FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 2G9VR

Calculation Name: 1D2O-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q53654

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2012877.622032
FMO2-HF: Nuclear repulsion 1939004.747721
FMO2-HF: Total energy -73872.87431
FMO2-MP2: Total energy -74092.001959


3D Structure Molmil
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:535:GLU)


Summations of interaction energy for fragment #1(A:535: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.
-4.0862.8783.591-4.035-6.521.7347234759768E-18
Interaction energy analysis for fragmet #1(A:535:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.038
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].
3A537THR00.006-0.0083.4659.77112.5600.107-1.312-1.584-0.001
55A589PRO00.0270.0184.7710.2160.236-0.001-0.0240.0050.000
56A590LYS10.9610.9682.419-10.553-7.2921.022-1.567-2.7160.010
57A591TYR0-0.093-0.0552.009-0.1120.7262.464-1.130-2.172-0.009
58A592ASP-1-0.820-0.9095.227-4.225-4.169-0.001-0.002-0.0530.000
4A538SER00.0070.0166.189-1.753-1.7530.0000.0000.0000.000
5A539SER0-0.012-0.0059.6780.0540.0540.0000.0000.0000.000
6A540ILE0-0.0020.00112.179-0.263-0.2630.0000.0000.0000.000
7A541GLY00.0580.03515.223-0.038-0.0380.0000.0000.0000.000
8A542GLU-1-0.920-0.95418.8321.1101.1100.0000.0000.0000.000
9A543LYS10.7980.90622.526-0.437-0.4370.0000.0000.0000.000
10A544VAL0-0.023-0.01625.7690.0210.0210.0000.0000.0000.000
11A545TRP00.006-0.00328.927-0.041-0.0410.0000.0000.0000.000
12A546ASP-1-0.907-0.94832.5900.3230.3230.0000.0000.0000.000
13A547ASP-1-0.691-0.82635.0130.2770.2770.0000.0000.0000.000
14A548LYS10.8390.91738.203-0.239-0.2390.0000.0000.0000.000
15A549ASP-1-0.912-0.95838.4520.3300.3300.0000.0000.0000.000
16A550ASN00.0140.01038.469-0.021-0.0210.0000.0000.0000.000
17A551GLN0-0.030-0.00940.301-0.006-0.0060.0000.0000.0000.000
18A552ASP-1-0.808-0.86443.4150.1560.1560.0000.0000.0000.000
19A553GLY0-0.058-0.03342.393-0.013-0.0130.0000.0000.0000.000
20A554LYS10.8890.94140.703-0.149-0.1490.0000.0000.0000.000
21A555ARG10.8480.90133.922-0.344-0.3440.0000.0000.0000.000
22A556PRO0-0.0340.00333.650-0.003-0.0030.0000.0000.0000.000
23A557GLU-1-0.913-0.97534.0580.3120.3120.0000.0000.0000.000
24A558LYS10.8090.88629.710-0.143-0.1430.0000.0000.0000.000
25A559VAL00.0100.02326.898-0.029-0.0290.0000.0000.0000.000
26A560SER0-0.004-0.02026.4640.0280.0280.0000.0000.0000.000
27A561VAL00.0030.01621.145-0.033-0.0330.0000.0000.0000.000
28A562ASN0-0.031-0.03021.271-0.031-0.0310.0000.0000.0000.000
29A563LEU0-0.025-0.00513.3660.0630.0630.0000.0000.0000.000
30A564LEU0-0.012-0.00917.220-0.147-0.1470.0000.0000.0000.000
31A565ALA00.016-0.00512.5650.0330.0330.0000.0000.0000.000
32A566ASN0-0.025-0.02511.9830.0390.0390.0000.0000.0000.000
33A567GLY00.0640.03115.3160.0390.0390.0000.0000.0000.000
34A568GLU-1-0.916-0.95717.280-1.036-1.0360.0000.0000.0000.000
35A569LYS10.9000.93917.6760.1540.1540.0000.0000.0000.000
36A570VAL00.0110.01314.158-0.013-0.0130.0000.0000.0000.000
37A571LYS10.8780.94113.0770.2010.2010.0000.0000.0000.000
38A572THR00.011-0.00418.549-0.008-0.0080.0000.0000.0000.000
39A573LEU0-0.057-0.02318.2830.0310.0310.0000.0000.0000.000
40A574ASP-1-0.814-0.87222.5230.1760.1760.0000.0000.0000.000
41A575VAL0-0.048-0.02023.1630.0700.0700.0000.0000.0000.000
42A576THR00.0430.00425.761-0.033-0.0330.0000.0000.0000.000
43A577SER00.0490.02327.8640.0580.0580.0000.0000.0000.000
44A578GLU-1-0.928-0.96228.7470.4390.4390.0000.0000.0000.000
45A579THR0-0.062-0.04223.5470.0230.0230.0000.0000.0000.000
46A580ASN0-0.046-0.03624.3620.0780.0780.0000.0000.0000.000
47A581TRP0-0.0050.01325.9840.0400.0400.0000.0000.0000.000
48A582LYS10.9120.96420.768-1.140-1.1400.0000.0000.0000.000
49A583TYR0-0.018-0.01917.953-0.088-0.0880.0000.0000.0000.000
50A584GLU-1-0.834-0.94612.4522.9602.9600.0000.0000.0000.000
51A585PHE0-0.044-0.00814.283-0.145-0.1450.0000.0000.0000.000
52A586LYS10.9310.95811.464-1.504-1.5040.0000.0000.0000.000
53A587ASP-1-0.935-0.9638.0432.3962.3960.0000.0000.0000.000
54A588LEU0-0.0110.0118.473-1.249-1.2490.0000.0000.0000.000
59A593GLU-1-0.919-0.9618.739-2.649-2.6490.0000.0000.0000.000
60A594GLY0-0.037-0.0097.8930.5220.5220.0000.0000.0000.000
61A595LYS10.9410.9828.4882.1992.1990.0000.0000.0000.000
62A596LYS10.8360.9006.3630.0140.0140.0000.0000.0000.000
63A597ILE0-0.0270.0007.2450.8600.8600.0000.0000.0000.000
64A598GLU-1-0.870-0.9279.4260.1270.1270.0000.0000.0000.000
65A599TYR0-0.064-0.0518.0170.1300.1300.0000.0000.0000.000
66A600THR00.0190.01913.3610.2300.2300.0000.0000.0000.000
67A601VAL0-0.004-0.00817.124-0.029-0.0290.0000.0000.0000.000
68A602THR00.010-0.01719.687-0.003-0.0030.0000.0000.0000.000
69A603GLU-1-0.771-0.88423.2820.3500.3500.0000.0000.0000.000
70A604ASP-1-0.875-0.91226.202-0.052-0.0520.0000.0000.0000.000
71A605HIS0-0.059-0.06228.8260.0320.0320.0000.0000.0000.000
72A606VAL0-0.020-0.00131.3380.0080.0080.0000.0000.0000.000
73A607LYS10.7980.87134.071-0.090-0.0900.0000.0000.0000.000
74A608ASP-1-0.847-0.91437.8540.1230.1230.0000.0000.0000.000
75A609TYR0-0.019-0.03334.7140.0190.0190.0000.0000.0000.000
76A610THR00.0050.01233.896-0.031-0.0310.0000.0000.0000.000
77A611THR0-0.035-0.02728.1210.0260.0260.0000.0000.0000.000
78A612ASP-1-0.927-0.95728.3370.2750.2750.0000.0000.0000.000
79A613ILE00.0000.00822.5160.0530.0530.0000.0000.0000.000
80A614ASN0-0.010-0.00623.561-0.011-0.0110.0000.0000.0000.000
81A615GLY00.0270.01119.2760.0750.0750.0000.0000.0000.000
82A616THR0-0.006-0.01516.8960.0930.0930.0000.0000.0000.000
83A617THR0-0.0110.01619.136-0.002-0.0020.0000.0000.0000.000
84A618ILE0-0.030-0.01322.195-0.083-0.0830.0000.0000.0000.000
85A619THR0-0.008-0.00725.2520.0190.0190.0000.0000.0000.000
86A620ASN0-0.033-0.01828.884-0.013-0.0130.0000.0000.0000.000
87A621LYS10.8950.94531.398-0.287-0.2870.0000.0000.0000.000
88A622TYR0-0.082-0.06535.210-0.023-0.0230.0000.0000.0000.000
89A623THR0-0.032-0.01338.3020.0030.0030.0000.0000.0000.000
90A624PRO00.0010.00940.514-0.014-0.0140.0000.0000.0000.000
91A625GLY0-0.042-0.02443.088-0.007-0.0070.0000.0000.0000.000
92A626GLU-1-0.929-0.97340.5210.0750.0750.0000.0000.0000.000
93A627THR0-0.034-0.00735.9040.0080.0080.0000.0000.0000.000
94A628SER00.0260.00832.1500.0050.0050.0000.0000.0000.000
95A629ALA0-0.048-0.02032.227-0.008-0.0080.0000.0000.0000.000
96A630THR0-0.020-0.02125.7750.0130.0130.0000.0000.0000.000
97A631VAL0-0.032-0.01127.465-0.025-0.0250.0000.0000.0000.000
98A632THR00.0160.00920.7560.0250.0250.0000.0000.0000.000
99A633LYS10.7320.88423.0680.5550.5550.0000.0000.0000.000
100A634ASN0-0.012-0.00219.686-0.118-0.1180.0000.0000.0000.000
101A635TRP0-0.024-0.03919.7940.1040.1040.0000.0000.0000.000
102A636ASP-1-0.867-0.92419.604-1.212-1.2120.0000.0000.0000.000
103A637ASP-1-0.727-0.87120.083-1.024-1.0240.0000.0000.0000.000
104A638ASN0-0.0260.00618.2400.0620.0620.0000.0000.0000.000
105A639ASN00.0380.01213.167-0.114-0.1140.0000.0000.0000.000
106A640ASN00.002-0.00816.9630.1900.1900.0000.0000.0000.000
107A641GLN0-0.014-0.00519.511-0.045-0.0450.0000.0000.0000.000
108A642ASP-1-0.864-0.92320.927-0.885-0.8850.0000.0000.0000.000
109A643GLY00.005-0.00323.3300.0500.0500.0000.0000.0000.000
110A644LYS10.8780.93724.1650.7620.7620.0000.0000.0000.000
111A645ARG10.8880.96317.7431.1601.1600.0000.0000.0000.000
112A646PRO0-0.045-0.00924.8210.0070.0070.0000.0000.0000.000
113A647THR00.022-0.01024.407-0.040-0.0400.0000.0000.0000.000
114A648GLU-1-0.947-0.97524.673-0.268-0.2680.0000.0000.0000.000
115A649ILE0-0.035-0.00426.643-0.017-0.0170.0000.0000.0000.000
116A650LYS10.9380.97229.0450.1960.1960.0000.0000.0000.000
117A651VAL00.0430.01929.397-0.018-0.0180.0000.0000.0000.000
118A652GLU-1-0.833-0.92732.449-0.101-0.1010.0000.0000.0000.000
119A653LEU00.0160.01934.248-0.013-0.0130.0000.0000.0000.000
120A654TYR0-0.030-0.01436.0640.0170.0170.0000.0000.0000.000
121A655GLN00.0220.00338.4970.0030.0030.0000.0000.0000.000
122A656ASP-1-0.836-0.92141.271-0.056-0.0560.0000.0000.0000.000
123A657GLY00.0050.00142.0310.0010.0010.0000.0000.0000.000
124A658LYS10.8300.92943.3290.0580.0580.0000.0000.0000.000
125A659ALA00.0820.05541.1910.0010.0010.0000.0000.0000.000
126A660THR0-0.057-0.06339.2490.0160.0160.0000.0000.0000.000
127A661GLY0-0.028-0.00340.8960.0140.0140.0000.0000.0000.000
128A662LYS10.9050.96836.7060.0070.0070.0000.0000.0000.000
129A663THR0-0.033-0.02534.655-0.019-0.0190.0000.0000.0000.000
130A664ALA0-0.0030.01630.0370.0240.0240.0000.0000.0000.000
131A665ILE00.000-0.00528.512-0.020-0.0200.0000.0000.0000.000
132A666LEU0-0.0250.01725.0740.0260.0260.0000.0000.0000.000
133A667ASN00.0720.02323.679-0.023-0.0230.0000.0000.0000.000
134A668GLU-1-0.855-0.92017.899-0.786-0.7860.0000.0000.0000.000
135A669SER0-0.126-0.07020.3720.0660.0660.0000.0000.0000.000
136A670ASN00.010-0.01522.7710.0290.0290.0000.0000.0000.000
137A671ASN00.0050.00817.224-0.001-0.0010.0000.0000.0000.000
138A672TRP0-0.070-0.02918.955-0.009-0.0090.0000.0000.0000.000
139A673THR00.010-0.00620.999-0.016-0.0160.0000.0000.0000.000
140A674HIS0-0.029-0.01723.6210.0520.0520.0000.0000.0000.000
141A675THR00.0020.01627.131-0.005-0.0050.0000.0000.0000.000
142A676TRP0-0.050-0.02429.5710.0130.0130.0000.0000.0000.000
143A677THR00.0330.00233.4010.0020.0020.0000.0000.0000.000
144A678GLY00.0360.02935.865-0.014-0.0140.0000.0000.0000.000
145A679LEU0-0.068-0.03335.595-0.019-0.0190.0000.0000.0000.000
146A680ASP-1-0.855-0.91539.8220.0360.0360.0000.0000.0000.000
147A681GLU-1-0.748-0.87739.3600.0630.0630.0000.0000.0000.000
148A682LYS10.8480.90242.098-0.036-0.0360.0000.0000.0000.000
149A683ALA00.0710.04745.6980.0030.0030.0000.0000.0000.000
150A684LYS10.9150.93648.1230.0080.0080.0000.0000.0000.000
151A685GLY00.0440.03850.389-0.003-0.0030.0000.0000.0000.000
152A686GLN0-0.024-0.01947.8150.0070.0070.0000.0000.0000.000
153A687GLN00.0160.02039.5640.0010.0010.0000.0000.0000.000
154A688VAL0-0.080-0.01341.645-0.012-0.0120.0000.0000.0000.000
155A689LYS10.8130.88439.6430.0630.0630.0000.0000.0000.000
156A690TYR0-0.010-0.03436.177-0.005-0.0050.0000.0000.0000.000
157A691THR0-0.012-0.00134.810-0.010-0.0100.0000.0000.0000.000
158A692VAL0-0.004-0.00230.4410.0180.0180.0000.0000.0000.000
159A693GLU-1-0.866-0.90733.807-0.221-0.2210.0000.0000.0000.000
160A694GLU-1-0.759-0.86028.895-0.441-0.4410.0000.0000.0000.000
161A695LEU0-0.013-0.00932.9500.0010.0010.0000.0000.0000.000
162A696THR0-0.042-0.01330.9590.0080.0080.0000.0000.0000.000
163A697LYS00.0950.06832.704-0.027-0.0270.0000.0000.0000.000
164A698VAL00.0040.00428.061-0.003-0.0030.0000.0000.0000.000
165A699LYS10.8630.90231.5090.3780.3780.0000.0000.0000.000
166A700GLY00.0350.01930.862-0.023-0.0230.0000.0000.0000.000
167A701TYR0-0.042-0.05023.508-0.024-0.0240.0000.0000.0000.000
168A702THR0-0.062-0.01129.6030.0560.0560.0000.0000.0000.000
169A703THR00.008-0.01529.181-0.056-0.0560.0000.0000.0000.000
170A704HIS0-0.014-0.00329.3200.0330.0330.0000.0000.0000.000
171A705VAL0-0.005-0.01029.046-0.026-0.0260.0000.0000.0000.000
172A706ASP-1-0.866-0.90627.769-0.261-0.2610.0000.0000.0000.000
173A707ASN00.026-0.02429.7250.0260.0260.0000.0000.0000.000
174A708ASN0-0.077-0.04730.8700.0450.0450.0000.0000.0000.000
175A709ASP-1-0.790-0.87729.5310.0120.0120.0000.0000.0000.000
176A710MET0-0.024-0.00930.290-0.017-0.0170.0000.0000.0000.000
177A711GLY00.0330.02129.4260.0040.0040.0000.0000.0000.000
178A712ASN0-0.006-0.00224.0190.0140.0140.0000.0000.0000.000
179A713LEU00.0090.02826.909-0.040-0.0400.0000.0000.0000.000
180A714ILE00.0030.00422.378-0.015-0.0150.0000.0000.0000.000
181A715THR0-0.0140.00325.9470.0060.0060.0000.0000.0000.000
182A716THR0-0.018-0.02324.005-0.050-0.0500.0000.0000.0000.000
183A717ASN0-0.048-0.03724.8470.0490.0490.0000.0000.0000.000
184A718LYS10.9410.97724.4570.6340.6340.0000.0000.0000.000
185A719TYR0-0.070-0.04124.7960.1020.1020.0000.0000.0000.000
186A720THR0-0.100-0.07126.574-0.024-0.0240.0000.0000.0000.000
187A721PRO-1-0.949-0.94828.611-0.510-0.5100.0000.0000.0000.000