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: G5VN1

Calculation Name: 2G5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G5X

Chain ID: A

ChEMBL ID:

UniProt ID: P85101

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2986727.113228
FMO2-HF: Nuclear repulsion 2895547.223954
FMO2-HF: Total energy -91179.889274
FMO2-MP2: Total energy -91447.805117


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:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
-12.854.33511.474-11.052-17.608-0.122
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.924
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].
3A3SER0-0.026-0.0282.657-10.008-7.5730.572-1.177-1.830-0.012
4A4TRP00.0740.0335.0513.7633.839-0.001-0.007-0.0680.000
5A5THR0-0.057-0.0228.614-0.679-0.6790.0000.0000.0000.000
6A6VAL0-0.018-0.01711.4271.2571.2570.0000.0000.0000.000
7A7ASP-1-0.840-0.92713.639-15.342-15.3420.0000.0000.0000.000
8A8SER0-0.059-0.03016.669-0.071-0.0710.0000.0000.0000.000
9A9ASP-1-0.845-0.91816.525-15.259-15.2590.0000.0000.0000.000
10A10SER00.045-0.01216.428-0.942-0.9420.0000.0000.0000.000
11A11ALA00.0610.05116.967-0.386-0.3860.0000.0000.0000.000
12A12LYS10.9200.95311.98118.16218.1620.0000.0000.0000.000
13A13TYR0-0.050-0.02712.106-1.224-1.2240.0000.0000.0000.000
14A14SER00.046-0.00212.623-0.850-0.8500.0000.0000.0000.000
15A15SER0-0.027-0.01411.387-0.048-0.0480.0000.0000.0000.000
16A16PHE0-0.059-0.0185.712-1.383-1.3830.0000.0000.0000.000
17A17LEU00.001-0.0058.860-1.637-1.6370.0000.0000.0000.000
18A18ASP-1-0.862-0.92511.066-16.973-16.9730.0000.0000.0000.000
19A19SER0-0.051-0.0225.869-1.496-1.4960.0000.0000.0000.000
20A20LEU0-0.016-0.0206.587-0.983-0.9830.0000.0000.0000.000
21A21ARG10.7290.8357.84517.28917.2890.0000.0000.0000.000
22A22GLU-1-0.817-0.8889.022-16.462-16.4620.0000.0000.0000.000
23A23GLU-1-0.927-0.9534.417-27.842-27.737-0.001-0.009-0.0950.000
24A24PHE0-0.066-0.0337.8360.1550.1550.0000.0000.0000.000
25A25GLY0-0.005-0.00110.8371.0861.0860.0000.0000.0000.000
26A26ARG10.8960.9596.33128.67828.6780.0000.0000.0000.000
27A27GLY00.000-0.00712.194-0.103-0.1030.0000.0000.0000.000
28A28THR0-0.024-0.00615.2150.5300.5300.0000.0000.0000.000
29A29PRO00.0080.00017.297-0.447-0.4470.0000.0000.0000.000
30A30LYS10.8430.91314.79715.15415.1540.0000.0000.0000.000
31A31VAL00.0470.02219.5900.5210.5210.0000.0000.0000.000
32A32CYS0-0.025-0.00822.176-0.346-0.3460.0000.0000.0000.000
33A33ASN0-0.030-0.01820.135-0.277-0.2770.0000.0000.0000.000
34A34ILE00.0190.03018.373-0.409-0.4090.0000.0000.0000.000
35A35PRO00.0020.00713.9330.3560.3560.0000.0000.0000.000
36A36VAL00.0630.03116.1830.1750.1750.0000.0000.0000.000
37A37THR00.0310.03114.652-0.226-0.2260.0000.0000.0000.000
38A38LYS10.8210.88714.72316.80116.8010.0000.0000.0000.000
39A39LYS10.9820.98617.49211.09311.0930.0000.0000.0000.000
40A40ALA0-0.009-0.00719.689-0.062-0.0620.0000.0000.0000.000
41A41ASN00.0120.02213.696-0.010-0.0100.0000.0000.0000.000
42A42ASN00.0340.00914.710-1.090-1.0900.0000.0000.0000.000
43A43ASP-1-0.876-0.94015.966-18.067-18.0670.0000.0000.0000.000
44A44LYS10.8680.93311.63918.11118.1110.0000.0000.0000.000
45A45PHE00.005-0.0098.9481.1781.1780.0000.0000.0000.000
46A46VAL00.0170.0265.327-2.013-2.0130.0000.0000.0000.000
47A47LEU0-0.051-0.0242.548-2.726-0.6081.809-0.838-3.0900.002
48A48VAL00.0280.0122.718-5.775-3.6081.078-1.170-2.075-0.014
49A49ASN00.0070.0182.136-19.771-16.5224.216-2.822-4.643-0.036
50A50LEU00.0330.0294.4734.5054.5910.000-0.032-0.0540.000
51A51VAL0-0.032-0.0267.475-0.762-0.7620.0000.0000.0000.000
52A52LEU00.0170.0169.9231.9061.9060.0000.0000.0000.000
53A53PRO00.0160.00113.577-0.533-0.5330.0000.0000.0000.000
54A54PHE0-0.015-0.00715.7050.2320.2320.0000.0000.0000.000
55A55ASN00.0600.02115.127-0.571-0.5710.0000.0000.0000.000
56A56ARG10.9510.98611.28922.47522.4750.0000.0000.0000.000
57A57ASN00.0140.02111.053-2.275-2.2750.0000.0000.0000.000
58A58THR0-0.036-0.0325.296-0.883-0.8830.0000.0000.0000.000
59A59ILE0-0.0310.0017.5960.3550.3550.0000.0000.0000.000
60A60THR0-0.061-0.0372.659-3.463-2.0691.204-0.832-1.767-0.002
61A61LEU00.009-0.0034.8994.4244.494-0.001-0.005-0.0650.000
62A62ALA00.0410.0215.417-5.292-5.2920.0000.0000.0000.000
63A63PHE00.006-0.0047.7483.6663.6660.0000.0000.0000.000
64A64ARG10.8270.9099.75516.65016.6500.0000.0000.0000.000
65A65ALA00.011-0.02210.5580.4910.4910.0000.0000.0000.000
66A66SER0-0.0010.00412.0460.5280.5280.0000.0000.0000.000
67A67ASP-1-0.887-0.96715.281-16.317-16.3170.0000.0000.0000.000
68A68ALA00.0190.02412.3960.4120.4120.0000.0000.0000.000
69A69TYR0-0.035-0.01213.4430.1230.1230.0000.0000.0000.000
70A70LEU0-0.030-0.00310.522-1.234-1.2340.0000.0000.0000.000
71A71VAL00.0200.00111.5261.3671.3670.0000.0000.0000.000
72A72GLY00.009-0.00511.6891.2641.2640.0000.0000.0000.000
73A73PHE0-0.038-0.0278.754-1.797-1.7970.0000.0000.0000.000
74A74GLN00.0520.0313.5024.1354.3030.000-0.033-0.1350.000
75A75ASP-1-0.739-0.8597.521-25.240-25.2400.0000.0000.0000.000
76A76ARG10.9230.9668.52227.11327.1130.0000.0000.0000.000
77A77ASP-1-0.904-0.95311.562-15.844-15.8440.0000.0000.0000.000
78A78SER00.0150.01214.9640.0120.0120.0000.0000.0000.000
79A79LYS10.9640.99117.80613.15413.1540.0000.0000.0000.000
80A80THR0-0.028-0.02716.5120.0210.0210.0000.0000.0000.000
81A81ASN00.0180.00614.293-0.532-0.5320.0000.0000.0000.000
82A82LYS10.9660.99712.41216.91016.9100.0000.0000.0000.000
83A83LEU0-0.043-0.0205.7280.2750.2750.0000.0000.0000.000
84A84ARG10.8320.8959.38821.09221.0920.0000.0000.0000.000
85A85ALA0-0.003-0.0049.709-1.773-1.7730.0000.0000.0000.000
86A86ASN0-0.008-0.01210.5973.6933.6930.0000.0000.0000.000
87A87PHE00.0220.00611.868-1.165-1.1650.0000.0000.0000.000
88A88PHE00.0300.01114.6640.9280.9280.0000.0000.0000.000
89A89SER0-0.009-0.02617.6690.2270.2270.0000.0000.0000.000
90A90ASP-1-0.821-0.90020.229-14.780-14.7800.0000.0000.0000.000
91A91GLU-1-0.759-0.87416.545-17.324-17.3240.0000.0000.0000.000
92A92TYR0-0.024-0.01117.460-0.105-0.1050.0000.0000.0000.000
93A93ARG10.9480.96118.91712.24112.2410.0000.0000.0000.000
94A94ALA00.0300.02219.6920.1540.1540.0000.0000.0000.000
95A95LEU0-0.018-0.01313.993-0.434-0.4340.0000.0000.0000.000
96A96SER0-0.029-0.00215.133-0.899-0.8990.0000.0000.0000.000
97A97GLY00.0380.01215.736-0.665-0.6650.0000.0000.0000.000
98A98LYS10.9090.97613.37720.60220.6020.0000.0000.0000.000
99A99TYR00.0710.01910.643-2.246-2.2460.0000.0000.0000.000
100A100LYS10.8990.9607.88928.23428.2340.0000.0000.0000.000
101A101SER0-0.075-0.0398.611-1.825-1.8250.0000.0000.0000.000
102A102ILE0-0.0330.0008.609-0.908-0.9080.0000.0000.0000.000
103A103PHE0-0.008-0.0135.339-4.769-4.7690.0000.0000.0000.000
104A104THR00.0170.0013.111-0.946-0.4390.060-0.130-0.4370.000
105A105ASP-1-0.872-0.9442.115-85.974-81.1972.539-3.996-3.319-0.060
106A106ALA0-0.033-0.0014.9294.5314.564-0.001-0.001-0.0300.000
107A107GLU-1-0.896-0.9497.882-23.342-23.3420.0000.0000.0000.000
108A108VAL0-0.036-0.01111.1092.2332.2330.0000.0000.0000.000
109A109LEU0-0.0140.00912.318-1.744-1.7440.0000.0000.0000.000
110A110ALA0-0.0090.00314.1911.1961.1960.0000.0000.0000.000
111A111PRO0-0.020-0.02715.9340.0700.0700.0000.0000.0000.000
112A112ALA0-0.0010.00717.593-0.748-0.7480.0000.0000.0000.000
113A113LEU00.0050.01014.5750.5640.5640.0000.0000.0000.000
114A114PRO0-0.039-0.01818.8050.5710.5710.0000.0000.0000.000
115A115CYS0-0.044-0.03019.9220.4490.4490.0000.0000.0000.000
116A116ALA0-0.048-0.00320.479-0.709-0.7090.0000.0000.0000.000
117A117SER00.018-0.01117.423-0.133-0.1330.0000.0000.0000.000
118A118THR00.0360.03918.978-0.150-0.1500.0000.0000.0000.000
119A119TYR00.041-0.02419.965-0.042-0.0420.0000.0000.0000.000
120A120THR0-0.017-0.00522.9110.0460.0460.0000.0000.0000.000
121A121ASP-1-0.768-0.87423.581-12.169-12.1690.0000.0000.0000.000
122A122LEU00.0160.01618.3750.1100.1100.0000.0000.0000.000
123A123GLN00.028-0.00922.5260.2420.2420.0000.0000.0000.000
124A124ASN0-0.0220.00025.3850.4850.4850.0000.0000.0000.000
125A125LYS10.8190.90423.95812.01212.0120.0000.0000.0000.000
126A126ALA0-0.046-0.02222.9790.0720.0720.0000.0000.0000.000
127A127GLY0-0.023-0.00224.9420.1870.1870.0000.0000.0000.000
128A128VAL0-0.090-0.04625.2720.3970.3970.0000.0000.0000.000
129A129SER00.0370.01826.342-0.340-0.3400.0000.0000.0000.000
130A130ARG10.8750.91823.06812.24312.2430.0000.0000.0000.000
131A131GLU-1-0.917-0.95225.113-10.726-10.7260.0000.0000.0000.000
132A132LYS10.9890.98827.84410.09710.0970.0000.0000.0000.000
133A133LEU0-0.0400.00020.7340.0280.0280.0000.0000.0000.000
134A134SER0-0.027-0.01724.637-0.002-0.0020.0000.0000.0000.000
135A135LEU0-0.032-0.01519.922-0.763-0.7630.0000.0000.0000.000
136A136GLY00.0690.01919.5250.6400.6400.0000.0000.0000.000
137A137VAL00.0190.01016.936-0.645-0.6450.0000.0000.0000.000
138A138SER00.0520.01818.519-0.688-0.6880.0000.0000.0000.000
139A139SER0-0.015-0.00620.7560.0250.0250.0000.0000.0000.000
140A140LEU00.0090.00813.010-0.111-0.1110.0000.0000.0000.000
141A141GLN0-0.001-0.01116.497-0.115-0.1150.0000.0000.0000.000
142A142THR0-0.009-0.00117.548-0.044-0.0440.0000.0000.0000.000
143A143ALA0-0.041-0.02517.6400.1120.1120.0000.0000.0000.000
144A144PHE00.0130.00710.1860.1240.1240.0000.0000.0000.000
145A145THR0-0.011-0.00715.371-0.417-0.4170.0000.0000.0000.000
146A146ALA0-0.076-0.03117.6850.3910.3910.0000.0000.0000.000
147A147VAL0-0.022-0.00714.1340.4990.4990.0000.0000.0000.000
148A148TYR00.015-0.01110.195-0.613-0.6130.0000.0000.0000.000
149A149GLY00.0170.01913.9881.0261.0260.0000.0000.0000.000
150A150LYS10.8580.94015.52616.11116.1110.0000.0000.0000.000
151A151VAL00.0150.01018.269-0.499-0.4990.0000.0000.0000.000
152A152PHE0-0.031-0.01514.1800.3780.3780.0000.0000.0000.000
153A153THR00.0300.00920.1820.5330.5330.0000.0000.0000.000
154A154GLY00.0590.01021.599-0.501-0.5010.0000.0000.0000.000
155A155LYS11.0051.00722.35110.98910.9890.0000.0000.0000.000
156A156ASN0-0.009-0.01120.0950.0590.0590.0000.0000.0000.000
157A157VAL00.0280.01616.535-0.603-0.6030.0000.0000.0000.000
158A158ALA00.0490.02517.727-0.750-0.7500.0000.0000.0000.000
159A159LYS10.9230.96119.53912.75712.7570.0000.0000.0000.000
160A160PHE00.0200.01711.050-0.009-0.0090.0000.0000.0000.000
161A161ALA00.0140.00714.712-0.867-0.8670.0000.0000.0000.000
162A162LEU00.0140.00315.753-0.347-0.3470.0000.0000.0000.000
163A163ILE00.0130.00716.7670.0950.0950.0000.0000.0000.000
164A164SER0-0.013-0.01112.067-0.663-0.6630.0000.0000.0000.000
165A165ILE0-0.021-0.00813.545-0.745-0.7450.0000.0000.0000.000
166A166GLN0-0.064-0.03415.3260.5240.5240.0000.0000.0000.000
167A167MET00.0090.01314.7840.1810.1810.0000.0000.0000.000
168A168VAL00.0000.0229.042-0.588-0.5880.0000.0000.0000.000
169A169ALA00.0060.00212.2370.0400.0400.0000.0000.0000.000
170A170GLU-1-0.771-0.87813.637-14.246-14.2460.0000.0000.0000.000
171A171ALA00.0200.01714.8390.6600.6600.0000.0000.0000.000
172A172ALA00.0070.01712.3090.3910.3910.0000.0000.0000.000
173A173ARG10.8410.92614.38616.79916.7990.0000.0000.0000.000
174A174PHE00.0240.01917.4310.7050.7050.0000.0000.0000.000
175A175LYS10.9340.95518.14113.97513.9750.0000.0000.0000.000
176A176TYR00.0420.03120.6110.0490.0490.0000.0000.0000.000
177A177ILE0-0.012-0.01119.2480.2410.2410.0000.0000.0000.000
178A178GLU-1-0.722-0.83817.023-15.723-15.7230.0000.0000.0000.000
179A179ASP-1-0.863-0.94018.786-12.304-12.3040.0000.0000.0000.000
180A180GLN0-0.046-0.00422.0790.3960.3960.0000.0000.0000.000
181A181VAL0-0.017-0.00317.2500.2200.2200.0000.0000.0000.000
182A182ILE0-0.037-0.01518.670-0.008-0.0080.0000.0000.0000.000
183A183ASN0-0.064-0.04920.8410.5340.5340.0000.0000.0000.000
184A184ARG10.8900.94223.76911.16911.1690.0000.0000.0000.000
185A185GLY0-0.0230.00121.2840.1360.1360.0000.0000.0000.000
186A186MET0-0.033-0.00216.863-0.842-0.8420.0000.0000.0000.000
187A187TYR00.0460.00521.084-0.247-0.2470.0000.0000.0000.000
188A188SER0-0.0070.00824.0110.3790.3790.0000.0000.0000.000
189A189SER0-0.046-0.02223.530-0.538-0.5380.0000.0000.0000.000
190A190PHE0-0.013-0.01121.4800.4660.4660.0000.0000.0000.000
191A191GLU-1-0.928-0.95624.810-10.616-10.6160.0000.0000.0000.000
192A192ALA00.0090.00923.7960.2270.2270.0000.0000.0000.000
193A193GLY00.0590.02625.7420.3040.3040.0000.0000.0000.000
194A194ALA00.0420.00428.301-0.264-0.2640.0000.0000.0000.000
195A195ARG10.8050.87930.1779.0499.0490.0000.0000.0000.000
196A196ILE00.0420.01924.007-0.031-0.0310.0000.0000.0000.000
197A197THR00.0180.01225.508-0.437-0.4370.0000.0000.0000.000
198A198LEU0-0.025-0.01226.462-0.195-0.1950.0000.0000.0000.000
199A199LEU0-0.006-0.00224.9020.0340.0340.0000.0000.0000.000
200A200GLU-1-0.790-0.89021.553-13.462-13.4620.0000.0000.0000.000
201A201ASN0-0.020-0.01623.551-0.626-0.6260.0000.0000.0000.000
202A202ASN0-0.084-0.04625.9040.3090.3090.0000.0000.0000.000
203A203TRP00.0340.02017.0960.0250.0250.0000.0000.0000.000
204A204SER00.012-0.00523.7020.0590.0590.0000.0000.0000.000
205A205LYS10.9850.98724.9049.6549.6540.0000.0000.0000.000
206A206ILE00.0320.02725.6750.2740.2740.0000.0000.0000.000
207A207SER00.0320.01322.8220.0000.0000.0000.0000.0000.000
208A208GLU-1-0.982-0.99324.699-9.841-9.8410.0000.0000.0000.000
209A209GLN0-0.014-0.01627.6680.4000.4000.0000.0000.0000.000
210A210TYR00.0480.02224.8240.2020.2020.0000.0000.0000.000
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