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: 3M8ML

Calculation Name: 3L9C-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3L9C

Chain ID: B

ChEMBL ID:

UniProt ID: Q8DUW4

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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2890836.687959
FMO2-HF: Nuclear repulsion 2800506.747915
FMO2-HF: Total energy -90329.940044
FMO2-MP2: Total energy -90591.81764


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.
-399.815-393.02239.606-19.326-27.076-0.157
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 : 0.780 / 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].
3A3ILE00.0290.0023.849-2.033-0.156-0.003-0.742-1.1320.002
187A187LEU00.0070.0202.688-7.365-5.9960.769-0.728-1.410-0.008
188A188ALA00.0050.0083.152-4.215-2.8570.204-0.614-0.948-0.007
189A189ALA00.0310.0172.535-0.222-0.3493.255-1.000-2.1280.001
190A190ASP-1-0.731-0.8761.755-124.624-125.48217.659-9.018-7.783-0.102
191A191LEU0-0.053-0.0103.8315.6345.7640.008-0.082-0.0550.000
195A195SER0-0.014-0.0403.791-11.817-10.9130.006-0.278-0.632-0.001
196A196TRP0-0.053-0.0322.288-24.802-22.6094.543-3.751-2.985-0.037
197A197THR00.022-0.0092.2524.5705.0644.528-1.257-3.766-0.001
198A198PHE0-0.007-0.0033.9371.9972.1780.003-0.058-0.1270.000
215A215MET0-0.018-0.0053.020-2.497-3.4403.330-0.479-1.909-0.004
216A216ARG10.8050.8914.11021.95422.1290.000-0.040-0.1360.000
218A218ILE00.001-0.0084.5191.0411.126-0.001-0.004-0.0800.000
219A219LYS10.8230.8792.59554.30453.9875.306-1.239-3.7490.000
220A220GLU-1-0.838-0.9004.998-21.719-21.641-0.001-0.010-0.0680.000
222A222LEU0-0.109-0.0583.8931.1241.3180.000-0.026-0.1680.000
4A4VAL00.0120.0185.4432.7082.7080.0000.0000.0000.000
5A5VAL00.004-0.0048.4860.4180.4180.0000.0000.0000.000
6A6PRO0-0.0370.00111.2610.9610.9610.0000.0000.0000.000
7A7VAL0-0.032-0.03014.2120.7010.7010.0000.0000.0000.000
8A8MET0-0.019-0.01516.018-0.015-0.0150.0000.0000.0000.000
9A9PRO0-0.0250.00820.6410.3850.3850.0000.0000.0000.000
10A10GLN00.012-0.01724.100-0.126-0.1260.0000.0000.0000.000
11A11ASN0-0.026-0.00827.1650.2840.2840.0000.0000.0000.000
12A12ILE00.0570.02528.239-0.410-0.4100.0000.0000.0000.000
13A13GLU-1-0.915-0.96429.515-9.499-9.4990.0000.0000.0000.000
14A14GLU-1-0.828-0.91425.511-11.172-11.1720.0000.0000.0000.000
15A15ALA00.0340.01824.762-0.455-0.4550.0000.0000.0000.000
16A16ASN0-0.014-0.01025.376-0.516-0.5160.0000.0000.0000.000
17A17GLN0-0.041-0.02325.778-0.240-0.2400.0000.0000.0000.000
18A18LEU0-0.0270.00719.924-0.309-0.3090.0000.0000.0000.000
19A19ASP-1-0.764-0.83821.153-13.557-13.5570.0000.0000.0000.000
20A20LEU00.020-0.00317.584-0.552-0.5520.0000.0000.0000.000
21A21THR0-0.063-0.05717.062-0.978-0.9780.0000.0000.0000.000
22A22ARG10.7600.87314.19214.32814.3280.0000.0000.0000.000
23A23ILE0-0.0080.01511.972-1.373-1.3730.0000.0000.0000.000
24A24ASP-1-0.859-0.92810.618-21.339-21.3390.0000.0000.0000.000
25A25SER0-0.041-0.03912.220-1.044-1.0440.0000.0000.0000.000
26A26THR0-0.039-0.0197.9710.5660.5660.0000.0000.0000.000
27A27ASP-1-0.830-0.9087.848-36.028-36.0280.0000.0000.0000.000
28A28ILE0-0.014-0.0057.8232.2042.2040.0000.0000.0000.000
29A29ILE00.0080.00610.845-0.322-0.3220.0000.0000.0000.000
30A30GLU-1-0.828-0.90113.096-19.752-19.7520.0000.0000.0000.000
31A31TRP00.0260.00914.6970.5770.5770.0000.0000.0000.000
32A32ARG10.7880.86116.81915.49315.4930.0000.0000.0000.000
33A33ALA00.0310.01719.5180.5940.5940.0000.0000.0000.000
34A34ASP-1-0.724-0.83521.293-13.447-13.4470.0000.0000.0000.000
35A35TYR0-0.005-0.01419.5220.3460.3460.0000.0000.0000.000
36A36LEU0-0.0280.01524.7770.3870.3870.0000.0000.0000.000
37A37VAL00.0310.01327.9170.0490.0490.0000.0000.0000.000
38A38LYS10.9190.93230.5998.6528.6520.0000.0000.0000.000
39A39ASP-1-0.877-0.92931.618-8.865-8.8650.0000.0000.0000.000
40A40ASP-1-0.894-0.95130.636-9.389-9.3890.0000.0000.0000.000
41A41ILE0-0.046-0.01026.315-0.223-0.2230.0000.0000.0000.000
42A42LEU00.0360.00128.248-0.292-0.2920.0000.0000.0000.000
43A43THR0-0.053-0.01730.4070.1040.1040.0000.0000.0000.000
44A44VAL0-0.023-0.02126.0990.0240.0240.0000.0000.0000.000
45A45ALA0-0.0110.00626.108-0.303-0.3030.0000.0000.0000.000
46A46PRO0-0.006-0.00226.308-0.382-0.3820.0000.0000.0000.000
47A47ALA00.0630.02727.346-0.294-0.2940.0000.0000.0000.000
48A48ILE0-0.037-0.01022.198-0.301-0.3010.0000.0000.0000.000
49A49PHE00.0630.01420.428-0.734-0.7340.0000.0000.0000.000
50A50GLU-1-0.992-0.98923.077-11.232-11.2320.0000.0000.0000.000
51A51LYS10.7260.84421.91112.04912.0490.0000.0000.0000.000
52A52PHE0-0.017-0.01318.787-0.692-0.6920.0000.0000.0000.000
53A53SER00.0060.01318.879-1.072-1.0720.0000.0000.0000.000
54A54GLY0-0.021-0.01518.944-0.064-0.0640.0000.0000.0000.000
55A55HIS10.7890.90713.32719.61519.6150.0000.0000.0000.000
56A56GLU-1-0.799-0.86610.453-29.089-29.0890.0000.0000.0000.000
57A57VAL0-0.037-0.02813.946-0.603-0.6030.0000.0000.0000.000
58A58ILE0-0.030-0.01210.633-0.240-0.2400.0000.0000.0000.000
59A59PHE0-0.0020.00315.2050.4380.4380.0000.0000.0000.000
60A60THR0-0.041-0.05616.053-0.111-0.1110.0000.0000.0000.000
61A61LEU00.0140.01019.0990.4460.4460.0000.0000.0000.000
62A62ARG10.7340.84516.64116.11916.1190.0000.0000.0000.000
63A63THR00.003-0.04921.6090.5810.5810.0000.0000.0000.000
64A64GLU-1-0.909-0.95124.322-10.387-10.3870.0000.0000.0000.000
65A65LYS10.8220.91726.30411.17711.1770.0000.0000.0000.000
66A66GLU-1-0.838-0.92221.286-14.000-14.0000.0000.0000.0000.000
67A67GLY0-0.020-0.02021.263-0.702-0.7020.0000.0000.0000.000
68A68GLY0-0.071-0.04721.479-0.496-0.4960.0000.0000.0000.000
69A69ASN0-0.063-0.03322.7520.5960.5960.0000.0000.0000.000
70A70ILE00.0230.02425.5300.3970.3970.0000.0000.0000.000
71A71SER00.0050.00527.681-0.270-0.2700.0000.0000.0000.000
72A72LEU0-0.018-0.01127.6310.2270.2270.0000.0000.0000.000
73A73SER0-0.012-0.00931.240-0.081-0.0810.0000.0000.0000.000
74A74ASN00.0480.00431.081-0.278-0.2780.0000.0000.0000.000
75A75GLU-1-0.939-0.96031.400-8.598-8.5980.0000.0000.0000.000
76A76ASP-1-0.843-0.91232.171-9.271-9.2710.0000.0000.0000.000
77A77TYR00.0050.01322.654-0.311-0.3110.0000.0000.0000.000
78A78LEU00.013-0.00527.557-0.395-0.3950.0000.0000.0000.000
79A79ALA0-0.049-0.01529.188-0.120-0.1200.0000.0000.0000.000
80A80ILE00.0160.00226.680-0.147-0.1470.0000.0000.0000.000
81A81ILE00.0010.00423.334-0.297-0.2970.0000.0000.0000.000
82A82ARG10.7870.87425.50510.04510.0450.0000.0000.0000.000
83A83ASP-1-0.904-0.95027.868-10.152-10.1520.0000.0000.0000.000
84A84ILE00.006-0.00423.355-0.102-0.1020.0000.0000.0000.000
85A85ALA0-0.010-0.00724.206-0.328-0.3280.0000.0000.0000.000
86A86ALA0-0.022-0.01125.148-0.073-0.0730.0000.0000.0000.000
87A87LEU0-0.077-0.04228.1990.1970.1970.0000.0000.0000.000
88A88TYR0-0.032-0.02223.9880.1880.1880.0000.0000.0000.000
89A89GLN0-0.104-0.03022.501-0.547-0.5470.0000.0000.0000.000
90A90PRO0-0.0040.01018.608-0.533-0.5330.0000.0000.0000.000
91A91ASP-1-0.810-0.90714.882-19.169-19.1690.0000.0000.0000.000
92A92TYR0-0.084-0.07010.947-0.894-0.8940.0000.0000.0000.000
93A93ILE00.0330.02215.8180.5000.5000.0000.0000.0000.000
94A94ASP-1-0.804-0.85516.306-17.943-17.9430.0000.0000.0000.000
95A95PHE00.0290.01118.0020.8030.8030.0000.0000.0000.000
96A96GLU-1-0.657-0.76420.269-13.534-13.5340.0000.0000.0000.000
97A97TYR0-0.026-0.02821.2500.7670.7670.0000.0000.0000.000
98A98PHE0-0.007-0.01921.5490.5650.5650.0000.0000.0000.000
99A99SER0-0.088-0.08025.0370.6460.6460.0000.0000.0000.000
100A100TYR0-0.010-0.01325.4160.3920.3920.0000.0000.0000.000
101A101ARG10.8740.93026.68211.17911.1790.0000.0000.0000.000
102A102ASP-1-0.974-0.98027.564-9.807-9.8070.0000.0000.0000.000
103A103VAL0-0.025-0.01228.6020.3290.3290.0000.0000.0000.000
104A104LEU00.0250.02323.148-0.262-0.2620.0000.0000.0000.000
105A105GLU-1-0.902-0.96026.917-10.885-10.8850.0000.0000.0000.000
106A106GLU-1-0.867-0.93329.497-9.527-9.5270.0000.0000.0000.000
107A107MET0-0.058-0.01724.4440.2100.2100.0000.0000.0000.000
108A108TYR0-0.067-0.02525.487-0.365-0.3650.0000.0000.0000.000
109A109ASP-1-0.880-0.93826.157-11.057-11.0570.0000.0000.0000.000
110A110PHE0-0.064-0.02822.070-0.248-0.2480.0000.0000.0000.000
111A111SER0-0.014-0.00919.827-0.385-0.3850.0000.0000.0000.000
112A112ASN0-0.033-0.04016.961-0.327-0.3270.0000.0000.0000.000
113A113LEU00.0190.01416.844-0.766-0.7660.0000.0000.0000.000
114A114ILE0-0.027-0.02512.128-1.012-1.0120.0000.0000.0000.000
115A115LEU00.0090.01815.6460.8860.8860.0000.0000.0000.000
116A116SER0-0.070-0.06816.341-0.813-0.8130.0000.0000.0000.000
117A117TYR00.0310.01017.0670.8680.8680.0000.0000.0000.000
118A118HIS0-0.058-0.02914.831-1.887-1.8870.0000.0000.0000.000
119A119ASN00.0600.04018.3760.8920.8920.0000.0000.0000.000
120A120PHE00.029-0.01916.918-0.774-0.7740.0000.0000.0000.000
121A121GLU-1-0.963-0.97220.099-11.055-11.0550.0000.0000.0000.000
122A122GLU-1-0.942-0.98221.539-10.967-10.9670.0000.0000.0000.000
123A123THR00.000-0.00918.366-1.010-1.0100.0000.0000.0000.000
124A124PRO00.0120.02720.3590.2910.2910.0000.0000.0000.000
125A125GLU-1-0.868-0.94922.855-11.335-11.3350.0000.0000.0000.000
126A126ASN0-0.086-0.05525.049-0.400-0.4000.0000.0000.0000.000
127A127LEU00.0270.02317.401-0.316-0.3160.0000.0000.0000.000
128A128MET00.013-0.00320.525-0.516-0.5160.0000.0000.0000.000
129A129GLU-1-0.885-0.92322.045-11.458-11.4580.0000.0000.0000.000
130A130VAL00.0060.01619.100-0.150-0.1500.0000.0000.0000.000
131A131PHE00.008-0.00813.598-0.545-0.5450.0000.0000.0000.000
132A132SER0-0.057-0.02218.637-0.390-0.3900.0000.0000.0000.000
133A133GLU-1-0.801-0.88121.551-11.922-11.9220.0000.0000.0000.000
134A134LEU00.0120.00317.8370.0510.0510.0000.0000.0000.000
135A135THR0-0.022-0.01617.554-0.990-0.9900.0000.0000.0000.000
136A136ALA0-0.063-0.03118.8300.0230.0230.0000.0000.0000.000
137A137LEU0-0.021-0.00621.3070.4740.4740.0000.0000.0000.000
138A138ALA0-0.053-0.00918.6750.0740.0740.0000.0000.0000.000
139A139PRO00.0340.03715.9800.0430.0430.0000.0000.0000.000
140A140ARG10.8990.9699.56025.27725.2770.0000.0000.0000.000
141A141VAL0-0.052-0.04110.200-2.369-2.3690.0000.0000.0000.000
142A142VAL00.0190.02812.6761.5461.5460.0000.0000.0000.000
143A143LYS10.8040.90611.93519.27119.2710.0000.0000.0000.000
144A144ILE00.0240.01512.7631.5791.5790.0000.0000.0000.000
145A145ALA0-0.016-0.00913.107-1.502-1.5020.0000.0000.0000.000
146A146VAL00.0180.00814.4441.1041.1040.0000.0000.0000.000
147A147MET00.0260.02715.275-1.136-1.1360.0000.0000.0000.000
148A148PRO0-0.086-0.02015.3170.4710.4710.0000.0000.0000.000
149A149LYS10.8650.90918.14611.59211.5920.0000.0000.0000.000
150A150ASN0-0.053-0.02520.5390.0670.0670.0000.0000.0000.000
151A151GLU-1-0.864-0.95617.623-13.297-13.2970.0000.0000.0000.000
152A152GLN0-0.088-0.04917.291-0.518-0.5180.0000.0000.0000.000
153A153ASP-1-0.736-0.86318.372-13.845-13.8450.0000.0000.0000.000
154A154VAL0-0.060-0.03112.343-0.979-0.9790.0000.0000.0000.000
155A155LEU0-0.020-0.01613.709-1.355-1.3550.0000.0000.0000.000
156A156ASP-1-0.832-0.90115.641-15.038-15.0380.0000.0000.0000.000
157A157LEU0-0.0080.01811.300-0.463-0.4630.0000.0000.0000.000
158A158MET0-0.056-0.0119.983-1.210-1.2100.0000.0000.0000.000
159A159ASN00.0240.00112.712-1.660-1.6600.0000.0000.0000.000
160A160TYR0-0.0010.00315.4780.1240.1240.0000.0000.0000.000
161A161THR0-0.0020.0069.520-0.165-0.1650.0000.0000.0000.000
162A162ARG10.8950.9578.67527.79627.7960.0000.0000.0000.000
163A163GLY00.0090.01612.7240.2590.2590.0000.0000.0000.000
164A164PHE0-0.012-0.00815.3740.4450.4450.0000.0000.0000.000
165A165LYS10.8830.9598.55931.69531.6950.0000.0000.0000.000
166A166THR0-0.101-0.07112.665-0.521-0.5210.0000.0000.0000.000
167A167LEU0-0.054-0.02814.9060.8500.8500.0000.0000.0000.000
168A168ASN0-0.038-0.02015.7471.6211.6210.0000.0000.0000.000
169A169PRO00.0130.01512.742-1.325-1.3250.0000.0000.0000.000
170A170ASN0-0.037-0.04611.916-2.671-2.6710.0000.0000.0000.000
171A171GLN0-0.0190.00413.5861.1321.1320.0000.0000.0000.000
172A172GLU-1-0.872-0.9077.433-40.041-40.0410.0000.0000.0000.000
173A173TYR00.037-0.0059.1122.6192.6190.0000.0000.0000.000
174A174VAL0-0.036-0.0156.500-4.833-4.8330.0000.0000.0000.000
175A175THR0-0.012-0.0298.2672.3462.3460.0000.0000.0000.000
176A176MET0-0.053-0.0248.425-2.393-2.3930.0000.0000.0000.000
177A177SER00.0640.04810.1071.8191.8190.0000.0000.0000.000
178A178MET0-0.0020.00611.176-1.130-1.1300.0000.0000.0000.000
179A179SER00.0540.01113.3810.7210.7210.0000.0000.0000.000
180A180LYS10.9860.98513.08312.32512.3250.0000.0000.0000.000
181A181LEU0-0.041-0.00513.744-0.526-0.5260.0000.0000.0000.000
182A182GLY00.0860.04812.402-0.257-0.2570.0000.0000.0000.000
183A183ARG10.7660.8719.23315.77915.7790.0000.0000.0000.000
184A184ILE00.0250.0097.532-1.957-1.9570.0000.0000.0000.000
185A185SER00.019-0.0077.147-2.193-2.1930.0000.0000.0000.000
186A186ARG10.8400.9184.84620.11020.1100.0000.0000.0000.000
192A192ILE0-0.027-0.0257.0493.0393.0390.0000.0000.0000.000
193A193GLY0-0.014-0.0036.7053.0463.0460.0000.0000.0000.000
194A194SER0-0.0150.0025.5494.1554.1550.0000.0000.0000.000
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