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: NNY4Q

Calculation Name: 1Q6H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q6H

Chain ID: A

ChEMBL ID:

UniProt ID: P45523

Base Structure: X-ray

Registration Date: 2023-09-24

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963272.439206
FMO2-HF: Nuclear repulsion 1884127.269249
FMO2-HF: Total energy -79145.169957
FMO2-MP2: Total energy -79380.085018


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:15:ALA)


Summations of interaction energy for fragment #1(A:15:ALA)
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.
-0.4561.4290.24-0.765-1.360.002
Interaction energy analysis for fragmet #1(A:15:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.002
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].
3A17LYS10.8850.9362.6361.2743.1590.240-0.765-1.3600.002
4A18ASN00.008-0.0076.1290.1380.1380.0000.0000.0000.000
5A19ASP-1-0.808-0.8848.9590.2440.2440.0000.0000.0000.000
6A20ASP-1-0.820-0.89211.517-0.042-0.0420.0000.0000.0000.000
7A21GLN0-0.015-0.0046.300-0.510-0.5100.0000.0000.0000.000
8A22LYS10.9240.9576.981-1.394-1.3940.0000.0000.0000.000
9A23SER00.011-0.0308.262-0.007-0.0070.0000.0000.0000.000
10A24ALA00.0130.02311.338-0.021-0.0210.0000.0000.0000.000
11A25TYR0-0.013-0.0117.833-0.043-0.0430.0000.0000.0000.000
12A26ALA0-0.009-0.0069.7980.0110.0110.0000.0000.0000.000
13A27LEU00.0250.01611.440-0.008-0.0080.0000.0000.0000.000
14A28GLY00.0470.02613.3670.0010.0010.0000.0000.0000.000
15A29ALA0-0.025-0.01611.3630.0050.0050.0000.0000.0000.000
16A30SER0-0.044-0.01813.4930.0110.0110.0000.0000.0000.000
17A31LEU00.0420.01216.4070.0010.0010.0000.0000.0000.000
18A32GLY00.0270.01516.7340.0010.0010.0000.0000.0000.000
19A33ARG10.8750.93716.9490.0040.0040.0000.0000.0000.000
20A34TYR00.0290.01818.6690.0090.0090.0000.0000.0000.000
21A35MET00.0410.02821.1590.0070.0070.0000.0000.0000.000
22A36GLU-1-0.852-0.92119.884-0.073-0.0730.0000.0000.0000.000
23A37ASN0-0.012-0.02121.8680.0150.0150.0000.0000.0000.000
24A38SER00.0370.02024.3700.0060.0060.0000.0000.0000.000
25A39LEU0-0.005-0.00525.0940.0030.0030.0000.0000.0000.000
26A40LYS10.8690.93723.2800.0630.0630.0000.0000.0000.000
27A41GLU-1-0.823-0.89827.783-0.013-0.0130.0000.0000.0000.000
28A42GLN00.0260.00629.347-0.001-0.0010.0000.0000.0000.000
29A43GLU-1-0.865-0.92028.747-0.050-0.0500.0000.0000.0000.000
30A44LYS10.7480.85930.4460.0180.0180.0000.0000.0000.000
31A45LEU0-0.054-0.03334.2730.0030.0030.0000.0000.0000.000
32A46GLY0-0.0010.00635.7790.0000.0000.0000.0000.0000.000
33A47ILE0-0.102-0.04133.072-0.002-0.0020.0000.0000.0000.000
34A48LYS10.8760.92231.1440.0510.0510.0000.0000.0000.000
35A49LEU0-0.0100.00029.042-0.001-0.0010.0000.0000.0000.000
36A50ASP-1-0.828-0.91328.057-0.099-0.0990.0000.0000.0000.000
37A51LYS10.9050.91822.1590.1000.1000.0000.0000.0000.000
38A52ASP-1-0.878-0.92223.632-0.150-0.1500.0000.0000.0000.000
39A53GLN0-0.024-0.01324.516-0.007-0.0070.0000.0000.0000.000
40A54LEU0-0.052-0.01522.7530.0000.0000.0000.0000.0000.000
41A55ILE0-0.021-0.02118.937-0.004-0.0040.0000.0000.0000.000
42A56ALA00.0310.02321.841-0.009-0.0090.0000.0000.0000.000
43A57GLY00.0540.03424.0450.0020.0020.0000.0000.0000.000
44A58VAL0-0.051-0.02619.6880.0020.0020.0000.0000.0000.000
45A59GLN0-0.029-0.02617.6820.0100.0100.0000.0000.0000.000
46A60ASP-1-0.821-0.89621.398-0.115-0.1150.0000.0000.0000.000
47A61ALA0-0.006-0.00624.9330.0050.0050.0000.0000.0000.000
48A62PHE0-0.061-0.01117.5290.0000.0000.0000.0000.0000.000
49A63ALA0-0.043-0.01722.292-0.002-0.0020.0000.0000.0000.000
50A64ASP-1-0.938-0.96323.664-0.083-0.0830.0000.0000.0000.000
51A65LYS10.8710.91926.5330.1150.1150.0000.0000.0000.000
52A66SER0-0.018-0.02128.520-0.004-0.0040.0000.0000.0000.000
53A67LYS10.8230.88828.0830.1080.1080.0000.0000.0000.000
54A68LEU0-0.043-0.00131.7800.0040.0040.0000.0000.0000.000
55A69SER00.037-0.01132.715-0.002-0.0020.0000.0000.0000.000
56A70ASP-1-0.844-0.93632.798-0.053-0.0530.0000.0000.0000.000
57A71GLN0-0.024-0.01234.8430.0010.0010.0000.0000.0000.000
58A72GLU-1-0.822-0.87436.420-0.050-0.0500.0000.0000.0000.000
59A73ILE0-0.0150.00830.5350.0010.0010.0000.0000.0000.000
60A74GLU-1-0.873-0.92834.364-0.029-0.0290.0000.0000.0000.000
61A75GLN00.0200.01136.4170.0010.0010.0000.0000.0000.000
62A76THR0-0.041-0.03434.8570.0010.0010.0000.0000.0000.000
63A77LEU0-0.020-0.02631.2290.0010.0010.0000.0000.0000.000
64A78GLN0-0.045-0.01835.3630.0040.0040.0000.0000.0000.000
65A79ALA0-0.017-0.00338.7190.0020.0020.0000.0000.0000.000
66A80PHE0-0.032-0.02832.2550.0010.0010.0000.0000.0000.000
67A81GLU-1-0.830-0.91335.870-0.022-0.0220.0000.0000.0000.000
68A82ALA0-0.0110.00237.5330.0020.0020.0000.0000.0000.000
69A83ARG10.9750.99136.3770.0430.0430.0000.0000.0000.000
70A84VAL0-0.0160.00034.6330.0010.0010.0000.0000.0000.000
71A85LYS10.9000.93337.8380.0220.0220.0000.0000.0000.000
72A86SER00.0100.01740.6530.0020.0020.0000.0000.0000.000
73A87SER0-0.054-0.04838.8570.0000.0000.0000.0000.0000.000
74A88ALA0-0.0090.00439.0890.0010.0010.0000.0000.0000.000
75A89GLN0-0.0070.00340.5710.0020.0020.0000.0000.0000.000
76A90ALA00.007-0.00543.2360.0010.0010.0000.0000.0000.000
77A91LYS10.8580.91038.0290.0160.0160.0000.0000.0000.000
78A92MET00.0210.01042.6360.0020.0020.0000.0000.0000.000
79A93GLU-1-0.816-0.88544.640-0.009-0.0090.0000.0000.0000.000
80A94LYS10.8610.92644.1890.0180.0180.0000.0000.0000.000
81A95ASP-1-0.863-0.90942.249-0.013-0.0130.0000.0000.0000.000
82A96ALA0-0.0010.00245.6820.0010.0010.0000.0000.0000.000
83A97ALA0-0.003-0.00248.9100.0010.0010.0000.0000.0000.000
84A98ASP-1-0.825-0.90846.372-0.014-0.0140.0000.0000.0000.000
85A99ASN0-0.041-0.02645.3080.0000.0000.0000.0000.0000.000
86A100GLH0-0.038-0.04449.3240.0010.0010.0000.0000.0000.000
87A101ALA0-0.063-0.02652.2950.0010.0010.0000.0000.0000.000
88A102LYS10.9670.97645.3370.0100.0100.0000.0000.0000.000
89A103GLY00.0350.01251.8710.0010.0010.0000.0000.0000.000
90A104LYS10.9330.97453.3000.0060.0060.0000.0000.0000.000
91A105GLU-1-0.939-0.96253.482-0.007-0.0070.0000.0000.0000.000
92A106TYR0-0.004-0.01151.8250.0010.0010.0000.0000.0000.000
93A107ARG10.9280.94955.2300.0030.0030.0000.0000.0000.000
94A108GLU-1-0.891-0.93658.036-0.002-0.0020.0000.0000.0000.000
95A109LYS10.8900.95156.6210.0020.0020.0000.0000.0000.000
96A110PHE00.0340.00457.5740.0000.0000.0000.0000.0000.000
97A111ALA00.017-0.00559.6300.0000.0000.0000.0000.0000.000
98A112LYS10.8110.90262.8130.0030.0030.0000.0000.0000.000
99A113GLU-1-0.908-0.92759.5050.0000.0000.0000.0000.0000.000
100A114LYS10.9950.98063.971-0.002-0.0020.0000.0000.0000.000
101A115GLY0-0.018-0.02464.9180.0000.0000.0000.0000.0000.000
102A116VAL0-0.0560.00361.8880.0010.0010.0000.0000.0000.000
103A117LYS10.9430.97764.829-0.003-0.0030.0000.0000.0000.000
104A118THR00.0420.01064.3000.0000.0000.0000.0000.0000.000
105A119SER0-0.070-0.05465.4050.0000.0000.0000.0000.0000.000
106A120SER00.020-0.00867.0970.0000.0000.0000.0000.0000.000
107A121THR0-0.074-0.06364.602-0.001-0.0010.0000.0000.0000.000
108A122GLY00.0050.00463.2480.0000.0000.0000.0000.0000.000
109A123LEU0-0.0320.00359.8960.0000.0000.0000.0000.0000.000
110A124VAL0-0.0220.00159.9280.0000.0000.0000.0000.0000.000
111A125TYR0-0.053-0.03960.4130.0000.0000.0000.0000.0000.000
112A126GLN00.0240.01260.4030.0000.0000.0000.0000.0000.000
113A127VAL0-0.0130.00562.1910.0010.0010.0000.0000.0000.000
114A128VAL0-0.032-0.00960.1640.0000.0000.0000.0000.0000.000
115A129GLU-1-0.850-0.92063.1660.0090.0090.0000.0000.0000.000
116A130ALA00.0100.00765.6680.0000.0000.0000.0000.0000.000
117A131GLY00.0610.03967.6790.0000.0000.0000.0000.0000.000
118A132LYS10.8780.91568.311-0.008-0.0080.0000.0000.0000.000
119A133GLY00.0100.00370.6850.0000.0000.0000.0000.0000.000
120A134GLU-1-0.858-0.93171.7310.0060.0060.0000.0000.0000.000
121A135ALA0-0.055-0.03370.3590.0000.0000.0000.0000.0000.000
122A136PRO00.0480.02465.9460.0000.0000.0000.0000.0000.000
123A137LYS10.8350.92268.202-0.007-0.0070.0000.0000.0000.000
124A138ASP-1-0.803-0.89666.8190.0050.0050.0000.0000.0000.000
125A139SER00.0400.02766.0550.0000.0000.0000.0000.0000.000
126A140ASP-1-0.893-0.93066.8290.0080.0080.0000.0000.0000.000
127A141THR0-0.049-0.03561.4000.0000.0000.0000.0000.0000.000
128A142VAL0-0.005-0.00160.0870.0000.0000.0000.0000.0000.000
129A143VAL0-0.020-0.00858.1470.0010.0010.0000.0000.0000.000
130A144VAL0-0.001-0.00955.7830.0000.0000.0000.0000.0000.000
131A145ASN00.0330.03154.0030.0010.0010.0000.0000.0000.000
132A146TYR0-0.067-0.08749.846-0.001-0.0010.0000.0000.0000.000
133A147LYS10.9130.96547.923-0.009-0.0090.0000.0000.0000.000
134A148GLY00.0170.00848.583-0.001-0.0010.0000.0000.0000.000
135A149THR0-0.013-0.00846.2310.0010.0010.0000.0000.0000.000
136A150LEU00.0220.01043.481-0.001-0.0010.0000.0000.0000.000
137A151ILE0-0.014-0.01647.3280.0000.0000.0000.0000.0000.000
138A152ASP-1-0.900-0.95042.9860.0000.0000.0000.0000.0000.000
139A153GLY0-0.0010.00245.0150.0000.0000.0000.0000.0000.000
140A154LYS10.8520.92638.976-0.009-0.0090.0000.0000.0000.000
141A155GLU-1-0.836-0.91642.9370.0150.0150.0000.0000.0000.000
142A156PHE0-0.041-0.03842.4250.0010.0010.0000.0000.0000.000
143A157ASP-1-0.760-0.84044.1030.0160.0160.0000.0000.0000.000
144A158ASN00.001-0.01445.375-0.001-0.0010.0000.0000.0000.000
145A159SER00.0690.04746.8520.0010.0010.0000.0000.0000.000
146A160TYR0-0.030-0.02148.7680.0010.0010.0000.0000.0000.000
147A161THR0-0.088-0.04743.7080.0020.0020.0000.0000.0000.000
148A162ARG10.8390.90145.005-0.017-0.0170.0000.0000.0000.000
149A163GLY0-0.028-0.00346.8090.0010.0010.0000.0000.0000.000
150A164GLU-1-0.993-0.98849.2400.0210.0210.0000.0000.0000.000
151A165PRO0-0.043-0.01451.6980.0000.0000.0000.0000.0000.000
152A166LEU00.0000.00251.3470.0000.0000.0000.0000.0000.000
153A167SER00.013-0.00854.289-0.001-0.0010.0000.0000.0000.000
154A168PHE0-0.047-0.03055.8730.0000.0000.0000.0000.0000.000
155A169ARG10.9991.00458.582-0.010-0.0100.0000.0000.0000.000
156A170LEU00.0060.01160.6940.0000.0000.0000.0000.0000.000
157A171ASP-1-0.908-0.94961.8620.0060.0060.0000.0000.0000.000
158A172GLY0-0.029-0.00859.7810.0000.0000.0000.0000.0000.000
159A173VAL0-0.064-0.02855.8850.0000.0000.0000.0000.0000.000
160A174ILE0-0.0150.00653.572-0.001-0.0010.0000.0000.0000.000
161A175PRO00.1040.03357.0650.0000.0000.0000.0000.0000.000
162A176GLY00.0410.01958.5900.0000.0000.0000.0000.0000.000
163A177TRP0-0.028-0.02154.0340.0000.0000.0000.0000.0000.000
164A178THR0-0.024-0.02359.2730.0000.0000.0000.0000.0000.000
165A179GLU-1-0.774-0.84162.3560.0020.0020.0000.0000.0000.000
166A180GLY00.0410.00661.7910.0000.0000.0000.0000.0000.000
167A181LEU00.001-0.00759.9110.0000.0000.0000.0000.0000.000
168A182LYS10.7750.88563.437-0.004-0.0040.0000.0000.0000.000
169A183ASN0-0.083-0.03265.5350.0000.0000.0000.0000.0000.000
170A184ILE0-0.054-0.00862.5320.0000.0000.0000.0000.0000.000
171A185LYS10.9030.95767.105-0.006-0.0060.0000.0000.0000.000
172A186LYS10.9170.94965.852-0.011-0.0110.0000.0000.0000.000
173A187GLY00.0010.00064.5470.0000.0000.0000.0000.0000.000
174A188GLY0-0.0100.00164.5730.0000.0000.0000.0000.0000.000
175A189LYS10.8320.90859.471-0.010-0.0100.0000.0000.0000.000
176A190ILE0-0.029-0.01560.100-0.001-0.0010.0000.0000.0000.000
177A191LYS10.9541.00854.972-0.003-0.0030.0000.0000.0000.000
178A192LEU0-0.024-0.01557.095-0.001-0.0010.0000.0000.0000.000
179A193VAL0-0.017-0.01455.1880.0000.0000.0000.0000.0000.000
180A194ILE00.0030.00055.2180.0000.0000.0000.0000.0000.000
181A195PRO00.0060.00954.9580.0000.0000.0000.0000.0000.000
182A196PRO00.0320.02952.5900.0010.0010.0000.0000.0000.000
183A197GLU-1-0.806-0.88654.486-0.002-0.0020.0000.0000.0000.000
184A198LEU0-0.042-0.01157.5510.0000.0000.0000.0000.0000.000
185A199ALA00.008-0.01553.1170.0010.0010.0000.0000.0000.000
186A200TYR00.0330.01250.1300.0000.0000.0000.0000.0000.000
187A201GLY0-0.0090.01151.490-0.001-0.0010.0000.0000.0000.000
188A202LYS10.8570.89450.4770.0090.0090.0000.0000.0000.000
189A203ALA0-0.013-0.00348.464-0.001-0.0010.0000.0000.0000.000
190A204GLY00.0110.02346.8170.0000.0000.0000.0000.0000.000
191A205VAL0-0.005-0.01245.8160.0000.0000.0000.0000.0000.000
192A206PRO00.0350.01040.629-0.001-0.0010.0000.0000.0000.000
193A207GLY0-0.0110.00140.9780.0010.0010.0000.0000.0000.000
194A208ILE0-0.059-0.03041.8970.0000.0000.0000.0000.0000.000
195A209PRO00.0220.01142.428-0.001-0.0010.0000.0000.0000.000
196A210PRO00.0450.05544.6080.0010.0010.0000.0000.0000.000
197A211ASN0-0.025-0.05247.5990.0000.0000.0000.0000.0000.000
198A212SER0-0.015-0.01547.3170.0000.0000.0000.0000.0000.000
199A213THR0-0.021-0.01249.7670.0000.0000.0000.0000.0000.000
200A214LEU0-0.048-0.01749.1620.0000.0000.0000.0000.0000.000
201A215VAL0-0.0090.00150.9470.0000.0000.0000.0000.0000.000
202A216PHE00.0070.01251.1360.0010.0010.0000.0000.0000.000
203A217ASP-1-0.862-0.92152.7740.0070.0070.0000.0000.0000.000
204A218VAL0-0.008-0.01654.3850.0010.0010.0000.0000.0000.000
205A219GLU-1-0.798-0.88756.5690.0130.0130.0000.0000.0000.000
206A220LEU0-0.011-0.00458.7030.0010.0010.0000.0000.0000.000
207A221LEU0-0.005-0.00557.4310.0000.0000.0000.0000.0000.000
208A222ASP-1-0.818-0.91261.8110.0120.0120.0000.0000.0000.000
209A223VAL00.0070.00763.6050.0000.0000.0000.0000.0000.000
210A224LYS10.9000.96062.098-0.013-0.0130.0000.0000.0000.000