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: 2J1MR

Calculation Name: 3D7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7L

Chain ID: A

ChEMBL ID:

UniProt ID: Q92AH8

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101203.977979
FMO2-HF: Nuclear repulsion 2026609.660083
FMO2-HF: Total energy -74594.317896
FMO2-MP2: Total energy -74811.901924


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:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-4.1250.64-0.143-1.628-2.995-0.004
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.075
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].
3A0ALA00.0020.0363.513-3.4321.060-0.147-1.571-2.775-0.004
4A1MET00.0230.0145.008-0.740-0.749-0.001-0.0050.0150.000
5A2LYS10.8910.9373.5470.4970.7790.005-0.052-0.2350.000
6A3ILE0-0.001-0.0067.6910.1050.1050.0000.0000.0000.000
7A4LEU00.0400.02811.4700.0230.0230.0000.0000.0000.000
8A5LEU0-0.044-0.02213.5570.0000.0000.0000.0000.0000.000
9A6ILE00.0450.00816.9470.0080.0080.0000.0000.0000.000
10A7GLY0-0.006-0.02719.836-0.003-0.0030.0000.0000.0000.000
11A8ALA0-0.010-0.00819.340-0.002-0.0020.0000.0000.0000.000
12A9SER0-0.0060.00121.4320.0000.0000.0000.0000.0000.000
13A10GLY0-0.0120.00924.4080.0000.0000.0000.0000.0000.000
14A11THR00.0340.00426.3190.0000.0000.0000.0000.0000.000
15A12LEU00.0210.01325.3770.0000.0000.0000.0000.0000.000
16A13GLY00.0360.01122.843-0.002-0.0020.0000.0000.0000.000
17A14SER0-0.0070.00622.065-0.002-0.0020.0000.0000.0000.000
18A15ALA00.0520.02123.0290.0000.0000.0000.0000.0000.000
19A16VAL0-0.035-0.02819.357-0.002-0.0020.0000.0000.0000.000
20A17LYS10.9000.94717.113-0.033-0.0330.0000.0000.0000.000
21A18GLU-1-0.907-0.93618.5500.0140.0140.0000.0000.0000.000
22A19ARG10.7560.85420.2200.0110.0110.0000.0000.0000.000
23A20LEU0-0.009-0.01415.398-0.001-0.0010.0000.0000.0000.000
24A21GLU-1-0.849-0.91714.7350.0180.0180.0000.0000.0000.000
25A22LYS10.8480.92814.691-0.004-0.0040.0000.0000.0000.000
26A23LYS10.8350.91413.7610.0490.0490.0000.0000.0000.000
27A24ALA0-0.0100.01210.447-0.035-0.0350.0000.0000.0000.000
28A25GLU-1-0.828-0.8846.253-0.225-0.2250.0000.0000.0000.000
29A26VAL0-0.073-0.0439.663-0.054-0.0540.0000.0000.0000.000
30A27ILE00.0390.0348.6450.0230.0230.0000.0000.0000.000
31A28THR0-0.060-0.04112.988-0.001-0.0010.0000.0000.0000.000
32A29ALA00.0750.03416.7510.0090.0090.0000.0000.0000.000
33A30GLY00.0280.01018.987-0.007-0.0070.0000.0000.0000.000
34A31ARG10.9090.96922.787-0.027-0.0270.0000.0000.0000.000
35A32HIS00.001-0.01725.8020.0020.0020.0000.0000.0000.000
36A33SER00.0070.00523.3310.0000.0000.0000.0000.0000.000
37A34GLY0-0.011-0.00219.674-0.002-0.0020.0000.0000.0000.000
38A35ASP-1-0.841-0.90614.4860.0420.0420.0000.0000.0000.000
39A36VAL0-0.021-0.00615.4690.0060.0060.0000.0000.0000.000
40A37THR0-0.035-0.02318.211-0.006-0.0060.0000.0000.0000.000
41A38VAL0-0.007-0.01420.8660.0040.0040.0000.0000.0000.000
42A39ASP-1-0.894-0.95622.9080.0240.0240.0000.0000.0000.000
43A40ILE0-0.003-0.01123.4170.0010.0010.0000.0000.0000.000
44A41THR0-0.042-0.01225.866-0.001-0.0010.0000.0000.0000.000
45A42ASN0-0.028-0.01127.7260.0020.0020.0000.0000.0000.000
46A43ILE00.0570.01225.6560.0030.0030.0000.0000.0000.000
47A44ASP-1-0.854-0.93024.5100.0610.0610.0000.0000.0000.000
48A45SER0-0.042-0.00623.6020.0040.0040.0000.0000.0000.000
49A46ILE0-0.026-0.00420.6210.0040.0040.0000.0000.0000.000
50A47LYS10.9590.97419.896-0.051-0.0510.0000.0000.0000.000
51A48LYS10.9580.98719.217-0.039-0.0390.0000.0000.0000.000
52A49MET0-0.0020.02416.9120.0050.0050.0000.0000.0000.000
53A50TYR0-0.040-0.06414.7070.0040.0040.0000.0000.0000.000
54A51GLU-1-0.972-0.97214.1550.1480.1480.0000.0000.0000.000
55A52GLN0-0.056-0.03514.4990.0230.0230.0000.0000.0000.000
56A53VAL0-0.050-0.01110.9740.0110.0110.0000.0000.0000.000
57A54GLY00.0030.0189.8120.0770.0770.0000.0000.0000.000
58A55LYS10.9100.9507.567-0.464-0.4640.0000.0000.0000.000
59A56VAL0-0.019-0.0057.1790.0620.0620.0000.0000.0000.000
60A57ASP-1-0.784-0.8806.653-0.745-0.7450.0000.0000.0000.000
61A58ALA0-0.034-0.0219.4320.0400.0400.0000.0000.0000.000
62A59ILE0-0.0010.02612.7410.0050.0050.0000.0000.0000.000
63A60VAL0-0.017-0.02215.311-0.003-0.0030.0000.0000.0000.000
64A61SER0-0.013-0.01518.1390.0080.0080.0000.0000.0000.000
65A62ALA00.0040.02321.468-0.003-0.0030.0000.0000.0000.000
66A63THR0-0.046-0.02623.4370.0030.0030.0000.0000.0000.000
67A64GLY00.0220.01325.881-0.001-0.0010.0000.0000.0000.000
68A65SER0-0.065-0.04428.681-0.001-0.0010.0000.0000.0000.000
69A66ALA00.028-0.01232.3080.0010.0010.0000.0000.0000.000
70A67THR0-0.027-0.01135.5990.0000.0000.0000.0000.0000.000
71A68PHE0-0.0190.00437.5520.0000.0000.0000.0000.0000.000
72A69SER00.009-0.02141.4980.0000.0000.0000.0000.0000.000
73A70PRO00.0380.04644.9780.0000.0000.0000.0000.0000.000
74A71LEU00.0470.01546.9180.0000.0000.0000.0000.0000.000
75A72THR0-0.001-0.01048.2220.0000.0000.0000.0000.0000.000
76A73GLU-1-0.947-0.97248.9030.0080.0080.0000.0000.0000.000
77A74LEU0-0.096-0.03442.4260.0010.0010.0000.0000.0000.000
78A75THR00.0560.03146.3890.0000.0000.0000.0000.0000.000
79A76PRO00.033-0.00244.2800.0000.0000.0000.0000.0000.000
80A77GLU-1-0.877-0.94542.6710.0120.0120.0000.0000.0000.000
81A78LYS10.9260.97341.602-0.009-0.0090.0000.0000.0000.000
82A79ASN00.0560.02640.2830.0000.0000.0000.0000.0000.000
83A80ALA00.0120.00938.5370.0000.0000.0000.0000.0000.000
84A81VAL00.0140.02036.1920.0010.0010.0000.0000.0000.000
85A82THR00.018-0.01934.8720.0010.0010.0000.0000.0000.000
86A83ILE0-0.027-0.00633.6040.0000.0000.0000.0000.0000.000
87A84SER0-0.0150.00132.5830.0010.0010.0000.0000.0000.000
88A85SER00.0320.02930.0090.0010.0010.0000.0000.0000.000
89A86LYS10.8170.90929.261-0.008-0.0080.0000.0000.0000.000
90A87LEU00.0070.01929.402-0.001-0.0010.0000.0000.0000.000
91A88GLY00.0270.00029.1420.0000.0000.0000.0000.0000.000
92A89GLY00.0400.02227.2080.0020.0020.0000.0000.0000.000
93A90GLN0-0.029-0.02124.5940.0010.0010.0000.0000.0000.000
94A91ILE00.0170.01124.0510.0010.0010.0000.0000.0000.000
95A92ASN00.018-0.00524.6340.0030.0030.0000.0000.0000.000
96A93LEU0-0.0260.00319.9670.0060.0060.0000.0000.0000.000
97A94VAL00.0090.03019.8520.0060.0060.0000.0000.0000.000
98A95LEU0-0.028-0.02520.6750.0060.0060.0000.0000.0000.000
99A96LEU0-0.054-0.03321.0620.0040.0040.0000.0000.0000.000
100A97GLY00.0510.03217.1440.0130.0130.0000.0000.0000.000
101A98ILE0-0.0010.00215.8010.0110.0110.0000.0000.0000.000
102A99ASP-1-0.917-0.96015.4780.1160.1160.0000.0000.0000.000
103A100SER0-0.079-0.03912.7500.0550.0550.0000.0000.0000.000
104A101LEU0-0.0230.00611.3460.0190.0190.0000.0000.0000.000
105A102ASN0-0.032-0.0335.8200.2830.2830.0000.0000.0000.000
106A103ASP-1-0.843-0.93910.0920.0260.0260.0000.0000.0000.000
107A104LYS10.8260.91011.5880.0100.0100.0000.0000.0000.000
108A105GLY00.0580.05412.442-0.026-0.0260.0000.0000.0000.000
109A106SER0-0.069-0.03913.1080.0160.0160.0000.0000.0000.000
110A107PHE00.1140.04415.4150.0010.0010.0000.0000.0000.000
111A108THR0-0.031-0.00318.253-0.007-0.0070.0000.0000.0000.000
112A109LEU00.0210.01420.5710.0030.0030.0000.0000.0000.000
113A110THR00.027-0.01623.559-0.003-0.0030.0000.0000.0000.000
114A111THR0-0.014-0.00626.5160.0020.0020.0000.0000.0000.000
115A112GLY00.012-0.01030.1350.0010.0010.0000.0000.0000.000
116A113ILE00.0470.02133.0720.0000.0000.0000.0000.0000.000
117A114MET0-0.0110.01836.1990.0000.0000.0000.0000.0000.000
118A115MET0-0.091-0.04432.8780.0010.0010.0000.0000.0000.000
119A116GLU-1-0.989-0.98737.7500.0000.0000.0000.0000.0000.000
120A117ASP-1-0.933-0.95739.6710.0020.0020.0000.0000.0000.000
121A118PRO0-0.045-0.02341.7990.0000.0000.0000.0000.0000.000
122A119ILE00.0560.04041.3080.0000.0000.0000.0000.0000.000
123A120VAL00.035-0.00744.6640.0000.0000.0000.0000.0000.000
124A121GLN0-0.016-0.02244.3130.0000.0000.0000.0000.0000.000
125A122GLY00.0580.03541.2420.0010.0010.0000.0000.0000.000
126A123ALA0-0.002-0.00440.5880.0000.0000.0000.0000.0000.000
127A124SER00.0170.01339.3190.0000.0000.0000.0000.0000.000
128A125ALA00.034-0.00336.3640.0000.0000.0000.0000.0000.000
129A126ALA00.0130.02435.9360.0000.0000.0000.0000.0000.000
130A127MET0-0.0090.00737.0180.0000.0000.0000.0000.0000.000
131A128ALA0-0.006-0.01132.8440.0000.0000.0000.0000.0000.000
132A129ASN00.0240.01332.2300.0010.0010.0000.0000.0000.000
133A130GLY00.0870.05632.663-0.001-0.0010.0000.0000.0000.000
134A131ALA0-0.024-0.01033.1470.0000.0000.0000.0000.0000.000
135A132VAL00.006-0.00327.3080.0000.0000.0000.0000.0000.000
136A133THR0-0.018-0.02728.774-0.001-0.0010.0000.0000.0000.000
137A134ALA0-0.026-0.01730.175-0.001-0.0010.0000.0000.0000.000
138A135PHE00.005-0.00124.6840.0000.0000.0000.0000.0000.000
139A136ALA00.0430.01825.6770.0010.0010.0000.0000.0000.000
140A137LYS10.9400.97326.4580.0010.0010.0000.0000.0000.000
141A138SER0-0.002-0.00828.828-0.001-0.0010.0000.0000.0000.000
142A139ALA00.0290.01024.6770.0000.0000.0000.0000.0000.000
143A140ALA0-0.017-0.00423.8790.0010.0010.0000.0000.0000.000
144A141ILE0-0.092-0.04024.492-0.002-0.0020.0000.0000.0000.000
145A142GLU-1-0.951-0.97525.6510.0160.0160.0000.0000.0000.000
146A143MET0-0.0570.00620.0680.0070.0070.0000.0000.0000.000
147A144PRO00.0240.02318.426-0.004-0.0040.0000.0000.0000.000
148A145ARG10.8330.88412.989-0.110-0.1100.0000.0000.0000.000
149A146GLY0-0.034-0.01415.919-0.011-0.0110.0000.0000.0000.000
150A147ILE0-0.0170.00714.795-0.014-0.0140.0000.0000.0000.000
151A148ARG10.8050.90716.1070.0680.0680.0000.0000.0000.000
152A149ILE00.0130.00318.7670.0010.0010.0000.0000.0000.000
153A150ASN0-0.034-0.00521.2450.0030.0030.0000.0000.0000.000
154A151THR0-0.014-0.00623.3070.0030.0030.0000.0000.0000.000
155A152VAL00.0080.01224.192-0.002-0.0020.0000.0000.0000.000
156A153SER00.022-0.00726.9310.0030.0030.0000.0000.0000.000
157A154PRO0-0.024-0.00529.220-0.001-0.0010.0000.0000.0000.000
158A155ASN00.0920.02931.6670.0010.0010.0000.0000.0000.000
159A156VAL00.0040.00833.9800.0000.0000.0000.0000.0000.000
160A157LEU0-0.023-0.02530.309-0.001-0.0010.0000.0000.0000.000
161A158GLU-1-0.861-0.94834.5770.0050.0050.0000.0000.0000.000
162A159GLU-1-0.832-0.92632.1460.0070.0070.0000.0000.0000.000
163A160SER0-0.113-0.06534.1520.0010.0010.0000.0000.0000.000
164A161TRP00.0490.02436.5250.0000.0000.0000.0000.0000.000
165A162ASP-1-0.862-0.93339.7960.0070.0070.0000.0000.0000.000
166A163LYS10.8480.93736.363-0.009-0.0090.0000.0000.0000.000
167A164LEU0-0.068-0.05736.6100.0000.0000.0000.0000.0000.000
168A165GLU-1-0.867-0.91741.0640.0050.0050.0000.0000.0000.000
169A166PRO00.0550.03043.7500.0000.0000.0000.0000.0000.000
170A167PHE0-0.087-0.03942.4150.0000.0000.0000.0000.0000.000
171A168PHE0-0.107-0.06838.6590.0000.0000.0000.0000.0000.000
172A169GLU-1-0.872-0.93043.7300.0050.0050.0000.0000.0000.000
173A170GLY0-0.022-0.01146.9420.0000.0000.0000.0000.0000.000
174A171PHE0-0.031-0.01240.4460.0000.0000.0000.0000.0000.000
175A172LEU0-0.029-0.02140.8950.0000.0000.0000.0000.0000.000
176A173PRO0-0.0160.00637.7440.0000.0000.0000.0000.0000.000
177A174VAL0-0.053-0.02432.933-0.001-0.0010.0000.0000.0000.000
178A175PRO00.0620.03632.1310.0000.0000.0000.0000.0000.000
179A176ALA00.0410.01028.589-0.001-0.0010.0000.0000.0000.000
180A177ALA00.0360.01027.177-0.002-0.0020.0000.0000.0000.000
181A178LYS10.9060.95027.275-0.001-0.0010.0000.0000.0000.000
182A179VAL00.0400.01927.019-0.002-0.0020.0000.0000.0000.000
183A180ALA00.0320.01623.501-0.003-0.0030.0000.0000.0000.000
184A181ARG10.9220.96022.9300.0000.0000.0000.0000.0000.000
185A182ALA0-0.0090.00823.615-0.005-0.0050.0000.0000.0000.000
186A183PHE00.0540.01620.557-0.003-0.0030.0000.0000.0000.000
187A184GLU-1-0.802-0.88418.711-0.031-0.0310.0000.0000.0000.000
188A185LYS10.8760.95019.3100.0140.0140.0000.0000.0000.000
189A186SER0-0.022-0.02020.034-0.005-0.0050.0000.0000.0000.000
190A187VAL00.0290.01714.291-0.004-0.0040.0000.0000.0000.000
191A188PHE0-0.005-0.01813.077-0.013-0.0130.0000.0000.0000.000
192A189GLY0-0.0290.01116.9640.0000.0000.0000.0000.0000.000
193A190ALA00.005-0.01218.401-0.008-0.0080.0000.0000.0000.000
194A191GLN00.0050.01020.4410.0060.0060.0000.0000.0000.000
195A192THR00.0630.02021.876-0.004-0.0040.0000.0000.0000.000
196A193GLY00.0620.03723.7270.0010.0010.0000.0000.0000.000
197A194GLU-1-0.979-0.97925.787-0.011-0.0110.0000.0000.0000.000
198A195SER0-0.020-0.01026.8220.0010.0010.0000.0000.0000.000
199A196TYR0-0.026-0.04823.382-0.002-0.0020.0000.0000.0000.000
200A197GLN00.0230.02228.7580.0000.0000.0000.0000.0000.000
201A198VAL0-0.069-0.03328.942-0.001-0.0010.0000.0000.0000.000
202A199TYR00.0810.06232.2100.0010.0010.0000.0000.0000.000