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: YVGR2

Calculation Name: 2GZ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D028

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2245793.646394
FMO2-HF: Nuclear repulsion 2167417.868818
FMO2-HF: Total energy -78375.777576
FMO2-MP2: Total energy -78602.506707


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:6:SER)


Summations of interaction energy for fragment #1(A:6:SER)
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.
1.8593.779-0.011-0.954-0.9550.005
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.012
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].
3A8ARG10.9230.9513.8151.2253.145-0.011-0.954-0.9550.005
4A9ALA00.0540.0266.3200.5190.5190.0000.0000.0000.000
5A10TRP00.0230.0028.1090.3120.3120.0000.0000.0000.000
6A11GLN0-0.021-0.01310.678-0.372-0.3720.0000.0000.0000.000
7A12ARG10.8630.92611.7500.5440.5440.0000.0000.0000.000
8A13MET00.0080.02314.273-0.050-0.0500.0000.0000.0000.000
9A14LEU00.011-0.00918.0360.0170.0170.0000.0000.0000.000
10A15SER0-0.051-0.03420.2260.0280.0280.0000.0000.0000.000
11A16GLY00.0180.02018.3270.0380.0380.0000.0000.0000.000
12A17ARG10.9120.97117.4680.2320.2320.0000.0000.0000.000
13A18ARG10.9180.93912.2010.2370.2370.0000.0000.0000.000
14A19LEU00.0590.05615.5120.0610.0610.0000.0000.0000.000
15A20ASP-1-0.884-0.94812.553-0.645-0.6450.0000.0000.0000.000
16A21LEU0-0.009-0.01511.0080.0290.0290.0000.0000.0000.000
17A22LEU0-0.038-0.02211.9260.0510.0510.0000.0000.0000.000
18A23ASP-1-0.993-0.99414.844-0.111-0.1110.0000.0000.0000.000
19A24PRO0-0.0170.01816.7240.0240.0240.0000.0000.0000.000
20A25SER00.0690.03218.2440.0450.0450.0000.0000.0000.000
21A26PRO00.030-0.00920.552-0.023-0.0230.0000.0000.0000.000
22A27LEU0-0.039-0.02522.965-0.003-0.0030.0000.0000.0000.000
23A28ASP-1-0.914-0.94018.170-0.224-0.2240.0000.0000.0000.000
24A29VAL0-0.094-0.03621.106-0.039-0.0390.0000.0000.0000.000
25A30GLU-1-0.835-0.93023.348-0.141-0.1410.0000.0000.0000.000
26A31ILE00.0380.02225.415-0.028-0.0280.0000.0000.0000.000
27A32ALA00.0080.00726.720-0.011-0.0110.0000.0000.0000.000
28A33ASP-1-0.776-0.87921.893-0.323-0.3230.0000.0000.0000.000
29A34ILE00.004-0.00123.718-0.030-0.0300.0000.0000.0000.000
30A35ALA00.0170.01225.281-0.013-0.0130.0000.0000.0000.000
31A36HIS0-0.031-0.00823.5310.0120.0120.0000.0000.0000.000
32A37GLY00.0240.01223.209-0.011-0.0110.0000.0000.0000.000
33A38LEU00.0390.00823.984-0.010-0.0100.0000.0000.0000.000
34A39ALA0-0.0120.00926.8470.0090.0090.0000.0000.0000.000
35A40ARG10.8330.90024.6860.3300.3300.0000.0000.0000.000
36A41VAL0-0.0250.01522.928-0.015-0.0150.0000.0000.0000.000
37A42ALA00.0200.01325.5600.0320.0320.0000.0000.0000.000
38A43ARG10.9050.95927.4690.2350.2350.0000.0000.0000.000
39A44TRP0-0.050-0.04330.1520.0000.0000.0000.0000.0000.000
40A45ASN0-0.030-0.01826.997-0.011-0.0110.0000.0000.0000.000
41A46GLY00.0250.01728.548-0.006-0.0060.0000.0000.0000.000
42A47GLN0-0.0410.00230.2150.0010.0010.0000.0000.0000.000
43A48THR0-0.025-0.03333.2990.0080.0080.0000.0000.0000.000
44A49ARG10.8800.94535.6930.1580.1580.0000.0000.0000.000
45A50GLY00.0350.00138.2300.0010.0010.0000.0000.0000.000
46A51ASP-1-0.925-0.94836.534-0.183-0.1830.0000.0000.0000.000
47A52HIS0-0.052-0.02133.684-0.021-0.0210.0000.0000.0000.000
48A53ALA00.0370.01130.1430.0030.0030.0000.0000.0000.000
49A54PHE00.0310.01532.0830.0060.0060.0000.0000.0000.000
50A55THR0-0.004-0.00429.648-0.012-0.0120.0000.0000.0000.000
51A56VAL00.0420.00827.0830.0190.0190.0000.0000.0000.000
52A57ALA0-0.0060.00430.0910.0160.0160.0000.0000.0000.000
53A58GLN00.0330.00431.5400.0070.0070.0000.0000.0000.000
54A59HIS10.7460.84632.6660.2340.2340.0000.0000.0000.000
55A60CYS0-0.032-0.01231.4470.0090.0090.0000.0000.0000.000
56A61LEU00.0040.01334.3750.0130.0130.0000.0000.0000.000
57A62ILE0-0.0140.00537.3550.0110.0110.0000.0000.0000.000
58A63VAL0-0.009-0.01035.8310.0110.0110.0000.0000.0000.000
59A64GLU-1-0.775-0.87337.764-0.123-0.1230.0000.0000.0000.000
60A65THR00.0380.02039.5020.0110.0110.0000.0000.0000.000
61A66ILE0-0.029-0.01841.4200.0090.0090.0000.0000.0000.000
62A67PHE0-0.004-0.01940.5520.0070.0070.0000.0000.0000.000
63A68CYS0-0.0130.00142.6700.0080.0080.0000.0000.0000.000
64A69ARG10.9060.96745.1190.1040.1040.0000.0000.0000.000
65A70MET0-0.060-0.04344.8310.0030.0030.0000.0000.0000.000
66A71CYS0-0.079-0.02144.8340.0040.0040.0000.0000.0000.000
67A72PRO00.0550.02347.0110.0000.0000.0000.0000.0000.000
68A73GLY0-0.037-0.01149.2420.0020.0020.0000.0000.0000.000
69A74ALA0-0.0280.00243.6550.0010.0010.0000.0000.0000.000
70A75THR0-0.032-0.02142.9010.0030.0030.0000.0000.0000.000
71A76PRO00.041-0.00342.322-0.005-0.0050.0000.0000.0000.000
72A77ASP-1-0.806-0.89238.699-0.107-0.1070.0000.0000.0000.000
73A78GLU-1-0.873-0.94437.835-0.109-0.1090.0000.0000.0000.000
74A79MET0-0.025-0.00538.596-0.008-0.0080.0000.0000.0000.000
75A80GLN00.001-0.00634.401-0.016-0.0160.0000.0000.0000.000
76A81MET0-0.027-0.01533.917-0.012-0.0120.0000.0000.0000.000
77A82ALA0-0.028-0.01034.050-0.012-0.0120.0000.0000.0000.000
78A83LEU0-0.040-0.00933.887-0.011-0.0110.0000.0000.0000.000
79A84LEU0-0.021-0.02230.045-0.017-0.0170.0000.0000.0000.000
80A85HIS0-0.0230.01429.756-0.012-0.0120.0000.0000.0000.000
81A86ASP-1-0.841-0.93728.534-0.275-0.2750.0000.0000.0000.000
82A87ALA00.002-0.00526.728-0.029-0.0290.0000.0000.0000.000
83A88PRO00.018-0.00323.251-0.035-0.0350.0000.0000.0000.000
84A89GLH0-0.051-0.06922.006-0.045-0.0450.0000.0000.0000.000
85A90TYR0-0.061-0.03021.311-0.047-0.0470.0000.0000.0000.000
86A91VAL0-0.035-0.01216.507-0.042-0.0420.0000.0000.0000.000
87A92ILE0-0.054-0.01617.566-0.092-0.0920.0000.0000.0000.000
88A93GLY0-0.0010.00819.505-0.034-0.0340.0000.0000.0000.000
89A94ASP-1-0.838-0.88421.481-0.312-0.3120.0000.0000.0000.000
90A95MET0-0.026-0.00423.553-0.028-0.0280.0000.0000.0000.000
91A96ILE00.0410.01925.4770.0300.0300.0000.0000.0000.000
92A97SER00.008-0.02628.523-0.011-0.0110.0000.0000.0000.000
93A98PRO00.0250.01330.5490.0000.0000.0000.0000.0000.000
94A99PHE00.0600.02525.6380.0050.0050.0000.0000.0000.000
95A100LYS10.9710.99025.7470.3170.3170.0000.0000.0000.000
96A101SER0-0.085-0.05427.338-0.002-0.0020.0000.0000.0000.000
97A102VAL0-0.0110.00524.9910.0140.0140.0000.0000.0000.000
98A103VAL0-0.0250.01421.370-0.010-0.0100.0000.0000.0000.000
99A104GLY00.0500.03221.629-0.029-0.0290.0000.0000.0000.000
100A105GLY0-0.004-0.02623.056-0.013-0.0130.0000.0000.0000.000
101A106GLY00.0340.01619.3330.0130.0130.0000.0000.0000.000
102A107TYR00.0690.03519.4600.0040.0040.0000.0000.0000.000
103A108LYS10.9620.97920.7000.2740.2740.0000.0000.0000.000
104A109THR0-0.053-0.02620.9650.0310.0310.0000.0000.0000.000
105A110VAL00.0390.02317.2560.0230.0230.0000.0000.0000.000
106A111GLU-1-0.891-0.95620.087-0.328-0.3280.0000.0000.0000.000
107A112LYS10.9260.96223.0610.2150.2150.0000.0000.0000.000
108A113ARG10.9220.95418.2830.2720.2720.0000.0000.0000.000
109A114LEU00.0300.01418.7050.0160.0160.0000.0000.0000.000
110A115GLU-1-0.831-0.91022.466-0.183-0.1830.0000.0000.0000.000
111A116ALA0-0.0120.00525.1530.0160.0160.0000.0000.0000.000
112A117ALA0-0.006-0.00222.2850.0180.0180.0000.0000.0000.000
113A118VAL00.013-0.00824.3230.0140.0140.0000.0000.0000.000
114A119HIS0-0.051-0.03526.3150.0070.0070.0000.0000.0000.000
115A120LEU00.003-0.00626.6770.0150.0150.0000.0000.0000.000
116A121ARG10.8040.92526.2640.1690.1690.0000.0000.0000.000
117A122PHE0-0.019-0.01428.2360.0100.0100.0000.0000.0000.000
118A123GLY00.0450.03031.6020.0080.0080.0000.0000.0000.000
119A124LEU0-0.040-0.01132.5220.0070.0070.0000.0000.0000.000
120A125PRO00.016-0.00332.7400.0000.0000.0000.0000.0000.000
121A126PRO00.0160.01429.464-0.010-0.0100.0000.0000.0000.000
122A127HIS0-0.085-0.05827.109-0.007-0.0070.0000.0000.0000.000
123A128ALA00.0470.03631.9230.0130.0130.0000.0000.0000.000
124A129SER00.0210.01635.057-0.001-0.0010.0000.0000.0000.000
125A130ARG10.9650.96336.9320.1110.1110.0000.0000.0000.000
126A131GLU-1-0.825-0.90938.579-0.104-0.1040.0000.0000.0000.000
127A132LEU00.0800.05137.238-0.002-0.0020.0000.0000.0000.000
128A133LYS10.9670.98032.0310.1820.1820.0000.0000.0000.000
129A134ASP-1-0.914-0.94837.058-0.127-0.1270.0000.0000.0000.000
130A135ARG10.8110.88739.8950.1010.1010.0000.0000.0000.000
131A136ILE00.0420.02735.212-0.001-0.0010.0000.0000.0000.000
132A137LYS10.9290.97233.6900.1960.1960.0000.0000.0000.000
133A138LYS10.8430.90437.6920.1160.1160.0000.0000.0000.000
134A139ALA00.0540.03139.7500.0010.0010.0000.0000.0000.000
135A140ASP-1-0.895-0.93034.448-0.217-0.2170.0000.0000.0000.000
136A141THR0-0.041-0.02837.654-0.007-0.0070.0000.0000.0000.000
137A142VAL00.0010.00339.3590.0020.0020.0000.0000.0000.000
138A143ALA00.0380.01738.1640.0020.0020.0000.0000.0000.000
139A144ALA0-0.035-0.01636.912-0.003-0.0030.0000.0000.0000.000
140A145PHE00.0110.00838.3950.0000.0000.0000.0000.0000.000
141A146PHE00.0370.00041.9100.0030.0030.0000.0000.0000.000
142A147GLU-1-0.709-0.82935.754-0.214-0.2140.0000.0000.0000.000
143A148ALA0-0.005-0.00138.634-0.003-0.0030.0000.0000.0000.000
144A149THR0-0.044-0.02839.5690.0020.0020.0000.0000.0000.000
145A150GLU-1-0.955-0.97642.284-0.131-0.1310.0000.0000.0000.000
146A151LEU0-0.078-0.03337.2080.0000.0000.0000.0000.0000.000
147A152ALA0-0.017-0.00536.216-0.004-0.0040.0000.0000.0000.000
148A153GLY0-0.043-0.01137.861-0.003-0.0030.0000.0000.0000.000
149A154PHE0-0.0130.00936.1600.0030.0030.0000.0000.0000.000
150A155SER00.008-0.00341.7630.0080.0080.0000.0000.0000.000
151A156THR00.0620.00644.874-0.004-0.0040.0000.0000.0000.000
152A157ALA00.0100.01247.0110.0000.0000.0000.0000.0000.000
153A158GLU-1-0.871-0.93141.769-0.157-0.1570.0000.0000.0000.000
154A159ALA00.0410.02442.184-0.003-0.0030.0000.0000.0000.000
155A160GLN0-0.026-0.01643.250-0.001-0.0010.0000.0000.0000.000
156A161LYS10.8880.94643.6070.1190.1190.0000.0000.0000.000
157A162PHE0-0.036-0.02239.1000.0000.0000.0000.0000.0000.000
158A163PHE0-0.032-0.02236.868-0.007-0.0070.0000.0000.0000.000
159A164GLY00.0100.02441.7750.0030.0030.0000.0000.0000.000
160A165LEU0-0.026-0.02045.410-0.003-0.0030.0000.0000.0000.000
161A166PRO00.0150.01645.4580.0030.0030.0000.0000.0000.000
162A167ARG10.9700.97947.8660.0900.0900.0000.0000.0000.000
163A168GLY0-0.026-0.02150.3980.0000.0000.0000.0000.0000.000
164A169ILE0-0.0060.00645.7830.0010.0010.0000.0000.0000.000
165A170THR00.017-0.01449.237-0.001-0.0010.0000.0000.0000.000
166A171ARG10.9980.99345.0780.1280.1280.0000.0000.0000.000
167A172ASP-1-0.938-0.96847.199-0.103-0.1030.0000.0000.0000.000
168A173MET0-0.058-0.00247.3130.0010.0010.0000.0000.0000.000
169A174PHE00.0080.00342.661-0.002-0.0020.0000.0000.0000.000
170A175ASP-1-0.895-0.93841.714-0.131-0.1310.0000.0000.0000.000
171A176ILE0-0.025-0.01939.694-0.008-0.0080.0000.0000.0000.000
172A177ILE00.001-0.00739.631-0.007-0.0070.0000.0000.0000.000
173A178PRO0-0.0020.00835.5090.0010.0010.0000.0000.0000.000
174A179LEU0-0.0120.00236.2590.0060.0060.0000.0000.0000.000
175A180PRO00.0320.01434.165-0.014-0.0140.0000.0000.0000.000
176A181SER00.014-0.00929.5160.0020.0020.0000.0000.0000.000
177A182THR0-0.027-0.02331.563-0.001-0.0010.0000.0000.0000.000
178A183GLU-1-0.735-0.83933.113-0.147-0.1470.0000.0000.0000.000
179A184ALA00.0040.00732.6670.0050.0050.0000.0000.0000.000
180A185GLN00.0410.00928.646-0.009-0.0090.0000.0000.0000.000
181A186ARG10.8090.88432.2170.1470.1470.0000.0000.0000.000
182A187LEU0-0.001-0.00135.3360.0080.0080.0000.0000.0000.000
183A188PHE00.0170.00530.3130.0050.0050.0000.0000.0000.000
184A189ILE0-0.005-0.00930.7420.0020.0020.0000.0000.0000.000
185A190ALA00.0380.02934.2440.0080.0080.0000.0000.0000.000
186A191ARG10.8150.88737.3790.1340.1340.0000.0000.0000.000
187A192PHE00.0470.01332.6150.0050.0050.0000.0000.0000.000
188A193GLU-1-0.891-0.96035.827-0.125-0.1250.0000.0000.0000.000
189A194ALA0-0.030-0.01337.8390.0090.0090.0000.0000.0000.000
190A195ILE0-0.028-0.02037.9320.0080.0080.0000.0000.0000.000
191A196GLU-1-0.808-0.88635.946-0.118-0.1180.0000.0000.0000.000
192A197THR0-0.012-0.00239.0300.0090.0090.0000.0000.0000.000
193A198LEU0-0.042-0.02442.5030.0070.0070.0000.0000.0000.000
194A199ARG10.7900.86335.1110.1190.1190.0000.0000.0000.000
195A200VAL00.0030.01741.0480.0050.0050.0000.0000.0000.000
196A201THR0-0.051-0.02143.3700.0060.0060.0000.0000.0000.000
197A202ARG10.8840.94044.8320.0790.0790.0000.0000.0000.000
198A203THR0-0.038-0.01742.6570.0020.0020.0000.0000.0000.000
199A204GLY0-0.0040.02045.2880.0040.0040.0000.0000.0000.000
200A205GLY0-0.028-0.01846.0930.0000.0000.0000.0000.0000.000