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: 2MRRR

Calculation Name: 2JEM-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JEM

Chain ID: A

ChEMBL ID:

UniProt ID: Q7X4S4

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3009170.917634
FMO2-HF: Nuclear repulsion 2919178.974234
FMO2-HF: Total energy -89991.9434
FMO2-MP2: Total energy -90260.467438


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:30:ALA)


Summations of interaction energy for fragment #1(A:30: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.
-62.424-60.36712.512-8.253-6.317-0.084
Interaction energy analysis for fragmet #1(A:30:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.810 / q_NPA : 0.893
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].
3A32SER0-0.042-0.0193.8542.2454.030-0.021-0.940-0.823-0.002
10A39LEU0-0.0130.0172.835-2.821-2.3230.298-0.182-0.615-0.001
37A66TYR0-0.014-0.0384.194-5.964-5.746-0.001-0.069-0.1480.000
38A67HIS0-0.035-0.0222.9803.7975.0360.012-0.512-0.740-0.002
39A68ASN0-0.067-0.0351.736-64.085-65.90412.225-6.523-3.882-0.079
40A69SER00.0260.0044.0006.3816.517-0.001-0.027-0.1090.000
4A33SER00.0340.0186.7030.1630.1630.0000.0000.0000.000
5A34ASN0-0.0140.01310.5302.9252.9250.0000.0000.0000.000
6A35PRO00.0410.01012.775-1.094-1.0940.0000.0000.0000.000
7A36SER0-0.039-0.02214.448-0.044-0.0440.0000.0000.0000.000
8A37ASP-1-0.735-0.8498.763-27.162-27.1620.0000.0000.0000.000
9A38LYS10.8700.9319.14519.93919.9390.0000.0000.0000.000
11A40TYR0-0.006-0.0206.1182.2892.2890.0000.0000.0000.000
12A41PHE00.0180.0106.594-3.168-3.1680.0000.0000.0000.000
13A42LYS10.8710.9238.51224.23124.2310.0000.0000.0000.000
14A43ASN00.000-0.00311.6890.5770.5770.0000.0000.0000.000
15A44LYS10.9160.96810.94422.99322.9930.0000.0000.0000.000
16A45LYS10.8840.97612.43917.30017.3000.0000.0000.0000.000
17A46TYR0-0.030-0.03011.5591.7061.7060.0000.0000.0000.000
18A47TYR00.015-0.0049.505-1.227-1.2270.0000.0000.0000.000
19A48ILE00.0240.0326.6842.1702.1700.0000.0000.0000.000
20A49PHE0-0.001-0.0159.363-1.064-1.0640.0000.0000.0000.000
21A50ASN00.032-0.00611.1370.7610.7610.0000.0000.0000.000
22A51ASN0-0.062-0.02612.7691.5411.5410.0000.0000.0000.000
23A52VAL00.0250.01415.5170.6270.6270.0000.0000.0000.000
24A53TRP0-0.044-0.04418.1450.4480.4480.0000.0000.0000.000
25A54GLY00.015-0.00221.8680.6330.6330.0000.0000.0000.000
26A55ALA0-0.008-0.00719.9120.1470.1470.0000.0000.0000.000
27A56ASP-1-0.907-0.94921.797-12.598-12.5980.0000.0000.0000.000
28A57GLN0-0.038-0.01225.1740.5840.5840.0000.0000.0000.000
29A58VAL0-0.041-0.01323.9420.3490.3490.0000.0000.0000.000
30A59SER00.0240.00924.211-0.428-0.4280.0000.0000.0000.000
31A60GLY00.010-0.00122.7180.0970.0970.0000.0000.0000.000
32A61TRP0-0.0120.00315.931-0.870-0.8700.0000.0000.0000.000
33A62TRP00.009-0.00213.482-0.582-0.5820.0000.0000.0000.000
34A63GLN0-0.001-0.01513.7051.5001.5000.0000.0000.0000.000
35A64THR0-0.0100.0008.0780.2410.2410.0000.0000.0000.000
36A65ILE0-0.0100.0047.1180.4140.4140.0000.0000.0000.000
41A70ASP-1-0.834-0.9347.166-29.490-29.4900.0000.0000.0000.000
42A71SER0-0.045-0.0219.9332.7322.7320.0000.0000.0000.000
43A72ASP-1-0.872-0.9297.837-35.287-35.2870.0000.0000.0000.000
44A73MET0-0.0080.0156.563-7.112-7.1120.0000.0000.0000.000
45A74GLY00.0100.0157.6274.9984.9980.0000.0000.0000.000
46A75TRP00.003-0.0178.830-3.891-3.8910.0000.0000.0000.000
47A76VAL0-0.0010.00610.3511.8601.8600.0000.0000.0000.000
48A77TRP00.018-0.00112.874-1.020-1.0200.0000.0000.0000.000
49A78ASN00.0100.02516.1581.0651.0650.0000.0000.0000.000
50A79TRP00.032-0.00118.3350.3760.3760.0000.0000.0000.000
51A80PRO0-0.0050.01022.1060.5370.5370.0000.0000.0000.000
52A81SER00.004-0.01125.2340.4750.4750.0000.0000.0000.000
53A82ASN00.018-0.00127.694-0.240-0.2400.0000.0000.0000.000
54A83THR00.0290.02829.9130.1910.1910.0000.0000.0000.000
55A84SER00.013-0.00429.480-0.363-0.3630.0000.0000.0000.000
56A85THR0-0.005-0.00128.166-0.010-0.0100.0000.0000.0000.000
57A86VAL00.0050.01122.904-0.189-0.1890.0000.0000.0000.000
58A87LYS10.8130.90322.38412.11312.1130.0000.0000.0000.000
59A88ALA00.0360.01817.866-0.419-0.4190.0000.0000.0000.000
60A89TYR00.0330.03818.8540.5680.5680.0000.0000.0000.000
61A90PRO0-0.0340.02813.803-0.390-0.3900.0000.0000.0000.000
62A91SER00.028-0.01813.8071.0311.0310.0000.0000.0000.000
63A92ILE0-0.049-0.01911.321-1.820-1.8200.0000.0000.0000.000
64A93VAL00.0040.00113.1941.7381.7380.0000.0000.0000.000
65A94SER00.014-0.00714.361-1.264-1.2640.0000.0000.0000.000
66A95GLY00.0060.00917.0760.9320.9320.0000.0000.0000.000
67A96TRP0-0.040-0.02218.614-0.822-0.8220.0000.0000.0000.000
68A97HIS10.8420.87717.87515.58915.5890.0000.0000.0000.000
69A98TRP0-0.0060.00819.369-0.720-0.7200.0000.0000.0000.000
70A99THR0-0.044-0.01817.668-0.579-0.5790.0000.0000.0000.000
71A100GLU-1-0.829-0.89320.926-10.933-10.9330.0000.0000.0000.000
72A101GLY0-0.0040.00821.937-0.344-0.3440.0000.0000.0000.000
73A102TYR00.015-0.00120.466-0.271-0.2710.0000.0000.0000.000
74A103THR0-0.024-0.01814.8140.2670.2670.0000.0000.0000.000
75A104ALA00.0410.02617.3270.6900.6900.0000.0000.0000.000
76A105GLY00.0150.00017.725-0.675-0.6750.0000.0000.0000.000
77A106SER0-0.031-0.03218.3270.2290.2290.0000.0000.0000.000
78A107GLY0-0.022-0.00719.7370.1500.1500.0000.0000.0000.000
79A108PHE0-0.050-0.01120.6460.5860.5860.0000.0000.0000.000
80A109PRO0-0.0150.00323.749-0.230-0.2300.0000.0000.0000.000
81A110THR0-0.009-0.01226.5520.3810.3810.0000.0000.0000.000
82A111ARG10.8910.94728.8098.5668.5660.0000.0000.0000.000
83A112LEU00.0030.00531.5370.0060.0060.0000.0000.0000.000
84A113SER0-0.019-0.03333.9460.1100.1100.0000.0000.0000.000
85A114ASP-1-0.925-0.95433.535-8.824-8.8240.0000.0000.0000.000
86A115GLN0-0.073-0.04834.552-0.065-0.0650.0000.0000.0000.000
87A116LYS10.9540.99729.7199.9059.9050.0000.0000.0000.000
88A117ASN0-0.041-0.02029.3450.1550.1550.0000.0000.0000.000
89A118ILE00.016-0.00124.592-0.280-0.2800.0000.0000.0000.000
90A119ASN00.0040.01325.1620.1540.1540.0000.0000.0000.000
91A120THR0-0.002-0.01721.118-0.370-0.3700.0000.0000.0000.000
92A121LYS10.8670.93418.88216.79616.7960.0000.0000.0000.000
93A122VAL00.0420.02916.474-0.987-0.9870.0000.0000.0000.000
94A123SER0-0.051-0.04616.9871.3171.3170.0000.0000.0000.000
95A124TYR0-0.021-0.01615.957-1.340-1.3400.0000.0000.0000.000
96A125SER0-0.023-0.01416.2021.1501.1500.0000.0000.0000.000
97A126ILE0-0.001-0.00616.414-1.352-1.3520.0000.0000.0000.000
98A127SER0-0.0170.01117.8451.1301.1300.0000.0000.0000.000
99A128ALA00.0380.01318.591-0.824-0.8240.0000.0000.0000.000
100A129ASN0-0.0090.01320.9450.6530.6530.0000.0000.0000.000
101A130GLY00.0280.01323.722-0.360-0.3600.0000.0000.0000.000
102A131THR0-0.018-0.01125.8220.3470.3470.0000.0000.0000.000
103A132TYR0-0.016-0.00921.978-0.496-0.4960.0000.0000.0000.000
104A133ASN0-0.047-0.02822.920-0.015-0.0150.0000.0000.0000.000
105A134ALA00.0300.00619.753-0.857-0.8570.0000.0000.0000.000
106A135ALA0-0.0100.00320.8180.8030.8030.0000.0000.0000.000
107A136TYR00.0110.01020.279-0.995-0.9950.0000.0000.0000.000
108A137ASP-1-0.779-0.88121.087-12.727-12.7270.0000.0000.0000.000
109A138ILE0-0.030-0.01821.936-0.431-0.4310.0000.0000.0000.000
110A139TRP00.0310.02421.9810.8360.8360.0000.0000.0000.000
111A140LEU0-0.010-0.01225.653-0.023-0.0230.0000.0000.0000.000
112A141HIS00.0590.05925.9690.1730.1730.0000.0000.0000.000
113A142ASN00.024-0.00130.9150.0390.0390.0000.0000.0000.000
114A143THR0-0.023-0.00330.1730.2190.2190.0000.0000.0000.000
115A144ASN00.0190.00429.697-0.204-0.2040.0000.0000.0000.000
116A145LYS10.9340.95828.4809.1069.1060.0000.0000.0000.000
117A146ALA00.0070.01325.9610.2790.2790.0000.0000.0000.000
118A147SER00.035-0.01025.749-0.375-0.3750.0000.0000.0000.000
119A148TRP0-0.004-0.00223.177-0.262-0.2620.0000.0000.0000.000
120A149ASP-1-0.865-0.93324.507-10.551-10.5510.0000.0000.0000.000
121A150SER0-0.052-0.02327.4390.5150.5150.0000.0000.0000.000
122A151ALA00.0320.01527.895-0.348-0.3480.0000.0000.0000.000
123A152PRO0-0.040-0.00826.5840.2370.2370.0000.0000.0000.000
124A153THR0-0.011-0.03029.3700.2470.2470.0000.0000.0000.000
125A154ASP-1-0.832-0.88330.898-8.913-8.9130.0000.0000.0000.000
126A155GLN00.0290.01525.0280.1290.1290.0000.0000.0000.000
127A156ILE0-0.054-0.03427.4730.4710.4710.0000.0000.0000.000
128A157MET00.0230.03324.453-0.270-0.2700.0000.0000.0000.000
129A158ILE0-0.025-0.01825.4460.5150.5150.0000.0000.0000.000
130A159TRP0-0.004-0.01024.821-0.682-0.6820.0000.0000.0000.000
131A160LEU0-0.016-0.01921.4310.5210.5210.0000.0000.0000.000
132A161ASN0-0.0150.00223.0050.3680.3680.0000.0000.0000.000
133A162ASN00.013-0.01325.029-0.358-0.3580.0000.0000.0000.000
134A163THR00.0090.00225.2670.2570.2570.0000.0000.0000.000
135A164ASN0-0.021-0.02327.3960.0820.0820.0000.0000.0000.000
136A165ALA00.0410.03927.7200.1690.1690.0000.0000.0000.000
137A166GLY0-0.007-0.00929.7870.3150.3150.0000.0000.0000.000
138A167PRO0-0.0170.00430.765-0.271-0.2710.0000.0000.0000.000
139A168ALA00.0400.02631.7370.2600.2600.0000.0000.0000.000
140A169GLY0-0.009-0.01433.604-0.036-0.0360.0000.0000.0000.000
141A170SER0-0.024-0.00636.8800.1180.1180.0000.0000.0000.000
142A171TYR0-0.036-0.03637.985-0.089-0.0890.0000.0000.0000.000
143A172VAL0-0.048-0.01539.4900.1990.1990.0000.0000.0000.000
144A173GLU-1-0.748-0.83339.939-7.541-7.5410.0000.0000.0000.000
145A174THR0-0.016-0.00937.588-0.309-0.3090.0000.0000.0000.000
146A175VAL00.0030.02136.0190.2070.2070.0000.0000.0000.000
147A176SER0-0.008-0.00536.096-0.353-0.3530.0000.0000.0000.000
148A177ILE00.0410.01232.3870.1540.1540.0000.0000.0000.000
149A178GLY00.0530.03030.995-0.274-0.2740.0000.0000.0000.000
150A179GLY0-0.012-0.00231.246-0.216-0.2160.0000.0000.0000.000
151A180HIS00.0190.03227.9110.0830.0830.0000.0000.0000.000
152A181SER00.003-0.00132.3900.3040.3040.0000.0000.0000.000
153A182TRP0-0.048-0.04027.248-0.401-0.4010.0000.0000.0000.000
154A183LYS10.9260.97533.4629.8049.8040.0000.0000.0000.000
155A184VAL00.0000.00034.193-0.348-0.3480.0000.0000.0000.000
156A185TYR00.026-0.00134.1150.2290.2290.0000.0000.0000.000
157A186LYS10.9350.98134.9818.0408.0400.0000.0000.0000.000
158A187GLY00.0220.00035.6410.2140.2140.0000.0000.0000.000
159A188TYR0-0.037-0.01035.114-0.022-0.0220.0000.0000.0000.000
160A189ILE0-0.0140.00329.8440.0340.0340.0000.0000.0000.000
161A190ASP-1-0.859-0.93233.209-8.748-8.7480.0000.0000.0000.000
162A191ALA0-0.031-0.01830.078-0.287-0.2870.0000.0000.0000.000
163A192GLY00.0210.02231.665-0.152-0.1520.0000.0000.0000.000
164A193GLY0-0.031-0.03334.318-0.071-0.0710.0000.0000.0000.000
165A194GLY0-0.0070.00136.2870.0950.0950.0000.0000.0000.000
166A195LYS10.8630.93430.8649.8519.8510.0000.0000.0000.000
167A196GLY00.0460.01832.422-0.028-0.0280.0000.0000.0000.000
168A197TRP0-0.055-0.01627.5490.0780.0780.0000.0000.0000.000
169A198ASN0-0.047-0.03432.9700.2590.2590.0000.0000.0000.000
170A199VAL00.0230.00929.885-0.321-0.3210.0000.0000.0000.000
171A200PHE00.002-0.00331.3870.4350.4350.0000.0000.0000.000
172A201SER00.0070.00230.265-0.530-0.5300.0000.0000.0000.000
173A202PHE00.0010.00430.0400.4130.4130.0000.0000.0000.000
174A203ILE00.0180.00929.463-0.420-0.4200.0000.0000.0000.000
175A204ARG10.8530.92628.14311.31811.3180.0000.0000.0000.000
176A205THR0-0.042-0.03530.875-0.043-0.0430.0000.0000.0000.000
177A206ALA00.0350.02031.7880.1570.1570.0000.0000.0000.000
178A207ASN00.0180.01726.2350.0100.0100.0000.0000.0000.000
179A208THR0-0.027-0.02024.6320.2830.2830.0000.0000.0000.000
180A209GLN00.0770.05521.240-0.803-0.8030.0000.0000.0000.000
181A210SER0-0.033-0.00920.532-0.721-0.7210.0000.0000.0000.000
182A211ALA00.0040.00321.9480.7350.7350.0000.0000.0000.000
183A212ASN0-0.008-0.00122.441-0.890-0.8900.0000.0000.0000.000
184A213LEU00.0060.00724.6130.6170.6170.0000.0000.0000.000
185A214ASN00.0910.04925.930-0.580-0.5800.0000.0000.0000.000
186A215ILE00.023-0.00224.5950.3660.3660.0000.0000.0000.000
187A216ARG10.8860.95028.1039.6679.6670.0000.0000.0000.000
188A217ASP-1-0.891-0.94031.318-9.415-9.4150.0000.0000.0000.000
189A218PHE00.007-0.00329.2670.2720.2720.0000.0000.0000.000
190A219THR0-0.001-0.00930.4990.2770.2770.0000.0000.0000.000
191A220ASN00.0400.00733.2270.2220.2220.0000.0000.0000.000
192A221TYR00.004-0.02635.6940.1780.1780.0000.0000.0000.000
193A222LEU0-0.004-0.01832.8860.2310.2310.0000.0000.0000.000
194A223ALA0-0.044-0.00637.0220.1860.1860.0000.0000.0000.000
195A224ASP-1-0.818-0.90938.842-7.804-7.8040.0000.0000.0000.000
196A225SER0-0.052-0.02840.4780.1350.1350.0000.0000.0000.000
197A226LYS10.8160.90039.4047.7977.7970.0000.0000.0000.000
198A227GLN0-0.0240.01141.5990.1670.1670.0000.0000.0000.000
199A228TRP00.010-0.00837.660-0.041-0.0410.0000.0000.0000.000
200A229LEU0-0.033-0.00533.074-0.095-0.0950.0000.0000.0000.000
201A230SER00.0430.03237.4380.0530.0530.0000.0000.0000.000
202A231LYS10.8720.91136.6618.0108.0100.0000.0000.0000.000
203A232THR0-0.0010.00337.100-0.121-0.1210.0000.0000.0000.000
204A233LYS10.8430.91633.0748.8078.8070.0000.0000.0000.000
205A234TYR00.027-0.00129.5150.1370.1370.0000.0000.0000.000
206A235VAL0-0.0040.00525.305-0.043-0.0430.0000.0000.0000.000
207A236SER0-0.014-0.05024.958-0.020-0.0200.0000.0000.0000.000
208A237SER0-0.022-0.03319.958-0.601-0.6010.0000.0000.0000.000
209A238VAL0-0.029-0.01320.5540.6750.6750.0000.0000.0000.000
210A239GLU-1-0.785-0.84417.633-16.691-16.6910.0000.0000.0000.000
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