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: 94NY2

Calculation Name: 3G9V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G9V

Chain ID: A

ChEMBL ID:

UniProt ID: Q969J5

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 186
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066530.568312
FMO2-HF: Nuclear repulsion 1988919.279585
FMO2-HF: Total energy -77611.288727
FMO2-MP2: Total energy -77838.42521


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:29:LEU)


Summations of interaction energy for fragment #1(A:29:LEU)
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.
-18.65-11.32210.465-6.324-11.47-0.01
Interaction energy analysis for fragmet #1(A:29:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.013
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].
3A31PRO00.0630.0523.668-2.243-0.649-0.005-0.773-0.8150.001
4A32GLN0-0.074-0.0414.0280.5990.737-0.001-0.023-0.1150.000
5A33ARG10.9160.9367.650-0.208-0.2080.0000.0000.0000.000
6A34VAL00.0100.0209.825-0.077-0.0770.0000.0000.0000.000
7A35GLN0-0.026-0.02112.4730.1480.1480.0000.0000.0000.000
8A36PHE00.0660.01716.242-0.059-0.0590.0000.0000.0000.000
9A37GLN0-0.030-0.00419.6150.0360.0360.0000.0000.0000.000
10A38SER0-0.025-0.01621.487-0.009-0.0090.0000.0000.0000.000
11A39ARG10.8250.88724.7280.1110.1110.0000.0000.0000.000
12A40ASN00.0250.00227.7400.0000.0000.0000.0000.0000.000
13A41PHE00.026-0.00528.863-0.004-0.0040.0000.0000.0000.000
14A42HIS00.0140.01827.229-0.010-0.0100.0000.0000.0000.000
15A43ASN00.0130.00323.9780.0080.0080.0000.0000.0000.000
16A44ILE00.0230.01219.746-0.016-0.0160.0000.0000.0000.000
17A45LEU0-0.0100.01015.3890.0150.0150.0000.0000.0000.000
18A46GLN00.0170.00415.537-0.014-0.0140.0000.0000.0000.000
19A47TRP0-0.033-0.0119.5070.1400.1400.0000.0000.0000.000
20A48GLN00.0500.0309.1470.0890.0890.0000.0000.0000.000
21A49PRO00.0270.0107.240-0.113-0.1130.0000.0000.0000.000
22A50GLY00.0470.0363.734-0.947-0.8730.000-0.032-0.0430.000
23A51ARG10.8790.9302.135-9.116-7.5815.905-2.380-5.0600.018
24A52ALA00.0490.0142.395-4.660-3.0254.174-2.444-3.365-0.027
25A53LEU0-0.061-0.0252.768-1.355-0.1410.345-0.427-1.132-0.002
26A54THR00.0350.0204.1540.0950.224-0.001-0.004-0.1250.000
27A55GLY00.0210.0157.013-0.135-0.1350.0000.0000.0000.000
28A56ASN0-0.002-0.0136.9750.3450.3450.0000.0000.0000.000
29A57SER00.0180.0199.2520.0940.0940.0000.0000.0000.000
30A58SER0-0.050-0.0017.117-0.368-0.3680.0000.0000.0000.000
31A59VAL00.0150.0288.6470.3310.3310.0000.0000.0000.000
32A60TYR0-0.001-0.0086.936-0.311-0.3110.0000.0000.0000.000
33A61PHE00.0150.02010.3080.1590.1590.0000.0000.0000.000
34A62VAL00.0250.01412.4530.0100.0100.0000.0000.0000.000
35A63GLN0-0.009-0.01715.1590.0770.0770.0000.0000.0000.000
36A64TYR00.0360.01617.3120.0140.0140.0000.0000.0000.000
37A65LYS10.7880.89619.993-0.043-0.0430.0000.0000.0000.000
38A66ILE00.0990.06922.6920.0020.0020.0000.0000.0000.000
39A67TYR0-0.052-0.05423.6410.0150.0150.0000.0000.0000.000
40A68GLY00.0560.03325.098-0.003-0.0030.0000.0000.0000.000
41A69GLN00.0000.00824.823-0.006-0.0060.0000.0000.0000.000
42A70ARG10.9760.98024.001-0.042-0.0420.0000.0000.0000.000
43A71GLN0-0.003-0.01122.1790.0230.0230.0000.0000.0000.000
44A72TRP00.0130.01217.4190.0120.0120.0000.0000.0000.000
45A73LYS10.9580.98820.6350.0650.0650.0000.0000.0000.000
46A74ASN00.0470.02218.773-0.002-0.0020.0000.0000.0000.000
47A75LYS10.7950.87618.6680.2610.2610.0000.0000.0000.000
48A76GLU-1-0.945-0.98519.018-0.254-0.2540.0000.0000.0000.000
49A77ASP-1-0.832-0.91220.281-0.312-0.3120.0000.0000.0000.000
50A78CYS0-0.052-0.00816.605-0.047-0.0470.0000.0000.0000.000
51A79TRP0-0.023-0.01415.714-0.061-0.0610.0000.0000.0000.000
52A80GLY00.0230.00713.7120.0290.0290.0000.0000.0000.000
53A81THR00.0290.02814.410-0.037-0.0370.0000.0000.0000.000
54A82GLN0-0.011-0.03512.706-0.066-0.0660.0000.0000.0000.000
55A83GLU-1-0.887-0.91213.598-0.487-0.4870.0000.0000.0000.000
56A84LEU0-0.057-0.04110.480-0.142-0.1420.0000.0000.0000.000
57A85SER0-0.022-0.04313.5590.0740.0740.0000.0000.0000.000
58A87ASP-1-0.759-0.83818.715-0.146-0.1460.0000.0000.0000.000
59A88LEU0-0.012-0.01219.249-0.007-0.0070.0000.0000.0000.000
60A89THR00.018-0.00823.2160.0290.0290.0000.0000.0000.000
61A90SER0-0.063-0.02226.7770.0160.0160.0000.0000.0000.000
62A91GLU-1-0.827-0.90224.123-0.160-0.1600.0000.0000.0000.000
63A92THR0-0.073-0.05823.7530.0130.0130.0000.0000.0000.000
64A93SER00.035-0.00327.0310.0070.0070.0000.0000.0000.000
65A94ASP-1-0.855-0.90130.562-0.036-0.0360.0000.0000.0000.000
66A95ILE0-0.034-0.02330.5440.0080.0080.0000.0000.0000.000
67A96GLN00.0170.00530.6900.0040.0040.0000.0000.0000.000
68A97GLU-1-0.915-0.94229.3710.0240.0240.0000.0000.0000.000
69A98PRO0-0.049-0.01526.4040.0000.0000.0000.0000.0000.000
70A99TYR0-0.026-0.03323.378-0.002-0.0020.0000.0000.0000.000
71A100TYR0-0.063-0.02618.5760.0250.0250.0000.0000.0000.000
72A101GLY00.0560.03017.924-0.028-0.0280.0000.0000.0000.000
73A102ARG10.7830.88813.1220.0470.0470.0000.0000.0000.000
74A103VAL00.0740.03910.041-0.054-0.0540.0000.0000.0000.000
75A104ARG10.7900.8947.7860.4010.4010.0000.0000.0000.000
76A105ALA00.0670.0304.523-0.0260.076-0.001-0.014-0.0860.000
77A106ALA0-0.013-0.0046.0630.2230.2230.0000.0000.0000.000
78A107SER0-0.003-0.0296.4040.0730.0730.0000.0000.0000.000
79A108ALA00.0230.0187.684-0.021-0.0210.0000.0000.0000.000
80A109GLY00.0210.02110.3460.1080.1080.0000.0000.0000.000
81A110SER0-0.056-0.0185.633-0.103-0.1030.0000.0000.0000.000
82A111TYR00.0370.0006.092-0.345-0.3450.0000.0000.0000.000
83A112SER0-0.029-0.0073.355-0.4780.2240.047-0.208-0.5410.000
84A113GLU-1-0.808-0.8984.1370.1740.3790.002-0.019-0.1880.000
85A114TRP0-0.004-0.0056.611-0.280-0.2800.0000.0000.0000.000
86A115SER0-0.088-0.0597.2580.5520.5520.0000.0000.0000.000
87A116MET0-0.034-0.0209.962-0.192-0.1920.0000.0000.0000.000
88A117THR00.0200.01713.6760.0490.0490.0000.0000.0000.000
89A118PRO00.0310.00016.1300.0450.0450.0000.0000.0000.000
90A119ARG10.8840.96018.952-0.162-0.1620.0000.0000.0000.000
91A120PHE00.0370.02221.148-0.006-0.0060.0000.0000.0000.000
92A121THR00.0440.01622.937-0.008-0.0080.0000.0000.0000.000
93A122PRO0-0.041-0.00226.3620.0020.0020.0000.0000.0000.000
94A123TRP0-0.036-0.03527.9170.0010.0010.0000.0000.0000.000
95A124TRP00.0340.03326.8020.0000.0000.0000.0000.0000.000
96A125GLU-1-0.856-0.94422.7860.0500.0500.0000.0000.0000.000
97A126THR0-0.058-0.02126.043-0.010-0.0100.0000.0000.0000.000
98A127LYS10.9160.95624.3210.0300.0300.0000.0000.0000.000
99A128ILE00.0010.00729.418-0.012-0.0120.0000.0000.0000.000
100A129ASP-1-0.759-0.84930.465-0.078-0.0780.0000.0000.0000.000
101A130PRO00.0260.00233.2010.0040.0040.0000.0000.0000.000
102A131PRO0-0.0400.00036.840-0.005-0.0050.0000.0000.0000.000
103A132VAL0-0.022-0.00839.6060.0000.0000.0000.0000.0000.000
104A133MET00.0090.00841.0080.0030.0030.0000.0000.0000.000
105A134ASN0-0.053-0.03144.471-0.004-0.0040.0000.0000.0000.000
106A135ILE00.0510.03447.5380.0020.0020.0000.0000.0000.000
107A136THR0-0.081-0.02651.026-0.001-0.0010.0000.0000.0000.000
108A137GLN00.0900.03954.5800.0000.0000.0000.0000.0000.000
109A138VAL0-0.016-0.02956.8410.0010.0010.0000.0000.0000.000
110A139ASN00.0170.00958.0650.0000.0000.0000.0000.0000.000
111A140GLY0-0.005-0.00160.5720.0020.0020.0000.0000.0000.000
112A141SER0-0.042-0.02158.113-0.001-0.0010.0000.0000.0000.000
113A142LEU00.0270.03053.8110.0010.0010.0000.0000.0000.000
114A143LEU0-0.028-0.01853.0640.0010.0010.0000.0000.0000.000
115A144VAL00.0220.00648.246-0.003-0.0030.0000.0000.0000.000
116A145ILE0-0.022-0.01247.3140.0010.0010.0000.0000.0000.000
117A146LEU00.0190.01144.118-0.002-0.0020.0000.0000.0000.000
118A147HIS0-0.047-0.02441.8440.0000.0000.0000.0000.0000.000
119A148ALA00.0110.01538.1760.0000.0000.0000.0000.0000.000
120A149PRO00.0060.01134.034-0.005-0.0050.0000.0000.0000.000
121A150ASN0-0.039-0.01332.6390.0090.0090.0000.0000.0000.000
122A151LEU00.0260.01533.247-0.002-0.0020.0000.0000.0000.000
123A152PRO00.0340.01830.9600.0010.0010.0000.0000.0000.000
124A153TYR0-0.002-0.01133.800-0.002-0.0020.0000.0000.0000.000
125A154ARG10.8990.94737.0520.0820.0820.0000.0000.0000.000
126A155TYR0-0.026-0.01934.6240.0010.0010.0000.0000.0000.000
127A156GLN0-0.035-0.00237.441-0.002-0.0020.0000.0000.0000.000
128A157LYS10.8150.89938.6420.0550.0550.0000.0000.0000.000
129A158GLU-1-0.787-0.86941.711-0.045-0.0450.0000.0000.0000.000
130A159LYS10.8110.88440.7850.0530.0530.0000.0000.0000.000
131A160ASN0-0.0020.00143.5050.0000.0000.0000.0000.0000.000
132A161VAL00.0140.02342.8170.0030.0030.0000.0000.0000.000
133A162SER00.019-0.02244.285-0.005-0.0050.0000.0000.0000.000
134A163ILE00.005-0.00838.6540.0000.0000.0000.0000.0000.000
135A164GLU-1-0.742-0.86039.770-0.036-0.0360.0000.0000.0000.000
136A165ASP-1-0.845-0.88041.115-0.015-0.0150.0000.0000.0000.000
137A166TYR0-0.047-0.01934.8930.0050.0050.0000.0000.0000.000
138A167TYR0-0.023-0.02133.480-0.002-0.0020.0000.0000.0000.000
139A168GLU-1-0.869-0.92637.2100.0050.0050.0000.0000.0000.000
140A169LEU0-0.057-0.02836.2060.0020.0020.0000.0000.0000.000
141A170LEU0-0.039-0.01740.2000.0010.0010.0000.0000.0000.000
142A171TYR0-0.064-0.04841.468-0.002-0.0020.0000.0000.0000.000
143A172ARG10.7810.87441.9530.0060.0060.0000.0000.0000.000
144A173VAL0-0.008-0.00144.728-0.003-0.0030.0000.0000.0000.000
145A174PHE0-0.008-0.01443.2140.0040.0040.0000.0000.0000.000
146A175ILE00.0140.01548.480-0.003-0.0030.0000.0000.0000.000
147A176ILE0-0.054-0.01546.9040.0030.0030.0000.0000.0000.000
148A177ASN0-0.006-0.02249.998-0.001-0.0010.0000.0000.0000.000
149A178ASN0-0.048-0.04351.614-0.001-0.0010.0000.0000.0000.000
150A179SER0-0.053-0.05549.1850.0000.0000.0000.0000.0000.000
151A180LEU0-0.055-0.01447.3790.0000.0000.0000.0000.0000.000
152A181GLU-1-0.790-0.86542.444-0.012-0.0120.0000.0000.0000.000
153A182LYN0-0.018-0.01643.4710.0000.0000.0000.0000.0000.000
154A183GLU-1-0.861-0.88047.488-0.004-0.0040.0000.0000.0000.000
155A184GLN00.006-0.00549.7110.0020.0020.0000.0000.0000.000
156A185LYS10.8900.94047.8920.0010.0010.0000.0000.0000.000
157A186VAL0-0.008-0.00649.7130.0020.0020.0000.0000.0000.000
158A187TYR0-0.035-0.03347.7570.0010.0010.0000.0000.0000.000
159A188GLU-1-0.806-0.90045.340-0.002-0.0020.0000.0000.0000.000
160A189GLY00.0070.01246.7790.0020.0020.0000.0000.0000.000
161A190ALA00.0460.02445.323-0.002-0.0020.0000.0000.0000.000
162A191HIS00.0050.00246.353-0.004-0.0040.0000.0000.0000.000
163A192ARG10.8110.90344.1800.0360.0360.0000.0000.0000.000
164A193ALA00.0180.02249.7250.0020.0020.0000.0000.0000.000
165A194VAL0-0.018-0.02652.123-0.002-0.0020.0000.0000.0000.000
166A195GLU-1-0.937-0.95152.796-0.015-0.0150.0000.0000.0000.000
167A206CYM-1-0.882-0.94149.680-0.025-0.0250.0000.0000.0000.000
168A207VAL0-0.045-0.03148.4540.0020.0020.0000.0000.0000.000
169A208VAL00.0360.03043.045-0.002-0.0020.0000.0000.0000.000
170A209ALA00.019-0.00443.4010.0030.0030.0000.0000.0000.000
171A210GLU-1-0.781-0.89539.369-0.013-0.0130.0000.0000.0000.000
172A211ILE0-0.024-0.02437.769-0.001-0.0010.0000.0000.0000.000
173A212TYR0-0.038-0.04438.1480.0000.0000.0000.0000.0000.000
174A213GLN00.0430.00233.540-0.002-0.0020.0000.0000.0000.000
175A214PRO00.0220.00638.4160.0050.0050.0000.0000.0000.000
176A215MET0-0.023-0.00438.1250.0050.0050.0000.0000.0000.000
177A216LEU0-0.085-0.04633.3600.0060.0060.0000.0000.0000.000
178A217ASP-1-0.873-0.90235.7740.0220.0220.0000.0000.0000.000
179A218ARG10.8040.91429.602-0.016-0.0160.0000.0000.0000.000
180A219ARG00.0320.03236.046-0.003-0.0030.0000.0000.0000.000
181A220SER0-0.048-0.02234.4920.0020.0020.0000.0000.0000.000
182A221GLN0-0.039-0.02231.265-0.003-0.0030.0000.0000.0000.000
183A222ARG10.8000.86535.5770.0130.0130.0000.0000.0000.000
184A223SER0-0.048-0.03038.080-0.004-0.0040.0000.0000.0000.000
185A224GLU-1-0.887-0.92340.165-0.049-0.0490.0000.0000.0000.000
186A225GLU-1-0.959-1.00141.566-0.032-0.0320.0000.0000.0000.000