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: RM5Z8

Calculation Name: 3BBD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine | glycerol

Ligand 3-letter code: SAH | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BBD

Chain ID: A

ChEMBL ID:

UniProt ID: Q57977

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2564794.037757
FMO2-HF: Nuclear repulsion 2481280.601692
FMO2-HF: Total energy -83513.436065
FMO2-MP2: Total energy -83757.590478


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
48.04955.5526.273-6.108-7.668-0.06
Interaction energy analysis for fragmet #1(A:2:THR)
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 : 0.897
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].
3A4ASN00.012-0.0033.497-3.937-2.1080.004-0.831-1.003-0.002
73A74LYS10.8160.9005.24723.29423.395-0.001-0.014-0.0850.000
74A75LYS10.8510.9152.18625.73027.3041.673-1.388-1.859-0.010
75A76LEU0-0.015-0.0012.304-22.224-19.8354.455-3.214-3.630-0.042
76A77ASN0-0.037-0.0052.7742.8954.5080.143-0.659-1.097-0.006
77A78ILE00.0180.0054.8311.6341.631-0.001-0.0020.0060.000
4A5ILE00.0000.0005.8643.3333.3330.0000.0000.0000.000
5A6ILE00.0220.0068.8310.5620.5620.0000.0000.0000.000
6A7LEU0-0.033-0.00311.9400.9440.9440.0000.0000.0000.000
7A8ALA00.0390.01415.4720.0400.0400.0000.0000.0000.000
8A9LYS10.8800.92617.82813.26013.2600.0000.0000.0000.000
9A10SER0-0.012-0.01118.5830.4570.4570.0000.0000.0000.000
10A11ALA0-0.0140.00821.2410.3580.3580.0000.0000.0000.000
11A12LEU0-0.072-0.04520.1870.3750.3750.0000.0000.0000.000
12A13GLU-1-0.729-0.85323.519-11.043-11.0430.0000.0000.0000.000
13A14LEU00.019-0.00226.2570.1980.1980.0000.0000.0000.000
14A15ILE0-0.072-0.03929.0500.0900.0900.0000.0000.0000.000
15A16PRO00.0530.02331.3440.1640.1640.0000.0000.0000.000
16A17GLU-1-0.767-0.88333.544-8.105-8.1050.0000.0000.0000.000
17A18GLU-1-0.875-0.94133.641-8.848-8.8480.0000.0000.0000.000
18A19ILE0-0.061-0.04634.9770.2670.2670.0000.0000.0000.000
19A20LYS10.8990.94734.8858.7618.7610.0000.0000.0000.000
20A21ASN00.0080.00139.2750.0180.0180.0000.0000.0000.000
21A22LYS10.9000.96140.6917.7757.7750.0000.0000.0000.000
22A23ILE0-0.048-0.01436.9470.0200.0200.0000.0000.0000.000
23A24ARG10.9710.99340.6706.7566.7560.0000.0000.0000.000
24A25LYS10.9050.95135.9258.3928.3920.0000.0000.0000.000
25A26SER00.0430.01440.3920.1660.1660.0000.0000.0000.000
26A27ARG10.9850.97840.0986.6476.6470.0000.0000.0000.000
27A28VAL00.0100.00939.371-0.086-0.0860.0000.0000.0000.000
28A29TYR0-0.032-0.02631.055-0.203-0.2030.0000.0000.0000.000
29A30LYS10.8570.93035.6738.1548.1540.0000.0000.0000.000
30A31TYR00.0360.02730.792-0.041-0.0410.0000.0000.0000.000
31A32ASP-1-0.827-0.90231.909-8.663-8.6630.0000.0000.0000.000
32A33ILE00.0060.01825.577-0.120-0.1200.0000.0000.0000.000
33A34LEU0-0.021-0.00129.1740.3820.3820.0000.0000.0000.000
34A35ASP-1-0.775-0.87629.095-10.377-10.3770.0000.0000.0000.000
35A36SER00.033-0.00831.1020.3940.3940.0000.0000.0000.000
36A37ASN0-0.079-0.05131.2510.4490.4490.0000.0000.0000.000
37A38TYR0-0.030-0.02032.8930.3900.3900.0000.0000.0000.000
38A39HIS0-0.020-0.01233.3390.1160.1160.0000.0000.0000.000
39A40TYR00.0490.02336.7430.1690.1690.0000.0000.0000.000
40A41LYS10.8880.94637.6757.1677.1670.0000.0000.0000.000
41A42ALA0-0.0070.00438.2650.0880.0880.0000.0000.0000.000
42A43MET0-0.036-0.01931.978-0.003-0.0030.0000.0000.0000.000
43A44GLU-1-0.848-0.90737.228-7.349-7.3490.0000.0000.0000.000
44A45LYS10.9140.96139.9557.4907.4900.0000.0000.0000.000
45A46LEU0-0.038-0.00632.4160.0780.0780.0000.0000.0000.000
46A47LYS10.9610.98531.1389.8169.8160.0000.0000.0000.000
47A48ASP-1-0.770-0.86730.005-10.250-10.2500.0000.0000.0000.000
48A49LYS10.8810.94930.7797.8577.8570.0000.0000.0000.000
49A50GLU-1-0.892-0.95631.960-9.133-9.1330.0000.0000.0000.000
50A51MET0-0.086-0.05126.665-0.350-0.3500.0000.0000.0000.000
51A52ARG10.8060.89126.6229.6409.6400.0000.0000.0000.000
52A53GLY00.0190.01528.1670.1870.1870.0000.0000.0000.000
53A54ARG10.8020.85826.57811.14011.1400.0000.0000.0000.000
54A55PRO00.0780.03924.071-0.538-0.5380.0000.0000.0000.000
55A56ASP-1-0.782-0.85723.182-11.989-11.9890.0000.0000.0000.000
56A57ILE00.0150.01321.260-0.420-0.4200.0000.0000.0000.000
57A58ILE00.0080.02717.859-0.742-0.7420.0000.0000.0000.000
58A59HIS0-0.072-0.03418.728-0.513-0.5130.0000.0000.0000.000
59A60ILE00.0320.00219.803-0.590-0.5900.0000.0000.0000.000
60A61SER0-0.004-0.03216.524-0.506-0.5060.0000.0000.0000.000
61A62LEU0-0.001-0.00113.742-1.055-1.0550.0000.0000.0000.000
62A63LEU0-0.058-0.02415.459-0.681-0.6810.0000.0000.0000.000
63A64ASN0-0.025-0.02016.6060.0090.0090.0000.0000.0000.000
64A65ILE00.007-0.00210.385-0.734-0.7340.0000.0000.0000.000
65A66LEU0-0.061-0.02311.553-1.504-1.5040.0000.0000.0000.000
66A67ASP-1-0.898-0.92212.914-17.595-17.5950.0000.0000.0000.000
67A68SER0-0.021-0.01011.131-0.455-0.4550.0000.0000.0000.000
68A69PRO00.0460.00611.291-1.232-1.2320.0000.0000.0000.000
69A70ILE00.0140.0185.145-1.769-1.7690.0000.0000.0000.000
70A71ASN0-0.048-0.0516.367-7.435-7.4350.0000.0000.0000.000
71A72HIS0-0.017-0.0117.941-1.600-1.6000.0000.0000.0000.000
72A73GLU-1-0.894-0.9307.536-30.307-30.3070.0000.0000.0000.000
78A79TYR00.0360.0086.5021.4381.4380.0000.0000.0000.000
79A80ILE0-0.040-0.02111.4070.4270.4270.0000.0000.0000.000
80A81HIS00.0610.03615.174-0.155-0.1550.0000.0000.0000.000
81A82THR0-0.014-0.03517.3100.0240.0240.0000.0000.0000.000
82A83TYR0-0.064-0.07421.0030.0070.0070.0000.0000.0000.000
83A84ASP-1-0.851-0.89724.260-11.942-11.9420.0000.0000.0000.000
84A85ASP-1-0.831-0.89621.674-13.233-13.2330.0000.0000.0000.000
85A86LYS10.9040.96220.72211.65511.6550.0000.0000.0000.000
86A87VAL0-0.006-0.01013.936-0.586-0.5860.0000.0000.0000.000
87A88LEU0-0.020-0.01215.7790.3530.3530.0000.0000.0000.000
88A89LYS10.8990.9476.38832.43632.4360.0000.0000.0000.000
89A90ILE0-0.043-0.03011.1431.5891.5890.0000.0000.0000.000
90A91ASN00.0270.0199.890-3.331-3.3310.0000.0000.0000.000
91A92PRO00.0720.0436.4952.1732.1730.0000.0000.0000.000
92A93GLU-1-0.827-0.8949.592-20.537-20.5370.0000.0000.0000.000
93A94THR0-0.066-0.04812.8322.1692.1690.0000.0000.0000.000
94A95ARG10.9890.99915.13412.97112.9710.0000.0000.0000.000
95A96LEU00.0060.00217.3380.9320.9320.0000.0000.0000.000
96A97PRO0-0.022-0.01019.3940.3460.3460.0000.0000.0000.000
97A98ARG11.0181.00418.60714.73614.7360.0000.0000.0000.000
98A99ASN0-0.0140.00124.4520.1910.1910.0000.0000.0000.000
99A100TYR00.060-0.00225.764-0.308-0.3080.0000.0000.0000.000
100A101PHE00.0450.01927.114-0.168-0.1680.0000.0000.0000.000
101A102ARG10.9330.96326.79210.29510.2950.0000.0000.0000.000
102A103PHE00.0160.01319.640-0.183-0.1830.0000.0000.0000.000
103A104LEU00.0090.01224.202-0.267-0.2670.0000.0000.0000.000
104A105GLY00.0300.01226.597-0.046-0.0460.0000.0000.0000.000
105A106VAL0-0.069-0.02821.5450.0230.0230.0000.0000.0000.000
106A107MET00.0230.00417.919-0.245-0.2450.0000.0000.0000.000
107A108GLU-1-0.784-0.88623.182-9.866-9.8660.0000.0000.0000.000
108A109LYS10.9370.97525.58210.53010.5300.0000.0000.0000.000
109A110VAL00.0030.00819.5840.0310.0310.0000.0000.0000.000
110A111LEU0-0.013-0.01321.893-0.092-0.0920.0000.0000.0000.000
111A112LYS10.7750.86124.3979.9009.9000.0000.0000.0000.000
112A113GLY00.0300.03724.5540.2990.2990.0000.0000.0000.000
113A114GLU-1-0.947-0.97525.594-10.415-10.4150.0000.0000.0000.000
114A115ARG10.9390.96121.92011.89811.8980.0000.0000.0000.000
115A116ASN00.0520.03018.704-0.283-0.2830.0000.0000.0000.000
116A117HIS00.011-0.00917.703-0.347-0.3470.0000.0000.0000.000
117A118LEU0-0.012-0.00814.343-0.922-0.9220.0000.0000.0000.000
118A119ILE0-0.013-0.00614.000-1.227-1.2270.0000.0000.0000.000
119A120LYS10.8750.95014.27617.91717.9170.0000.0000.0000.000
120A121MET0-0.0020.00016.006-0.739-0.7390.0000.0000.0000.000
121A122GLU-1-0.871-0.92615.701-17.043-17.0430.0000.0000.0000.000
122A123GLU-1-0.933-0.97019.031-11.987-11.9870.0000.0000.0000.000
123A124LYS10.7690.86414.98717.06817.0680.0000.0000.0000.000
124A125THR0-0.007-0.01019.364-0.366-0.3660.0000.0000.0000.000
125A126LEU0-0.013-0.02115.594-0.942-0.9420.0000.0000.0000.000
126A127GLU-1-0.799-0.90716.090-15.468-15.4680.0000.0000.0000.000
127A128ASP-1-0.818-0.87716.641-15.288-15.2880.0000.0000.0000.000
128A129LEU0-0.006-0.00211.582-0.972-0.9720.0000.0000.0000.000
129A130LEU0-0.039-0.03112.096-1.927-1.9270.0000.0000.0000.000
130A131ASN00.001-0.00712.212-1.810-1.8100.0000.0000.0000.000
131A132GLU-1-0.836-0.90112.732-18.520-18.5200.0000.0000.0000.000
132A133ILE0-0.101-0.0427.416-1.326-1.3260.0000.0000.0000.000
133A134ASN0-0.060-0.0307.723-2.668-2.6680.0000.0000.0000.000
134A135ALA00.0010.0079.255-2.526-2.5260.0000.0000.0000.000
135A136LYS10.9250.9607.88934.08534.0850.0000.0000.0000.000
136A137LYS10.8960.96010.61027.81327.8130.0000.0000.0000.000
137A138ILE00.013-0.00111.298-2.203-2.2030.0000.0000.0000.000
138A139ALA0-0.0020.00013.0801.8241.8240.0000.0000.0000.000
139A140ILE00.0100.00314.758-0.459-0.4590.0000.0000.0000.000
140A141MET0-0.0040.00015.3170.5670.5670.0000.0000.0000.000
141A142THR0-0.003-0.01618.1910.8700.8700.0000.0000.0000.000
142A143LYS10.9830.98922.01710.85610.8560.0000.0000.0000.000
143A144THR0-0.057-0.03524.9200.4660.4660.0000.0000.0000.000
144A145GLY00.0520.03922.6690.2100.2100.0000.0000.0000.000
145A146LYS10.9370.95721.76012.71512.7150.0000.0000.0000.000
146A147LEU00.0080.01921.788-0.747-0.7470.0000.0000.0000.000
147A148THR0-0.019-0.00817.3350.0640.0640.0000.0000.0000.000
148A149HIS00.0410.00820.007-0.717-0.7170.0000.0000.0000.000
149A150PRO00.0790.01316.313-0.710-0.7100.0000.0000.0000.000
150A151LYS10.9630.99814.82714.41714.4170.0000.0000.0000.000
151A152LEU0-0.020-0.01814.192-0.777-0.7770.0000.0000.0000.000
152A153LEU0-0.011-0.00112.065-0.481-0.4810.0000.0000.0000.000
153A154LYS10.8460.8968.90322.81922.8190.0000.0000.0000.000
154A155GLU-1-0.909-0.9448.303-28.032-28.0320.0000.0000.0000.000
155A156TYR0-0.054-0.0359.9811.6021.6020.0000.0000.0000.000
156A157ASP-1-0.744-0.8416.059-36.359-36.3590.0000.0000.0000.000
157A158THR00.009-0.0166.576-5.253-5.2530.0000.0000.0000.000
158A159PHE0-0.014-0.0067.6444.0574.0570.0000.0000.0000.000
159A160ILE00.0200.00811.399-0.223-0.2230.0000.0000.0000.000
160A161ILE0-0.014-0.00913.1911.1541.1540.0000.0000.0000.000
161A162GLY00.0250.00916.6420.0410.0410.0000.0000.0000.000
162A163GLY00.0110.00119.6080.0160.0160.0000.0000.0000.000
163A164PHE0-0.048-0.01220.1000.4170.4170.0000.0000.0000.000
164A165PRO0-0.032-0.01023.896-0.197-0.1970.0000.0000.0000.000
165A166TYR00.0070.00126.8040.1460.1460.0000.0000.0000.000
166A167GLY00.0340.02927.404-0.143-0.1430.0000.0000.0000.000
167A168LYS10.7950.86724.43712.18812.1880.0000.0000.0000.000
168A169LEU00.0240.01717.8820.3780.3780.0000.0000.0000.000
169A170LYS10.9320.95622.58511.16411.1640.0000.0000.0000.000
170A171ILE00.0340.01917.722-0.091-0.0910.0000.0000.0000.000
171A172ASN0-0.116-0.06721.9270.8140.8140.0000.0000.0000.000
172A173LYS11.0000.99021.81912.81212.8120.0000.0000.0000.000
173A174GLU-1-0.834-0.93122.150-12.502-12.5020.0000.0000.0000.000
174A175LYS10.8820.95821.95212.13312.1330.0000.0000.0000.000
175A176VAL0-0.034-0.00316.117-0.571-0.5710.0000.0000.0000.000
176A177PHE00.0120.00915.5810.4350.4350.0000.0000.0000.000
177A178GLY00.0150.02314.513-0.158-0.1580.0000.0000.0000.000
178A179ASP-1-0.924-0.96515.370-16.407-16.4070.0000.0000.0000.000
179A180ILE0-0.033-0.01415.861-1.011-1.0110.0000.0000.0000.000
180A181LYS10.8880.94217.55318.38318.3830.0000.0000.0000.000
181A182GLU-1-0.829-0.88018.308-13.717-13.7170.0000.0000.0000.000
182A183ILE0-0.030-0.02016.5180.4720.4720.0000.0000.0000.000
183A184SER00.0090.01319.705-0.106-0.1060.0000.0000.0000.000
184A185ILE00.0380.00917.487-0.240-0.2400.0000.0000.0000.000
185A186TYR0-0.003-0.01020.8990.3880.3880.0000.0000.0000.000
186A187ASN00.0210.01524.458-0.329-0.3290.0000.0000.0000.000
187A188LYS10.9690.98326.90610.63310.6330.0000.0000.0000.000
188A189GLY0-0.026-0.00526.280-0.439-0.4390.0000.0000.0000.000
189A190LEU00.007-0.00122.5110.2570.2570.0000.0000.0000.000
190A191MET00.0220.02123.542-0.070-0.0700.0000.0000.0000.000
191A192ALA00.0890.04319.021-0.473-0.4730.0000.0000.0000.000
192A193TRP00.1220.05318.093-0.918-0.9180.0000.0000.0000.000
193A194THR0-0.049-0.01318.277-0.414-0.4140.0000.0000.0000.000
194A195VAL0-0.020-0.00516.647-0.476-0.4760.0000.0000.0000.000
195A196CYS00.002-0.00314.103-1.088-1.0880.0000.0000.0000.000
196A197GLY00.0460.03613.701-1.479-1.4790.0000.0000.0000.000
197A198ILE0-0.012-0.01214.801-0.663-0.6630.0000.0000.0000.000
198A199ILE0-0.0010.00910.343-0.430-0.4300.0000.0000.0000.000
199A200CYS00.0120.00810.021-1.909-1.9090.0000.0000.0000.000
200A201TYR00.0060.00410.727-1.256-1.2560.0000.0000.0000.000
201A202SER0-0.056-0.03212.312-0.223-0.2230.0000.0000.0000.000
202A203LEU0-0.029-0.0216.529-0.209-0.2090.0000.0000.0000.000
203A204SER0-0.038-0.0288.757-2.305-2.3050.0000.0000.0000.000
204A205PHE-1-0.873-0.89610.721-21.300-21.3000.0000.0000.0000.000