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: 2MLRR

Calculation Name: 2BB3-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: 2BB3

Chain ID: A

ChEMBL ID:

UniProt ID: O29536

Base Structure: X-ray

Registration Date: 2025-10-05

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2152204.824254
FMO2-HF: Nuclear repulsion 2073796.959588
FMO2-HF: Total energy -78407.864666
FMO2-MP2: Total energy -78635.593823


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-157.037-153.1710.429-2.051-2.245-0.019
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.887
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].
3A0HIS00.011-0.0013.221-11.695-9.6780.006-1.171-0.853-0.006
4A1MET0-0.0050.0112.492-0.3031.5460.423-0.880-1.392-0.013
5A2ILE00.0470.0385.8460.1460.1460.0000.0000.0000.000
6A3TRP00.008-0.0046.203-0.252-0.2520.0000.0000.0000.000
7A4ILE0-0.008-0.0069.6782.2402.2400.0000.0000.0000.000
8A5VAL00.0290.00512.615-0.085-0.0850.0000.0000.0000.000
9A6GLY00.0010.00115.0710.9430.9430.0000.0000.0000.000
10A7SER0-0.045-0.04318.760-0.228-0.2280.0000.0000.0000.000
11A8GLY0-0.0140.01321.2090.3530.3530.0000.0000.0000.000
12A9THR0-0.015-0.03423.5340.0870.0870.0000.0000.0000.000
13A10CYS0-0.144-0.08227.1200.0080.0080.0000.0000.0000.000
14A11ARG10.9740.96727.18510.47610.4760.0000.0000.0000.000
15A12GLY00.0160.00426.4330.2670.2670.0000.0000.0000.000
16A13GLN00.0290.02224.884-0.254-0.2540.0000.0000.0000.000
17A14THR00.0080.02619.405-0.391-0.3910.0000.0000.0000.000
18A15THR00.0650.01116.9510.2310.2310.0000.0000.0000.000
19A16GLU-1-0.932-0.97117.718-15.476-15.4760.0000.0000.0000.000
20A17ARG10.9430.95910.24725.21525.2150.0000.0000.0000.000
21A18ALA00.0220.01012.846-1.527-1.5270.0000.0000.0000.000
22A19LYS10.8990.95614.57214.29314.2930.0000.0000.0000.000
23A20GLU-1-0.928-0.95911.602-22.337-22.3370.0000.0000.0000.000
24A21ILE0-0.041-0.0159.185-1.105-1.1050.0000.0000.0000.000
25A22ILE0-0.024-0.01711.019-0.410-0.4100.0000.0000.0000.000
26A23GLU-1-0.932-0.94913.450-20.724-20.7240.0000.0000.0000.000
27A24ARG10.8630.9158.96926.38226.3820.0000.0000.0000.000
28A25ALA0-0.0080.02110.822-0.254-0.2540.0000.0000.0000.000
29A26GLU-1-0.764-0.88911.222-23.399-23.3990.0000.0000.0000.000
30A27VAL0-0.099-0.04613.4012.0562.0560.0000.0000.0000.000
31A28ILE00.0180.01914.332-1.276-1.2760.0000.0000.0000.000
32A29TYR0-0.001-0.03015.8352.1122.1120.0000.0000.0000.000
33A30GLY00.0760.02518.291-0.497-0.4970.0000.0000.0000.000
34A31SER00.0030.01720.8760.5440.5440.0000.0000.0000.000
35A32ARG10.8890.92624.31710.57910.5790.0000.0000.0000.000
36A33ARG11.0271.01426.37410.51210.5120.0000.0000.0000.000
37A34ALA00.0060.01421.6010.0450.0450.0000.0000.0000.000
38A35LEU00.0450.02120.381-0.205-0.2050.0000.0000.0000.000
39A36GLU-1-0.862-0.92623.075-10.688-10.6880.0000.0000.0000.000
40A37LEU0-0.172-0.07924.7550.2940.2940.0000.0000.0000.000
41A38ALA00.0190.00420.1000.0820.0820.0000.0000.0000.000
42A39GLY0-0.051-0.00521.758-0.295-0.2950.0000.0000.0000.000
43A40VAL00.0240.00019.1630.0500.0500.0000.0000.0000.000
44A41VAL0-0.068-0.03622.326-0.190-0.1900.0000.0000.0000.000
45A42ASP-1-0.894-0.95424.788-11.018-11.0180.0000.0000.0000.000
46A43ASP-1-0.803-0.86920.284-15.435-15.4350.0000.0000.0000.000
47A44SER0-0.012-0.00521.456-0.165-0.1650.0000.0000.0000.000
48A45ARG10.8060.87715.03218.65718.6570.0000.0000.0000.000
49A46ALA0-0.0030.01818.866-0.717-0.7170.0000.0000.0000.000
50A47ARG10.8150.90219.69116.00716.0070.0000.0000.0000.000
51A48ILE0-0.006-0.00521.731-0.205-0.2050.0000.0000.0000.000
52A49LEU00.0090.01119.9030.2960.2960.0000.0000.0000.000
53A50ARG10.8900.93924.28610.84810.8480.0000.0000.0000.000
54A51SER00.0020.00525.4390.3760.3760.0000.0000.0000.000
55A52PHE00.0750.01221.535-0.383-0.3830.0000.0000.0000.000
56A53LYS10.9330.98023.62510.82510.8250.0000.0000.0000.000
57A54GLY00.1020.03921.569-0.452-0.4520.0000.0000.0000.000
58A55ASP-1-0.937-0.97521.260-13.062-13.0620.0000.0000.0000.000
59A56GLU-1-0.862-0.92221.300-14.365-14.3650.0000.0000.0000.000
60A57ILE00.005-0.00116.702-0.568-0.5680.0000.0000.0000.000
61A58ARG10.9230.94616.90313.42413.4240.0000.0000.0000.000
62A59ARG10.8280.91617.38913.30613.3060.0000.0000.0000.000
63A60ILE0-0.012-0.00614.407-0.509-0.5090.0000.0000.0000.000
64A61MET0-0.001-0.00112.773-0.848-0.8480.0000.0000.0000.000
65A62GLU-1-0.902-0.94612.492-23.141-23.1410.0000.0000.0000.000
66A63GLU-1-0.776-0.86413.742-20.643-20.6430.0000.0000.0000.000
67A64GLY0-0.002-0.01710.523-0.884-0.8840.0000.0000.0000.000
68A65ARG10.8800.9528.84318.99618.9960.0000.0000.0000.000
69A66GLU-1-1.022-1.00710.122-21.394-21.3940.0000.0000.0000.000
70A67ARG10.7880.89710.98621.12321.1230.0000.0000.0000.000
71A68GLU-1-0.933-0.9766.857-40.378-40.3780.0000.0000.0000.000
72A69VAL0-0.017-0.0019.2393.0253.0250.0000.0000.0000.000
73A70ALA0-0.005-0.00110.088-2.346-2.3460.0000.0000.0000.000
74A71VAL0-0.022-0.01412.4191.9861.9860.0000.0000.0000.000
75A72ILE0-0.018-0.00315.239-0.360-0.3600.0000.0000.0000.000
76A73SER0-0.026-0.01217.9410.8670.8670.0000.0000.0000.000
77A74THR0-0.011-0.01220.2160.0880.0880.0000.0000.0000.000
78A75GLY0-0.033-0.00723.2410.0260.0260.0000.0000.0000.000
79A76ASP-1-0.815-0.92819.832-15.818-15.8180.0000.0000.0000.000
80A77PRO00.0100.00316.2610.5140.5140.0000.0000.0000.000
81A78MET0-0.043-0.02217.1900.0630.0630.0000.0000.0000.000
82A79VAL0-0.016-0.00120.4330.6460.6460.0000.0000.0000.000
83A80ALA0-0.022-0.00924.070-0.022-0.0220.0000.0000.0000.000
84A81GLY00.0380.03421.5960.1910.1910.0000.0000.0000.000
85A82LEU00.006-0.01817.6430.3600.3600.0000.0000.0000.000
86A83GLY00.0390.02218.783-0.238-0.2380.0000.0000.0000.000
87A84ARG10.7980.88419.81911.20611.2060.0000.0000.0000.000
88A85VAL00.0530.02120.082-0.055-0.0550.0000.0000.0000.000
89A86LEU00.0350.02214.9700.0980.0980.0000.0000.0000.000
90A87ARG10.9330.97018.08414.00914.0090.0000.0000.0000.000
91A88GLU-1-0.962-0.96820.357-12.069-12.0690.0000.0000.0000.000
92A89ILE0-0.067-0.03016.5870.5780.5780.0000.0000.0000.000
93A90ALA0-0.028-0.00918.095-0.099-0.0990.0000.0000.0000.000
94A91GLU-1-0.875-0.94411.763-24.795-24.7950.0000.0000.0000.000
95A92ASP-1-0.968-0.97912.153-24.153-24.1530.0000.0000.0000.000
96A93VAL0-0.040-0.0078.491-2.601-2.6010.0000.0000.0000.000
97A94GLU-1-0.927-0.9555.829-46.625-46.6250.0000.0000.0000.000
98A95ILE0-0.032-0.0217.887-1.918-1.9180.0000.0000.0000.000
99A96LYS10.8870.9544.99949.04649.0460.0000.0000.0000.000
100A97ILE00.000-0.0129.2271.3151.3150.0000.0000.0000.000
101A98GLU-1-0.832-0.90812.052-23.470-23.4700.0000.0000.0000.000
102A99PRO0-0.026-0.02113.6150.9110.9110.0000.0000.0000.000
103A100ALA0-0.031-0.00317.400-0.110-0.1100.0000.0000.0000.000
104A101ILE0-0.025-0.00420.4510.3840.3840.0000.0000.0000.000
105A102SER00.0420.00624.2840.3160.3160.0000.0000.0000.000
106A103SER00.0400.00525.7250.2190.2190.0000.0000.0000.000
107A104VAL00.0700.03628.1640.3810.3810.0000.0000.0000.000
108A105GLN00.0660.04924.5720.0890.0890.0000.0000.0000.000
109A106VAL0-0.022-0.00829.2900.2770.2770.0000.0000.0000.000
110A107ALA00.0320.01431.7110.3160.3160.0000.0000.0000.000
111A108LEU00.0260.01431.5070.2510.2510.0000.0000.0000.000
112A109ALA0-0.028-0.01132.8860.2440.2440.0000.0000.0000.000
113A110ARG10.7500.84734.5909.0689.0680.0000.0000.0000.000
114A111LEU00.005-0.00337.0570.2260.2260.0000.0000.0000.000
115A112LYS10.8410.93337.9248.1008.1000.0000.0000.0000.000
116A113VAL00.0240.03336.5020.1420.1420.0000.0000.0000.000
117A114ASP-1-0.812-0.88633.702-9.827-9.8270.0000.0000.0000.000
118A115LEU0-0.012-0.02827.5540.0190.0190.0000.0000.0000.000
119A116SER0-0.134-0.08632.0490.0360.0360.0000.0000.0000.000
120A117GLU-1-0.855-0.92533.743-8.053-8.0530.0000.0000.0000.000
121A118VAL0-0.022-0.00832.9990.2130.2130.0000.0000.0000.000
122A119ALA0-0.0230.00433.440-0.203-0.2030.0000.0000.0000.000
123A120VAL0-0.013-0.00928.9370.1440.1440.0000.0000.0000.000
124A121VAL00.0020.01431.136-0.232-0.2320.0000.0000.0000.000
125A122ASP-1-0.764-0.87229.042-10.685-10.6850.0000.0000.0000.000
126A123CYS0-0.053-0.00231.838-0.026-0.0260.0000.0000.0000.000
127A124HIS10.8630.91527.76510.91710.9170.0000.0000.0000.000
128A125ALA0-0.072-0.02628.971-0.238-0.2380.0000.0000.0000.000
129A126LYS10.7660.84730.7769.5279.5270.0000.0000.0000.000
130A127ASP-1-0.771-0.87133.746-8.156-8.1560.0000.0000.0000.000
131A128PHE0-0.029-0.02435.3350.0760.0760.0000.0000.0000.000
132A129ASP-1-0.837-0.92140.115-7.038-7.0380.0000.0000.0000.000
133A130ALA0-0.006-0.00839.7020.0270.0270.0000.0000.0000.000
134A131GLU-1-0.832-0.91135.197-9.223-9.2230.0000.0000.0000.000
135A132LEU00.0020.01438.991-0.036-0.0360.0000.0000.0000.000
136A133THR00.0230.00342.2600.0180.0180.0000.0000.0000.000
137A134GLU-1-0.829-0.89640.855-7.248-7.2480.0000.0000.0000.000
138A135LEU0-0.025-0.01135.909-0.049-0.0490.0000.0000.0000.000
139A136LEU00.0480.02839.673-0.044-0.0440.0000.0000.0000.000
140A137LYS10.8570.92842.5847.1867.1860.0000.0000.0000.000
141A138TYR0-0.109-0.06539.6230.1400.1400.0000.0000.0000.000
142A139ARG10.8120.90533.0988.9668.9660.0000.0000.0000.000
143A140HIS00.0910.06538.5410.1840.1840.0000.0000.0000.000
144A141LEU0-0.017-0.01237.188-0.291-0.2910.0000.0000.0000.000
145A142LEU0-0.008-0.00532.2390.0860.0860.0000.0000.0000.000
146A143ILE00.0060.00233.945-0.323-0.3230.0000.0000.0000.000
147A144LEU0-0.033-0.01628.8800.0430.0430.0000.0000.0000.000
148A145ALA00.0510.00133.1040.0080.0080.0000.0000.0000.000
149A146ASP-1-0.813-0.88034.755-8.836-8.8360.0000.0000.0000.000
150A147SER0-0.054-0.07236.5600.2400.2400.0000.0000.0000.000
151A148HIS10.7820.86837.3928.5108.5100.0000.0000.0000.000
152A149PHE00.0190.00838.4850.0110.0110.0000.0000.0000.000
153A150PRO0-0.0010.01240.3080.1390.1390.0000.0000.0000.000
154A151LEU00.0450.02243.479-0.053-0.0530.0000.0000.0000.000
155A152GLU-1-0.837-0.93345.278-6.824-6.8240.0000.0000.0000.000
156A153ARG10.7560.87039.8167.9687.9680.0000.0000.0000.000
157A154LEU00.0010.00042.217-0.141-0.1410.0000.0000.0000.000
158A155GLY00.0070.01645.6620.0770.0770.0000.0000.0000.000
159A156LYS10.9400.95449.5055.7345.7340.0000.0000.0000.000
160A157ARG10.7840.89045.8826.8606.8600.0000.0000.0000.000
161A158ARG10.9110.95247.0716.3946.3940.0000.0000.0000.000
162A159VAL0-0.018-0.01743.481-0.146-0.1460.0000.0000.0000.000
163A160VAL00.0150.00541.6590.1130.1130.0000.0000.0000.000
164A161LEU0-0.0040.00640.670-0.234-0.2340.0000.0000.0000.000
165A162LEU0-0.003-0.01237.0580.0680.0680.0000.0000.0000.000
166A163GLU-1-0.773-0.86837.067-7.777-7.7770.0000.0000.0000.000
167A164ASN0-0.007-0.00635.385-0.126-0.1260.0000.0000.0000.000
168A165LEU00.0080.00433.150-0.032-0.0320.0000.0000.0000.000
169A167MET0-0.075-0.02231.486-0.250-0.2500.0000.0000.0000.000
170A168GLU-1-0.901-0.95635.257-7.855-7.8550.0000.0000.0000.000
171A169GLY00.0450.03438.6950.1730.1730.0000.0000.0000.000
172A170GLU-1-0.848-0.87636.553-8.682-8.6820.0000.0000.0000.000
173A171ARG10.7650.85039.2327.6327.6320.0000.0000.0000.000
174A172ILE0-0.008-0.00639.612-0.209-0.2090.0000.0000.0000.000
175A173ARG10.8090.90342.5477.2577.2570.0000.0000.0000.000
176A174GLU-1-0.864-0.92744.559-6.863-6.8630.0000.0000.0000.000
177A175GLY00.0060.00447.1030.1420.1420.0000.0000.0000.000
178A176ASN00.0050.00548.498-0.141-0.1410.0000.0000.0000.000
179A177ALA00.0110.00446.1930.0050.0050.0000.0000.0000.000
180A178ASP-1-0.887-0.93947.969-6.099-6.0990.0000.0000.0000.000
181A179SER0-0.084-0.05450.8960.1020.1020.0000.0000.0000.000
182A180ILE0-0.021-0.00846.5170.0260.0260.0000.0000.0000.000
183A181GLU-1-0.882-0.93047.560-6.485-6.4850.0000.0000.0000.000
184A182LEU00.0010.00540.781-0.107-0.1070.0000.0000.0000.000
185A183GLU-1-0.876-0.93442.699-7.017-7.0170.0000.0000.0000.000
186A184SER0-0.008-0.02637.679-0.123-0.1230.0000.0000.0000.000
187A185ASP-1-0.853-0.89034.962-8.554-8.5540.0000.0000.0000.000
188A186TYR0-0.051-0.03230.471-0.540-0.5400.0000.0000.0000.000
189A187THR00.0370.01134.5890.1660.1660.0000.0000.0000.000
190A188ILE0-0.056-0.02431.803-0.257-0.2570.0000.0000.0000.000
191A189ILE00.0200.01435.9900.2200.2200.0000.0000.0000.000
192A190PHE0-0.003-0.00537.949-0.186-0.1860.0000.0000.0000.000
193A191VAL00.007-0.00439.5060.2320.2320.0000.0000.0000.000
194A192GLU-1-0.922-0.95741.353-7.206-7.2060.0000.0000.0000.000
195A193ARG10.9130.94442.2517.4347.4340.0000.0000.0000.000
196A194GLU-1-0.883-0.92043.877-6.574-6.5740.0000.0000.0000.000
197A195VAL-1-0.986-0.98046.675-6.419-6.4190.0000.0000.0000.000