Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G5ZM1

Calculation Name: 4GJ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GJ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PM74

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2909767.741848
FMO2-HF: Nuclear repulsion 2819714.930491
FMO2-HF: Total energy -90052.811357
FMO2-MP2: Total energy -90314.760535


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-32.446-31.9732.124-14.564-18.036-0.051
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.027
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].
3A4ILE00.0140.0113.721-1.5600.3640.001-0.889-1.0360.001
4A5ILE0-0.011-0.0015.4180.3290.3290.0000.0000.0000.000
5A6PRO0-0.021-0.0088.2820.0870.0870.0000.0000.0000.000
6A7ALA0-0.010-0.00411.3010.0610.0610.0000.0000.0000.000
7A8LEU0-0.063-0.02713.9290.0280.0280.0000.0000.0000.000
8A9ASP-1-0.760-0.85017.704-0.355-0.3550.0000.0000.0000.000
9A10LEU0-0.010-0.01720.2700.0140.0140.0000.0000.0000.000
10A11ILE00.0000.00423.6350.0000.0000.0000.0000.0000.000
11A12ASP-1-0.844-0.89827.169-0.126-0.1260.0000.0000.0000.000
12A13GLY00.0000.00727.8390.0090.0090.0000.0000.0000.000
13A14GLU-1-0.877-0.92327.215-0.148-0.1480.0000.0000.0000.000
14A15VAL0-0.005-0.00620.975-0.013-0.0130.0000.0000.0000.000
15A16VAL0-0.032-0.02922.6510.0120.0120.0000.0000.0000.000
16A17ARG10.8100.87115.1840.3820.3820.0000.0000.0000.000
17A18LEU00.0060.01921.5970.0190.0190.0000.0000.0000.000
18A19VAL0-0.013-0.00421.469-0.030-0.0300.0000.0000.0000.000
19A20LYS10.8270.88619.6510.3250.3250.0000.0000.0000.000
20A21GLY00.0370.01623.333-0.010-0.0100.0000.0000.0000.000
21A22ASP-1-0.927-0.94925.364-0.144-0.1440.0000.0000.0000.000
22A23TYR0-0.012-0.00928.2360.0100.0100.0000.0000.0000.000
23A24GLU-1-0.897-0.92825.834-0.196-0.1960.0000.0000.0000.000
24A25GLN0-0.011-0.02226.3090.0150.0150.0000.0000.0000.000
25A26LYS10.8520.91425.7850.1340.1340.0000.0000.0000.000
26A27LYS10.8530.94022.6390.2280.2280.0000.0000.0000.000
27A28VAL00.0320.00825.103-0.014-0.0140.0000.0000.0000.000
28A29TYR0-0.047-0.05920.7770.0000.0000.0000.0000.0000.000
29A30LYS10.9730.98125.6510.1490.1490.0000.0000.0000.000
30A31TYR0-0.065-0.03521.2810.0150.0150.0000.0000.0000.000
31A32ASN00.0600.02224.806-0.003-0.0030.0000.0000.0000.000
32A33PRO00.0700.02822.385-0.007-0.0070.0000.0000.0000.000
33A34LEU00.0470.03321.665-0.016-0.0160.0000.0000.0000.000
34A35LYS10.9380.96022.4050.1050.1050.0000.0000.0000.000
35A36LYS10.8160.91118.2760.2750.2750.0000.0000.0000.000
36A37PHE00.0610.02115.732-0.020-0.0200.0000.0000.0000.000
37A38LYS10.8040.88317.7730.1010.1010.0000.0000.0000.000
38A39GLU-1-0.883-0.91618.461-0.252-0.2520.0000.0000.0000.000
39A40TYR00.0580.00314.034-0.007-0.0070.0000.0000.0000.000
40A41GLU-1-0.763-0.86914.541-0.160-0.1600.0000.0000.0000.000
41A42LYS10.9190.96216.1760.1390.1390.0000.0000.0000.000
42A43ALA0-0.023-0.00415.1860.0210.0210.0000.0000.0000.000
43A44GLY00.0420.01713.263-0.034-0.0340.0000.0000.0000.000
44A45ALA0-0.0140.00810.8430.0100.0100.0000.0000.0000.000
45A46LYS10.8690.90410.0110.2320.2320.0000.0000.0000.000
46A47GLU-1-0.743-0.8297.950-0.016-0.0160.0000.0000.0000.000
47A48LEU0-0.016-0.00110.684-0.135-0.1350.0000.0000.0000.000
48A49HIS00.0530.02712.4090.0350.0350.0000.0000.0000.000
49A50LEU00.0330.01814.2390.0050.0050.0000.0000.0000.000
50A51VAL00.001-0.00117.0310.0060.0060.0000.0000.0000.000
51A52ASP-1-0.726-0.85419.558-0.149-0.1490.0000.0000.0000.000
52A53LEU0-0.001-0.01421.9130.0070.0070.0000.0000.0000.000
53A54THR0-0.005-0.02124.7230.0030.0030.0000.0000.0000.000
54A55GLY00.0310.00927.0730.0080.0080.0000.0000.0000.000
55A56ALA0-0.085-0.02924.0330.0030.0030.0000.0000.0000.000
56A57LYS10.8490.90926.0640.1790.1790.0000.0000.0000.000
57A58ASP-1-0.757-0.84929.295-0.092-0.0920.0000.0000.0000.000
58A59PRO00.0000.01829.564-0.002-0.0020.0000.0000.0000.000
59A60SER0-0.096-0.07630.6130.0050.0050.0000.0000.0000.000
60A61LYS10.8530.90832.2300.0950.0950.0000.0000.0000.000
61A62ARG10.8180.89924.8520.1470.1470.0000.0000.0000.000
62A63GLN0-0.053-0.03825.9380.0130.0130.0000.0000.0000.000
63A64PHE00.017-0.01827.325-0.005-0.0050.0000.0000.0000.000
64A65ALA00.0550.03027.849-0.001-0.0010.0000.0000.0000.000
65A66LEU0-0.037-0.00525.5160.0020.0020.0000.0000.0000.000
66A67ILE00.009-0.00822.440-0.007-0.0070.0000.0000.0000.000
67A68GLU-1-0.832-0.89423.869-0.072-0.0720.0000.0000.0000.000
68A69LYS10.7760.87125.8390.0940.0940.0000.0000.0000.000
69A70LEU0-0.059-0.02721.701-0.001-0.0010.0000.0000.0000.000
70A71ALA00.019-0.00321.163-0.001-0.0010.0000.0000.0000.000
71A72LYS10.8030.90822.2380.0710.0710.0000.0000.0000.000
72A73GLU-1-0.796-0.87123.994-0.078-0.0780.0000.0000.0000.000
73A74VAL0-0.070-0.03117.836-0.003-0.0030.0000.0000.0000.000
74A75SER0-0.049-0.02819.4920.0140.0140.0000.0000.0000.000
75A76VAL0-0.067-0.02314.2440.0270.0270.0000.0000.0000.000
76A77ASN0-0.024-0.01911.578-0.013-0.0130.0000.0000.0000.000
77A78LEU00.0190.02313.783-0.071-0.0710.0000.0000.0000.000
78A79GLN00.000-0.00811.4590.0740.0740.0000.0000.0000.000
79A80VAL00.0250.00715.489-0.023-0.0230.0000.0000.0000.000
80A81GLY00.0490.01818.2700.0020.0020.0000.0000.0000.000
81A82GLY00.0100.00219.0780.0060.0060.0000.0000.0000.000
82A83GLY00.0060.00622.0190.0200.0200.0000.0000.0000.000
83A84ILE0-0.054-0.00920.9080.0170.0170.0000.0000.0000.000
84A85ARG10.8520.91623.8660.1330.1330.0000.0000.0000.000
85A86SER00.001-0.00626.7180.0110.0110.0000.0000.0000.000
86A87LYS10.8740.90726.9140.0420.0420.0000.0000.0000.000
87A88GLU-1-0.855-0.93327.846-0.069-0.0690.0000.0000.0000.000
88A89GLU-1-0.778-0.86826.409-0.132-0.1320.0000.0000.0000.000
89A90VAL00.0050.00322.489-0.006-0.0060.0000.0000.0000.000
90A91LYS10.8730.92224.4600.0410.0410.0000.0000.0000.000
91A92ALA00.0440.03226.8070.0040.0040.0000.0000.0000.000
92A93LEU0-0.007-0.01122.404-0.002-0.0020.0000.0000.0000.000
93A94LEU0-0.015-0.00320.5720.0000.0000.0000.0000.0000.000
94A95ASP-1-0.827-0.89123.678-0.036-0.0360.0000.0000.0000.000
95A96CYS0-0.102-0.05624.9760.0030.0030.0000.0000.0000.000
96A97GLY00.0230.00423.240-0.002-0.0020.0000.0000.0000.000
97A98VAL0-0.080-0.03118.653-0.003-0.0030.0000.0000.0000.000
98A99LYS10.8540.93014.271-0.011-0.0110.0000.0000.0000.000
99A100ARG10.7260.82510.7110.2490.2490.0000.0000.0000.000
100A101VAL00.0130.00816.288-0.033-0.0330.0000.0000.0000.000
101A102VAL0-0.031-0.02115.068-0.002-0.0020.0000.0000.0000.000
102A103ILE00.0330.03317.8110.0090.0090.0000.0000.0000.000
103A104GLY00.0800.01918.890-0.035-0.0350.0000.0000.0000.000
104A105SER0-0.0060.00520.7030.0070.0070.0000.0000.0000.000
105A106MET00.0240.00623.7510.0080.0080.0000.0000.0000.000
106A107ALA00.0570.03121.5350.0140.0140.0000.0000.0000.000
107A108ILE00.0030.00823.5700.0070.0070.0000.0000.0000.000
108A109LYS10.8450.92426.2710.1570.1570.0000.0000.0000.000
109A110ASP-1-0.793-0.87628.043-0.071-0.0710.0000.0000.0000.000
110A111ALA00.0360.02126.279-0.005-0.0050.0000.0000.0000.000
111A112THR0-0.016-0.02726.9960.0030.0030.0000.0000.0000.000
112A113LEU00.0510.03027.8250.0030.0030.0000.0000.0000.000
113A114CYS0-0.065-0.02923.393-0.007-0.0070.0000.0000.0000.000
114A115LEU0-0.017-0.01323.7580.0010.0010.0000.0000.0000.000
115A116GLU-1-0.900-0.93325.580-0.041-0.0410.0000.0000.0000.000
116A117ILE00.0020.00122.4990.0070.0070.0000.0000.0000.000
117A118LEU0-0.010-0.01618.6990.0050.0050.0000.0000.0000.000
118A119LYS10.8780.93822.3870.0260.0260.0000.0000.0000.000
119A120GLU-1-0.895-0.91825.158-0.033-0.0330.0000.0000.0000.000
120A121PHE00.012-0.00822.3900.0050.0050.0000.0000.0000.000
121A122GLY00.0400.03320.9400.0120.0120.0000.0000.0000.000
122A123SER00.005-0.01016.751-0.009-0.0090.0000.0000.0000.000
123A124GLU-1-0.778-0.85812.8050.1230.1230.0000.0000.0000.000
124A125ALA00.0190.00715.473-0.006-0.0060.0000.0000.0000.000
125A126ILE0-0.032-0.00817.231-0.031-0.0310.0000.0000.0000.000
126A127VAL0-0.034-0.01613.034-0.005-0.0050.0000.0000.0000.000
127A128LEU00.0020.00215.3410.0230.0230.0000.0000.0000.000
128A129ALA0-0.014-0.01215.179-0.063-0.0630.0000.0000.0000.000
129A130LEU0-0.036-0.03115.5080.0580.0580.0000.0000.0000.000
130A131ASP-1-0.833-0.89215.981-0.420-0.4200.0000.0000.0000.000
131A132THR0-0.072-0.05615.8670.0400.0400.0000.0000.0000.000
132A133ILE00.0270.00418.640-0.014-0.0140.0000.0000.0000.000
133A134LEU0-0.0340.00020.3540.0070.0070.0000.0000.0000.000
134A135LYS10.8810.93421.9230.1320.1320.0000.0000.0000.000
135A136GLU-1-0.906-0.95525.719-0.106-0.1060.0000.0000.0000.000
136A137ASP-1-0.816-0.91721.928-0.130-0.1300.0000.0000.0000.000
137A138TYR00.001-0.00317.476-0.021-0.0210.0000.0000.0000.000
138A139VAL00.0040.01120.7910.0080.0080.0000.0000.0000.000
139A140VAL00.0180.02120.170-0.028-0.0280.0000.0000.0000.000
140A141ALA0-0.071-0.03621.1270.0260.0260.0000.0000.0000.000
141A150ASP-1-0.846-0.91726.349-0.120-0.1200.0000.0000.0000.000
142A151LYS10.8330.90625.2160.1070.1070.0000.0000.0000.000
143A152LYS10.9170.94523.1850.0710.0710.0000.0000.0000.000
144A153LEU00.012-0.01215.4600.0040.0040.0000.0000.0000.000
145A154MET00.0390.01417.711-0.020-0.0200.0000.0000.0000.000
146A155GLU-1-0.803-0.87719.539-0.078-0.0780.0000.0000.0000.000
147A156VAL0-0.041-0.01620.5240.0140.0140.0000.0000.0000.000
148A157LEU0-0.016-0.01215.0450.0010.0010.0000.0000.0000.000
149A158ASP-1-0.842-0.92618.455-0.043-0.0430.0000.0000.0000.000
150A159PHE0-0.026-0.00720.5690.0180.0180.0000.0000.0000.000
151A160TYR0-0.004-0.03719.5210.0160.0160.0000.0000.0000.000
152A161SER00.0230.02917.3510.0140.0140.0000.0000.0000.000
153A162ASN0-0.079-0.02618.7790.0390.0390.0000.0000.0000.000
154A163LYS10.8270.89621.5130.0380.0380.0000.0000.0000.000
155A164GLY00.0070.01919.5650.0030.0030.0000.0000.0000.000
156A165LEU0-0.037-0.01815.6890.0170.0170.0000.0000.0000.000
157A166LYS10.8890.94510.653-0.311-0.3110.0000.0000.0000.000
158A167HIS0-0.014-0.0279.403-0.182-0.1820.0000.0000.0000.000
159A168ILE00.0150.00610.9460.0620.0620.0000.0000.0000.000
160A169LEU0-0.013-0.00110.388-0.182-0.1820.0000.0000.0000.000
161A170CYS0-0.038-0.00710.8520.1280.1280.0000.0000.0000.000
162A171THR00.0120.00011.797-0.123-0.1230.0000.0000.0000.000
163A172ASP-1-0.746-0.84113.723-0.267-0.2670.0000.0000.0000.000
164A173ILE0-0.019-0.01715.655-0.007-0.0070.0000.0000.0000.000
165A174SER00.020-0.00318.7070.0400.0400.0000.0000.0000.000
166A175LYS10.7460.87214.9000.3380.3380.0000.0000.0000.000
167A176ASP-1-0.836-0.91316.169-0.357-0.3570.0000.0000.0000.000
168A177GLY00.0350.02616.188-0.047-0.0470.0000.0000.0000.000
169A178THR0-0.007-0.02018.7020.0140.0140.0000.0000.0000.000
170A179MET0-0.044-0.01317.4310.0240.0240.0000.0000.0000.000
171A180GLN00.0210.02017.063-0.013-0.0130.0000.0000.0000.000
172A181GLY00.0480.03313.5630.0160.0160.0000.0000.0000.000
173A182VAL00.0170.0018.4770.0100.0100.0000.0000.0000.000
174A183ASN0-0.054-0.04011.6120.1030.1030.0000.0000.0000.000
175A184VAL00.021-0.0079.279-0.053-0.0530.0000.0000.0000.000
176A185ARG10.9420.97910.7630.0890.0890.0000.0000.0000.000
177A186LEU00.0300.02212.6800.0230.0230.0000.0000.0000.000
178A187TYR00.016-0.0228.003-0.058-0.0580.0000.0000.0000.000
179A188LYS10.8940.9558.493-0.168-0.1680.0000.0000.0000.000
180A189LEU00.0400.03510.5790.0550.0550.0000.0000.0000.000
181A190ILE0-0.009-0.01411.2160.0260.0260.0000.0000.0000.000
182A191HIS0-0.017-0.0117.4290.0060.0060.0000.0000.0000.000
183A192GLU-1-0.968-0.98610.2550.1000.1000.0000.0000.0000.000
184A193ILE0-0.028-0.00713.2950.0380.0380.0000.0000.0000.000
185A194PHE0-0.043-0.02513.2960.0310.0310.0000.0000.0000.000
186A195PRO00.0320.01710.726-0.072-0.0720.0000.0000.0000.000
187A196ASN0-0.037-0.02110.0600.0570.0570.0000.0000.0000.000
188A197ILE0-0.0170.00410.6630.0350.0350.0000.0000.0000.000
189A198CYS0-0.041-0.0187.621-0.024-0.0240.0000.0000.0000.000
190A199ILE00.0220.0056.666-0.034-0.0340.0000.0000.0000.000
191A200GLN0-0.0030.0215.786-0.981-0.9810.0000.0000.0000.000
192A201ALA00.0440.0125.7980.3780.3780.0000.0000.0000.000
193A202SER0-0.031-0.0297.500-0.017-0.0170.0000.0000.0000.000
194A203GLY00.0580.03410.6150.0760.0760.0000.0000.0000.000
195A204GLY0-0.026-0.01612.204-0.058-0.0580.0000.0000.0000.000
196A205VAL0-0.081-0.0388.9530.0320.0320.0000.0000.0000.000
197A206ALA0-0.0060.00611.6510.0300.0300.0000.0000.0000.000
198A207SER0-0.051-0.04712.0660.0550.0550.0000.0000.0000.000
199A208LEU00.0690.0199.487-0.087-0.0870.0000.0000.0000.000
200A209LYS10.8800.9268.6640.0240.0240.0000.0000.0000.000
201A210ASP-1-0.776-0.8658.815-0.404-0.4040.0000.0000.0000.000
202A211LEU00.006-0.0024.953-0.052-0.0520.0000.0000.0000.000
203A212GLU-1-0.839-0.9104.009-0.1440.0490.000-0.045-0.1480.000
204A213ASN0-0.077-0.0456.2640.4870.4870.0000.0000.0000.000
205A214LEU00.000-0.0123.704-0.0670.1460.003-0.043-0.1720.000
206A215LYS10.8480.9302.499-3.221-0.8781.994-1.839-2.4980.004
207A216GLY0-0.033-0.0111.887-5.630-9.8869.026-2.051-2.7190.029
208A217ILE0-0.049-0.0153.630-2.922-2.4650.008-0.011-0.4530.001
209A218CYS0-0.0090.0122.799-0.8590.4730.175-0.542-0.9650.000
210A219SER0-0.005-0.0011.703-16.651-20.88815.506-6.519-4.750-0.066
211A220GLY00.008-0.0092.508-0.8930.7262.428-2.130-1.916-0.018
212A221VAL0-0.0040.0022.923-0.1430.3040.2150.078-0.7410.000
213A222ILE00.0150.0165.3410.2290.219-0.001-0.0010.0120.000
214A223VAL0-0.032-0.0157.6370.0770.0770.0000.0000.0000.000
215A224GLY00.0500.02410.4540.0600.0600.0000.0000.0000.000
216A225LYS10.9160.93814.2450.3060.3060.0000.0000.0000.000
217A226ALA00.0380.02012.6830.0380.0380.0000.0000.0000.000
218A227LEU00.0130.02111.1520.0250.0250.0000.0000.0000.000
219A228LEU0-0.053-0.02615.0480.0490.0490.0000.0000.0000.000
220A229ASP-1-0.802-0.87018.190-0.224-0.2240.0000.0000.0000.000
221A230GLY0-0.0110.00618.2740.0220.0220.0000.0000.0000.000
222A231VAL0-0.039-0.01315.7140.0160.0160.0000.0000.0000.000
223A232PHE00.0020.0019.580-0.006-0.0060.0000.0000.0000.000
224A233SER0-0.022-0.04214.200-0.024-0.0240.0000.0000.0000.000
225A234VAL00.0240.00010.782-0.085-0.0850.0000.0000.0000.000
226A235GLU-1-0.825-0.89010.482-0.423-0.4230.0000.0000.0000.000
227A236GLU-1-0.906-0.95611.655-0.317-0.3170.0000.0000.0000.000
228A237GLY00.0510.0178.053-0.010-0.0100.0000.0000.0000.000
229A238ILE0-0.018-0.0146.591-0.316-0.3160.0000.0000.0000.000
230A239ARG10.9180.9667.4570.1860.1860.0000.0000.0000.000
231A240CYS0-0.057-0.0127.7740.0410.0410.0000.0000.0000.000
232A241LEU00.0320.0182.322-0.199-0.1432.768-0.479-2.346-0.002
233A242ALA0-0.0190.0114.082-0.185-0.0140.000-0.064-0.1070.000
234A243ASN0-0.0020.0003.7110.3510.5750.001-0.029-0.1970.000