FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 3M1YL

Calculation Name: 4XBS-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 4XBS

Chain ID: A

ChEMBL ID:

UniProt ID: U2PI02

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2453517.925084
FMO2-HF: Nuclear repulsion 2372292.362081
FMO2-HF: Total energy -81225.563003
FMO2-MP2: Total energy -81460.61434


3D Structure
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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-150.337-143.62412.77-7.041-12.444-0.059
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.921
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].
3A5THR00.032-0.0063.080-4.147-1.9690.118-1.100-1.196-0.005
5A7GLN00.0230.0082.119-19.180-18.9208.950-4.209-5.001-0.040
6A8LEU00.0010.0102.333-1.0100.4991.557-0.668-2.398-0.004
7A9ALA00.0570.0293.7743.7243.9000.0140.004-0.1940.000
9A11TYR00.0040.0112.7830.5991.7720.180-0.431-0.921-0.004
193A195ARG10.9830.9803.61851.00351.4100.000-0.114-0.2940.000
197A199LEU0-0.027-0.0152.524-3.955-3.6051.575-0.352-1.574-0.004
198A200ALA00.0500.0295.3930.6740.718-0.0010.000-0.0430.000
200A202ILE0-0.009-0.0042.7340.1900.8060.377-0.171-0.823-0.002
4A6GLU-1-0.769-0.8585.784-37.029-37.0290.0000.0000.0000.000
8A10LYS10.8200.9086.96823.16123.1610.0000.0000.0000.000
10A12ILE0-0.046-0.0236.5382.3462.3460.0000.0000.0000.000
11A13ASP-1-0.697-0.8039.186-16.950-16.9500.0000.0000.0000.000
12A14HIS0-0.016-0.00712.910-0.368-0.3680.0000.0000.0000.000
13A15THR0-0.041-0.03614.4391.0231.0230.0000.0000.0000.000
14A16ASN0-0.043-0.03217.2730.2370.2370.0000.0000.0000.000
15A17LEU00.0150.01020.2780.2810.2810.0000.0000.0000.000
16A18LYS10.9360.98123.18511.99511.9950.0000.0000.0000.000
17A19ALA00.009-0.00126.0010.0610.0610.0000.0000.0000.000
18A20ASP-1-0.916-0.95928.973-9.700-9.7000.0000.0000.0000.000
19A21ALA0-0.044-0.00626.0560.0030.0030.0000.0000.0000.000
20A22THR0-0.022-0.04927.9800.2400.2400.0000.0000.0000.000
21A23GLU-1-0.898-0.96128.049-9.486-9.4860.0000.0000.0000.000
22A24ALA00.0010.00227.875-0.309-0.3090.0000.0000.0000.000
23A25ASP-1-0.792-0.85925.107-11.030-11.0300.0000.0000.0000.000
24A26ILE00.0180.02023.557-0.729-0.7290.0000.0000.0000.000
25A27LYS10.8680.94223.18310.93810.9380.0000.0000.0000.000
26A28GLN0-0.026-0.01520.9770.0750.0750.0000.0000.0000.000
27A29THR0-0.023-0.03118.644-0.670-0.6700.0000.0000.0000.000
28A30CYS0-0.010-0.00718.529-0.776-0.7760.0000.0000.0000.000
29A31ASP-1-0.862-0.93519.580-12.775-12.7750.0000.0000.0000.000
30A32GLU-1-0.853-0.92616.473-15.893-15.8930.0000.0000.0000.000
31A33ALA00.0180.00314.814-1.122-1.1220.0000.0000.0000.000
32A34LYS10.8300.93314.86012.07712.0770.0000.0000.0000.000
33A35LYS10.8930.95915.30316.71616.7160.0000.0000.0000.000
34A36PHE0-0.027-0.02510.780-0.504-0.5040.0000.0000.0000.000
35A37ASN00.0040.00810.729-1.210-1.2100.0000.0000.0000.000
36A38THR00.0090.00010.569-1.148-1.1480.0000.0000.0000.000
37A39ALA0-0.0180.01110.0610.8570.8570.0000.0000.0000.000
38A40SER00.001-0.01811.8621.2641.2640.0000.0000.0000.000
39A41VAL0-0.0050.00114.714-0.741-0.7410.0000.0000.0000.000
40A42CYS0-0.043-0.01716.9570.5280.5280.0000.0000.0000.000
41A43VAL00.010-0.00118.7760.0180.0180.0000.0000.0000.000
42A44ASN00.015-0.01522.447-0.021-0.0210.0000.0000.0000.000
43A45SER0-0.005-0.03825.7770.0470.0470.0000.0000.0000.000
44A46TYR0-0.0080.00427.7960.0900.0900.0000.0000.0000.000
45A47TRP00.0390.01326.2250.1460.1460.0000.0000.0000.000
46A48ILE0-0.0070.01123.681-0.220-0.2200.0000.0000.0000.000
47A49PRO00.0200.01626.541-0.239-0.2390.0000.0000.0000.000
48A50PHE00.0230.01827.150-0.123-0.1230.0000.0000.0000.000
49A51VAL00.0350.00021.579-0.216-0.2160.0000.0000.0000.000
50A52THR0-0.020-0.01923.785-0.461-0.4610.0000.0000.0000.000
51A53GLU-1-0.936-0.95325.506-9.859-9.8590.0000.0000.0000.000
52A54GLN0-0.036-0.03724.348-0.496-0.4960.0000.0000.0000.000
53A55LEU00.0160.01419.109-0.393-0.3930.0000.0000.0000.000
54A56LYS10.9010.97222.26910.52710.5270.0000.0000.0000.000
55A57GLY0-0.027-0.01423.9560.1170.1170.0000.0000.0000.000
56A58THR0-0.073-0.04918.739-0.528-0.5280.0000.0000.0000.000
57A59ASP-1-0.901-0.94915.234-16.160-16.1600.0000.0000.0000.000
58A60VAL0-0.069-0.02115.055-0.796-0.7960.0000.0000.0000.000
59A61ASN00.0480.01916.2731.1181.1180.0000.0000.0000.000
60A62PRO00.0340.01918.068-0.409-0.4090.0000.0000.0000.000
61A63ILE0-0.071-0.02016.3660.1320.1320.0000.0000.0000.000
62A64ALA00.0490.02120.4180.0700.0700.0000.0000.0000.000
63A65VAL0-0.051-0.01221.369-0.247-0.2470.0000.0000.0000.000
64A66VAL00.0080.00123.5270.3430.3430.0000.0000.0000.000
65A67GLY00.018-0.01026.794-0.123-0.1230.0000.0000.0000.000
66A68PHE0-0.0300.00822.379-0.089-0.0890.0000.0000.0000.000
67A69PRO0-0.008-0.01525.9680.2490.2490.0000.0000.0000.000
68A70LEU00.034-0.01327.120-0.100-0.1000.0000.0000.0000.000
69A71GLY00.0510.04029.3320.1130.1130.0000.0000.0000.000
70A72ALA0-0.059-0.04029.9010.1150.1150.0000.0000.0000.000
71A73MET0-0.0440.01131.9100.2260.2260.0000.0000.0000.000
72A74ALA00.0440.01934.200-0.065-0.0650.0000.0000.0000.000
73A75THR00.028-0.01433.072-0.019-0.0190.0000.0000.0000.000
74A76GLU-1-0.917-0.95334.200-7.322-7.3220.0000.0000.0000.000
75A77SER0-0.026-0.01535.400-0.028-0.0280.0000.0000.0000.000
76A78LYS10.8250.89029.5689.1009.1000.0000.0000.0000.000
77A79ILE00.0150.02130.754-0.247-0.2470.0000.0000.0000.000
78A80PHE0-0.0020.02232.432-0.109-0.1090.0000.0000.0000.000
79A81GLU-1-0.802-0.87129.333-9.590-9.5900.0000.0000.0000.000
80A82ALA00.0140.00227.876-0.198-0.1980.0000.0000.0000.000
81A83THR0-0.043-0.04928.640-0.116-0.1160.0000.0000.0000.000
82A84THR0-0.004-0.01031.1740.0220.0220.0000.0000.0000.000
83A85ALA0-0.003-0.00726.553-0.085-0.0850.0000.0000.0000.000
84A86ILE0-0.013-0.00525.694-0.181-0.1810.0000.0000.0000.000
85A87ASP-1-0.836-0.89427.698-8.951-8.9510.0000.0000.0000.000
86A88GLN0-0.070-0.03829.6750.0140.0140.0000.0000.0000.000
87A89GLY0-0.011-0.01326.631-0.077-0.0770.0000.0000.0000.000
88A90ALA0-0.053-0.01723.329-0.452-0.4520.0000.0000.0000.000
89A91GLU-1-0.805-0.90320.100-11.672-11.6720.0000.0000.0000.000
90A92GLU-1-0.781-0.85716.254-16.199-16.1990.0000.0000.0000.000
91A93ILE00.0010.00420.7130.2270.2270.0000.0000.0000.000
92A94ASP-1-0.713-0.83617.848-14.876-14.8760.0000.0000.0000.000
93A95MET00.0210.02721.1000.2760.2760.0000.0000.0000.000
94A96VAL0-0.054-0.00923.473-0.403-0.4030.0000.0000.0000.000
95A97LEU00.0290.03125.6190.3820.3820.0000.0000.0000.000
96A98ASN00.0330.01927.4000.1100.1100.0000.0000.0000.000
97A99VAL00.0320.00227.7990.1300.1300.0000.0000.0000.000
98A100GLY00.0000.00530.5390.1060.1060.0000.0000.0000.000
99A101GLU-1-0.790-0.89234.347-7.429-7.4290.0000.0000.0000.000
100A102LEU0-0.028-0.00729.3130.0910.0910.0000.0000.0000.000
101A103LYS10.8100.88330.9009.2049.2040.0000.0000.0000.000
102A104GLY0-0.032-0.00234.0920.1650.1650.0000.0000.0000.000
103A105GLY00.0010.00835.7320.1930.1930.0000.0000.0000.000
104A106ASN0-0.060-0.03536.6740.1790.1790.0000.0000.0000.000
105A107ASP-1-0.773-0.89433.950-8.669-8.6690.0000.0000.0000.000
106A108GLU-1-0.942-0.97634.132-7.528-7.5280.0000.0000.0000.000
107A109LYS10.8420.91836.2277.2787.2780.0000.0000.0000.000
108A110VAL0-0.0180.00230.287-0.105-0.1050.0000.0000.0000.000
109A111LEU0-0.018-0.00631.224-0.217-0.2170.0000.0000.0000.000
110A112ALA00.0240.00732.051-0.147-0.1470.0000.0000.0000.000
111A113ASP-1-0.825-0.88830.812-9.093-9.0930.0000.0000.0000.000
112A114ILE0-0.004-0.01126.488-0.142-0.1420.0000.0000.0000.000
113A115GLN00.0030.00528.956-0.002-0.0020.0000.0000.0000.000
114A116GLY00.0390.02231.0640.0010.0010.0000.0000.0000.000
115A117LEU0-0.032-0.03027.4810.0270.0270.0000.0000.0000.000
116A118ALA0-0.002-0.00127.039-0.146-0.1460.0000.0000.0000.000
117A119ASP-1-0.893-0.94528.046-8.928-8.9280.0000.0000.0000.000
118A120ALA0-0.039-0.02130.9730.0040.0040.0000.0000.0000.000
119A121VAL0-0.032-0.01624.449-0.001-0.0010.0000.0000.0000.000
120A122HIS10.8030.88823.70510.87310.8730.0000.0000.0000.000
121A123ALA0-0.0130.00127.9030.0120.0120.0000.0000.0000.000
122A124LYS10.7470.86528.7019.0689.0680.0000.0000.0000.000
123A125GLY0-0.023-0.00526.757-0.176-0.1760.0000.0000.0000.000
124A126LYS10.7820.89823.29810.93610.9360.0000.0000.0000.000
125A127ILE0-0.013-0.00117.1010.1620.1620.0000.0000.0000.000
126A128LEU0-0.016-0.02121.7190.0800.0800.0000.0000.0000.000
127A129LYS10.7540.86214.92615.22215.2220.0000.0000.0000.000
128A130VAL00.0290.00619.9670.3730.3730.0000.0000.0000.000
129A131ILE0-0.043-0.03020.227-0.503-0.5030.0000.0000.0000.000
130A132LEU00.032-0.00621.0970.5800.5800.0000.0000.0000.000
131A133GLU-1-0.759-0.84722.375-11.246-11.2460.0000.0000.0000.000
132A134ASN00.044-0.02019.4310.6610.6610.0000.0000.0000.000
133A135ALA0-0.083-0.01923.1280.1920.1920.0000.0000.0000.000
134A136LEU0-0.030-0.01324.9830.3570.3570.0000.0000.0000.000
135A137LEU0-0.063-0.01324.8260.3930.3930.0000.0000.0000.000
136A138THR0-0.030-0.04126.828-0.234-0.2340.0000.0000.0000.000
137A139LYS10.8650.89022.63711.79811.7980.0000.0000.0000.000
138A140ASP-1-0.837-0.91326.016-9.815-9.8150.0000.0000.0000.000
139A141GLU-1-0.764-0.85428.449-9.290-9.2900.0000.0000.0000.000
140A142ILE0-0.0160.00521.632-0.078-0.0780.0000.0000.0000.000
141A143VAL00.0520.03324.106-0.191-0.1910.0000.0000.0000.000
142A144ARG10.8170.88725.2758.9688.9680.0000.0000.0000.000
143A145ALA00.0520.01425.3790.1080.1080.0000.0000.0000.000
144A146CYS0-0.058-0.00221.707-0.301-0.3010.0000.0000.0000.000
145A147GLN00.0460.02123.8220.3260.3260.0000.0000.0000.000
146A148LEU0-0.063-0.02826.8190.1790.1790.0000.0000.0000.000
147A149SER00.022-0.01123.6140.1330.1330.0000.0000.0000.000
148A150GLU-1-0.824-0.87523.940-11.608-11.6080.0000.0000.0000.000
149A151LYS10.8750.94325.3298.8298.8290.0000.0000.0000.000
150A152ALA0-0.012-0.01227.6260.3090.3090.0000.0000.0000.000
151A153GLY00.0100.01926.4460.1460.1460.0000.0000.0000.000
152A154ALA0-0.021-0.00922.898-0.093-0.0930.0000.0000.0000.000
153A155ASP-1-0.756-0.87719.504-12.437-12.4370.0000.0000.0000.000
154A156PHE0-0.028-0.01512.708-0.941-0.9410.0000.0000.0000.000
155A157VAL00.0200.03117.5990.6970.6970.0000.0000.0000.000
156A158LYS10.8510.91216.43913.15713.1570.0000.0000.0000.000
157A159THR00.0290.01815.7930.3640.3640.0000.0000.0000.000
158A160SER0-0.017-0.01118.2170.5670.5670.0000.0000.0000.000
159A161THR0-0.045-0.05719.204-0.568-0.5680.0000.0000.0000.000
160A162GLY0-0.027-0.01820.728-0.307-0.3070.0000.0000.0000.000
161A163PHE0-0.046-0.02521.2460.1260.1260.0000.0000.0000.000
162A164SER00.0140.03024.5340.4780.4780.0000.0000.0000.000
163A165THR00.004-0.01224.920-0.390-0.3900.0000.0000.0000.000
164A166SER0-0.035-0.02621.657-0.170-0.1700.0000.0000.0000.000
165A167GLY00.0150.01518.3760.1780.1780.0000.0000.0000.000
166A168ALA0-0.0170.00214.4930.3950.3950.0000.0000.0000.000
167A169LYS10.9130.94416.47312.67812.6780.0000.0000.0000.000
168A170VAL00.0610.03312.4160.1750.1750.0000.0000.0000.000
169A171GLU-1-0.809-0.90814.695-15.228-15.2280.0000.0000.0000.000
170A172ASP-1-0.834-0.89317.764-12.572-12.5720.0000.0000.0000.000
171A173VAL0-0.013-0.01911.8260.3600.3600.0000.0000.0000.000
172A174LYS10.8960.96215.07715.18515.1850.0000.0000.0000.000
173A175LEU00.0070.01415.9170.3060.3060.0000.0000.0000.000
174A176MET0-0.0130.00917.2270.4050.4050.0000.0000.0000.000
175A177ARG10.7770.87712.17918.57918.5790.0000.0000.0000.000
176A178GLU-1-0.943-0.98616.670-13.988-13.9880.0000.0000.0000.000
177A179THR0-0.083-0.03419.5030.7150.7150.0000.0000.0000.000
178A180VAL0-0.001-0.00417.9610.4380.4380.0000.0000.0000.000
179A181GLY0-0.0120.00918.7920.1690.1690.0000.0000.0000.000
180A182ASP-1-0.936-0.98116.302-15.230-15.2300.0000.0000.0000.000
181A183ARG10.7680.86017.29812.12312.1230.0000.0000.0000.000
182A184LEU00.0040.01918.5580.3710.3710.0000.0000.0000.000
183A185GLY00.0070.00214.416-0.846-0.8460.0000.0000.0000.000
184A186VAL0-0.008-0.01013.1740.8710.8710.0000.0000.0000.000
185A187LYS10.7300.83912.01015.06615.0660.0000.0000.0000.000
186A188ALA00.0440.03310.9911.0931.0930.0000.0000.0000.000
187A189SER0-0.006-0.02312.349-0.790-0.7900.0000.0000.0000.000
188A190GLY00.0180.01914.9040.7960.7960.0000.0000.0000.000
189A191GLY0-0.010-0.02216.043-0.284-0.2840.0000.0000.0000.000
190A192ILE0-0.0150.0129.878-0.254-0.2540.0000.0000.0000.000
191A193HIS0-0.028-0.02913.0690.7760.7760.0000.0000.0000.000
192A194SER0-0.033-0.02911.389-0.526-0.5260.0000.0000.0000.000
194A196GLU-1-0.871-0.9476.546-35.836-35.8360.0000.0000.0000.000
195A197GLU-1-0.835-0.8918.849-19.017-19.0170.0000.0000.0000.000
196A198ALA00.008-0.0126.2060.1770.1770.0000.0000.0000.000
199A201MET0-0.027-0.0178.5842.0812.0810.0000.0000.0000.000
201A203ASP-1-0.928-0.9576.300-34.763-34.7630.0000.0000.0000.000
202A204ALA0-0.087-0.0357.9452.0042.0040.0000.0000.0000.000
203A205GLY00.0270.0149.5211.7741.7740.0000.0000.0000.000
204A206ALA0-0.034-0.0138.6971.2621.2620.0000.0000.0000.000
205A207SER00.005-0.0057.978-1.765-1.7650.0000.0000.0000.000
206A208ARG10.7390.8228.86118.46518.4650.0000.0000.0000.000
207A209MET00.0050.0085.5170.6320.6320.0000.0000.0000.000
208A210GLY0-0.008-0.02210.2100.5280.5280.0000.0000.0000.000
209A211VAL0-0.032-0.0109.7750.3410.3410.0000.0000.0000.000
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