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: QY84Y

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 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 398
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5954031.309826
FMO2-HF: Nuclear repulsion 5798862.497594
FMO2-HF: Total energy -155168.812233
FMO2-MP2: Total energy -155623.96653


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.
-0.4491.386-0.022-0.978-0.8340
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 : 0.020 / 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].
3A7ALA00.0040.0103.8720.1321.967-0.022-0.978-0.8340.000
4A8ALA00.0850.0666.930-0.209-0.2090.0000.0000.0000.000
5A9ASP-1-0.785-0.8755.8681.0831.0830.0000.0000.0000.000
6A10ARG10.8430.8845.308-0.715-0.7150.0000.0000.0000.000
7A11ASN0-0.017-0.0216.959-0.051-0.0510.0000.0000.0000.000
8A12VAL00.0800.05210.345-0.031-0.0310.0000.0000.0000.000
9A13GLU-1-0.826-0.8998.6620.9040.9040.0000.0000.0000.000
10A14ILE0-0.040-0.02210.315-0.103-0.1030.0000.0000.0000.000
11A15TRP00.0040.01212.859-0.077-0.0770.0000.0000.0000.000
12A16LYS10.8360.90512.343-0.704-0.7040.0000.0000.0000.000
13A17ILE0-0.0050.00213.596-0.046-0.0460.0000.0000.0000.000
14A18LYS10.9380.96416.391-0.309-0.3090.0000.0000.0000.000
15A19LYS10.8760.95118.900-0.213-0.2130.0000.0000.0000.000
16A20LEU0-0.0020.00718.559-0.025-0.0250.0000.0000.0000.000
17A21ILE0-0.010-0.01518.797-0.023-0.0230.0000.0000.0000.000
18A22LYS10.9330.97122.231-0.168-0.1680.0000.0000.0000.000
19A23SER00.0050.00124.033-0.014-0.0140.0000.0000.0000.000
20A24LEU0-0.025-0.00922.503-0.013-0.0130.0000.0000.0000.000
21A25GLU-1-0.810-0.89125.8880.1810.1810.0000.0000.0000.000
22A26ALA0-0.064-0.01428.264-0.013-0.0130.0000.0000.0000.000
23A27ALA0-0.0140.00929.993-0.010-0.0100.0000.0000.0000.000
24A28ARG10.8760.91431.697-0.105-0.1050.0000.0000.0000.000
25A29GLY00.0460.02834.722-0.004-0.0040.0000.0000.0000.000
26A30ASN0-0.052-0.02836.9440.0000.0000.0000.0000.0000.000
27A31GLY00.0150.00239.151-0.005-0.0050.0000.0000.0000.000
28A32THR0-0.010-0.00637.4480.0040.0040.0000.0000.0000.000
29A33SER00.002-0.01736.079-0.001-0.0010.0000.0000.0000.000
30A34MET0-0.0660.01131.2960.0040.0040.0000.0000.0000.000
31A35ILE00.0170.00628.269-0.001-0.0010.0000.0000.0000.000
32A36SER00.006-0.00426.1660.0120.0120.0000.0000.0000.000
33A37LEU0-0.011-0.01324.180-0.016-0.0160.0000.0000.0000.000
34A38ILE0-0.018-0.00519.4990.0270.0270.0000.0000.0000.000
35A39ILE00.0080.00920.449-0.029-0.0290.0000.0000.0000.000
36A40PRO0-0.0110.01518.0470.0490.0490.0000.0000.0000.000
37A41PRO00.001-0.01813.928-0.024-0.0240.0000.0000.0000.000
38A42LYS10.8440.91414.984-0.414-0.4140.0000.0000.0000.000
39A43ASP-1-0.743-0.80918.5850.2030.2030.0000.0000.0000.000
40A44GLN0-0.006-0.01121.1430.0240.0240.0000.0000.0000.000
41A45ILE00.0750.03120.337-0.009-0.0090.0000.0000.0000.000
42A46SER0-0.007-0.00824.209-0.007-0.0070.0000.0000.0000.000
43A47ARG10.8100.87125.037-0.215-0.2150.0000.0000.0000.000
44A48VAL00.0280.01124.848-0.011-0.0110.0000.0000.0000.000
45A49ALA00.0280.00627.907-0.009-0.0090.0000.0000.0000.000
46A50LYS10.8330.89729.586-0.124-0.1240.0000.0000.0000.000
47A51MET0-0.0190.01629.558-0.010-0.0100.0000.0000.0000.000
48A52LEU00.0420.00028.486-0.007-0.0070.0000.0000.0000.000
49A53ALA0-0.021-0.00532.783-0.006-0.0060.0000.0000.0000.000
50A54ASP-1-0.794-0.87735.6170.1060.1060.0000.0000.0000.000
51A55GLU-1-0.831-0.87634.2840.1220.1220.0000.0000.0000.000
52A56PHE0-0.0010.00336.584-0.006-0.0060.0000.0000.0000.000
53A57GLY00.0240.01638.346-0.006-0.0060.0000.0000.0000.000
54A58THR0-0.008-0.02240.460-0.007-0.0070.0000.0000.0000.000
55A59ALA00.0230.00039.876-0.005-0.0050.0000.0000.0000.000
56A60SER0-0.052-0.03541.910-0.005-0.0050.0000.0000.0000.000
57A61ASN0-0.082-0.05744.184-0.009-0.0090.0000.0000.0000.000
58A62ILE00.0540.05642.254-0.003-0.0030.0000.0000.0000.000
59A63LYS10.9010.96346.737-0.072-0.0720.0000.0000.0000.000
60A64SER00.0430.00648.226-0.002-0.0020.0000.0000.0000.000
61A65ARG10.9390.96847.357-0.062-0.0620.0000.0000.0000.000
62A66VAL00.0690.04144.7760.0030.0030.0000.0000.0000.000
63A67ASN00.0400.01842.4190.0030.0030.0000.0000.0000.000
64A68ARG10.9030.95142.421-0.070-0.0700.0000.0000.0000.000
65A69LEU00.0130.00541.5540.0040.0040.0000.0000.0000.000
66A70SER0-0.0120.00539.1280.0060.0060.0000.0000.0000.000
67A71VAL00.0190.01037.8910.0070.0070.0000.0000.0000.000
68A72LEU0-0.0020.00137.1880.0060.0060.0000.0000.0000.000
69A73GLY00.0140.02336.9620.0050.0050.0000.0000.0000.000
70A74ALA00.0110.00933.7180.0080.0080.0000.0000.0000.000
71A75ILE00.0190.00332.5100.0120.0120.0000.0000.0000.000
72A76THR0-0.036-0.03732.3520.0070.0070.0000.0000.0000.000
73A77SER0-0.022-0.01030.0960.0040.0040.0000.0000.0000.000
74A78VAL00.0400.01426.8060.0120.0120.0000.0000.0000.000
75A79GLN00.0080.00527.4600.0130.0130.0000.0000.0000.000
76A80GLN0-0.027-0.02028.3370.0040.0040.0000.0000.0000.000
77A81ARG10.8240.89823.544-0.253-0.2530.0000.0000.0000.000
78A82LEU0-0.004-0.00423.0250.0170.0170.0000.0000.0000.000
79A83LYS10.8400.90723.850-0.142-0.1420.0000.0000.0000.000
80A84LEU0-0.0220.01122.162-0.012-0.0120.0000.0000.0000.000
81A85TYR0-0.071-0.05216.5470.0370.0370.0000.0000.0000.000
82A86ASN00.0120.00118.3990.0040.0040.0000.0000.0000.000
83A87LYN0-0.017-0.01218.676-0.025-0.0250.0000.0000.0000.000
84A88VAL00.0050.01416.3420.0320.0320.0000.0000.0000.000
85A89PRO00.0380.04012.337-0.052-0.0520.0000.0000.0000.000
86A90PRO00.003-0.0159.056-0.086-0.0860.0000.0000.0000.000
87A91ASN0-0.022-0.0327.588-0.096-0.0960.0000.0000.0000.000
88A92GLY0-0.026-0.02111.614-0.081-0.0810.0000.0000.0000.000
89A93LEU0-0.0040.00015.1200.0580.0580.0000.0000.0000.000
90A94VAL0-0.0310.00117.377-0.045-0.0450.0000.0000.0000.000
91A95VAL00.001-0.01319.5760.0080.0080.0000.0000.0000.000
92A96TYR0-0.030-0.02821.166-0.008-0.0080.0000.0000.0000.000
93A97CYS0-0.046-0.00325.3880.0040.0040.0000.0000.0000.000
94A98GLY00.0530.01328.722-0.006-0.0060.0000.0000.0000.000
95A99THR0-0.055-0.01732.0560.0030.0030.0000.0000.0000.000
96A100ILE0-0.006-0.01232.353-0.001-0.0010.0000.0000.0000.000
97A101VAL00.0050.01535.558-0.003-0.0030.0000.0000.0000.000
98A102THR0-0.028-0.01235.5910.0090.0090.0000.0000.0000.000
99A103GLU-1-0.876-0.94936.9920.0800.0800.0000.0000.0000.000
100A104GLU-1-0.807-0.90338.9750.0680.0680.0000.0000.0000.000
101A105GLY0-0.0130.01041.630-0.003-0.0030.0000.0000.0000.000
102A106LYS10.7790.89039.610-0.072-0.0720.0000.0000.0000.000
103A107GLU-1-0.843-0.92838.0940.1030.1030.0000.0000.0000.000
104A108LYS10.9050.93732.655-0.121-0.1210.0000.0000.0000.000
105A109LYS10.8740.93432.992-0.113-0.1130.0000.0000.0000.000
106A110VAL00.0060.02227.5830.0030.0030.0000.0000.0000.000
107A111ASN00.018-0.02526.9360.0020.0020.0000.0000.0000.000
108A112ILE00.0290.03220.8670.0050.0050.0000.0000.0000.000
109A113ASP-1-0.786-0.86520.2500.3400.3400.0000.0000.0000.000
110A114PHE00.0410.01714.648-0.001-0.0010.0000.0000.0000.000
111A115GLU-1-0.781-0.8769.7431.2961.2960.0000.0000.0000.000
112A116PRO0-0.072-0.01412.7670.0720.0720.0000.0000.0000.000
113A117PHE00.018-0.0168.5480.2150.2150.0000.0000.0000.000
114A118LYS10.9440.9789.380-0.791-0.7910.0000.0000.0000.000
115A119PRO00.0620.03912.547-0.083-0.0830.0000.0000.0000.000
116A120ILE00.005-0.01513.907-0.020-0.0200.0000.0000.0000.000
117A121ASN0-0.034-0.03617.162-0.022-0.0220.0000.0000.0000.000
118A122THR00.0050.01319.931-0.013-0.0130.0000.0000.0000.000
119A123SER0-0.020-0.02221.895-0.019-0.0190.0000.0000.0000.000
120A124LEU00.0120.04423.746-0.022-0.0220.0000.0000.0000.000
121A125TYR0-0.029-0.06625.6880.0180.0180.0000.0000.0000.000
122A126LEU0-0.0010.00528.503-0.013-0.0130.0000.0000.0000.000
123A127CYS00.0020.01230.7820.0060.0060.0000.0000.0000.000
124A128ASP-1-0.771-0.83332.8700.1270.1270.0000.0000.0000.000
125A129ASN00.021-0.00634.751-0.001-0.0010.0000.0000.0000.000
126A130LYS10.9100.93031.908-0.139-0.1390.0000.0000.0000.000
127A131PHE0-0.0030.00026.8630.0030.0030.0000.0000.0000.000
128A132HIS10.8250.87026.761-0.187-0.1870.0000.0000.0000.000
129A133THR00.000-0.01122.4350.0260.0260.0000.0000.0000.000
130A134GLU-1-0.780-0.86022.2970.2210.2210.0000.0000.0000.000
131A135ALA00.008-0.00220.2670.0080.0080.0000.0000.0000.000
132A136LEU0-0.022-0.00917.1250.0440.0440.0000.0000.0000.000
133A137THR00.009-0.02317.8640.0200.0200.0000.0000.0000.000
134A138ALA00.0070.01519.282-0.002-0.0020.0000.0000.0000.000
135A139LEU0-0.027-0.01613.1420.0070.0070.0000.0000.0000.000
136A140LEU0-0.072-0.02814.2500.0330.0330.0000.0000.0000.000
137A141SER0-0.012-0.00316.605-0.049-0.0490.0000.0000.0000.000
138A142ASP-1-0.838-0.87810.8430.5360.5360.0000.0000.0000.000
139A143ASP-1-0.891-0.95814.1360.0790.0790.0000.0000.0000.000
140A144SER0-0.005-0.00113.7360.0010.0010.0000.0000.0000.000
141A145LYS10.8340.91314.066-0.089-0.0890.0000.0000.0000.000
142A146PHE00.0180.00414.395-0.029-0.0290.0000.0000.0000.000
143A147GLY00.0390.00716.9190.0180.0180.0000.0000.0000.000
144A148PHE0-0.051-0.01918.508-0.012-0.0120.0000.0000.0000.000
145A149ILE00.0200.00921.2090.0060.0060.0000.0000.0000.000
146A150VAL0-0.021-0.00724.528-0.003-0.0030.0000.0000.0000.000
147A151ILE00.000-0.00427.0050.0040.0040.0000.0000.0000.000
148A152ASP-1-0.798-0.88430.575-0.035-0.0350.0000.0000.0000.000
149A153GLY0-0.0150.00834.381-0.003-0.0030.0000.0000.0000.000
150A154SER0-0.050-0.04937.0950.0010.0010.0000.0000.0000.000
151A155GLY0-0.046-0.02234.5030.0030.0030.0000.0000.0000.000
152A156ALA0-0.0020.02029.090-0.002-0.0020.0000.0000.0000.000
153A157LEU0-0.016-0.00926.7510.0060.0060.0000.0000.0000.000
154A158PHE00.0090.00923.265-0.008-0.0080.0000.0000.0000.000
155A159GLY00.0560.02123.1690.0100.0100.0000.0000.0000.000
156A160THR0-0.030-0.01618.195-0.007-0.0070.0000.0000.0000.000
157A161LEU00.0250.02319.8570.0050.0050.0000.0000.0000.000
158A162GLN0-0.013-0.01315.861-0.025-0.0250.0000.0000.0000.000
159A163GLY00.1100.06519.4080.0090.0090.0000.0000.0000.000
160A164ASN0-0.054-0.03221.566-0.020-0.0200.0000.0000.0000.000
161A165THR0-0.037-0.01021.560-0.004-0.0040.0000.0000.0000.000
162A166ARG10.9570.98022.543-0.033-0.0330.0000.0000.0000.000
163A167GLU-1-0.855-0.92520.9170.0700.0700.0000.0000.0000.000
164A168VAL0-0.021-0.00323.893-0.010-0.0100.0000.0000.0000.000
165A169LEU0-0.044-0.01320.3910.0050.0050.0000.0000.0000.000
166A170HIS00.0420.01324.8890.0050.0050.0000.0000.0000.000
167A171LYS10.8220.89327.1840.0030.0030.0000.0000.0000.000
168A172PHE0-0.016-0.00328.4510.0040.0040.0000.0000.0000.000
169A173THR00.024-0.01032.674-0.001-0.0010.0000.0000.0000.000
170A174VAL0-0.032-0.03134.736-0.002-0.0020.0000.0000.0000.000
171A175ASP-1-0.834-0.88837.451-0.030-0.0300.0000.0000.0000.000
172A176LEU00.0220.01937.059-0.001-0.0010.0000.0000.0000.000
173A177PRO00.0080.00641.0380.0030.0030.0000.0000.0000.000
174A178LYS10.8840.92342.6380.0320.0320.0000.0000.0000.000
175A179LYS10.9410.97446.5210.0250.0250.0000.0000.0000.000
176A180HIS00.0700.04749.2100.0000.0000.0000.0000.0000.000
177A181GLY00.0130.00352.3320.0000.0000.0000.0000.0000.000
178A182ARG10.9640.97155.6980.0190.0190.0000.0000.0000.000
179A183GLY00.0740.03658.0280.0010.0010.0000.0000.0000.000
180A184GLY0-0.0120.00658.2920.0000.0000.0000.0000.0000.000
181A185GLN0-0.031-0.02551.133-0.002-0.0020.0000.0000.0000.000
182A186SER00.0410.03154.3350.0000.0000.0000.0000.0000.000
183A187ALA00.0830.02952.337-0.001-0.0010.0000.0000.0000.000
184A188LEU00.0420.02748.747-0.001-0.0010.0000.0000.0000.000
185A189ARG10.9060.94348.9690.0340.0340.0000.0000.0000.000
186A190PHE00.0100.00447.301-0.001-0.0010.0000.0000.0000.000
187A191ALA00.0350.01046.064-0.001-0.0010.0000.0000.0000.000
188A192ARG10.9740.99144.4340.0440.0440.0000.0000.0000.000
189A193LEU0-0.005-0.00543.432-0.002-0.0020.0000.0000.0000.000
190A194ARG10.9000.93941.6860.0430.0430.0000.0000.0000.000
191A195MET00.0470.02038.6410.0000.0000.0000.0000.0000.000
192A196GLU-1-0.816-0.89338.473-0.060-0.0600.0000.0000.0000.000
193A197LYS10.8360.91237.8560.0470.0470.0000.0000.0000.000
194A198ARG10.7990.90335.2470.0710.0710.0000.0000.0000.000
195A199HIS00.0770.04932.195-0.001-0.0010.0000.0000.0000.000
196A200ASN00.000-0.01332.906-0.007-0.0070.0000.0000.0000.000
197A201TYR0-0.082-0.04832.419-0.001-0.0010.0000.0000.0000.000
198A202VAL00.0370.01529.2690.0000.0000.0000.0000.0000.000
199A203ARG10.9170.94528.5550.0830.0830.0000.0000.0000.000
200A204LYS10.8830.96427.9250.0450.0450.0000.0000.0000.000
201A205VAL0-0.027-0.01226.4340.0030.0030.0000.0000.0000.000
202A206ALA00.0480.02724.365-0.001-0.0010.0000.0000.0000.000
203A207GLU-1-0.889-0.94723.210-0.130-0.1300.0000.0000.0000.000
204A208THR0-0.090-0.06323.5200.0020.0020.0000.0000.0000.000
205A209ALA0-0.0080.00221.3330.0070.0070.0000.0000.0000.000
206A210VAL00.0300.01418.560-0.005-0.0050.0000.0000.0000.000
207A211GLN0-0.068-0.04118.550-0.014-0.0140.0000.0000.0000.000
208A212LEU0-0.038-0.00819.0860.0200.0200.0000.0000.0000.000
209A213PHE0-0.024-0.00916.3870.0120.0120.0000.0000.0000.000
210A214ILE0-0.0260.00412.754-0.021-0.0210.0000.0000.0000.000
211A215SER0-0.014-0.00514.527-0.010-0.0100.0000.0000.0000.000
212A216GLY0-0.031-0.02011.7190.0410.0410.0000.0000.0000.000
213A217ASP-1-0.852-0.91610.063-0.398-0.3980.0000.0000.0000.000
214A218LYN00.0070.0136.154-0.120-0.1200.0000.0000.0000.000
215A219VAL00.0310.0079.7380.0880.0880.0000.0000.0000.000
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