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: RM8L8

Calculation Name: 3ID5-B-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ID5

Chain ID: B

ChEMBL ID:

UniProt ID: P58032

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2893731.227809
FMO2-HF: Nuclear repulsion 2804129.106579
FMO2-HF: Total energy -89602.12123
FMO2-MP2: Total energy -89867.689643


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:5:ILE)


Summations of interaction energy for fragment #1(A:5:ILE)
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.
-86.059-76.5169.44-8.169-10.813-0.079
Interaction energy analysis for fragmet #1(A:5:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.780 / q_NPA : 0.888
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].
3A7VAL0-0.0030.0083.8124.0535.538-0.023-0.527-0.9340.000
14A18CYS0-0.090-0.0374.577-1.346-1.257-0.001-0.008-0.0800.000
15A19GLU-1-0.805-0.8663.009-71.322-68.4510.041-1.660-1.252-0.016
16A20PHE0-0.010-0.0252.112-30.210-27.8888.064-5.439-4.947-0.049
17A21ASN0-0.002-0.0122.598-8.619-7.1631.290-0.267-2.479-0.013
18A22ASP-1-0.854-0.9104.016-32.353-32.1210.003-0.069-0.1670.000
40A44ILE0-0.001-0.0094.059-2.382-2.0740.001-0.032-0.2770.000
42A46TYR0-0.021-0.0152.875-8.089-7.3300.066-0.167-0.658-0.001
43A47GLU-1-0.856-0.9325.306-26.554-26.533-0.0010.000-0.0190.000
4A8LYS10.9430.9776.17029.39629.3960.0000.0000.0000.000
5A9GLN0-0.042-0.0299.9310.4980.4980.0000.0000.0000.000
6A10THR00.0120.00013.1300.4600.4600.0000.0000.0000.000
7A11ASN00.023-0.00115.2210.1740.1740.0000.0000.0000.000
8A12MET0-0.0310.00217.9821.0191.0190.0000.0000.0000.000
9A13GLU-1-0.818-0.92817.594-14.022-14.0220.0000.0000.0000.000
10A14ASN0-0.065-0.05716.2450.4020.4020.0000.0000.0000.000
11A15ILE0-0.0220.00514.684-0.606-0.6060.0000.0000.0000.000
12A16TYR00.0200.0059.9610.2640.2640.0000.0000.0000.000
13A17GLU-1-0.908-0.9559.296-23.888-23.8880.0000.0000.0000.000
19A23GLY00.0140.0136.0564.3474.3470.0000.0000.0000.000
20A24SER0-0.098-0.0567.3793.3643.3640.0000.0000.0000.000
21A25PHE00.0890.0316.810-5.291-5.2910.0000.0000.0000.000
22A26ARG10.8230.9098.31630.01730.0170.0000.0000.0000.000
23A27LEU00.0660.0499.321-1.755-1.7550.0000.0000.0000.000
24A28CYS0-0.044-0.0197.520-0.144-0.1440.0000.0000.0000.000
25A29THR00.0020.01310.5101.0491.0490.0000.0000.0000.000
26A30ARG10.9700.98711.70917.85117.8510.0000.0000.0000.000
27A31ASN0-0.051-0.03412.3301.7491.7490.0000.0000.0000.000
28A32LEU0-0.024-0.00214.1240.2370.2370.0000.0000.0000.000
29A33VAL0-0.053-0.02917.1650.7150.7150.0000.0000.0000.000
30A34PRO00.0360.02515.030-0.358-0.3580.0000.0000.0000.000
31A35ASN0-0.030-0.01614.9040.6260.6260.0000.0000.0000.000
32A36PHE00.0510.02016.4220.5040.5040.0000.0000.0000.000
33A37ASN0-0.011-0.00414.944-1.731-1.7310.0000.0000.0000.000
34A38VAL0-0.010-0.01315.9020.4520.4520.0000.0000.0000.000
35A39TYR00.0010.01015.422-0.819-0.8190.0000.0000.0000.000
36A40GLY00.0380.00415.6120.8300.8300.0000.0000.0000.000
37A41GLU-1-0.893-0.93012.584-17.144-17.1440.0000.0000.0000.000
38A42ARG10.8960.9446.36430.31530.3150.0000.0000.0000.000
39A43LEU00.0110.0099.183-1.106-1.1060.0000.0000.0000.000
41A45LYS10.9430.9664.86424.43924.4390.0000.0000.0000.000
44A48GLY0-0.0120.0058.6042.3112.3110.0000.0000.0000.000
45A49VAL0-0.047-0.0169.6501.5291.5290.0000.0000.0000.000
46A50GLU-1-0.858-0.9458.429-22.378-22.3780.0000.0000.0000.000
47A51TYR0-0.020-0.0177.1051.2141.2140.0000.0000.0000.000
48A52ARG10.7740.8779.14317.17117.1710.0000.0000.0000.000
49A53GLU-1-0.838-0.9088.492-26.556-26.5560.0000.0000.0000.000
50A54TRP0-0.005-0.01810.0121.9291.9290.0000.0000.0000.000
51A55ASN00.006-0.01213.258-0.708-0.7080.0000.0000.0000.000
52A56ALA00.0560.01614.6260.9570.9570.0000.0000.0000.000
53A57PHE00.0220.01816.2330.5610.5610.0000.0000.0000.000
54A58ARG10.9110.96217.64215.39415.3940.0000.0000.0000.000
55A59SER0-0.036-0.01419.1770.5300.5300.0000.0000.0000.000
56A60LYS10.8890.95420.93910.33110.3310.0000.0000.0000.000
57A61LEU00.0100.01220.915-0.147-0.1470.0000.0000.0000.000
58A62ALA00.0110.00516.981-0.171-0.1710.0000.0000.0000.000
59A63GLY00.0530.01818.876-0.547-0.5470.0000.0000.0000.000
60A64ALA00.0140.00220.940-0.035-0.0350.0000.0000.0000.000
61A65ILE0-0.045-0.02217.4480.0680.0680.0000.0000.0000.000
62A66LEU0-0.024-0.01514.691-0.210-0.2100.0000.0000.0000.000
63A67LYS10.8230.93018.73513.54313.5430.0000.0000.0000.000
64A68GLY00.0000.01421.5450.5270.5270.0000.0000.0000.000
65A69LEU0-0.021-0.01122.8790.6150.6150.0000.0000.0000.000
66A70LYS10.9170.95323.21710.91510.9150.0000.0000.0000.000
67A71THR0-0.007-0.00524.889-0.194-0.1940.0000.0000.0000.000
68A72ASN00.0480.02221.1810.7680.7680.0000.0000.0000.000
69A73PRO00.0050.01324.694-0.137-0.1370.0000.0000.0000.000
70A74ILE0-0.039-0.02223.1620.0770.0770.0000.0000.0000.000
71A75ARG10.8990.96422.21811.50111.5010.0000.0000.0000.000
72A76LYS10.8980.94920.17514.14014.1400.0000.0000.0000.000
73A77GLY0-0.040-0.02623.3070.3550.3550.0000.0000.0000.000
74A78THR0-0.027-0.02225.7610.4260.4260.0000.0000.0000.000
75A79LYS10.8480.91227.7848.8298.8290.0000.0000.0000.000
76A80VAL00.0050.00026.5460.0550.0550.0000.0000.0000.000
77A81LEU00.0180.01529.8150.0830.0830.0000.0000.0000.000
78A82TYR0-0.0050.00924.874-0.195-0.1950.0000.0000.0000.000
79A83LEU00.0150.00630.2120.1040.1040.0000.0000.0000.000
80A84GLY00.0300.02131.286-0.058-0.0580.0000.0000.0000.000
81A85ALA0-0.043-0.03728.111-0.376-0.3760.0000.0000.0000.000
82A86ALA00.0500.01726.861-0.418-0.4180.0000.0000.0000.000
83A87SER00.0130.00124.7230.0580.0580.0000.0000.0000.000
84A88GLY00.0290.00024.338-0.351-0.3510.0000.0000.0000.000
85A89THR0-0.0040.00218.903-0.520-0.5200.0000.0000.0000.000
86A90THR00.0070.00219.712-0.725-0.7250.0000.0000.0000.000
87A91ILE00.0520.03220.696-0.468-0.4680.0000.0000.0000.000
88A92SER0-0.005-0.00718.653-0.376-0.3760.0000.0000.0000.000
89A93HIS10.8040.89313.68017.49717.4970.0000.0000.0000.000
90A94VAL00.0390.01817.921-0.253-0.2530.0000.0000.0000.000
91A95SER0-0.015-0.01721.006-0.051-0.0510.0000.0000.0000.000
92A96ASP-1-0.714-0.84015.702-16.687-16.6870.0000.0000.0000.000
93A97ILE0-0.059-0.01817.434-0.270-0.2700.0000.0000.0000.000
94A98ILE0-0.0070.02019.1440.1560.1560.0000.0000.0000.000
95A99GLU-1-0.787-0.86419.227-13.864-13.8640.0000.0000.0000.000
96A100LEU00.0300.00522.0850.4330.4330.0000.0000.0000.000
97A101ASN00.0070.00325.0730.5970.5970.0000.0000.0000.000
98A102GLY00.0250.03526.2400.4100.4100.0000.0000.0000.000
99A103LYS10.8240.90127.62510.04810.0480.0000.0000.0000.000
100A104ALA00.0200.01226.1740.0310.0310.0000.0000.0000.000
101A105TYR0-0.008-0.00728.2730.0240.0240.0000.0000.0000.000
102A106GLY00.0090.00629.695-0.058-0.0580.0000.0000.0000.000
103A107VAL00.0120.00330.5400.1490.1490.0000.0000.0000.000
104A108GLU-1-0.835-0.91331.444-9.443-9.4430.0000.0000.0000.000
105A109PHE00.0330.02633.5540.2030.2030.0000.0000.0000.000
106A110SER00.015-0.00234.2520.1810.1810.0000.0000.0000.000
107A111PRO00.0590.01334.517-0.260-0.2600.0000.0000.0000.000
108A112ARG10.8970.94431.7498.8198.8190.0000.0000.0000.000
109A113VAL00.0140.01529.132-0.171-0.1710.0000.0000.0000.000
110A114VAL00.0810.03330.024-0.308-0.3080.0000.0000.0000.000
111A115ARG10.9070.94931.2378.5658.5650.0000.0000.0000.000
112A116GLU-1-0.908-0.94825.673-11.054-11.0540.0000.0000.0000.000
113A117LEU0-0.019-0.00226.766-0.333-0.3330.0000.0000.0000.000
114A118LEU00.005-0.00527.536-0.163-0.1630.0000.0000.0000.000
115A119LEU0-0.0180.00225.908-0.059-0.0590.0000.0000.0000.000
116A120VAL0-0.057-0.02321.951-0.345-0.3450.0000.0000.0000.000
117A121ALA00.018-0.00524.007-0.279-0.2790.0000.0000.0000.000
118A122GLN0-0.015-0.00126.726-0.171-0.1710.0000.0000.0000.000
119A123ARG10.8710.93922.11712.13412.1340.0000.0000.0000.000
120A124ARG10.8180.89517.08614.30814.3080.0000.0000.0000.000
121A125PRO00.0320.00924.2180.2150.2150.0000.0000.0000.000
122A126ASN0-0.0370.00222.6870.2450.2450.0000.0000.0000.000
123A127ILE0-0.0070.00423.0620.0100.0100.0000.0000.0000.000
124A128PHE00.0060.00327.4290.1880.1880.0000.0000.0000.000
125A129PRO0-0.030-0.00230.0650.0560.0560.0000.0000.0000.000
126A130LEU00.007-0.00831.7620.2870.2870.0000.0000.0000.000
127A131LEU00.0010.00034.783-0.154-0.1540.0000.0000.0000.000
128A132ALA0-0.004-0.00737.0510.2300.2300.0000.0000.0000.000
129A133ASP-1-0.839-0.92438.058-7.521-7.5210.0000.0000.0000.000
130A134ALA00.0380.01637.1730.0840.0840.0000.0000.0000.000
131A135ARG10.8340.90839.2427.2757.2750.0000.0000.0000.000
132A136PHE0-0.043-0.00842.4260.1960.1960.0000.0000.0000.000
133A137PRO00.0550.05041.106-0.030-0.0300.0000.0000.0000.000
134A138GLN00.017-0.02142.263-0.148-0.1480.0000.0000.0000.000
135A139SER0-0.074-0.04342.466-0.005-0.0050.0000.0000.0000.000
136A140TYR00.036-0.00338.225-0.021-0.0210.0000.0000.0000.000
137A141LYS10.9330.97640.4076.6246.6240.0000.0000.0000.000
138A142SER0-0.035-0.01942.7390.0350.0350.0000.0000.0000.000
139A143VAL0-0.041-0.01437.3050.0180.0180.0000.0000.0000.000
140A144VAL0-0.028-0.00335.965-0.195-0.1950.0000.0000.0000.000
141A145GLU-1-0.821-0.88634.489-8.577-8.5770.0000.0000.0000.000
142A146ASN0-0.006-0.01436.551-0.088-0.0880.0000.0000.0000.000
143A147VAL0-0.047-0.01432.699-0.135-0.1350.0000.0000.0000.000
144A148ASP-1-0.770-0.88231.003-9.167-9.1670.0000.0000.0000.000
145A149VAL0-0.009-0.00928.352-0.038-0.0380.0000.0000.0000.000
146A150LEU00.0020.00131.2170.0040.0040.0000.0000.0000.000
147A151TYR0-0.060-0.04425.861-0.310-0.3100.0000.0000.0000.000
148A152VAL0-0.009-0.01230.2130.1840.1840.0000.0000.0000.000
149A153ASP-1-0.751-0.86827.573-10.783-10.7830.0000.0000.0000.000
150A154ILE00.0180.01231.034-0.029-0.0290.0000.0000.0000.000
151A155ALA00.0170.00833.6350.0680.0680.0000.0000.0000.000
152A156GLN0-0.022-0.01235.2330.4150.4150.0000.0000.0000.000
153A157PRO00.0150.00238.591-0.129-0.1290.0000.0000.0000.000
154A158ASP-1-0.782-0.88641.325-7.289-7.2890.0000.0000.0000.000
155A159GLN0-0.053-0.02834.2690.1150.1150.0000.0000.0000.000
156A160THR00.0500.02238.476-0.144-0.1440.0000.0000.0000.000
157A161ASP-1-0.839-0.92939.750-7.149-7.1490.0000.0000.0000.000
158A162ILE0-0.042-0.00638.5640.0450.0450.0000.0000.0000.000
159A163ALA00.0010.00536.680-0.019-0.0190.0000.0000.0000.000
160A164ILE00.0240.01238.3230.0170.0170.0000.0000.0000.000
161A165TYR0-0.046-0.02241.1980.1460.1460.0000.0000.0000.000
162A166ASN0-0.020-0.02838.0910.0010.0010.0000.0000.0000.000
163A167ALA00.0100.00838.393-0.027-0.0270.0000.0000.0000.000
164A168LYS10.9150.96739.4626.8396.8390.0000.0000.0000.000
165A169PHE0-0.054-0.01741.8870.2180.2180.0000.0000.0000.000
166A170PHE0-0.014-0.01737.8520.0660.0660.0000.0000.0000.000
167A171LEU0-0.062-0.00434.855-0.163-0.1630.0000.0000.0000.000
168A172LYS10.7890.88634.9228.8778.8770.0000.0000.0000.000
169A173VAL00.0480.01638.428-0.099-0.0990.0000.0000.0000.000
170A174ASN00.0040.00837.965-0.257-0.2570.0000.0000.0000.000
171A175GLY00.0320.04734.780-0.239-0.2390.0000.0000.0000.000
172A176ASP-1-0.877-0.95131.417-9.517-9.5170.0000.0000.0000.000
173A177MET0-0.038-0.01632.6040.0180.0180.0000.0000.0000.000
174A178LEU0-0.023-0.01126.416-0.204-0.2040.0000.0000.0000.000
175A179LEU00.0240.01830.567-0.015-0.0150.0000.0000.0000.000
176A180VAL0-0.003-0.00228.854-0.222-0.2220.0000.0000.0000.000
177A181ILE0-0.022-0.01731.6080.3000.3000.0000.0000.0000.000
178A182LYS10.8280.92630.5399.8159.8150.0000.0000.0000.000
179A183ALA0-0.011-0.01233.8430.0650.0650.0000.0000.0000.000
180A184ARG10.8230.89136.4607.8397.8390.0000.0000.0000.000
181A185SER00.059-0.01731.8190.0540.0540.0000.0000.0000.000
182A186ILE00.0200.03033.687-0.113-0.1130.0000.0000.0000.000
183A187ASP-1-0.793-0.88234.784-8.594-8.5940.0000.0000.0000.000
184A188VAL0-0.110-0.03134.5620.0750.0750.0000.0000.0000.000
185A189THR0-0.0050.00530.456-0.183-0.1830.0000.0000.0000.000
186A190LYS10.7860.85533.5418.8408.8400.0000.0000.0000.000
187A191ASP-1-0.846-0.91935.891-8.928-8.9280.0000.0000.0000.000
188A192PRO0-0.103-0.04237.5810.0900.0900.0000.0000.0000.000
189A193LYS10.8730.92836.1378.2128.2120.0000.0000.0000.000
190A194GLU-1-0.789-0.88236.192-8.642-8.6420.0000.0000.0000.000
191A195ILE00.0140.00038.2520.1030.1030.0000.0000.0000.000
192A196TYR00.0100.00838.4480.1470.1470.0000.0000.0000.000
193A197LYS10.8990.94434.0289.1429.1420.0000.0000.0000.000
194A198THR0-0.017-0.01439.2270.1150.1150.0000.0000.0000.000
195A199GLU-1-0.895-0.91742.499-7.114-7.1140.0000.0000.0000.000
196A200VAL00.007-0.00637.8650.0950.0950.0000.0000.0000.000
197A201GLU-1-0.838-0.92239.397-7.887-7.8870.0000.0000.0000.000
198A202LYS10.9390.96340.6876.9566.9560.0000.0000.0000.000
199A203LEU0-0.047-0.00442.8790.1170.1170.0000.0000.0000.000
200A204GLU-1-0.801-0.88837.405-8.373-8.3730.0000.0000.0000.000
201A205ASN0-0.069-0.04041.1450.1370.1370.0000.0000.0000.000
202A206SER00.0010.01343.8420.1660.1660.0000.0000.0000.000
203A207ASN0-0.125-0.09443.5040.2160.2160.0000.0000.0000.000
204A208PHE00.0280.01336.983-0.050-0.0500.0000.0000.0000.000
205A209GLU-1-0.955-0.96838.842-7.811-7.8110.0000.0000.0000.000
206A210THR00.0340.00835.953-0.183-0.1830.0000.0000.0000.000
207A211ILE0-0.0180.00231.8840.0130.0130.0000.0000.0000.000
208A212GLN0-0.033-0.03127.040-0.366-0.3660.0000.0000.0000.000
209A213ILE00.0180.01931.9280.0630.0630.0000.0000.0000.000
210A214ILE0-0.033-0.00925.693-0.091-0.0910.0000.0000.0000.000
211A215ASN00.0620.03728.985-0.058-0.0580.0000.0000.0000.000
212A216LEU00.0080.00424.460-0.427-0.4270.0000.0000.0000.000
213A217ASP-1-0.843-0.88224.385-11.458-11.4580.0000.0000.0000.000
214A218PRO0-0.058-0.04521.714-0.245-0.2450.0000.0000.0000.000
215A219TYR0-0.052-0.04717.699-0.177-0.1770.0000.0000.0000.000
216A220ASP-1-0.797-0.93322.021-11.371-11.3710.0000.0000.0000.000
217A221LYS0-0.046-0.01325.2870.1550.1550.0000.0000.0000.000
218A222ASP-1-0.825-0.91328.040-9.297-9.2970.0000.0000.0000.000
219A223HIS-1-0.848-0.94228.258-9.696-9.6960.0000.0000.0000.000
220A224ALA00.0030.00329.131-0.272-0.2720.0000.0000.0000.000
221A225ILE0-0.037-0.01925.6430.0780.0780.0000.0000.0000.000
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223A227LEU0-0.043-0.01128.617-0.107-0.1070.0000.0000.0000.000
224A228SER00.007-0.04131.5150.0800.0800.0000.0000.0000.000
225A229LYS10.8850.93834.6658.6258.6250.0000.0000.0000.000
226A230TYR0-0.052-0.03136.4020.2710.2710.0000.0000.0000.000
227A231LYS0-0.0070.00938.991-0.403-0.4030.0000.0000.0000.000