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: GYQJ1

Calculation Name: 1TUA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YE16

Base Structure: X-ray

Registration Date: 2023-09-26

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017379.657095
FMO2-HF: Nuclear repulsion 1941216.101814
FMO2-HF: Total energy -76163.555281
FMO2-MP2: Total energy -76382.462885


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:0:ALA)


Summations of interaction energy for fragment #1(A:0: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.
-2.524-0.642-0.005-0.848-1.0280.003
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.010
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].
3A2LYS10.8630.9293.818-1.688-0.299-0.005-0.602-0.7810.002
4A3PRO00.0170.0076.1530.0860.0860.0000.0000.0000.000
5A4ARG10.8220.9014.035-2.149-1.6560.000-0.246-0.2470.001
6A5ILE0-0.0090.00010.867-0.062-0.0620.0000.0000.0000.000
7A6TYR00.0070.00110.0040.0320.0320.0000.0000.0000.000
8A7VAL00.001-0.00615.714-0.027-0.0270.0000.0000.0000.000
9A8LYS10.8850.92919.288-0.056-0.0560.0000.0000.0000.000
10A9VAL0-0.040-0.02321.536-0.007-0.0070.0000.0000.0000.000
11A10LYS10.8660.93124.045-0.035-0.0350.0000.0000.0000.000
12A11PRO00.0700.02826.7380.0050.0050.0000.0000.0000.000
13A12GLU-1-0.879-0.94227.7250.0530.0530.0000.0000.0000.000
14A13ARG10.7950.88728.327-0.056-0.0560.0000.0000.0000.000
15A14LEU00.0390.02721.9590.0050.0050.0000.0000.0000.000
16A15GLY00.0220.00825.6190.0090.0090.0000.0000.0000.000
17A16ALA0-0.034-0.01327.9390.0020.0020.0000.0000.0000.000
18A17VAL00.0050.00122.2800.0010.0010.0000.0000.0000.000
19A18ILE0-0.025-0.00122.2770.0100.0100.0000.0000.0000.000
20A19GLY00.0430.01924.0940.0030.0030.0000.0000.0000.000
21A20PRO00.0230.00026.8630.0080.0080.0000.0000.0000.000
22A21ARG10.8310.89027.075-0.080-0.0800.0000.0000.0000.000
23A22GLY0-0.0060.00023.4350.0090.0090.0000.0000.0000.000
24A23GLU-1-0.830-0.90223.2970.0920.0920.0000.0000.0000.000
25A24VAL00.0250.01724.612-0.002-0.0020.0000.0000.0000.000
26A25LYS10.9390.96317.053-0.257-0.2570.0000.0000.0000.000
27A26ALA0-0.017-0.01220.1170.0120.0120.0000.0000.0000.000
28A27GLU-1-0.806-0.89621.1130.0900.0900.0000.0000.0000.000
29A28ILE0-0.026-0.01119.484-0.005-0.0050.0000.0000.0000.000
30A29MET0-0.0280.03616.2110.0160.0160.0000.0000.0000.000
31A30ARG10.9060.95018.129-0.116-0.1160.0000.0000.0000.000
32A31ARG10.8810.93320.495-0.077-0.0770.0000.0000.0000.000
33A32THR0-0.052-0.01418.181-0.004-0.0040.0000.0000.0000.000
34A33GLY00.0940.07116.206-0.012-0.0120.0000.0000.0000.000
35A34THR0-0.060-0.05013.1960.0190.0190.0000.0000.0000.000
36A35VAL00.017-0.00610.703-0.003-0.0030.0000.0000.0000.000
37A36ILE0-0.023-0.02812.6400.0120.0120.0000.0000.0000.000
38A37THR0-0.026-0.01411.901-0.014-0.0140.0000.0000.0000.000
39A38VAL0-0.014-0.02614.842-0.032-0.0320.0000.0000.0000.000
40A39ASP-1-0.800-0.86416.1160.1780.1780.0000.0000.0000.000
41A40THR00.028-0.03218.025-0.019-0.0190.0000.0000.0000.000
42A41GLU-1-0.968-0.96220.8080.1000.1000.0000.0000.0000.000
43A42ASN0-0.039-0.02518.013-0.031-0.0310.0000.0000.0000.000
44A43SER0-0.052-0.04121.149-0.009-0.0090.0000.0000.0000.000
45A44MET0-0.0160.01816.608-0.020-0.0200.0000.0000.0000.000
46A45VAL0-0.0040.00117.3020.0230.0230.0000.0000.0000.000
47A46ILE00.0130.01010.880-0.034-0.0340.0000.0000.0000.000
48A47VAL00.0020.00213.7680.0440.0440.0000.0000.0000.000
49A48GLU-1-0.763-0.8757.4191.3671.3670.0000.0000.0000.000
50A49PRO00.0290.0258.5780.0000.0000.0000.0000.0000.000
51A50GLU-1-0.923-0.9758.9460.3190.3190.0000.0000.0000.000
52A51ALA0-0.011-0.0129.0790.0460.0460.0000.0000.0000.000
53A52GLU-1-0.955-0.9907.426-0.265-0.2650.0000.0000.0000.000
54A53GLY00.0020.0059.362-0.027-0.0270.0000.0000.0000.000
55A54ILE0-0.055-0.00112.411-0.002-0.0020.0000.0000.0000.000
56A55PRO00.0160.01513.860-0.021-0.0210.0000.0000.0000.000
57A56PRO00.0580.00115.4790.0170.0170.0000.0000.0000.000
58A57VAL00.0380.01716.6920.0120.0120.0000.0000.0000.000
59A58ASN00.003-0.00117.053-0.005-0.0050.0000.0000.0000.000
60A59LEU00.0170.01612.4750.0130.0130.0000.0000.0000.000
61A60MET0-0.030-0.03016.0060.0050.0050.0000.0000.0000.000
62A61LYS10.8530.91718.839-0.025-0.0250.0000.0000.0000.000
63A62ALA00.0280.02617.4990.0020.0020.0000.0000.0000.000
64A63ALA0-0.011-0.01117.6210.0070.0070.0000.0000.0000.000
65A64GLU-1-0.778-0.88919.4930.0240.0240.0000.0000.0000.000
66A65VAL00.0000.01122.756-0.002-0.0020.0000.0000.0000.000
67A66VAL00.004-0.00319.719-0.002-0.0020.0000.0000.0000.000
68A67LYS10.8320.90822.948-0.029-0.0290.0000.0000.0000.000
69A68ALA00.0160.00224.720-0.005-0.0050.0000.0000.0000.000
70A69ILE0-0.0150.00425.208-0.004-0.0040.0000.0000.0000.000
71A70SER00.0120.01225.525-0.003-0.0030.0000.0000.0000.000
72A71LEU0-0.021-0.02227.656-0.004-0.0040.0000.0000.0000.000
73A72GLY00.0050.01330.524-0.004-0.0040.0000.0000.0000.000
74A73PHE0-0.067-0.03530.766-0.001-0.0010.0000.0000.0000.000
75A74PRO0-0.031-0.00230.9790.0040.0040.0000.0000.0000.000
76A75PRO00.0830.01727.964-0.002-0.0020.0000.0000.0000.000
77A76GLU-1-0.869-0.94029.4810.0580.0580.0000.0000.0000.000
78A77LYS10.8620.94231.885-0.034-0.0340.0000.0000.0000.000
79A78ALA00.0090.00527.583-0.003-0.0030.0000.0000.0000.000
80A79PHE00.0210.00125.3540.0000.0000.0000.0000.0000.000
81A80ARG10.8920.96727.928-0.025-0.0250.0000.0000.0000.000
82A81LEU0-0.054-0.02326.075-0.004-0.0040.0000.0000.0000.000
83A82LEU0-0.054-0.03022.610-0.001-0.0010.0000.0000.0000.000
84A83GLU-1-0.915-0.95825.5970.0320.0320.0000.0000.0000.000
85A84GLU-1-0.911-0.94928.1290.0130.0130.0000.0000.0000.000
86A85ASP-1-0.888-0.94928.9780.0070.0070.0000.0000.0000.000
87A86GLN0-0.049-0.00529.542-0.001-0.0010.0000.0000.0000.000
88A87ILE0-0.031-0.02328.2200.0010.0010.0000.0000.0000.000
89A88LEU00.005-0.01026.9420.0020.0020.0000.0000.0000.000
90A89VAL0-0.033-0.01129.573-0.003-0.0030.0000.0000.0000.000
91A90VAL0-0.002-0.01430.2100.0030.0030.0000.0000.0000.000
92A91VAL0-0.024-0.00533.178-0.003-0.0030.0000.0000.0000.000
93A92ASP-1-0.809-0.90233.9210.0140.0140.0000.0000.0000.000
94A93LEU00.011-0.02135.947-0.002-0.0020.0000.0000.0000.000
95A94LYS10.8980.95036.590-0.014-0.0140.0000.0000.0000.000
96A95GLN0-0.047-0.01735.669-0.001-0.0010.0000.0000.0000.000
97A96VAL0-0.049-0.01439.190-0.001-0.0010.0000.0000.0000.000
98A97VAL0-0.058-0.04042.444-0.001-0.0010.0000.0000.0000.000
99A98GLY00.0420.02740.8780.0000.0000.0000.0000.0000.000
100A99ASP-1-0.836-0.92039.1920.0100.0100.0000.0000.0000.000
101A100SER0-0.040-0.01241.8470.0010.0010.0000.0000.0000.000
102A101GLN00.1040.03841.2870.0000.0000.0000.0000.0000.000
103A102ASN00.003-0.01444.8870.0010.0010.0000.0000.0000.000
104A103HIS00.0430.02746.7190.0010.0010.0000.0000.0000.000
105A104LEU00.0480.05340.3900.0000.0000.0000.0000.0000.000
106A105LYS10.9580.96144.604-0.016-0.0160.0000.0000.0000.000
107A106ARG10.8890.94246.538-0.008-0.0080.0000.0000.0000.000
108A107ILE00.0240.01543.3670.0000.0000.0000.0000.0000.000
109A108LYS10.8410.91840.461-0.021-0.0210.0000.0000.0000.000
110A109GLY00.0090.01345.2280.0010.0010.0000.0000.0000.000
111A110ARG10.8410.92048.602-0.008-0.0080.0000.0000.0000.000
112A111ILE00.0290.01642.6480.0000.0000.0000.0000.0000.000
113A112ILE0-0.0170.00543.5500.0010.0010.0000.0000.0000.000
114A113GLY00.0160.00546.3630.0000.0000.0000.0000.0000.000
115A114GLU-1-0.820-0.90449.9380.0130.0130.0000.0000.0000.000
116A115GLY00.0470.01950.9330.0000.0000.0000.0000.0000.000
117A116GLY0-0.011-0.00847.2480.0010.0010.0000.0000.0000.000
118A117ARG10.8470.90547.382-0.013-0.0130.0000.0000.0000.000
119A118ALA0-0.0110.01448.2720.0000.0000.0000.0000.0000.000
120A119ARG10.8340.89740.278-0.023-0.0230.0000.0000.0000.000
121A120ARG10.9050.94744.143-0.020-0.0200.0000.0000.0000.000
122A121THR00.0220.02045.7810.0000.0000.0000.0000.0000.000
123A122ILE00.002-0.00642.687-0.001-0.0010.0000.0000.0000.000
124A123GLU-1-0.797-0.87339.8740.0230.0230.0000.0000.0000.000
125A124GLU-1-0.917-0.96042.6360.0160.0160.0000.0000.0000.000
126A125MET0-0.087-0.03145.265-0.001-0.0010.0000.0000.0000.000
127A126THR0-0.066-0.06341.072-0.001-0.0010.0000.0000.0000.000
128A127ASP-1-0.913-0.94540.1250.0180.0180.0000.0000.0000.000
129A128THR0-0.017-0.01337.2590.0010.0010.0000.0000.0000.000
130A129TYR0-0.050-0.01933.8870.0000.0000.0000.0000.0000.000
131A130ILE00.025-0.00336.2290.0000.0000.0000.0000.0000.000
132A131ASN0-0.057-0.01634.9710.0000.0000.0000.0000.0000.000
133A132VAL0-0.008-0.00936.919-0.001-0.0010.0000.0000.0000.000
134A133GLY00.1010.06135.9380.0010.0010.0000.0000.0000.000
135A134GLU-1-0.942-0.98435.6850.0240.0240.0000.0000.0000.000
136A135TYR0-0.019-0.02031.694-0.002-0.0020.0000.0000.0000.000
137A136GLU-1-0.778-0.84431.4260.0260.0260.0000.0000.0000.000
138A137VAL0-0.041-0.02835.5640.0020.0020.0000.0000.0000.000
139A138ALA0-0.0050.01332.117-0.002-0.0020.0000.0000.0000.000
140A139ILE0-0.003-0.01433.5730.0010.0010.0000.0000.0000.000
141A140ILE00.0240.01730.6000.0000.0000.0000.0000.0000.000
142A141GLY00.0550.02232.8720.0000.0000.0000.0000.0000.000
143A142ASP-1-0.765-0.84832.9970.0090.0090.0000.0000.0000.000
144A143TYR00.033-0.00632.4840.0000.0000.0000.0000.0000.000
145A144GLU-1-0.787-0.88434.5030.0000.0000.0000.0000.0000.000
146A145ARG10.7880.85237.931-0.010-0.0100.0000.0000.0000.000
147A146ALA00.0080.00534.7950.0010.0010.0000.0000.0000.000
148A147MET0-0.005-0.00635.8150.0000.0000.0000.0000.0000.000
149A148ALA0-0.0130.00238.079-0.001-0.0010.0000.0000.0000.000
150A149ALA00.003-0.00339.0960.0000.0000.0000.0000.0000.000
151A150LYS10.8490.92036.013-0.003-0.0030.0000.0000.0000.000
152A151GLN00.0720.05439.4780.0000.0000.0000.0000.0000.000
153A152ALA0-0.005-0.00842.6310.0000.0000.0000.0000.0000.000
154A153ILE0-0.007-0.01740.3540.0000.0000.0000.0000.0000.000
155A154GLU-1-0.790-0.89939.2070.0030.0030.0000.0000.0000.000
156A155MET0-0.039-0.01843.4550.0000.0000.0000.0000.0000.000
157A156LEU0-0.055-0.03146.2830.0000.0000.0000.0000.0000.000
158A157ALA0-0.039-0.01543.8400.0000.0000.0000.0000.0000.000
159A158GLU-1-0.826-0.89545.9120.0010.0010.0000.0000.0000.000
160A159GLY0-0.043-0.01848.254-0.001-0.0010.0000.0000.0000.000
161A160ARG10.7990.91049.803-0.002-0.0020.0000.0000.0000.000
162A161MET00.0200.00552.4530.0010.0010.0000.0000.0000.000
163A162HIS00.0720.01850.004-0.001-0.0010.0000.0000.0000.000
164A163SER00.0040.00752.6380.0000.0000.0000.0000.0000.000
165A164THR0-0.035-0.01753.0650.0000.0000.0000.0000.0000.000
166A165VAL00.0550.03347.8150.0000.0000.0000.0000.0000.000
167A166TYR00.0610.01749.2830.0000.0000.0000.0000.0000.000
168A167ARG10.9570.98451.281-0.005-0.0050.0000.0000.0000.000
169A168HIS0-0.030-0.02946.7890.0000.0000.0000.0000.0000.000
170A169LEU00.0500.01744.365-0.001-0.0010.0000.0000.0000.000
171A170GLU-1-0.918-0.95947.9330.0070.0070.0000.0000.0000.000
172A171ARG10.8580.92750.364-0.003-0.0030.0000.0000.0000.000
173A172ILE00.0490.02644.4880.0000.0000.0000.0000.0000.000
174A173MET00.0480.03142.7690.0000.0000.0000.0000.0000.000
175A174ARG10.9210.96746.544-0.003-0.0030.0000.0000.0000.000
176A175GLU-1-0.901-0.93946.577-0.001-0.0010.0000.0000.0000.000
177A176ILE00.0380.01941.9490.0000.0000.0000.0000.0000.000
178A177LYS10.9740.99744.702-0.009-0.0090.0000.0000.0000.000
179A178ARG10.8870.95646.1780.0000.0000.0000.0000.0000.000
180A179ARG10.7480.83242.3080.0000.0000.0000.0000.0000.000
181A180GLU-1-0.810-0.86641.0210.0060.0060.0000.0000.0000.000
182A181ARG10.9260.97344.547-0.004-0.0040.0000.0000.0000.000
183A182LEU0-0.057-0.03447.6520.0000.0000.0000.0000.0000.000
184A183LYS10.9770.99440.6980.0010.0010.0000.0000.0000.000
185A184MET0-0.0030.00344.1260.0000.0000.0000.0000.0000.000
186A185TRP00.007-0.02245.8440.0000.0000.0000.0000.0000.000
187A186ALA0-0.032-0.01747.5690.0000.0000.0000.0000.0000.000
188A187ARG10.7970.89841.601-0.003-0.0030.0000.0000.0000.000
189A188GLU-1-0.832-0.88544.8240.0040.0040.0000.0000.0000.000