FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2N48R

Calculation Name: 3MDN-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3MDN

Chain ID: A

ChEMBL ID:
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UniProt ID: Q5LRU5

Base Structure: X-ray

Registration Date: 2023-09-22

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 220
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2693501.002456
FMO2-HF: Nuclear repulsion 2606995.371587
FMO2-HF: Total energy -86505.630869
FMO2-MP2: Total energy -86758.922775


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-8.005-6.90214.975-6.185-9.891-0.037
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.037
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].
3A4TRP00.0270.0213.686-1.1970.585-0.013-0.788-0.9810.001
4A5ALA0-0.015-0.0215.7570.4590.4590.0000.0000.0000.000
5A6ALA00.0160.0139.5320.0460.0460.0000.0000.0000.000
6A7TYR0-0.037-0.03712.1580.0050.0050.0000.0000.0000.000
7A8HIS00.004-0.00115.9210.0130.0130.0000.0000.0000.000
8A9GLY00.026-0.00119.1540.0040.0040.0000.0000.0000.000
9A10THR0-0.019-0.00222.5900.0110.0110.0000.0000.0000.000
10A11PRO0-0.035-0.02222.745-0.018-0.0180.0000.0000.0000.000
11A12ILE00.0070.02918.1690.0080.0080.0000.0000.0000.000
12A13PHE0-0.010-0.00920.9550.0100.0100.0000.0000.0000.000
13A14LEU00.0090.00615.927-0.024-0.0240.0000.0000.0000.000
14A15GLU-1-0.787-0.89616.082-0.289-0.2890.0000.0000.0000.000
15A16ASP-1-0.908-0.93716.979-0.257-0.2570.0000.0000.0000.000
16A17VAL0-0.141-0.06512.874-0.005-0.0050.0000.0000.0000.000
17A18ILE0-0.058-0.02611.539-0.071-0.0710.0000.0000.0000.000
18A43GLY0-0.008-0.0117.342-0.001-0.0010.0000.0000.0000.000
19A44PHE00.005-0.0277.358-0.257-0.2570.0000.0000.0000.000
20A45GLY00.0650.0338.9460.1340.1340.0000.0000.0000.000
21A46VAL0-0.043-0.0319.728-0.201-0.2010.0000.0000.0000.000
22A47ALA0-0.0180.00912.1700.0850.0850.0000.0000.0000.000
23A48TRP0-0.006-0.01314.250-0.050-0.0500.0000.0000.0000.000
24A49TYR00.0310.03017.1600.0230.0230.0000.0000.0000.000
25A50ASP-1-0.917-0.96220.553-0.114-0.1140.0000.0000.0000.000
26A51ALA00.0040.00923.7480.0060.0060.0000.0000.0000.000
27A52ARG10.8900.95024.7340.0430.0430.0000.0000.0000.000
28A53PRO00.0010.00124.369-0.008-0.0080.0000.0000.0000.000
29A54GLU-1-0.928-0.97022.003-0.023-0.0230.0000.0000.0000.000
30A55PRO0-0.0110.01417.318-0.008-0.0080.0000.0000.0000.000
31A56GLY0-0.014-0.00319.4080.0220.0220.0000.0000.0000.000
32A57LEU0-0.024-0.03212.818-0.023-0.0230.0000.0000.0000.000
33A58TYR0-0.070-0.05714.3280.0240.0240.0000.0000.0000.000
34A59ARG10.9040.94311.763-0.276-0.2760.0000.0000.0000.000
35A60ASP-1-0.859-0.93112.3070.0580.0580.0000.0000.0000.000
36A61VAL0-0.025-0.00211.7070.0410.0410.0000.0000.0000.000
37A62TYR0-0.031-0.00312.568-0.008-0.0080.0000.0000.0000.000
38A63PRO0-0.0100.00710.629-0.020-0.0200.0000.0000.0000.000
39A64ALA00.0840.02910.088-0.008-0.0080.0000.0000.0000.000
40A65TRP0-0.057-0.0377.3990.0420.0420.0000.0000.0000.000
41A66SER0-0.054-0.04513.9210.0160.0160.0000.0000.0000.000
42A67ASP-1-0.734-0.81615.395-0.047-0.0470.0000.0000.0000.000
43A68PRO0-0.027-0.02617.123-0.025-0.0250.0000.0000.0000.000
44A69ASN00.0190.00319.771-0.010-0.0100.0000.0000.0000.000
45A70LEU00.0310.03713.207-0.011-0.0110.0000.0000.0000.000
46A71ARG10.9290.97017.2650.2130.2130.0000.0000.0000.000
47A72ALA0-0.012-0.01218.559-0.007-0.0070.0000.0000.0000.000
48A73VAL00.0330.00618.1870.0020.0020.0000.0000.0000.000
49A74ALA0-0.009-0.01116.468-0.002-0.0020.0000.0000.0000.000
50A75HIS10.8190.89818.4690.1630.1630.0000.0000.0000.000
51A76HIS0-0.058-0.03021.6120.0110.0110.0000.0000.0000.000
52A77VAL0-0.0120.01020.5440.0140.0140.0000.0000.0000.000
53A78ARG10.9150.95621.2040.1040.1040.0000.0000.0000.000
54A79SER00.002-0.02119.2520.0060.0060.0000.0000.0000.000
55A80GLY00.0310.02220.564-0.018-0.0180.0000.0000.0000.000
56A81LEU0-0.0250.00116.730-0.006-0.0060.0000.0000.0000.000
57A82PHE00.0000.00613.8100.0230.0230.0000.0000.0000.000
58A83LEU0-0.004-0.00510.400-0.046-0.0460.0000.0000.0000.000
59A84SER0-0.032-0.0189.4440.1190.1190.0000.0000.0000.000
60A85HIS00.0530.0072.187-1.735-4.4237.143-1.595-2.859-0.004
61A86VAL0-0.0010.0082.449-2.783-2.1143.298-1.755-2.212-0.013
62A99CYM-1-0.899-0.9457.8570.8110.8110.0000.0000.0000.000
63A100HIS0-0.105-0.0216.040-0.294-0.2940.0000.0000.0000.000
64A101PRO00.028-0.0127.993-0.084-0.0840.0000.0000.0000.000
65A102PHE0-0.001-0.0188.9410.0540.0540.0000.0000.0000.000
66A103ALA00.0350.00312.737-0.060-0.0600.0000.0000.0000.000
67A104ALA0-0.025-0.00516.1340.0260.0260.0000.0000.0000.000
68A105ARG10.8050.90719.514-0.052-0.0520.0000.0000.0000.000
69A106ARG11.0010.99121.3240.0280.0280.0000.0000.0000.000
70A107TRP00.0430.04717.519-0.019-0.0190.0000.0000.0000.000
71A108CYS0-0.031-0.01313.6060.0020.0020.0000.0000.0000.000
72A109PHE00.011-0.00310.390-0.037-0.0370.0000.0000.0000.000
73A110MET0-0.0080.0056.412-0.036-0.0360.0000.0000.0000.000
74A111HIS00.0060.0185.9770.1000.1000.0000.0000.0000.000
75A112ASN00.0760.0462.295-1.199-0.1234.547-2.040-3.582-0.021
76A113GLY0-0.006-0.0114.599-0.804-0.7260.0010.018-0.0970.000
77A114GLN0-0.023-0.0146.3180.2600.2600.0000.0000.0000.000
78A115VAL00.0100.0129.431-0.129-0.1290.0000.0000.0000.000
79A116GLY00.0350.03213.2090.0170.0170.0000.0000.0000.000
80A117GLY00.0610.00514.973-0.037-0.0370.0000.0000.0000.000
81A118PHE00.0370.01914.169-0.028-0.0280.0000.0000.0000.000
82A119GLU-1-0.942-0.98114.0520.3720.3720.0000.0000.0000.000
83A120ALA0-0.043-0.01317.550-0.027-0.0270.0000.0000.0000.000
84A121PHE0-0.027-0.01417.569-0.022-0.0220.0000.0000.0000.000
85A122ARG10.9470.98716.815-0.282-0.2820.0000.0000.0000.000
86A123LYS10.9590.98019.499-0.134-0.1340.0000.0000.0000.000
87A124GLN00.029-0.00322.900-0.002-0.0020.0000.0000.0000.000
88A125ALA00.0140.02118.591-0.009-0.0090.0000.0000.0000.000
89A126ASP-1-0.785-0.90219.0210.2460.2460.0000.0000.0000.000
90A127MET0-0.092-0.05021.248-0.018-0.0180.0000.0000.0000.000
91A128ALA0-0.025-0.01422.378-0.013-0.0130.0000.0000.0000.000
92A129ILE0-0.075-0.02319.086-0.005-0.0050.0000.0000.0000.000
93A130ALA00.0300.02123.076-0.008-0.0080.0000.0000.0000.000
94A131ASP-1-0.871-0.95125.4200.0850.0850.0000.0000.0000.000
95A132GLU-1-0.936-0.95626.9340.0520.0520.0000.0000.0000.000
96A133PHE00.005-0.01521.732-0.001-0.0010.0000.0000.0000.000
97A134TYR00.0420.02222.0880.0180.0180.0000.0000.0000.000
98A135THR0-0.020-0.01322.6380.0090.0090.0000.0000.0000.000
99A136TYR0-0.041-0.02819.319-0.007-0.0070.0000.0000.0000.000
100A137ARG10.7530.89414.392-0.323-0.3230.0000.0000.0000.000
101A138LYS10.8630.92417.320-0.141-0.1410.0000.0000.0000.000
102A139GLY0-0.0070.00415.000-0.006-0.0060.0000.0000.0000.000
103A140SER0-0.049-0.03814.499-0.012-0.0120.0000.0000.0000.000
104A141THR00.0420.0309.366-0.056-0.0560.0000.0000.0000.000
105A142ASP-1-0.750-0.8949.6890.8530.8530.0000.0000.0000.000
106A143SER0-0.030-0.0597.8270.0300.0300.0000.0000.0000.000
107A144GLU-1-0.817-0.88710.1720.1860.1860.0000.0000.0000.000
108A145VAL00.0220.00112.914-0.078-0.0780.0000.0000.0000.000
109A146LEU00.0150.00211.587-0.058-0.0580.0000.0000.0000.000
110A147PHE0-0.0200.01113.217-0.058-0.0580.0000.0000.0000.000
111A148LEU00.0350.01514.991-0.036-0.0360.0000.0000.0000.000
112A149LEU0-0.025-0.00217.865-0.026-0.0260.0000.0000.0000.000
113A150ALA00.014-0.00317.223-0.020-0.0200.0000.0000.0000.000
114A151LEU0-0.030-0.02418.957-0.018-0.0180.0000.0000.0000.000
115A152SER0-0.025-0.01521.029-0.012-0.0120.0000.0000.0000.000
116A153GLU-1-0.922-0.94722.2160.0810.0810.0000.0000.0000.000
117A154GLY00.0430.02924.021-0.008-0.0080.0000.0000.0000.000
118A155LEU0-0.025-0.01917.616-0.009-0.0090.0000.0000.0000.000
119A156GLU-1-0.952-0.98421.8410.0160.0160.0000.0000.0000.000
120A157HIS0-0.022-0.01023.983-0.004-0.0040.0000.0000.0000.000
121A158ASP-1-0.892-0.95424.7240.0170.0170.0000.0000.0000.000
122A159PRO00.0490.02919.9230.0100.0100.0000.0000.0000.000
123A160HIS0-0.061-0.05520.1510.0120.0120.0000.0000.0000.000
124A161GLY00.0600.02321.1370.0120.0120.0000.0000.0000.000
125A162ALA0-0.0100.01121.2350.0120.0120.0000.0000.0000.000
126A163LEU00.0220.00614.4160.0200.0200.0000.0000.0000.000
127A164ALA0-0.0080.00318.3520.0250.0250.0000.0000.0000.000
128A165ARG10.8550.91820.579-0.042-0.0420.0000.0000.0000.000
129A166ALA00.0000.01117.9980.0120.0120.0000.0000.0000.000
130A167ILE00.009-0.00815.0640.0260.0260.0000.0000.0000.000
131A168ALA00.0080.01217.9160.0160.0160.0000.0000.0000.000
132A169ARG10.9130.97321.222-0.118-0.1180.0000.0000.0000.000
133A170LEU00.0250.00915.1450.0040.0040.0000.0000.0000.000
134A171GLU-1-0.774-0.85417.7840.1790.1790.0000.0000.0000.000
135A172GLY0-0.015-0.00318.857-0.006-0.0060.0000.0000.0000.000
136A173LEU0-0.036-0.03320.507-0.007-0.0070.0000.0000.0000.000
137A174SER00.0100.00917.522-0.010-0.0100.0000.0000.0000.000
138A175ARG10.7990.87819.772-0.159-0.1590.0000.0000.0000.000
139A176ALA0-0.063-0.01522.430-0.009-0.0090.0000.0000.0000.000
140A177HIS0-0.020-0.01922.720-0.009-0.0090.0000.0000.0000.000
141A178GLY0-0.0170.00819.3980.0080.0080.0000.0000.0000.000
142A179THR0-0.056-0.03117.683-0.018-0.0180.0000.0000.0000.000
143A180THR0-0.0270.02217.4220.0120.0120.0000.0000.0000.000
144A181PRO0-0.009-0.01912.276-0.006-0.0060.0000.0000.0000.000
145A182HIS00.026-0.01114.5220.0160.0160.0000.0000.0000.000
146A183MET0-0.021-0.01013.5210.0430.0430.0000.0000.0000.000
147A184ARG10.7900.8969.047-0.413-0.4130.0000.0000.0000.000
148A185LEU00.016-0.0079.1420.1220.1220.0000.0000.0000.000
149A186SER00.0230.0276.862-0.101-0.1010.0000.0000.0000.000
150A187ALA00.0220.0047.6260.0310.0310.0000.0000.0000.000
151A188ALA00.0320.0259.376-0.021-0.0210.0000.0000.0000.000
152A189PHE0-0.021-0.03110.8780.0420.0420.0000.0000.0000.000
153A190SER00.000-0.00713.615-0.012-0.0120.0000.0000.0000.000
154A191ASP-1-0.806-0.90916.937-0.049-0.0490.0000.0000.0000.000
155A192GLY00.005-0.01719.4120.0110.0110.0000.0000.0000.000
156A193GLN0-0.081-0.03621.103-0.005-0.0050.0000.0000.0000.000
157A194THR0-0.016-0.00720.286-0.007-0.0070.0000.0000.0000.000
158A195LEU0-0.0180.01213.631-0.004-0.0040.0000.0000.0000.000
159A196TYR00.0070.00516.0360.0170.0170.0000.0000.0000.000
160A197ALA00.0220.00012.526-0.051-0.0510.0000.0000.0000.000
161A198ALA0-0.0170.00712.5130.0430.0430.0000.0000.0000.000
162A199ARG10.8030.86711.278-0.092-0.0920.0000.0000.0000.000
163A200TYR0-0.029-0.05012.440-0.012-0.0120.0000.0000.0000.000
164A201SER0-0.007-0.01512.6170.0500.0500.0000.0000.0000.000
165A202SER0-0.0130.02314.381-0.022-0.0220.0000.0000.0000.000
166A203ASP-1-0.799-0.88514.6450.2460.2460.0000.0000.0000.000
167A204HIS00.0220.00316.574-0.003-0.0030.0000.0000.0000.000
168A205ILE0-0.025-0.00310.737-0.004-0.0040.0000.0000.0000.000
169A206ALA00.011-0.00510.9850.0220.0220.0000.0000.0000.000
170A207PRO0-0.0070.0075.690-0.001-0.0010.0000.0000.0000.000
171A208SER0-0.010-0.0147.737-0.059-0.0590.0000.0000.0000.000
172A209VAL0-0.009-0.0068.424-0.152-0.1520.0000.0000.0000.000
173A210TYR00.0020.01410.6950.1040.1040.0000.0000.0000.000
174A211TYR0-0.061-0.06913.558-0.083-0.0830.0000.0000.0000.000
175A212ARG10.9340.99116.1920.2780.2780.0000.0000.0000.000
176A213TYR0-0.0070.01119.163-0.021-0.0210.0000.0000.0000.000
177A214SER0-0.0030.00420.8340.0080.0080.0000.0000.0000.000
178A215HIS00.0640.00622.5230.0080.0080.0000.0000.0000.000
179A216ALA0-0.0020.00324.0520.0100.0100.0000.0000.0000.000
180A217ARG10.9290.97216.5970.3380.3380.0000.0000.0000.000
181A218GLN0-0.042-0.00723.7740.0120.0120.0000.0000.0000.000
182A219GLY00.0430.01221.8750.0090.0090.0000.0000.0000.000
183A220TRP0-0.0210.00118.770-0.007-0.0070.0000.0000.0000.000
184A221ALA00.0000.00115.069-0.020-0.0200.0000.0000.0000.000
185A222VAL00.009-0.00311.7160.0440.0440.0000.0000.0000.000
186A223VAL0-0.007-0.0069.702-0.113-0.1130.0000.0000.0000.000
187A224SER00.0460.0345.547-0.392-0.3920.0000.0000.0000.000
188A225GLU-1-0.925-0.9704.310-0.0430.143-0.001-0.025-0.1600.000
189A226PRO00.0390.0238.153-0.160-0.1600.0000.0000.0000.000
190A227LEU0-0.042-0.00710.298-0.010-0.0100.0000.0000.0000.000
191A228GLU-1-0.969-1.00512.512-0.201-0.2010.0000.0000.0000.000
192A229THR0-0.049-0.00514.816-0.003-0.0030.0000.0000.0000.000
193A230ASP-1-0.864-0.93118.105-0.198-0.1980.0000.0000.0000.000
194A231GLU-1-0.929-0.97121.200-0.197-0.1970.0000.0000.0000.000
195A232GLY0-0.047-0.03121.4850.0180.0180.0000.0000.0000.000
196A233ASP-1-0.870-0.92519.888-0.145-0.1450.0000.0000.0000.000
197A234TRP0-0.083-0.06714.950-0.030-0.0300.0000.0000.0000.000
198A235THR0-0.008-0.00517.7610.0320.0320.0000.0000.0000.000
199A236GLU-1-0.852-0.90314.829-0.029-0.0290.0000.0000.0000.000
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