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: 3M5GL

Calculation Name: 5Y9P-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5Y9P

Chain ID: A

ChEMBL ID:

UniProt ID: Q2FZ38

Base Structure: X-ray

Registration Date: 2025-10-06

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 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2488109.828005
FMO2-HF: Nuclear repulsion 2403077.824419
FMO2-HF: Total energy -85032.003586
FMO2-MP2: Total energy -85279.360273


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:44:ALA)


Summations of interaction energy for fragment #1(A:44:ALA)
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.
-72.752-68.9280.065-1.591-2.299-0.007
Interaction energy analysis for fragmet #1(A:44:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.908
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].
3A46GLU-1-0.891-0.9193.095-51.012-47.825-0.003-1.430-1.754-0.006
4A47LYS10.9580.9683.10958.94959.5860.068-0.161-0.545-0.001
5A48GLU-1-0.919-0.9375.179-34.206-34.2060.0000.0000.0000.000
6A49GLN00.0900.0356.6513.7663.7660.0000.0000.0000.000
7A50ALA00.0180.0038.4833.4373.4370.0000.0000.0000.000
8A51LEU0-0.033-0.0089.6752.5372.5370.0000.0000.0000.000
9A52LYS10.8840.9339.03532.80232.8020.0000.0000.0000.000
10A53GLU-1-0.901-0.93212.817-21.160-21.1600.0000.0000.0000.000
11A54LYS10.7650.85014.24921.16021.1600.0000.0000.0000.000
12A55TYR-1-0.716-0.84115.582-14.880-14.8800.0000.0000.0000.000
13A56VAL0-0.0060.00817.1661.0891.0890.0000.0000.0000.000
14A57GLU-1-0.893-0.93418.247-16.317-16.3170.0000.0000.0000.000
15A58MET0-0.062-0.01820.0250.5030.5030.0000.0000.0000.000
16A59THR00.0140.00420.9460.6210.6210.0000.0000.0000.000
17A60TYR0-0.093-0.04523.3420.4610.4610.0000.0000.0000.000
18A61PHE00.023-0.00125.4830.4210.4210.0000.0000.0000.000
19A62GLU-1-0.711-0.83126.010-11.550-11.5500.0000.0000.0000.000
20A63ASN0-0.002-0.00423.3110.4200.4200.0000.0000.0000.000
21A64GLU-1-0.877-0.93427.673-10.371-10.3710.0000.0000.0000.000
22A65ILE0-0.025-0.01830.6460.3890.3890.0000.0000.0000.000
23A66LEU0-0.009-0.01028.1330.2930.2930.0000.0000.0000.000
24A67LYS10.7790.89730.6679.9519.9510.0000.0000.0000.000
25A68GLU-1-0.873-0.92432.345-9.012-9.0120.0000.0000.0000.000
26A69HIS0-0.067-0.03434.9990.5790.5790.0000.0000.0000.000
27A70PRO00.0330.02433.244-0.144-0.1440.0000.0000.0000.000
28A71ASN0-0.078-0.05733.991-0.090-0.0900.0000.0000.0000.000
29A72ALA0-0.0180.00833.6470.1310.1310.0000.0000.0000.000
30A73ILE0-0.0100.00733.277-0.315-0.3150.0000.0000.0000.000
31A74ILE00.0120.00630.4030.2370.2370.0000.0000.0000.000
32A75CYS0-0.040-0.00931.872-0.228-0.2280.0000.0000.0000.000
33A76GLY00.0170.01030.2140.0850.0850.0000.0000.0000.000
34A77ILE0-0.017-0.02531.2760.1190.1190.0000.0000.0000.000
35A78ASP-1-0.748-0.86929.748-10.483-10.4830.0000.0000.0000.000
36A79GLU-1-0.855-0.92132.814-8.590-8.5900.0000.0000.0000.000
37A80VAL0-0.0140.00531.417-0.223-0.2230.0000.0000.0000.000
38A81GLY00.029-0.00434.5240.2420.2420.0000.0000.0000.000
39A82ARG10.8500.91936.1778.7478.7470.0000.0000.0000.000
40A83GLY00.015-0.00738.0060.1920.1920.0000.0000.0000.000
41A84PRO0-0.074-0.03537.9540.1150.1150.0000.0000.0000.000
42A85LEU00.0140.01840.7470.0830.0830.0000.0000.0000.000
43A86ALA00.0020.00343.1670.1840.1840.0000.0000.0000.000
44A87GLY00.0360.02342.177-0.242-0.2420.0000.0000.0000.000
45A88PRO00.0270.02140.6540.0510.0510.0000.0000.0000.000
46A89VAL0-0.043-0.00738.895-0.180-0.1800.0000.0000.0000.000
47A90VAL0-0.020-0.02535.7060.1580.1580.0000.0000.0000.000
48A91ALA00.0540.03035.756-0.242-0.2420.0000.0000.0000.000
49A92CYS0-0.115-0.04632.1410.0030.0030.0000.0000.0000.000
50A93ALA00.0540.03233.798-0.046-0.0460.0000.0000.0000.000
51A94THR00.000-0.03128.110-0.131-0.1310.0000.0000.0000.000
52A95ILE00.0190.02330.834-0.124-0.1240.0000.0000.0000.000
53A96LEU00.0390.01824.173-0.014-0.0140.0000.0000.0000.000
54A97ASN00.0610.05623.0930.3980.3980.0000.0000.0000.000
55A98SER00.019-0.01325.441-0.424-0.4240.0000.0000.0000.000
56A99ASN0-0.046-0.01922.0740.0610.0610.0000.0000.0000.000
57A100HIS0-0.066-0.02521.284-0.055-0.0550.0000.0000.0000.000
58A101ASN00.039-0.00514.282-0.840-0.8400.0000.0000.0000.000
59A102TYR0-0.026-0.03116.964-0.896-0.8960.0000.0000.0000.000
60A103LEU0-0.086-0.02512.898-0.439-0.4390.0000.0000.0000.000
61A104GLY0-0.008-0.01413.864-0.843-0.8430.0000.0000.0000.000
62A105LEU0-0.129-0.08514.5190.5560.5560.0000.0000.0000.000
63A106ASP-1-0.760-0.89016.969-16.072-16.0720.0000.0000.0000.000
64A107ASP00.0280.01319.783-0.255-0.2550.0000.0000.0000.000
65A108SER00.0430.03222.332-0.373-0.3730.0000.0000.0000.000
66A109LYS0-0.108-0.04715.973-0.780-0.7800.0000.0000.0000.000
67A110LYS10.8840.92718.16216.25116.2510.0000.0000.0000.000
68A111VAL00.0750.06620.1230.4270.4270.0000.0000.0000.000
69A112PRO0-0.027-0.01817.6830.6410.6410.0000.0000.0000.000
70A113VAL00.028-0.00120.910-0.194-0.1940.0000.0000.0000.000
71A114THR00.014-0.00518.8390.1260.1260.0000.0000.0000.000
72A115LYS10.8860.95414.53719.24519.2450.0000.0000.0000.000
73A116ARG10.9450.98619.06212.07212.0720.0000.0000.0000.000
74A117LEU00.0150.00322.4450.3330.3330.0000.0000.0000.000
75A118GLU-1-0.917-0.94916.402-17.772-17.7720.0000.0000.0000.000
76A119LEU00.0080.00017.9310.2050.2050.0000.0000.0000.000
77A120ASN0-0.015-0.01221.2840.4730.4730.0000.0000.0000.000
78A121GLU-1-0.822-0.90824.153-10.516-10.5160.0000.0000.0000.000
79A122ALA00.0060.01320.6690.2350.2350.0000.0000.0000.000
80A123LEU0-0.002-0.00122.6620.2710.2710.0000.0000.0000.000
81A124LYS10.8290.89024.76310.72910.7290.0000.0000.0000.000
82A125ASN0-0.115-0.04524.9790.4870.4870.0000.0000.0000.000
83A126GLU-1-0.955-0.97221.238-13.902-13.9020.0000.0000.0000.000
84A127VAL0-0.062-0.01425.592-0.012-0.0120.0000.0000.0000.000
85A128THR0-0.073-0.03627.5340.2690.2690.0000.0000.0000.000
86A129ALA0-0.001-0.00630.6850.3780.3780.0000.0000.0000.000
87A130PHE00.0070.01130.494-0.212-0.2120.0000.0000.0000.000
88A131ALA00.0160.02032.6280.2220.2220.0000.0000.0000.000
89A132TYR00.0220.00231.474-0.129-0.1290.0000.0000.0000.000
90A133GLY00.0300.02237.0400.2230.2230.0000.0000.0000.000
91A134ILE0-0.045-0.02139.218-0.122-0.1220.0000.0000.0000.000
92A135ALA00.0100.02041.8590.1860.1860.0000.0000.0000.000
93A136THR00.001-0.03043.884-0.095-0.0950.0000.0000.0000.000
94A137ALA00.0250.01246.3490.0120.0120.0000.0000.0000.000
95A138GLU-1-0.785-0.89147.525-6.018-6.0180.0000.0000.0000.000
96A139GLU-1-0.726-0.82747.832-6.632-6.6320.0000.0000.0000.000
97A140ILE0-0.056-0.02943.744-0.022-0.0220.0000.0000.0000.000
98A141ASP-1-0.790-0.86848.031-6.294-6.2940.0000.0000.0000.000
99A142GLU-1-0.979-0.97451.432-5.823-5.8230.0000.0000.0000.000
100A143PHE00.004-0.01749.3060.0510.0510.0000.0000.0000.000
101A144ASN00.0240.01847.609-0.191-0.1910.0000.0000.0000.000
102A145ILE00.0710.01942.036-0.067-0.0670.0000.0000.0000.000
103A146TYR0-0.0070.02842.409-0.228-0.2280.0000.0000.0000.000
104A147LYS10.9140.97443.9596.2286.2280.0000.0000.0000.000
105A148ALA0-0.010-0.00145.214-0.028-0.0280.0000.0000.0000.000
106A149THR00.006-0.02239.091-0.142-0.1420.0000.0000.0000.000
107A150GLN0-0.008-0.01841.113-0.024-0.0240.0000.0000.0000.000
108A151ILE0-0.023-0.00342.987-0.016-0.0160.0000.0000.0000.000
109A152ALA0-0.024-0.00440.300-0.016-0.0160.0000.0000.0000.000
110A153MET00.017-0.00535.802-0.065-0.0650.0000.0000.0000.000
111A154GLN0-0.044-0.02139.572-0.134-0.1340.0000.0000.0000.000
112A155ARG10.8100.86342.1906.8526.8520.0000.0000.0000.000
113A156ALA0-0.0060.00736.910-0.022-0.0220.0000.0000.0000.000
114A157ILE0-0.028-0.01738.284-0.160-0.1600.0000.0000.0000.000
115A158ASP-1-0.884-0.94039.612-7.211-7.2110.0000.0000.0000.000
116A159GLY0-0.018-0.00140.2800.1260.1260.0000.0000.0000.000
117A160LEU0-0.061-0.02434.879-0.161-0.1610.0000.0000.0000.000
118A161SER0-0.028-0.02136.3410.1970.1970.0000.0000.0000.000
119A162VAL0-0.032-0.01735.9540.1300.1300.0000.0000.0000.000
120A163GLN00.0200.01838.090-0.183-0.1830.0000.0000.0000.000
121A164PRO00.0100.00536.202-0.062-0.0620.0000.0000.0000.000
122A165THR0-0.026-0.04137.3820.1910.1910.0000.0000.0000.000
123A166HIS00.0110.02135.4330.0830.0830.0000.0000.0000.000
124A167LEU0-0.0030.00435.297-0.164-0.1640.0000.0000.0000.000
125A168LEU0-0.015-0.00429.4310.0290.0290.0000.0000.0000.000
126A169ILE00.0480.00833.004-0.052-0.0520.0000.0000.0000.000
127A170ASP-1-0.774-0.88830.345-10.368-10.3680.0000.0000.0000.000
128A171ALA0-0.079-0.04733.0370.3020.3020.0000.0000.0000.000
129A172MET0-0.0250.01035.7720.3660.3660.0000.0000.0000.000
130A173THR0-0.054-0.03838.358-0.087-0.0870.0000.0000.0000.000
131A174LEU00.0230.01239.4190.1290.1290.0000.0000.0000.000
132A175ASP-1-0.908-0.94543.014-6.891-6.8910.0000.0000.0000.000
133A176ASN0-0.041-0.02541.7140.1340.1340.0000.0000.0000.000
134A177ALA0-0.009-0.02245.312-0.040-0.0400.0000.0000.0000.000
135A178LEU00.0010.01840.3070.0160.0160.0000.0000.0000.000
136A179PRO0-0.036-0.00639.631-0.007-0.0070.0000.0000.0000.000
137A180GLN00.0300.00137.511-0.291-0.2910.0000.0000.0000.000
138A181VAL0-0.018-0.00833.5340.1260.1260.0000.0000.0000.000
139A182SER00.0040.02134.718-0.245-0.2450.0000.0000.0000.000
140A183LEU0-0.025-0.01029.360-0.082-0.0820.0000.0000.0000.000
141A184ILE00.000-0.00832.0370.0430.0430.0000.0000.0000.000
142A185LYS10.9130.96327.48610.98610.9860.0000.0000.0000.000
143A186GLY00.0650.01927.800-0.404-0.4040.0000.0000.0000.000
144A187ASP-1-0.783-0.89026.305-12.090-12.0900.0000.0000.0000.000
145A188ALA0-0.030-0.03923.422-0.542-0.5420.0000.0000.0000.000
146A189ARG10.8150.90423.31911.48111.4810.0000.0000.0000.000
147A190SER00.011-0.00425.4270.0720.0720.0000.0000.0000.000
148A191VAL00.0430.01720.8310.1750.1750.0000.0000.0000.000
149A192SER0-0.017-0.03023.6560.1230.1230.0000.0000.0000.000
150A193ILE0-0.081-0.02927.1680.2730.2730.0000.0000.0000.000
151A194ALA0-0.012-0.01323.1030.1390.1390.0000.0000.0000.000
152A195ALA00.007-0.00424.954-0.046-0.0460.0000.0000.0000.000
153A196ALA00.0250.02325.7810.1860.1860.0000.0000.0000.000
154A197SER0-0.004-0.02827.6360.0490.0490.0000.0000.0000.000
155A198ILE0-0.060-0.02421.9880.1210.1210.0000.0000.0000.000
156A199MET00.0130.01226.4800.2530.2530.0000.0000.0000.000
157A200ALA0-0.004-0.00129.2210.3300.3300.0000.0000.0000.000
158A201LYS10.7640.85828.15410.39310.3930.0000.0000.0000.000
159A202VAL0-0.018-0.01027.3150.1620.1620.0000.0000.0000.000
160A203PHE00.0400.03530.3510.3110.3110.0000.0000.0000.000
161A204ARG10.8010.88833.7518.4988.4980.0000.0000.0000.000
162A205ASP-1-0.827-0.89230.735-9.740-9.7400.0000.0000.0000.000
163A206ASP-1-0.887-0.93233.045-9.319-9.3190.0000.0000.0000.000
164A207TYR0-0.080-0.05535.2470.2400.2400.0000.0000.0000.000
165A208MET0-0.053-0.02037.5490.2690.2690.0000.0000.0000.000
166A209THR0-0.004-0.01635.5210.1770.1770.0000.0000.0000.000
167A210GLN0-0.051-0.01737.6230.2890.2890.0000.0000.0000.000
168A211LEU00.0710.03540.8060.1560.1560.0000.0000.0000.000
169A212SER0-0.082-0.04940.6280.1470.1470.0000.0000.0000.000
170A213LYS10.8280.90939.0207.9297.9290.0000.0000.0000.000
171A214ASP-1-0.912-0.94544.711-6.650-6.6500.0000.0000.0000.000
172A215TYR0-0.021-0.01446.4640.2070.2070.0000.0000.0000.000
173A216PRO00.0050.00545.064-0.143-0.1430.0000.0000.0000.000
174A217GLU-1-0.875-0.94045.278-6.566-6.5660.0000.0000.0000.000
175A218TYR0-0.027-0.04045.627-0.100-0.1000.0000.0000.0000.000
176A219GLY0-0.030-0.01342.482-0.119-0.1190.0000.0000.0000.000
177A220PHE00.013-0.00840.402-0.240-0.2400.0000.0000.0000.000
178A221GLU-1-0.777-0.89037.708-8.039-8.0390.0000.0000.0000.000
179A222LYS10.7400.87035.8847.6237.6230.0000.0000.0000.000
180A223ASN0-0.032-0.01835.904-0.268-0.2680.0000.0000.0000.000
181A224ALA00.0420.03035.528-0.027-0.0270.0000.0000.0000.000
182A225GLY00.0830.04937.6790.0300.0300.0000.0000.0000.000
183A226TYR0-0.012-0.01334.7180.2000.2000.0000.0000.0000.000
184A227GLY00.0430.04140.5290.0750.0750.0000.0000.0000.000
185A228THR0-0.020-0.01939.5380.1000.1000.0000.0000.0000.000
186A229LYS10.9890.98842.7506.5306.5300.0000.0000.0000.000
187A230GLN00.0330.01942.615-0.055-0.0550.0000.0000.0000.000
188A231HIS00.000-0.00243.3090.2510.2510.0000.0000.0000.000
189A232LEU0-0.006-0.01345.9190.1170.1170.0000.0000.0000.000
190A233LEU0-0.003-0.00448.6810.1040.1040.0000.0000.0000.000
191A234ALA00.0250.02148.5280.1130.1130.0000.0000.0000.000
192A235ILE0-0.040-0.01748.4800.0770.0770.0000.0000.0000.000
193A236ASP-1-0.966-0.99052.001-5.917-5.9170.0000.0000.0000.000
194A237ASP-1-1.002-0.98653.763-5.661-5.6610.0000.0000.0000.000
195A238ILE0-0.029-0.01251.8040.1060.1060.0000.0000.0000.000
196A239GLY00.0200.03155.0220.0550.0550.0000.0000.0000.000
197A240ILE0-0.037-0.01851.792-0.141-0.1410.0000.0000.0000.000
198A241MET00.0310.02547.8840.0700.0700.0000.0000.0000.000
199A242LYS10.9130.93147.7316.5036.5030.0000.0000.0000.000
200A243GLU-1-0.841-0.90645.627-7.075-7.0750.0000.0000.0000.000
201A244HIS00.0150.00746.695-0.073-0.0730.0000.0000.0000.000
202A245ARG10.7530.89241.2747.5517.5510.0000.0000.0000.000
203A246LYS10.8840.92348.9086.0126.0120.0000.0000.0000.000
204A247SER0-0.059-0.05849.6720.0340.0340.0000.0000.0000.000
205A248PHE0-0.052-0.02942.994-0.058-0.0580.0000.0000.0000.000
206A249GLU-1-0.807-0.85748.532-6.002-6.0020.0000.0000.0000.000
207A250PRO0-0.053-0.04447.393-0.182-0.1820.0000.0000.0000.000
208A251ILE00.0300.01149.0630.1240.1240.0000.0000.0000.000
209A252LYS10.9350.97251.8236.0406.0400.0000.0000.0000.000
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