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: R9978

Calculation Name: 5F5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F5U

Chain ID: A

ChEMBL ID:

UniProt ID: G0S6R0

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152523.651653
FMO2-HF: Nuclear repulsion 2076775.150456
FMO2-HF: Total energy -75748.501197
FMO2-MP2: Total energy -75970.695987


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:22:GLY)


Summations of interaction energy for fragment #1(A:22: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.
-0.8780.114-0.009-0.458-0.5260.001
Interaction energy analysis for fragmet #1(A:22:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.023
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].
3A24LEU0-0.005-0.0093.840-0.4440.548-0.009-0.458-0.5260.001
4A25ALA0-0.037-0.0126.5650.1610.1610.0000.0000.0000.000
5A26PRO00.0240.0159.6640.0520.0520.0000.0000.0000.000
6A27ASN00.0070.01412.9230.0200.0200.0000.0000.0000.000
7A28GLY00.0330.00312.088-0.057-0.0570.0000.0000.0000.000
8A29LEU0-0.043-0.01211.275-0.018-0.0180.0000.0000.0000.000
9A30ASN00.0840.0305.967-0.434-0.4340.0000.0000.0000.000
10A31PRO00.0740.0235.7950.3090.3090.0000.0000.0000.000
11A32ALA0-0.0180.0026.9680.1660.1660.0000.0000.0000.000
12A33THR0-0.083-0.0648.5990.0860.0860.0000.0000.0000.000
13A34ILE0-0.0070.03010.8540.0440.0440.0000.0000.0000.000
14A35MET0-0.0010.01713.1920.0450.0450.0000.0000.0000.000
15A36GLU-1-0.776-0.89914.892-0.105-0.1050.0000.0000.0000.000
16A37LYS10.9550.96915.3980.0000.0000.0000.0000.0000.000
17A38ALA00.0440.02717.1630.0030.0030.0000.0000.0000.000
18A39VAL0-0.0020.00117.9880.0060.0060.0000.0000.0000.000
19A40ARG10.9290.97612.4190.1190.1190.0000.0000.0000.000
20A41GLU-1-0.911-0.95016.252-0.022-0.0220.0000.0000.0000.000
21A42ARG10.9580.97018.6480.0460.0460.0000.0000.0000.000
22A43ILE0-0.013-0.00216.3640.0020.0020.0000.0000.0000.000
23A44VAL0-0.0100.03614.9570.0020.0020.0000.0000.0000.000
24A45GLU-1-0.956-0.98417.779-0.022-0.0220.0000.0000.0000.000
25A46SER0-0.107-0.08420.5720.0030.0030.0000.0000.0000.000
26A47TYR00.0500.00322.139-0.001-0.0010.0000.0000.0000.000
27A48PHE00.016-0.00220.9290.0000.0000.0000.0000.0000.000
28A49TRP00.0300.01012.904-0.009-0.0090.0000.0000.0000.000
29A50LYS10.9180.95719.0930.0280.0280.0000.0000.0000.000
30A51GLU-1-0.941-0.96420.813-0.047-0.0470.0000.0000.0000.000
31A52GLN00.0100.00022.123-0.005-0.0050.0000.0000.0000.000
32A53CYS0-0.0310.00916.551-0.014-0.0140.0000.0000.0000.000
33A54PHE00.0290.02016.505-0.017-0.0170.0000.0000.0000.000
34A55GLY0-0.008-0.00816.6750.0020.0020.0000.0000.0000.000
35A56VAL0-0.066-0.01616.439-0.005-0.0050.0000.0000.0000.000
36A57ASN00.0490.01814.776-0.027-0.0270.0000.0000.0000.000
37A58GLU-1-0.763-0.90613.165-0.304-0.3040.0000.0000.0000.000
38A59ALA00.0160.00616.7730.0140.0140.0000.0000.0000.000
39A60ASP-1-0.801-0.89518.679-0.122-0.1220.0000.0000.0000.000
40A61ILE0-0.106-0.05015.5080.0100.0100.0000.0000.0000.000
41A62VAL0-0.034-0.02419.1400.0100.0100.0000.0000.0000.000
42A63ASP-1-0.865-0.92522.360-0.093-0.0930.0000.0000.0000.000
43A64ARG10.8940.93820.5350.1090.1090.0000.0000.0000.000
44A65VAL0-0.044-0.03021.5340.0070.0070.0000.0000.0000.000
45A66VAL0-0.024-0.01724.1140.0080.0080.0000.0000.0000.000
46A67GLU-1-0.921-0.95626.472-0.072-0.0720.0000.0000.0000.000
47A68HIS0-0.035-0.01925.0070.0070.0070.0000.0000.0000.000
48A69VAL0-0.070-0.00623.5890.0020.0020.0000.0000.0000.000
49A70ARG10.8440.92126.7480.0780.0780.0000.0000.0000.000
50A71PHE0-0.064-0.06427.5590.0060.0060.0000.0000.0000.000
51A72VAL00.0560.04825.446-0.005-0.0050.0000.0000.0000.000
52A73GLY00.053-0.00525.0380.0090.0090.0000.0000.0000.000
53A74GLY00.0240.01622.938-0.009-0.0090.0000.0000.0000.000
54A75VAL0-0.021-0.01022.6940.0020.0020.0000.0000.0000.000
55A76THR0-0.081-0.04025.1540.0040.0040.0000.0000.0000.000
56A77GLY00.0250.00528.8340.0020.0020.0000.0000.0000.000
57A78VAL00.0600.01431.508-0.001-0.0010.0000.0000.0000.000
58A79THR0-0.0040.00229.5060.0010.0010.0000.0000.0000.000
59A80GLN0-0.026-0.00225.9050.0040.0040.0000.0000.0000.000
60A81LYS11.0000.99826.0140.0620.0620.0000.0000.0000.000
61A82PRO00.0160.01421.425-0.003-0.0030.0000.0000.0000.000
62A83SER0-0.048-0.02423.4810.0000.0000.0000.0000.0000.000
63A84PRO00.0680.01922.130-0.006-0.0060.0000.0000.0000.000
64A85PHE00.0160.02021.130-0.009-0.0090.0000.0000.0000.000
65A86LEU00.0020.01118.516-0.013-0.0130.0000.0000.0000.000
66A87CYS0-0.044-0.01817.632-0.014-0.0140.0000.0000.0000.000
67A88LEU00.0490.01916.344-0.016-0.0160.0000.0000.0000.000
68A89ALA00.0120.01515.813-0.026-0.0260.0000.0000.0000.000
69A90PHE0-0.004-0.01911.639-0.044-0.0440.0000.0000.0000.000
70A91LYS10.8740.93911.6410.1590.1590.0000.0000.0000.000
71A92LEU00.0290.01811.521-0.036-0.0360.0000.0000.0000.000
72A93LEU0-0.062-0.0289.625-0.080-0.0800.0000.0000.0000.000
73A94GLN0-0.071-0.0387.352-0.126-0.1260.0000.0000.0000.000
74A95LEU0-0.056-0.0246.832-0.095-0.0950.0000.0000.0000.000
75A96ALA0-0.058-0.0116.731-0.110-0.1100.0000.0000.0000.000
76A97PRO00.0180.0238.735-0.014-0.0140.0000.0000.0000.000
77A98GLY00.0760.02712.104-0.031-0.0310.0000.0000.0000.000
78A99ASP-1-0.804-0.91513.757-0.298-0.2980.0000.0000.0000.000
79A100ASP-1-0.943-0.96716.845-0.234-0.2340.0000.0000.0000.000
80A101ILE00.0830.04114.9500.0200.0200.0000.0000.0000.000
81A102LEU0-0.038-0.00914.9140.0240.0240.0000.0000.0000.000
82A103LYS10.9420.97218.5260.2090.2090.0000.0000.0000.000
83A104GLU-1-0.897-0.93821.352-0.119-0.1190.0000.0000.0000.000
84A105TYR0-0.052-0.03516.8590.0060.0060.0000.0000.0000.000
85A106LEU00.0040.00921.9190.0170.0170.0000.0000.0000.000
86A107TYR00.0320.01124.1210.0090.0090.0000.0000.0000.000
87A108PHE00.1210.06626.1350.0130.0130.0000.0000.0000.000
88A109GLY00.016-0.01525.2160.0090.0090.0000.0000.0000.000
89A110GLY00.003-0.01226.1230.0070.0070.0000.0000.0000.000
90A111GLU-1-0.934-0.95127.403-0.078-0.0780.0000.0000.0000.000
91A112LYS10.8270.93229.7800.0880.0880.0000.0000.0000.000
92A113PHE0-0.026-0.02527.2460.0050.0050.0000.0000.0000.000
93A114LYS10.9210.93327.4270.0660.0660.0000.0000.0000.000
94A115TYR00.0280.00625.977-0.003-0.0030.0000.0000.0000.000
95A116LEU00.0290.04421.283-0.007-0.0070.0000.0000.0000.000
96A117ARG10.9230.97322.6370.0930.0930.0000.0000.0000.000
97A118ALA0-0.032-0.01023.610-0.009-0.0090.0000.0000.0000.000
98A119LEU0-0.014-0.01518.407-0.006-0.0060.0000.0000.0000.000
99A120ALA00.0330.01618.963-0.020-0.0200.0000.0000.0000.000
100A121ALA00.0350.01719.280-0.019-0.0190.0000.0000.0000.000
101A122PHE0-0.010-0.01718.177-0.009-0.0090.0000.0000.0000.000
102A123TYR00.0540.01610.142-0.006-0.0060.0000.0000.0000.000
103A124ILE00.0470.02215.687-0.037-0.0370.0000.0000.0000.000
104A125ARG10.8540.92617.5350.1540.1540.0000.0000.0000.000
105A126LEU0-0.080-0.04614.6880.0020.0020.0000.0000.0000.000
106A127THR0-0.067-0.03311.513-0.026-0.0260.0000.0000.0000.000
107A128ARG10.8820.93012.2520.3990.3990.0000.0000.0000.000
108A129PRO00.0240.00816.0900.0220.0220.0000.0000.0000.000
109A130ASP-1-0.744-0.87518.763-0.140-0.1400.0000.0000.0000.000
110A131LYS10.9971.01122.1160.1380.1380.0000.0000.0000.000
111A132GLU-1-0.906-0.97618.604-0.248-0.2480.0000.0000.0000.000
112A133VAL0-0.033-0.01919.9830.0050.0050.0000.0000.0000.000
113A134TYR00.005-0.00222.2270.0080.0080.0000.0000.0000.000
114A135THR0-0.042-0.02224.4990.0030.0030.0000.0000.0000.000
115A136LEU0-0.025-0.01320.6780.0050.0050.0000.0000.0000.000
116A137LEU0-0.035-0.02722.2240.0060.0060.0000.0000.0000.000
117A138GLU-1-0.780-0.86525.868-0.086-0.0860.0000.0000.0000.000
118A139PRO00.0240.01928.1640.0070.0070.0000.0000.0000.000
119A140PHE0-0.040-0.02025.6420.0060.0060.0000.0000.0000.000
120A141LEU0-0.005-0.01030.4710.0010.0010.0000.0000.0000.000
121A142GLU-1-0.914-0.94532.803-0.064-0.0640.0000.0000.0000.000
122A143ASP-1-0.843-0.91131.089-0.085-0.0850.0000.0000.0000.000
123A144ARG11.0581.02433.7570.0550.0550.0000.0000.0000.000
124A145ARG10.6940.83629.9140.0910.0910.0000.0000.0000.000
125A146LYS10.9490.98334.1070.0500.0500.0000.0000.0000.000
126A147LEU00.0100.01728.763-0.002-0.0020.0000.0000.0000.000
127A148ARG10.9070.95631.6890.0650.0650.0000.0000.0000.000
128A149ARG10.9731.00528.2670.0800.0800.0000.0000.0000.000
129A150LYS10.8830.93529.8280.0650.0650.0000.0000.0000.000
130A151GLY0-0.027-0.02529.387-0.006-0.0060.0000.0000.0000.000
131A152LYS10.9510.97928.6420.0750.0750.0000.0000.0000.000
132A153ASN00.0540.03232.511-0.001-0.0010.0000.0000.0000.000
133A154GLY00.0530.04535.2440.0010.0010.0000.0000.0000.000
134A155THR0-0.052-0.04334.184-0.005-0.0050.0000.0000.0000.000
135A156SER00.0430.02734.8350.0020.0020.0000.0000.0000.000
136A157LEU0-0.051-0.02835.025-0.003-0.0030.0000.0000.0000.000
137A158THR00.0010.00331.076-0.001-0.0010.0000.0000.0000.000
138A159TYR00.019-0.00533.6900.0030.0030.0000.0000.0000.000
139A160MET0-0.081-0.02228.078-0.006-0.0060.0000.0000.0000.000
140A161ASP-1-0.785-0.89530.084-0.079-0.0790.0000.0000.0000.000
141A162GLU-1-0.810-0.90931.895-0.067-0.0670.0000.0000.0000.000
142A163PHE0-0.101-0.04423.508-0.004-0.0040.0000.0000.0000.000
143A164ILE0-0.016-0.01826.039-0.008-0.0080.0000.0000.0000.000
144A165ASP-1-0.823-0.91827.688-0.085-0.0850.0000.0000.0000.000
145A166ASP-1-0.885-0.94028.094-0.085-0.0850.0000.0000.0000.000
146A167LEU0-0.101-0.05822.246-0.006-0.0060.0000.0000.0000.000
147A168LEU0-0.0140.00724.635-0.010-0.0100.0000.0000.0000.000
148A169THR0-0.0220.00126.8770.0020.0020.0000.0000.0000.000
149A170LYS10.8580.94227.5050.0830.0830.0000.0000.0000.000
150A171ASP-1-0.849-0.92125.177-0.096-0.0960.0000.0000.0000.000
151A172ARG10.8100.89822.6240.0850.0850.0000.0000.0000.000
152A173VAL00.0610.02723.0480.0100.0100.0000.0000.0000.000
153A174CYS0-0.071-0.02421.986-0.004-0.0040.0000.0000.0000.000
154A175SER0-0.090-0.05321.663-0.002-0.0020.0000.0000.0000.000
155A176THR00.0870.04617.315-0.002-0.0020.0000.0000.0000.000
156A177SER0-0.039-0.02119.6880.0100.0100.0000.0000.0000.000
157A178LEU0-0.038-0.01518.924-0.023-0.0230.0000.0000.0000.000
158A179TRP0-0.030-0.00917.3630.0230.0230.0000.0000.0000.000
159A180LYS10.9600.96719.8410.0870.0870.0000.0000.0000.000
160A181MET00.0000.01821.911-0.013-0.0130.0000.0000.0000.000
161A182ARG10.8880.94723.9710.1220.1220.0000.0000.0000.000
162A183ARG10.9520.97226.7040.0550.0550.0000.0000.0000.000
163A184ARG10.7500.79729.7990.0820.0820.0000.0000.0000.000
164A185ASP-1-0.796-0.90130.727-0.064-0.0640.0000.0000.0000.000
165A186ILE0-0.0020.00729.5240.0010.0010.0000.0000.0000.000
166A187LEU0-0.077-0.04625.923-0.001-0.0010.0000.0000.0000.000
167A188GLU-1-0.868-0.92629.851-0.067-0.0670.0000.0000.0000.000
168A189ASP-1-0.886-0.92933.225-0.050-0.0500.0000.0000.0000.000
169A190LEU0-0.188-0.09628.7460.0020.0020.0000.0000.0000.000
170A191ASP-1-0.906-0.94831.495-0.061-0.0610.0000.0000.0000.000
171A192LEU0-0.105-0.04525.898-0.007-0.0070.0000.0000.0000.000
172A193LEU0-0.094-0.06827.502-0.012-0.0120.0000.0000.0000.000
173A194GLU-1-0.842-0.90430.735-0.061-0.0610.0000.0000.0000.000
174A195PRO00.0420.03133.470-0.005-0.0050.0000.0000.0000.000
175A196ARG10.9270.98033.0510.0730.0730.0000.0000.0000.000
176A197VAL00.0380.01935.4020.0040.0040.0000.0000.0000.000
177A198SER0-0.037-0.01837.917-0.003-0.0030.0000.0000.0000.000
178A199PRO00.0480.00939.0810.0030.0030.0000.0000.0000.000
179A200LEU0-0.003-0.02441.7130.0020.0020.0000.0000.0000.000
180A201GLY00.0190.02742.4740.0010.0010.0000.0000.0000.000
181A202SER00.0110.01743.5450.0020.0020.0000.0000.0000.000
182A203LEU0-0.044-0.03446.0710.0020.0020.0000.0000.0000.000
183A204GLU-1-0.921-0.97945.781-0.038-0.0380.0000.0000.0000.000
184A205ASP-1-0.906-0.93547.024-0.038-0.0380.0000.0000.0000.000
185A206ILE0-0.062-0.03249.1960.0020.0020.0000.0000.0000.000
186A207LEU0-0.129-0.06549.1910.0020.0020.0000.0000.0000.000
187A208GLU-1-0.977-0.97447.989-0.035-0.0350.0000.0000.0000.000
188A209GLU-1-1.057-1.01552.385-0.028-0.0280.0000.0000.0000.000