Manual

About

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: QV8LY

Calculation Name: 3M65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M65

Chain ID: A

ChEMBL ID:

UniProt ID: P37945

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130550.663197
FMO2-HF: Nuclear repulsion 2047534.524765
FMO2-HF: Total energy -83016.138432
FMO2-MP2: Total energy -83257.976204


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
10.71120.9145.52-6.548-9.1740.06
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.896 / q_NPA : -0.959
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].
3A6LYS10.8590.9442.178-94.693-88.5083.359-4.639-4.9050.051
4A7ARG10.9340.9565.469-28.211-28.2110.0000.0000.0000.000
5A8SER0-0.053-0.0309.050-0.279-0.2790.0000.0000.0000.000
6A9ILE0-0.028-0.0018.3510.1610.1610.0000.0000.0000.000
7A10PRO00.0230.02111.832-0.948-0.9480.0000.0000.0000.000
8A11LEU00.0220.00514.9180.9960.9960.0000.0000.0000.000
9A12LEU0-0.035-0.02116.593-1.006-1.0060.0000.0000.0000.000
10A13PRO00.0270.02018.8820.4170.4170.0000.0000.0000.000
11A14LEU0-0.036-0.01719.358-0.584-0.5840.0000.0000.0000.000
12A15ARG10.9310.96622.672-11.004-11.0040.0000.0000.0000.000
13A16GLY00.0080.01026.155-0.162-0.1620.0000.0000.0000.000
14A17LEU00.0350.01922.551-0.124-0.1240.0000.0000.0000.000
15A18LEU00.0270.01918.3770.3930.3930.0000.0000.0000.000
16A19VAL00.0030.00617.039-0.257-0.2570.0000.0000.0000.000
17A20TYR00.019-0.01316.4400.8480.8480.0000.0000.0000.000
18A21PRO0-0.014-0.01612.463-0.301-0.3010.0000.0000.0000.000
19A22THR0-0.050-0.03614.529-1.528-1.5280.0000.0000.0000.000
20A23MET00.0240.05716.406-0.944-0.9440.0000.0000.0000.000
21A24VAL0-0.007-0.01218.4070.8340.8340.0000.0000.0000.000
22A25LEU00.0170.01720.682-0.717-0.7170.0000.0000.0000.000
23A26HIS0-0.014-0.02022.5780.3960.3960.0000.0000.0000.000
24A27LEU00.0040.00721.351-0.053-0.0530.0000.0000.0000.000
25A28ASP-1-0.896-0.95425.50010.61410.6140.0000.0000.0000.000
26A29VAL0-0.046-0.02923.470-0.012-0.0120.0000.0000.0000.000
27A30GLY00.0380.00626.868-0.217-0.2170.0000.0000.0000.000
28A31ARG10.8840.95024.386-12.285-12.2850.0000.0000.0000.000
29A32ASP-1-0.809-0.89626.88510.56410.5640.0000.0000.0000.000
30A33LYS10.9680.98924.045-11.834-11.8340.0000.0000.0000.000
31A34SER0-0.076-0.03422.4500.5110.5110.0000.0000.0000.000
32A35VAL00.010-0.00822.4890.6350.6350.0000.0000.0000.000
33A36GLN00.0490.03623.4600.3800.3800.0000.0000.0000.000
34A37ALA00.0120.02418.5490.5210.5210.0000.0000.0000.000
35A38LEU0-0.028-0.02618.8440.8880.8880.0000.0000.0000.000
36A39GLU-1-0.902-0.97419.97512.50612.5060.0000.0000.0000.000
37A40GLN00.0370.02117.817-0.555-0.5550.0000.0000.0000.000
38A41ALA00.0340.02115.7640.6840.6840.0000.0000.0000.000
39A42MET0-0.096-0.06616.7241.0391.0390.0000.0000.0000.000
40A43MET0-0.063-0.00319.232-0.548-0.5480.0000.0000.0000.000
41A44HIS0-0.056-0.03514.7170.1400.1400.0000.0000.0000.000
42A45ASP-1-0.872-0.93710.15927.21527.2150.0000.0000.0000.000
43A46HIS10.7820.88612.953-17.679-17.6790.0000.0000.0000.000
44A47MET0-0.037-0.0019.310-0.246-0.2460.0000.0000.0000.000
45A48ILE00.0440.01812.482-1.045-1.0450.0000.0000.0000.000
46A49PHE0-0.018-0.00410.7781.9101.9100.0000.0000.0000.000
47A50LEU00.0180.01013.200-1.490-1.4900.0000.0000.0000.000
48A51ALA00.0340.01915.5090.8550.8550.0000.0000.0000.000
49A52THR0-0.042-0.02017.383-0.404-0.4040.0000.0000.0000.000
50A53GLN00.0390.01320.7720.3510.3510.0000.0000.0000.000
51A54GLN0-0.054-0.03821.4900.3660.3660.0000.0000.0000.000
52A55ASP-1-0.829-0.92424.85410.65310.6530.0000.0000.0000.000
53A56ILE0-0.073-0.05228.2280.0950.0950.0000.0000.0000.000
54A57SER0-0.051-0.04029.4780.0360.0360.0000.0000.0000.000
55A58ILE00.0170.04428.429-0.302-0.3020.0000.0000.0000.000
56A59ASP-1-0.909-0.96829.1839.9919.9910.0000.0000.0000.000
57A60GLU-1-1.003-1.01627.22610.63610.6360.0000.0000.0000.000
58A61PRO0-0.082-0.02723.824-0.115-0.1150.0000.0000.0000.000
59A62GLY00.0690.04023.8850.3420.3420.0000.0000.0000.000
60A63GLU-1-0.963-1.00516.54416.23616.2360.0000.0000.0000.000
61A64ASP-1-0.937-0.96420.39912.28312.2830.0000.0000.0000.000
62A65GLU-1-0.853-0.92722.77211.02111.0210.0000.0000.0000.000
63A66ILE0-0.101-0.03518.5150.0200.0200.0000.0000.0000.000
64A67PHE00.0200.01517.4890.0340.0340.0000.0000.0000.000
65A68THR00.0570.02113.7000.6170.6170.0000.0000.0000.000
66A69VAL0-0.027-0.01011.7581.5921.5920.0000.0000.0000.000
67A70GLY00.0150.00412.233-1.459-1.4590.0000.0000.0000.000
68A71THR0-0.045-0.03711.8011.9931.9930.0000.0000.0000.000
69A72TYR00.0020.0176.1092.0712.0710.0000.0000.0000.000
70A73THR00.025-0.02110.273-0.094-0.0940.0000.0000.0000.000
71A74LYS10.9400.97612.397-22.907-22.9070.0000.0000.0000.000
72A75ILE00.0040.01013.863-1.294-1.2940.0000.0000.0000.000
73A76LYS10.8510.91916.559-18.189-18.1890.0000.0000.0000.000
74A77GLN0-0.002-0.00119.083-0.307-0.3070.0000.0000.0000.000
75A78MET00.0190.02022.1970.2640.2640.0000.0000.0000.000
76A79LEU0-0.043-0.00924.038-0.265-0.2650.0000.0000.0000.000
77A80LYS10.9250.98727.784-10.727-10.7270.0000.0000.0000.000
78A81LEU00.004-0.00329.764-0.314-0.3140.0000.0000.0000.000
79A82PRO0-0.014-0.02132.818-0.031-0.0310.0000.0000.0000.000
80A83ASN00.026-0.00234.3520.1520.1520.0000.0000.0000.000
81A84GLY00.0410.03032.930-0.068-0.0680.0000.0000.0000.000
82A85THR00.0000.01530.1240.3390.3390.0000.0000.0000.000
83A86ILE0-0.040-0.01924.913-0.035-0.0350.0000.0000.0000.000
84A87ARG10.9771.00427.307-10.988-10.9880.0000.0000.0000.000
85A88VAL0-0.031-0.02520.8120.0830.0830.0000.0000.0000.000
86A89LEU0-0.0160.00521.468-0.205-0.2050.0000.0000.0000.000
87A90VAL0-0.003-0.01417.6200.6940.6940.0000.0000.0000.000
88A91GLU-1-0.870-0.95415.18520.01520.0150.0000.0000.0000.000
89A92GLY00.0240.02614.3551.5231.5230.0000.0000.0000.000
90A93LEU0-0.068-0.0239.4430.5940.5940.0000.0000.0000.000
91A94LYS10.9980.9915.100-50.150-50.058-0.0010.000-0.0900.000
92A95ARG11.0181.0169.374-22.605-22.6050.0000.0000.0000.000
93A96ALA0-0.025-0.0157.2163.9733.9730.0000.0000.0000.000
94A97HIS00.009-0.0026.610-3.527-3.5270.0000.0000.0000.000
95A98ILE00.0150.0078.7021.9961.9960.0000.0000.0000.000
96A99VAL0-0.045-0.0208.097-0.622-0.6220.0000.0000.0000.000
97A100LYS10.8450.90410.718-19.008-19.0080.0000.0000.0000.000
98A101TYR00.0690.05213.5251.1381.1380.0000.0000.0000.000
99A102ASN0-0.028-0.00714.121-1.331-1.3310.0000.0000.0000.000
100A103GLU-1-0.865-0.94217.88812.74312.7430.0000.0000.0000.000
101A104HIS0-0.076-0.03518.6360.3310.3310.0000.0000.0000.000
102A105GLU-1-0.955-0.98622.55110.42310.4230.0000.0000.0000.000
103A106ASP-1-0.811-0.90524.42711.42811.4280.0000.0000.0000.000
104A107TYR0-0.086-0.07117.7100.5440.5440.0000.0000.0000.000
105A108THR00.0100.01418.022-0.268-0.2680.0000.0000.0000.000
106A109SER0-0.0150.00114.8981.0331.0330.0000.0000.0000.000
107A110VAL00.0130.00411.600-0.552-0.5520.0000.0000.0000.000
108A111ASP-1-0.849-0.9099.65025.38725.3870.0000.0000.0000.000
109A112ILE00.0220.0066.209-0.780-0.7800.0000.0000.0000.000
110A113GLN0-0.016-0.0163.5040.0610.6540.006-0.228-0.3710.001
111A114LEU0-0.046-0.0342.277-5.526-2.7702.152-1.435-3.4730.010
112A115ILE0-0.034-0.0133.637-1.714-1.1370.004-0.246-0.335-0.002
113A116HIS0-0.099-0.0446.3581.8151.8150.0000.0000.0000.000
114A117GLU-1-0.901-0.9018.04024.76424.7640.0000.0000.0000.000
115A118ASP-1-0.901-1.03010.96525.15225.1520.0000.0000.0000.000
116A119ASP-1-1.035-0.98513.35817.49817.4980.0000.0000.0000.000
117A120SER00.0360.01316.347-0.920-0.9200.0000.0000.0000.000
118A121LYS10.8050.91217.328-13.100-13.1000.0000.0000.0000.000
119A122ASP-1-0.886-0.93019.84513.90813.9080.0000.0000.0000.000
120A123THR0-0.039-0.03722.896-0.125-0.1250.0000.0000.0000.000
121A124GLU-1-0.930-0.97225.20811.43611.4360.0000.0000.0000.000
122A125ASP-1-0.718-0.85720.48714.55714.5570.0000.0000.0000.000
123A126GLU-1-0.933-0.98023.98911.70511.7050.0000.0000.0000.000
124A127ALA0-0.083-0.04626.466-0.407-0.4070.0000.0000.0000.000
125A128LEU00.0700.02724.835-0.356-0.3560.0000.0000.0000.000
126A129MET0-0.0080.00323.603-0.016-0.0160.0000.0000.0000.000
127A130ARG10.8990.96126.879-10.144-10.1440.0000.0000.0000.000
128A131THR0-0.005-0.00230.206-0.391-0.3910.0000.0000.0000.000
129A132LEU0-0.010-0.00325.212-0.248-0.2480.0000.0000.0000.000
130A133LEU0-0.015-0.01728.400-0.214-0.2140.0000.0000.0000.000
131A134ASP-1-0.894-0.93331.0018.3848.3840.0000.0000.0000.000
132A135HIS0-0.021-0.01832.404-0.224-0.2240.0000.0000.0000.000
133A136PHE00.0170.01330.823-0.193-0.1930.0000.0000.0000.000
134A137ASP-1-0.869-0.93932.9628.3718.3710.0000.0000.0000.000
135A138GLN0-0.066-0.04435.829-0.341-0.3410.0000.0000.0000.000
136A139TYR00.0100.00933.826-0.201-0.2010.0000.0000.0000.000
137A140ILE00.0260.01633.395-0.226-0.2260.0000.0000.0000.000
138A141LYS10.8540.92437.526-8.031-8.0310.0000.0000.0000.000
139A142ILE0-0.009-0.01040.294-0.259-0.2590.0000.0000.0000.000
140A143SER00.0290.02038.589-0.174-0.1740.0000.0000.0000.000
141A144LYS10.9330.97541.237-7.620-7.6200.0000.0000.0000.000
142A145LYS10.8660.92543.143-6.836-6.8360.0000.0000.0000.000
143A146ILE00.0510.02443.344-0.168-0.1680.0000.0000.0000.000
144A147SER0-0.022-0.00643.979-0.165-0.1650.0000.0000.0000.000
145A148ALA00.0030.00146.094-0.122-0.1220.0000.0000.0000.000
146A149GLU-1-0.891-0.95048.8206.3246.3240.0000.0000.0000.000
147A150THR0-0.0200.00048.486-0.130-0.1300.0000.0000.0000.000
148A151TYR0-0.018-0.01549.833-0.108-0.1080.0000.0000.0000.000
149A152ALA0-0.012-0.01151.514-0.109-0.1090.0000.0000.0000.000
150A153ALA00.0020.00953.944-0.117-0.1170.0000.0000.0000.000
151A154VAL0-0.012-0.02952.503-0.102-0.1020.0000.0000.0000.000
152A155THR0-0.059-0.02755.196-0.064-0.0640.0000.0000.0000.000
153A156ASP-1-0.946-0.94857.2355.2985.2980.0000.0000.0000.000
154A157ILE0-0.122-0.05256.604-0.075-0.0750.0000.0000.0000.000
155A158GLU-1-0.896-0.94960.4985.0395.0390.0000.0000.0000.000
156A159GLU-1-0.921-0.96262.4965.0795.0790.0000.0000.0000.000
157A160PRO00.0310.01160.2940.0990.0990.0000.0000.0000.000
158A161GLY00.034-0.01458.7340.1030.1030.0000.0000.0000.000
159A162ARG10.9360.97557.964-5.272-5.2720.0000.0000.0000.000
160A163MET00.0250.01455.6500.1140.1140.0000.0000.0000.000
161A164ALA0-0.015-0.01354.2550.1330.1330.0000.0000.0000.000
162A165ASP-1-0.853-0.92752.9655.8645.8640.0000.0000.0000.000
163A166ILE0-0.043-0.01952.2430.1360.1360.0000.0000.0000.000
164A167VAL00.0350.01949.6030.1360.1360.0000.0000.0000.000
165A168ALA00.0280.01648.5330.1800.1800.0000.0000.0000.000
166A169SER0-0.140-0.07847.4400.1550.1550.0000.0000.0000.000
167A170HIS00.007-0.00946.5030.1810.1810.0000.0000.0000.000
168A171LEU0-0.0090.01744.1420.1810.1810.0000.0000.0000.000
169A172PRO0-0.036-0.01138.951-0.072-0.0720.0000.0000.0000.000
170A173LEU00.0230.02640.1520.1210.1210.0000.0000.0000.000
171A174LYS10.9680.96337.547-8.222-8.2220.0000.0000.0000.000
172A175LEU00.0800.01941.272-0.149-0.1490.0000.0000.0000.000
173A176LYS10.9270.96940.730-7.795-7.7950.0000.0000.0000.000
174A177ASP-1-0.853-0.91942.8847.2817.2810.0000.0000.0000.000
175A178LYS10.8960.95844.231-7.225-7.2250.0000.0000.0000.000
176A179GLN0-0.075-0.03447.688-0.096-0.0960.0000.0000.0000.000
177A180ASP-1-0.823-0.91148.7596.2246.2240.0000.0000.0000.000
178A181ILE0-0.044-0.01849.612-0.154-0.1540.0000.0000.0000.000
179A182LEU0-0.022-0.00952.076-0.144-0.1440.0000.0000.0000.000
180A183GLU-1-0.927-0.96452.5285.9395.9390.0000.0000.0000.000
181A184THR0-0.045-0.00154.017-0.062-0.0620.0000.0000.0000.000
182A185ALA00.008-0.00756.509-0.031-0.0310.0000.0000.0000.000
183A186ASP-1-0.891-0.94560.0625.1595.1590.0000.0000.0000.000
184A187VAL00.0540.01059.2640.0890.0890.0000.0000.0000.000
185A188LYS10.9490.97258.919-5.194-5.1940.0000.0000.0000.000
186A189ASP-1-0.895-0.93756.9835.5845.5840.0000.0000.0000.000
187A190ARG10.8020.92654.814-5.483-5.4830.0000.0000.0000.000
188A191LEU0-0.016-0.02153.9840.1150.1150.0000.0000.0000.000
189A192ASN0-0.053-0.02853.7360.1480.1480.0000.0000.0000.000
190A193LYS10.9000.96050.727-6.011-6.0110.0000.0000.0000.000
191A194VAL0-0.0050.00149.4700.1640.1640.0000.0000.0000.000
192A195ILE0-0.012-0.00848.9000.1420.1420.0000.0000.0000.000
193A196ASP-1-0.900-0.95748.0956.5926.5920.0000.0000.0000.000
194A197PHE0-0.040-0.03044.8280.1860.1860.0000.0000.0000.000
195A198ILE0-0.009-0.00144.1660.1940.1940.0000.0000.0000.000
196A199ASN0-0.039-0.02844.0580.2490.2490.0000.0000.0000.000
197A200ASN00.0460.03741.2490.1390.1390.0000.0000.0000.000
198A201GLU-1-0.928-0.97139.8098.2658.2650.0000.0000.0000.000
199A202LYS10.8540.93939.391-7.079-7.0790.0000.0000.0000.000
200A203GLU-1-0.883-0.96339.4698.0398.0390.0000.0000.0000.000
201A204VAL0-0.032-0.01834.5940.2630.2630.0000.0000.0000.000
202A205LEU00.005-0.00134.7040.2960.2960.0000.0000.0000.000
203A206GLU-1-1.029-1.01134.7038.4038.4030.0000.0000.0000.000
204A207ILE0-0.030-0.00831.8560.2330.2330.0000.0000.0000.000
205A208GLU-1-1.026-0.98330.33910.52410.5240.0000.0000.0000.000
206A209LYS10.8750.93130.335-9.131-9.1310.0000.0000.0000.000