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

tag_button

FMODB ID: Z62RN

Calculation Name: 5GNG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNG

Chain ID: A

ChEMBL ID:

UniProt ID: P44251

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 OptH
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842980.561838
FMO2-HF: Nuclear repulsion 2755466.084293
FMO2-HF: Total energy -87514.477544
FMO2-MP2: Total energy -87771.621739


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-40.634-42.87753.828-21.758-29.829-0.137
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.101 / q_NPA : -0.039
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].
3A3THR00.023-0.0092.972-2.6331.1530.192-2.041-1.9380.001
4A4LYS10.8630.9375.146-0.388-0.348-0.001-0.005-0.0340.000
5A5PHE00.0410.0208.8130.2320.2320.0000.0000.0000.000
6A6TYR0-0.047-0.03010.903-0.077-0.0770.0000.0000.0000.000
7A7ASP-1-0.839-0.93214.4250.1880.1880.0000.0000.0000.000
8A8TYR0-0.055-0.03416.664-0.034-0.0340.0000.0000.0000.000
9A9GLN0-0.055-0.01819.102-0.022-0.0220.0000.0000.0000.000
10A10GLY0-0.040-0.00419.104-0.013-0.0130.0000.0000.0000.000
11A11GLU-1-0.818-0.92619.2340.1600.1600.0000.0000.0000.000
12A12HIS0-0.044-0.02118.4670.0110.0110.0000.0000.0000.000
13A13LEU00.0320.03110.8490.0010.0010.0000.0000.0000.000
14A14ILE0-0.053-0.02312.9310.0190.0190.0000.0000.0000.000
15A15LEU00.0400.0177.0190.0520.0520.0000.0000.0000.000
16A16TYR00.0350.0029.053-0.093-0.0930.0000.0000.0000.000
17A17PHE00.0440.0182.785-0.3290.7250.470-0.318-1.207-0.001
18A18ALA00.0150.0136.907-0.890-0.8900.0000.0000.0000.000
19A19GLY00.0600.0398.2100.2870.2870.0000.0000.0000.000
20A20TRP00.007-0.0148.7150.1190.1190.0000.0000.0000.000
21A21GLY0-0.043-0.0288.919-0.078-0.0780.0000.0000.0000.000
22A22THR0-0.102-0.04410.177-0.075-0.0750.0000.0000.0000.000
23A23PRO00.0320.01410.2100.0800.0800.0000.0000.0000.000
24A24PRO00.018-0.0068.7630.0460.0460.0000.0000.0000.000
25A25ASP-1-0.869-0.94211.2620.3480.3480.0000.0000.0000.000
26A26ALA0-0.056-0.01314.162-0.038-0.0380.0000.0000.0000.000
27A27VAL00.0120.00512.962-0.021-0.0210.0000.0000.0000.000
28A28ASN0-0.039-0.02015.9680.0010.0010.0000.0000.0000.000
29A29HIS0-0.069-0.02517.226-0.028-0.0280.0000.0000.0000.000
30A30LEU0-0.074-0.01516.619-0.031-0.0310.0000.0000.0000.000
31A31ILE00.0210.00019.5050.0020.0020.0000.0000.0000.000
32A32LEU0-0.020-0.01216.5450.0320.0320.0000.0000.0000.000
33A33PRO0-0.056-0.01519.719-0.035-0.0350.0000.0000.0000.000
34A34GLU-1-0.791-0.89721.8320.2070.2070.0000.0000.0000.000
35A35ASN0-0.050-0.02622.7320.0180.0180.0000.0000.0000.000
36A36HIS0-0.135-0.08617.9290.0320.0320.0000.0000.0000.000
37A37ASP-1-0.666-0.77414.5300.2670.2670.0000.0000.0000.000
38A38LEU0-0.066-0.03511.9020.0780.0780.0000.0000.0000.000
39A39LEU0-0.0080.0086.736-0.082-0.0820.0000.0000.0000.000
40A40ILE0-0.053-0.0187.8050.3810.3810.0000.0000.0000.000
41A41CYS00.007-0.0032.831-2.428-2.0911.801-0.642-1.4950.005
42A42TYR00.010-0.0193.405-0.6650.2410.056-0.232-0.7300.000
43A43ASP-1-0.870-0.9452.295-3.746-3.2592.755-1.163-2.079-0.018
44A44TYR0-0.022-0.0422.315-5.455-2.3274.467-2.247-5.348-0.008
45A45GLN00.017-0.0133.566-0.447-0.1730.005-0.010-0.2700.000
46A46ASP-1-0.853-0.9071.705-13.112-22.52420.122-6.593-4.117-0.049
47A47LEU0-0.036-0.0462.383-3.651-1.5533.022-2.094-3.026-0.019
48A48ASN0-0.024-0.0052.8111.5042.5980.7810.146-2.021-0.002
49A49LEU00.0210.0081.779-8.803-15.39517.705-6.117-4.997-0.045
50A50ASP-1-0.954-0.9653.6400.0010.3840.009-0.006-0.3850.000
51A51PHE0-0.009-0.0216.3050.3890.3890.0000.0000.0000.000
52A52ASP-1-0.840-0.8878.501-0.017-0.0170.0000.0000.0000.000
53A53LEU0-0.011-0.0218.8840.1190.1190.0000.0000.0000.000
54A54SER0-0.089-0.06512.6870.0440.0440.0000.0000.0000.000
55A55ALA0-0.008-0.00116.0420.0050.0050.0000.0000.0000.000
56A56TYR0-0.046-0.05113.5070.0280.0280.0000.0000.0000.000
57A57ARG10.8520.93617.883-0.191-0.1910.0000.0000.0000.000
58A58HIS0-0.060-0.04118.9120.0120.0120.0000.0000.0000.000
59A59ILE00.1100.05812.1520.0100.0100.0000.0000.0000.000
60A60ARG10.8680.92514.990-0.464-0.4640.0000.0000.0000.000
61A61LEU00.0340.0338.6930.0810.0810.0000.0000.0000.000
62A62VAL0-0.005-0.00411.512-0.197-0.1970.0000.0000.0000.000
63A63ALA00.0190.0199.2810.3360.3360.0000.0000.0000.000
64A64TRP0-0.042-0.02510.497-0.301-0.3010.0000.0000.0000.000
65A65SER0-0.001-0.01510.8010.1650.1650.0000.0000.0000.000
66A66MET0-0.022-0.0299.400-0.003-0.0030.0000.0000.0000.000
67A67GLY00.0370.0276.7140.0330.0330.0000.0000.0000.000
68A68VAL0-0.043-0.0137.2020.2050.2050.0000.0000.0000.000
69A69TRP00.004-0.0016.7600.0020.0020.0000.0000.0000.000
70A70VAL00.0030.0042.652-0.855-0.4960.617-0.123-0.8530.000
71A71ALA00.0280.0134.969-0.295-0.253-0.001-0.003-0.0380.000
72A72GLU-1-0.865-0.9276.3120.1240.1240.0000.0000.0000.000
73A73ARG10.7660.8685.544-0.214-0.2140.0000.0000.0000.000
74A74VAL0-0.024-0.0152.148-0.399-0.6261.828-0.310-1.291-0.001
75A75LEU0-0.009-0.0095.457-0.080-0.0800.0000.0000.0000.000
76A76GLN00.0040.0128.675-0.048-0.0480.0000.0000.0000.000
77A77GLY0-0.014-0.00511.179-0.091-0.0910.0000.0000.0000.000
78A78ILE0-0.0120.0059.896-0.035-0.0350.0000.0000.0000.000
79A79ARG10.8550.92513.581-0.219-0.2190.0000.0000.0000.000
80A80LEU00.0490.02711.6920.0280.0280.0000.0000.0000.000
81A81LYS10.8270.92615.794-0.332-0.3320.0000.0000.0000.000
82A82SER00.008-0.00617.057-0.065-0.0650.0000.0000.0000.000
83A83ALA00.0340.04113.5540.0710.0710.0000.0000.0000.000
84A84THR00.005-0.00114.464-0.105-0.1050.0000.0000.0000.000
85A85ALA00.0150.02013.9210.1430.1430.0000.0000.0000.000
86A86VAL00.0010.00114.284-0.104-0.1040.0000.0000.0000.000
87A87ASN0-0.007-0.01315.1120.0460.0460.0000.0000.0000.000
88A88GLY00.0350.00813.8470.0280.0280.0000.0000.0000.000
89A89THR0-0.043-0.02614.417-0.005-0.0050.0000.0000.0000.000
90A90GLY00.0720.02612.8770.0570.0570.0000.0000.0000.000
91A91LEU0-0.047-0.02613.835-0.056-0.0560.0000.0000.0000.000
92A92PRO00.0250.01311.551-0.009-0.0090.0000.0000.0000.000
93A93CYS0-0.048-0.00714.694-0.014-0.0140.0000.0000.0000.000
94A94ASP-1-0.789-0.90716.9840.0720.0720.0000.0000.0000.000
95A95ASP-1-0.895-0.96120.0870.0890.0890.0000.0000.0000.000
96A96SER0-0.068-0.02022.9380.0010.0010.0000.0000.0000.000
97A97PHE0-0.020-0.00719.6660.0100.0100.0000.0000.0000.000
98A98GLY0-0.0150.00717.7620.0460.0460.0000.0000.0000.000
99A99ILE0-0.051-0.01615.648-0.013-0.0130.0000.0000.0000.000
100A100PRO00.0500.02019.122-0.023-0.0230.0000.0000.0000.000
101A101TYR00.0820.03420.0180.0040.0040.0000.0000.0000.000
102A102ALA0-0.042-0.02721.244-0.009-0.0090.0000.0000.0000.000
103A103ILE0-0.013-0.00220.561-0.008-0.0080.0000.0000.0000.000
104A104PHE00.0340.01712.6210.0020.0020.0000.0000.0000.000
105A105LYS10.9840.99018.4200.0100.0100.0000.0000.0000.000
106A106GLY0-0.019-0.00720.428-0.013-0.0130.0000.0000.0000.000
107A107THR0-0.038-0.03417.6060.0010.0010.0000.0000.0000.000
108A108LEU00.0230.00615.2230.0020.0020.0000.0000.0000.000
109A109GLU-1-0.974-0.98418.432-0.075-0.0750.0000.0000.0000.000
110A110ASN0-0.081-0.03321.519-0.009-0.0090.0000.0000.0000.000
111A111LEU0-0.0280.00815.4760.0150.0150.0000.0000.0000.000
112A112THR00.024-0.00219.930-0.016-0.0160.0000.0000.0000.000
113A113GLU-1-0.752-0.89719.0410.0920.0920.0000.0000.0000.000
114A114ASN0-0.001-0.00221.0330.0260.0260.0000.0000.0000.000
115A115THR0-0.068-0.04621.6220.0170.0170.0000.0000.0000.000
116A116ARG10.9080.95214.500-0.121-0.1210.0000.0000.0000.000
117A117LEU00.0410.03119.3850.0310.0310.0000.0000.0000.000
118A118LYS10.8510.92621.722-0.068-0.0680.0000.0000.0000.000
119A119PHE00.0410.01615.8920.0010.0010.0000.0000.0000.000
120A120GLU-1-0.817-0.92116.6030.2800.2800.0000.0000.0000.000
121A121ARG10.8370.91019.740-0.133-0.1330.0000.0000.0000.000
122A122ARG10.8670.93322.052-0.164-0.1640.0000.0000.0000.000
123A123ILE00.0080.01915.9650.0060.0060.0000.0000.0000.000
124A124CYS0-0.024-0.00520.2280.0210.0210.0000.0000.0000.000
125A125GLY00.0470.04522.634-0.007-0.0070.0000.0000.0000.000
126A126ASP-1-0.867-0.91725.8420.1670.1670.0000.0000.0000.000
127A127LYS10.8230.90627.091-0.111-0.1110.0000.0000.0000.000
128A128ALA00.0420.02027.9550.0020.0020.0000.0000.0000.000
129A129SER0-0.036-0.02724.5130.0080.0080.0000.0000.0000.000
130A130PHE0-0.029-0.02321.9950.0120.0120.0000.0000.0000.000
131A131GLU-1-0.797-0.92323.6320.1330.1330.0000.0000.0000.000
132A132ARG10.9280.97023.761-0.229-0.2290.0000.0000.0000.000
133A133TYR00.0170.00215.2700.0070.0070.0000.0000.0000.000
134A134GLN0-0.032-0.01719.851-0.007-0.0070.0000.0000.0000.000
135A135LEU0-0.039-0.01021.795-0.019-0.0190.0000.0000.0000.000
136A136PHE0-0.052-0.00816.7190.0050.0050.0000.0000.0000.000
137A137PRO00.0180.01015.506-0.022-0.0220.0000.0000.0000.000
138A138ALA00.0240.02015.3930.0420.0420.0000.0000.0000.000
139A139ARG10.8110.9277.340-0.375-0.3750.0000.0000.0000.000
140A140PRO00.0690.03411.2740.0120.0120.0000.0000.0000.000
141A141PHE00.0100.00712.8170.0040.0040.0000.0000.0000.000
142A142ASP-1-0.860-0.94213.834-0.117-0.1170.0000.0000.0000.000
143A143GLU-1-0.953-0.9798.654-0.334-0.3340.0000.0000.0000.000
144A144ILE0-0.0010.0079.242-0.033-0.0330.0000.0000.0000.000
145A145HIS00.0140.01911.0230.0000.0000.0000.0000.0000.000
146A146GLN00.0170.0229.539-0.066-0.0660.0000.0000.0000.000
147A147GLU-1-0.709-0.8466.2060.7830.7830.0000.0000.0000.000
148A148LEU0-0.053-0.0228.5470.0050.0050.0000.0000.0000.000
149A149THR0-0.012-0.01811.8270.0070.0070.0000.0000.0000.000
150A150ALA00.0250.0218.2970.0210.0210.0000.0000.0000.000
151A151LEU0-0.019-0.0096.3700.0220.0220.0000.0000.0000.000
152A152PHE00.0090.0009.4800.0350.0350.0000.0000.0000.000
153A153ALA0-0.024-0.00912.5100.0250.0250.0000.0000.0000.000
154A154MET00.0320.0095.712-0.039-0.0390.0000.0000.0000.000
155A155ILE00.000-0.00110.2850.0590.0590.0000.0000.0000.000
156A156GLN0-0.108-0.05512.5330.0550.0550.0000.0000.0000.000
157A157GLN0-0.044-0.02413.545-0.034-0.0340.0000.0000.0000.000
158A158ASP-1-0.786-0.82811.256-0.226-0.2260.0000.0000.0000.000
159A159LYS10.9530.96313.3670.0810.0810.0000.0000.0000.000
160A160ARG10.8390.90711.3940.2680.2680.0000.0000.0000.000
161A161ILE0-0.001-0.00214.3280.0290.0290.0000.0000.0000.000
162A162ASP-1-0.826-0.88815.5260.1690.1690.0000.0000.0000.000
163A163LEU0-0.027-0.00510.850-0.040-0.0400.0000.0000.0000.000
164A164ILE0-0.017-0.00610.320-0.004-0.0040.0000.0000.0000.000
165A165HIS0-0.016-0.00113.964-0.021-0.0210.0000.0000.0000.000
166A166TRP0-0.035-0.04310.5620.0960.0960.0000.0000.0000.000
167A167ALA0-0.053-0.03016.959-0.049-0.0490.0000.0000.0000.000
168A168ASN0-0.035-0.03018.562-0.051-0.0510.0000.0000.0000.000
169A169ALA00.0440.01918.0170.0720.0720.0000.0000.0000.000
170A170TRP0-0.023-0.01418.762-0.068-0.0680.0000.0000.0000.000
171A171VAL00.0140.00919.5730.0320.0320.0000.0000.0000.000
172A172SER0-0.038-0.03021.758-0.020-0.0200.0000.0000.0000.000
173A173SER00.0140.00823.640-0.006-0.0060.0000.0000.0000.000
174A174ARG10.8810.93026.325-0.216-0.2160.0000.0000.0000.000
175A175ASP-1-0.716-0.85119.9310.3680.3680.0000.0000.0000.000
176A176LYS10.7960.88122.989-0.220-0.2200.0000.0000.0000.000
177A177ILE0-0.066-0.02617.095-0.030-0.0300.0000.0000.0000.000
178A178PHE00.0500.02813.946-0.016-0.0160.0000.0000.0000.000
179A179THR00.0150.01519.6340.0110.0110.0000.0000.0000.000
180A180PRO00.0470.01522.7250.0070.0070.0000.0000.0000.000
181A181ALA0-0.0070.00524.5070.0030.0030.0000.0000.0000.000
182A182ASN00.0010.00021.595-0.014-0.0140.0000.0000.0000.000
183A183GLN0-0.056-0.03719.2050.0310.0310.0000.0000.0000.000
184A184HIS0-0.009-0.01421.2360.0040.0040.0000.0000.0000.000
185A185GLN0-0.0290.00023.996-0.003-0.0030.0000.0000.0000.000
186A186TYR00.0190.01215.964-0.020-0.0200.0000.0000.0000.000
187A187TRP00.030-0.01215.041-0.017-0.0170.0000.0000.0000.000
188A188ALA0-0.0050.02021.495-0.003-0.0030.0000.0000.0000.000
189A189LEU0-0.039-0.02724.729-0.006-0.0060.0000.0000.0000.000
190A190ARG10.7520.86618.710-0.214-0.2140.0000.0000.0000.000
191A191CYS0-0.054-0.01518.8640.0040.0040.0000.0000.0000.000
192A192ALA00.0000.01122.281-0.017-0.0170.0000.0000.0000.000
193A193VAL00.0250.00422.3950.0320.0320.0000.0000.0000.000
194A194GLN0-0.011-0.00422.560-0.020-0.0200.0000.0000.0000.000
195A195GLU-1-0.906-0.95123.9720.2230.2230.0000.0000.0000.000
196A196ILE0-0.017-0.00923.297-0.011-0.0110.0000.0000.0000.000
197A197GLU-1-0.920-0.97026.2170.1870.1870.0000.0000.0000.000
198A198GLY0-0.030-0.03525.6530.0060.0060.0000.0000.0000.000
199A199GLU-1-0.803-0.89123.5290.2050.2050.0000.0000.0000.000
200A200HIS0-0.0070.01716.1710.0670.0670.0000.0000.0000.000
201A201TYR0-0.017-0.01416.9960.0360.0360.0000.0000.0000.000
202A202VAL00.0250.01019.177-0.051-0.0510.0000.0000.0000.000
203A203PHE00.0880.02414.395-0.032-0.0320.0000.0000.0000.000
204A204SER0-0.034-0.01619.765-0.029-0.0290.0000.0000.0000.000
205A205ARG10.8490.94022.913-0.279-0.2790.0000.0000.0000.000
206A206PHE0-0.0090.00920.988-0.008-0.0080.0000.0000.0000.000
207A207THR00.029-0.01622.8640.0010.0010.0000.0000.0000.000
208A208HIS00.0490.05322.3190.0060.0060.0000.0000.0000.000
209A209TRP00.0950.02813.0810.0440.0440.0000.0000.0000.000
210A210SER00.007-0.00619.2910.0240.0240.0000.0000.0000.000
211A211ALA0-0.0020.00721.507-0.011-0.0110.0000.0000.0000.000
212A212LEU0-0.020-0.00916.6410.0020.0020.0000.0000.0000.000
213A213TRP0-0.0090.00116.8980.0210.0210.0000.0000.0000.000
214A214ASP-1-0.996-0.97620.6910.2350.2350.0000.0000.0000.000