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: 6YZ8Z

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 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 220
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2696323.626535
FMO2-HF: Nuclear repulsion 2609817.073675
FMO2-HF: Total energy -86506.55286
FMO2-MP2: Total energy -86759.902001


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.
-5.09-0.8487.615-4.226-7.63-0.03
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 : -0.063 / q_NPA : -0.039
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].
3A4TRP00.0210.0143.825-1.1130.453-0.014-0.676-0.8760.001
4A5ALA0-0.008-0.0145.8440.4390.4390.0000.0000.0000.000
5A6ALA00.0150.0119.6180.0550.0550.0000.0000.0000.000
6A7TYR0-0.024-0.03012.2640.0100.0100.0000.0000.0000.000
7A8HIS00.004-0.00616.0180.0100.0100.0000.0000.0000.000
8A9GLY00.023-0.00119.273-0.001-0.0010.0000.0000.0000.000
9A10THR0-0.017-0.00622.6940.0130.0130.0000.0000.0000.000
10A11PRO0-0.043-0.02922.732-0.011-0.0110.0000.0000.0000.000
11A12ILE0-0.0240.01818.4350.0110.0110.0000.0000.0000.000
12A13PHE00.000-0.01120.8980.0000.0000.0000.0000.0000.000
13A14LEU00.0200.01115.831-0.015-0.0150.0000.0000.0000.000
14A15GLU-1-0.759-0.86915.988-0.018-0.0180.0000.0000.0000.000
15A16ASP-1-0.882-0.92116.954-0.078-0.0780.0000.0000.0000.000
16A17VAL0-0.111-0.05812.866-0.020-0.0200.0000.0000.0000.000
17A18ILE0-0.041-0.01511.4950.0160.0160.0000.0000.0000.000
18A43GLY00.0380.0237.0350.0720.0720.0000.0000.0000.000
19A44PHE0-0.045-0.0517.374-0.055-0.0550.0000.0000.0000.000
20A45GLY00.0670.0308.6660.0520.0520.0000.0000.0000.000
21A46VAL0-0.048-0.0349.532-0.200-0.2000.0000.0000.0000.000
22A47ALA0-0.0180.00912.0080.0800.0800.0000.0000.0000.000
23A48TRP0-0.003-0.01214.158-0.053-0.0530.0000.0000.0000.000
24A49TYR00.0300.01217.1680.0180.0180.0000.0000.0000.000
25A50ASP-1-0.909-0.96320.523-0.063-0.0630.0000.0000.0000.000
26A51ALA0-0.0020.01523.6930.0000.0000.0000.0000.0000.000
27A52ARG10.8900.95624.6030.0240.0240.0000.0000.0000.000
28A53PRO00.0060.00224.343-0.010-0.0100.0000.0000.0000.000
29A54GLU-1-0.921-0.97122.039-0.050-0.0500.0000.0000.0000.000
30A55PRO0-0.0090.01117.2520.0000.0000.0000.0000.0000.000
31A56GLY0-0.020-0.00219.2770.0250.0250.0000.0000.0000.000
32A57LEU0-0.017-0.02812.679-0.032-0.0320.0000.0000.0000.000
33A58TYR0-0.076-0.05514.1320.0180.0180.0000.0000.0000.000
34A59ARG10.8830.92411.402-0.326-0.3260.0000.0000.0000.000
35A60ASP-1-0.856-0.91611.9890.3030.3030.0000.0000.0000.000
36A61VAL0-0.005-0.00511.4440.0960.0960.0000.0000.0000.000
37A62TYR0-0.046-0.00912.5240.0450.0450.0000.0000.0000.000
38A63PRO0-0.004-0.00710.6290.0380.0380.0000.0000.0000.000
39A64ALA00.0610.03010.186-0.084-0.0840.0000.0000.0000.000
40A65TRP0-0.033-0.0317.287-0.087-0.0870.0000.0000.0000.000
41A66SER0-0.078-0.04813.895-0.054-0.0540.0000.0000.0000.000
42A67ASP-1-0.693-0.81715.4300.1980.1980.0000.0000.0000.000
43A68PRO0-0.025-0.01617.120-0.022-0.0220.0000.0000.0000.000
44A69ASN0-0.014-0.01919.632-0.040-0.0400.0000.0000.0000.000
45A70LEU00.0380.05012.836-0.028-0.0280.0000.0000.0000.000
46A71ARG10.8190.90217.219-0.113-0.1130.0000.0000.0000.000
47A72ALA0-0.007-0.01018.550-0.024-0.0240.0000.0000.0000.000
48A73VAL00.0270.00518.073-0.017-0.0170.0000.0000.0000.000
49A74ALA0-0.004-0.00716.285-0.022-0.0220.0000.0000.0000.000
50A75HIS10.8440.91718.274-0.030-0.0300.0000.0000.0000.000
51A76HIS0-0.049-0.03221.5630.0020.0020.0000.0000.0000.000
52A77VAL0-0.0070.01320.349-0.003-0.0030.0000.0000.0000.000
53A78ARG10.9040.95721.0790.0410.0410.0000.0000.0000.000
54A79SER00.017-0.01919.164-0.005-0.0050.0000.0000.0000.000
55A80GLY00.0260.01920.556-0.010-0.0100.0000.0000.0000.000
56A81LEU0-0.028-0.00616.800-0.020-0.0200.0000.0000.0000.000
57A82PHE0-0.0040.00813.7880.0280.0280.0000.0000.0000.000
58A83LEU0-0.0010.00010.480-0.071-0.0710.0000.0000.0000.000
59A84SER0-0.042-0.0249.3600.1770.1770.0000.0000.0000.000
60A85HIS00.0460.0022.928-3.945-3.3352.137-0.790-1.957-0.007
61A86VAL00.0050.0102.469-1.848-1.9184.191-1.742-2.379-0.014
62A99CYM-1-0.890-0.9387.7101.1061.1060.0000.0000.0000.000
63A100HIS0-0.085-0.0335.278-0.422-0.2970.000-0.022-0.1030.000
64A101PRO00.016-0.0157.846-0.025-0.0250.0000.0000.0000.000
65A102PHE00.002-0.0098.9270.0970.0970.0000.0000.0000.000
66A103ALA00.0330.00312.678-0.075-0.0750.0000.0000.0000.000
67A104ALA0-0.031-0.01216.0930.0360.0360.0000.0000.0000.000
68A105ARG10.7780.86319.4950.0070.0070.0000.0000.0000.000
69A106ARG10.9300.94621.3100.1040.1040.0000.0000.0000.000
70A107TRP00.0040.03617.767-0.031-0.0310.0000.0000.0000.000
71A108CYS0-0.033-0.01313.7180.0150.0150.0000.0000.0000.000
72A109PHE00.0190.00110.730-0.068-0.0680.0000.0000.0000.000
73A110MET0-0.0290.0066.5400.0070.0070.0000.0000.0000.000
74A111HIS00.0000.0026.1740.1070.1070.0000.0000.0000.000
75A112ASN00.0410.0282.563-0.9010.8891.302-0.978-2.113-0.010
76A113GLY00.012-0.0014.550-0.603-0.5080.000-0.010-0.0850.000
77A114GLN0-0.039-0.0176.2720.4900.4900.0000.0000.0000.000
78A115VAL00.0110.0139.359-0.133-0.1330.0000.0000.0000.000
79A116GLY00.0300.03213.1310.0530.0530.0000.0000.0000.000
80A117GLY00.0580.01014.9710.0030.0030.0000.0000.0000.000
81A118PHE00.0120.01314.1050.0090.0090.0000.0000.0000.000
82A119GLU-1-0.930-0.97314.3210.2630.2630.0000.0000.0000.000
83A120ALA0-0.042-0.01017.575-0.006-0.0060.0000.0000.0000.000
84A121PHE0-0.033-0.02417.758-0.014-0.0140.0000.0000.0000.000
85A122ARG10.8870.94716.733-0.202-0.2020.0000.0000.0000.000
86A123LYS10.9660.98119.556-0.069-0.0690.0000.0000.0000.000
87A124GLN00.0310.00222.9520.0040.0040.0000.0000.0000.000
88A125ALA00.0140.01918.653-0.011-0.0110.0000.0000.0000.000
89A126ASP-1-0.736-0.85419.0400.1470.1470.0000.0000.0000.000
90A127MET0-0.083-0.03921.327-0.009-0.0090.0000.0000.0000.000
91A128ALA0-0.020-0.01022.533-0.010-0.0100.0000.0000.0000.000
92A129ILE0-0.079-0.02819.160-0.009-0.0090.0000.0000.0000.000
93A130ALA00.0380.02323.1990.0030.0030.0000.0000.0000.000
94A131ASP-1-0.873-0.94925.5230.0200.0200.0000.0000.0000.000
95A132GLU-1-0.915-0.93127.061-0.015-0.0150.0000.0000.0000.000
96A133PHE00.011-0.01521.7960.0020.0020.0000.0000.0000.000
97A134TYR00.0410.02522.1110.0180.0180.0000.0000.0000.000
98A135THR0-0.017-0.00522.6640.0200.0200.0000.0000.0000.000
99A136TYR0-0.012-0.00719.3500.0050.0050.0000.0000.0000.000
100A137ARG10.7250.85414.384-0.215-0.2150.0000.0000.0000.000
101A138LYS10.8390.90717.203-0.111-0.1110.0000.0000.0000.000
102A139GLY00.0090.01314.9240.0130.0130.0000.0000.0000.000
103A140SER0-0.023-0.02814.410-0.034-0.0340.0000.0000.0000.000
104A141THR00.0300.0159.245-0.083-0.0830.0000.0000.0000.000
105A142ASP-1-0.737-0.8939.7830.4130.4130.0000.0000.0000.000
106A143SER0-0.013-0.0237.9200.0620.0620.0000.0000.0000.000
107A144GLU-1-0.812-0.87210.3070.1330.1330.0000.0000.0000.000
108A145VAL00.0290.00312.995-0.067-0.0670.0000.0000.0000.000
109A146LEU00.0050.00411.766-0.051-0.0510.0000.0000.0000.000
110A147PHE0-0.0200.00913.295-0.046-0.0460.0000.0000.0000.000
111A148LEU00.0380.01715.106-0.019-0.0190.0000.0000.0000.000
112A149LEU0-0.0190.00517.978-0.012-0.0120.0000.0000.0000.000
113A150ALA00.008-0.00617.409-0.011-0.0110.0000.0000.0000.000
114A151LEU0-0.029-0.02218.661-0.006-0.0060.0000.0000.0000.000
115A152SER0-0.038-0.02521.1560.0050.0050.0000.0000.0000.000
116A153GLU-1-0.831-0.88122.311-0.063-0.0630.0000.0000.0000.000
117A154GLY00.0420.03324.165-0.008-0.0080.0000.0000.0000.000
118A155LEU0-0.032-0.02517.823-0.010-0.0100.0000.0000.0000.000
119A156GLU-1-0.915-0.96422.022-0.073-0.0730.0000.0000.0000.000
120A157HIS0-0.0030.00224.1320.0050.0050.0000.0000.0000.000
121A158ASP-1-0.839-0.92124.909-0.129-0.1290.0000.0000.0000.000
122A159PRO00.0470.03620.083-0.004-0.0040.0000.0000.0000.000
123A160HIS0-0.035-0.04020.4050.0030.0030.0000.0000.0000.000
124A161GLY00.0510.01721.426-0.008-0.0080.0000.0000.0000.000
125A162ALA0-0.0080.00721.5240.0040.0040.0000.0000.0000.000
126A163LEU00.0300.00914.7070.0100.0100.0000.0000.0000.000
127A164ALA0-0.0090.00118.622-0.001-0.0010.0000.0000.0000.000
128A165ARG10.7820.87720.7550.1080.1080.0000.0000.0000.000
129A166ALA0-0.0100.00118.2580.0130.0130.0000.0000.0000.000
130A167ILE00.008-0.00714.9800.0180.0180.0000.0000.0000.000
131A168ALA00.0120.01217.8720.0090.0090.0000.0000.0000.000
132A169ARG10.8290.91321.1430.0540.0540.0000.0000.0000.000
133A170LEU00.0290.00815.2980.0130.0130.0000.0000.0000.000
134A171GLU-1-0.760-0.84717.723-0.175-0.1750.0000.0000.0000.000
135A172GLY0-0.0080.00218.7900.0040.0040.0000.0000.0000.000
136A173LEU0-0.055-0.03720.5970.0080.0080.0000.0000.0000.000
137A174SER00.0280.00117.507-0.001-0.0010.0000.0000.0000.000
138A175ARG10.7950.87619.7070.1280.1280.0000.0000.0000.000
139A176ALA0-0.060-0.01522.3890.0030.0030.0000.0000.0000.000
140A177HIS0-0.031-0.02122.7350.0070.0070.0000.0000.0000.000
141A178GLY0-0.0170.01019.3980.0150.0150.0000.0000.0000.000
142A179THR0-0.073-0.04417.9030.0030.0030.0000.0000.0000.000
143A180THR0-0.0110.03217.442-0.001-0.0010.0000.0000.0000.000
144A181PRO00.002-0.01412.3740.0160.0160.0000.0000.0000.000
145A182HIS00.015-0.01114.5130.0080.0080.0000.0000.0000.000
146A183MET0-0.023-0.01113.4980.0300.0300.0000.0000.0000.000
147A184ARG10.7840.8839.0990.4310.4310.0000.0000.0000.000
148A185LEU00.022-0.0089.0750.0520.0520.0000.0000.0000.000
149A186SER00.0320.0367.035-0.097-0.0970.0000.0000.0000.000
150A187ALA00.0100.0007.951-0.071-0.0710.0000.0000.0000.000
151A188ALA00.0310.0189.5770.0220.0220.0000.0000.0000.000
152A189PHE0-0.009-0.02511.0520.0550.0550.0000.0000.0000.000
153A190SER0-0.002-0.01613.7820.0020.0020.0000.0000.0000.000
154A191ASP-1-0.749-0.87117.070-0.141-0.1410.0000.0000.0000.000
155A192GLY00.0290.01419.5050.0250.0250.0000.0000.0000.000
156A193GLN0-0.087-0.03721.1730.0130.0130.0000.0000.0000.000
157A194THR0-0.016-0.00720.900-0.001-0.0010.0000.0000.0000.000
158A195LEU0-0.0170.01613.852-0.007-0.0070.0000.0000.0000.000
159A196TYR00.0080.00516.2400.0210.0210.0000.0000.0000.000
160A197ALA00.0230.00112.805-0.074-0.0740.0000.0000.0000.000
161A198ALA0-0.0130.00912.8380.0950.0950.0000.0000.0000.000
162A199ARG10.7970.86711.2340.6330.6330.0000.0000.0000.000
163A200TYR0-0.042-0.06212.4420.0900.0900.0000.0000.0000.000
164A201SER00.011-0.00912.624-0.052-0.0520.0000.0000.0000.000
165A202SER0-0.0280.01714.4070.0450.0450.0000.0000.0000.000
166A203ASP-1-0.797-0.87814.819-0.326-0.3260.0000.0000.0000.000
167A204HIS00.0140.00316.650-0.025-0.0250.0000.0000.0000.000
168A205ILE0-0.0160.00410.815-0.027-0.0270.0000.0000.0000.000
169A206ALA00.0180.00111.0640.0200.0200.0000.0000.0000.000
170A207PRO0-0.0020.0085.7370.0400.0400.0000.0000.0000.000
171A208SER00.0120.0007.4160.1730.1730.0000.0000.0000.000
172A209VAL0-0.024-0.0188.503-0.328-0.3280.0000.0000.0000.000
173A210TYR0-0.029-0.01710.2380.1620.1620.0000.0000.0000.000
174A211TYR0-0.047-0.05913.492-0.057-0.0570.0000.0000.0000.000
175A212ARG10.8580.92516.2790.2660.2660.0000.0000.0000.000
176A213TYR00.0000.02019.155-0.008-0.0080.0000.0000.0000.000
177A214SER0-0.022-0.03920.7750.0170.0170.0000.0000.0000.000
178A215HIS00.0590.00522.6590.0100.0100.0000.0000.0000.000
179A216ALA0-0.021-0.00824.3850.0100.0100.0000.0000.0000.000
180A217ARG10.8640.93017.7650.1840.1840.0000.0000.0000.000
181A218GLN0-0.036-0.00223.8330.0060.0060.0000.0000.0000.000
182A219GLY00.0470.01721.9870.0060.0060.0000.0000.0000.000
183A220TRP0-0.023-0.00318.945-0.006-0.0060.0000.0000.0000.000
184A221ALA00.0130.01015.271-0.010-0.0100.0000.0000.0000.000
185A222VAL0-0.001-0.00912.2060.0140.0140.0000.0000.0000.000
186A223VAL0-0.004-0.0059.899-0.076-0.0760.0000.0000.0000.000
187A224SER00.0530.0285.144-0.316-0.3160.0000.0000.0000.000
188A225GLU-1-0.862-0.9124.7371.7841.910-0.001-0.008-0.1170.000
189A226PRO00.0250.0198.0980.0300.0300.0000.0000.0000.000
190A227LEU0-0.0250.00210.8460.1060.1060.0000.0000.0000.000
191A228GLU-1-0.967-0.99413.110-0.023-0.0230.0000.0000.0000.000
192A229THR0-0.065-0.01615.3570.0010.0010.0000.0000.0000.000
193A230ASP-1-0.855-0.93318.598-0.093-0.0930.0000.0000.0000.000
194A231GLU-1-0.794-0.84021.500-0.162-0.1620.0000.0000.0000.000
195A232GLY0-0.031-0.02421.7710.0070.0070.0000.0000.0000.000
196A233ASP-1-0.884-0.93119.904-0.175-0.1750.0000.0000.0000.000
197A234TRP0-0.075-0.06415.013-0.052-0.0520.0000.0000.0000.000
198A235THR0-0.0120.00017.5540.0260.0260.0000.0000.0000.000
199A236GLU-1-0.820-0.88014.006-0.577-0.5770.0000.0000.0000.000
200A237LEU0-0.015-0.00214.1030.0500.0500.0000.0000.0000.000
201A238ARG10.9530.99114.9660.2110.2110.0000.0000.0000.000
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