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

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FMODB ID: 5JV5Z

Calculation Name: 2G7S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G7S

Chain ID: A

ChEMBL ID:

UniProt ID: A9CKG4

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 OptHSide
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 190
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1942034.713613
FMO2-HF: Nuclear repulsion 1868817.827315
FMO2-HF: Total energy -73216.886299
FMO2-MP2: Total energy -73429.214047


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-21.983-15.6097.84-5.833-8.3810.019
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.031
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].
3A5GLN00.010-0.0032.629-4.884-1.3811.731-2.000-3.2340.016
4A6SER00.0120.0062.030-14.944-12.5936.092-3.653-4.7900.002
5A7LYS10.8870.9413.761-2.057-1.5370.017-0.180-0.3570.001
6A8ALA00.0210.0155.989-0.601-0.6010.0000.0000.0000.000
7A9ASP-1-0.832-0.9136.6641.9911.9910.0000.0000.0000.000
8A10ASP-1-0.861-0.9237.506-0.619-0.6190.0000.0000.0000.000
9A11ILE0-0.073-0.0419.723-0.221-0.2210.0000.0000.0000.000
10A12LEU0-0.004-0.00111.094-0.158-0.1580.0000.0000.0000.000
11A13GLN00.0330.02812.358-0.125-0.1250.0000.0000.0000.000
12A14CYS0-0.068-0.01813.867-0.091-0.0910.0000.0000.0000.000
13A15ALA00.0370.00815.746-0.048-0.0480.0000.0000.0000.000
14A16ARG10.7750.84616.179-0.376-0.3760.0000.0000.0000.000
15A17THR00.0390.01718.100-0.042-0.0420.0000.0000.0000.000
16A18LEU0-0.059-0.03319.107-0.026-0.0260.0000.0000.0000.000
17A19ILE00.0030.01221.552-0.018-0.0180.0000.0000.0000.000
18A20ILE00.0320.02222.324-0.015-0.0150.0000.0000.0000.000
19A21ARG10.8960.95423.760-0.117-0.1170.0000.0000.0000.000
20A22GLY00.011-0.00226.684-0.012-0.0120.0000.0000.0000.000
21A23GLY00.0420.04226.962-0.003-0.0030.0000.0000.0000.000
22A24TYR0-0.004-0.02823.6010.0050.0050.0000.0000.0000.000
23A25ASN0-0.067-0.04025.4690.0160.0160.0000.0000.0000.000
24A26SER0-0.043-0.00126.535-0.010-0.0100.0000.0000.0000.000
25A27PHE0-0.0120.00119.764-0.002-0.0020.0000.0000.0000.000
26A28SER0-0.004-0.03722.3200.0140.0140.0000.0000.0000.000
27A29TYR00.024-0.01917.602-0.004-0.0040.0000.0000.0000.000
28A30ALA00.0220.01417.780-0.005-0.0050.0000.0000.0000.000
29A31ASP-1-0.789-0.85619.1120.0970.0970.0000.0000.0000.000
30A32ILE00.014-0.01313.948-0.014-0.0140.0000.0000.0000.000
31A33SER0-0.079-0.06214.344-0.009-0.0090.0000.0000.0000.000
32A34GLN0-0.052-0.01515.051-0.031-0.0310.0000.0000.0000.000
33A35VAL0-0.021-0.00414.914-0.024-0.0240.0000.0000.0000.000
34A36VAL0-0.013-0.0159.729-0.037-0.0370.0000.0000.0000.000
35A37GLY00.0060.01310.501-0.100-0.1000.0000.0000.0000.000
36A38ILE0-0.045-0.0048.269-0.046-0.0460.0000.0000.0000.000
37A39ARG11.0141.01111.057-0.027-0.0270.0000.0000.0000.000
38A40ASN00.0940.01813.6100.0530.0530.0000.0000.0000.000
39A41ALA00.004-0.00915.3700.0360.0360.0000.0000.0000.000
40A42SER00.0040.00010.0140.0060.0060.0000.0000.0000.000
41A43ILE0-0.0040.00611.6050.1200.1200.0000.0000.0000.000
42A44HIS00.003-0.00313.3480.1100.1100.0000.0000.0000.000
43A45HIS0-0.078-0.03110.9800.0160.0160.0000.0000.0000.000
44A46HIS0-0.036-0.0066.4570.3200.3200.0000.0000.0000.000
45A47PHE00.0140.00711.2870.0580.0580.0000.0000.0000.000
46A48PRO00.0170.02215.000-0.074-0.0740.0000.0000.0000.000
47A49SER00.0210.00118.215-0.050-0.0500.0000.0000.0000.000
48A50LYS10.8900.94819.126-0.169-0.1690.0000.0000.0000.000
49A51SER00.0270.01020.6580.0090.0090.0000.0000.0000.000
50A52ASP-1-0.800-0.87816.7130.6170.6170.0000.0000.0000.000
51A53LEU00.0020.00915.1700.0260.0260.0000.0000.0000.000
52A54VAL00.0280.00217.2440.0190.0190.0000.0000.0000.000
53A55CYS0-0.071-0.01419.981-0.025-0.0250.0000.0000.0000.000
54A56LYS10.8610.91414.511-0.707-0.7070.0000.0000.0000.000
55A57LEU0-0.0020.01916.5090.0160.0160.0000.0000.0000.000
56A58VAL0-0.008-0.02017.407-0.031-0.0310.0000.0000.0000.000
57A59SER0-0.011-0.02518.338-0.020-0.0200.0000.0000.0000.000
58A60GLN0-0.0020.01812.345-0.100-0.1000.0000.0000.0000.000
59A61TYR00.007-0.09617.375-0.046-0.0460.0000.0000.0000.000
60A62ARG10.8150.89320.126-0.267-0.2670.0000.0000.0000.000
61A63GLN0-0.0150.00417.1570.0080.0080.0000.0000.0000.000
62A64GLU-1-0.780-0.85616.6060.2900.2900.0000.0000.0000.000
63A65ALA0-0.026-0.00520.629-0.035-0.0350.0000.0000.0000.000
64A66GLU-1-0.823-0.92224.0570.1640.1640.0000.0000.0000.000
65A67ALA00.0080.01321.789-0.019-0.0190.0000.0000.0000.000
66A68GLY00.0120.00623.738-0.022-0.0220.0000.0000.0000.000
67A69ILE00.005-0.01525.300-0.016-0.0160.0000.0000.0000.000
68A70ALA00.0070.01326.517-0.011-0.0110.0000.0000.0000.000
69A71GLU-1-0.795-0.85625.6420.0100.0100.0000.0000.0000.000
70A72LEU0-0.040-0.02827.768-0.012-0.0120.0000.0000.0000.000
71A73GLU-1-0.837-0.89630.9130.0570.0570.0000.0000.0000.000
72A74LYS10.7550.86826.587-0.023-0.0230.0000.0000.0000.000
73A75ASN0-0.065-0.04728.316-0.009-0.0090.0000.0000.0000.000
74A76ILE0-0.046-0.01232.553-0.006-0.0060.0000.0000.0000.000
75A77SER00.0170.01535.7040.0040.0040.0000.0000.0000.000
76A78ASP-1-0.814-0.89838.8530.0240.0240.0000.0000.0000.000
77A79PRO00.0190.00239.2310.0010.0010.0000.0000.0000.000
78A80LEU00.0290.01739.5760.0040.0040.0000.0000.0000.000
79A81GLU-1-0.805-0.88838.8840.0180.0180.0000.0000.0000.000
80A82GLN0-0.0010.00835.2970.0050.0050.0000.0000.0000.000
81A83LEU0-0.009-0.00135.3340.0040.0040.0000.0000.0000.000
82A84ARG10.7820.84636.877-0.017-0.0170.0000.0000.0000.000
83A85ALA0-0.015-0.00633.228-0.001-0.0010.0000.0000.0000.000
84A86TYR00.0220.01030.5320.0010.0010.0000.0000.0000.000
85A87ILE0-0.025-0.02332.7080.0040.0040.0000.0000.0000.000
86A88GLY00.0170.01334.0790.0000.0000.0000.0000.0000.000
87A89TYR0-0.011-0.00125.162-0.002-0.0020.0000.0000.0000.000
88A90TRP00.0380.00126.8310.0030.0030.0000.0000.0000.000
89A91GLU-1-0.778-0.85031.2160.0240.0240.0000.0000.0000.000
90A92GLY00.0170.01229.948-0.004-0.0040.0000.0000.0000.000
91A93CYS0-0.022-0.00326.9530.0000.0000.0000.0000.0000.000
92A94ILE0-0.085-0.06628.1850.0010.0010.0000.0000.0000.000
93A95ALA0-0.060-0.01430.987-0.002-0.0020.0000.0000.0000.000
94A96ASP-1-0.899-0.95025.8470.0000.0000.0000.0000.0000.000
95A97ALA0-0.081-0.04027.036-0.003-0.0030.0000.0000.0000.000
96A98THR0-0.0080.01421.1630.0010.0010.0000.0000.0000.000
97A99HIS0-0.078-0.07718.8700.0150.0150.0000.0000.0000.000
98A100PRO00.0230.03124.6490.0030.0030.0000.0000.0000.000
99A101PHE0-0.006-0.02027.207-0.005-0.0050.0000.0000.0000.000
100A102CYM-1-0.857-0.77326.5420.1550.1550.0000.0000.0000.000
101A103VAL00.0400.00821.882-0.002-0.0020.0000.0000.0000.000
102A104CYS0-0.012-0.00425.0560.0070.0070.0000.0000.0000.000
103A105ALA00.024-0.03727.339-0.007-0.0070.0000.0000.0000.000
104A106LEU0-0.029-0.00427.553-0.007-0.0070.0000.0000.0000.000
105A107LEU00.0100.00824.246-0.002-0.0020.0000.0000.0000.000
106A108ALA00.000-0.00628.891-0.003-0.0030.0000.0000.0000.000
107A109SER0-0.095-0.04231.952-0.008-0.0080.0000.0000.0000.000
108A110GLU-1-0.755-0.88029.0760.1430.1430.0000.0000.0000.000
109A111ILE0-0.035-0.02331.7640.0050.0050.0000.0000.0000.000
110A112PRO0-0.035-0.01833.0850.0050.0050.0000.0000.0000.000
111A113VAL00.0020.00731.799-0.001-0.0010.0000.0000.0000.000
112A114LEU0-0.061-0.01327.4120.0110.0110.0000.0000.0000.000
113A115PRO00.011-0.00225.663-0.002-0.0020.0000.0000.0000.000
114A116GLU-1-0.861-0.93428.4780.1650.1650.0000.0000.0000.000
115A117THR0-0.011-0.03424.180-0.005-0.0050.0000.0000.0000.000
116A118VAL00.013-0.00623.5300.0120.0120.0000.0000.0000.000
117A119VAL00.0060.00625.772-0.005-0.0050.0000.0000.0000.000
118A120LEU0-0.038-0.01327.473-0.009-0.0090.0000.0000.0000.000
119A121GLU-1-0.801-0.88222.3010.2990.2990.0000.0000.0000.000
120A122VAL00.0070.00725.903-0.010-0.0100.0000.0000.0000.000
121A123ARG10.9450.95827.944-0.147-0.1470.0000.0000.0000.000
122A124ALA0-0.035-0.01927.322-0.013-0.0130.0000.0000.0000.000
123A125HIS00.0520.02426.6980.0010.0010.0000.0000.0000.000
124A126PHE0-0.025-0.01228.469-0.014-0.0140.0000.0000.0000.000
125A127ARG10.9390.96830.592-0.157-0.1570.0000.0000.0000.000
126A128SER00.0050.01128.604-0.013-0.0130.0000.0000.0000.000
127A129LEU00.0350.02030.612-0.008-0.0080.0000.0000.0000.000
128A130SER0-0.021-0.04232.051-0.011-0.0110.0000.0000.0000.000
129A131ASP-1-0.836-0.90133.7380.0960.0960.0000.0000.0000.000
130A132TRP0-0.034-0.01832.167-0.006-0.0060.0000.0000.0000.000
131A133LEU00.012-0.00434.318-0.008-0.0080.0000.0000.0000.000
132A134THR0-0.032-0.03336.881-0.008-0.0080.0000.0000.0000.000
133A135ALA00.0500.03636.780-0.005-0.0050.0000.0000.0000.000
134A136VAL0-0.024-0.00236.003-0.006-0.0060.0000.0000.0000.000
135A137LEU0-0.031-0.02938.917-0.006-0.0060.0000.0000.0000.000
136A138GLU-1-0.934-0.97141.8160.0540.0540.0000.0000.0000.000
137A139ARG10.7970.87435.490-0.057-0.0570.0000.0000.0000.000
138A140GLY00.0270.00342.828-0.004-0.0040.0000.0000.0000.000
139A141ILE0-0.035-0.01744.465-0.003-0.0030.0000.0000.0000.000
140A142ALA0-0.044-0.01845.527-0.002-0.0020.0000.0000.0000.000
141A143GLN0-0.039-0.02241.775-0.004-0.0040.0000.0000.0000.000
142A144GLY0-0.026-0.01047.335-0.003-0.0030.0000.0000.0000.000
143A145ARG10.8460.91544.963-0.018-0.0180.0000.0000.0000.000
144A146LEU0-0.015-0.00143.1790.0000.0000.0000.0000.0000.000
145A147VAL0-0.025-0.01147.8870.0000.0000.0000.0000.0000.000
146A148LEU00.003-0.00145.6820.0010.0010.0000.0000.0000.000
147A149THR0-0.0110.00049.940-0.002-0.0020.0000.0000.0000.000
148A150GLY00.0140.00750.0390.0020.0020.0000.0000.0000.000
149A151THR00.0200.00446.9570.0000.0000.0000.0000.0000.000
150A152ALA00.0910.05443.3700.0000.0000.0000.0000.0000.000
151A153ARG10.8660.91437.156-0.083-0.0830.0000.0000.0000.000
152A154ALA0-0.014-0.00942.3850.0020.0020.0000.0000.0000.000
153A155ASN0-0.029-0.04144.176-0.001-0.0010.0000.0000.0000.000
154A156ALA00.0460.02938.8280.0000.0000.0000.0000.0000.000
155A157GLU-1-0.861-0.89938.9240.0880.0880.0000.0000.0000.000
156A158ILE0-0.029-0.01040.4310.0010.0010.0000.0000.0000.000
157A159PHE00.0410.02136.7200.0000.0000.0000.0000.0000.000
158A160MET0-0.0010.00734.7610.0040.0040.0000.0000.0000.000
159A161ALA0-0.034-0.01836.6380.0030.0030.0000.0000.0000.000
160A162THR0-0.031-0.02439.028-0.002-0.0020.0000.0000.0000.000
161A163VAL00.0450.02233.852-0.002-0.0020.0000.0000.0000.000
162A164HIS10.8710.91831.283-0.101-0.1010.0000.0000.0000.000
163A165GLY00.0200.01735.4850.0010.0010.0000.0000.0000.000
164A166ALA0-0.001-0.00337.674-0.003-0.0030.0000.0000.0000.000
165A167MET0-0.0130.01430.5820.0000.0000.0000.0000.0000.000
166A168LEU0-0.021-0.00434.874-0.001-0.0010.0000.0000.0000.000
167A169SER0-0.032-0.02536.482-0.004-0.0040.0000.0000.0000.000
168A170ALA0-0.0090.00235.611-0.003-0.0030.0000.0000.0000.000
169A171ARG10.8190.91628.493-0.087-0.0870.0000.0000.0000.000
170A172ALA0-0.017-0.00735.467-0.002-0.0020.0000.0000.0000.000
171A173HIS0-0.0450.00138.928-0.001-0.0010.0000.0000.0000.000
172A174GLY00.0300.00339.032-0.004-0.0040.0000.0000.0000.000
173A175ASP-1-0.824-0.94138.2270.0180.0180.0000.0000.0000.000
174A176ALA0-0.040-0.01136.4750.0030.0030.0000.0000.0000.000
175A177ALA0-0.0100.00137.6620.0000.0000.0000.0000.0000.000
176A178THR00.0010.00139.5450.0010.0010.0000.0000.0000.000
177A179PHE00.0280.01134.7790.0020.0020.0000.0000.0000.000
178A180GLY00.0810.03738.3410.0020.0020.0000.0000.0000.000
179A181ALA0-0.051-0.02240.1240.0000.0000.0000.0000.0000.000
180A182ILE0-0.026-0.01141.0850.0000.0000.0000.0000.0000.000
181A183THR0-0.055-0.04337.8450.0000.0000.0000.0000.0000.000
182A184ARG10.8230.87837.746-0.022-0.0220.0000.0000.0000.000
183A185PRO00.0220.01442.845-0.001-0.0010.0000.0000.0000.000
184A186MET0-0.054-0.00243.508-0.001-0.0010.0000.0000.0000.000
185A187LEU00.0370.02639.7860.0010.0010.0000.0000.0000.000
186A188GLU-1-0.836-0.91544.2360.0200.0200.0000.0000.0000.000
187A189ARG10.8560.92946.837-0.036-0.0360.0000.0000.0000.000
188A190ILE0-0.050-0.01643.629-0.001-0.0010.0000.0000.0000.000
189A191THR00.0180.01546.6960.0000.0000.0000.0000.0000.000
190A192ALA0-0.035-0.00348.370-0.002-0.0020.0000.0000.0000.000