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: 3M3YL

Calculation Name: 1JFL-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JFL

Chain ID: A

ChEMBL ID:

UniProt ID: O58403

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2770424.715342
FMO2-HF: Nuclear repulsion 2681684.429273
FMO2-HF: Total energy -88740.286069
FMO2-MP2: Total energy -88996.390485


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.
-142.212-132.75410.101-7.329-12.235-0.067
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 : 0.811 / q_NPA : 0.911
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].
3A3THR0-0.027-0.0193.046-0.8131.8930.126-1.353-1.480-0.007
33A33GLU-1-0.828-0.9082.815-29.829-29.2670.131-0.202-0.491-0.001
34A34HIS00.0060.0132.989-6.512-5.3490.467-0.632-0.999-0.007
35A35PRO0-0.0010.0032.861-4.392-2.6402.851-2.026-2.578-0.007
36A36LYS10.9540.9753.37438.53838.3950.1051.085-1.0480.000
225A225ALA0-0.018-0.0053.978-4.913-4.6330.000-0.099-0.1820.000
226A226LEU0-0.011-0.0152.229-28.732-25.9396.423-4.052-5.165-0.045
227A227GLU-1-0.919-0.9393.903-31.363-31.190-0.001-0.006-0.1650.000
228A228LYS0-0.092-0.0454.358-37.273-37.101-0.001-0.044-0.1270.000
4A4ILE00.0020.0065.5792.5292.5290.0000.0000.0000.000
5A5GLY00.0570.0208.2571.6481.6480.0000.0000.0000.000
6A6ILE0-0.028-0.02311.6790.6440.6440.0000.0000.0000.000
7A7LEU00.0100.00714.5280.6160.6160.0000.0000.0000.000
8A8GLY00.0470.00017.8740.3680.3680.0000.0000.0000.000
9A9GLY0-0.002-0.00519.9000.3740.3740.0000.0000.0000.000
10A10MET0-0.100-0.02422.4190.8080.8080.0000.0000.0000.000
11A11GLY00.0760.03124.9310.0400.0400.0000.0000.0000.000
12A12PRO00.0310.00223.024-0.510-0.5100.0000.0000.0000.000
13A13LEU00.0160.01622.381-0.497-0.4970.0000.0000.0000.000
14A14ALA00.0480.02122.327-0.353-0.3530.0000.0000.0000.000
15A15THR00.005-0.00618.145-0.669-0.6690.0000.0000.0000.000
16A16ALA00.0050.00517.832-0.830-0.8300.0000.0000.0000.000
17A17GLU-1-0.757-0.82317.779-13.990-13.9900.0000.0000.0000.000
18A18LEU00.0360.00414.964-0.395-0.3950.0000.0000.0000.000
19A19PHE00.010-0.00110.701-0.833-0.8330.0000.0000.0000.000
20A20ARG10.8450.88713.08812.99812.9980.0000.0000.0000.000
21A21ARG10.7790.84014.40813.63513.6350.0000.0000.0000.000
22A22ILE00.0180.0109.139-0.489-0.4890.0000.0000.0000.000
23A23VAL0-0.0120.0149.707-1.338-1.3380.0000.0000.0000.000
24A24ILE0-0.049-0.03510.781-0.159-0.1590.0000.0000.0000.000
25A25LYS10.7680.88612.21216.97916.9790.0000.0000.0000.000
26A26THR0-0.019-0.0125.754-2.320-2.3200.0000.0000.0000.000
27A27PRO0-0.063-0.0197.4181.4051.4050.0000.0000.0000.000
28A28ALA00.0100.0076.571-2.494-2.4940.0000.0000.0000.000
29A29LYS10.8880.9358.28420.99120.9910.0000.0000.0000.000
30A30ARG10.8820.9417.31426.63426.6340.0000.0000.0000.000
31A31ASP-1-0.829-0.9227.175-21.319-21.3190.0000.0000.0000.000
32A32GLN0-0.068-0.0485.607-1.842-1.8420.0000.0000.0000.000
37A37VAL00.0110.0065.427-1.576-1.5760.0000.0000.0000.000
38A38ILE0-0.0060.0068.7181.4401.4400.0000.0000.0000.000
39A39ILE00.0230.00411.5830.1890.1890.0000.0000.0000.000
40A40PHE00.0350.02014.9760.9090.9090.0000.0000.0000.000
41A41ASN0-0.008-0.01717.8730.2420.2420.0000.0000.0000.000
42A42ASN00.020-0.01020.5790.7480.7480.0000.0000.0000.000
43A43PRO0-0.035-0.02923.7360.0870.0870.0000.0000.0000.000
44A44GLN0-0.0060.00526.8290.0890.0890.0000.0000.0000.000
45A45ILE0-0.044-0.00123.5690.2100.2100.0000.0000.0000.000
46A46PRO00.0610.03228.1970.0410.0410.0000.0000.0000.000
47A47ASP-1-0.836-0.91830.367-9.679-9.6790.0000.0000.0000.000
48A48ARG10.9020.94227.34510.75010.7500.0000.0000.0000.000
49A49THR00.0190.00831.1320.1120.1120.0000.0000.0000.000
50A50ALA0-0.038-0.03533.9680.2500.2500.0000.0000.0000.000
51A51TYR0-0.0280.00532.8080.2320.2320.0000.0000.0000.000
52A52ILE0-0.021-0.00832.0100.1400.1400.0000.0000.0000.000
53A53LEU0-0.057-0.03135.5400.1740.1740.0000.0000.0000.000
54A54GLY00.0160.01738.5210.2280.2280.0000.0000.0000.000
55A55LYS10.8890.95438.7958.0008.0000.0000.0000.0000.000
56A56GLY00.012-0.00537.1200.0010.0010.0000.0000.0000.000
57A57GLU-1-0.920-0.95234.540-8.607-8.6070.0000.0000.0000.000
58A58ASP-1-0.763-0.87032.013-9.937-9.9370.0000.0000.0000.000
59A59PRO0-0.010-0.00228.670-0.110-0.1100.0000.0000.0000.000
60A60ARG10.8070.86127.7309.5259.5250.0000.0000.0000.000
61A61PRO00.0220.01527.214-0.467-0.4670.0000.0000.0000.000
62A62GLN00.0560.02626.963-0.328-0.3280.0000.0000.0000.000
63A63LEU0-0.0060.01823.789-0.501-0.5010.0000.0000.0000.000
64A64ILE00.0240.00822.561-0.705-0.7050.0000.0000.0000.000
65A65TRP0-0.0080.00222.777-0.641-0.6410.0000.0000.0000.000
66A66THR00.002-0.02419.787-0.314-0.3140.0000.0000.0000.000
67A67ALA0-0.007-0.00818.426-0.708-0.7080.0000.0000.0000.000
68A68LYS10.9690.99817.85011.90311.9030.0000.0000.0000.000
69A69ARG10.8920.95718.71712.90012.9000.0000.0000.0000.000
70A70LEU0-0.062-0.01613.296-0.366-0.3660.0000.0000.0000.000
71A71GLU-1-0.805-0.90914.055-18.974-18.9740.0000.0000.0000.000
72A72GLU-1-0.923-0.97114.594-15.102-15.1020.0000.0000.0000.000
73A73CYS0-0.101-0.04313.5660.1580.1580.0000.0000.0000.000
74A74GLY00.0230.02411.315-0.539-0.5390.0000.0000.0000.000
75A75ALA0-0.042-0.0199.394-2.589-2.5890.0000.0000.0000.000
76A76ASP-1-0.800-0.9036.439-41.705-41.7050.0000.0000.0000.000
77A77PHE0-0.048-0.0336.9141.5871.5870.0000.0000.0000.000
78A78ILE0-0.019-0.00111.152-0.013-0.0130.0000.0000.0000.000
79A79ILE00.0040.01212.4350.4710.4710.0000.0000.0000.000
80A80MET00.0230.00415.4710.5610.5610.0000.0000.0000.000
81A81PRO0-0.0040.01318.2560.1440.1440.0000.0000.0000.000
82A82CYS0-0.041-0.01820.3500.8980.8980.0000.0000.0000.000
83A83ASN00.0310.01723.734-0.611-0.6110.0000.0000.0000.000
84A84THR00.0470.01425.859-0.115-0.1150.0000.0000.0000.000
85A85ALA00.014-0.00323.8950.2370.2370.0000.0000.0000.000
86A86HIS0-0.028-0.01720.909-0.798-0.7980.0000.0000.0000.000
87A87ALA00.0120.01524.996-0.001-0.0010.0000.0000.0000.000
88A88PHE00.017-0.00226.7050.2350.2350.0000.0000.0000.000
89A89VAL0-0.0040.00521.497-0.242-0.2420.0000.0000.0000.000
90A90GLU-1-0.827-0.91923.252-13.818-13.8180.0000.0000.0000.000
91A91ASP-1-0.899-0.93625.410-10.745-10.7450.0000.0000.0000.000
92A92ILE0-0.026-0.02020.746-0.058-0.0580.0000.0000.0000.000
93A93ARG10.7800.87618.70715.03415.0340.0000.0000.0000.000
94A94LYS10.9310.97621.65011.02711.0270.0000.0000.0000.000
95A95ALA0-0.032-0.00423.6470.2770.2770.0000.0000.0000.000
96A96ILE0-0.050-0.02817.3010.3140.3140.0000.0000.0000.000
97A97LYS10.9090.95017.40415.81815.8180.0000.0000.0000.000
98A98ILE0-0.0180.01412.891-0.538-0.5380.0000.0000.0000.000
99A99PRO0-0.012-0.01212.3661.2681.2680.0000.0000.0000.000
100A100ILE00.0180.02014.509-0.612-0.6120.0000.0000.0000.000
101A101ILE00.0080.00711.4640.6900.6900.0000.0000.0000.000
102A102SER00.0260.00815.9680.5140.5140.0000.0000.0000.000
103A103MET00.0200.01118.961-0.174-0.1740.0000.0000.0000.000
104A104ILE0-0.0200.00619.8280.1760.1760.0000.0000.0000.000
105A105GLU-1-0.848-0.93620.788-13.803-13.8030.0000.0000.0000.000
106A106GLU-1-0.829-0.90516.261-18.099-18.0990.0000.0000.0000.000
107A107THR0-0.010-0.02119.5720.1670.1670.0000.0000.0000.000
108A108ALA0-0.0180.00222.4810.3650.3650.0000.0000.0000.000
109A109LYS10.8280.89917.64217.47417.4740.0000.0000.0000.000
110A110LYS10.9260.97719.59315.76215.7620.0000.0000.0000.000
111A111VAL00.027-0.00122.4740.2970.2970.0000.0000.0000.000
112A112LYS10.9520.98725.74611.76411.7640.0000.0000.0000.000
113A113GLU-1-0.993-1.00720.060-15.392-15.3920.0000.0000.0000.000
114A114LEU0-0.068-0.03124.1020.0650.0650.0000.0000.0000.000
115A115GLY0-0.0060.00526.9300.3620.3620.0000.0000.0000.000
116A116PHE00.0040.00427.6190.2970.2970.0000.0000.0000.000
117A117LYS10.8250.90131.7039.4009.4000.0000.0000.0000.000
118A118LYS10.8320.91034.3878.1498.1490.0000.0000.0000.000
119A119ALA00.0110.00031.000-0.100-0.1000.0000.0000.0000.000
120A120GLY00.0390.02033.0940.1270.1270.0000.0000.0000.000
121A121LEU0-0.071-0.02829.694-0.299-0.2990.0000.0000.0000.000
122A122LEU00.0280.01131.5380.3150.3150.0000.0000.0000.000
123A123ALA00.013-0.00930.235-0.377-0.3770.0000.0000.0000.000
124A124THR00.0520.01530.9380.3000.3000.0000.0000.0000.000
125A125THR00.0630.01233.189-0.150-0.1500.0000.0000.0000.000
126A126GLY00.0130.01534.0230.0560.0560.0000.0000.0000.000
127A127THR0-0.043-0.02929.422-0.304-0.3040.0000.0000.0000.000
128A128ILE00.0630.04731.663-0.119-0.1190.0000.0000.0000.000
129A129VAL0-0.004-0.00234.5010.0400.0400.0000.0000.0000.000
130A130SER0-0.083-0.05431.157-0.114-0.1140.0000.0000.0000.000
131A131GLY00.0500.03832.511-0.159-0.1590.0000.0000.0000.000
132A132VAL0-0.041-0.02127.549-0.149-0.1490.0000.0000.0000.000
133A133TYR00.005-0.02325.436-0.425-0.4250.0000.0000.0000.000
134A134GLU-1-0.797-0.90829.439-9.692-9.6920.0000.0000.0000.000
135A135LYS10.8880.95427.91311.23211.2320.0000.0000.0000.000
136A136GLU-1-0.799-0.88625.343-12.259-12.2590.0000.0000.0000.000
137A137PHE00.051-0.00426.365-0.275-0.2750.0000.0000.0000.000
138A138SER00.006-0.00229.2890.1930.1930.0000.0000.0000.000
139A139LYS10.7550.87325.20512.46612.4660.0000.0000.0000.000
140A140TYR0-0.055-0.02922.881-0.235-0.2350.0000.0000.0000.000
141A141GLY0-0.0060.01028.4930.0430.0430.0000.0000.0000.000
142A142VAL0-0.056-0.03529.4260.1850.1850.0000.0000.0000.000
143A143GLU-1-0.841-0.90332.340-8.176-8.1760.0000.0000.0000.000
144A144ILE0-0.032-0.01430.492-0.102-0.1020.0000.0000.0000.000
145A145MET00.0040.01534.5290.2920.2920.0000.0000.0000.000
146A146THR00.001-0.00435.633-0.233-0.2330.0000.0000.0000.000
147A147PRO0-0.014-0.00536.7790.1890.1890.0000.0000.0000.000
148A148THR00.000-0.01740.0510.0290.0290.0000.0000.0000.000
149A149GLU-1-0.901-0.96842.519-6.960-6.9600.0000.0000.0000.000
150A150ASP-1-0.855-0.92343.562-6.652-6.6520.0000.0000.0000.000
151A151GLU-1-0.713-0.79941.761-7.290-7.2900.0000.0000.0000.000
152A152GLN00.013-0.00635.676-0.183-0.1830.0000.0000.0000.000
153A153LYS10.8430.91239.4686.5886.5880.0000.0000.0000.000
154A154ASP-1-0.782-0.88141.299-7.105-7.1050.0000.0000.0000.000
155A155VAL00.0160.00535.084-0.136-0.1360.0000.0000.0000.000
156A156MET0-0.044-0.00835.951-0.329-0.3290.0000.0000.0000.000
157A157ARG10.8810.94437.3586.9806.9800.0000.0000.0000.000
158A158GLY00.0490.02037.266-0.021-0.0210.0000.0000.0000.000
159A159ILE0-0.024-0.02231.832-0.176-0.1760.0000.0000.0000.000
160A160TYR0-0.054-0.04332.434-0.279-0.2790.0000.0000.0000.000
161A161GLU-1-0.877-0.94936.165-7.238-7.2380.0000.0000.0000.000
162A162GLY0-0.016-0.00437.1420.1410.1410.0000.0000.0000.000
163A163VAL0-0.046-0.02930.458-0.013-0.0130.0000.0000.0000.000
164A164LYS10.8550.93829.7929.7909.7900.0000.0000.0000.000
165A165ALA00.0080.02633.279-0.011-0.0110.0000.0000.0000.000
166A166GLY00.0030.00734.1230.1600.1600.0000.0000.0000.000
167A167ASN0-0.0030.00635.1600.0370.0370.0000.0000.0000.000
168A168LEU00.044-0.00231.935-0.001-0.0010.0000.0000.0000.000
169A169LYS10.9340.97435.5677.1727.1720.0000.0000.0000.000
170A170LEU00.0180.01638.9340.0320.0320.0000.0000.0000.000
171A171GLY00.0480.01435.672-0.013-0.0130.0000.0000.0000.000
172A172ARG10.7510.82934.2198.3988.3980.0000.0000.0000.000
173A173GLU-1-0.852-0.91736.632-7.140-7.1400.0000.0000.0000.000
174A174LEU00.0120.01439.0440.0060.0060.0000.0000.0000.000
175A175LEU0-0.0120.00433.060-0.033-0.0330.0000.0000.0000.000
176A176LEU0-0.0200.00135.736-0.093-0.0930.0000.0000.0000.000
177A177LYS10.8110.91137.3667.0867.0860.0000.0000.0000.000
178A178THR0-0.006-0.02238.0690.0940.0940.0000.0000.0000.000
179A179ALA00.001-0.00235.166-0.043-0.0430.0000.0000.0000.000
180A180LYS10.9450.98236.8897.7207.7200.0000.0000.0000.000
181A181ILE00.0200.02339.6710.0460.0460.0000.0000.0000.000
182A182LEU0-0.018-0.01435.9110.0400.0400.0000.0000.0000.000
183A183GLU-1-0.802-0.91336.553-8.384-8.3840.0000.0000.0000.000
184A184GLU-1-1.001-1.00039.089-7.033-7.0330.0000.0000.0000.000
185A185ARG10.7810.85541.2957.4167.4160.0000.0000.0000.000
186A186GLY00.0010.01240.4740.0140.0140.0000.0000.0000.000
187A187ALA0-0.056-0.02935.290-0.156-0.1560.0000.0000.0000.000
188A188GLU-1-0.798-0.90634.178-9.067-9.0670.0000.0000.0000.000
189A189CYS0-0.039-0.00529.814-0.297-0.2970.0000.0000.0000.000
190A190ILE00.0220.01331.0470.2010.2010.0000.0000.0000.000
191A191ILE00.0100.00026.700-0.437-0.4370.0000.0000.0000.000
192A192ALA00.0480.01326.4970.3500.3500.0000.0000.0000.000
193A193GLY00.0240.01326.315-0.429-0.4290.0000.0000.0000.000
194A194CYS0-0.084-0.03726.9470.1340.1340.0000.0000.0000.000
195A195THR00.0590.03422.932-0.008-0.0080.0000.0000.0000.000
196A196GLU-1-0.894-0.96925.732-10.498-10.4980.0000.0000.0000.000
197A197VAL00.0230.01229.0190.2560.2560.0000.0000.0000.000
198A198SER00.041-0.01424.6840.3340.3340.0000.0000.0000.000
199A199VAL0-0.061-0.00626.625-0.055-0.0550.0000.0000.0000.000
200A200VAL0-0.043-0.02228.1720.1470.1470.0000.0000.0000.000
201A201LEU0-0.0190.00730.4170.3170.3170.0000.0000.0000.000
202A202LYS10.8370.90527.0109.9549.9540.0000.0000.0000.000
203A203GLN00.0410.00327.105-0.109-0.1090.0000.0000.0000.000
204A204ASP-1-0.883-0.93429.790-9.399-9.3990.0000.0000.0000.000
205A205ASP-1-0.827-0.86832.856-8.486-8.4860.0000.0000.0000.000
206A206LEU0-0.090-0.04331.7240.2580.2580.0000.0000.0000.000
207A207LYS10.9170.95534.8537.5357.5350.0000.0000.0000.000
208A208VAL0-0.0300.00833.056-0.063-0.0630.0000.0000.0000.000
209A209PRO0-0.017-0.00928.358-0.123-0.1230.0000.0000.0000.000
210A210LEU0-0.019-0.00227.1920.1410.1410.0000.0000.0000.000
211A211ILE00.000-0.00423.718-0.508-0.5080.0000.0000.0000.000
212A212ASP-1-0.739-0.83622.286-12.772-12.7720.0000.0000.0000.000
213A213PRO00.0290.00121.480-0.687-0.6870.0000.0000.0000.000
214A214MET0-0.034-0.00318.482-0.765-0.7650.0000.0000.0000.000
215A215ASP-1-0.804-0.89417.388-15.981-15.9810.0000.0000.0000.000
216A216VAL00.0120.01816.496-1.072-1.0720.0000.0000.0000.000
217A217ILE0-0.016-0.01415.083-1.061-1.0610.0000.0000.0000.000
218A218ALA00.0080.00913.097-1.576-1.5760.0000.0000.0000.000
219A219GLU-1-0.864-0.92311.704-19.118-19.1180.0000.0000.0000.000
220A220VAL0-0.045-0.02111.696-1.995-1.9950.0000.0000.0000.000
221A221ALA0-0.010-0.00510.098-2.374-2.3740.0000.0000.0000.000
222A222VAL00.0340.0107.153-4.047-4.0470.0000.0000.0000.000
223A223LYS10.9460.9806.64218.76118.7610.0000.0000.0000.000
224A224VAL0-0.013-0.0116.662-4.559-4.5590.0000.0000.0000.000