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: GRZ31

Calculation Name: 5EJ3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5EJ3

Chain ID: A

ChEMBL ID:

UniProt ID: P26515

Base Structure: X-ray

Registration Date: 2025-10-04

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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2126027.51056
FMO2-HF: Nuclear repulsion 2052043.310948
FMO2-HF: Total energy -73984.199612
FMO2-MP2: Total energy -74200.314907


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-32.161-29.49220.806-11.544-11.9290.017
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.020
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].
3A3VAL00.019-0.0023.1223.3635.7660.133-1.202-1.334-0.005
4A4VAL0-0.0050.0075.069-0.637-0.610-0.001-0.003-0.0230.000
12A12ASN00.0350.0064.7331.1871.250-0.001-0.001-0.0600.000
13A13ASN0-0.054-0.0354.6150.5050.550-0.001-0.001-0.0420.000
30A30ASN0-0.076-0.0351.758-19.344-24.61113.504-4.611-3.6260.054
31A31MET0-0.0140.0022.3253.9915.9111.230-1.071-2.079-0.002
32A32GLY00.0890.0542.181-14.210-11.0225.924-4.553-4.559-0.031
33A33SER0-0.002-0.0123.932-5.443-5.2790.019-0.076-0.1070.001
38A38SER00.0010.0204.131-0.999-0.873-0.001-0.026-0.0990.000
5A5THR00.0350.0078.3770.8150.8150.0000.0000.0000.000
6A6THR0-0.0010.00311.5390.0500.0500.0000.0000.0000.000
7A7ASN00.0030.00213.4510.1000.1000.0000.0000.0000.000
8A8GLN00.0150.03110.824-0.440-0.4400.0000.0000.0000.000
9A9GLU-1-0.869-0.90113.8150.2800.2800.0000.0000.0000.000
10A10GLY00.0200.01313.217-0.302-0.3020.0000.0000.0000.000
11A11THR0-0.022-0.01312.1210.2850.2850.0000.0000.0000.000
14A14GLY00.0330.0188.6970.6500.6500.0000.0000.0000.000
15A15TYR0-0.050-0.01610.9060.2020.2020.0000.0000.0000.000
16A16TYR0-0.032-0.04611.569-0.287-0.2870.0000.0000.0000.000
17A17TYR0-0.054-0.05610.2040.4130.4130.0000.0000.0000.000
18A18SER00.0510.02412.175-0.388-0.3880.0000.0000.0000.000
19A19PHE0-0.014-0.01710.6490.4520.4520.0000.0000.0000.000
20A20TRP00.0180.01113.522-0.299-0.2990.0000.0000.0000.000
21A21THR00.015-0.02316.3800.2040.2040.0000.0000.0000.000
22A22ASP-1-0.811-0.87218.3630.4640.4640.0000.0000.0000.000
23A23SER0-0.051-0.03319.828-0.102-0.1020.0000.0000.0000.000
24A24GLN00.000-0.01314.9180.1100.1100.0000.0000.0000.000
25A25GLY00.0030.01315.422-0.038-0.0380.0000.0000.0000.000
26A26THR0-0.041-0.01816.1910.1430.1430.0000.0000.0000.000
27A27VAL0-0.002-0.00612.7020.2800.2800.0000.0000.0000.000
28A28SER0-0.045-0.0198.833-0.184-0.1840.0000.0000.0000.000
29A29MET00.0120.0046.6590.7670.7670.0000.0000.0000.000
34A34GLY00.0720.0396.8651.3451.3450.0000.0000.0000.000
35A35GLY00.0530.0259.0400.0080.0080.0000.0000.0000.000
36A36GLN0-0.090-0.0416.1581.1361.1360.0000.0000.0000.000
37A37TYR0-0.044-0.0345.3000.6930.6930.0000.0000.0000.000
39A39THR00.010-0.0176.554-0.720-0.7200.0000.0000.0000.000
40A40SER00.0210.0149.127-0.183-0.1830.0000.0000.0000.000
41A41TRP00.0070.01511.179-0.302-0.3020.0000.0000.0000.000
42A42ARG10.8550.90412.943-2.285-2.2850.0000.0000.0000.000
43A43ASN00.003-0.00717.953-0.059-0.0590.0000.0000.0000.000
44A44THR0-0.020-0.00118.291-0.097-0.0970.0000.0000.0000.000
45A45GLY00.0470.02420.349-0.013-0.0130.0000.0000.0000.000
46A46ASN0-0.075-0.07221.2470.0010.0010.0000.0000.0000.000
47A47PHE0-0.0090.01613.806-0.065-0.0650.0000.0000.0000.000
48A48VAL00.0490.02717.0180.1340.1340.0000.0000.0000.000
49A49ALA0-0.002-0.00511.627-0.153-0.1530.0000.0000.0000.000
50A50GLY00.0120.00411.2140.3680.3680.0000.0000.0000.000
51A51LYS10.8010.8996.400-3.847-3.8470.0000.0000.0000.000
52A52GLY0-0.001-0.00812.2240.0930.0930.0000.0000.0000.000
53A53TRP0-0.055-0.04315.382-0.130-0.1300.0000.0000.0000.000
54A54ALA00.0520.01818.0530.0250.0250.0000.0000.0000.000
55A55ASN0-0.061-0.02219.493-0.077-0.0770.0000.0000.0000.000
56A56GLY00.0260.00322.3690.0750.0750.0000.0000.0000.000
57A57GLY00.001-0.00524.009-0.067-0.0670.0000.0000.0000.000
58A58ARG10.7640.83426.102-0.366-0.3660.0000.0000.0000.000
59A59ARG10.9000.94320.918-0.742-0.7420.0000.0000.0000.000
60A60THR00.0130.00424.4700.0190.0190.0000.0000.0000.000
61A61VAL0-0.0120.01218.5660.0270.0270.0000.0000.0000.000
62A62GLN00.0430.04618.659-0.130-0.1300.0000.0000.0000.000
63A63TYR0-0.029-0.04115.0830.2500.2500.0000.0000.0000.000
64A64SER0-0.016-0.00714.443-0.161-0.1610.0000.0000.0000.000
65A65GLY00.0370.01812.4940.5270.5270.0000.0000.0000.000
66A66SER0-0.029-0.01811.614-0.418-0.4180.0000.0000.0000.000
67A67PHE00.034-0.00312.8960.4550.4550.0000.0000.0000.000
68A68ASN0-0.041-0.01414.966-0.050-0.0500.0000.0000.0000.000
69A69PRO00.0060.01516.5560.0550.0550.0000.0000.0000.000
70A70SER0-0.007-0.00718.632-0.133-0.1330.0000.0000.0000.000
71A71GLY00.0410.00521.231-0.095-0.0950.0000.0000.0000.000
72A72ASN00.0150.00923.1080.1310.1310.0000.0000.0000.000
73A73ALA00.0450.03218.7410.0680.0680.0000.0000.0000.000
74A74TYR0-0.005-0.01019.571-0.099-0.0990.0000.0000.0000.000
75A75LEU0-0.0030.01314.9210.1980.1980.0000.0000.0000.000
76A76ALA00.015-0.01318.131-0.180-0.1800.0000.0000.0000.000
77A77LEU00.0190.02218.6160.1140.1140.0000.0000.0000.000
78A78TYR0-0.029-0.04219.209-0.099-0.0990.0000.0000.0000.000
79A79GLY00.0370.00920.4910.0380.0380.0000.0000.0000.000
80A80TRP00.0220.01322.715-0.073-0.0730.0000.0000.0000.000
81A81THR0-0.0230.00125.6640.0000.0000.0000.0000.0000.000
82A82SER00.0420.02228.936-0.004-0.0040.0000.0000.0000.000
83A83ASN0-0.045-0.00931.6600.0000.0000.0000.0000.0000.000
84A84PRO00.0750.04034.643-0.005-0.0050.0000.0000.0000.000
85A85LEU0-0.035-0.02329.4530.0160.0160.0000.0000.0000.000
86A86VAL0-0.059-0.02629.8700.0040.0040.0000.0000.0000.000
87A87GLU-1-0.771-0.83824.7400.6160.6160.0000.0000.0000.000
88A88TYR0-0.026-0.04924.249-0.019-0.0190.0000.0000.0000.000
89A89TYR0-0.015-0.02822.1170.0490.0490.0000.0000.0000.000
90A90ILE0-0.039-0.01623.628-0.076-0.0760.0000.0000.0000.000
91A91VAL0-0.003-0.00522.6050.1310.1310.0000.0000.0000.000
92A92ASP-1-0.728-0.82020.8431.3501.3500.0000.0000.0000.000
93A93ASN00.000-0.01119.717-0.156-0.1560.0000.0000.0000.000
94A94TRP00.0600.01821.6050.0070.0070.0000.0000.0000.000
95A95GLY00.0140.01222.2830.0610.0610.0000.0000.0000.000
96A96THR0-0.046-0.03722.885-0.036-0.0360.0000.0000.0000.000
97A97TYR00.0070.01326.018-0.068-0.0680.0000.0000.0000.000
98A98ARG10.7760.88126.285-0.717-0.7170.0000.0000.0000.000
99A99PRO00.0190.02025.471-0.057-0.0570.0000.0000.0000.000
100A100THR0-0.035-0.02928.518-0.020-0.0200.0000.0000.0000.000
101A101GLY00.0300.00632.101-0.002-0.0020.0000.0000.0000.000
102A102GLU-1-0.850-0.91734.6600.3520.3520.0000.0000.0000.000
103A103TYR0-0.017-0.01236.4540.0040.0040.0000.0000.0000.000
104A104LYS10.8360.90837.161-0.395-0.3950.0000.0000.0000.000
105A105GLY00.0260.02738.174-0.021-0.0210.0000.0000.0000.000
106A106THR0-0.050-0.02735.3570.0210.0210.0000.0000.0000.000
107A107VAL00.0230.01531.458-0.029-0.0290.0000.0000.0000.000
108A108THR0-0.018-0.02132.8380.0310.0310.0000.0000.0000.000
109A109SER00.007-0.02228.723-0.059-0.0590.0000.0000.0000.000
110A110ASP-1-0.796-0.84926.1150.9590.9590.0000.0000.0000.000
111A111GLY00.0320.01427.3430.0770.0770.0000.0000.0000.000
112A112GLY0-0.041-0.02529.0420.0170.0170.0000.0000.0000.000
113A113THR00.0170.01629.991-0.029-0.0290.0000.0000.0000.000
114A114TYR0-0.076-0.04724.9780.0330.0330.0000.0000.0000.000
115A115ASP-1-0.746-0.84931.1580.6020.6020.0000.0000.0000.000
116A116ILE0-0.019-0.00631.7620.0440.0440.0000.0000.0000.000
117A117TYR00.008-0.00631.390-0.020-0.0200.0000.0000.0000.000
118A118LYS10.8870.94732.816-0.327-0.3270.0000.0000.0000.000
119A119THR00.005-0.00931.4260.0020.0020.0000.0000.0000.000
120A120THR0-0.009-0.02234.130-0.003-0.0030.0000.0000.0000.000
121A121ARG10.8840.96228.222-0.468-0.4680.0000.0000.0000.000
122A122VAL00.0750.02833.649-0.022-0.0220.0000.0000.0000.000
123A123ASN0-0.017-0.01135.4120.0060.0060.0000.0000.0000.000
124A124LYS10.8360.91230.301-0.280-0.2800.0000.0000.0000.000
125A125PRO00.0410.01226.794-0.023-0.0230.0000.0000.0000.000
126A126SER00.006-0.00426.9100.0440.0440.0000.0000.0000.000
127A127VAL00.0390.02123.297-0.039-0.0390.0000.0000.0000.000
128A128GLU-1-0.847-0.90125.8940.1040.1040.0000.0000.0000.000
129A129GLY00.0130.01128.225-0.032-0.0320.0000.0000.0000.000
130A130THR0-0.041-0.02029.6560.0400.0400.0000.0000.0000.000
131A131ARG10.9010.96332.042-0.133-0.1330.0000.0000.0000.000
132A132THR00.0220.01433.8650.0220.0220.0000.0000.0000.000
133A133PHE0-0.025-0.00328.849-0.021-0.0210.0000.0000.0000.000
134A134ASP-1-0.765-0.86433.5540.3460.3460.0000.0000.0000.000
135A135GLN0-0.007-0.01427.624-0.008-0.0080.0000.0000.0000.000
136A136TYR0-0.056-0.05529.855-0.018-0.0180.0000.0000.0000.000
137A137TRP00.015-0.00425.2530.0880.0880.0000.0000.0000.000
138A138SER00.0040.01027.957-0.072-0.0720.0000.0000.0000.000
139A139VAL0-0.017-0.00727.0350.0840.0840.0000.0000.0000.000
140A140ARG10.8770.96025.244-1.170-1.1700.0000.0000.0000.000
141A141GLN0-0.038-0.04228.1100.0080.0080.0000.0000.0000.000
142A142SER0-0.023-0.00828.932-0.001-0.0010.0000.0000.0000.000
143A143LYS10.8430.94023.669-1.282-1.2820.0000.0000.0000.000
144A144ARG10.8110.88721.988-1.407-1.4070.0000.0000.0000.000
145A145THR0-0.016-0.00816.005-0.010-0.0100.0000.0000.0000.000
146A146GLY00.0160.01517.8600.0830.0830.0000.0000.0000.000
147A147GLY0-0.034-0.01518.592-0.200-0.2000.0000.0000.0000.000
148A148THR0-0.013-0.02720.3140.0990.0990.0000.0000.0000.000
149A149ILE0-0.044-0.02020.756-0.013-0.0130.0000.0000.0000.000
150A150THR00.010-0.02123.804-0.018-0.0180.0000.0000.0000.000
151A151THR0-0.005-0.00923.894-0.064-0.0640.0000.0000.0000.000
152A152GLY00.0000.00126.762-0.038-0.0380.0000.0000.0000.000
153A153ASN00.0350.00930.179-0.069-0.0690.0000.0000.0000.000
154A154HIS00.0200.01727.479-0.051-0.0510.0000.0000.0000.000
155A155PHE00.011-0.00126.122-0.033-0.0330.0000.0000.0000.000
156A156ASP-1-0.772-0.83531.8960.4020.4020.0000.0000.0000.000
157A157ALA0-0.009-0.00434.168-0.030-0.0300.0000.0000.0000.000
158A158TRP00.015-0.01927.349-0.028-0.0280.0000.0000.0000.000
159A159ALA00.0170.01835.093-0.028-0.0280.0000.0000.0000.000
160A160ARG10.8810.93537.469-0.353-0.3530.0000.0000.0000.000
161A161ALA0-0.0090.00337.682-0.021-0.0210.0000.0000.0000.000
162A162GLY0-0.0180.00139.732-0.004-0.0040.0000.0000.0000.000
163A163MET0-0.082-0.02633.350-0.011-0.0110.0000.0000.0000.000
164A164PRO00.0260.01735.3160.0240.0240.0000.0000.0000.000
165A165LEU0-0.0060.00629.5770.0020.0020.0000.0000.0000.000
166A166GLY00.0080.01632.327-0.025-0.0250.0000.0000.0000.000
167A167ASN0-0.003-0.00431.8120.0310.0310.0000.0000.0000.000
168A168PHE00.0300.01926.5620.0040.0040.0000.0000.0000.000
169A169SER0-0.043-0.04526.626-0.010-0.0100.0000.0000.0000.000
170A170TYR0-0.061-0.04423.990-0.055-0.0550.0000.0000.0000.000
171A171TYR00.0610.03918.9490.0730.0730.0000.0000.0000.000
172A172MET0-0.0410.00819.9160.0030.0030.0000.0000.0000.000
173A173ILE0-0.022-0.00115.1110.0050.0050.0000.0000.0000.000
174A174MET00.0030.01814.735-0.179-0.1790.0000.0000.0000.000
175A175ALA00.0050.01814.0900.4660.4660.0000.0000.0000.000
176A176THR0-0.019-0.00412.9610.1880.1880.0000.0000.0000.000
177A177GLU-1-0.776-0.87415.0730.9690.9690.0000.0000.0000.000
178A178GLY00.004-0.00117.9330.1200.1200.0000.0000.0000.000
179A179TYR0-0.036-0.02419.078-0.133-0.1330.0000.0000.0000.000
180A180GLN00.010-0.00122.5820.0150.0150.0000.0000.0000.000
181A181SER0-0.043-0.00820.6380.0180.0180.0000.0000.0000.000
182A182SER00.0190.01418.440-0.011-0.0110.0000.0000.0000.000
183A183GLY00.008-0.01216.291-0.082-0.0820.0000.0000.0000.000
184A184SER0-0.035-0.00511.3100.1590.1590.0000.0000.0000.000
185A185SER00.0040.00110.752-0.310-0.3100.0000.0000.0000.000
186A186SER00.0180.0117.4571.7801.7800.0000.0000.0000.000
187A187ILE00.0010.0138.622-1.236-1.2360.0000.0000.0000.000
188A188ASN00.0290.0109.0251.1621.1620.0000.0000.0000.000
189A189VAL0-0.044-0.01411.006-0.627-0.6270.0000.0000.0000.000
190A190GLY00.0470.01113.6300.0430.0430.0000.0000.0000.000
191A191GLY-1-0.751-0.84616.4940.9290.9290.0000.0000.0000.000