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: 7YL3K

Calculation Name: 2BID-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BID

Chain ID: A

ChEMBL ID:

UniProt ID: P55957

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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 -2061853.441638
FMO2-HF: Nuclear repulsion 1983181.554297
FMO2-HF: Total energy -78671.887341
FMO2-MP2: Total energy -78898.181041


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-101.001-99.6630.011-0.793-0.556-0.005
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.909
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].
3A3MET0-0.037-0.0273.603-12.080-10.7420.011-0.793-0.556-0.005
4A4ASP-1-0.892-0.9365.883-26.525-26.5250.0000.0000.0000.000
5A5CYS0-0.009-0.0016.245-1.264-1.2640.0000.0000.0000.000
6A6GLU-1-0.887-0.9288.209-25.102-25.1020.0000.0000.0000.000
7A7VAL0-0.077-0.0389.1192.1542.1540.0000.0000.0000.000
8A8ASN0-0.034-0.02110.917-0.844-0.8440.0000.0000.0000.000
9A9ASN00.000-0.00413.6301.2501.2500.0000.0000.0000.000
10A10GLY00.0240.00014.022-1.557-1.5570.0000.0000.0000.000
11A11SER0-0.046-0.02215.7711.1751.1750.0000.0000.0000.000
12A12SER00.0380.01118.792-0.445-0.4450.0000.0000.0000.000
13A13LEU0-0.046-0.00321.6810.4640.4640.0000.0000.0000.000
14A14ARG10.8600.90524.48411.05911.0590.0000.0000.0000.000
15A15ASP-1-0.874-0.93627.507-11.084-11.0840.0000.0000.0000.000
16A16GLU-1-0.834-0.91330.149-10.166-10.1660.0000.0000.0000.000
17A17CYS00.0500.04532.7420.2490.2490.0000.0000.0000.000
18A18ILE00.0130.01832.0340.2800.2800.0000.0000.0000.000
19A19THR0-0.042-0.05133.8580.1220.1220.0000.0000.0000.000
20A20ASN00.0300.00935.9620.1490.1490.0000.0000.0000.000
21A21LEU00.0330.02737.8780.2360.2360.0000.0000.0000.000
22A22LEU0-0.021-0.00636.3800.2300.2300.0000.0000.0000.000
23A23VAL0-0.0250.00940.1680.2390.2390.0000.0000.0000.000
24A24PHE00.0050.00342.5410.2300.2300.0000.0000.0000.000
25A25GLY00.0200.00243.6390.2050.2050.0000.0000.0000.000
26A26PHE0-0.040-0.03740.2360.1570.1570.0000.0000.0000.000
27A27LEU0-0.013-0.01945.5730.1630.1630.0000.0000.0000.000
28A28GLN0-0.045-0.01647.9060.2400.2400.0000.0000.0000.000
29A29SER0-0.054-0.03149.1040.1320.1320.0000.0000.0000.000
30A30CYS0-0.0450.01449.7850.0820.0820.0000.0000.0000.000
31A31SER00.0340.01451.6410.0920.0920.0000.0000.0000.000
32A32ASP-1-0.846-0.88653.782-5.777-5.7770.0000.0000.0000.000
33A33ASN0-0.048-0.02654.9970.0330.0330.0000.0000.0000.000
34A34SER0-0.039-0.03357.3510.0530.0530.0000.0000.0000.000
35A35PHE00.0730.02255.6850.0550.0550.0000.0000.0000.000
36A36ARG10.9340.96654.0335.7255.7250.0000.0000.0000.000
37A37ARG10.9180.97553.7255.6815.6810.0000.0000.0000.000
38A38GLU-1-0.857-0.94854.091-5.752-5.7520.0000.0000.0000.000
39A39LEU0-0.012-0.00249.616-0.120-0.1200.0000.0000.0000.000
40A40ASP-1-0.861-0.92649.382-6.361-6.3610.0000.0000.0000.000
41A41ALA0-0.053-0.03250.212-0.087-0.0870.0000.0000.0000.000
42A42LEU0-0.055-0.01847.142-0.039-0.0390.0000.0000.0000.000
43A43GLY00.0340.02145.385-0.121-0.1210.0000.0000.0000.000
44A44HIS0-0.086-0.04445.453-0.014-0.0140.0000.0000.0000.000
45A45GLU-1-0.973-0.98946.205-7.047-7.0470.0000.0000.0000.000
46A46LEU0-0.075-0.02040.928-0.107-0.1070.0000.0000.0000.000
47A47PRO00.0360.02940.300-0.098-0.0980.0000.0000.0000.000
48A48VAL0-0.027-0.03034.213-0.117-0.1170.0000.0000.0000.000
49A49LEU0-0.024-0.00531.6180.0240.0240.0000.0000.0000.000
50A50ALA00.0380.01831.731-0.016-0.0160.0000.0000.0000.000
51A51PRO0-0.045-0.03727.488-0.068-0.0680.0000.0000.0000.000
52A52GLN0-0.014-0.00529.5570.1320.1320.0000.0000.0000.000
53A53TRP00.0010.00432.6010.0060.0060.0000.0000.0000.000
54A54GLU-1-0.911-0.96736.227-7.939-7.9390.0000.0000.0000.000
55A55GLY0-0.015-0.00536.0460.1300.1300.0000.0000.0000.000
56A56TYR0-0.088-0.03431.164-0.197-0.1970.0000.0000.0000.000
57A57ASP-1-0.926-0.97036.435-7.739-7.7390.0000.0000.0000.000
58A58GLU-1-0.934-0.96440.208-7.307-7.3070.0000.0000.0000.000
59A59LEU0-0.049-0.00343.5410.2470.2470.0000.0000.0000.000
60A60GLN0-0.034-0.02944.8140.0600.0600.0000.0000.0000.000
61A61THR00.0330.00741.424-0.042-0.0420.0000.0000.0000.000
62A62ASP-1-0.990-0.99044.179-6.691-6.6910.0000.0000.0000.000
63A63GLY00.0550.04046.117-0.065-0.0650.0000.0000.0000.000
64A64ASN0-0.037-0.03847.0580.0890.0890.0000.0000.0000.000
65A65ARG11.0011.01049.3626.1516.1510.0000.0000.0000.000
66A66SER0-0.015-0.00152.5780.0770.0770.0000.0000.0000.000
67A67SER00.005-0.00254.984-0.072-0.0720.0000.0000.0000.000
68A68HIS00.0530.02449.0770.0740.0740.0000.0000.0000.000
69A69SER0-0.0120.00054.3840.0960.0960.0000.0000.0000.000
70A70ARG10.9830.98151.8555.9135.9130.0000.0000.0000.000
71A71LEU0-0.010-0.01353.847-0.023-0.0230.0000.0000.0000.000
72A72GLY00.0040.00054.1660.0740.0740.0000.0000.0000.000
73A73ARG10.8730.92453.0795.5895.5890.0000.0000.0000.000
74A74ILE00.0520.03947.817-0.007-0.0070.0000.0000.0000.000
75A75GLU-1-0.876-0.93147.341-6.746-6.7460.0000.0000.0000.000
76A76ALA0-0.051-0.03046.964-0.096-0.0960.0000.0000.0000.000
77A77ASP-1-0.904-0.94444.554-6.915-6.9150.0000.0000.0000.000
78A78SER0-0.094-0.04542.362-0.088-0.0880.0000.0000.0000.000
79A79GLU-1-0.885-0.93139.870-7.927-7.9270.0000.0000.0000.000
80A80SER0-0.044-0.03738.280-0.288-0.2880.0000.0000.0000.000
81A81GLN00.002-0.01532.0700.2730.2730.0000.0000.0000.000
82A82GLU-1-0.881-0.95236.444-7.919-7.9190.0000.0000.0000.000
83A83ASP-1-0.837-0.90838.900-7.300-7.3000.0000.0000.0000.000
84A84ILE0-0.025-0.00737.0850.1100.1100.0000.0000.0000.000
85A85ILE0-0.021-0.01434.6160.0740.0740.0000.0000.0000.000
86A86ARG10.8830.93639.1007.2947.2940.0000.0000.0000.000
87A87ASN0-0.027-0.00542.6310.2220.2220.0000.0000.0000.000
88A88ILE00.0010.01238.8680.1600.1600.0000.0000.0000.000
89A89ALA00.002-0.00341.4920.1040.1040.0000.0000.0000.000
90A90ARG10.8920.93543.1396.4216.4210.0000.0000.0000.000
91A91HIS00.0120.01245.8050.2020.2020.0000.0000.0000.000
92A92LEU00.0150.00643.1790.1580.1580.0000.0000.0000.000
93A93ALA00.0010.01746.0670.0930.0930.0000.0000.0000.000
94A94GLN00.0000.00247.5300.2370.2370.0000.0000.0000.000
95A95VAL0-0.0160.00448.7490.1460.1460.0000.0000.0000.000
96A96GLY00.0330.02549.1490.1040.1040.0000.0000.0000.000
97A97ASP0-0.019-0.05050.0980.0900.0900.0000.0000.0000.000
98A98SER0-0.135-0.07253.0380.1590.1590.0000.0000.0000.000
99A99MET0-0.005-0.00950.7650.1220.1220.0000.0000.0000.000
100A100ASP-1-0.783-0.87052.161-6.196-6.1960.0000.0000.0000.000
101A101ARG10.9210.95654.9455.4225.4220.0000.0000.0000.000
102A102SER0-0.078-0.01857.8620.1270.1270.0000.0000.0000.000
103A103ILE00.0070.01156.645-0.060-0.0600.0000.0000.0000.000
104A104PRO00.016-0.00254.5970.0860.0860.0000.0000.0000.000
105A105PRO00.001-0.01757.9350.0300.0300.0000.0000.0000.000
106A106GLY00.0190.02359.214-0.040-0.0400.0000.0000.0000.000
107A107LEU0-0.0200.00452.103-0.045-0.0450.0000.0000.0000.000
108A108VAL00.0530.00954.123-0.069-0.0690.0000.0000.0000.000
109A109ASN00.0130.01755.1440.0160.0160.0000.0000.0000.000
110A110GLY00.0300.01556.205-0.001-0.0010.0000.0000.0000.000
111A111LEU00.0230.02448.721-0.058-0.0580.0000.0000.0000.000
112A112ALA00.0590.01652.257-0.095-0.0950.0000.0000.0000.000
113A113LEU0-0.107-0.05154.5080.0230.0230.0000.0000.0000.000
114A114GLN00.0060.00550.5860.0890.0890.0000.0000.0000.000
115A115LEU0-0.040-0.02048.002-0.068-0.0680.0000.0000.0000.000
116A116ARG10.9280.96550.7765.5875.5870.0000.0000.0000.000
117A117ASN00.0380.01651.3000.1250.1250.0000.0000.0000.000
118A118THR0-0.089-0.04352.639-0.008-0.0080.0000.0000.0000.000
119A119SER00.0380.01049.996-0.033-0.0330.0000.0000.0000.000
120A120ARG10.9430.98949.2956.0416.0410.0000.0000.0000.000
121A121SER0-0.0130.01447.773-0.144-0.1440.0000.0000.0000.000
122A122GLU-1-0.927-0.96943.680-7.405-7.4050.0000.0000.0000.000
123A123GLU-1-0.957-0.97243.214-7.567-7.5670.0000.0000.0000.000
124A124ASP-1-0.903-0.97844.691-6.601-6.6010.0000.0000.0000.000
125A125ARG10.9200.95342.7367.3077.3070.0000.0000.0000.000
126A126ASN0-0.002-0.00439.375-0.009-0.0090.0000.0000.0000.000
127A127ARG10.9120.96139.2157.8097.8090.0000.0000.0000.000
128A128ASP-1-0.843-0.91544.249-6.608-6.6080.0000.0000.0000.000
129A129LEU0-0.044-0.02243.4320.0090.0090.0000.0000.0000.000
130A130ALA00.0060.00640.311-0.056-0.0560.0000.0000.0000.000
131A131THR0-0.025-0.02341.817-0.073-0.0730.0000.0000.0000.000
132A132ALA00.003-0.01344.5940.0330.0330.0000.0000.0000.000
133A133LEU0-0.043-0.01340.4770.0400.0400.0000.0000.0000.000
134A134GLU-1-0.846-0.91337.912-8.490-8.4900.0000.0000.0000.000
135A135GLN0-0.055-0.02442.3810.1410.1410.0000.0000.0000.000
136A136LEU0-0.033-0.01245.8640.0830.0830.0000.0000.0000.000
137A137LEU00.003-0.02339.513-0.008-0.0080.0000.0000.0000.000
138A138GLN0-0.056-0.01542.469-0.063-0.0630.0000.0000.0000.000
139A139ALA0-0.044-0.00644.0290.0530.0530.0000.0000.0000.000
140A140TYR0-0.060-0.02843.0840.1090.1090.0000.0000.0000.000
141A141PRO0-0.018-0.01540.974-0.181-0.1810.0000.0000.0000.000
142A142ARG10.9650.98734.1558.8568.8560.0000.0000.0000.000
143A143ASP-1-0.967-0.98933.367-9.393-9.3930.0000.0000.0000.000
144A144MET0-0.0020.01132.014-0.155-0.1550.0000.0000.0000.000
145A145GLU-1-0.823-0.93829.525-10.774-10.7740.0000.0000.0000.000
146A146LYS10.7830.88333.1339.2289.2280.0000.0000.0000.000
147A147GLU-1-0.933-0.95830.000-10.232-10.2320.0000.0000.0000.000
148A148LYS11.0030.99334.0439.3249.3240.0000.0000.0000.000
149A149THR00.0530.02537.1470.1150.1150.0000.0000.0000.000
150A150MET0-0.0060.00936.1250.2620.2620.0000.0000.0000.000
151A151LEU0-0.016-0.00535.3160.1680.1680.0000.0000.0000.000
152A152VAL00.0380.01539.6950.1720.1720.0000.0000.0000.000
153A153LEU00.0280.01442.1030.2260.2260.0000.0000.0000.000
154A154ALA00.0250.01041.7150.1370.1370.0000.0000.0000.000
155A155LEU00.0130.02338.6610.1110.1110.0000.0000.0000.000
156A156LEU0-0.0230.00243.3430.1500.1500.0000.0000.0000.000
157A157LEU0-0.070-0.03246.4690.1800.1800.0000.0000.0000.000
158A158ALA00.0150.00445.4570.1390.1390.0000.0000.0000.000
159A159LYS10.8900.92843.2507.4877.4870.0000.0000.0000.000
160A160LYS10.8660.90748.4736.5306.5300.0000.0000.0000.000
161A161VAL0-0.0120.00850.7470.1590.1590.0000.0000.0000.000
162A162ALA0-0.013-0.00650.8640.1150.1150.0000.0000.0000.000
163A163SER0-0.013-0.01252.8490.1320.1320.0000.0000.0000.000
164A164HIS0-0.020-0.00855.2900.0930.0930.0000.0000.0000.000
165A165THR0-0.090-0.05955.8230.1260.1260.0000.0000.0000.000
166A166PRO00.0690.05254.714-0.116-0.1160.0000.0000.0000.000
167A167SER0-0.039-0.03154.885-0.075-0.0750.0000.0000.0000.000
168A168LEU00.0130.01651.800-0.029-0.0290.0000.0000.0000.000
169A169LEU0-0.0010.01450.588-0.165-0.1650.0000.0000.0000.000
170A170ARG10.9900.98247.6546.4706.4700.0000.0000.0000.000
171A171ASP-1-0.762-0.86246.366-6.962-6.9620.0000.0000.0000.000
172A172VAL0-0.0140.02146.174-0.179-0.1790.0000.0000.0000.000
173A173PHE00.016-0.01144.088-0.151-0.1510.0000.0000.0000.000
174A174HIS00.0440.01841.866-0.320-0.3200.0000.0000.0000.000
175A175THR0-0.055-0.05541.413-0.176-0.1760.0000.0000.0000.000
176A176THR0-0.019-0.03040.612-0.100-0.1000.0000.0000.0000.000
177A177VAL00.0220.01936.764-0.200-0.2000.0000.0000.0000.000
178A178ASN0-0.013-0.00736.698-0.499-0.4990.0000.0000.0000.000
179A179PHE00.022-0.00336.595-0.240-0.2400.0000.0000.0000.000
180A180ILE00.0000.01033.770-0.199-0.1990.0000.0000.0000.000
181A181ASN00.027-0.02532.635-0.452-0.4520.0000.0000.0000.000
182A182GLN0-0.047-0.00531.798-0.181-0.1810.0000.0000.0000.000
183A183ASN0-0.025-0.03029.612-0.061-0.0610.0000.0000.0000.000
184A184LEU00.0500.03829.292-0.329-0.3290.0000.0000.0000.000
185A185ARG10.9541.00526.84311.41011.4100.0000.0000.0000.000
186A186THR00.006-0.01526.5480.1390.1390.0000.0000.0000.000
187A187TYR00.0440.03029.2380.0910.0910.0000.0000.0000.000
188A188VAL00.0130.00532.5250.2510.2510.0000.0000.0000.000
189A189ARG10.9870.98925.75511.69211.6920.0000.0000.0000.000
190A190SER0-0.017-0.00932.3680.0280.0280.0000.0000.0000.000
191A191LEU00.0040.01633.9820.2130.2130.0000.0000.0000.000
192A192ALA00.0170.02335.6910.2470.2470.0000.0000.0000.000
193A193ARG10.8100.89131.8819.4409.4400.0000.0000.0000.000
194A194ASN0-0.024-0.02035.641-0.087-0.0870.0000.0000.0000.000
195A195GLY00.0400.01238.4670.2170.2170.0000.0000.0000.000
196A196MET0-0.078-0.03841.0310.2050.2050.0000.0000.0000.000
197A197ASP-2-1.789-1.89137.583-16.225-16.2250.0000.0000.0000.000