Manual

About

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: 3JZ7L

Calculation Name: 5I32-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I32

Chain ID: A

ChEMBL ID:

UniProt ID: Q41951

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2531506.973289
FMO2-HF: Nuclear repulsion 2449588.478631
FMO2-HF: Total energy -81918.494658
FMO2-MP2: Total energy -82161.341578


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-5.434-0.5663.283-3.774-4.377-0.029
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.019
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].
3A3GLY00.0260.0143.818-0.4330.463-0.002-0.397-0.4970.002
4A4VAL00.014-0.0016.4030.6120.6120.0000.0000.0000.000
5A5ALA00.0410.0289.5120.0660.0660.0000.0000.0000.000
6A6PHE00.020-0.00212.1400.1030.1030.0000.0000.0000.000
7A7GLY00.0460.01115.7580.0560.0560.0000.0000.0000.000
8A8SER00.0080.00517.3580.0230.0230.0000.0000.0000.000
9A9PHE00.0640.01321.0140.0060.0060.0000.0000.0000.000
10A10ASP-1-0.900-0.94024.314-0.167-0.1670.0000.0000.0000.000
11A11ASP-1-0.947-0.97419.148-0.270-0.2700.0000.0000.0000.000
12A12SER0-0.030-0.02320.6010.0110.0110.0000.0000.0000.000
13A13PHE00.0170.00622.9040.0110.0110.0000.0000.0000.000
14A14SER00.0250.04023.8530.0260.0260.0000.0000.0000.000
15A15LEU00.036-0.00826.6530.0010.0010.0000.0000.0000.000
16A16ALA0-0.027-0.01123.8390.0060.0060.0000.0000.0000.000
17A17SER00.0320.00722.7190.0010.0010.0000.0000.0000.000
18A18LEU0-0.009-0.00424.3170.0010.0010.0000.0000.0000.000
19A19ARG10.9110.95227.1410.0790.0790.0000.0000.0000.000
20A20ALA00.0330.03422.6260.0080.0080.0000.0000.0000.000
21A21TYR0-0.022-0.03622.268-0.005-0.0050.0000.0000.0000.000
22A22LEU00.0010.00526.0810.0050.0050.0000.0000.0000.000
23A23ALA00.0330.01125.8550.0070.0070.0000.0000.0000.000
24A24GLU-1-0.697-0.80822.093-0.144-0.1440.0000.0000.0000.000
25A25PHE0-0.0460.00025.7150.0050.0050.0000.0000.0000.000
26A26ILE00.000-0.00729.0450.0060.0060.0000.0000.0000.000
27A27SER0-0.001-0.01026.5620.0070.0070.0000.0000.0000.000
28A28THR0-0.024-0.03526.3090.0030.0030.0000.0000.0000.000
29A29LEU0-0.0300.00128.3290.0050.0050.0000.0000.0000.000
30A30LEU0-0.010-0.01431.7490.0060.0060.0000.0000.0000.000
31A31PHE0-0.027-0.01227.0270.0050.0050.0000.0000.0000.000
32A32VAL0-0.004-0.00529.5980.0040.0040.0000.0000.0000.000
33A33PHE0-0.020-0.00432.0230.0040.0040.0000.0000.0000.000
34A34ALA00.0300.01133.8670.0040.0040.0000.0000.0000.000
35A35GLY00.0420.01432.8520.0040.0040.0000.0000.0000.000
36A36VAL0-0.002-0.01533.5520.0020.0020.0000.0000.0000.000
37A37GLY00.0510.02835.8420.0030.0030.0000.0000.0000.000
38A38SER0-0.051-0.03936.2280.0040.0040.0000.0000.0000.000
39A39ALA00.0030.00137.1780.0030.0030.0000.0000.0000.000
40A40ILE00.0130.00739.1310.0010.0010.0000.0000.0000.000
41A41ALA0-0.031-0.01941.6930.0020.0020.0000.0000.0000.000
42A42TYR0-0.040-0.03241.8300.0030.0030.0000.0000.0000.000
43A43ALA00.0390.03543.4110.0020.0020.0000.0000.0000.000
44A44LYS10.9560.97645.2770.0260.0260.0000.0000.0000.000
45A45LEU0-0.097-0.06045.7770.0020.0020.0000.0000.0000.000
46A46THR0-0.041-0.02046.4090.0010.0010.0000.0000.0000.000
47A47SER0-0.054-0.01149.1220.0000.0000.0000.0000.0000.000
48A48ASP-1-0.951-0.98046.608-0.035-0.0350.0000.0000.0000.000
49A49ALA0-0.0120.01047.052-0.001-0.0010.0000.0000.0000.000
50A50ALA00.022-0.00244.179-0.002-0.0020.0000.0000.0000.000
51A51LEU0-0.0220.00837.4720.0020.0020.0000.0000.0000.000
52A52ASP-1-0.797-0.89941.968-0.016-0.0160.0000.0000.0000.000
53A53THR0-0.010-0.02239.7240.0000.0000.0000.0000.0000.000
54A54PRO00.0160.00340.2250.0000.0000.0000.0000.0000.000
55A55GLY00.0680.03040.9000.0000.0000.0000.0000.0000.000
56A56LEU0-0.043-0.00934.234-0.002-0.0020.0000.0000.0000.000
57A57VAL0-0.015-0.01036.012-0.001-0.0010.0000.0000.0000.000
58A58ALA00.0010.00736.5600.0000.0000.0000.0000.0000.000
59A59ILE00.0180.00834.034-0.001-0.0010.0000.0000.0000.000
60A60ALA0-0.0010.01432.165-0.004-0.0040.0000.0000.0000.000
61A61VAL00.002-0.00331.8630.0000.0000.0000.0000.0000.000
62A62CYS0-0.0610.00433.249-0.001-0.0010.0000.0000.0000.000
63A63HIS00.0110.00129.535-0.009-0.0090.0000.0000.0000.000
64A64GLY00.0220.01828.387-0.003-0.0030.0000.0000.0000.000
65A65PHE0-0.021-0.03128.8470.0030.0030.0000.0000.0000.000
66A66ALA00.0250.01630.7050.0000.0000.0000.0000.0000.000
67A67LEU0-0.023-0.00123.391-0.004-0.0040.0000.0000.0000.000
68A68PHE00.0110.00626.080-0.001-0.0010.0000.0000.0000.000
69A69VAL0-0.011-0.00326.8290.0010.0010.0000.0000.0000.000
70A70ALA00.0160.00727.114-0.002-0.0020.0000.0000.0000.000
71A71VAL00.0070.01221.668-0.007-0.0070.0000.0000.0000.000
72A72ALA0-0.009-0.01424.157-0.001-0.0010.0000.0000.0000.000
73A73ILE0-0.076-0.03526.0410.0020.0020.0000.0000.0000.000
74A74GLY00.0470.02824.865-0.004-0.0040.0000.0000.0000.000
75A75ALA0-0.0100.00921.783-0.012-0.0120.0000.0000.0000.000
76A76ASN0-0.035-0.02621.2630.0000.0000.0000.0000.0000.000
77A77ILE0-0.069-0.02723.4940.0000.0000.0000.0000.0000.000
78A78SER0-0.030-0.04921.808-0.004-0.0040.0000.0000.0000.000
79A79GLY0-0.0030.02718.758-0.030-0.0300.0000.0000.0000.000
80A80GLY0-0.056-0.01819.6320.0110.0110.0000.0000.0000.000
81A81HIS00.0310.02016.133-0.009-0.0090.0000.0000.0000.000
82A82VAL0-0.039-0.02520.1020.0080.0080.0000.0000.0000.000
83A83ASN00.018-0.01620.488-0.010-0.0100.0000.0000.0000.000
84A84PRO00.0500.03719.757-0.019-0.0190.0000.0000.0000.000
85A85ALA00.0350.01017.938-0.046-0.0460.0000.0000.0000.000
86A86VAL0-0.0110.00815.987-0.036-0.0360.0000.0000.0000.000
87A87THR00.008-0.01514.745-0.031-0.0310.0000.0000.0000.000
88A88PHE0-0.040-0.01314.376-0.080-0.0800.0000.0000.0000.000
89A89GLY00.0410.02211.929-0.110-0.1100.0000.0000.0000.000
90A90LEU00.0050.00510.121-0.125-0.1250.0000.0000.0000.000
91A91ALA0-0.0100.0059.827-0.147-0.1470.0000.0000.0000.000
92A92VAL0-0.054-0.0267.880-0.223-0.2230.0000.0000.0000.000
93A93GLY00.0150.0185.473-0.475-0.4750.0000.0000.0000.000
94A94GLY0-0.013-0.0026.076-0.099-0.0990.0000.0000.0000.000
95A95GLN0-0.099-0.0606.9880.4810.4810.0000.0000.0000.000
96A96ILE0-0.021-0.00210.3340.1490.1490.0000.0000.0000.000
97A97THR00.0100.01412.723-0.104-0.1040.0000.0000.0000.000
98A98VAL00.0230.00114.0390.0560.0560.0000.0000.0000.000
99A99ILE0-0.0240.00216.2040.0580.0580.0000.0000.0000.000
100A100THR00.0470.02918.0080.0370.0370.0000.0000.0000.000
101A101GLY00.0270.02017.4260.0390.0390.0000.0000.0000.000
102A102VAL0-0.0010.00018.3370.0340.0340.0000.0000.0000.000
103A103PHE00.015-0.00221.2510.0330.0330.0000.0000.0000.000
104A104TYR0-0.019-0.03819.4140.0240.0240.0000.0000.0000.000
105A105TRP0-0.040-0.00518.6680.0240.0240.0000.0000.0000.000
106A106ILE0-0.021-0.00123.1100.0220.0220.0000.0000.0000.000
107A107ALA00.0150.00825.5640.0170.0170.0000.0000.0000.000
108A108GLN00.004-0.02020.6110.0080.0080.0000.0000.0000.000
109A109LEU0-0.009-0.00725.8330.0140.0140.0000.0000.0000.000
110A110LEU0-0.0060.00528.4190.0130.0130.0000.0000.0000.000
111A111GLY00.0150.00829.8890.0100.0100.0000.0000.0000.000
112A112SER0-0.016-0.03729.4400.0130.0130.0000.0000.0000.000
113A113THR00.027-0.00631.3710.0080.0080.0000.0000.0000.000
114A114ALA0-0.0010.00434.0990.0070.0070.0000.0000.0000.000
115A115ALA0-0.0080.00734.2010.0070.0070.0000.0000.0000.000
116A116CYS0-0.021-0.00134.5120.0060.0060.0000.0000.0000.000
117A117PHE00.005-0.00237.3830.0050.0050.0000.0000.0000.000
118A118LEU0-0.012-0.00738.0350.0050.0050.0000.0000.0000.000
119A119LEU0-0.0010.01237.3650.0040.0040.0000.0000.0000.000
120A120LYS10.9210.98241.2420.0570.0570.0000.0000.0000.000
121A121TYR0-0.020-0.00543.5470.0030.0030.0000.0000.0000.000
122A122VAL0-0.003-0.01543.1260.0030.0030.0000.0000.0000.000
123A123THR0-0.077-0.03843.4660.0030.0030.0000.0000.0000.000
124A124GLY0-0.020-0.00546.4390.0020.0020.0000.0000.0000.000
125A125GLY0-0.014-0.00647.2720.0010.0010.0000.0000.0000.000
126A126LEU0-0.018-0.00145.410-0.001-0.0010.0000.0000.0000.000
127A127ALA0-0.013-0.01643.599-0.003-0.0030.0000.0000.0000.000
128A128VAL00.0180.00437.7570.0020.0020.0000.0000.0000.000
129A129PRO0-0.0130.00637.715-0.003-0.0030.0000.0000.0000.000
130A130THR00.0140.00035.403-0.002-0.0020.0000.0000.0000.000
131A131HIS00.0260.03429.629-0.003-0.0030.0000.0000.0000.000
132A132SER00.0090.00133.479-0.004-0.0040.0000.0000.0000.000
133A133VAL0-0.015-0.00731.3720.0020.0020.0000.0000.0000.000
134A134ALA0-0.0070.01134.0420.0020.0020.0000.0000.0000.000
135A135ALA00.0420.00736.966-0.002-0.0020.0000.0000.0000.000
136A136GLY0-0.028-0.01539.8430.0040.0040.0000.0000.0000.000
137A137LEU0-0.046-0.00232.7930.0010.0010.0000.0000.0000.000
138A138GLY00.0620.03534.165-0.004-0.0040.0000.0000.0000.000
139A139SER00.002-0.02731.183-0.003-0.0030.0000.0000.0000.000
140A140ILE0-0.0020.00327.359-0.008-0.0080.0000.0000.0000.000
141A141GLU-1-0.835-0.91727.747-0.077-0.0770.0000.0000.0000.000
142A142GLY00.0010.00828.3980.0020.0020.0000.0000.0000.000
143A143VAL00.001-0.01724.024-0.004-0.0040.0000.0000.0000.000
144A144VAL0-0.001-0.00723.568-0.010-0.0100.0000.0000.0000.000
145A145MET00.0200.02223.6000.0040.0040.0000.0000.0000.000
146A146GLU-1-0.711-0.85123.873-0.100-0.1000.0000.0000.0000.000
147A147ILE0-0.0380.00318.528-0.008-0.0080.0000.0000.0000.000
148A148ILE00.0020.00419.279-0.004-0.0040.0000.0000.0000.000
149A149ILE0-0.016-0.00820.1680.0110.0110.0000.0000.0000.000
150A150THR0-0.003-0.01218.0980.0090.0090.0000.0000.0000.000
151A151PHE0-0.0220.00912.950-0.003-0.0030.0000.0000.0000.000
152A152ALA00.0000.00516.0520.0210.0210.0000.0000.0000.000
153A153LEU00.0010.01217.8440.0240.0240.0000.0000.0000.000
154A154VAL00.009-0.00112.7070.0140.0140.0000.0000.0000.000
155A155TYR00.0030.00812.1190.0240.0240.0000.0000.0000.000
156A156THR0-0.031-0.02113.9010.0690.0690.0000.0000.0000.000
157A157VAL00.0040.01014.3320.0330.0330.0000.0000.0000.000
158A158TYR0-0.027-0.0407.376-0.031-0.0310.0000.0000.0000.000
159A159ALA0-0.0070.00012.0850.0730.0730.0000.0000.0000.000
160A160THR0-0.088-0.04813.7090.0250.0250.0000.0000.0000.000
161A161ALA00.012-0.00415.2860.0020.0020.0000.0000.0000.000
162A162ALA00.0050.00910.755-0.009-0.0090.0000.0000.0000.000
163A163ASP-1-0.725-0.8339.7480.8540.8540.0000.0000.0000.000
164A164PRO00.0200.0038.861-0.066-0.0660.0000.0000.0000.000
165A165LYS10.8040.90210.195-1.045-1.0450.0000.0000.0000.000
166A166LYS10.8610.94813.527-0.162-0.1620.0000.0000.0000.000
167A167GLY00.0360.01215.560-0.025-0.0250.0000.0000.0000.000
168A168SER0-0.010-0.01818.721-0.022-0.0220.0000.0000.0000.000
169A169LEU00.0480.02316.897-0.030-0.0300.0000.0000.0000.000
170A170GLY00.0100.00319.108-0.025-0.0250.0000.0000.0000.000
171A171THR0-0.062-0.03119.758-0.026-0.0260.0000.0000.0000.000
172A172ILE0-0.0020.00022.425-0.016-0.0160.0000.0000.0000.000
173A173ALA00.0180.02019.278-0.012-0.0120.0000.0000.0000.000
174A174PRO00.0290.00921.120-0.012-0.0120.0000.0000.0000.000
175A175LEU00.0030.00923.432-0.011-0.0110.0000.0000.0000.000
176A176ALA0-0.006-0.00121.260-0.005-0.0050.0000.0000.0000.000
177A177ILE00.0190.00518.513-0.009-0.0090.0000.0000.0000.000
178A178GLY00.0140.00821.785-0.013-0.0130.0000.0000.0000.000
179A179LEU0-0.022-0.02825.433-0.006-0.0060.0000.0000.0000.000
180A180ILE0-0.0120.00820.770-0.001-0.0010.0000.0000.0000.000
181A181VAL00.0390.01223.291-0.008-0.0080.0000.0000.0000.000
182A182GLY00.0140.00725.501-0.003-0.0030.0000.0000.0000.000
183A183ALA0-0.006-0.01426.597-0.001-0.0010.0000.0000.0000.000
184A184ASN00.023-0.00622.7230.0060.0060.0000.0000.0000.000
185A185ILE0-0.0190.00227.098-0.005-0.0050.0000.0000.0000.000
186A186LEU0-0.029-0.01830.013-0.001-0.0010.0000.0000.0000.000
187A187ALA0-0.0170.01328.8680.0020.0020.0000.0000.0000.000
188A188ALA00.0480.00128.157-0.002-0.0020.0000.0000.0000.000
189A189GLY0-0.0170.00330.292-0.006-0.0060.0000.0000.0000.000
190A190PRO0-0.021-0.02232.983-0.004-0.0040.0000.0000.0000.000
191A191PHE0-0.051-0.00531.7430.0000.0000.0000.0000.0000.000
192A192SER00.015-0.02828.195-0.001-0.0010.0000.0000.0000.000
193A193GLY00.0370.03531.059-0.007-0.0070.0000.0000.0000.000
194A194GLY0-0.043-0.02127.9900.0040.0040.0000.0000.0000.000
195A195SER0-0.054-0.03626.6330.0000.0000.0000.0000.0000.000
196A196MET0-0.055-0.02122.1780.0070.0070.0000.0000.0000.000
197A197ASN00.005-0.00921.968-0.025-0.0250.0000.0000.0000.000
198A198PRO00.0690.03921.8920.0110.0110.0000.0000.0000.000
199A199ALA00.0390.01524.8350.0080.0080.0000.0000.0000.000
200A200ARG10.8590.93526.6150.0850.0850.0000.0000.0000.000
201A201SER00.016-0.01528.0210.0070.0070.0000.0000.0000.000
202A202PHE0-0.020-0.00328.7370.0050.0050.0000.0000.0000.000
203A203GLY0-0.0020.00730.5790.0040.0040.0000.0000.0000.000
204A204PRO00.021-0.01732.3640.0040.0040.0000.0000.0000.000
205A205ALA00.0020.02533.4180.0040.0040.0000.0000.0000.000
206A206VAL0-0.017-0.00733.8640.0030.0030.0000.0000.0000.000
207A207ALA0-0.057-0.02936.4760.0040.0040.0000.0000.0000.000
208A208ALA0-0.060-0.02938.5220.0050.0050.0000.0000.0000.000
209A209GLY0-0.025-0.00239.4780.0030.0030.0000.0000.0000.000
210A210ASP-1-0.899-0.95438.299-0.078-0.0780.0000.0000.0000.000
211A211PHE0-0.021-0.02432.221-0.004-0.0040.0000.0000.0000.000
212A212SER0-0.0250.00534.621-0.009-0.0090.0000.0000.0000.000
213A213GLY00.0250.00933.5350.0020.0020.0000.0000.0000.000
214A214HIS00.0520.01729.669-0.013-0.0130.0000.0000.0000.000
215A215TRP00.0460.01027.340-0.011-0.0110.0000.0000.0000.000
216A216VAL00.0300.02426.752-0.016-0.0160.0000.0000.0000.000
217A217TYR0-0.062-0.05125.718-0.010-0.0100.0000.0000.0000.000
218A218TRP0-0.046-0.02722.792-0.015-0.0150.0000.0000.0000.000
219A219VAL00.001-0.00921.980-0.020-0.0200.0000.0000.0000.000
220A220GLY00.0330.01921.159-0.018-0.0180.0000.0000.0000.000
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225A225GLY00.012-0.01014.8510.0070.0070.0000.0000.0000.000
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227A227LEU0-0.015-0.01410.726-0.117-0.1170.0000.0000.0000.000
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229A229GLY00.0120.0008.5960.1050.1050.0000.0000.0000.000
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233A233GLY00.0250.0044.3200.4480.528-0.001-0.023-0.0560.000
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235A235VAL0-0.0260.0063.4691.4301.4660.0080.136-0.1790.000
236A236PHE0-0.048-0.0326.7320.1810.1810.0000.0000.0000.000
237A237MET0-0.071-0.0204.809-0.479-0.4790.0000.0000.0000.000
238A238GLY0-0.0020.0243.177-0.8440.3360.086-0.607-0.660-0.002