869-42.326-41.4378.626-4.838-4.677-0.064
131X131GLU-1-0.913-0.9673.040-47.650-45.2680.166-1.216-1.332-0.012
132X132THR0-0.045-0.0032.8405.6216.1630.073-0.187-0.428-0.001
133X133GLU-1-0.893-0.9662.145-96.141-94.7094.027-2.762-2.698-0.032
134X134LYS10.9200.9874.57833.07533.126-0.001-0.006-0.0440.000
135X135PRO00.0120.0124.182-11.284-11.208-0.001-0.025-0.0500.000
188X188TYR-1-1.002-1.0114.456-33.078-32.978-0.001-0.016-0.0830.000
5X5VAL00.0060.0244.9431.2681.2680.0000.0000.0000.000
6X6TYR0-0.049-0.0517.0255.1565.1560.0000.0000.0000.000
7X7VAL0-0.0020.00110.701-0.023-0.0230.0000.0000.0000.000
8X8ALA00.0310.01013.9120.8310.8310.0000.0000.0000.000
9X9LEU0-0.046-0.00417.2390.1430.1430.0000.0000.0000.000
10X10ILE00.0140.00619.4830.4410.4410.0000.0000.0000.000
11X11HIS0-0.034-0.02322.7730.5740.5740.0000.0000.0000.000
12X12TYR00.0020.00125.8210.6760.6760.0000.0000.0000.000
13X13PRO00.0310.03324.799-0.426-0.4260.0000.0000.0000.000
14X14ILE0-0.035-0.03124.628-0.461-0.4610.0000.0000.0000.000
15X15LYS10.9300.98427.94011.38611.3860.0000.0000.0000.000
16X16GLY00.0480.01430.402-0.035-0.0350.0000.0000.0000.000
17X17LYS10.8970.93633.6978.1298.1290.0000.0000.0000.000
18X18ASP-1-0.839-0.89935.882-8.507-8.5070.0000.0000.0000.000
19X19GLY0-0.050-0.01833.1800.0340.0340.0000.0000.0000.000
20X20SER0-0.045-0.03133.664-0.171-0.1710.0000.0000.0000.000
21X21ILE00.0080.00629.768-0.260-0.2600.0000.0000.0000.000
22X22ILE0-0.035-0.02031.6150.3480.3480.0000.0000.0000.000
23X23SER0-0.011-0.01630.568-0.425-0.4250.0000.0000.0000.000
24X24THR0-0.049-0.03828.3370.3430.3430.0000.0000.0000.000
25X25ALA0-0.021-0.02330.560-0.102-0.1020.0000.0000.0000.000
26X26VAL00.0240.01326.506-0.194-0.1940.0000.0000.0000.000
27X27THR0-0.058-0.04828.1630.4190.4190.0000.0000.0000.000
28X28ASN00.0780.01528.085-0.592-0.5920.0000.0000.0000.000
29X29LEU00.003-0.00627.997-0.297-0.2970.0000.0000.0000.000
30X30ASP-1-0.732-0.82124.192-12.529-12.5290.0000.0000.0000.000
31X31VAL0-0.0010.01623.084-0.695-0.6950.0000.0000.0000.000
32X32HIS0-0.017-0.02523.093-0.630-0.6300.0000.0000.0000.000
33X33ASP-1-0.907-0.95222.723-13.995-13.9950.0000.0000.0000.000
34X34ILE00.0630.02618.000-0.479-0.4790.0000.0000.0000.000
35X35ALA00.0250.02418.193-1.028-1.0280.0000.0000.0000.000
36X36ARG10.8610.92918.03712.34212.3420.0000.0000.0000.000
37X37THR00.0190.03315.972-0.382-0.3820.0000.0000.0000.000
38X38ALA00.0270.00814.182-0.881-0.8810.0000.0000.0000.000
39X39ARG10.7750.87512.93218.01918.0190.0000.0000.0000.000
40X40THR0-0.056-0.03313.742-0.096-0.0960.0000.0000.0000.000
41X41TYR0-0.041-0.03810.6610.3450.3450.0000.0000.0000.000
42X42ASN0-0.023-0.0138.397-1.004-1.0040.0000.0000.0000.000
43X43LEU00.0400.0288.786-1.932-1.9320.0000.0000.0000.000
44X44LYS10.8500.9178.38735.21135.2110.0000.0000.0000.000
45X45GLY0-0.018-0.02110.7792.1422.1420.0000.0000.0000.000
46X46TYR0-0.085-0.06213.521-0.818-0.8180.0000.0000.0000.000
47X47TYR0-0.029-0.03913.8731.0061.0060.0000.0000.0000.000
48X48ILE0-0.030-0.01618.5530.2520.2520.0000.0000.0000.000
49X49VAL00.0530.02920.3600.3020.3020.0000.0000.0000.000
50X50THR00.0220.00323.1430.4710.4710.0000.0000.0000.000
51X51ASN00.1010.07226.989-0.002-0.0020.0000.0000.0000.000
52X52LEU0-0.0030.01329.6730.4630.4630.0000.0000.0000.000
53X53ARG11.0150.99432.0898.6638.6630.0000.0000.0000.000
54X54ALA0-0.012-0.00633.447-0.020-0.0200.0000.0000.0000.000
55X55GLN00.0310.02030.467-0.133-0.1330.0000.0000.0000.000
56X56GLN00.0240.01128.0930.1340.1340.0000.0000.0000.000
57X57ASP-1-0.833-0.89630.089-9.230-9.2300.0000.0000.0000.000
58X58MET0-0.028-0.00130.974-0.139-0.1390.0000.0000.0000.000
59X59VAL00.0660.01025.967-0.027-0.0270.0000.0000.0000.000
60X60SER0-0.007-0.01028.621-0.336-0.3360.0000.0000.0000.000
61X61LYS10.8120.89529.6938.8628.8620.0000.0000.0000.000
62X62MET0-0.0380.01126.9600.0200.0200.0000.0000.0000.000
63X63LEU00.0550.00623.987-0.039-0.0390.0000.0000.0000.000
64X64LYS10.8520.91027.9949.6279.6270.0000.0000.0000.000
65X65PHE00.0090.00730.1800.1790.1790.0000.0000.0000.000
66X66TRP0-0.022-0.02727.4530.1130.1130.0000.0000.0000.000
67X67ARG10.8220.89422.56113.31213.3120.0000.0000.0000.000
68X68GLU-1-0.873-0.89827.335-9.841-9.8410.0000.0000.0000.000
69X69GLY00.0110.00630.6240.2940.2940.0000.0000.0000.000
70X70PHE00.0290.01232.528-0.207-0.2070.0000.0000.0000.000
71X71GLY00.0690.03231.4610.0010.0010.0000.0000.0000.000
72X72SER0-0.065-0.05228.542-0.223-0.2230.0000.0000.0000.000
73X73ARG10.9150.94029.4239.4939.4930.0000.0000.0000.000
74X74TYR00.0080.02532.0600.1710.1710.0000.0000.0000.000
75X75ASN0-0.008-0.00227.583-0.022-0.0220.0000.0000.0000.000
76X76PRO0-0.0120.01225.3090.0590.0590.0000.0000.0000.000
77X77SER00.0680.03322.268-0.254-0.2540.0000.0000.0000.000
78X78ARG10.8420.92323.79310.93210.9320.0000.0000.0000.000
79X79ALA00.0750.03023.451-0.429-0.4290.0000.0000.0000.000
80X80GLU-1-0.775-0.86717.238-16.489-16.4890.0000.0000.0000.000
81X81SER00.0310.01218.559-0.641-0.6410.0000.0000.0000.000
82X82LEU0-0.002-0.01719.255-0.518-0.5180.0000.0000.0000.000
83X83LYS10.8140.91616.49916.93916.9390.0000.0000.0000.000
84X84LEU00.0460.03614.0630.2560.2560.0000.0000.0000.000
85X85VAL0-0.048-0.00117.368-0.439-0.4390.0000.0000.0000.000
86X86LYS10.8560.93016.96218.55118.5510.0000.0000.0000.000
87X87LEU0-0.028-0.01220.684-0.009-0.0090.0000.0000.0000.000
88X88LYS10.8680.93819.72314.88414.8840.0000.0000.0000.000
89X89SER0-0.032-0.00823.4210.3710.3710.0000.0000.0000.000
90X90TYR0-0.039-0.02924.3160.4430.4430.0000.0000.0000.000
91X91LEU00.0550.02017.527-0.284-0.2840.0000.0000.0000.000
92X92GLU-1-0.782-0.86019.356-15.921-15.9210.0000.0000.0000.000
93X93ASP-1-0.760-0.90419.991-13.485-13.4850.0000.0000.0000.000
94X94VAL0-0.074-0.04515.604-0.183-0.1830.0000.0000.0000.000
95X95LEU0-0.0180.00115.059-1.217-1.2170.0000.0000.0000.000
96X96GLU-1-0.873-0.93215.792-14.889-14.8890.0000.0000.0000.000
97X97ASP-1-0.817-0.87216.899-17.789-17.7890.0000.0000.0000.000
98X98ILE00.0200.00210.772-0.366-0.3660.0000.0000.0000.000
99X99GLU-1-0.854-0.91912.754-19.121-19.1210.0000.0000.0000.000
100X100SER0-0.070-0.04814.5450.2570.2570.0000.0000.0000.000
101X101VAL0-0.110-0.05111.8940.4240.4240.0000.0000.0000.000
102X102GLU-1-0.787-0.8598.697-35.150-35.1500.0000.0000.0000.000
103X103GLY0-0.038-0.00211.141-0.938-0.9380.0000.0000.0000.000
104X104GLU-1-0.887-0.9639.263-30.516-30.5160.0000.0000.0000.000
105X105ARG10.7990.87311.59016.27616.2760.0000.0000.0000.000
106X106PRO0-0.058-0.0259.444-1.296-1.2960.0000.0000.0000.000
107X107LEU00.0200.0146.9091.8101.8100.0000.0000.0000.000
108X108ILE0-0.022-0.01910.229-1.360-1.3600.0000.0000.0000.000
109X109PHE00.0060.0008.4580.7370.7370.0000.0000.0000.000
110X110PHE00.0170.00613.2670.7760.7760.0000.0000.0000.000
111X111THR0-0.027-0.03416.1080.1370.1370.0000.0000.0000.000
112X112SER0-0.011-0.02718.5891.0261.0260.0000.0000.0000.000
113X113ALA00.0260.02322.214-0.237-0.2370.0000.0000.0000.000
114X114LYS10.9060.96324.76011.39911.3990.0000.0000.0000.000
115X115LYS10.8470.89021.86513.40513.4050.0000.0000.0000.000
116X116ARG10.8840.94822.51213.22113.2210.0000.0000.0000.000
117X117GLU-1-0.875-0.93723.805-12.248-12.2480.0000.0000.0000.000
118X118ASN0-0.044-0.03321.212-0.153-0.1530.0000.0000.0000.000
119X119ASP-1-0.801-0.87118.633-15.146-15.1460.0000.0000.0000.000
120X120ILE00.0090.01512.3190.0080.0080.0000.0000.0000.000
121X121SER0-0.009-0.03915.999-0.146-0.1460.0000.0000.0000.000
122X122PHE0-0.006-0.03713.527-1.224-1.2240.0000.0000.0000.000
123X123GLU-1-0.990-0.98312.344-20.633-20.6330.0000.0000.0000.000
124X124GLU-1-0.814-0.87911.465-20.693-20.6930.0000.0000.0000.000
125X125GLY00.0380.0139.901-2.347-2.3470.0000.0000.0000.000
126X126ARG10.8550.9287.84520.22620.2260.0000.0000.0000.000
127X127ARG10.9000.9596.75520.74720.7470.0000.0000.0000.000
128X128ILE00.0340.0226.473-4.720-4.7200.0000.0000.0000.000
136X136VAL0-0.018-0.0054.9802.8112.8110.0000.0000.0000.000
137X137LEU0-0.018-0.0127.4591.3601.3600.0000.0000.0000.000
138X138ILE00.0120.01210.0941.5051.5050.0000.0000.0000.000
139X139LEU00.0160.01012.7611.1631.1630.0000.0000.0000.000
140X140LEU00.0180.01716.4970.5120.5120.0000.0000.0000.000
141X141GLY00.0400.01719.2850.3380.3380.0000.0000.0000.000
142X142THR00.000-0.00522.9300.3640.3640.0000.0000.0000.000
143X143GLY00.0300.00726.3290.0460.0460.0000.0000.0000.000
144X144TRP0-0.032-0.01729.4340.0440.0440.0000.0000.0000.000
145X145GLY0-0.011-0.00225.584-0.004-0.0040.0000.0000.0000.000
146X146LEU00.0250.01319.6330.4310.4310.0000.0000.0000.000
147X147PRO0-0.014-0.00624.2040.2200.2200.0000.0000.0000.000
148X148ASP-1-0.823-0.93024.729-11.908-11.9080.0000.0000.0000.000
149X149GLU-1-0.917-0.96825.156-11.489-11.4890.0000.0000.0000.000
150X150ILE0-0.013-0.01220.175-0.328-0.3280.0000.0000.0000.000
151X151LEU0-0.051-0.00920.599-0.775-0.7750.0000.0000.0000.000
152X152GLU-1-0.926-0.97120.884-12.994-12.9940.0000.0000.0000.000
153X153ILE0-0.064-0.01919.137-0.034-0.0340.0000.0000.0000.000
154X154SER0-0.043-0.04116.591-1.080-1.0800.0000.0000.0000.000
155X155ASP-1-0.856-0.90912.908-22.087-22.0870.0000.0000.0000.000
156X156TYR00.0130.00010.303-0.544-0.5440.0000.0000.0000.000
157X157VAL00.0140.00714.7030.1850.1850.0000.0000.0000.000
158X158LEU0-0.014-0.00312.474-0.439-0.4390.0000.0000.0000.000
159X159GLU-1-0.869-0.93016.337-15.215-15.2150.0000.0000.0000.000
160X160PRO0-0.047-0.01618.937-0.317-0.3170.0000.0000.0000.000
161X161ILE00.0100.00219.0950.1170.1170.0000.0000.0000.000
162X162ARG10.8710.91521.63011.81711.8170.0000.0000.0000.000
163X163ALA00.0520.03223.6410.5500.5500.0000.0000.0000.000
164X164GLN00.0080.01024.4140.2050.2050.0000.0000.0000.000
165X165SER0-0.064-0.02628.4240.2790.2790.0000.0000.0000.000
166X166ASP-1-0.858-0.91830.225-9.447-9.4470.0000.0000.0000.000
167X167PHE0-0.039-0.02830.4780.0960.0960.0000.0000.0000.000
168X168ASN0-0.029-0.02625.1590.1960.1960.0000.0000.0000.000
169X169HIS0-0.0110.00826.376-0.685-0.6850.0000.0000.0000.000
170X170LEU0-0.012-0.00523.2050.3030.3030.0000.0000.0000.000
171X171SER0-0.033-0.01526.094-0.102-0.1020.0000.0000.0000.000
172X172VAL00.0870.02721.604-0.333-0.3330.0000.0000.0000.000
173X173ARG10.8630.92821.37111.15111.1510.0000.0000.0000.000
174X174ALA00.0130.00921.249-0.571-0.5710.0000.0000.0000.000
175X175ALA00.000-0.00120.747-0.412-0.4120.0000.0000.0000.000
176X176ALA00.0470.01817.355-0.791-0.7910.0000.0000.0000.000
177X177ALA00.0190.00616.442-1.170-1.1700.0000.0000.0000.000
178X178ILE0-0.004-0.00216.839-0.708-0.7080.0000.0000.0000.000
179X179ILE0-0.035-0.02213.465-0.550-0.5500.0000.0000.0000.000
180X180ILE00.000-0.00611.752-1.395-1.3950.0000.0000.0000.000
181X181ASP-1-0.854-0.90311.948-20.491-20.4910.0000.0000.0000.000
182X182ARG10.8680.93813.01716.02316.0230.0000.0000.0000.000
183X183LEU0-0.028-0.0078.973-0.116-0.1160.0000.0000.0000.000
184X184ILE0-0.039-0.0016.864-3.619-3.6190.0000.0000.0000.000
185X185GLY00.0400.0318.8820.0530.0530.0000.0000.0000.000
186X186GLU-1-0.916-0.94210.062-19.240-19.2400.0000.0000.0000.000
187X187ASN0-0.132-0.0765.6410.7190.7190.0000.0000.0000.000