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: QVV2Y

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2497009.110353
FMO2-HF: Nuclear repulsion 2412945.610365
FMO2-HF: Total energy -84063.499989
FMO2-MP2: Total energy -84308.701981


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.
-0.470.738-0.008-0.526-0.6730.002
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 : 0.017 / q_NPA : -0.008
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].
3A24CYS0-0.0380.0203.7641.0671.985-0.011-0.443-0.4640.002
4A25PRO0-0.003-0.0036.3800.3620.3620.0000.0000.0000.000
5A26PHE0-0.007-0.0278.1230.2410.2410.0000.0000.0000.000
6A27SER00.0680.0359.833-0.022-0.0220.0000.0000.0000.000
7A28GLN00.0670.01511.8980.0640.0640.0000.0000.0000.000
8A29ARG10.8070.9018.0590.0200.0200.0000.0000.0000.000
9A30LEU0-0.005-0.00112.1500.0830.0830.0000.0000.0000.000
10A31PHE0-0.028-0.03113.9500.0470.0470.0000.0000.0000.000
11A32MET00.0100.02316.8350.0280.0280.0000.0000.0000.000
12A33VAL00.0170.01114.8000.0310.0310.0000.0000.0000.000
13A34LEU0-0.024-0.01717.3830.0250.0250.0000.0000.0000.000
14A35TRP00.0290.00019.8430.0200.0200.0000.0000.0000.000
15A36LEU00.0030.00820.2880.0110.0110.0000.0000.0000.000
16A37LYS10.6870.83920.296-0.058-0.0580.0000.0000.0000.000
17A38GLY00.0180.00623.4460.0110.0110.0000.0000.0000.000
18A39VAL0-0.108-0.04922.4540.0020.0020.0000.0000.0000.000
19A40THR00.0130.01222.935-0.013-0.0130.0000.0000.0000.000
20A41PHE0-0.031-0.01418.706-0.007-0.0070.0000.0000.0000.000
21A42ASN0-0.022-0.00224.7680.0150.0150.0000.0000.0000.000
22A43VAL00.0450.02126.217-0.017-0.0170.0000.0000.0000.000
23A44THR0-0.018-0.01927.3670.0040.0040.0000.0000.0000.000
24A45THR00.0510.00826.860-0.012-0.0120.0000.0000.0000.000
25A46VAL00.0220.01126.398-0.016-0.0160.0000.0000.0000.000
26A47ASP-1-0.847-0.92325.045-0.149-0.1490.0000.0000.0000.000
27A48THR0-0.012-0.00321.770-0.020-0.0200.0000.0000.0000.000
28A49LYS10.9801.00221.4560.1720.1720.0000.0000.0000.000
29A50ARG11.0131.01221.6740.1250.1250.0000.0000.0000.000
30A51ARG10.9430.97317.9220.2880.2880.0000.0000.0000.000
31A52THR0-0.003-0.01317.323-0.050-0.0500.0000.0000.0000.000
32A53GLU-1-0.907-0.94816.923-0.296-0.2960.0000.0000.0000.000
33A54THR0-0.069-0.03916.776-0.008-0.0080.0000.0000.0000.000
34A55VAL0-0.002-0.01312.142-0.009-0.0090.0000.0000.0000.000
35A56GLN00.0380.01912.544-0.080-0.0800.0000.0000.0000.000
36A57LYS10.9160.96613.3580.1650.1650.0000.0000.0000.000
37A58LEU0-0.073-0.03812.0600.0290.0290.0000.0000.0000.000
38A60PRO00.0410.0289.359-0.122-0.1220.0000.0000.0000.000
39A61GLY0-0.031-0.0157.5930.0620.0620.0000.0000.0000.000
40A62GLY00.0320.0238.586-0.084-0.0840.0000.0000.0000.000
41A63GLN0-0.034-0.0438.162-0.326-0.3260.0000.0000.0000.000
42A64LEU00.0190.0199.9610.0090.0090.0000.0000.0000.000
43A65PRO0-0.061-0.0177.163-0.374-0.3740.0000.0000.0000.000
44A66PHE00.0520.0393.7970.3660.6560.003-0.083-0.2090.000
45A67LEU0-0.021-0.0077.2340.2870.2870.0000.0000.0000.000
46A68LEU00.0050.0137.557-0.123-0.1230.0000.0000.0000.000
47A69TYR0-0.016-0.0228.4780.0960.0960.0000.0000.0000.000
48A70GLY0-0.011-0.01911.1440.0620.0620.0000.0000.0000.000
49A71THR0-0.052-0.03213.2650.0070.0070.0000.0000.0000.000
50A72GLU-1-0.903-0.9325.688-0.218-0.2180.0000.0000.0000.000
51A73VAL00.013-0.0019.432-0.053-0.0530.0000.0000.0000.000
52A74HIS0-0.006-0.0118.8960.0290.0290.0000.0000.0000.000
53A75THR0-0.021-0.0097.340-0.063-0.0630.0000.0000.0000.000
54A76ASP-1-0.769-0.8665.204-0.464-0.4640.0000.0000.0000.000
55A77THR00.0160.0255.404-0.175-0.1750.0000.0000.0000.000
56A78ASN00.0540.0245.5250.1630.1630.0000.0000.0000.000
57A79LYS11.0300.9998.046-1.400-1.4000.0000.0000.0000.000
58A80ILE0-0.0010.01010.086-0.054-0.0540.0000.0000.0000.000
59A81GLU-1-0.775-0.88411.4890.0520.0520.0000.0000.0000.000
60A82GLU-1-0.955-0.97511.1350.7360.7360.0000.0000.0000.000
61A83PHE0-0.047-0.02314.072-0.036-0.0360.0000.0000.0000.000
62A84LEU00.011-0.01215.870-0.031-0.0310.0000.0000.0000.000
63A85GLU-1-0.749-0.87517.0470.0880.0880.0000.0000.0000.000
64A86ALA0-0.054-0.01618.448-0.011-0.0110.0000.0000.0000.000
65A87VAL0-0.042-0.03219.919-0.014-0.0140.0000.0000.0000.000
66A88LEU0-0.0340.00421.138-0.018-0.0180.0000.0000.0000.000
67A89CYS0-0.0040.01423.116-0.004-0.0040.0000.0000.0000.000
68A90PRO00.0110.01625.097-0.009-0.0090.0000.0000.0000.000
69A91PRO0-0.017-0.03028.5480.0080.0080.0000.0000.0000.000
70A92ARG10.9090.95728.724-0.043-0.0430.0000.0000.0000.000
71A93TYR00.0280.01825.071-0.004-0.0040.0000.0000.0000.000
72A94PRO00.0520.04025.0930.0120.0120.0000.0000.0000.000
73A95LYS10.9280.95223.284-0.092-0.0920.0000.0000.0000.000
74A96LEU00.0220.01319.747-0.010-0.0100.0000.0000.0000.000
75A97ALA0-0.038-0.00519.594-0.007-0.0070.0000.0000.0000.000
76A98ALA0-0.009-0.00220.109-0.012-0.0120.0000.0000.0000.000
77A99LEU0-0.062-0.03622.0520.0210.0210.0000.0000.0000.000
78A100ASN0-0.0030.00424.6280.0110.0110.0000.0000.0000.000
79A101PRO00.002-0.00821.4570.0040.0040.0000.0000.0000.000
80A102GLU-1-0.871-0.94720.5010.0970.0970.0000.0000.0000.000
81A103SER0-0.019-0.03221.044-0.014-0.0140.0000.0000.0000.000
82A104ASN0-0.028-0.01716.500-0.030-0.0300.0000.0000.0000.000
83A105THR0-0.085-0.04815.7090.0210.0210.0000.0000.0000.000
84A106ALA00.0470.03417.402-0.017-0.0170.0000.0000.0000.000
85A107GLY00.0250.00418.104-0.014-0.0140.0000.0000.0000.000
86A108LEU0-0.022-0.00412.433-0.040-0.0400.0000.0000.0000.000
87A109ASP-1-0.873-0.93613.166-0.062-0.0620.0000.0000.0000.000
88A110ILE00.0030.00415.239-0.039-0.0390.0000.0000.0000.000
89A111PHE00.0320.0109.5840.0190.0190.0000.0000.0000.000
90A112ALA00.0300.03512.209-0.061-0.0610.0000.0000.0000.000
91A113LYS10.8560.93013.0410.0500.0500.0000.0000.0000.000
92A114PHE00.0500.01913.7600.0130.0130.0000.0000.0000.000
93A115SER00.008-0.00311.783-0.059-0.0590.0000.0000.0000.000
94A116ALA0-0.028-0.02414.061-0.002-0.0020.0000.0000.0000.000
95A117TYR0-0.036-0.02516.5380.0060.0060.0000.0000.0000.000
96A118ILE00.0040.00215.8120.0180.0180.0000.0000.0000.000
97A119LYS10.9040.96711.8690.5850.5850.0000.0000.0000.000
98A120ASN0-0.053-0.02317.3530.0240.0240.0000.0000.0000.000
99A121SER00.0220.00420.7270.0030.0030.0000.0000.0000.000
100A122ASN00.0280.01823.7140.0180.0180.0000.0000.0000.000
101A123PRO00.0470.02026.2150.0010.0010.0000.0000.0000.000
102A124ALA0-0.008-0.00128.6260.0050.0050.0000.0000.0000.000
103A125LEU0-0.029-0.01524.0260.0080.0080.0000.0000.0000.000
104A126ASN00.0210.01024.892-0.022-0.0220.0000.0000.0000.000
105A127ASP-1-0.846-0.92125.704-0.105-0.1050.0000.0000.0000.000
106A128ASN0-0.095-0.06025.838-0.001-0.0010.0000.0000.0000.000
107A129LEU00.003-0.00320.0280.0070.0070.0000.0000.0000.000
108A130GLU-1-0.849-0.91422.198-0.137-0.1370.0000.0000.0000.000
109A131LYS10.9420.96724.3370.0760.0760.0000.0000.0000.000
110A132GLY0-0.054-0.01922.0240.0110.0110.0000.0000.0000.000
111A133LEU00.0480.02118.6490.0100.0100.0000.0000.0000.000
112A134LEU00.0140.00721.2850.0080.0080.0000.0000.0000.000
113A135LYS10.9120.95323.7450.0550.0550.0000.0000.0000.000
114A136ALA00.0260.01819.3810.0120.0120.0000.0000.0000.000
115A137LEU00.012-0.00421.0760.0070.0070.0000.0000.0000.000
116A138LYS10.8490.94922.9010.0500.0500.0000.0000.0000.000
117A139VAL0-0.005-0.01522.7880.0070.0070.0000.0000.0000.000
118A140LEU00.0190.01820.2350.0090.0090.0000.0000.0000.000
119A141ASP-1-0.799-0.91323.340-0.048-0.0480.0000.0000.0000.000
120A142ASN0-0.001-0.01526.7400.0000.0000.0000.0000.0000.000
121A143TYR00.004-0.00323.6270.0050.0050.0000.0000.0000.000
122A144LEU0-0.034-0.01124.0460.0030.0030.0000.0000.0000.000
123A145THR0-0.062-0.02227.5570.0010.0010.0000.0000.0000.000
124A146SER0-0.0020.01730.1610.0020.0020.0000.0000.0000.000
125A147PRO0-0.010-0.00630.6510.0010.0010.0000.0000.0000.000
126A148LEU0-0.038-0.01026.9720.0060.0060.0000.0000.0000.000
127A149PRO00.004-0.01829.742-0.003-0.0030.0000.0000.0000.000
128A150GLU-1-1.009-1.00531.9690.0150.0150.0000.0000.0000.000
129A151GLU-1-0.663-0.81532.139-0.001-0.0010.0000.0000.0000.000
130A152VAL0-0.079-0.01235.369-0.003-0.0030.0000.0000.0000.000
131A153ASP-1-0.947-0.97337.7410.0210.0210.0000.0000.0000.000
132A154GLU-1-0.984-0.98936.2330.0020.0020.0000.0000.0000.000
133A155THR0-0.065-0.03339.8030.0000.0000.0000.0000.0000.000
134A156SER0-0.012-0.01538.066-0.001-0.0010.0000.0000.0000.000
135A157ALA0-0.046-0.01939.5320.0000.0000.0000.0000.0000.000
136A158GLU-1-0.992-0.99741.050-0.029-0.0290.0000.0000.0000.000
137A159ASP-1-0.941-0.96639.755-0.021-0.0210.0000.0000.0000.000
138A160GLU-1-0.965-0.99440.2870.0020.0020.0000.0000.0000.000
139A161GLY00.0180.00838.6560.0000.0000.0000.0000.0000.000
140A162VAL0-0.054-0.01834.7780.0000.0000.0000.0000.0000.000
141A163SER0-0.089-0.05631.749-0.002-0.0020.0000.0000.0000.000
142A164GLN0-0.031-0.03533.603-0.009-0.0090.0000.0000.0000.000
143A165ARG10.7470.90125.892-0.004-0.0040.0000.0000.0000.000
144A166LYS10.8770.93528.8760.0280.0280.0000.0000.0000.000
145A167PHE0-0.019-0.03123.945-0.015-0.0150.0000.0000.0000.000
146A168LEU0-0.002-0.00519.2080.0080.0080.0000.0000.0000.000
147A169ASP-1-0.693-0.83723.1370.0650.0650.0000.0000.0000.000
148A170GLY00.0950.05825.0820.0080.0080.0000.0000.0000.000
149A171ASN00.014-0.00427.798-0.015-0.0150.0000.0000.0000.000
150A172GLU-1-0.936-0.96326.735-0.017-0.0170.0000.0000.0000.000
151A173LEU0-0.060-0.01721.8350.0010.0010.0000.0000.0000.000
152A174THR00.017-0.00320.8420.0150.0150.0000.0000.0000.000
153A175LEU0-0.018-0.03515.779-0.023-0.0230.0000.0000.0000.000
154A176ALA00.0090.02115.854-0.019-0.0190.0000.0000.0000.000
155A177ASP-1-0.696-0.84316.563-0.068-0.0680.0000.0000.0000.000
156A178CYS0-0.043-0.00215.579-0.040-0.0400.0000.0000.0000.000
157A179ASN00.0320.01210.741-0.141-0.1410.0000.0000.0000.000
158A180LEU0-0.0030.00613.328-0.079-0.0790.0000.0000.0000.000
159A181LEU00.0220.01415.677-0.044-0.0440.0000.0000.0000.000
160A182PRO00.001-0.00213.828-0.023-0.0230.0000.0000.0000.000
161A183LYS10.8050.8938.3170.3890.3890.0000.0000.0000.000
162A184LEU00.0190.00414.261-0.008-0.0080.0000.0000.0000.000
163A185HIS10.9360.97717.8050.2860.2860.0000.0000.0000.000
164A186ILE00.0200.00713.1610.0070.0070.0000.0000.0000.000
165A187VAL0-0.016-0.00915.7240.0120.0120.0000.0000.0000.000
166A188GLN00.0270.04417.8890.0150.0150.0000.0000.0000.000
167A189VAL00.0130.01919.9550.0180.0180.0000.0000.0000.000
168A190VAL00.0360.01916.7720.0180.0180.0000.0000.0000.000
169A191CYS0-0.054-0.02619.6830.0210.0210.0000.0000.0000.000
170A192LYS10.9760.99622.0740.1960.1960.0000.0000.0000.000
171A193LYS10.8980.95423.1050.2480.2480.0000.0000.0000.000
172A194TYR0-0.030-0.02120.4570.0220.0220.0000.0000.0000.000
173A195ARG10.8340.92521.8680.2440.2440.0000.0000.0000.000
174A196GLY0-0.0140.02025.6060.0160.0160.0000.0000.0000.000
175A197PHE0-0.032-0.00623.4320.0130.0130.0000.0000.0000.000
176A198THR0-0.015-0.02425.490-0.013-0.0130.0000.0000.0000.000
177A199ILE00.0250.01422.2950.0050.0050.0000.0000.0000.000
178A200PRO00.0250.02226.3680.0050.0050.0000.0000.0000.000
179A201GLU-1-0.849-0.93729.749-0.095-0.0950.0000.0000.0000.000
180A202ALA0-0.031-0.02132.1580.0050.0050.0000.0000.0000.000
181A203PHE0-0.066-0.02126.2040.0090.0090.0000.0000.0000.000
182A204ARG11.0010.98729.2720.0600.0600.0000.0000.0000.000
183A205GLY00.0400.02929.1060.0000.0000.0000.0000.0000.000
184A206VAL00.003-0.01123.653-0.003-0.0030.0000.0000.0000.000
185A207HIS0-0.039-0.02626.099-0.008-0.0080.0000.0000.0000.000
186A208ARG10.9520.96828.4250.0340.0340.0000.0000.0000.000
187A209TYR0-0.052-0.03320.606-0.010-0.0100.0000.0000.0000.000
188A210LEU00.001-0.01721.709-0.005-0.0050.0000.0000.0000.000
189A211SER0-0.027-0.00425.312-0.007-0.0070.0000.0000.0000.000
190A212ASN0-0.034-0.01927.8940.0000.0000.0000.0000.0000.000
191A213ALA0-0.010-0.00223.1540.0020.0020.0000.0000.0000.000
192A214TYR0-0.074-0.08522.366-0.016-0.0160.0000.0000.0000.000
193A215ALA0-0.0050.01126.390-0.003-0.0030.0000.0000.0000.000
194A216ARG10.8330.92425.5770.0660.0660.0000.0000.0000.000
195A217GLU-1-0.874-0.94625.773-0.100-0.1000.0000.0000.0000.000
196A218GLU-1-0.795-0.89222.588-0.091-0.0910.0000.0000.0000.000
197A219PHE0-0.0060.00818.964-0.023-0.0230.0000.0000.0000.000
198A220ALA00.016-0.00721.901-0.027-0.0270.0000.0000.0000.000
199A221SER0-0.021-0.01824.177-0.015-0.0150.0000.0000.0000.000
200A222THR0-0.109-0.06518.871-0.022-0.0220.0000.0000.0000.000
201A223CYS0-0.044-0.01918.912-0.055-0.0550.0000.0000.0000.000
202A224PRO0-0.069-0.01316.6750.0140.0140.0000.0000.0000.000
203A225ASP-1-0.864-0.95019.833-0.288-0.2880.0000.0000.0000.000
204A226ASP-1-0.928-0.97821.261-0.282-0.2820.0000.0000.0000.000
205A227GLU-1-0.918-0.94821.658-0.264-0.2640.0000.0000.0000.000
206A228GLU-1-0.931-0.96217.884-0.470-0.4700.0000.0000.0000.000
207A229ILE0-0.080-0.04416.814-0.069-0.0690.0000.0000.0000.000
208A230GLU-1-0.908-0.98917.622-0.312-0.3120.0000.0000.0000.000
209A231LEU00.0040.00419.622-0.008-0.0080.0000.0000.0000.000
210A232ALA0-0.074-0.01314.102-0.036-0.0360.0000.0000.0000.000
211A233TYR0-0.098-0.08910.822-0.051-0.0510.0000.0000.0000.000
212A234GLU-1-0.993-0.97216.146-0.308-0.3080.0000.0000.0000.000