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: Z62GN

Calculation Name: 1DT9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DT9

Chain ID: A

ChEMBL ID:

UniProt ID: P62495

Base Structure: X-ray

Registration Date: 2023-06-21

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 398
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5947857.638142
FMO2-HF: Nuclear repulsion 5792698.001568
FMO2-HF: Total energy -155159.636573
FMO2-MP2: Total energy -155616.104748


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:5:PRO)


Summations of interaction energy for fragment #1(A:5:PRO)
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.
-1.5650.691-0.018-1.306-0.932-0.002
Interaction energy analysis for fragmet #1(A:5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.014
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].
3A7ALA00.0070.0133.932-0.8531.403-0.018-1.306-0.932-0.002
4A8ALA00.0920.0616.853-0.300-0.3000.0000.0000.0000.000
5A9ASP-1-0.806-0.8546.406-0.569-0.5690.0000.0000.0000.000
6A10ARG10.8350.8985.449-0.793-0.7930.0000.0000.0000.000
7A11ASN0-0.011-0.0257.1800.0260.0260.0000.0000.0000.000
8A12VAL00.0720.06710.4610.0320.0320.0000.0000.0000.000
9A13GLU-1-0.828-0.9238.8880.5420.5420.0000.0000.0000.000
10A14ILE0-0.020-0.00510.576-0.017-0.0170.0000.0000.0000.000
11A15TRP00.0820.03013.162-0.017-0.0170.0000.0000.0000.000
12A16LYS10.9170.95312.421-0.308-0.3080.0000.0000.0000.000
13A17ILE00.0120.03114.077-0.021-0.0210.0000.0000.0000.000
14A18LYS10.9760.98616.846-0.211-0.2110.0000.0000.0000.000
15A19LYS10.8640.95519.178-0.099-0.0990.0000.0000.0000.000
16A20LEU00.0090.00118.924-0.017-0.0170.0000.0000.0000.000
17A21ILE0-0.037-0.04119.098-0.013-0.0130.0000.0000.0000.000
18A22LYS10.9320.98222.503-0.106-0.1060.0000.0000.0000.000
19A23SER0-0.001-0.00924.516-0.007-0.0070.0000.0000.0000.000
20A24LEU0-0.054-0.02923.079-0.008-0.0080.0000.0000.0000.000
21A25GLU-1-0.921-0.97326.5870.1350.1350.0000.0000.0000.000
22A26ALA0-0.066-0.00828.624-0.009-0.0090.0000.0000.0000.000
23A27ALA0-0.027-0.00130.563-0.009-0.0090.0000.0000.0000.000
24A28ARG10.9310.92932.325-0.084-0.0840.0000.0000.0000.000
25A29GLY00.0150.03135.179-0.006-0.0060.0000.0000.0000.000
26A30ASN0-0.013-0.00637.4480.0000.0000.0000.0000.0000.000
27A31GLY0-0.012-0.00339.884-0.001-0.0010.0000.0000.0000.000
28A32THR0-0.004-0.01437.3440.0010.0010.0000.0000.0000.000
29A33SER00.0000.00135.571-0.002-0.0020.0000.0000.0000.000
30A34MET0-0.1010.00231.8270.0000.0000.0000.0000.0000.000
31A35ILE00.0360.01728.6140.0010.0010.0000.0000.0000.000
32A36SER00.0070.00726.4660.0080.0080.0000.0000.0000.000
33A37LEU0-0.006-0.01324.395-0.006-0.0060.0000.0000.0000.000
34A38ILE00.005-0.00219.9930.0210.0210.0000.0000.0000.000
35A39ILE0-0.015-0.01620.511-0.027-0.0270.0000.0000.0000.000
36A40PRO0-0.0080.03518.9470.0460.0460.0000.0000.0000.000
37A41PRO00.0280.00414.907-0.020-0.0200.0000.0000.0000.000
38A42LYS10.9130.94915.978-0.384-0.3840.0000.0000.0000.000
39A43ASP-1-0.790-0.86518.6470.2090.2090.0000.0000.0000.000
40A44GLN0-0.025-0.03921.2090.0210.0210.0000.0000.0000.000
41A45ILE00.1260.03820.787-0.013-0.0130.0000.0000.0000.000
42A46SER0-0.037-0.01024.325-0.006-0.0060.0000.0000.0000.000
43A47ARG10.9130.96625.911-0.218-0.2180.0000.0000.0000.000
44A48VAL00.0120.00125.115-0.012-0.0120.0000.0000.0000.000
45A49ALA0-0.011-0.02328.029-0.012-0.0120.0000.0000.0000.000
46A50LYS10.9460.98329.794-0.123-0.1230.0000.0000.0000.000
47A51MET00.0350.04030.018-0.009-0.0090.0000.0000.0000.000
48A52LEU00.0060.00828.865-0.007-0.0070.0000.0000.0000.000
49A53ALA0-0.022-0.01033.023-0.008-0.0080.0000.0000.0000.000
50A54ASP-1-0.869-0.94035.6820.0960.0960.0000.0000.0000.000
51A55GLU-1-0.880-0.93634.5550.1080.1080.0000.0000.0000.000
52A56PHE0-0.039-0.03036.844-0.007-0.0070.0000.0000.0000.000
53A57GLY00.0000.00038.526-0.006-0.0060.0000.0000.0000.000
54A58THR0-0.030-0.03740.404-0.006-0.0060.0000.0000.0000.000
55A59ALA00.000-0.00640.464-0.004-0.0040.0000.0000.0000.000
56A60SER0-0.038-0.02842.400-0.006-0.0060.0000.0000.0000.000
57A61ASN0-0.051-0.02844.395-0.007-0.0070.0000.0000.0000.000
58A62ILE00.0030.01742.859-0.004-0.0040.0000.0000.0000.000
59A63LYS10.8430.93447.068-0.056-0.0560.0000.0000.0000.000
60A64SER00.1100.04648.134-0.002-0.0020.0000.0000.0000.000
61A65ARG10.9120.94848.064-0.046-0.0460.0000.0000.0000.000
62A66VAL00.0920.07945.5690.0020.0020.0000.0000.0000.000
63A67ASN00.0540.01543.3510.0040.0040.0000.0000.0000.000
64A68ARG10.9700.98643.046-0.054-0.0540.0000.0000.0000.000
65A69LEU0-0.042-0.03640.7970.0030.0030.0000.0000.0000.000
66A70SER0-0.0210.00040.0850.0050.0050.0000.0000.0000.000
67A71VAL00.0760.03137.9400.0050.0050.0000.0000.0000.000
68A72LEU0-0.027-0.00837.4920.0040.0040.0000.0000.0000.000
69A73GLY00.0390.02837.1520.0050.0050.0000.0000.0000.000
70A74ALA00.0430.03533.7870.0050.0050.0000.0000.0000.000
71A75ILE00.0280.01032.8390.0080.0080.0000.0000.0000.000
72A76THR0-0.041-0.04132.7160.0040.0040.0000.0000.0000.000
73A77SER0-0.021-0.01630.2110.0020.0020.0000.0000.0000.000
74A78VAL00.0410.01827.1840.0060.0060.0000.0000.0000.000
75A79GLN0-0.028-0.01727.7780.0070.0070.0000.0000.0000.000
76A80GLN00.001-0.01828.6580.0050.0050.0000.0000.0000.000
77A81ARG10.8520.94324.038-0.162-0.1620.0000.0000.0000.000
78A82LEU00.0320.00123.4480.0100.0100.0000.0000.0000.000
79A83LYS10.8430.92524.236-0.100-0.1000.0000.0000.0000.000
80A84LEU0-0.035-0.00222.576-0.011-0.0110.0000.0000.0000.000
81A85TYR0-0.070-0.02716.7200.0220.0220.0000.0000.0000.000
82A86ASN00.0210.00118.4420.0110.0110.0000.0000.0000.000
83A87LYN0-0.003-0.00418.500-0.015-0.0150.0000.0000.0000.000
84A88VAL0-0.0700.00016.4840.0230.0230.0000.0000.0000.000
85A89PRO00.0320.04812.762-0.023-0.0230.0000.0000.0000.000
86A90PRO00.0220.0029.299-0.037-0.0370.0000.0000.0000.000
87A91ASN0-0.034-0.0308.335-0.031-0.0310.0000.0000.0000.000
88A92GLY0-0.027-0.03612.564-0.084-0.0840.0000.0000.0000.000
89A93LEU0-0.0010.00215.6810.0220.0220.0000.0000.0000.000
90A94VAL0-0.0180.02317.602-0.034-0.0340.0000.0000.0000.000
91A95VAL00.030-0.00319.848-0.007-0.0070.0000.0000.0000.000
92A96TYR0-0.041-0.02821.647-0.002-0.0020.0000.0000.0000.000
93A97CYS0-0.078-0.02525.651-0.008-0.0080.0000.0000.0000.000
94A98GLY00.0780.03728.9680.0000.0000.0000.0000.0000.000
95A99THR0-0.027-0.01232.3230.0000.0000.0000.0000.0000.000
96A100ILE0-0.022-0.01132.4690.0010.0010.0000.0000.0000.000
97A101VAL00.0300.02735.588-0.004-0.0040.0000.0000.0000.000
98A102THR0-0.019-0.02335.5250.0040.0040.0000.0000.0000.000
99A103GLU-1-0.876-0.95237.1890.0390.0390.0000.0000.0000.000
100A104GLU-1-0.920-0.98139.2020.0350.0350.0000.0000.0000.000
101A105GLY0-0.0260.00241.670-0.002-0.0020.0000.0000.0000.000
102A106LYS10.8860.96039.802-0.038-0.0380.0000.0000.0000.000
103A107GLU-1-0.941-0.96238.4860.0670.0670.0000.0000.0000.000
104A108LYS10.9410.96432.344-0.073-0.0730.0000.0000.0000.000
105A109LYS10.9620.97632.894-0.071-0.0710.0000.0000.0000.000
106A110VAL00.0020.01127.233-0.001-0.0010.0000.0000.0000.000
107A111ASN0-0.037-0.04526.8830.0050.0050.0000.0000.0000.000
108A112ILE00.0320.02121.097-0.001-0.0010.0000.0000.0000.000
109A113ASP-1-0.825-0.89520.2390.2430.2430.0000.0000.0000.000
110A114PHE00.0390.01615.067-0.016-0.0160.0000.0000.0000.000
111A115GLU-1-0.804-0.91010.5711.0541.0540.0000.0000.0000.000
112A116PRO0-0.038-0.00812.5840.0390.0390.0000.0000.0000.000
113A117PHE00.001-0.0308.0400.2370.2370.0000.0000.0000.000
114A118LYS10.8930.96110.072-0.952-0.9520.0000.0000.0000.000
115A119PRO00.0250.04412.802-0.049-0.0490.0000.0000.0000.000
116A120ILE00.040-0.00915.152-0.014-0.0140.0000.0000.0000.000
117A121ASN0-0.020-0.03218.027-0.027-0.0270.0000.0000.0000.000
118A122THR00.0150.03120.605-0.020-0.0200.0000.0000.0000.000
119A123SER0-0.024-0.05722.441-0.023-0.0230.0000.0000.0000.000
120A124LEU0-0.064-0.00924.253-0.019-0.0190.0000.0000.0000.000
121A125TYR00.019-0.00826.0590.0100.0100.0000.0000.0000.000
122A126LEU0-0.0050.01229.021-0.011-0.0110.0000.0000.0000.000
123A127CYS00.0200.01130.9110.0030.0030.0000.0000.0000.000
124A128ASP-1-0.831-0.89733.4190.1080.1080.0000.0000.0000.000
125A129ASN0-0.039-0.05635.0220.0020.0020.0000.0000.0000.000
126A130LYS10.9950.98331.593-0.120-0.1200.0000.0000.0000.000
127A131PHE00.0110.00227.1520.0050.0050.0000.0000.0000.000
128A132HIS10.8530.91527.348-0.158-0.1580.0000.0000.0000.000
129A133THR00.0990.06223.2640.0160.0160.0000.0000.0000.000
130A134GLU-1-0.872-0.92322.4440.2080.2080.0000.0000.0000.000
131A135ALA0-0.012-0.01020.6190.0150.0150.0000.0000.0000.000
132A136LEU0-0.036-0.01917.6580.0410.0410.0000.0000.0000.000
133A137THR00.028-0.00518.0010.0330.0330.0000.0000.0000.000
134A138ALA00.0300.03319.145-0.003-0.0030.0000.0000.0000.000
135A139LEU0-0.023-0.02112.9960.0230.0230.0000.0000.0000.000
136A140LEU0-0.117-0.05014.4720.0250.0250.0000.0000.0000.000
137A141SER00.0190.01215.877-0.061-0.0610.0000.0000.0000.000
138A142ASP-1-0.903-0.94510.8920.6350.6350.0000.0000.0000.000
139A143ASP-1-0.908-0.94014.3210.1420.1420.0000.0000.0000.000
140A144SER0-0.028-0.02213.4080.0390.0390.0000.0000.0000.000
141A145LYS10.9290.98313.737-0.276-0.2760.0000.0000.0000.000
142A146PHE00.018-0.00514.602-0.016-0.0160.0000.0000.0000.000
143A147GLY0-0.013-0.05317.0380.0110.0110.0000.0000.0000.000
144A148PHE00.0210.03018.333-0.020-0.0200.0000.0000.0000.000
145A149ILE00.0300.01921.2760.0070.0070.0000.0000.0000.000
146A150VAL0-0.027-0.02724.193-0.007-0.0070.0000.0000.0000.000
147A151ILE0-0.028-0.00127.0860.0030.0030.0000.0000.0000.000
148A152ASP-1-0.781-0.89530.1330.0060.0060.0000.0000.0000.000
149A153GLY0-0.028-0.03533.898-0.002-0.0020.0000.0000.0000.000
150A154SER0-0.144-0.08537.047-0.001-0.0010.0000.0000.0000.000
151A155GLY00.0250.00834.4550.0030.0030.0000.0000.0000.000
152A156ALA0-0.0060.03028.889-0.002-0.0020.0000.0000.0000.000
153A157LEU0-0.0190.00126.7970.0030.0030.0000.0000.0000.000
154A158PHE0-0.001-0.00223.056-0.007-0.0070.0000.0000.0000.000
155A159GLY00.0520.02023.3140.0070.0070.0000.0000.0000.000
156A160THR0-0.026-0.03818.3750.0010.0010.0000.0000.0000.000
157A161LEU00.0290.04120.3170.0000.0000.0000.0000.0000.000
158A162GLN00.0540.00516.4020.0370.0370.0000.0000.0000.000
159A163GLY00.0760.06719.6620.0040.0040.0000.0000.0000.000
160A164ASN0-0.011-0.02121.572-0.019-0.0190.0000.0000.0000.000
161A165THR0-0.062-0.03322.153-0.012-0.0120.0000.0000.0000.000
162A166ARG10.9540.98922.851-0.074-0.0740.0000.0000.0000.000
163A167GLU-1-0.920-0.98222.5040.1610.1610.0000.0000.0000.000
164A168VAL0-0.0170.02524.221-0.003-0.0030.0000.0000.0000.000
165A169LEU0-0.0340.01020.6500.0040.0040.0000.0000.0000.000
166A170HIS00.0330.01625.1440.0000.0000.0000.0000.0000.000
167A171LYS10.9560.96627.221-0.045-0.0450.0000.0000.0000.000
168A172PHE0-0.0100.01328.4840.0000.0000.0000.0000.0000.000
169A173THR0-0.020-0.05232.383-0.002-0.0020.0000.0000.0000.000
170A174VAL0-0.030-0.01034.415-0.001-0.0010.0000.0000.0000.000
171A175ASP-1-0.874-0.93537.1430.0040.0040.0000.0000.0000.000
172A176LEU00.002-0.00637.270-0.001-0.0010.0000.0000.0000.000
173A177PRO00.0090.01540.9110.0010.0010.0000.0000.0000.000
174A178LYS10.8930.95441.126-0.003-0.0030.0000.0000.0000.000
175A179LYS10.9510.97146.023-0.001-0.0010.0000.0000.0000.000
176A180HIS00.0950.05849.137-0.001-0.0010.0000.0000.0000.000
177A181GLY0-0.029-0.01552.2470.0000.0000.0000.0000.0000.000
178A182ARG10.9790.97555.5940.0020.0020.0000.0000.0000.000
179A183GLY00.0670.04258.0980.0000.0000.0000.0000.0000.000
180A184GLY0-0.0010.01758.1490.0000.0000.0000.0000.0000.000
181A185GLN0-0.027-0.03751.387-0.001-0.0010.0000.0000.0000.000
182A186SER00.0010.00253.8280.0000.0000.0000.0000.0000.000
183A187ALA00.1250.06652.1910.0000.0000.0000.0000.0000.000
184A188LEU00.0900.04548.3980.0000.0000.0000.0000.0000.000
185A189ARG10.8990.94648.5650.0100.0100.0000.0000.0000.000
186A190PHE0-0.022-0.02047.0540.0000.0000.0000.0000.0000.000
187A191ALA00.0840.03945.7030.0000.0000.0000.0000.0000.000
188A192ARG10.9610.97944.0840.0180.0180.0000.0000.0000.000
189A193LEU0-0.012-0.00243.1680.0000.0000.0000.0000.0000.000
190A194ARG10.9470.95941.7040.0120.0120.0000.0000.0000.000
191A195MET0-0.0280.00638.6880.0020.0020.0000.0000.0000.000
192A196GLU-1-0.964-0.97938.940-0.022-0.0220.0000.0000.0000.000
193A197LYS10.9380.94337.6620.0070.0070.0000.0000.0000.000
194A198ARG10.9150.98435.0470.0270.0270.0000.0000.0000.000
195A199HIS00.1170.06333.2230.0010.0010.0000.0000.0000.000
196A200ASN0-0.106-0.05132.6260.0010.0010.0000.0000.0000.000
197A201TYR0-0.057-0.04032.4660.0040.0040.0000.0000.0000.000
198A202VAL0-0.017-0.02629.1340.0030.0030.0000.0000.0000.000
199A203ARG10.9890.98528.2170.0230.0230.0000.0000.0000.000
200A204LYS10.9420.97327.472-0.012-0.0120.0000.0000.0000.000
201A205VAL0-0.009-0.00526.1950.0070.0070.0000.0000.0000.000
202A206ALA00.0010.00224.1680.0050.0050.0000.0000.0000.000
203A207GLU-1-0.851-0.91723.167-0.032-0.0320.0000.0000.0000.000
204A208THR0-0.187-0.08623.4560.0080.0080.0000.0000.0000.000
205A209ALA00.0430.00521.0090.0100.0100.0000.0000.0000.000
206A210VAL00.0510.01517.9000.0120.0120.0000.0000.0000.000
207A211GLN0-0.018-0.01618.2870.0080.0080.0000.0000.0000.000
208A212LEU0-0.035-0.01319.0520.0120.0120.0000.0000.0000.000
209A213PHE0-0.0650.01916.1460.0190.0190.0000.0000.0000.000
210A214ILE0-0.0330.02312.8580.0230.0230.0000.0000.0000.000
211A215SER0-0.0020.01013.922-0.015-0.0150.0000.0000.0000.000
212A216GLY0-0.013-0.01311.7230.0360.0360.0000.0000.0000.000
213A217ASP-1-0.905-0.96210.0240.0230.0230.0000.0000.0000.000
214A218LYN0-0.0340.0306.336-0.083-0.0830.0000.0000.0000.000
215A219VAL00.067-0.0039.6940.0370.0370.0000.0000.0000.000
216A220ASN0-0.0210.00210.0830.0260.0260.0000.0000.0000.000
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