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: 46L8N

Calculation Name: 3O7B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine

Ligand 3-letter code: SAH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3O7B

Chain ID: A

ChEMBL ID:

UniProt ID: O29524

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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2737834.446401
FMO2-HF: Nuclear repulsion 2650674.515344
FMO2-HF: Total energy -87159.931057
FMO2-MP2: Total energy -87416.424232


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:1:MET)


Summations of interaction energy for fragment #1(A: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.
-228.255-220.02826.124-16.802-17.545-0.167
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.678 / q_NPA : 0.834
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].
3A3SER00.0850.0453.579-1.4890.7480.758-1.183-1.812-0.006
81A81GLU-1-0.785-0.8605.146-33.911-33.808-0.001-0.001-0.1000.000
139A139VAL00.0060.0104.415-3.914-3.838-0.001-0.015-0.0600.000
140A140ARG10.9180.9694.53929.19329.402-0.001-0.016-0.1910.000
141A141GLY0-0.040-0.0232.739-7.734-6.4680.860-0.832-1.294-0.009
142A142ARG10.7740.8702.75137.72640.0015.800-2.204-5.871-0.014
143A143ASP-1-0.838-0.9095.079-26.852-26.7830.003-0.040-0.0320.000
163A163ASP-1-0.789-0.8721.732-140.310-138.47218.707-12.499-8.045-0.138
164A164VAL00.0420.0244.9214.4154.569-0.001-0.012-0.1400.000
4A4ALA0-0.055-0.0235.5580.5320.5320.0000.0000.0000.000
5A5PHE00.0150.0207.3021.4951.4950.0000.0000.0000.000
6A6VAL00.002-0.0139.0490.1460.1460.0000.0000.0000.000
7A7PHE0-0.020-0.01411.7080.9070.9070.0000.0000.0000.000
8A8LEU00.0460.01313.0040.1430.1430.0000.0000.0000.000
9A9GLU-1-0.747-0.84916.356-12.053-12.0530.0000.0000.0000.000
10A10ALA00.0160.01318.6020.6260.6260.0000.0000.0000.000
11A11SER0-0.045-0.04720.3560.3190.3190.0000.0000.0000.000
12A12LEU0-0.067-0.04319.9380.3880.3880.0000.0000.0000.000
13A13GLU-1-0.723-0.82722.822-10.406-10.4060.0000.0000.0000.000
14A14LEU00.0080.01025.4640.2740.2740.0000.0000.0000.000
15A15ILE0-0.029-0.00728.4370.0730.0730.0000.0000.0000.000
16A16PRO00.0620.03230.0600.1380.1380.0000.0000.0000.000
17A17GLN00.0540.00629.9950.3980.3980.0000.0000.0000.000
18A18LYS10.9160.95534.5988.1928.1920.0000.0000.0000.000
19A19ILE00.0150.01834.5440.2110.2110.0000.0000.0000.000
20A20ARG10.8680.93131.3278.7808.7800.0000.0000.0000.000
21A21GLY0-0.0020.00338.2540.0870.0870.0000.0000.0000.000
22A22HIS00.0400.03340.7430.1660.1660.0000.0000.0000.000
23A23PRO00.0260.00642.460-0.081-0.0810.0000.0000.0000.000
24A24ALA00.0100.00541.4470.0170.0170.0000.0000.0000.000
25A25VAL00.0350.02337.267-0.077-0.0770.0000.0000.0000.000
26A26ARG10.9390.97039.7116.5296.5290.0000.0000.0000.000
27A27ALA00.0200.01042.3860.0120.0120.0000.0000.0000.000
28A28ASP-1-0.814-0.90236.799-7.928-7.9280.0000.0000.0000.000
29A29ALA00.004-0.01138.727-0.058-0.0580.0000.0000.0000.000
30A30ILE0-0.032-0.01839.695-0.006-0.0060.0000.0000.0000.000
31A31ARG10.8580.92639.7277.2927.2920.0000.0000.0000.000
32A32ARG10.7670.85432.7358.5898.5890.0000.0000.0000.000
33A33GLY00.0170.02938.284-0.127-0.1270.0000.0000.0000.000
34A34LYS10.7920.88331.8429.0029.0020.0000.0000.0000.000
35A35ARG10.8960.92435.7397.9837.9830.0000.0000.0000.000
36A36PRO00.0430.00835.674-0.200-0.2000.0000.0000.0000.000
37A37GLU-1-0.839-0.91833.053-8.475-8.4750.0000.0000.0000.000
38A38LYS10.8210.90731.2488.7228.7220.0000.0000.0000.000
39A39ILE0-0.049-0.01031.456-0.120-0.1200.0000.0000.0000.000
40A40LEU00.0160.00625.329-0.065-0.0650.0000.0000.0000.000
41A41LEU0-0.053-0.03328.9950.3540.3540.0000.0000.0000.000
42A42ASP-1-0.754-0.86729.479-9.189-9.1890.0000.0000.0000.000
43A43ASP-1-0.782-0.89932.033-8.461-8.4610.0000.0000.0000.000
44A44SER0-0.0090.00134.0270.2990.2990.0000.0000.0000.000
45A45LYS10.7740.88933.8168.8228.8220.0000.0000.0000.000
46A46HIS0-0.039-0.03933.6270.1210.1210.0000.0000.0000.000
47A47HIS00.1110.07236.836-0.051-0.0510.0000.0000.0000.000
48A48THR0-0.055-0.04137.7140.0320.0320.0000.0000.0000.000
49A49ALA0-0.040-0.02738.2510.1660.1660.0000.0000.0000.000
50A50MET0-0.010-0.00432.0260.0340.0340.0000.0000.0000.000
51A51LYS10.9390.97836.1776.6896.6890.0000.0000.0000.000
52A52SER00.0130.02238.106-0.008-0.0080.0000.0000.0000.000
53A53LEU0-0.063-0.02731.773-0.014-0.0140.0000.0000.0000.000
54A54GLU-1-0.854-0.92631.027-8.271-8.2710.0000.0000.0000.000
55A55PHE00.0800.03826.316-0.184-0.1840.0000.0000.0000.000
56A56ARG10.8080.87129.6998.3308.3300.0000.0000.0000.000
57A57GLU-1-0.871-0.93629.957-9.317-9.3170.0000.0000.0000.000
58A58LYS10.8700.94223.72111.17311.1730.0000.0000.0000.000
59A59ARG10.7810.88226.9239.4969.4960.0000.0000.0000.000
60A60GLY00.001-0.00428.3080.2550.2550.0000.0000.0000.000
61A61ARG10.8520.90127.5519.9669.9660.0000.0000.0000.000
62A62PRO00.0760.03524.741-0.380-0.3800.0000.0000.0000.000
63A63ASP-1-0.834-0.90124.747-10.563-10.5630.0000.0000.0000.000
64A64ILE00.0350.03222.914-0.229-0.2290.0000.0000.0000.000
65A65VAL00.0730.02718.777-0.365-0.3650.0000.0000.0000.000
66A66HIS0-0.090-0.03820.776-0.290-0.2900.0000.0000.0000.000
67A67GLN0-0.007-0.01622.701-0.323-0.3230.0000.0000.0000.000
68A68CYS0-0.042-0.00819.534-0.028-0.0280.0000.0000.0000.000
69A69LEU00.0180.00516.214-0.614-0.6140.0000.0000.0000.000
70A70LEU0-0.077-0.03619.121-0.333-0.3330.0000.0000.0000.000
71A71LEU00.0190.01621.527-0.193-0.1930.0000.0000.0000.000
72A72LEU00.0190.01613.823-0.073-0.0730.0000.0000.0000.000
73A73LEU0-0.040-0.02015.635-0.792-0.7920.0000.0000.0000.000
74A74ASP-1-0.807-0.86118.522-13.087-13.0870.0000.0000.0000.000
75A75SER0-0.044-0.01917.201-0.023-0.0230.0000.0000.0000.000
76A76PRO00.0160.00418.571-0.341-0.3410.0000.0000.0000.000
77A77LEU00.0170.02612.221-0.288-0.2880.0000.0000.0000.000
78A78ARG10.8020.86112.81818.32718.3270.0000.0000.0000.000
79A79ASP-1-0.789-0.8647.868-32.587-32.5870.0000.0000.0000.000
80A80PHE0-0.018-0.0117.492-4.451-4.4510.0000.0000.0000.000
82A82VAL0-0.002-0.0098.7900.7620.7620.0000.0000.0000.000
83A83TYR0-0.036-0.0425.8961.7271.7270.0000.0000.0000.000
84A84VAL0-0.051-0.02811.5100.8240.8240.0000.0000.0000.000
85A85HIS00.0870.05713.707-0.432-0.4320.0000.0000.0000.000
86A86THR0-0.042-0.03515.4010.4440.4440.0000.0000.0000.000
87A87LEU0-0.026-0.01119.205-0.023-0.0230.0000.0000.0000.000
88A88ASN0-0.109-0.05921.8590.4270.4270.0000.0000.0000.000
89A89GLY00.0180.01218.1980.1170.1170.0000.0000.0000.000
90A90GLU-1-0.870-0.92516.836-12.977-12.9770.0000.0000.0000.000
91A91ILE00.0300.02810.862-0.143-0.1430.0000.0000.0000.000
92A92ILE0-0.035-0.01714.1590.4090.4090.0000.0000.0000.000
93A93TRP0-0.029-0.0208.6121.2411.2410.0000.0000.0000.000
94A94VAL0-0.038-0.03812.3271.6921.6920.0000.0000.0000.000
95A95ASN0-0.013-0.00712.745-1.923-1.9230.0000.0000.0000.000
96A96ARG10.8480.93012.35921.33121.3310.0000.0000.0000.000
97A97GLU-1-0.831-0.90114.275-17.607-17.6070.0000.0000.0000.000
98A98THR0-0.079-0.04417.2701.3461.3460.0000.0000.0000.000
99A99ARG10.9590.98019.22312.54312.5430.0000.0000.0000.000
100A100LEU00.0440.02719.2430.6490.6490.0000.0000.0000.000
101A101PRO0-0.045-0.02523.1350.3550.3550.0000.0000.0000.000
102A102ARG10.8780.89024.93412.00212.0020.0000.0000.0000.000
103A103ASN0-0.043-0.01628.1610.1770.1770.0000.0000.0000.000
104A104TYR00.0800.02228.479-0.196-0.1960.0000.0000.0000.000
105A105ASN00.015-0.00129.493-0.130-0.1300.0000.0000.0000.000
106A106ARG10.9170.95930.1439.0249.0240.0000.0000.0000.000
107A107PHE00.0670.04021.673-0.049-0.0490.0000.0000.0000.000
108A108VAL00.0190.01026.286-0.187-0.1870.0000.0000.0000.000
109A109GLY0-0.014-0.00528.135-0.051-0.0510.0000.0000.0000.000
110A110LEU0-0.006-0.00823.3410.0480.0480.0000.0000.0000.000
111A111MET00.0240.02620.829-0.400-0.4000.0000.0000.0000.000
112A112GLU-1-0.711-0.81024.641-9.236-9.2360.0000.0000.0000.000
113A113LYS10.8580.94526.55010.61210.6120.0000.0000.0000.000
114A114LEU00.0190.01819.0940.0260.0260.0000.0000.0000.000
115A115PHE0-0.022-0.01722.214-0.169-0.1690.0000.0000.0000.000
116A116GLU-1-0.864-0.89624.424-9.281-9.2810.0000.0000.0000.000
117A117GLU-1-0.872-0.95625.338-10.512-10.5120.0000.0000.0000.000
118A118ARG10.8370.93620.62711.99411.9940.0000.0000.0000.000
119A119ARG10.8830.90917.47313.94413.9440.0000.0000.0000.000
120A120ILE0-0.017-0.00720.0020.7570.7570.0000.0000.0000.000
121A121THR0-0.035-0.02919.938-0.653-0.6530.0000.0000.0000.000
122A122ALA00.0020.00721.4610.5790.5790.0000.0000.0000.000
123A123GLY00.001-0.00123.001-0.201-0.2010.0000.0000.0000.000
124A124ASP-1-0.860-0.93021.659-12.546-12.5460.0000.0000.0000.000
125A125THR0-0.047-0.00917.613-0.879-0.8790.0000.0000.0000.000
126A126THR0-0.007-0.01215.5490.7840.7840.0000.0000.0000.000
127A127LEU0-0.024-0.00616.444-0.792-0.7920.0000.0000.0000.000
128A128ILE00.012-0.00216.433-0.539-0.5390.0000.0000.0000.000
129A129GLU-1-0.782-0.86115.198-15.927-15.9270.0000.0000.0000.000
130A130PHE0-0.0030.00514.978-0.794-0.7940.0000.0000.0000.000
131A131LYS10.8110.89410.89920.00420.0040.0000.0000.0000.000
132A132ASP-1-0.927-0.95613.813-14.278-14.2780.0000.0000.0000.000
133A133VAL0-0.044-0.0249.826-0.478-0.4780.0000.0000.0000.000
134A134GLY00.0310.02112.3140.8260.8260.0000.0000.0000.000
135A135LEU0-0.016-0.02310.474-1.219-1.2190.0000.0000.0000.000
136A136ARG10.8810.9099.46215.19515.1950.0000.0000.0000.000
137A137ASP-1-0.902-0.9588.021-22.676-22.6760.0000.0000.0000.000
138A138ILE0-0.037-0.0175.434-2.982-2.9820.0000.0000.0000.000
144A144VAL0-0.026-0.0138.6320.3890.3890.0000.0000.0000.000
145A145LEU0-0.018-0.00410.5342.0962.0960.0000.0000.0000.000
146A146LEU00.0000.01213.4960.1440.1440.0000.0000.0000.000
147A147PHE00.017-0.00515.1500.8990.8990.0000.0000.0000.000
148A148ARG10.8500.90718.67013.17113.1710.0000.0000.0000.000
149A149GLU-1-0.834-0.89822.036-10.250-10.2500.0000.0000.0000.000
150A150LYS10.8290.90523.44312.16812.1680.0000.0000.0000.000
151A151GLY00.0010.00922.331-0.047-0.0470.0000.0000.0000.000
152A152GLY0-0.008-0.00922.1190.5080.5080.0000.0000.0000.000
153A153ARG10.9320.95522.59810.74510.7450.0000.0000.0000.000
154A154PHE00.016-0.00919.8790.0200.0200.0000.0000.0000.000
155A155GLU-1-0.868-0.91920.498-14.152-14.1520.0000.0000.0000.000
156A156PHE00.030-0.01117.519-0.641-0.6410.0000.0000.0000.000
157A157SER0-0.006-0.00416.195-1.256-1.2560.0000.0000.0000.000
158A158GLU-1-0.890-0.94815.104-18.657-18.6570.0000.0000.0000.000
159A159LEU0-0.132-0.05514.605-0.831-0.8310.0000.0000.0000.000
160A160LEU0-0.051-0.02312.025-1.545-1.5450.0000.0000.0000.000
161A161ASP-1-0.867-0.91111.113-27.246-27.2460.0000.0000.0000.000
162A162GLY00.0520.0277.286-1.998-1.9980.0000.0000.0000.000
165A165ALA00.017-0.0086.380-1.441-1.4410.0000.0000.0000.000
166A166VAL00.0070.0278.1022.4862.4860.0000.0000.0000.000
167A167CYS0-0.040-0.01810.8810.1170.1170.0000.0000.0000.000
168A168ILE00.0240.00613.3761.0321.0320.0000.0000.0000.000
169A169GLY00.0370.03316.871-0.140-0.1400.0000.0000.0000.000
170A170ALA0-0.018-0.00719.3870.2380.2380.0000.0000.0000.000
171A171PHE0-0.033-0.01520.6520.3070.3070.0000.0000.0000.000
172A172PRO0-0.060-0.01724.287-0.087-0.0870.0000.0000.0000.000
173A173HIS0-0.051-0.03427.6440.3050.3050.0000.0000.0000.000
174A174GLY00.0410.01927.561-0.117-0.1170.0000.0000.0000.000
175A175ASP-1-0.880-0.93225.118-10.889-10.8890.0000.0000.0000.000
176A176PHE0-0.012-0.01718.4760.0650.0650.0000.0000.0000.000
177A177PHE0-0.004-0.01121.4840.5010.5010.0000.0000.0000.000
178A178GLU-1-0.859-0.95720.787-12.280-12.2800.0000.0000.0000.000
179A179GLU-1-1.035-1.01119.113-12.709-12.7090.0000.0000.0000.000
180A180THR0-0.004-0.04416.257-0.567-0.5670.0000.0000.0000.000
181A181LEU0-0.013-0.00715.964-0.845-0.8450.0000.0000.0000.000
182A182ARG10.9310.97116.82511.93011.9300.0000.0000.0000.000
183A183GLU-1-0.808-0.88213.567-17.412-17.4120.0000.0000.0000.000
184A184LEU0-0.029-0.01611.557-1.186-1.1860.0000.0000.0000.000
185A185GLY0-0.0110.00611.754-1.190-1.1900.0000.0000.0000.000
186A186GLU-1-0.967-0.97512.378-19.673-19.6730.0000.0000.0000.000
187A187PHE0-0.019-0.02012.084-1.064-1.0640.0000.0000.0000.000
188A188LYS10.9500.98914.19019.78619.7860.0000.0000.0000.000
189A189GLU-1-0.792-0.88016.397-13.225-13.2250.0000.0000.0000.000
190A190VAL0-0.006-0.00417.0840.4310.4310.0000.0000.0000.000
191A191SER0-0.0060.00320.0050.1360.1360.0000.0000.0000.000
192A192LEU0-0.021-0.01121.104-0.191-0.1910.0000.0000.0000.000
193A193GLY0-0.004-0.00624.6590.2590.2590.0000.0000.0000.000
194A194THR0-0.056-0.02128.057-0.159-0.1590.0000.0000.0000.000
195A195GLU-1-0.838-0.90229.321-9.251-9.2510.0000.0000.0000.000
196A196SER0-0.005-0.00527.829-0.441-0.4410.0000.0000.0000.000
197A197TYR0-0.098-0.06225.7530.0180.0180.0000.0000.0000.000
198A198THR00.009-0.00526.020-0.311-0.3110.0000.0000.0000.000
199A199SER00.054-0.00221.338-0.026-0.0260.0000.0000.0000.000
200A200LEU00.0100.01321.616-0.597-0.5970.0000.0000.0000.000
201A201TYR00.0070.01723.395-0.384-0.3840.0000.0000.0000.000
202A202VAL00.0220.00519.399-0.249-0.2490.0000.0000.0000.000
203A203THR0-0.001-0.02617.951-0.752-0.7520.0000.0000.0000.000
204A204SER0-0.026-0.01619.585-0.648-0.6480.0000.0000.0000.000
205A205ARG10.9020.94621.91912.05112.0510.0000.0000.0000.000
206A206VAL00.0080.00316.085-0.166-0.1660.0000.0000.0000.000
207A207LEU0-0.025-0.00516.822-1.013-1.0130.0000.0000.0000.000
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212A212ARG10.7360.79616.71813.93613.9360.0000.0000.0000.000
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215A215ALA0-0.061-0.02212.962-0.880-0.8800.0000.0000.0000.000
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