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: KGG43

Calculation Name: 1RK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RK4

Chain ID: A

ChEMBL ID:

UniProt ID: O00299

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptHSide
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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499696.5114
FMO2-HF: Nuclear repulsion 2415631.793617
FMO2-HF: Total energy -84064.717783
FMO2-MP2: Total energy -84309.89664


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.
-0.7711.171-0.014-1.012-0.9170.005
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 : 0.033 / q_NPA : 0.015
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].
3A24CYS0-0.0350.0223.764-0.8210.844-0.014-0.940-0.7110.005
4A25PRO0-0.002-0.0036.1820.5510.5510.0000.0000.0000.000
5A26PHE0-0.015-0.0318.1240.4000.4000.0000.0000.0000.000
6A27SER00.0690.0309.4310.0860.0860.0000.0000.0000.000
7A28GLN00.0470.01211.8980.0810.0810.0000.0000.0000.000
8A29ARG10.7880.8728.3270.3400.3400.0000.0000.0000.000
9A30LEU0-0.0010.00112.1040.0960.0960.0000.0000.0000.000
10A31PHE0-0.026-0.02913.9510.0680.0680.0000.0000.0000.000
11A32MET00.0090.02616.8350.0430.0430.0000.0000.0000.000
12A33VAL00.0140.01015.0270.0460.0460.0000.0000.0000.000
13A34LEU0-0.026-0.01817.2840.0380.0380.0000.0000.0000.000
14A35TRP00.0430.00219.8440.0390.0390.0000.0000.0000.000
15A36LEU0-0.0040.00820.2670.0220.0220.0000.0000.0000.000
16A37LYS10.6820.83120.4280.1140.1140.0000.0000.0000.000
17A38GLY00.0070.00423.4470.0160.0160.0000.0000.0000.000
18A39VAL0-0.107-0.05022.4810.0070.0070.0000.0000.0000.000
19A40THR00.0170.01422.936-0.026-0.0260.0000.0000.0000.000
20A41PHE0-0.044-0.01718.532-0.013-0.0130.0000.0000.0000.000
21A42ASN0-0.022-0.01024.7690.0280.0280.0000.0000.0000.000
22A43VAL00.0450.02026.218-0.023-0.0230.0000.0000.0000.000
23A44THR0-0.020-0.03327.3660.0150.0150.0000.0000.0000.000
24A45THR00.0430.00426.863-0.020-0.0200.0000.0000.0000.000
25A46VAL00.0200.01426.440-0.021-0.0210.0000.0000.0000.000
26A47ASP-1-0.843-0.90325.186-0.269-0.2690.0000.0000.0000.000
27A48THR00.0230.00921.682-0.037-0.0370.0000.0000.0000.000
28A49LYS10.9741.00921.5110.2310.2310.0000.0000.0000.000
29A50ARG11.0041.01522.0200.2280.2280.0000.0000.0000.000
30A51ARG10.9130.96718.0360.4190.4190.0000.0000.0000.000
31A52THR00.001-0.01317.518-0.080-0.0800.0000.0000.0000.000
32A53GLU-1-0.888-0.94717.319-0.438-0.4380.0000.0000.0000.000
33A54THR0-0.086-0.05616.909-0.024-0.0240.0000.0000.0000.000
34A55VAL0-0.002-0.01412.291-0.049-0.0490.0000.0000.0000.000
35A56GLN00.0270.01612.855-0.133-0.1330.0000.0000.0000.000
36A57LYS10.9140.96413.8180.3900.3900.0000.0000.0000.000
37A58LEU0-0.063-0.03511.9740.0080.0080.0000.0000.0000.000
38A60PRO00.0380.0249.721-0.029-0.0290.0000.0000.0000.000
39A61GLY0-0.029-0.0147.7470.1300.1300.0000.0000.0000.000
40A62GLY00.0290.0208.7500.0300.0300.0000.0000.0000.000
41A63GLN0-0.026-0.0338.474-0.425-0.4250.0000.0000.0000.000
42A64LEU00.0230.0219.961-0.051-0.0510.0000.0000.0000.000
43A65PRO0-0.061-0.0187.180-0.352-0.3520.0000.0000.0000.000
44A66PHE00.0550.0373.9360.3460.5820.001-0.067-0.1710.000
45A67LEU0-0.004-0.0017.2380.3100.3100.0000.0000.0000.000
46A68LEU0-0.0040.0157.393-0.022-0.0220.0000.0000.0000.000
47A69TYR00.000-0.0088.271-0.121-0.1210.0000.0000.0000.000
48A70GLY0-0.005-0.01111.1450.0520.0520.0000.0000.0000.000
49A71THR0-0.024-0.02013.016-0.044-0.0440.0000.0000.0000.000
50A72GLU-1-0.891-0.9205.7851.0921.0920.0000.0000.0000.000
51A73VAL00.0300.0039.238-0.182-0.1820.0000.0000.0000.000
52A74HIS0-0.019-0.0188.8970.0590.0590.0000.0000.0000.000
53A75THR0-0.0160.0027.478-0.198-0.1980.0000.0000.0000.000
54A76ASP-1-0.762-0.8675.088-0.603-0.562-0.001-0.005-0.0350.000
55A77THR00.0040.0285.234-0.143-0.1430.0000.0000.0000.000
56A78ASN00.0330.0095.526-0.285-0.2850.0000.0000.0000.000
57A79LYS11.0211.0027.949-0.318-0.3180.0000.0000.0000.000
58A80ILE0-0.0120.00610.0880.0590.0590.0000.0000.0000.000
59A81GLU-1-0.770-0.85711.493-0.171-0.1710.0000.0000.0000.000
60A82GLU-1-0.900-0.96110.1990.3360.3360.0000.0000.0000.000
61A83PHE0-0.032-0.01914.0740.0200.0200.0000.0000.0000.000
62A84LEU00.011-0.00915.8520.0150.0150.0000.0000.0000.000
63A85GLU-1-0.741-0.85717.047-0.035-0.0350.0000.0000.0000.000
64A86ALA0-0.054-0.01818.4550.0160.0160.0000.0000.0000.000
65A87VAL0-0.032-0.02319.9730.0080.0080.0000.0000.0000.000
66A88LEU0-0.0340.00021.136-0.002-0.0020.0000.0000.0000.000
67A89CYS0-0.027-0.00223.117-0.003-0.0030.0000.0000.0000.000
68A90PRO00.0260.02425.098-0.003-0.0030.0000.0000.0000.000
69A91PRO0-0.026-0.03328.5480.0060.0060.0000.0000.0000.000
70A92ARG10.9020.95328.7950.0640.0640.0000.0000.0000.000
71A93TYR00.0330.02225.124-0.007-0.0070.0000.0000.0000.000
72A94PRO00.0500.04325.0410.0150.0150.0000.0000.0000.000
73A95LYS10.9200.95223.330-0.017-0.0170.0000.0000.0000.000
74A96LEU00.0350.01219.684-0.004-0.0040.0000.0000.0000.000
75A97ALA0-0.039-0.01119.592-0.003-0.0030.0000.0000.0000.000
76A98ALA0-0.0080.00020.106-0.004-0.0040.0000.0000.0000.000
77A99LEU0-0.062-0.03722.0510.0170.0170.0000.0000.0000.000
78A100ASN00.001-0.00924.6150.0180.0180.0000.0000.0000.000
79A101PRO0-0.006-0.01321.4600.0020.0020.0000.0000.0000.000
80A102GLU-1-0.858-0.94020.5000.1100.1100.0000.0000.0000.000
81A103SER0-0.012-0.03021.042-0.003-0.0030.0000.0000.0000.000
82A104ASN0-0.053-0.02416.520-0.035-0.0350.0000.0000.0000.000
83A105THR0-0.062-0.04615.7070.0300.0300.0000.0000.0000.000
84A106ALA00.0250.03317.4000.0050.0050.0000.0000.0000.000
85A107GLY00.0350.00418.102-0.022-0.0220.0000.0000.0000.000
86A108LEU0-0.0130.00412.147-0.030-0.0300.0000.0000.0000.000
87A109ASP-1-0.842-0.91413.1710.1220.1220.0000.0000.0000.000
88A110ILE0-0.0120.00515.243-0.015-0.0150.0000.0000.0000.000
89A111PHE00.0420.0159.7040.0160.0160.0000.0000.0000.000
90A112ALA00.0340.03812.175-0.036-0.0360.0000.0000.0000.000
91A113LYS10.8300.90113.045-0.144-0.1440.0000.0000.0000.000
92A114PHE00.0380.01213.7960.0050.0050.0000.0000.0000.000
93A115SER00.0100.00011.779-0.051-0.0510.0000.0000.0000.000
94A116ALA0-0.032-0.02314.064-0.004-0.0040.0000.0000.0000.000
95A117TYR0-0.081-0.07716.540-0.007-0.0070.0000.0000.0000.000
96A118ILE00.0080.00615.8500.0060.0060.0000.0000.0000.000
97A119LYS10.8370.92411.1850.1080.1080.0000.0000.0000.000
98A120ASN0-0.054-0.01617.3550.0240.0240.0000.0000.0000.000
99A121SER00.0420.01620.729-0.009-0.0090.0000.0000.0000.000
100A122ASN00.0140.00623.716-0.002-0.0020.0000.0000.0000.000
101A123PRO00.0550.01826.2170.0050.0050.0000.0000.0000.000
102A124ALA0-0.0080.00328.6280.0020.0020.0000.0000.0000.000
103A125LEU0-0.020-0.01323.4870.0080.0080.0000.0000.0000.000
104A126ASN00.0130.00724.895-0.005-0.0050.0000.0000.0000.000
105A127ASP-1-0.773-0.87225.707-0.016-0.0160.0000.0000.0000.000
106A128ASN0-0.062-0.03925.898-0.003-0.0030.0000.0000.0000.000
107A129LEU00.000-0.00319.8760.0090.0090.0000.0000.0000.000
108A130GLU-1-0.807-0.87122.201-0.061-0.0610.0000.0000.0000.000
109A131LYS10.8510.91024.341-0.002-0.0020.0000.0000.0000.000
110A132GLY0-0.058-0.02222.0270.0070.0070.0000.0000.0000.000
111A133LEU00.0450.01918.6070.0120.0120.0000.0000.0000.000
112A134LEU00.0130.00721.289-0.001-0.0010.0000.0000.0000.000
113A135LYS10.9070.95023.928-0.052-0.0520.0000.0000.0000.000
114A136ALA00.0260.02519.3470.0050.0050.0000.0000.0000.000
115A137LEU00.013-0.00921.220-0.002-0.0020.0000.0000.0000.000
116A138LYS10.8350.92222.906-0.001-0.0010.0000.0000.0000.000
117A139VAL0-0.017-0.01622.6350.0010.0010.0000.0000.0000.000
118A140LEU00.0190.01520.2300.0030.0030.0000.0000.0000.000
119A141ASP-1-0.763-0.87623.345-0.027-0.0270.0000.0000.0000.000
120A142ASN00.003-0.00326.745-0.007-0.0070.0000.0000.0000.000
121A143TYR0-0.003-0.00623.4210.0040.0040.0000.0000.0000.000
122A144LEU0-0.035-0.01224.055-0.003-0.0030.0000.0000.0000.000
123A145THR0-0.033-0.02127.556-0.002-0.0020.0000.0000.0000.000
124A146SER0-0.0150.00530.0520.0020.0020.0000.0000.0000.000
125A147PRO0-0.021-0.01330.649-0.001-0.0010.0000.0000.0000.000
126A148LEU0-0.0240.00026.9380.0080.0080.0000.0000.0000.000
127A149PRO00.012-0.01429.783-0.003-0.0030.0000.0000.0000.000
128A150GLU-1-0.989-0.99331.964-0.009-0.0090.0000.0000.0000.000
129A151GLU-1-0.732-0.85531.976-0.008-0.0080.0000.0000.0000.000
130A152VAL0-0.065-0.00135.367-0.001-0.0010.0000.0000.0000.000
131A153ASP-1-0.931-0.96437.7400.0150.0150.0000.0000.0000.000
132A154GLU-1-0.951-0.97236.527-0.018-0.0180.0000.0000.0000.000
133A155THR0-0.064-0.02839.8020.0020.0020.0000.0000.0000.000
134A156SER0-0.014-0.01337.981-0.002-0.0020.0000.0000.0000.000
135A157ALA0-0.039-0.01739.5290.0000.0000.0000.0000.0000.000
136A158GLU-1-0.996-1.00441.051-0.027-0.0270.0000.0000.0000.000
137A159ASP-1-0.937-0.95839.788-0.009-0.0090.0000.0000.0000.000
138A160GLU-1-0.977-1.00540.2850.0080.0080.0000.0000.0000.000
139A161GLY00.0230.01238.6530.0020.0020.0000.0000.0000.000
140A162VAL0-0.043-0.00834.8890.0030.0030.0000.0000.0000.000
141A163SER0-0.081-0.04631.617-0.005-0.0050.0000.0000.0000.000
142A164GLN0-0.025-0.05533.601-0.006-0.0060.0000.0000.0000.000
143A165ARG10.7550.90325.960-0.007-0.0070.0000.0000.0000.000
144A166LYS10.8710.94328.8920.0540.0540.0000.0000.0000.000
145A167PHE0-0.023-0.03523.947-0.014-0.0140.0000.0000.0000.000
146A168LEU0-0.002-0.00419.1810.0150.0150.0000.0000.0000.000
147A169ASP-1-0.704-0.82023.0750.0360.0360.0000.0000.0000.000
148A170GLY00.1090.06225.0800.0070.0070.0000.0000.0000.000
149A171ASN0-0.013-0.02427.797-0.015-0.0150.0000.0000.0000.000
150A172GLU-1-0.821-0.90926.614-0.092-0.0920.0000.0000.0000.000
151A173LEU0-0.067-0.00721.8270.0020.0020.0000.0000.0000.000
152A174THR00.016-0.00920.8010.0100.0100.0000.0000.0000.000
153A175LEU0-0.011-0.03115.759-0.026-0.0260.0000.0000.0000.000
154A176ALA00.0070.01915.853-0.027-0.0270.0000.0000.0000.000
155A177ASP-1-0.704-0.84416.562-0.101-0.1010.0000.0000.0000.000
156A178CYS0-0.047-0.00815.659-0.038-0.0380.0000.0000.0000.000
157A179ASN00.0190.00210.897-0.171-0.1710.0000.0000.0000.000
158A180LEU00.0010.01113.327-0.061-0.0610.0000.0000.0000.000
159A181LEU00.0250.01915.675-0.027-0.0270.0000.0000.0000.000
160A182PRO00.011-0.00213.822-0.008-0.0080.0000.0000.0000.000
161A183LYS10.8190.9048.4550.4180.4180.0000.0000.0000.000
162A184LEU00.0160.00414.2670.0150.0150.0000.0000.0000.000
163A185HIS10.9160.96517.8110.3230.3230.0000.0000.0000.000
164A186ILE00.0120.00013.1980.0120.0120.0000.0000.0000.000
165A187VAL0-0.014-0.00515.7680.0240.0240.0000.0000.0000.000
166A188GLN00.0230.01717.8950.0100.0100.0000.0000.0000.000
167A189VAL0-0.0250.00519.9170.0210.0210.0000.0000.0000.000
168A190VAL00.0220.01216.7990.0180.0180.0000.0000.0000.000
169A191CYS0-0.046-0.02819.7130.0300.0300.0000.0000.0000.000
170A192LYS10.9460.98622.0790.2190.2190.0000.0000.0000.000
171A193LYS10.7890.88823.1700.2440.2440.0000.0000.0000.000
172A194TYR0-0.037-0.04020.6860.0280.0280.0000.0000.0000.000
173A195ARG10.8010.90021.8810.1320.1320.0000.0000.0000.000
174A196GLY0-0.0020.02525.6100.0150.0150.0000.0000.0000.000
175A197PHE0-0.035-0.00823.1950.0130.0130.0000.0000.0000.000
176A198THR0-0.009-0.01825.495-0.014-0.0140.0000.0000.0000.000
177A199ILE00.0180.00822.2890.0100.0100.0000.0000.0000.000
178A200PRO00.0290.01826.374-0.001-0.0010.0000.0000.0000.000
179A201GLU-1-0.811-0.90329.755-0.077-0.0770.0000.0000.0000.000
180A202ALA0-0.026-0.00932.1640.0030.0030.0000.0000.0000.000
181A203PHE0-0.052-0.01626.0510.0090.0090.0000.0000.0000.000
182A204ARG10.9410.93229.2780.0490.0490.0000.0000.0000.000
183A205GLY00.0450.03429.107-0.005-0.0050.0000.0000.0000.000
184A206VAL00.003-0.01423.675-0.008-0.0080.0000.0000.0000.000
185A207HIS0-0.026-0.01226.105-0.018-0.0180.0000.0000.0000.000
186A208ARG10.8940.96428.4310.0250.0250.0000.0000.0000.000
187A209TYR0-0.026-0.01620.637-0.014-0.0140.0000.0000.0000.000
188A210LEU00.003-0.01321.661-0.013-0.0130.0000.0000.0000.000
189A211SER0-0.038-0.02625.319-0.014-0.0140.0000.0000.0000.000
190A212ASN0-0.047-0.03827.981-0.003-0.0030.0000.0000.0000.000
191A213ALA0-0.0060.00323.125-0.004-0.0040.0000.0000.0000.000
192A214TYR0-0.049-0.04122.274-0.026-0.0260.0000.0000.0000.000
193A215ALA0-0.0110.00826.389-0.005-0.0050.0000.0000.0000.000
194A216ARG10.7730.88525.6280.1260.1260.0000.0000.0000.000
195A217GLU-1-0.868-0.93525.773-0.178-0.1780.0000.0000.0000.000
196A218GLU-1-0.810-0.90322.646-0.177-0.1770.0000.0000.0000.000
197A219PHE0-0.0090.00218.813-0.037-0.0370.0000.0000.0000.000
198A220ALA00.021-0.00621.901-0.031-0.0310.0000.0000.0000.000
199A221SER0-0.030-0.02124.177-0.012-0.0120.0000.0000.0000.000
200A222THR0-0.098-0.05718.905-0.033-0.0330.0000.0000.0000.000
201A223CYS0-0.057-0.02118.912-0.066-0.0660.0000.0000.0000.000
202A224PRO0-0.040-0.00616.5970.0130.0130.0000.0000.0000.000
203A225ASP-1-0.839-0.93119.833-0.337-0.3370.0000.0000.0000.000
204A226ASP-1-0.873-0.98021.266-0.292-0.2920.0000.0000.0000.000
205A227GLU-1-0.953-0.96321.664-0.274-0.2740.0000.0000.0000.000
206A228GLU-1-0.884-0.93817.526-0.591-0.5910.0000.0000.0000.000
207A229ILE0-0.077-0.04716.664-0.059-0.0590.0000.0000.0000.000
208A230GLU-1-0.856-0.93717.627-0.271-0.2710.0000.0000.0000.000
209A231LEU00.0380.03219.6270.0060.0060.0000.0000.0000.000
210A232ALA0-0.071-0.01014.140-0.028-0.0280.0000.0000.0000.000
211A233TYR0-0.073-0.07410.791-0.024-0.0240.0000.0000.0000.000
212A234GLU-1-1.035-0.99616.150-0.237-0.2370.0000.0000.0000.000