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: N8N3Q

Calculation Name: 3GYQ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GYQ

Chain ID: B

ChEMBL ID:

UniProt ID: P18644

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3122775.458469
FMO2-HF: Nuclear repulsion 3025190.12904
FMO2-HF: Total energy -97585.329429
FMO2-MP2: Total energy -97871.472393


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:8:ALA)


Summations of interaction energy for fragment #1(A:8:ALA)
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.
-27.689-23.1777.308-6.112-5.708-0.056
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.919
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].
3A10PRO00.0440.0253.8592.5214.004-0.009-0.631-0.843-0.001
50A57ASP-1-0.787-0.9033.789-36.434-36.3400.001-0.025-0.0710.000
70A77ARG10.8420.9353.83541.32041.5050.000-0.034-0.1500.000
71A78LEU0-0.0040.0012.4362.2403.0210.761-0.489-1.053-0.003
72A79ILE0-0.021-0.0132.170-23.576-21.8716.555-4.856-3.404-0.052
73A80ASP-1-0.739-0.8474.101-31.169-30.9140.001-0.074-0.1830.000
74A81SER0-0.011-0.0184.8134.5384.547-0.001-0.003-0.0040.000
4A11SER00.0020.0105.7715.2545.2540.0000.0000.0000.000
5A12ASP-1-0.853-0.9149.052-26.671-26.6710.0000.0000.0000.000
6A13PRO0-0.014-0.02311.8911.3591.3590.0000.0000.0000.000
7A14ALA00.0310.0039.535-2.811-2.8110.0000.0000.0000.000
8A15VAL0-0.008-0.01811.1041.6081.6080.0000.0000.0000.000
9A16GLN0-0.016-0.0018.6883.2243.2240.0000.0000.0000.000
10A17ARG10.8780.93210.75518.30018.3000.0000.0000.0000.000
11A18ILE00.0420.01914.1201.3271.3270.0000.0000.0000.000
12A19ILE00.0610.0429.7071.3131.3130.0000.0000.0000.000
13A20ASP-1-0.833-0.90214.314-16.094-16.0940.0000.0000.0000.000
14A21VAL0-0.089-0.04916.5891.2371.2370.0000.0000.0000.000
15A22THR0-0.047-0.03416.8650.7520.7520.0000.0000.0000.000
16A23LYS10.9571.00817.17916.19816.1980.0000.0000.0000.000
17A24PRO0-0.017-0.01218.8070.8080.8080.0000.0000.0000.000
18A25SER0-0.0150.00121.8500.0600.0600.0000.0000.0000.000
19A26ARG10.8900.94722.32312.82112.8210.0000.0000.0000.000
20A27SER00.0490.00525.2870.0800.0800.0000.0000.0000.000
21A28ASN0-0.068-0.02622.7600.4510.4510.0000.0000.0000.000
22A29ILE00.1070.05824.608-0.222-0.2220.0000.0000.0000.000
23A30LYS10.9570.97024.45811.28311.2830.0000.0000.0000.000
24A31THR0-0.0200.00019.488-0.294-0.2940.0000.0000.0000.000
25A32THR00.007-0.00920.7690.0900.0900.0000.0000.0000.000
26A33LEU0-0.042-0.01314.459-0.841-0.8410.0000.0000.0000.000
27A34ILE0-0.0190.00017.3870.9030.9030.0000.0000.0000.000
28A35GLU-1-0.900-0.98216.578-17.276-17.2760.0000.0000.0000.000
29A36ASP-1-0.863-0.94016.769-14.813-14.8130.0000.0000.0000.000
30A37VAL00.023-0.00216.329-0.240-0.2400.0000.0000.0000.000
31A38GLU-1-0.813-0.91317.466-13.399-13.3990.0000.0000.0000.000
32A39PRO00.0000.01020.0940.4180.4180.0000.0000.0000.000
33A40LEU0-0.0320.01714.6370.1730.1730.0000.0000.0000.000
34A41MET00.0150.02218.674-0.072-0.0720.0000.0000.0000.000
35A42HIS10.8730.93220.44712.82512.8250.0000.0000.0000.000
36A43SER0-0.002-0.01320.9760.6350.6350.0000.0000.0000.000
37A44ILE0-0.031-0.02316.8030.2740.2740.0000.0000.0000.000
38A45ALA0-0.016-0.00321.4440.3310.3310.0000.0000.0000.000
39A46ALA0-0.0280.00224.6830.4840.4840.0000.0000.0000.000
40A47GLY0-0.0140.00224.8380.3450.3450.0000.0000.0000.000
41A48VAL0-0.060-0.03121.1630.0300.0300.0000.0000.0000.000
42A49GLU-1-0.897-0.95221.028-13.940-13.9400.0000.0000.0000.000
43A50PHE00.019-0.00815.605-0.173-0.1730.0000.0000.0000.000
44A51ILE0-0.057-0.01514.4460.4350.4350.0000.0000.0000.000
45A52GLU-1-0.819-0.9048.840-34.376-34.3760.0000.0000.0000.000
46A53VAL0-0.0040.00110.7891.2311.2310.0000.0000.0000.000
47A54TYR0-0.041-0.0616.663-2.334-2.3340.0000.0000.0000.000
48A55GLY00.0390.0107.0143.6923.6920.0000.0000.0000.000
49A56SER0-0.042-0.0076.212-3.894-3.8940.0000.0000.0000.000
51A58SER0-0.024-0.0085.8292.4592.4590.0000.0000.0000.000
52A59SER0-0.051-0.0498.9753.2833.2830.0000.0000.0000.000
53A60PRO0-0.0060.0129.590-2.152-2.1520.0000.0000.0000.000
54A61PHE00.0110.0058.8850.2410.2410.0000.0000.0000.000
55A62PRO00.0340.01111.0040.5900.5900.0000.0000.0000.000
56A63SER0-0.0150.00114.524-0.725-0.7250.0000.0000.0000.000
57A64GLU-1-0.864-0.94315.815-14.194-14.1940.0000.0000.0000.000
58A65LEU00.0450.01413.5830.1270.1270.0000.0000.0000.000
59A66LEU0-0.037-0.01110.147-0.607-0.6070.0000.0000.0000.000
60A67ASP-1-0.885-0.93513.498-18.448-18.4480.0000.0000.0000.000
61A68LEU0-0.016-0.00916.7240.3920.3920.0000.0000.0000.000
62A69CYS0-0.056-0.03713.5220.3650.3650.0000.0000.0000.000
63A70GLY00.0180.01015.2290.2480.2480.0000.0000.0000.000
64A71ARG10.8840.93115.90214.51614.5160.0000.0000.0000.000
65A72GLN0-0.0020.01018.4071.0841.0840.0000.0000.0000.000
66A73ASN0-0.048-0.01616.767-0.126-0.1260.0000.0000.0000.000
67A74ILE0-0.0080.00413.457-0.380-0.3800.0000.0000.0000.000
68A75PRO00.0000.00310.807-1.349-1.3490.0000.0000.0000.000
69A76VAL00.0460.0188.0450.6060.6060.0000.0000.0000.000
75A82SER0-0.081-0.0518.4512.8562.8560.0000.0000.0000.000
76A83ILE00.0410.0157.7652.1122.1120.0000.0000.0000.000
77A84VAL0-0.047-0.0337.7392.0592.0590.0000.0000.0000.000
78A85ASN0-0.024-0.02710.2451.6991.6990.0000.0000.0000.000
79A86GLN0-0.045-0.00112.7341.7691.7690.0000.0000.0000.000
80A87LEU0-0.039-0.01111.4201.2781.2780.0000.0000.0000.000
81A88PHE0-0.056-0.03212.2270.7860.7860.0000.0000.0000.000
82A89LYS10.9921.00316.92316.02816.0280.0000.0000.0000.000
83A90GLY00.0130.01019.5330.1950.1950.0000.0000.0000.000
84A91GLU-1-0.906-0.94620.501-13.071-13.0710.0000.0000.0000.000
85A92ARG10.8650.91418.17713.50513.5050.0000.0000.0000.000
86A93LYS10.9320.96114.09616.26816.2680.0000.0000.0000.000
87A94ALA00.1030.08114.4470.5250.5250.0000.0000.0000.000
88A95LYS10.8210.90310.51523.77123.7710.0000.0000.0000.000
89A96THR0-0.021-0.02510.839-1.991-1.9910.0000.0000.0000.000
90A97PHE00.0230.0089.6901.4811.4810.0000.0000.0000.000
91A98GLY00.0410.02212.037-2.064-2.0640.0000.0000.0000.000
92A99ILE0-0.024-0.00313.4621.3351.3350.0000.0000.0000.000
93A100ALA00.0480.03115.703-0.306-0.3060.0000.0000.0000.000
94A101ARG10.8670.92418.98715.08015.0800.0000.0000.0000.000
95A102VAL0-0.036-0.01621.9520.0700.0700.0000.0000.0000.000
96A103PRO0-0.0060.00224.7160.2120.2120.0000.0000.0000.000
97A104ARG10.7550.84127.3039.7509.7500.0000.0000.0000.000
98A105PRO00.0300.00430.928-0.095-0.0950.0000.0000.0000.000
99A106ALA00.0110.02533.0260.0070.0070.0000.0000.0000.000
100A107ARG10.9340.94934.4888.8568.8560.0000.0000.0000.000
101A108PHE00.1100.05037.968-0.184-0.1840.0000.0000.0000.000
102A109GLY00.0260.02139.9140.0110.0110.0000.0000.0000.000
103A110ASP-1-0.767-0.84134.381-9.161-9.1610.0000.0000.0000.000
104A111ILE0-0.0080.00036.079-0.175-0.1750.0000.0000.0000.000
105A112ALA00.0050.01038.2140.0140.0140.0000.0000.0000.000
106A113SER0-0.051-0.02937.233-0.001-0.0010.0000.0000.0000.000
107A114ARG10.8270.92130.8319.4809.4800.0000.0000.0000.000
108A115ARG10.8490.91637.1288.5058.5050.0000.0000.0000.000
109A116GLY00.1070.05438.035-0.215-0.2150.0000.0000.0000.000
110A117ASP-1-0.755-0.83440.399-7.196-7.1960.0000.0000.0000.000
111A118VAL0-0.037-0.00740.061-0.303-0.3030.0000.0000.0000.000
112A119VAL0-0.0050.00938.9510.1590.1590.0000.0000.0000.000
113A120VAL00.010-0.00341.013-0.129-0.1290.0000.0000.0000.000
114A121LEU0-0.030-0.01739.1330.0510.0510.0000.0000.0000.000
115A122ASP-1-0.711-0.84943.286-6.573-6.5730.0000.0000.0000.000
116A123GLY00.0790.03645.6710.0660.0660.0000.0000.0000.000
117A124VAL0-0.048-0.01940.471-0.063-0.0630.0000.0000.0000.000
118A125LYS10.8230.89440.9016.8206.8200.0000.0000.0000.000
119A126ILE0-0.070-0.01738.426-0.235-0.2350.0000.0000.0000.000
120A127VAL00.0440.00133.824-0.102-0.1020.0000.0000.0000.000
121A128GLY0-0.023-0.00434.124-0.238-0.2380.0000.0000.0000.000
122A129ASN00.0460.02135.121-0.206-0.2060.0000.0000.0000.000
123A130ILE00.0430.02834.903-0.104-0.1040.0000.0000.0000.000
124A131GLY00.0320.01132.097-0.118-0.1180.0000.0000.0000.000
125A132ALA0-0.029-0.02232.125-0.231-0.2310.0000.0000.0000.000
126A133ILE00.0670.04434.126-0.061-0.0610.0000.0000.0000.000
127A134VAL0-0.0100.01430.106-0.014-0.0140.0000.0000.0000.000
128A135ARG10.9000.94928.29510.38810.3880.0000.0000.0000.000
129A136THR0-0.026-0.01831.369-0.089-0.0890.0000.0000.0000.000
130A137SER00.027-0.01034.5090.1790.1790.0000.0000.0000.000
131A138LEU0-0.059-0.02127.492-0.050-0.0500.0000.0000.0000.000
132A139ALA0-0.063-0.03331.499-0.067-0.0670.0000.0000.0000.000
133A140LEU0-0.021-0.00632.4700.0230.0230.0000.0000.0000.000
134A141GLY00.0200.02234.5410.2220.2220.0000.0000.0000.000
135A142ALA00.0060.01135.6470.1580.1580.0000.0000.0000.000
136A143SER0-0.030-0.01735.383-0.280-0.2800.0000.0000.0000.000
137A144GLY00.008-0.02735.337-0.345-0.3450.0000.0000.0000.000
138A145ILE0-0.046-0.00434.7560.1510.1510.0000.0000.0000.000
139A146ILE00.0260.01237.902-0.131-0.1310.0000.0000.0000.000
140A147LEU0-0.063-0.03036.2920.0610.0610.0000.0000.0000.000
141A148VAL00.0430.02640.714-0.002-0.0020.0000.0000.0000.000
142A149ASP-1-0.825-0.91444.121-6.748-6.7480.0000.0000.0000.000
143A150SER00.0340.01839.1610.0420.0420.0000.0000.0000.000
144A151ASP-1-0.859-0.92940.219-7.395-7.3950.0000.0000.0000.000
145A152ILE0-0.072-0.03034.829-0.195-0.1950.0000.0000.0000.000
146A153THR00.0290.01236.546-0.032-0.0320.0000.0000.0000.000
147A154SER00.011-0.01131.401-0.099-0.0990.0000.0000.0000.000
148A155ILE00.0380.02129.734-0.080-0.0800.0000.0000.0000.000
149A156ALA00.0000.00027.051-0.265-0.2650.0000.0000.0000.000
150A157ASP-1-0.806-0.88828.092-9.964-9.9640.0000.0000.0000.000
151A158ARG10.9700.97323.25812.28212.2820.0000.0000.0000.000
152A159ARG10.8620.93027.2888.7998.7990.0000.0000.0000.000
153A160LEU00.0580.04129.956-0.044-0.0440.0000.0000.0000.000
154A161GLN00.0400.03622.6270.1100.1100.0000.0000.0000.000
155A162ARG10.9370.97423.96511.84111.8410.0000.0000.0000.000
156A163ALA0-0.0040.00526.466-0.095-0.0950.0000.0000.0000.000
157A164SER0-0.002-0.01527.9760.2610.2610.0000.0000.0000.000
158A165ARG10.8830.93923.76411.96311.9630.0000.0000.0000.000
159A166GLY00.0240.01122.767-0.405-0.4050.0000.0000.0000.000
160A167TYR00.015-0.00123.814-0.217-0.2170.0000.0000.0000.000
161A168VAL0-0.022-0.01026.1880.2480.2480.0000.0000.0000.000
162A169PHE0-0.013-0.01323.7540.2400.2400.0000.0000.0000.000
163A170SER00.003-0.00725.315-0.251-0.2510.0000.0000.0000.000
164A171LEU0-0.0160.00227.3510.1100.1100.0000.0000.0000.000
165A172PRO0-0.018-0.00531.125-0.114-0.1140.0000.0000.0000.000
166A173VAL00.0190.00832.4050.2280.2280.0000.0000.0000.000
167A174VAL0-0.030-0.01334.767-0.119-0.1190.0000.0000.0000.000
168A175LEU0-0.048-0.02035.5900.0580.0580.0000.0000.0000.000
169A176SER0-0.017-0.02539.2300.0110.0110.0000.0000.0000.000
170A177GLY00.0360.02042.9540.0400.0400.0000.0000.0000.000
171A178ARG10.8670.91946.6096.3096.3090.0000.0000.0000.000
172A179GLU-1-0.853-0.93548.868-6.226-6.2260.0000.0000.0000.000
173A180GLU-1-0.922-0.95445.432-6.962-6.9620.0000.0000.0000.000
174A181ALA0-0.006-0.00145.445-0.043-0.0430.0000.0000.0000.000
175A182ILE00.0040.00946.674-0.013-0.0130.0000.0000.0000.000
176A183ALA0-0.031-0.01649.7620.0610.0610.0000.0000.0000.000
177A184PHE00.005-0.00642.502-0.018-0.0180.0000.0000.0000.000
178A185ILE0-0.004-0.01245.925-0.033-0.0330.0000.0000.0000.000
179A186ARG10.8710.91748.1276.0076.0070.0000.0000.0000.000
180A187ASP-1-0.837-0.88950.127-6.040-6.0400.0000.0000.0000.000
181A188SER0-0.110-0.05845.963-0.076-0.0760.0000.0000.0000.000
182A189GLY0-0.020-0.00448.225-0.074-0.0740.0000.0000.0000.000
183A190MET0-0.064-0.02344.096-0.099-0.0990.0000.0000.0000.000
184A191GLN00.0520.02748.9410.0210.0210.0000.0000.0000.000
185A192LEU0-0.025-0.01348.753-0.163-0.1630.0000.0000.0000.000
186A193MET00.0150.01749.4240.1580.1580.0000.0000.0000.000
187A194THR00.0220.02249.582-0.204-0.2040.0000.0000.0000.000
188A195LEU0-0.056-0.02446.7650.0680.0680.0000.0000.0000.000
189A196LYS00.0250.02350.327-0.071-0.0710.0000.0000.0000.000
190A197ALA0-0.017-0.02352.6730.0360.0360.0000.0000.0000.000
191A198ASP-1-0.927-0.96354.050-5.543-5.5430.0000.0000.0000.000
192A199GLY00.0050.01555.7010.0780.0780.0000.0000.0000.000
193A200ASP-1-0.890-0.94256.704-5.345-5.3450.0000.0000.0000.000
194A201ILE0-0.042-0.01054.8210.0480.0480.0000.0000.0000.000
195A202SER00.0070.01154.586-0.141-0.1410.0000.0000.0000.000
196A203VAL00.015-0.01148.106-0.065-0.0650.0000.0000.0000.000
197A204LYS10.7800.85648.4186.4346.4340.0000.0000.0000.000
198A205GLU-1-0.835-0.91751.601-5.672-5.6720.0000.0000.0000.000
199A206LEU0-0.042-0.01847.292-0.017-0.0170.0000.0000.0000.000
200A207GLY00.0440.03148.166-0.093-0.0930.0000.0000.0000.000
201A208ASP-1-0.899-0.94849.162-6.030-6.0300.0000.0000.0000.000
202A209ASN0-0.055-0.03750.5330.0140.0140.0000.0000.0000.000
203A210PRO0-0.038-0.02949.837-0.151-0.1510.0000.0000.0000.000
204A211ASP-1-0.878-0.92149.280-6.234-6.2340.0000.0000.0000.000
205A212ARG10.7860.88140.0157.5247.5240.0000.0000.0000.000
206A213LEU00.0190.00445.8000.0990.0990.0000.0000.0000.000
207A214ALA0-0.022-0.01244.787-0.227-0.2270.0000.0000.0000.000
208A215LEU00.0030.00242.9370.1390.1390.0000.0000.0000.000
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