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: YNQV2

Calculation Name: 1G0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NHL6

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075698.818436
FMO2-HF: Nuclear repulsion 1998559.604364
FMO2-HF: Total energy -77139.214071
FMO2-MP2: Total energy -77364.641749


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:2:HIS)


Summations of interaction energy for fragment #1(A:2:HIS)
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.
-43.906-35.32527.174-13.299-22.455-0.07
Interaction energy analysis for fragmet #1(A:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.041
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].
3A4PRO00.0230.0133.891-1.8700.235-0.019-1.110-0.9760.000
4A5LYS10.8700.9385.9170.0170.0170.0000.0000.0000.000
5A6PRO0-0.050-0.0167.1730.1090.1090.0000.0000.0000.000
6A7THR0-0.009-0.0099.237-0.316-0.3160.0000.0000.0000.000
7A8LEU0-0.045-0.02912.8290.0150.0150.0000.0000.0000.000
8A9TRP0-0.054-0.03914.403-0.001-0.0010.0000.0000.0000.000
9A10ALA00.014-0.00518.872-0.033-0.0330.0000.0000.0000.000
10A11GLU-1-0.807-0.84620.6500.2000.2000.0000.0000.0000.000
11A12PRO00.0460.00323.564-0.025-0.0250.0000.0000.0000.000
12A13GLY00.0640.02525.4040.0190.0190.0000.0000.0000.000
13A14SER0-0.026-0.01223.647-0.010-0.0100.0000.0000.0000.000
14A15VAL00.0390.02025.472-0.010-0.0100.0000.0000.0000.000
15A16ILE0-0.047-0.01327.4720.0020.0020.0000.0000.0000.000
16A17THR00.0190.01830.744-0.003-0.0030.0000.0000.0000.000
17A18GLN0-0.046-0.03232.988-0.004-0.0040.0000.0000.0000.000
18A19GLY00.0470.03532.9810.0030.0030.0000.0000.0000.000
19A20SER0-0.0170.00231.623-0.009-0.0090.0000.0000.0000.000
20A21PRO0-0.0100.00727.683-0.006-0.0060.0000.0000.0000.000
21A22VAL0-0.005-0.00123.7920.0170.0170.0000.0000.0000.000
22A23THR0-0.043-0.02119.237-0.040-0.0400.0000.0000.0000.000
23A24LEU00.0210.01818.4720.0390.0390.0000.0000.0000.000
24A25ARG10.8320.90615.693-0.274-0.2740.0000.0000.0000.000
25A26CYS0-0.040-0.00710.7940.0230.0230.0000.0000.0000.000
26A27GLN00.0300.00610.273-0.153-0.1530.0000.0000.0000.000
27A28GLY00.0590.0107.357-0.094-0.0940.0000.0000.0000.000
28A29GLY00.0010.0136.5920.6210.6210.0000.0000.0000.000
29A30GLN0-0.016-0.0082.131-4.646-4.4633.616-1.667-2.132-0.016
30A31GLH00.0780.0192.7770.4534.1471.354-2.177-2.8710.010
31A32THR0-0.015-0.0052.644-7.575-7.1600.8080.182-1.405-0.009
32A33GLN00.002-0.0014.0180.0050.090-0.001-0.017-0.0670.000
33A34GLU-1-0.849-0.8771.764-27.571-31.27311.971-4.378-3.891-0.051
34A35TYR0-0.021-0.0135.3051.2511.325-0.0010.000-0.0730.000
35A36ARG10.9030.9517.7860.8530.8530.0000.0000.0000.000
36A37LEU00.0160.01510.5050.1890.1890.0000.0000.0000.000
37A38TYR0-0.070-0.04811.895-0.134-0.1340.0000.0000.0000.000
38A39ARG10.7850.86215.9170.1650.1650.0000.0000.0000.000
39A40GLU-1-0.761-0.87518.4710.0530.0530.0000.0000.0000.000
40A41LYS10.8880.94220.080-0.014-0.0140.0000.0000.0000.000
41A42LYS10.9931.00122.7520.0920.0920.0000.0000.0000.000
42A43THR00.0620.03920.2090.0150.0150.0000.0000.0000.000
43A44ALA00.0690.03720.3590.0240.0240.0000.0000.0000.000
44A45PRO00.0170.01120.893-0.024-0.0240.0000.0000.0000.000
45A46TRP0-0.005-0.00919.719-0.023-0.0230.0000.0000.0000.000
46A47ILE00.0450.03115.904-0.018-0.0180.0000.0000.0000.000
47A48THR0-0.029-0.02517.310-0.038-0.0380.0000.0000.0000.000
48A49ARG10.8670.93318.3860.2370.2370.0000.0000.0000.000
49A50ILE0-0.0210.01316.8850.0330.0330.0000.0000.0000.000
50A51PRO00.0360.02417.423-0.079-0.0790.0000.0000.0000.000
51A52GLN00.0630.02211.331-0.185-0.1850.0000.0000.0000.000
52A53GLU-1-0.864-0.95013.508-0.589-0.5890.0000.0000.0000.000
53A54LEU0-0.049-0.03014.6380.0610.0610.0000.0000.0000.000
54A55VAL00.0350.02710.8250.0720.0720.0000.0000.0000.000
55A56LYS10.8860.9399.4511.7231.7230.0000.0000.0000.000
56A57LYS10.8520.9319.6330.2790.2790.0000.0000.0000.000
57A58GLY00.0240.02310.9640.1670.1670.0000.0000.0000.000
58A59GLN0-0.014-0.00611.8260.0500.0500.0000.0000.0000.000
59A60PHE00.029-0.00712.090-0.102-0.1020.0000.0000.0000.000
60A61PRO00.0010.00317.6320.0360.0360.0000.0000.0000.000
61A62ILE0-0.006-0.00521.260-0.034-0.0340.0000.0000.0000.000
62A63PRO0-0.018-0.02324.4320.0180.0180.0000.0000.0000.000
63A64SER0-0.033-0.02527.2690.0090.0090.0000.0000.0000.000
64A65ILE0-0.045-0.00426.614-0.015-0.0150.0000.0000.0000.000
65A66THR00.009-0.03629.3590.0030.0030.0000.0000.0000.000
66A67TRP00.0880.03429.9110.0050.0050.0000.0000.0000.000
67A68GLU-1-0.853-0.90229.035-0.084-0.0840.0000.0000.0000.000
68A69HIS00.0230.02424.550-0.005-0.0050.0000.0000.0000.000
69A70ALA00.0560.06525.0600.0100.0100.0000.0000.0000.000
70A71GLY0-0.015-0.01324.486-0.019-0.0190.0000.0000.0000.000
71A72ARG10.8120.90220.354-0.093-0.0930.0000.0000.0000.000
72A73TYR0-0.023-0.04117.786-0.045-0.0450.0000.0000.0000.000
73A74ARG10.8150.88713.658-0.162-0.1620.0000.0000.0000.000
74A76TYR0-0.0130.0186.1870.0930.0930.0000.0000.0000.000
75A77TYR0-0.021-0.0251.965-3.988-2.0495.171-2.732-4.3780.012
76A78GLY00.0680.0412.6360.2841.6682.465-1.804-2.0450.005
77A79SER0-0.045-0.0573.2473.3461.4920.1012.350-0.5970.001
78A80ASP-1-0.869-0.9435.117-1.488-1.416-0.001-0.001-0.0690.000
79A81THR0-0.038-0.0167.8070.3370.3370.0000.0000.0000.000
80A82ALA0-0.0030.0043.7170.3900.5560.001-0.028-0.1400.000
81A83GLY00.0130.0343.7270.5381.0040.006-0.163-0.309-0.001
82A84ARG10.8290.8882.522-6.991-4.0121.625-1.817-2.787-0.019
83A85SER00.0040.0103.189-0.2390.1790.0780.080-0.575-0.002
84A86GLU-1-0.829-0.9164.3610.4890.6460.000-0.017-0.1400.000
85A87SER0-0.041-0.0277.7570.1670.1670.0000.0000.0000.000
86A88SER00.0320.02210.3140.0130.0130.0000.0000.0000.000
87A89ASP-1-0.845-0.90112.2470.4020.4020.0000.0000.0000.000
88A90PRO0-0.048-0.02215.917-0.002-0.0020.0000.0000.0000.000
89A91LEU00.0300.02218.1400.0040.0040.0000.0000.0000.000
90A92GLU-1-0.814-0.89919.7510.0630.0630.0000.0000.0000.000
91A93LEU0-0.033-0.00522.8830.0100.0100.0000.0000.0000.000
92A94VAL00.004-0.00124.651-0.019-0.0190.0000.0000.0000.000
93A95VAL0-0.016-0.00128.4540.0010.0010.0000.0000.0000.000
94A96THR0-0.026-0.01530.957-0.002-0.0020.0000.0000.0000.000
95A97GLY00.009-0.02434.512-0.004-0.0040.0000.0000.0000.000
96A98ALA0-0.0250.00936.203-0.004-0.0040.0000.0000.0000.000
97A99TYR0-0.025-0.02035.945-0.004-0.0040.0000.0000.0000.000
98A100ILE00.0150.00341.4900.0020.0020.0000.0000.0000.000
99A101LYS10.8290.91342.714-0.011-0.0110.0000.0000.0000.000
100A102PRO0-0.0070.00441.727-0.001-0.0010.0000.0000.0000.000
101A103THR0-0.017-0.02044.8350.0000.0000.0000.0000.0000.000
102A104LEU0-0.024-0.00642.5150.0020.0020.0000.0000.0000.000
103A105SER0-0.0090.00446.191-0.002-0.0020.0000.0000.0000.000
104A106ALA00.011-0.00247.8960.0030.0030.0000.0000.0000.000
105A107GLN0-0.035-0.00149.755-0.005-0.0050.0000.0000.0000.000
106A108PRO0-0.004-0.02351.8160.0030.0030.0000.0000.0000.000
107A109SER00.018-0.01053.239-0.003-0.0030.0000.0000.0000.000
108A110PRO00.0380.01049.9490.0030.0030.0000.0000.0000.000
109A111VAL0-0.0240.01150.3820.0030.0030.0000.0000.0000.000
110A112VAL00.0240.01749.336-0.001-0.0010.0000.0000.0000.000
111A113ASN00.0160.00952.1780.0000.0000.0000.0000.0000.000
112A114SER00.0600.01249.5170.0030.0030.0000.0000.0000.000
113A115GLY0-0.079-0.02448.457-0.002-0.0020.0000.0000.0000.000
114A116GLY0-0.0110.00749.4140.0000.0000.0000.0000.0000.000
115A117ASN0-0.010-0.02146.2630.0070.0070.0000.0000.0000.000
116A118VAL0-0.0070.00446.794-0.004-0.0040.0000.0000.0000.000
117A119THR00.0170.01946.8580.0030.0030.0000.0000.0000.000
118A120LEU0-0.014-0.01142.956-0.003-0.0030.0000.0000.0000.000
119A121GLN00.002-0.00546.1670.0000.0000.0000.0000.0000.000
120A122CYS0-0.064-0.01539.1230.0030.0030.0000.0000.0000.000
121A123ASP-1-0.792-0.87945.2470.0190.0190.0000.0000.0000.000
122A124SER00.028-0.00345.095-0.001-0.0010.0000.0000.0000.000
123A125GLN0-0.030-0.01947.244-0.002-0.0020.0000.0000.0000.000
124A126VAL0-0.024-0.00645.552-0.003-0.0030.0000.0000.0000.000
125A127ALA0-0.006-0.00246.2170.0030.0030.0000.0000.0000.000
126A128PHE0-0.008-0.00440.621-0.003-0.0030.0000.0000.0000.000
127A129ASP-1-0.791-0.85638.7490.0200.0200.0000.0000.0000.000
128A130GLY00.0140.01737.3800.0060.0060.0000.0000.0000.000
129A131PHE00.018-0.01038.264-0.004-0.0040.0000.0000.0000.000
130A132ILE0-0.0310.00133.5410.0060.0060.0000.0000.0000.000
131A133LEU0-0.0050.00436.971-0.006-0.0060.0000.0000.0000.000
132A134CYS0-0.087-0.02730.977-0.006-0.0060.0000.0000.0000.000
133A135LYS10.8320.91035.549-0.109-0.1090.0000.0000.0000.000
134A136GLU-1-0.867-0.93634.8390.0720.0720.0000.0000.0000.000
135A137GLY0-0.027-0.02533.4280.0000.0000.0000.0000.0000.000
136A138GLU-1-0.914-0.98231.4800.1220.1220.0000.0000.0000.000
137A139ASP-1-0.873-0.93134.4190.1030.1030.0000.0000.0000.000
138A140GLU-1-0.912-0.90828.3960.2010.2010.0000.0000.0000.000
139A141HIS00.0520.00624.299-0.002-0.0020.0000.0000.0000.000
140A142PRO0-0.025-0.00229.2560.0020.0020.0000.0000.0000.000
141A143GLN00.000-0.00330.574-0.009-0.0090.0000.0000.0000.000
142A145LEU00.0270.00531.6080.0090.0090.0000.0000.0000.000
143A146ASN00.0450.02032.527-0.015-0.0150.0000.0000.0000.000
144A147SER00.001-0.00635.2130.0030.0030.0000.0000.0000.000
145A148GLN0-0.023-0.01436.4050.0020.0020.0000.0000.0000.000
146A149PRO00.017-0.00238.662-0.005-0.0050.0000.0000.0000.000
147A150HIS00.0020.00541.433-0.005-0.0050.0000.0000.0000.000
148A151ALA0-0.024-0.00642.856-0.001-0.0010.0000.0000.0000.000
149A152ARG10.8420.91537.943-0.045-0.0450.0000.0000.0000.000
150A153GLY00.0260.02245.0480.0000.0000.0000.0000.0000.000
151A154SER0-0.006-0.01345.7160.0010.0010.0000.0000.0000.000
152A155SER00.0250.02146.011-0.002-0.0020.0000.0000.0000.000
153A156ARG10.8320.90146.334-0.025-0.0250.0000.0000.0000.000
154A157ALA00.0040.01142.5130.0010.0010.0000.0000.0000.000
155A158ILE0-0.028-0.01744.444-0.001-0.0010.0000.0000.0000.000
156A159PHE00.0110.00538.1760.0030.0030.0000.0000.0000.000
157A160SER00.0100.00242.909-0.005-0.0050.0000.0000.0000.000
158A161VAL0-0.047-0.00941.0580.0050.0050.0000.0000.0000.000
159A162GLY00.0440.02242.503-0.005-0.0050.0000.0000.0000.000
160A163PRO0-0.005-0.01042.5120.0040.0040.0000.0000.0000.000
161A164VAL0-0.0280.00643.7410.0040.0040.0000.0000.0000.000
162A165SER00.001-0.01943.999-0.001-0.0010.0000.0000.0000.000
163A166PRO00.0310.01545.1500.0020.0020.0000.0000.0000.000
164A167SER0-0.038-0.00343.644-0.001-0.0010.0000.0000.0000.000
165A168ARG10.8890.94236.565-0.110-0.1100.0000.0000.0000.000
166A169ARG10.9510.99738.187-0.085-0.0850.0000.0000.0000.000
167A170TRP0-0.027-0.03740.5770.0070.0070.0000.0000.0000.000
168A171TRP0-0.010-0.00439.190-0.005-0.0050.0000.0000.0000.000
169A172TYR00.0340.00238.9960.0070.0070.0000.0000.0000.000
170A173ARG10.8940.94137.102-0.047-0.0470.0000.0000.0000.000
171A175TYR00.0530.01435.489-0.007-0.0070.0000.0000.0000.000
172A176ALA00.0300.02138.8940.0040.0040.0000.0000.0000.000
173A177TYR0-0.043-0.04134.219-0.002-0.0020.0000.0000.0000.000
174A178ASP-1-0.760-0.86036.977-0.003-0.0030.0000.0000.0000.000
175A179SER0-0.060-0.07734.560-0.002-0.0020.0000.0000.0000.000
176A180ASN0-0.089-0.05633.377-0.001-0.0010.0000.0000.0000.000
177A181SER0-0.040-0.03531.989-0.008-0.0080.0000.0000.0000.000
178A182PRO0-0.013-0.00429.1930.0030.0030.0000.0000.0000.000
179A183TYR0-0.088-0.05125.2720.0040.0040.0000.0000.0000.000
180A184GLU-1-0.842-0.90529.663-0.038-0.0380.0000.0000.0000.000
181A185TRP0-0.019-0.02030.9730.0040.0040.0000.0000.0000.000
182A186SER00.0370.00335.369-0.005-0.0050.0000.0000.0000.000
183A187LEU0-0.002-0.00237.6650.0030.0030.0000.0000.0000.000
184A188PRO0-0.0200.00038.0280.0030.0030.0000.0000.0000.000
185A189SER00.0040.00039.710-0.002-0.0020.0000.0000.0000.000
186A190ASP-1-0.836-0.90542.2220.0190.0190.0000.0000.0000.000
187A191LEU0-0.029-0.01041.1750.0030.0030.0000.0000.0000.000
188A192LEU00.0050.01843.782-0.002-0.0020.0000.0000.0000.000
189A193GLU-1-0.869-0.94443.8330.0600.0600.0000.0000.0000.000
190A194LEU0-0.054-0.02044.663-0.003-0.0030.0000.0000.0000.000
191A195LEU00.0080.00847.1660.0030.0030.0000.0000.0000.000
192A196VAL00.001-0.00846.599-0.002-0.0020.0000.0000.0000.000
193A197LEU00.0200.00949.8370.0000.0000.0000.0000.0000.000
194A198GLY00.0070.00051.9610.0030.0030.0000.0000.0000.000