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: YV1R2

Calculation Name: 1KUT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KUT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0X0

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2585264.620208
FMO2-HF: Nuclear repulsion 2500140.5147
FMO2-HF: Total energy -85124.105508
FMO2-MP2: Total energy -85373.637481


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:7:THR)


Summations of interaction energy for fragment #1(A:7: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.
-42.816-61.38558.255-23.524-16.161-0.09
Interaction energy analysis for fragmet #1(A:7:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.012
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].
3A9ILE0-0.0230.0093.9050.7743.211-0.012-1.306-1.1190.003
4A10VAL00.0310.0176.408-0.547-0.5470.0000.0000.0000.000
5A11LYS10.9100.94610.0220.1670.1670.0000.0000.0000.000
6A12VAL00.0200.01313.233-0.063-0.0630.0000.0000.0000.000
7A13THR0-0.040-0.03216.8120.0000.0000.0000.0000.0000.000
8A14GLY00.0110.02019.321-0.003-0.0030.0000.0000.0000.000
9A15ASP-1-0.921-0.96221.551-0.096-0.0960.0000.0000.0000.000
10A16TYR0-0.025-0.01419.519-0.009-0.0090.0000.0000.0000.000
11A17ALA0-0.018-0.01314.6630.0290.0290.0000.0000.0000.000
12A18LEU00.0020.00713.802-0.039-0.0390.0000.0000.0000.000
13A19LEU0-0.002-0.0067.4130.1310.1310.0000.0000.0000.000
14A20GLU-1-0.889-0.9447.112-1.551-1.5510.0000.0000.0000.000
15A21PHE00.027-0.0054.984-0.427-0.4270.0000.0000.0000.000
16A22LYS10.8580.9102.3073.2875.8281.105-1.477-2.1680.007
17A23ASP-1-0.782-0.8832.061-9.063-9.0585.172-2.698-2.480-0.031
18A24ASP-1-0.767-0.8831.728-35.867-59.74351.987-17.967-10.144-0.069
19A36LEU0-0.032-0.0226.172-0.210-0.2100.0000.0000.0000.000
20A37THR0-0.052-0.0467.3990.2630.2630.0000.0000.0000.000
21A38GLY00.0530.0337.198-0.026-0.0260.0000.0000.0000.000
22A39LYS10.8540.8933.626-1.512-1.2190.005-0.065-0.2330.000
23A40GLY00.0200.0224.750-0.219-0.202-0.001-0.011-0.0050.000
24A41SER00.019-0.0245.2840.2350.249-0.0010.000-0.0120.000
25A42ILE00.0110.0228.9440.1430.1430.0000.0000.0000.000
26A43CYS0-0.0070.0136.6250.2750.2750.0000.0000.0000.000
27A44ALA00.0140.0368.5380.1660.1660.0000.0000.0000.000
28A45GLU-1-0.769-0.8579.984-0.267-0.2670.0000.0000.0000.000
29A46THR0-0.026-0.03812.0020.1420.1420.0000.0000.0000.000
30A47THR00.002-0.00810.3660.1200.1200.0000.0000.0000.000
31A48ALA0-0.020-0.01013.0430.0910.0910.0000.0000.0000.000
32A49ILE0-0.026-0.00215.6860.0690.0690.0000.0000.0000.000
33A50LEU00.0270.01515.3200.0450.0450.0000.0000.0000.000
34A51MET00.0020.01613.5700.0430.0430.0000.0000.0000.000
35A52LYS10.8730.94017.7380.2460.2460.0000.0000.0000.000
36A53TYR0-0.034-0.04320.6450.0320.0320.0000.0000.0000.000
37A54LEU00.019-0.00818.6100.0250.0250.0000.0000.0000.000
38A55SER0-0.013-0.01120.8900.0220.0220.0000.0000.0000.000
39A56GLU-1-0.893-0.90923.400-0.138-0.1380.0000.0000.0000.000
40A57LYS10.8540.92925.6670.1400.1400.0000.0000.0000.000
41A58GLY00.0020.01127.0900.0120.0120.0000.0000.0000.000
42A59ILE0-0.043-0.01821.0670.0140.0140.0000.0000.0000.000
43A60LYS10.8560.92022.2960.0970.0970.0000.0000.0000.000
44A61THR0-0.007-0.01417.887-0.005-0.0050.0000.0000.0000.000
45A62HIS00.020-0.00411.7360.0620.0620.0000.0000.0000.000
46A63LEU0-0.0040.00715.688-0.016-0.0160.0000.0000.0000.000
47A64VAL0-0.073-0.01917.5190.0450.0450.0000.0000.0000.000
48A65GLU-1-0.858-0.92318.373-0.263-0.2630.0000.0000.0000.000
49A66TYR00.002-0.02312.3340.0090.0090.0000.0000.0000.000
50A67ILE00.0030.00614.7550.0700.0700.0000.0000.0000.000
51A68PRO0-0.0010.02213.871-0.123-0.1230.0000.0000.0000.000
52A69PRO0-0.009-0.01211.4250.0290.0290.0000.0000.0000.000
53A70ARG10.8670.9247.1361.8171.8170.0000.0000.0000.000
54A71THR00.0380.0208.824-0.448-0.4480.0000.0000.0000.000
55A72LEU0-0.0090.01611.3140.1430.1430.0000.0000.0000.000
56A73LYS10.8620.92913.4370.2700.2700.0000.0000.0000.000
57A74VAL00.021-0.00313.6320.0040.0040.0000.0000.0000.000
58A75ILE00.0140.00216.8130.0340.0340.0000.0000.0000.000
59A76PRO0-0.006-0.00416.957-0.008-0.0080.0000.0000.0000.000
60A77LEU0-0.020-0.01115.6540.0100.0100.0000.0000.0000.000
61A78LYS10.8330.90816.1230.0370.0370.0000.0000.0000.000
62A79MET00.0080.00211.974-0.024-0.0240.0000.0000.0000.000
63A80PHE00.0190.00115.6680.0220.0220.0000.0000.0000.000
64A81PRO00.0060.01514.7270.0020.0020.0000.0000.0000.000
65A82LEU0-0.037-0.02915.1790.0110.0110.0000.0000.0000.000
66A83GLU-1-0.811-0.88710.8650.1450.1450.0000.0000.0000.000
67A84VAL0-0.040-0.02315.3030.0090.0090.0000.0000.0000.000
68A85VAL0-0.004-0.00916.000-0.019-0.0190.0000.0000.0000.000
69A86VAL0-0.023-0.00718.5110.0050.0050.0000.0000.0000.000
70A87ARG10.8020.86418.536-0.076-0.0760.0000.0000.0000.000
71A88LEU00.004-0.00422.821-0.004-0.0040.0000.0000.0000.000
72A89LYS10.8020.90624.496-0.004-0.0040.0000.0000.0000.000
73A90LYS10.7840.90924.765-0.030-0.0300.0000.0000.0000.000
74A91ALA00.0600.01321.9410.0000.0000.0000.0000.0000.000
75A92GLY0-0.004-0.02320.2290.0060.0060.0000.0000.0000.000
76A93SER0-0.008-0.00519.117-0.002-0.0020.0000.0000.0000.000
77A94PHE00.0120.02721.184-0.003-0.0030.0000.0000.0000.000
78A95VAL00.0320.01624.311-0.001-0.0010.0000.0000.0000.000
79A96ARG10.9170.95418.902-0.160-0.1600.0000.0000.0000.000
80A97ARG10.7670.86522.736-0.092-0.0920.0000.0000.0000.000
81A98TYR0-0.029-0.02125.583-0.002-0.0020.0000.0000.0000.000
82A99GLY00.0090.03029.145-0.006-0.0060.0000.0000.0000.000
83A100GLY0-0.015-0.02529.827-0.002-0.0020.0000.0000.0000.000
84A101ALA00.0000.00230.6510.0050.0050.0000.0000.0000.000
85A102GLU-1-0.829-0.92822.7330.0950.0950.0000.0000.0000.000
86A103GLY0-0.002-0.00426.627-0.002-0.0020.0000.0000.0000.000
87A104GLU-1-0.829-0.90627.5700.0260.0260.0000.0000.0000.000
88A105ASP-1-0.849-0.91328.8700.0030.0030.0000.0000.0000.000
89A106LEU0-0.027-0.01426.4540.0040.0040.0000.0000.0000.000
90A107PRO0-0.026-0.02130.308-0.005-0.0050.0000.0000.0000.000
91A108VAL0-0.0040.00230.632-0.004-0.0040.0000.0000.0000.000
92A109PRO0-0.016-0.01725.3900.0050.0050.0000.0000.0000.000
93A110LEU00.0150.03625.3860.0000.0000.0000.0000.0000.000
94A111VAL0-0.013-0.02022.440-0.004-0.0040.0000.0000.0000.000
95A112GLU-1-0.735-0.83221.4000.0820.0820.0000.0000.0000.000
96A113PHE00.015-0.00419.996-0.008-0.0080.0000.0000.0000.000
97A114PHE0-0.007-0.00616.7140.0000.0000.0000.0000.0000.000
98A115ILE0-0.016-0.00417.243-0.011-0.0110.0000.0000.0000.000
99A116LYS10.7570.8579.620-0.156-0.1560.0000.0000.0000.000
100A117ASP-1-0.885-0.97514.4360.2410.2410.0000.0000.0000.000
101A118ASP-1-0.885-0.93911.8470.4340.4340.0000.0000.0000.000
102A119GLU-1-0.880-0.91113.9930.2020.2020.0000.0000.0000.000
103A120ARG10.7440.85417.123-0.202-0.2020.0000.0000.0000.000
104A121HIS0-0.064-0.02516.324-0.037-0.0370.0000.0000.0000.000
105A122ASP-1-0.861-0.91913.3520.2950.2950.0000.0000.0000.000
106A123PRO00.0040.01716.549-0.023-0.0230.0000.0000.0000.000
107A124MET0-0.034-0.03020.306-0.008-0.0080.0000.0000.0000.000
108A125VAL0-0.035-0.01321.458-0.003-0.0030.0000.0000.0000.000
109A126CYS0-0.010-0.01324.147-0.009-0.0090.0000.0000.0000.000
110A127VAL00.028-0.01126.7540.0020.0020.0000.0000.0000.000
111A128ASP-1-0.843-0.93328.0670.0330.0330.0000.0000.0000.000
112A129HIS00.0430.03026.3920.0020.0020.0000.0000.0000.000
113A130LEU00.0040.00322.1760.0040.0040.0000.0000.0000.000
114A131GLU-1-0.801-0.88125.4830.0260.0260.0000.0000.0000.000
115A132ILE0-0.035-0.02028.5140.0010.0010.0000.0000.0000.000
116A133LEU0-0.026-0.00924.1380.0030.0030.0000.0000.0000.000
117A134GLY0-0.017-0.00425.3450.0060.0060.0000.0000.0000.000
118A135ILE0-0.036-0.00420.372-0.002-0.0020.0000.0000.0000.000
119A136ALA0-0.041-0.04022.472-0.007-0.0070.0000.0000.0000.000
120A137THR00.012-0.00324.6890.0000.0000.0000.0000.0000.000
121A138LYS10.8740.91127.515-0.032-0.0320.0000.0000.0000.000
122A139LYS10.9400.97829.2280.0130.0130.0000.0000.0000.000
123A140GLN00.0250.03024.340-0.002-0.0020.0000.0000.0000.000
124A141ALA00.0490.02124.577-0.006-0.0060.0000.0000.0000.000
125A142GLU-1-0.820-0.90425.655-0.001-0.0010.0000.0000.0000.000
126A143LYS10.8370.89825.7100.0350.0350.0000.0000.0000.000
127A144MET0-0.0220.00620.655-0.011-0.0110.0000.0000.0000.000
128A145LYS10.8510.92522.981-0.012-0.0120.0000.0000.0000.000
129A146GLU-1-0.819-0.89525.285-0.039-0.0390.0000.0000.0000.000
130A147ALA0-0.028-0.00722.549-0.007-0.0070.0000.0000.0000.000
131A148ALA00.0660.03320.757-0.012-0.0120.0000.0000.0000.000
132A149VAL00.0120.02421.833-0.005-0.0050.0000.0000.0000.000
133A150LYS10.8630.91924.9620.0810.0810.0000.0000.0000.000
134A151ILE0-0.019-0.00718.717-0.006-0.0060.0000.0000.0000.000
135A152THR00.0400.01220.914-0.009-0.0090.0000.0000.0000.000
136A153LEU0-0.0210.00122.0750.0020.0020.0000.0000.0000.000
137A154ALA00.0040.00223.7530.0000.0000.0000.0000.0000.000
138A155LEU00.0110.00817.166-0.008-0.0080.0000.0000.0000.000
139A156LYS10.8460.91321.7100.0360.0360.0000.0000.0000.000
140A157GLU-1-0.802-0.86823.756-0.100-0.1000.0000.0000.0000.000
141A158PHE0-0.006-0.00620.5200.0010.0010.0000.0000.0000.000
142A159PHE00.049-0.00217.4450.0010.0010.0000.0000.0000.000
143A160GLU-1-0.807-0.87023.546-0.033-0.0330.0000.0000.0000.000
144A161ARG10.8110.88826.2920.1210.1210.0000.0000.0000.000
145A162ALA00.0040.01424.8290.0010.0010.0000.0000.0000.000
146A163ASN0-0.039-0.01526.9690.0060.0060.0000.0000.0000.000
147A164PHE00.0240.00621.4430.0090.0090.0000.0000.0000.000
148A165GLU-1-0.807-0.90823.736-0.005-0.0050.0000.0000.0000.000
149A166LEU0-0.016-0.00418.0210.0050.0050.0000.0000.0000.000
150A167TRP0-0.070-0.04820.5030.0110.0110.0000.0000.0000.000
151A168ASP-1-0.842-0.93118.7040.0720.0720.0000.0000.0000.000
152A169ILE0-0.027-0.01014.866-0.003-0.0030.0000.0000.0000.000
153A170LYS10.8400.9428.8230.0930.0930.0000.0000.0000.000
154A171TYR0-0.008-0.03713.876-0.057-0.0570.0000.0000.0000.000
155A172GLU-1-0.771-0.8659.8080.0270.0270.0000.0000.0000.000
156A173PHE00.0300.00214.339-0.043-0.0430.0000.0000.0000.000
157A174GLY00.0630.03016.5990.0270.0270.0000.0000.0000.000
158A175LEU0-0.0270.00818.164-0.012-0.0120.0000.0000.0000.000
159A176ASP-1-0.697-0.82520.657-0.073-0.0730.0000.0000.0000.000
160A177LYS10.8260.88221.8890.0950.0950.0000.0000.0000.000
161A178ASP-1-0.833-0.89224.706-0.067-0.0670.0000.0000.0000.000
162A179GLY0-0.0060.01125.3990.0060.0060.0000.0000.0000.000
163A180ASN0-0.088-0.04325.019-0.003-0.0030.0000.0000.0000.000
164A181VAL00.017-0.00321.544-0.002-0.0020.0000.0000.0000.000
165A182VAL0-0.044-0.01318.779-0.007-0.0070.0000.0000.0000.000
166A183LEU00.0000.00116.0300.0120.0120.0000.0000.0000.000
167A184GLY00.037-0.00514.019-0.020-0.0200.0000.0000.0000.000
168A185ASP-1-0.808-0.9078.275-0.538-0.5380.0000.0000.0000.000
169A186GLU-1-0.786-0.8635.627-1.840-1.8400.0000.0000.0000.000
170A187ILE0-0.022-0.00210.1580.1460.1460.0000.0000.0000.000
171A188SER00.041-0.0147.9880.0790.0790.0000.0000.0000.000
172A189PRO00.0480.01610.7760.0750.0750.0000.0000.0000.000
173A190ASP-1-0.772-0.8165.9540.3460.3460.0000.0000.0000.000
174A191THR0-0.047-0.0238.5010.0640.0640.0000.0000.0000.000
175A192PHE00.0160.01310.8800.0330.0330.0000.0000.0000.000
176A193ARG10.8740.95614.177-0.091-0.0910.0000.0000.0000.000
177A194LEU00.0040.00516.848-0.014-0.0140.0000.0000.0000.000
178A195ARG10.8980.95318.362-0.044-0.0440.0000.0000.0000.000
179A196LYS10.9280.95022.285-0.011-0.0110.0000.0000.0000.000
180A197LYS10.8400.90225.2100.0480.0480.0000.0000.0000.000
181A198GLY00.0410.01528.466-0.003-0.0030.0000.0000.0000.000
182A199GLU-1-0.896-0.93123.2360.0170.0170.0000.0000.0000.000
183A200ILE0-0.0020.00627.5310.0080.0080.0000.0000.0000.000
184A201PHE0-0.023-0.01122.4920.0000.0000.0000.0000.0000.000
185A202ASP-1-0.783-0.89926.5680.0480.0480.0000.0000.0000.000
186A203LYS10.9400.97626.336-0.053-0.0530.0000.0000.0000.000
187A204ASP-1-0.846-0.92726.3140.0760.0760.0000.0000.0000.000
188A205VAL00.0140.00524.1570.0040.0040.0000.0000.0000.000
189A206TYR00.0090.01118.7040.0110.0110.0000.0000.0000.000
190A207ARG10.8400.89721.805-0.074-0.0740.0000.0000.0000.000
191A208ARG10.8380.90222.840-0.030-0.0300.0000.0000.0000.000
192A209ASP-1-0.786-0.87719.6560.0280.0280.0000.0000.0000.000
193A210LEU0-0.063-0.02017.4210.0120.0120.0000.0000.0000.000
194A211GLY0-0.0040.00817.6230.0350.0350.0000.0000.0000.000
195A212ASP-1-0.812-0.89115.395-0.009-0.0090.0000.0000.0000.000
196A213PRO00.0200.00111.557-0.018-0.0180.0000.0000.0000.000
197A214LEU0-0.003-0.0019.7090.0140.0140.0000.0000.0000.000
198A215LYS10.7990.90512.295-0.097-0.0970.0000.0000.0000.000
199A216LYS10.8680.93010.561-0.289-0.2890.0000.0000.0000.000
200A217TYR0-0.052-0.0618.0670.0040.0040.0000.0000.0000.000
201A218ARG10.8490.90812.6260.0330.0330.0000.0000.0000.000
202A219GLU-1-0.817-0.90215.299-0.030-0.0300.0000.0000.0000.000
203A220VAL00.0080.00114.938-0.006-0.0060.0000.0000.0000.000
204A221LEU0-0.0010.02013.397-0.009-0.0090.0000.0000.0000.000
205A222GLU-1-0.933-0.98516.045-0.190-0.1900.0000.0000.0000.000
206A223LEU0-0.0330.00319.4390.0100.0100.0000.0000.0000.000
207A224CYS0-0.042-0.03417.6840.0050.0050.0000.0000.0000.000
208A225ARG10.8290.87316.3990.3600.3600.0000.0000.0000.000
209A226SER0-0.0190.00520.9870.0140.0140.0000.0000.0000.000
210A227LEU00.004-0.00523.1810.0100.0100.0000.0000.0000.000
211A228ASN0-0.106-0.04221.8730.0000.0000.0000.0000.0000.000
212A229SER0-0.031-0.02023.967-0.001-0.0010.0000.0000.0000.000
213A230GLN0-0.0350.00123.0190.0110.0110.0000.0000.0000.000