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: 2N63R

Calculation Name: 4MEM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MEM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5D006

Base Structure: X-ray

Registration Date: 2023-09-24

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2380493.439753
FMO2-HF: Nuclear repulsion 2294989.320795
FMO2-HF: Total energy -85504.118959
FMO2-MP2: Total energy -85755.656536


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:26:ALA)


Summations of interaction energy for fragment #1(A:26:ALA)
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.
1.5982.605-0.008-0.403-0.5960.001
Interaction energy analysis for fragmet #1(A:26:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.024
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].
3A28PRO0-0.029-0.0133.8750.6011.608-0.008-0.403-0.5960.001
4A29ASP-1-0.857-0.9226.2920.5720.5720.0000.0000.0000.000
5A30LEU00.0240.0299.381-0.196-0.1960.0000.0000.0000.000
6A31ASP-1-0.813-0.89112.361-0.033-0.0330.0000.0000.0000.000
7A32GLN0-0.029-0.0158.5850.0300.0300.0000.0000.0000.000
8A33GLN00.0430.0268.642-0.081-0.0810.0000.0000.0000.000
9A34TRP00.0520.01112.288-0.006-0.0060.0000.0000.0000.000
10A35ARG10.7810.86515.7390.0480.0480.0000.0000.0000.000
11A36GLN0-0.0050.0089.739-0.013-0.0130.0000.0000.0000.000
12A37ILE0-0.013-0.00512.8660.0000.0000.0000.0000.0000.000
13A38GLY00.0120.00716.2120.0200.0200.0000.0000.0000.000
14A39ASN0-0.025-0.02618.3430.0250.0250.0000.0000.0000.000
15A40GLY0-0.018-0.00318.374-0.001-0.0010.0000.0000.0000.000
16A41ARG10.8780.92819.1450.1000.1000.0000.0000.0000.000
17A42GLU-1-0.931-0.95022.427-0.081-0.0810.0000.0000.0000.000
18A43ARG10.7610.87720.4070.1830.1830.0000.0000.0000.000
19A44PRO00.0020.00023.8800.0050.0050.0000.0000.0000.000
20A45LEU00.0530.02026.671-0.008-0.0080.0000.0000.0000.000
21A46ARG10.8470.90725.4070.1350.1350.0000.0000.0000.000
22A47ALA00.0580.02728.625-0.006-0.0060.0000.0000.0000.000
23A48GLY00.0390.02628.924-0.003-0.0030.0000.0000.0000.000
24A49GLU-1-0.791-0.85224.335-0.160-0.1600.0000.0000.0000.000
25A50SER0-0.024-0.03021.4950.0100.0100.0000.0000.0000.000
26A51TRP0-0.036-0.04121.812-0.020-0.0200.0000.0000.0000.000
27A52PHE00.0190.01419.5020.0040.0040.0000.0000.0000.000
28A53LEU00.0070.01821.5980.0010.0010.0000.0000.0000.000
29A54VAL0-0.0140.00218.526-0.011-0.0110.0000.0000.0000.000
30A55GLU-1-0.735-0.83621.151-0.016-0.0160.0000.0000.0000.000
31A56LYS10.8760.92922.3080.0280.0280.0000.0000.0000.000
32A57HIS10.8140.86123.7540.0190.0190.0000.0000.0000.000
33A58TRP00.0220.03013.684-0.002-0.0020.0000.0000.0000.000
34A59TYR00.0410.01118.9270.0140.0140.0000.0000.0000.000
35A60LYS10.8270.88519.6630.0120.0120.0000.0000.0000.000
36A61GLN00.0320.02618.1400.0110.0110.0000.0000.0000.000
37A62TRP00.0040.00412.7520.0270.0270.0000.0000.0000.000
38A63GLU-1-0.806-0.87116.3290.0020.0020.0000.0000.0000.000
39A64ALA0-0.038-0.02118.8810.0110.0110.0000.0000.0000.000
40A65TYR0-0.069-0.05410.782-0.003-0.0030.0000.0000.0000.000
41A66VAL0-0.008-0.00413.3780.0250.0250.0000.0000.0000.000
42A67LYS10.7630.85515.7240.0140.0140.0000.0000.0000.000
43A68GLY0-0.0030.01418.301-0.005-0.0050.0000.0000.0000.000
44A69GLY0-0.053-0.02016.8050.0070.0070.0000.0000.0000.000
45A70ASP-1-0.874-0.94615.4570.4260.4260.0000.0000.0000.000
46A71GLN00.0260.0027.739-0.206-0.2060.0000.0000.0000.000
47A72ASP-1-0.910-0.93611.3560.9930.9930.0000.0000.0000.000
48A73ALA0-0.0010.02013.368-0.070-0.0700.0000.0000.0000.000
49A74SER0-0.039-0.03815.4000.0100.0100.0000.0000.0000.000
50A75THR00.002-0.00917.723-0.012-0.0120.0000.0000.0000.000
51A76PHE00.0450.0229.079-0.055-0.0550.0000.0000.0000.000
52A77PRO0-0.046-0.01412.884-0.017-0.0170.0000.0000.0000.000
53A78GLY0-0.0130.00313.429-0.030-0.0300.0000.0000.0000.000
54A79SER0-0.029-0.03112.128-0.010-0.0100.0000.0000.0000.000
55A80ILE0-0.026-0.01213.3270.0250.0250.0000.0000.0000.000
56A81ASN0-0.008-0.00315.947-0.009-0.0090.0000.0000.0000.000
57A82ASN00.025-0.01519.4460.0110.0110.0000.0000.0000.000
58A83SER0-0.029-0.00922.2280.0050.0050.0000.0000.0000.000
59A84GLY00.0220.00624.8490.0010.0010.0000.0000.0000.000
60A85LEU0-0.025-0.01624.0050.0010.0010.0000.0000.0000.000
61A86PHE0-0.032-0.00723.639-0.004-0.0040.0000.0000.0000.000
62A87GLU-1-0.806-0.88529.133-0.027-0.0270.0000.0000.0000.000
63A88ASP-1-0.775-0.85831.523-0.042-0.0420.0000.0000.0000.000
64A89GLN0-0.0010.00126.111-0.005-0.0050.0000.0000.0000.000
65A90ILE0-0.042-0.01428.8960.0000.0000.0000.0000.0000.000
66A91SER0-0.052-0.07030.420-0.005-0.0050.0000.0000.0000.000
67A92TRP00.0030.00824.579-0.006-0.0060.0000.0000.0000.000
68A93HIS10.8260.89428.5470.0520.0520.0000.0000.0000.000
69A94LEU0-0.004-0.00627.6050.0010.0010.0000.0000.0000.000
70A95ARG10.8500.90830.4070.0340.0340.0000.0000.0000.000
71A96GLU-1-0.773-0.85032.974-0.039-0.0390.0000.0000.0000.000
72A97ARG10.7370.82635.5830.0370.0370.0000.0000.0000.000
73A98LEU00.0180.04529.6480.0020.0020.0000.0000.0000.000
74A99VAL0-0.022-0.03032.369-0.004-0.0040.0000.0000.0000.000
75A100GLU-1-0.820-0.90926.453-0.085-0.0850.0000.0000.0000.000
76A101GLY0-0.020-0.00428.4510.0040.0040.0000.0000.0000.000
77A102ASP-1-0.955-0.98429.477-0.020-0.0200.0000.0000.0000.000
78A103ASP-1-0.819-0.89529.182-0.031-0.0310.0000.0000.0000.000
79A104TYR0-0.039-0.02925.074-0.004-0.0040.0000.0000.0000.000
80A105VAL0-0.046-0.01521.8010.0060.0060.0000.0000.0000.000
81A106LEU0-0.0100.00022.977-0.010-0.0100.0000.0000.0000.000
82A107LEU0-0.007-0.00816.654-0.004-0.0040.0000.0000.0000.000
83A108PRO0-0.0020.02118.996-0.001-0.0010.0000.0000.0000.000
84A109ALA00.0510.00617.922-0.028-0.0280.0000.0000.0000.000
85A110PRO0-0.046-0.01414.814-0.032-0.0320.0000.0000.0000.000
86A111ALA00.0330.01613.514-0.068-0.0680.0000.0000.0000.000
87A112TRP00.0480.02413.755-0.037-0.0370.0000.0000.0000.000
88A113ASN00.0360.00012.265-0.010-0.0100.0000.0000.0000.000
89A114TYR0-0.027-0.0058.435-0.030-0.0300.0000.0000.0000.000
90A115LEU00.0510.0488.908-0.162-0.1620.0000.0000.0000.000
91A116VAL00.022-0.00110.4550.0010.0010.0000.0000.0000.000
92A117SER0-0.125-0.0746.118-0.110-0.1100.0000.0000.0000.000
93A118TRP0-0.026-0.0215.423-0.170-0.1700.0000.0000.0000.000
94A119TYR0-0.013-0.0246.9400.3450.3450.0000.0000.0000.000
95A120GLY00.0100.0249.5720.0910.0910.0000.0000.0000.000
96A121LEU0-0.008-0.01011.4380.0270.0270.0000.0000.0000.000
97A122LYS10.7750.87115.2720.0210.0210.0000.0000.0000.000
98A123ASP-1-0.801-0.89417.422-0.019-0.0190.0000.0000.0000.000
99A124ASP-1-0.909-0.95618.735-0.079-0.0790.0000.0000.0000.000
100A125GLN0-0.034-0.01220.055-0.008-0.0080.0000.0000.0000.000
101A126PRO00.0210.02619.715-0.020-0.0200.0000.0000.0000.000
102A127PRO0-0.013-0.01718.0460.0020.0020.0000.0000.0000.000
103A128ILE0-0.0010.00219.9920.0080.0080.0000.0000.0000.000
104A129GLU-1-0.828-0.88521.978-0.166-0.1660.0000.0000.0000.000
105A130ARG10.8290.91623.2890.1070.1070.0000.0000.0000.000
106A131LYS10.9090.93924.6650.1260.1260.0000.0000.0000.000
107A132VAL0-0.047-0.00826.8420.0080.0080.0000.0000.0000.000
108A133ILE0-0.0150.00029.339-0.001-0.0010.0000.0000.0000.000
109A134GLU-1-0.837-0.91933.064-0.074-0.0740.0000.0000.0000.000
110A135LEU00.0520.02836.2980.0010.0010.0000.0000.0000.000
111A136PRO00.009-0.00339.776-0.001-0.0010.0000.0000.0000.000
112A137GLY00.0080.00941.7530.0020.0020.0000.0000.0000.000
113A138ILE0-0.060-0.02436.4680.0000.0000.0000.0000.0000.000
114A139ARG10.8010.88231.4230.0780.0780.0000.0000.0000.000
115A140LYS10.8860.94232.1340.0620.0620.0000.0000.0000.000
116A141VAL00.0450.02126.652-0.004-0.0040.0000.0000.0000.000
117A142GLU-1-0.742-0.85029.774-0.058-0.0580.0000.0000.0000.000
118A143VAL0-0.001-0.01828.353-0.004-0.0040.0000.0000.0000.000
119A144TYR0-0.056-0.04230.365-0.001-0.0010.0000.0000.0000.000
120A145PRO0-0.0130.00731.2160.0030.0030.0000.0000.0000.000
121A146ILE0-0.0200.00834.2470.0030.0030.0000.0000.0000.000
122A147GLU-1-0.806-0.87834.001-0.062-0.0620.0000.0000.0000.000
123A148LEU0-0.0070.00137.9950.0040.0040.0000.0000.0000.000
124A149LEU00.0090.00940.560-0.002-0.0020.0000.0000.0000.000
125A150LEU00.0320.01640.7150.0020.0020.0000.0000.0000.000
126A151VAL00.0090.00943.8810.0000.0000.0000.0000.0000.000
127A152GLN00.0150.00446.7910.0000.0000.0000.0000.0000.000
128A153HIS0-0.005-0.03149.2360.0010.0010.0000.0000.0000.000
129A154SER0-0.049-0.03952.6220.0010.0010.0000.0000.0000.000
130A155ASP-1-0.825-0.88947.830-0.034-0.0340.0000.0000.0000.000
131A156MET0-0.037-0.02049.088-0.001-0.0010.0000.0000.0000.000
132A157GLU-1-0.968-0.96448.747-0.027-0.0270.0000.0000.0000.000
133A158THR0-0.045-0.03343.573-0.001-0.0010.0000.0000.0000.000
134A159ALA0-0.042-0.02344.471-0.001-0.0010.0000.0000.0000.000
135A160LEU0-0.015-0.01039.336-0.002-0.0020.0000.0000.0000.000
136A161THR0-0.016-0.01737.3530.0010.0010.0000.0000.0000.000
137A162ILE0-0.028-0.00635.878-0.003-0.0030.0000.0000.0000.000
138A163GLN0-0.086-0.05130.934-0.003-0.0030.0000.0000.0000.000
139A164PHE00.0320.01534.742-0.002-0.0020.0000.0000.0000.000
140A165SER0-0.057-0.03134.3040.0000.0000.0000.0000.0000.000
141A166TYR00.009-0.02235.9050.0020.0020.0000.0000.0000.000
142A167SER0-0.072-0.05836.2760.0020.0020.0000.0000.0000.000
143A168ASP-1-0.802-0.89036.583-0.068-0.0680.0000.0000.0000.000
144A169SER00.000-0.00739.1940.0030.0030.0000.0000.0000.000
145A170VAL00.0470.01142.328-0.001-0.0010.0000.0000.0000.000
146A171ASP-1-0.868-0.90344.584-0.044-0.0440.0000.0000.0000.000
147A172LEU00.0170.02236.7840.0000.0000.0000.0000.0000.000
148A173VAL00.0200.02840.629-0.001-0.0010.0000.0000.0000.000
149A174LEU0-0.022-0.01341.8890.0010.0010.0000.0000.0000.000
150A175GLN0-0.070-0.05241.614-0.001-0.0010.0000.0000.0000.000
151A176THR00.026-0.00437.202-0.001-0.0010.0000.0000.0000.000
152A177ALA0-0.011-0.00939.8050.0000.0000.0000.0000.0000.000
153A178ARG10.7930.86342.5230.0420.0420.0000.0000.0000.000
154A179GLU-1-0.950-0.96137.219-0.065-0.0650.0000.0000.0000.000
155A180GLN0-0.020-0.01636.275-0.002-0.0020.0000.0000.0000.000
156A181PHE0-0.054-0.02640.0240.0010.0010.0000.0000.0000.000
157A182LEU0-0.071-0.03040.7960.0020.0020.0000.0000.0000.000
158A183VAL0-0.0210.00043.7980.0020.0020.0000.0000.0000.000
159A184GLU-1-0.872-0.91945.980-0.037-0.0370.0000.0000.0000.000
160A185PRO0-0.013-0.01446.2740.0000.0000.0000.0000.0000.000
161A186GLN0-0.057-0.05047.916-0.001-0.0010.0000.0000.0000.000
162A187GLU-1-0.843-0.88950.979-0.032-0.0320.0000.0000.0000.000
163A188ASP-1-0.785-0.87551.417-0.033-0.0330.0000.0000.0000.000
164A189THR00.0190.01149.0170.0000.0000.0000.0000.0000.000
165A190ARG10.7710.88251.0240.0280.0280.0000.0000.0000.000
166A191LEU00.0550.03246.0120.0000.0000.0000.0000.0000.000
167A192TRP0-0.011-0.02850.4380.0020.0020.0000.0000.0000.000
168A193THR0-0.005-0.01248.637-0.001-0.0010.0000.0000.0000.000
169A194LYS10.8930.94750.6790.0280.0280.0000.0000.0000.000
170A195ASN00.0380.03450.7290.0000.0000.0000.0000.0000.000
171A196SER0-0.014-0.06549.6000.0010.0010.0000.0000.0000.000
172A197GLU-1-0.988-0.95052.310-0.021-0.0210.0000.0000.0000.000
173A198GLY0-0.034-0.01655.6050.0010.0010.0000.0000.0000.000
174A199SER0-0.084-0.06756.0230.0010.0010.0000.0000.0000.000
175A200LEU0-0.043-0.02654.645-0.001-0.0010.0000.0000.0000.000
176A201ASP-1-0.801-0.86954.604-0.025-0.0250.0000.0000.0000.000
177A202ARG10.8960.94054.0610.0260.0260.0000.0000.0000.000
178A203LEU00.0170.01648.2310.0010.0010.0000.0000.0000.000
179A204CYS0-0.069-0.04651.744-0.001-0.0010.0000.0000.0000.000
180A205ASN0-0.013-0.00851.393-0.001-0.0010.0000.0000.0000.000
181A206THR00.028-0.01947.6690.0000.0000.0000.0000.0000.000
182A207GLN0-0.037-0.02046.748-0.003-0.0030.0000.0000.0000.000
183A208ILE0-0.0530.00046.731-0.001-0.0010.0000.0000.0000.000
184A209THR0-0.023-0.04642.137-0.001-0.0010.0000.0000.0000.000
185A210LEU00.019-0.00539.9150.0030.0030.0000.0000.0000.000
186A211LEU0-0.031-0.00441.6180.0020.0020.0000.0000.0000.000
187A212ASP-1-0.847-0.89343.826-0.039-0.0390.0000.0000.0000.000
188A213ALA0-0.048-0.02446.2100.0020.0020.0000.0000.0000.000
189A214CYS0-0.102-0.04646.9000.0020.0020.0000.0000.0000.000
190A215LEU0-0.0260.00343.7960.0010.0010.0000.0000.0000.000
191A216GLU-1-0.791-0.88343.867-0.034-0.0340.0000.0000.0000.000
192A217THR0-0.021-0.01938.192-0.002-0.0020.0000.0000.0000.000
193A218GLY00.003-0.00641.1330.0020.0020.0000.0000.0000.000
194A219GLN0-0.045-0.02242.2840.0020.0020.0000.0000.0000.000
195A220LEU00.0090.00844.647-0.002-0.0020.0000.0000.0000.000
196A221VAL0-0.022-0.00645.0710.0010.0010.0000.0000.0000.000
197A222ILE00.0140.01746.934-0.001-0.0010.0000.0000.0000.000
198A223MET00.0140.02046.7970.0000.0000.0000.0000.0000.000
199A224GLU-1-0.707-0.79349.154-0.026-0.0260.0000.0000.0000.000
200A225THR00.0620.01650.987-0.001-0.0010.0000.0000.0000.000
201A226ARG10.7370.85753.3070.0290.0290.0000.0000.0000.000
202A227ASN00.0150.00656.544-0.001-0.0010.0000.0000.0000.000
203A228LYS10.8590.89354.8370.0310.0310.0000.0000.0000.000
204A229ASP-1-0.828-0.87960.236-0.023-0.0230.0000.0000.0000.000
205A230GLY00.0060.00561.4160.0010.0010.0000.0000.0000.000
206A231THR0-0.066-0.04561.6530.0000.0000.0000.0000.0000.000
207A232TRP00.010-0.00554.178-0.001-0.0010.0000.0000.0000.000
208A233PRO00.0520.03756.3550.0010.0010.0000.0000.0000.000
209A234SER0-0.085-0.07457.9640.0010.0010.0000.0000.0000.000
210A235ALA0-0.062-0.03859.8940.0010.0010.0000.0000.0000.000
211A236GLN0-0.056-0.02962.5660.0010.0010.0000.0000.0000.000
212A237LEU0-0.023-0.00265.1620.0010.0010.0000.0000.0000.000