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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: XYQQ2

Calculation Name: 4JER-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JER

Chain ID: A

ChEMBL ID:

UniProt ID: A0A384

Base Structure: X-ray

Registration Date: 2018-02-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181208
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1901575.129883
FMO2-HF: Nuclear repulsion 1829862.547227
FMO2-HF: Total energy -71712.582656
FMO2-MP2: Total energy -71917.891479


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:1:ACE)


Summations of interaction energy for fragment #1(A:1:ACE)
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.
-0.0571.7332.797-2.601-1.986-0.02
Interaction energy analysis for fragmet #1(A:1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.026
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].
3A3THR0-0.0140.0053.8390.8151.502-0.010-0.272-0.4050.000
4A4THR0-0.035-0.0086.4750.2200.2200.0000.0000.0000.000
5A5ILE00.0050.0018.8750.0800.0800.0000.0000.0000.000
6A6GLN0-0.0070.01411.2500.0390.0390.0000.0000.0000.000
7A7TYR00.2790.22615.214-0.003-0.0030.0000.0000.0000.000
8A8ASN00.0340.02118.8130.0120.0120.0000.0000.0000.000
9A9SER00.0460.01522.256-0.008-0.0080.0000.0000.0000.000
10A10ASN00.0070.00424.2890.0000.0000.0000.0000.0000.000
11A11TYR0-0.028-0.01422.9310.0040.0040.0000.0000.0000.000
12A12ALA00.0140.00922.868-0.014-0.0140.0000.0000.0000.000
13A13ASP-1-0.854-0.92123.745-0.109-0.1090.0000.0000.0000.000
14A14TYR0-0.108-0.06223.927-0.001-0.0010.0000.0000.0000.000
15A15SER00.0320.03621.476-0.008-0.0080.0000.0000.0000.000
16A16ILE00.0210.00515.6140.0100.0100.0000.0000.0000.000
17A17SER00.029-0.00119.9080.0140.0140.0000.0000.0000.000
18A18SER0-0.059-0.02622.7220.0110.0110.0000.0000.0000.000
19A19TYR0-0.006-0.02221.5570.0100.0100.0000.0000.0000.000
20A20LEU00.0370.01018.7950.0120.0120.0000.0000.0000.000
21A21ARG10.9520.98723.3020.1130.1130.0000.0000.0000.000
22A22GLU-1-0.897-0.93326.776-0.082-0.0820.0000.0000.0000.000
23A23TRP0-0.0010.00924.5220.0050.0050.0000.0000.0000.000
24A24ALA00.0340.01025.6090.0080.0080.0000.0000.0000.000
25A25ASN0-0.039-0.03227.3060.0060.0060.0000.0000.0000.000
26A26ASN0-0.085-0.03330.1110.0100.0100.0000.0000.0000.000
27A27PHE0-0.0310.00927.0800.0060.0060.0000.0000.0000.000
28A28GLY00.0580.03729.8730.0060.0060.0000.0000.0000.000
29A29ASP-1-0.827-0.91230.996-0.059-0.0590.0000.0000.0000.000
30A30ILE00.0410.01529.8440.0060.0060.0000.0000.0000.000
31A31ASP-1-0.885-0.93832.481-0.046-0.0460.0000.0000.0000.000
32A32GLN0-0.072-0.03934.9070.0030.0030.0000.0000.0000.000
33A33ALA00.0100.03035.9170.0020.0020.0000.0000.0000.000
34A34PRO00.0020.00037.6600.0010.0010.0000.0000.0000.000
35A35ALA0-0.038-0.03838.5460.0000.0000.0000.0000.0000.000
36A36GLU-1-0.942-0.97938.788-0.022-0.0220.0000.0000.0000.000
37A37THR0-0.007-0.01038.4140.0010.0010.0000.0000.0000.000
38A38LYS10.8760.96733.6430.0330.0330.0000.0000.0000.000
39A39ASP-1-0.804-0.89530.015-0.031-0.0310.0000.0000.0000.000
40A40ARG10.9010.92530.3730.0210.0210.0000.0000.0000.000
41A41GLY00.0360.04226.786-0.003-0.0030.0000.0000.0000.000
42A42SER0-0.114-0.06626.2660.0060.0060.0000.0000.0000.000
43A43PHE00.0240.01421.927-0.004-0.0040.0000.0000.0000.000
44A44SER0-0.019-0.00823.2520.0050.0050.0000.0000.0000.000
45A45GLY00.0820.04221.8200.0000.0000.0000.0000.0000.000
46A46SER0-0.015-0.00822.2610.0080.0080.0000.0000.0000.000
47A47SER0-0.032-0.00324.561-0.005-0.0050.0000.0000.0000.000
48A48THR0-0.038-0.03026.205-0.001-0.0010.0000.0000.0000.000
49A49LEU00.0260.01826.918-0.002-0.0020.0000.0000.0000.000
50A50PHE0-0.023-0.01927.0650.0000.0000.0000.0000.0000.000
51A51SER0-0.016-0.01522.884-0.001-0.0010.0000.0000.0000.000
52A52GLY00.0070.00121.6050.0010.0010.0000.0000.0000.000
53A53THR00.0260.02117.411-0.008-0.0080.0000.0000.0000.000
54A54GLN00.0160.01717.404-0.007-0.0070.0000.0000.0000.000
55A55TYR0-0.048-0.04319.7540.0020.0020.0000.0000.0000.000
56A56ALA00.0090.01520.973-0.010-0.0100.0000.0000.0000.000
57A57ILE0-0.045-0.02623.5250.0060.0060.0000.0000.0000.000
58A58GLY00.0520.01725.667-0.007-0.0070.0000.0000.0000.000
59A59SER0-0.018-0.01228.4210.0030.0030.0000.0000.0000.000
60A60SER0-0.014-0.01530.8050.0050.0050.0000.0000.0000.000
61A61HIS0-0.068-0.03933.6130.0060.0060.0000.0000.0000.000
62A62SER0-0.074-0.02735.6710.0010.0010.0000.0000.0000.000
63A63ASN0-0.0120.00632.8230.0040.0040.0000.0000.0000.000
64A64PRO00.0360.01530.7130.0000.0000.0000.0000.0000.000
65A65GLU-1-0.875-0.94927.236-0.066-0.0660.0000.0000.0000.000
66A66GLY00.0370.00925.6880.0060.0060.0000.0000.0000.000
67A67MET0-0.063-0.01920.025-0.016-0.0160.0000.0000.0000.000
68A68ILE0-0.003-0.00118.5610.0130.0130.0000.0000.0000.000
69A69ALA00.0000.00416.422-0.021-0.0210.0000.0000.0000.000
70A70GLU-1-0.883-0.95014.2730.0330.0330.0000.0000.0000.000
71A71GLY00.0450.01413.213-0.029-0.0290.0000.0000.0000.000
72A72ASP-1-0.977-0.97714.0250.0790.0790.0000.0000.0000.000
73A73LEU0-0.024-0.00216.003-0.019-0.0190.0000.0000.0000.000
74A74LYS10.9410.96918.956-0.009-0.0090.0000.0000.0000.000
75A75TYR0-0.011-0.05522.175-0.011-0.0110.0000.0000.0000.000
76A76SER0-0.031-0.00225.1410.0050.0050.0000.0000.0000.000
77A77PHE00.0310.02527.9220.0030.0030.0000.0000.0000.000
78A78MET0-0.0480.00630.789-0.003-0.0030.0000.0000.0000.000
79A79PRO00.004-0.01833.5860.0020.0020.0000.0000.0000.000
80A80GLN00.041-0.00330.058-0.006-0.0060.0000.0000.0000.000
81A81HIS00.0050.05729.341-0.006-0.0060.0000.0000.0000.000
82A82THR0-0.005-0.01123.681-0.005-0.0050.0000.0000.0000.000
83A83PHE00.0150.00221.2730.0080.0080.0000.0000.0000.000
84A84HIS0-0.040-0.03219.493-0.009-0.0090.0000.0000.0000.000
85A85GLY0-0.005-0.00217.3640.0090.0090.0000.0000.0000.000
86A86GLN00.012-0.0119.129-0.013-0.0130.0000.0000.0000.000
87A87ILE0-0.021-0.02412.8000.0290.0290.0000.0000.0000.000
88A88ASP-1-0.873-0.9368.745-0.048-0.0480.0000.0000.0000.000
89A89THR0-0.020-0.0149.370-0.110-0.1100.0000.0000.0000.000
90A90LEU0-0.031-0.01211.9570.0320.0320.0000.0000.0000.000
91A91GLN0-0.016-0.01814.869-0.016-0.0160.0000.0000.0000.000
92A92PHE00.0350.01417.3470.0100.0100.0000.0000.0000.000
93A93GLY00.030-0.00120.796-0.002-0.0020.0000.0000.0000.000
94A94LYS10.8190.91323.9300.0800.0800.0000.0000.0000.000
95A95ASP-1-0.864-0.93527.366-0.038-0.0380.0000.0000.0000.000
96A96LEU0-0.038-0.01124.2590.0030.0030.0000.0000.0000.000
97A97ALA00.0420.03227.5440.0030.0030.0000.0000.0000.000
98A98THR0-0.080-0.04727.6820.0000.0000.0000.0000.0000.000
99A99ASN00.0320.03623.769-0.005-0.0050.0000.0000.0000.000
100A100ALA00.0270.00328.2770.0000.0000.0000.0000.0000.000
101A101GLY0-0.009-0.00829.8260.0040.0040.0000.0000.0000.000
102A102GLY0-0.023-0.00931.2480.0010.0010.0000.0000.0000.000
103A103PRO00.047-0.00629.1330.0020.0020.0000.0000.0000.000
104A104SER0-0.043-0.01427.5930.0000.0000.0000.0000.0000.000
105A105ALA00.0040.00726.3280.0050.0050.0000.0000.0000.000
106A106GLY00.0350.03223.8830.0030.0030.0000.0000.0000.000
107A107LYS10.8680.92823.8760.0180.0180.0000.0000.0000.000
108A108HIS00.005-0.01223.0260.0000.0000.0000.0000.0000.000
109A109LEU0-0.009-0.00821.291-0.001-0.0010.0000.0000.0000.000
110A110GLU-1-0.929-0.95424.808-0.020-0.0200.0000.0000.0000.000
111A111LYS10.8550.92626.0540.0720.0720.0000.0000.0000.000
112A112ILE0-0.0050.00219.237-0.006-0.0060.0000.0000.0000.000
113A113ASP-1-0.785-0.86522.096-0.088-0.0880.0000.0000.0000.000
114A114ILE0-0.022-0.02216.694-0.008-0.0080.0000.0000.0000.000
115A115THR00.0120.01213.2400.0230.0230.0000.0000.0000.000
116A116PHE0-0.014-0.01011.702-0.034-0.0340.0000.0000.0000.000
117A117ASN0-0.003-0.0158.5040.1370.1370.0000.0000.0000.000
118A118GLU-1-0.848-0.9412.573-0.4730.6302.807-2.329-1.581-0.020
119A119LEU0-0.038-0.0136.024-0.463-0.4630.0000.0000.0000.000
120A120ASP-1-0.879-0.9426.339-0.467-0.4670.0000.0000.0000.000
121A121LEU0-0.0420.0078.3660.0070.0070.0000.0000.0000.000
122A122SER00.0720.03412.1410.0460.0460.0000.0000.0000.000
123A123GLY0-0.008-0.01714.189-0.018-0.0180.0000.0000.0000.000
124A124GLU-1-0.896-0.93617.155-0.012-0.0120.0000.0000.0000.000
125A125PHE0-0.030-0.02820.324-0.005-0.0050.0000.0000.0000.000
126A126ASP-1-0.865-0.93223.915-0.006-0.0060.0000.0000.0000.000
127A127SER0-0.030-0.02126.832-0.003-0.0030.0000.0000.0000.000
128A128GLY0-0.012-0.00130.0460.0000.0000.0000.0000.0000.000
129A129LYS10.8250.91527.9300.0330.0330.0000.0000.0000.000
130A130SER00.0200.00530.8360.0000.0000.0000.0000.0000.000
131A131MET00.0260.00929.864-0.003-0.0030.0000.0000.0000.000
132A132THR0-0.017-0.00929.011-0.003-0.0030.0000.0000.0000.000
133A133GLU-1-0.856-0.91326.853-0.050-0.0500.0000.0000.0000.000
134A134ASN00.027-0.00525.288-0.007-0.0070.0000.0000.0000.000
135A135HIS0-0.100-0.06124.250-0.009-0.0090.0000.0000.0000.000
136A136GLN0-0.050-0.03124.069-0.004-0.0040.0000.0000.0000.000
137A137GLY00.0020.01820.288-0.012-0.0120.0000.0000.0000.000
138A138ASP-1-0.853-0.93215.505-0.224-0.2240.0000.0000.0000.000
139A139MET0-0.0300.00616.262-0.003-0.0030.0000.0000.0000.000
140A140HIS00.0520.04217.7660.0060.0060.0000.0000.0000.000
141A141LYS10.9370.97020.0190.1630.1630.0000.0000.0000.000
142A142SER0-0.026-0.02118.1220.0010.0010.0000.0000.0000.000
143A143VAL00.0390.02018.8000.0040.0040.0000.0000.0000.000
144A144ARG10.8690.92821.2910.0690.0690.0000.0000.0000.000
145A145GLY00.001-0.00323.9420.0070.0070.0000.0000.0000.000
146A146LEU00.0220.00919.8800.0050.0050.0000.0000.0000.000
147A147MET0-0.049-0.00824.3540.0070.0070.0000.0000.0000.000
148A148LYS10.7940.88526.8030.0690.0690.0000.0000.0000.000
149A149GLY00.0100.01628.0090.0030.0030.0000.0000.0000.000
150A150ASN0-0.021-0.01827.172-0.007-0.0070.0000.0000.0000.000
151A151PRO00.0210.00023.105-0.004-0.0040.0000.0000.0000.000
152A152ASP-1-0.862-0.92922.305-0.146-0.1460.0000.0000.0000.000
153A153PRO0-0.018-0.01422.384-0.016-0.0160.0000.0000.0000.000
154A154MET00.0250.01414.980-0.012-0.0120.0000.0000.0000.000
155A155LEU0-0.0110.00117.761-0.039-0.0390.0000.0000.0000.000
156A156GLU-1-0.978-0.98918.778-0.179-0.1790.0000.0000.0000.000
157A157VAL0-0.005-0.00314.560-0.017-0.0170.0000.0000.0000.000
158A158MET0-0.027-0.01613.958-0.045-0.0450.0000.0000.0000.000
159A159LYS10.9470.96914.5060.1740.1740.0000.0000.0000.000
160A160ALA0-0.040-0.00716.302-0.017-0.0170.0000.0000.0000.000
161A161LYS10.8530.9339.3490.6280.6280.0000.0000.0000.000
162A162GLY0-0.028-0.00611.355-0.126-0.1260.0000.0000.0000.000
163A163ILE0-0.022-0.00510.714-0.005-0.0050.0000.0000.0000.000
164A164ASN00.0070.00213.8790.0810.0810.0000.0000.0000.000
165A165VAL00.0350.00217.193-0.005-0.0050.0000.0000.0000.000
166A166ASP-1-0.915-0.95619.128-0.177-0.1770.0000.0000.0000.000
167A167THR0-0.091-0.04319.2820.0150.0150.0000.0000.0000.000
168A168ALA00.1070.04120.716-0.009-0.0090.0000.0000.0000.000
169A169PHE00.5070.43417.240-0.018-0.0180.0000.0000.0000.000
170A170LYS11.0151.04118.9650.0990.0990.0000.0000.0000.000
171A171ASP-1-0.693-0.76520.783-0.145-0.1450.0000.0000.0000.000
172A172LEU00.0640.07015.037-0.014-0.0140.0000.0000.0000.000
173A173SER00.047-0.00413.706-0.016-0.0160.0000.0000.0000.000
174A174ILE00.0780.05210.2040.0320.0320.0000.0000.0000.000
175A175ALA00.2350.21611.484-0.021-0.0210.0000.0000.0000.000
176A176SER00.011-0.01013.8910.0460.0460.0000.0000.0000.000
177A177GLN0-0.029-0.02215.861-0.006-0.0060.0000.0000.0000.000
178A178TYR00.0240.00716.5870.0050.0050.0000.0000.0000.000
179A179PRO0-0.013-0.00919.0540.0010.0010.0000.0000.0000.000
180A180ASP-1-0.869-0.91822.191-0.057-0.0570.0000.0000.0000.000
181A181SER0-0.047-0.03525.7700.0080.0080.0000.0000.0000.000
182A182GLY00.025-0.00527.615-0.003-0.0030.0000.0000.0000.000
183A183TYR0-0.032-0.01325.6740.0010.0010.0000.0000.0000.000
184A184MET00.0040.00624.982-0.001-0.0010.0000.0000.0000.000
185A185NME0-0.0100.01430.746-0.001-0.0010.0000.0000.0000.000
186A201NA+1-0.901-0.44917.8270.2260.2260.0000.0000.0000.000