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: 9MGJ2

Calculation Name: 3ZIN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JIK5

Base Structure: X-ray

Registration Date: 2023-09-26

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 426
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6699619.11822
FMO2-HF: Nuclear repulsion 6539177.203646
FMO2-HF: Total energy -160441.914574
FMO2-MP2: Total energy -160914.728803


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:72:GLY)


Summations of interaction energy for fragment #1(A:72:GLY)
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.
-2.020.4570.158-1.222-1.4120.003
Interaction energy analysis for fragmet #1(A:72:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.013
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].
3A74VAL00.004-0.0162.9750.3432.4510.161-1.060-1.2090.003
4A75ASN0-0.042-0.0254.547-0.783-0.717-0.001-0.009-0.0560.000
5A76TRP00.0310.0154.2350.5570.816-0.001-0.150-0.1080.000
6A77SER0-0.016-0.0358.8250.2680.2680.0000.0000.0000.000
7A78VAL00.026-0.01812.244-0.021-0.0210.0000.0000.0000.000
8A79GLU-1-0.858-0.91514.865-0.290-0.2900.0000.0000.0000.000
9A80ASP-1-0.812-0.87310.030-0.752-0.7520.0000.0000.0000.000
10A81ILE0-0.0070.00210.8660.0240.0240.0000.0000.0000.000
11A82VAL0-0.0010.00312.5220.0610.0610.0000.0000.0000.000
12A83LYS10.8670.92913.7060.3780.3780.0000.0000.0000.000
13A84GLY00.0350.02312.1610.0310.0310.0000.0000.0000.000
14A85ILE00.0060.00113.1620.0640.0640.0000.0000.0000.000
15A86ASN0-0.048-0.02415.5980.0640.0640.0000.0000.0000.000
16A87SER0-0.0070.00315.0480.0160.0160.0000.0000.0000.000
17A88ASN0-0.006-0.00917.4290.0230.0230.0000.0000.0000.000
18A89ASN00.001-0.01014.0880.0190.0190.0000.0000.0000.000
19A90LEU00.0850.04114.816-0.023-0.0230.0000.0000.0000.000
20A91GLU-1-0.829-0.91010.7050.1970.1970.0000.0000.0000.000
21A92SER0-0.023-0.01310.404-0.037-0.0370.0000.0000.0000.000
22A93GLN0-0.052-0.02311.087-0.049-0.0490.0000.0000.0000.000
23A94LEU00.0130.02410.427-0.007-0.0070.0000.0000.0000.000
24A95GLN0-0.059-0.0396.521-0.120-0.1200.0000.0000.0000.000
25A96ALA00.0130.0097.896-0.092-0.0920.0000.0000.0000.000
26A97THR0-0.017-0.02710.0300.0110.0110.0000.0000.0000.000
27A98GLN0-0.028-0.0166.7880.7220.7220.0000.0000.0000.000
28A99ALA0-0.008-0.0017.0050.1370.1370.0000.0000.0000.000
29A100ALA0-0.024-0.0118.4610.0270.0270.0000.0000.0000.000
30A101ARG10.8410.90211.198-0.603-0.6030.0000.0000.0000.000
31A102LYS10.8550.9355.255-3.414-3.370-0.001-0.003-0.0390.000
32A103LEU0-0.013-0.00910.432-0.020-0.0200.0000.0000.0000.000
33A104LEU0-0.064-0.03312.032-0.005-0.0050.0000.0000.0000.000
34A105SER0-0.011-0.00812.9150.0130.0130.0000.0000.0000.000
35A106ARG10.8190.92612.9700.1350.1350.0000.0000.0000.000
36A107GLU-1-0.869-0.94014.5820.1010.1010.0000.0000.0000.000
37A108LYS10.9100.95817.096-0.004-0.0040.0000.0000.0000.000
38A109GLN00.0180.00017.837-0.015-0.0150.0000.0000.0000.000
39A110PRO00.0980.07316.646-0.033-0.0330.0000.0000.0000.000
40A111PRO0-0.0190.00015.193-0.003-0.0030.0000.0000.0000.000
41A112ILE00.0720.01718.337-0.018-0.0180.0000.0000.0000.000
42A113ASP-1-0.805-0.89620.454-0.044-0.0440.0000.0000.0000.000
43A114ASN0-0.052-0.02618.9730.0090.0090.0000.0000.0000.000
44A115ILE00.0120.00815.209-0.018-0.0180.0000.0000.0000.000
45A116ILE00.0070.01119.2830.0000.0000.0000.0000.0000.000
46A117ARG10.8840.93122.9910.0880.0880.0000.0000.0000.000
47A118ALA0-0.0330.00319.316-0.005-0.0050.0000.0000.0000.000
48A119GLY00.0010.00121.266-0.005-0.0050.0000.0000.0000.000
49A120LEU0-0.025-0.02616.3310.0030.0030.0000.0000.0000.000
50A121ILE00.0340.03320.2530.0120.0120.0000.0000.0000.000
51A122PRO00.0550.01322.4750.0110.0110.0000.0000.0000.000
52A123LYS10.8660.95919.3860.0890.0890.0000.0000.0000.000
53A124PHE00.0440.02015.5880.0130.0130.0000.0000.0000.000
54A125VAL00.0430.01819.9750.0180.0180.0000.0000.0000.000
55A126SER0-0.082-0.04821.6460.0050.0050.0000.0000.0000.000
56A127PHE0-0.017-0.03016.2700.0050.0050.0000.0000.0000.000
57A128LEU00.0420.03320.3030.0180.0180.0000.0000.0000.000
58A129GLY00.0340.02622.4070.0080.0080.0000.0000.0000.000
59A130LYS10.7840.88919.322-0.059-0.0590.0000.0000.0000.000
60A131THR00.024-0.00221.2900.0170.0170.0000.0000.0000.000
61A132ASP-1-0.858-0.90221.6540.0780.0780.0000.0000.0000.000
62A133CYS0-0.057-0.02616.6550.0100.0100.0000.0000.0000.000
63A134SER00.0820.03918.0840.0150.0150.0000.0000.0000.000
64A135PRO00.008-0.00513.4970.0110.0110.0000.0000.0000.000
65A136ILE00.0250.01414.3910.0230.0230.0000.0000.0000.000
66A137GLN0-0.0200.02015.774-0.002-0.0020.0000.0000.0000.000
67A138PHE00.0090.00814.991-0.002-0.0020.0000.0000.0000.000
68A139GLU-1-0.733-0.83411.3850.6540.6540.0000.0000.0000.000
69A140SER0-0.034-0.04114.799-0.031-0.0310.0000.0000.0000.000
70A141ALA00.0430.02017.575-0.018-0.0180.0000.0000.0000.000
71A142TRP00.0020.00814.4600.0360.0360.0000.0000.0000.000
72A143ALA0-0.032-0.02015.644-0.016-0.0160.0000.0000.0000.000
73A144LEU00.008-0.01217.405-0.023-0.0230.0000.0000.0000.000
74A145THR00.003-0.00120.715-0.010-0.0100.0000.0000.0000.000
75A146ASN0-0.021-0.02616.560-0.003-0.0030.0000.0000.0000.000
76A147ILE0-0.054-0.02119.528-0.017-0.0170.0000.0000.0000.000
77A148ALA0-0.011-0.01022.345-0.009-0.0090.0000.0000.0000.000
78A149SER0-0.049-0.01722.8420.0020.0020.0000.0000.0000.000
79A150GLY0-0.0010.00925.291-0.002-0.0020.0000.0000.0000.000
80A151THR0-0.018-0.02525.8980.0020.0020.0000.0000.0000.000
81A152SER00.052-0.00829.133-0.001-0.0010.0000.0000.0000.000
82A153GLU-1-1.012-0.98930.063-0.020-0.0200.0000.0000.0000.000
83A154GLN0-0.023-0.03324.8570.0070.0070.0000.0000.0000.000
84A155THR00.0530.01626.8420.0010.0010.0000.0000.0000.000
85A156LYS10.8400.90328.4460.0050.0050.0000.0000.0000.000
86A157ALA0-0.0100.00526.6330.0000.0000.0000.0000.0000.000
87A158VAL0-0.026-0.01724.254-0.002-0.0020.0000.0000.0000.000
88A159VAL0-0.033-0.01326.8060.0030.0030.0000.0000.0000.000
89A160ASP-1-0.816-0.89330.296-0.003-0.0030.0000.0000.0000.000
90A161GLY0-0.047-0.01827.148-0.004-0.0040.0000.0000.0000.000
91A162GLY00.008-0.00127.8960.0010.0010.0000.0000.0000.000
92A163ALA0-0.001-0.00726.1070.0050.0050.0000.0000.0000.000
93A164ILE00.0090.02027.7580.0080.0080.0000.0000.0000.000
94A165PRO00.0600.02130.7430.0060.0060.0000.0000.0000.000
95A166ALA0-0.0050.01926.3620.0040.0040.0000.0000.0000.000
96A167PHE00.036-0.00323.1110.0090.0090.0000.0000.0000.000
97A168ILE00.012-0.00127.6300.0070.0070.0000.0000.0000.000
98A169SER0-0.047-0.02829.0240.0010.0010.0000.0000.0000.000
99A170LEU0-0.032-0.02123.0780.0060.0060.0000.0000.0000.000
100A171LEU0-0.0220.01226.9560.0120.0120.0000.0000.0000.000
101A172ALA00.0190.02329.3210.0050.0050.0000.0000.0000.000
102A173SER0-0.013-0.00224.0140.0010.0010.0000.0000.0000.000
103A174PRO00.001-0.00426.0870.0050.0050.0000.0000.0000.000
104A175HIS0-0.018-0.00421.6270.0260.0260.0000.0000.0000.000
105A176ALA00.0730.03223.6980.0020.0020.0000.0000.0000.000
106A177HIS00.0670.03017.920-0.030-0.0300.0000.0000.0000.000
107A178ILE0-0.031-0.02419.5170.0020.0020.0000.0000.0000.000
108A179SER0-0.0090.00922.110-0.013-0.0130.0000.0000.0000.000
109A180GLU-1-0.822-0.91823.6380.1680.1680.0000.0000.0000.000
110A181GLN0-0.063-0.03719.5410.0170.0170.0000.0000.0000.000
111A182ALA00.0010.00322.873-0.013-0.0130.0000.0000.0000.000
112A183VAL00.0210.01025.730-0.013-0.0130.0000.0000.0000.000
113A184TRP00.0320.02920.741-0.004-0.0040.0000.0000.0000.000
114A185ALA0-0.0170.00024.342-0.011-0.0110.0000.0000.0000.000
115A186LEU0-0.004-0.01226.055-0.012-0.0120.0000.0000.0000.000
116A187GLY00.0330.02529.314-0.008-0.0080.0000.0000.0000.000
117A188ASN0-0.058-0.04025.466-0.011-0.0110.0000.0000.0000.000
118A189ILE0-0.023-0.01527.850-0.008-0.0080.0000.0000.0000.000
119A190ALA0-0.022-0.01730.967-0.006-0.0060.0000.0000.0000.000
120A191GLY0-0.007-0.00332.602-0.003-0.0030.0000.0000.0000.000
121A192ASP-1-0.879-0.91332.1540.0180.0180.0000.0000.0000.000
122A193GLY00.0560.01733.904-0.004-0.0040.0000.0000.0000.000
123A194SER0-0.045-0.04237.6090.0020.0020.0000.0000.0000.000
124A195ALA00.0150.02039.1790.0010.0010.0000.0000.0000.000
125A196PHE00.0290.00533.261-0.001-0.0010.0000.0000.0000.000
126A197ARG10.7710.87036.108-0.026-0.0260.0000.0000.0000.000
127A198ASP-1-0.793-0.88737.5610.0280.0280.0000.0000.0000.000
128A199LEU0-0.047-0.01635.3360.0000.0000.0000.0000.0000.000
129A200VAL00.0310.01533.1560.0010.0010.0000.0000.0000.000
130A201ILE0-0.002-0.00135.8900.0020.0020.0000.0000.0000.000
131A202LYS10.9080.94839.164-0.022-0.0220.0000.0000.0000.000
132A203HIS0-0.080-0.04035.401-0.003-0.0030.0000.0000.0000.000
133A204GLY00.0110.00936.8120.0020.0020.0000.0000.0000.000
134A205ALA0-0.004-0.01034.6320.0030.0030.0000.0000.0000.000
135A206ILE00.0070.00835.9140.0050.0050.0000.0000.0000.000
136A207ASP-1-0.817-0.91538.1290.0480.0480.0000.0000.0000.000
137A208PRO0-0.021-0.00833.8700.0030.0030.0000.0000.0000.000
138A209LEU00.014-0.00231.8680.0060.0060.0000.0000.0000.000
139A210LEU0-0.009-0.00835.1230.0030.0030.0000.0000.0000.000
140A211ALA0-0.017-0.00636.5590.0010.0010.0000.0000.0000.000
141A212LEU0-0.055-0.01730.8570.0020.0020.0000.0000.0000.000
142A213LEU0-0.001-0.00134.5340.0050.0050.0000.0000.0000.000
143A214ALA0-0.045-0.01637.139-0.003-0.0030.0000.0000.0000.000
144A215VAL00.0130.02235.926-0.002-0.0020.0000.0000.0000.000
145A216PRO00.0330.00439.229-0.003-0.0030.0000.0000.0000.000
146A217ASP-1-0.835-0.90440.2480.0720.0720.0000.0000.0000.000
147A218LEU00.0290.02937.4970.0050.0050.0000.0000.0000.000
148A219SER0-0.027-0.04335.9810.0060.0060.0000.0000.0000.000
149A220THR0-0.108-0.05635.4110.0050.0050.0000.0000.0000.000
150A221LEU0-0.0170.00532.2800.0070.0070.0000.0000.0000.000
151A222ALA00.0030.00127.2710.0010.0010.0000.0000.0000.000
152A223CYS0-0.008-0.00628.838-0.002-0.0020.0000.0000.0000.000
153A224GLY00.0270.01526.091-0.006-0.0060.0000.0000.0000.000
154A225TYR00.0240.01126.525-0.011-0.0110.0000.0000.0000.000
155A226LEU00.0240.01728.292-0.009-0.0090.0000.0000.0000.000
156A227ARG10.7890.88929.495-0.118-0.1180.0000.0000.0000.000
157A228ASN0-0.027-0.02924.965-0.017-0.0170.0000.0000.0000.000
158A229LEU0-0.011-0.00729.256-0.008-0.0080.0000.0000.0000.000
159A230THR0-0.031-0.02632.157-0.009-0.0090.0000.0000.0000.000
160A231TRP00.0130.02328.518-0.006-0.0060.0000.0000.0000.000
161A232THR0-0.013-0.02130.029-0.007-0.0070.0000.0000.0000.000
162A233LEU0-0.005-0.00232.733-0.007-0.0070.0000.0000.0000.000
163A234SER0-0.046-0.03134.915-0.007-0.0070.0000.0000.0000.000
164A235ASN0-0.002-0.02732.055-0.009-0.0090.0000.0000.0000.000
165A236LEU0-0.011-0.01035.423-0.005-0.0050.0000.0000.0000.000
166A237CYS0-0.084-0.02937.952-0.004-0.0040.0000.0000.0000.000
167A238ARG10.9150.97434.659-0.048-0.0480.0000.0000.0000.000
168A239ASN0-0.0170.00037.139-0.002-0.0020.0000.0000.0000.000
169A240LYS10.8530.89641.504-0.022-0.0220.0000.0000.0000.000
170A241ASN0-0.0540.00244.4000.0000.0000.0000.0000.0000.000
171A242PRO00.0490.03644.677-0.001-0.0010.0000.0000.0000.000
172A243ALA00.0360.00944.8940.0010.0010.0000.0000.0000.000
173A244PRO00.0270.02942.396-0.001-0.0010.0000.0000.0000.000
174A245PRO00.0140.01643.799-0.001-0.0010.0000.0000.0000.000
175A246LEU00.0130.00446.8230.0020.0020.0000.0000.0000.000
176A247ASP-1-0.861-0.93546.7710.0290.0290.0000.0000.0000.000
177A248ALA00.0570.02243.0630.0020.0020.0000.0000.0000.000
178A249VAL0-0.008-0.00144.3470.0030.0030.0000.0000.0000.000
179A250GLU-1-0.806-0.89946.2680.0320.0320.0000.0000.0000.000
180A251GLN0-0.085-0.03042.8930.0000.0000.0000.0000.0000.000
181A252ILE00.0190.00240.1070.0030.0030.0000.0000.0000.000
182A253LEU0-0.003-0.00143.2070.0030.0030.0000.0000.0000.000
183A254PRO0-0.043-0.02145.6750.0010.0010.0000.0000.0000.000
184A255THR00.0280.02239.7240.0020.0020.0000.0000.0000.000
185A256LEU0-0.010-0.00140.4560.0030.0030.0000.0000.0000.000
186A257VAL00.0230.00542.4530.0010.0010.0000.0000.0000.000
187A258ARG10.8230.92240.853-0.063-0.0630.0000.0000.0000.000
188A259LEU0-0.0080.00137.1480.0010.0010.0000.0000.0000.000
189A260LEU0-0.0030.00040.6140.0020.0020.0000.0000.0000.000
190A261HIS0-0.052-0.04643.062-0.004-0.0040.0000.0000.0000.000
191A262HIS00.0280.02836.242-0.004-0.0040.0000.0000.0000.000
192A263ASN0-0.014-0.02137.410-0.001-0.0010.0000.0000.0000.000
193A264ASP-1-0.776-0.86433.6940.0990.0990.0000.0000.0000.000
194A265PRO00.0550.00735.852-0.002-0.0020.0000.0000.0000.000
195A266GLU-1-0.865-0.92930.4200.1030.1030.0000.0000.0000.000
196A267VAL0-0.0050.00234.197-0.003-0.0030.0000.0000.0000.000
197A268LEU00.0040.01836.092-0.005-0.0050.0000.0000.0000.000
198A269ALA00.0090.01436.472-0.004-0.0040.0000.0000.0000.000
199A270ASP-1-0.827-0.93033.4600.0700.0700.0000.0000.0000.000
200A271SER0-0.044-0.04037.123-0.003-0.0030.0000.0000.0000.000
201A272CYS0-0.030-0.01940.117-0.004-0.0040.0000.0000.0000.000
202A273TRP0-0.033-0.00937.172-0.006-0.0060.0000.0000.0000.000
203A274ALA00.0250.02639.386-0.003-0.0030.0000.0000.0000.000
204A275ILE00.0190.00441.051-0.003-0.0030.0000.0000.0000.000
205A276SER0-0.059-0.02642.680-0.003-0.0030.0000.0000.0000.000
206A277TYR0-0.010-0.02237.217-0.003-0.0030.0000.0000.0000.000
207A278LEU0-0.028-0.01843.975-0.002-0.0020.0000.0000.0000.000
208A279THR0-0.012-0.02846.388-0.002-0.0020.0000.0000.0000.000
209A280ASP-1-0.836-0.88946.6940.0230.0230.0000.0000.0000.000
210A281GLY0-0.027-0.02948.730-0.001-0.0010.0000.0000.0000.000
211A282PRO00.0190.01451.5300.0000.0000.0000.0000.0000.000
212A283ASN00.0790.03054.5870.0010.0010.0000.0000.0000.000
213A284GLU-1-0.840-0.91256.0080.0200.0200.0000.0000.0000.000
214A285ARG10.7820.88147.378-0.025-0.0250.0000.0000.0000.000
215A286ILE00.0440.03751.6920.0020.0020.0000.0000.0000.000
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