FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: G5G61

Calculation Name: 3GNL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNL

Chain ID: A

ChEMBL ID:

UniProt ID:

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2827142.7551
FMO2-HF: Nuclear repulsion 2736392.725045
FMO2-HF: Total energy -90750.030055
FMO2-MP2: Total energy -91018.826136


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:9:GLU)


Summations of interaction energy for fragment #1(A:9:GLU)
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.
-161.131-175.07453.774-21.703-18.1260.226
Interaction energy analysis for fragmet #1(A:9:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.785 / q_NPA : -0.871
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].
3A11GLN00.0020.0113.8770.4281.797-0.009-0.642-0.7180.002
4A12LEU00.0090.0146.455-0.870-0.8700.0000.0000.0000.000
5A13SER0-0.011-0.0298.116-1.623-1.6230.0000.0000.0000.000
6A14LYS10.8440.87511.642-20.577-20.5770.0000.0000.0000.000
7A15ARG10.8500.92313.827-19.307-19.3070.0000.0000.0000.000
8A16LEU0-0.015-0.0029.981-0.345-0.3450.0000.0000.0000.000
9A17GLU-1-0.828-0.90610.51723.01123.0110.0000.0000.0000.000
10A18LYS10.8340.93711.814-16.729-16.7290.0000.0000.0000.000
11A19VAL00.0080.00713.963-0.759-0.7590.0000.0000.0000.000
12A20ALA00.0400.01110.566-0.432-0.4320.0000.0000.0000.000
13A21SER0-0.021-0.02012.547-0.615-0.6150.0000.0000.0000.000
14A22TYR0-0.014-0.01214.713-1.064-1.0640.0000.0000.0000.000
15A23ILE0-0.048-0.00912.042-1.014-1.0140.0000.0000.0000.000
16A24THR0-0.019-0.02914.7100.4800.4800.0000.0000.0000.000
17A25LYS10.8370.91416.468-14.759-14.7590.0000.0000.0000.000
18A26ASN00.0490.02614.5620.5500.5500.0000.0000.0000.000
19A27GLU-1-0.739-0.80115.24417.35617.3560.0000.0000.0000.000
20A28ARG10.8780.93814.544-15.730-15.7300.0000.0000.0000.000
21A29ILE00.0320.01110.916-1.265-1.2650.0000.0000.0000.000
22A30ALA00.0020.00015.3330.2990.2990.0000.0000.0000.000
23A31ASP-1-0.817-0.88212.29423.40823.4080.0000.0000.0000.000
24A32ILE0-0.019-0.01314.9190.1570.1570.0000.0000.0000.000
25A33GLY0-0.031-0.02017.641-0.617-0.6170.0000.0000.0000.000
26A34SER0-0.051-0.04111.8541.0411.0410.0000.0000.0000.000
27A35ASP-1-0.759-0.86711.24222.53222.5320.0000.0000.0000.000
28A36HIS0-0.053-0.0438.6441.5801.5800.0000.0000.0000.000
29A37ALA00.0250.0068.1082.9282.9280.0000.0000.0000.000
30A38TYR0-0.032-0.0324.1384.1764.326-0.001-0.016-0.1340.000
31A39LEU0-0.0040.0065.5025.1525.1520.0000.0000.0000.000
32A40PRO0-0.010-0.0157.6171.1501.1500.0000.0000.0000.000
33A41CYS0-0.014-0.0012.494-8.899-7.3491.215-1.147-1.6160.018
34A42PHE00.0220.0073.9882.4293.0150.015-0.163-0.4380.001
35A43ALA00.017-0.0044.887-2.747-2.745-0.001-0.0040.0030.000
36A44VAL0-0.0080.0106.516-2.869-2.8690.0000.0000.0000.000
37A45LYS10.7730.8811.847-144.229-151.52825.204-9.580-8.3250.126
38A46ASN0-0.0250.0055.604-6.004-6.011-0.0010.0000.0080.000
39A47GLN0-0.009-0.0038.630-3.841-3.8410.0000.0000.0000.000
40A48THR0-0.020-0.01310.417-2.602-2.6020.0000.0000.0000.000
41A49ALA0-0.058-0.02910.327-2.235-2.2350.0000.0000.0000.000
42A50SER0-0.017-0.02111.0591.7841.7840.0000.0000.0000.000
43A51PHE0-0.042-0.02612.4170.4310.4310.0000.0000.0000.000
44A52ALA00.0230.01110.563-0.528-0.5280.0000.0000.0000.000
45A53ILE0-0.027-0.00212.5840.0860.0860.0000.0000.0000.000
46A54ALA00.0230.00311.2700.4300.4300.0000.0000.0000.000
47A55GLY00.0110.01013.408-0.516-0.5160.0000.0000.0000.000
48A56GLH0-0.064-0.06013.767-0.131-0.1310.0000.0000.0000.000
49A57VAL00.0580.02818.088-0.571-0.5710.0000.0000.0000.000
50A58VAL00.001-0.00620.205-0.649-0.6490.0000.0000.0000.000
51A59ASP-1-0.749-0.88019.22315.55115.5510.0000.0000.0000.000
52A60GLY0-0.0060.02017.9980.6850.6850.0000.0000.0000.000
53A61PRO00.0630.01514.7361.0701.0700.0000.0000.0000.000
54A62PHE00.0040.01914.0641.5941.5940.0000.0000.0000.000
55A63GLN00.008-0.01314.5781.7281.7280.0000.0000.0000.000
56A64SER0-0.022-0.01411.5211.2431.2430.0000.0000.0000.000
57A65ALA00.0470.03410.0302.7532.7530.0000.0000.0000.000
58A66GLN00.0120.0069.7373.3303.3300.0000.0000.0000.000
59A67LYS10.8750.94310.315-21.017-21.0170.0000.0000.0000.000
60A68GLN00.0290.0293.145-8.115-6.7570.090-0.744-0.7030.001
61A69VAL00.0490.0145.3638.5658.671-0.0010.000-0.1050.000
62A70ARG10.8390.9136.812-23.218-23.2180.0000.0000.0000.000
63A71SER0-0.028-0.0105.739-2.478-2.4780.0000.0000.0000.000
64A72SER0-0.042-0.0441.565-20.874-32.07827.265-10.555-5.5050.074
65A73GLY0-0.0100.0033.3330.716-0.080-0.0031.201-0.4020.004
66A74LEU00.0150.0004.202-1.827-1.5850.001-0.053-0.1910.000
67A75THR00.006-0.0177.729-2.580-2.5800.0000.0000.0000.000
68A76GLU-1-0.973-0.96910.90920.93220.9320.0000.0000.0000.000
69A77GLN0-0.061-0.0419.6720.4500.4500.0000.0000.0000.000
70A78ILE0-0.024-0.0086.639-0.341-0.3410.0000.0000.0000.000
71A79ASP-1-0.764-0.86610.98119.24719.2470.0000.0000.0000.000
72A80VAL0-0.044-0.01611.541-0.595-0.5950.0000.0000.0000.000
73A81ARG10.6630.78614.281-18.383-18.3830.0000.0000.0000.000
74A82LYS10.8310.89617.965-14.250-14.2500.0000.0000.0000.000
75A83GLY00.001-0.01220.647-0.644-0.6440.0000.0000.0000.000
76A84ASN0-0.003-0.00222.7010.7500.7500.0000.0000.0000.000
77A85GLY00.0590.02223.310-0.097-0.0970.0000.0000.0000.000
78A86LEU00.0290.01522.0170.6950.6950.0000.0000.0000.000
79A87ALA0-0.034-0.00823.604-0.004-0.0040.0000.0000.0000.000
80A88VAL0-0.031-0.00119.121-0.026-0.0260.0000.0000.0000.000
81A89ILE00.0310.02919.9700.6680.6680.0000.0000.0000.000
82A90GLU-1-0.832-0.92222.11411.06111.0610.0000.0000.0000.000
83A91LYS10.9150.95324.084-10.470-10.4700.0000.0000.0000.000
84A92LYS10.8700.92022.954-13.933-13.9330.0000.0000.0000.000
85A93ASP-1-0.741-0.82520.08615.31715.3170.0000.0000.0000.000
86A94ALA0-0.0060.01020.4850.7960.7960.0000.0000.0000.000
87A95ILE00.0140.01217.8280.4940.4940.0000.0000.0000.000
88A96ASP-1-0.799-0.88118.60614.96814.9680.0000.0000.0000.000
89A97THR0-0.040-0.05317.422-1.119-1.1190.0000.0000.0000.000
90A98ILE0-0.014-0.00417.9930.8130.8130.0000.0000.0000.000
91A99VAL0-0.0030.00014.434-0.559-0.5590.0000.0000.0000.000
92A100ILE00.0340.00617.3380.1420.1420.0000.0000.0000.000
93A101ALA00.0230.00815.910-0.532-0.5320.0000.0000.0000.000
94A102GLY00.0160.01818.0620.1400.1400.0000.0000.0000.000
95A103MET0-0.0060.01418.895-0.712-0.7120.0000.0000.0000.000
96A104GLY00.005-0.00222.409-0.178-0.1780.0000.0000.0000.000
97A105GLY00.0390.01426.0310.1350.1350.0000.0000.0000.000
98A106THR00.0440.01027.4080.0750.0750.0000.0000.0000.000
99A107LEU0-0.0100.02724.591-0.159-0.1590.0000.0000.0000.000
100A108ILE00.0180.00422.2600.0870.0870.0000.0000.0000.000
101A109ARG10.7480.83425.458-9.206-9.2060.0000.0000.0000.000
102A110THR00.001-0.00928.960-0.190-0.1900.0000.0000.0000.000
103A111ILE0-0.020-0.01023.025-0.008-0.0080.0000.0000.0000.000
104A112LEU0-0.022-0.01424.3970.1520.1520.0000.0000.0000.000
105A113GLU-1-0.847-0.91027.4969.3739.3730.0000.0000.0000.000
106A114GLU-1-0.924-0.97129.33610.49110.4910.0000.0000.0000.000
107A115GLY0-0.017-0.01227.105-0.022-0.0220.0000.0000.0000.000
108A116ALA00.0660.04127.9070.2420.2420.0000.0000.0000.000
109A117ALA0-0.011-0.01229.9280.0460.0460.0000.0000.0000.000
110A118LYS10.7460.85225.094-12.197-12.1970.0000.0000.0000.000
111A119LEU00.0320.02625.1250.4790.4790.0000.0000.0000.000
112A120ALA0-0.046-0.02226.869-0.039-0.0390.0000.0000.0000.000
113A121GLY0-0.001-0.00526.5520.0400.0400.0000.0000.0000.000
114A122VAL0-0.0570.00222.1470.2470.2470.0000.0000.0000.000
115A123THR0-0.048-0.03622.520-0.392-0.3920.0000.0000.0000.000
116A124LYS10.7760.86018.151-16.788-16.7880.0000.0000.0000.000
117A125LEU0-0.0040.01021.4080.4730.4730.0000.0000.0000.000
118A126ILE0-0.018-0.01216.639-0.303-0.3030.0000.0000.0000.000
119A127LEU00.0100.00619.2230.5610.5610.0000.0000.0000.000
120A128GLN00.010-0.00917.9950.5940.5940.0000.0000.0000.000
121A129PRO00.0100.01520.3880.2160.2160.0000.0000.0000.000
122A130ASN0-0.012-0.01220.8720.4280.4280.0000.0000.0000.000
123A131ILE00.0190.00423.714-0.365-0.3650.0000.0000.0000.000
124A132ALA00.002-0.00527.5420.1810.1810.0000.0000.0000.000
125A133ALA00.0710.03027.054-0.015-0.0150.0000.0000.0000.000
126A134TRP00.0580.03628.3890.1110.1110.0000.0000.0000.000
127A135GLN0-0.0050.00830.672-0.037-0.0370.0000.0000.0000.000
128A136LEU00.0170.00125.251-0.055-0.0550.0000.0000.0000.000
129A137ARG10.7430.87927.704-10.571-10.5710.0000.0000.0000.000
130A138GLU-1-0.827-0.89931.5928.4838.4830.0000.0000.0000.000
131A139TRP0-0.017-0.00128.182-0.015-0.0150.0000.0000.0000.000
132A140SER0-0.023-0.03430.399-0.143-0.1430.0000.0000.0000.000
133A141GLU-1-0.874-0.93532.0038.1578.1570.0000.0000.0000.000
134A142GLN0-0.026-0.02235.806-0.022-0.0220.0000.0000.0000.000
135A143ASN0-0.066-0.02832.455-0.132-0.1320.0000.0000.0000.000
136A144ASN0-0.0100.00133.6010.0580.0580.0000.0000.0000.000
137A145TRP00.0400.01725.4180.3490.3490.0000.0000.0000.000
138A146LEU00.0180.03330.906-0.055-0.0550.0000.0000.0000.000
139A147ILE00.006-0.00527.3110.4310.4310.0000.0000.0000.000
140A148THR0-0.023-0.01725.416-0.217-0.2170.0000.0000.0000.000
141A149SER0-0.018-0.03723.7610.0840.0840.0000.0000.0000.000
142A150GLU-1-0.756-0.87624.01610.90410.9040.0000.0000.0000.000
143A151ALA00.0210.01621.1400.1130.1130.0000.0000.0000.000
144A152ILE0-0.0160.00123.2910.0370.0370.0000.0000.0000.000
145A153LEU0-0.0030.00718.063-0.035-0.0350.0000.0000.0000.000
146A154ARG10.9100.94021.682-11.071-11.0710.0000.0000.0000.000
147A155GLU-1-0.743-0.83014.96218.49618.4960.0000.0000.0000.000
148A156ASP-1-0.779-0.88918.20615.40515.4050.0000.0000.0000.000
149A157ASN0-0.040-0.02221.002-0.398-0.3980.0000.0000.0000.000
150A158LYS10.8260.91619.384-14.936-14.9360.0000.0000.0000.000
151A159VAL0-0.009-0.01522.9110.2940.2940.0000.0000.0000.000
152A160TYR0-0.029-0.01719.4260.0830.0830.0000.0000.0000.000
153A161GLU-1-0.804-0.89922.60410.70810.7080.0000.0000.0000.000
154A162ILE0-0.025-0.02317.6330.4020.4020.0000.0000.0000.000
155A163MET0-0.022-0.00221.721-0.586-0.5860.0000.0000.0000.000
156A164VAL00.0040.00620.8690.6610.6610.0000.0000.0000.000
157A165LEU0-0.006-0.00223.397-0.622-0.6220.0000.0000.0000.000
158A166ALA00.0270.01524.7070.6110.6110.0000.0000.0000.000
159A167PRO00.0100.00726.974-0.377-0.3770.0000.0000.0000.000
160A168SER0-0.055-0.03830.173-0.026-0.0260.0000.0000.0000.000
161A169GLU-1-0.940-0.96633.6618.3518.3510.0000.0000.0000.000
162A170LYS10.9010.95736.864-8.216-8.2160.0000.0000.0000.000
163A171PRO00.0320.01337.3040.2070.2070.0000.0000.0000.000
164A172VAL0-0.0280.01033.7480.0080.0080.0000.0000.0000.000
165A173THR0-0.023-0.01537.031-0.118-0.1180.0000.0000.0000.000
166A174TRP0-0.018-0.01132.3080.0340.0340.0000.0000.0000.000
167A175THR0-0.004-0.02038.148-0.212-0.2120.0000.0000.0000.000
168A176LYS10.9170.93738.318-6.910-6.9100.0000.0000.0000.000
169A177GLN00.005-0.01438.1520.2130.2130.0000.0000.0000.000
170A178GLU-1-0.806-0.88134.8788.7488.7480.0000.0000.0000.000
171A179ILE00.0080.00833.5570.3500.3500.0000.0000.0000.000
172A180PHE0-0.059-0.03533.4160.2670.2670.0000.0000.0000.000
173A181PHE0-0.028-0.03332.4590.2210.2210.0000.0000.0000.000
174A182GLY00.0570.02630.0980.3040.3040.0000.0000.0000.000
175A183PRO0-0.0090.00530.438-0.206-0.2060.0000.0000.0000.000
176A184CYS0-0.052-0.01828.034-0.263-0.2630.0000.0000.0000.000
177A185LEU00.0210.01725.880-0.111-0.1110.0000.0000.0000.000
178A186LEU0-0.025-0.01029.839-0.169-0.1690.0000.0000.0000.000
179A187LYS10.8190.89832.691-9.254-9.2540.0000.0000.0000.000
180A188GLU-1-0.889-0.90826.47511.04811.0480.0000.0000.0000.000
181A189GLN0-0.080-0.05631.090-0.099-0.0990.0000.0000.0000.000
182A190SER00.011-0.00828.094-0.164-0.1640.0000.0000.0000.000
183A191ALA00.0470.01229.583-0.157-0.1570.0000.0000.0000.000
184A192ILE0-0.0350.00824.145-0.159-0.1590.0000.0000.0000.000
185A193PHE00.0400.02628.303-0.117-0.1170.0000.0000.0000.000
186A194LYS10.8750.92730.277-8.372-8.3720.0000.0000.0000.000
187A195SER0-0.044-0.04330.532-0.078-0.0780.0000.0000.0000.000
188A196LYS10.8390.92228.427-10.343-10.3430.0000.0000.0000.000
189A197TRP00.0450.01230.698-0.276-0.2760.0000.0000.0000.000
190A198ARG10.8570.92234.505-7.659-7.6590.0000.0000.0000.000
191A199HIS0-0.039-0.01533.732-0.290-0.2900.0000.0000.0000.000
192A200GLU-1-0.826-0.89231.7519.3219.3210.0000.0000.0000.000
193A201ALA00.0180.00936.141-0.201-0.2010.0000.0000.0000.000
194A202ASN00.0400.01639.274-0.264-0.2640.0000.0000.0000.000
195A203THR0-0.032-0.01537.324-0.177-0.1770.0000.0000.0000.000
196A204TRP0-0.001-0.02535.948-0.152-0.1520.0000.0000.0000.000
197A205GLN00.0580.02341.649-0.042-0.0420.0000.0000.0000.000
198A206ASN00.0340.02341.936-0.304-0.3040.0000.0000.0000.000
199A207ILE0-0.042-0.00140.184-0.126-0.1260.0000.0000.0000.000
200A208ILE00.0400.01844.677-0.128-0.1280.0000.0000.0000.000
201A209GLN0-0.034-0.00247.644-0.129-0.1290.0000.0000.0000.000
202A210THR0-0.015-0.02746.468-0.125-0.1250.0000.0000.0000.000
203A211ILE0-0.031-0.01346.454-0.097-0.0970.0000.0000.0000.000
204A212SER0-0.009-0.01950.180-0.147-0.1470.0000.0000.0000.000
205A213ASN0-0.025-0.00852.595-0.063-0.0630.0000.0000.0000.000
206A214ASN0-0.086-0.03751.243-0.133-0.1330.0000.0000.0000.000
207A215GLN0-0.0090.00454.338-0.016-0.0160.0000.0000.0000.000
208A216PRO0-0.016-0.00457.420-0.040-0.0400.0000.0000.0000.000
209A217VAL00.012-0.00252.6440.0730.0730.0000.0000.0000.000
210A218SER00.015-0.01252.843-0.032-0.0320.0000.0000.0000.000
211A219THR00.0460.00953.5660.0580.0580.0000.0000.0000.000
212A220GLU-1-0.822-0.89449.4026.0756.0750.0000.0000.0000.000
213A221ASN0-0.039-0.03148.6140.2790.2790.0000.0000.0000.000
214A222GLN00.0280.01650.0190.1070.1070.0000.0000.0000.000
215A223ALA0-0.065-0.02949.2100.0100.0100.0000.0000.0000.000
216A224LYS10.9520.97643.317-7.000-7.0000.0000.0000.0000.000
217A225ILE00.0120.00845.9300.1540.1540.0000.0000.0000.000
218A226ARG10.9991.01247.312-6.016-6.0160.0000.0000.0000.000
219A227GLU-1-0.863-0.90241.7257.7097.7090.0000.0000.0000.000
220A228LEU0-0.020-0.01341.5060.1760.1760.0000.0000.0000.000
221A229GLU-1-0.860-0.94443.5916.3496.3490.0000.0000.0000.000
222A230HIS00.0160.02842.9080.0050.0050.0000.0000.0000.000
223A231LYS10.7990.88038.388-7.802-7.8020.0000.0000.0000.000
224A232ILE00.0140.00340.5980.1490.1490.0000.0000.0000.000
225A233ALA00.0040.00642.5470.0490.0490.0000.0000.0000.000
226A234LEU0-0.030-0.01639.7050.0120.0120.0000.0000.0000.000
227A235VAL00.0110.00137.0830.1170.1170.0000.0000.0000.000
228A236GLU-1-0.794-0.86039.5016.9826.9820.0000.0000.0000.000
229A237ASP-1-0.848-0.90342.4607.1817.1810.0000.0000.0000.000
230A238VAL0-0.036-0.02836.5770.0080.0080.0000.0000.0000.000
231A239LEU0-0.057-0.01936.3400.1630.1630.0000.0000.0000.000
232A240LYS10.8270.91739.375-7.218-7.2180.0000.0000.0000.000
233A241GLU-1-0.871-0.91739.6007.6937.6930.0000.0000.0000.000
234A242GLY0-0.078-0.05843.247-0.029-0.0290.0000.0000.0000.000