FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: YY882

Calculation Name: 2X9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPF9

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 236
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2960247.267469
FMO2-HF: Nuclear repulsion 2867095.927418
FMO2-HF: Total energy -93151.34005
FMO2-MP2: Total energy -93420.773714


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:49:DPN)


Summations of interaction energy for fragment #1(A:49:DPN)
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.
-5.753-2.5451.589-1.748-3.051-0.008
Interaction energy analysis for fragmet #1(A:49:DPN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.015
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].
3A51LEU00.0730.0352.555-4.703-1.9101.585-1.694-2.685-0.008
4A52GLY0-0.0200.0075.3200.0570.203-0.001-0.007-0.1380.000
5A53ARG10.9390.9455.9360.1590.1590.0000.0000.0000.000
6A54ARG10.8640.9138.1750.0520.0520.0000.0000.0000.000
7A55ILE0-0.016-0.0073.547-0.2480.0210.005-0.047-0.2280.000
8A56PRO00.0170.0357.9230.0490.0490.0000.0000.0000.000
9A57GLU-1-0.946-0.9719.8970.7210.7210.0000.0000.0000.000
10A58ALA0-0.058-0.04511.718-0.062-0.0620.0000.0000.0000.000
11A59THR00.0040.00914.082-0.041-0.0410.0000.0000.0000.000
12A60ALA00.0330.01317.8060.0130.0130.0000.0000.0000.000
13A61GLN00.0610.04420.414-0.017-0.0170.0000.0000.0000.000
14A62GLU-1-0.855-0.93422.9290.1660.1660.0000.0000.0000.000
15A63GLY00.0020.00323.924-0.005-0.0050.0000.0000.0000.000
16A64PHE0-0.065-0.03019.2680.0070.0070.0000.0000.0000.000
17A65LEU00.0240.02415.4620.0060.0060.0000.0000.0000.000
18A66VAL0-0.007-0.00816.0330.0330.0330.0000.0000.0000.000
19A67ARG10.9650.9796.987-1.649-1.6490.0000.0000.0000.000
20A68PRO00.0230.01911.9900.0530.0530.0000.0000.0000.000
21A69PHE00.001-0.0016.1710.1560.1560.0000.0000.0000.000
22A70THR0-0.012-0.0559.654-0.030-0.0300.0000.0000.0000.000
23A71GLN00.0740.02211.6310.0480.0480.0000.0000.0000.000
24A72GLN00.0280.01313.846-0.020-0.0200.0000.0000.0000.000
25A73CYM-1-0.784-0.78314.3320.1110.1110.0000.0000.0000.000
26A74GLN00.001-0.01715.3700.0570.0570.0000.0000.0000.000
27A75ILE0-0.039-0.01017.103-0.002-0.0020.0000.0000.0000.000
28A76ILE00.0160.00719.0490.0010.0010.0000.0000.0000.000
29A77HIS0-0.076-0.03918.5860.0130.0130.0000.0000.0000.000
30A78THR0-0.065-0.03620.6540.0010.0010.0000.0000.0000.000
31A79GLU-1-0.942-0.96323.1780.0340.0340.0000.0000.0000.000
32A80GLY00.0030.02724.357-0.004-0.0040.0000.0000.0000.000
33A81ASP-1-0.785-0.86825.8800.0410.0410.0000.0000.0000.000
34A82HIS0-0.038-0.04725.1990.0000.0000.0000.0000.0000.000
35A83ALA00.0390.03321.8410.0090.0090.0000.0000.0000.000
36A84VAL0-0.0040.00521.028-0.011-0.0110.0000.0000.0000.000
37A85ILE00.0050.01320.4590.0200.0200.0000.0000.0000.000
38A86GLY00.0570.03219.924-0.016-0.0160.0000.0000.0000.000
39A87VAL0-0.049-0.03920.6580.0170.0170.0000.0000.0000.000
40A88SER00.0420.03619.968-0.005-0.0050.0000.0000.0000.000
41A89PRO00.0310.01322.3150.0080.0080.0000.0000.0000.000
42A90GLY0-0.039-0.03224.302-0.002-0.0020.0000.0000.0000.000
43A91ASN00.0270.02918.6530.0080.0080.0000.0000.0000.000
44A92SER0-0.019-0.03023.0710.0060.0060.0000.0000.0000.000
45A93TYR00.0740.04318.7100.0070.0070.0000.0000.0000.000
46A94PHE00.0350.02119.2620.0050.0050.0000.0000.0000.000
47A95SER0-0.045-0.01924.196-0.015-0.0150.0000.0000.0000.000
48A96ARG10.9940.97427.257-0.065-0.0650.0000.0000.0000.000
49A97GLN0-0.016-0.00428.351-0.010-0.0100.0000.0000.0000.000
50A98ARG10.9480.99021.554-0.178-0.1780.0000.0000.0000.000
51A99LEU00.005-0.00724.9410.0060.0060.0000.0000.0000.000
52A100ARG10.9420.96926.641-0.083-0.0830.0000.0000.0000.000
53A101ASP-1-0.818-0.89825.5540.1340.1340.0000.0000.0000.000
54A102LEU0-0.027-0.01820.5340.0030.0030.0000.0000.0000.000
55A103GLY00.0350.01724.607-0.001-0.0010.0000.0000.0000.000
56A104LEU0-0.046-0.02427.699-0.006-0.0060.0000.0000.0000.000
57A105TRP0-0.0100.00319.930-0.004-0.0040.0000.0000.0000.000
58A106GLY00.0480.00324.9210.0000.0000.0000.0000.0000.000
59A107LEU0-0.038-0.02825.796-0.007-0.0070.0000.0000.0000.000
60A108THR0-0.051-0.02727.633-0.010-0.0100.0000.0000.0000.000
61A109ASN0-0.125-0.07524.434-0.003-0.0030.0000.0000.0000.000
62A110PHE0-0.0020.01621.1730.0060.0060.0000.0000.0000.000
63A111ASP-1-0.860-0.91727.2320.0550.0550.0000.0000.0000.000
64A112ARG10.8230.92028.855-0.043-0.0430.0000.0000.0000.000
65A113VAL00.0140.00525.3340.0070.0070.0000.0000.0000.000
66A114ASP-1-0.768-0.85126.0210.0390.0390.0000.0000.0000.000
67A115PHE0-0.012-0.00624.9660.0080.0080.0000.0000.0000.000
68A116VAL00.0120.00023.890-0.009-0.0090.0000.0000.0000.000
69A117TYR0-0.033-0.01223.9670.0040.0040.0000.0000.0000.000
70A118THR0-0.016-0.02221.794-0.004-0.0040.0000.0000.0000.000
71A119ASP-1-0.844-0.91224.9110.0160.0160.0000.0000.0000.000
72A120VAL00.0100.01125.476-0.003-0.0030.0000.0000.0000.000
73A121HIS00.0720.03424.7700.0020.0020.0000.0000.0000.000
74A122VAL00.0040.02225.341-0.001-0.0010.0000.0000.0000.000
75A123ALA0-0.060-0.03926.9670.0000.0000.0000.0000.0000.000
76A124GLU-1-0.775-0.90227.544-0.015-0.0150.0000.0000.0000.000
77A125SER00.000-0.00823.625-0.006-0.0060.0000.0000.0000.000
78A126TYR0-0.079-0.03925.4100.0020.0020.0000.0000.0000.000
79A127GLU-1-0.897-0.95127.913-0.019-0.0190.0000.0000.0000.000
80A128ALA0-0.0340.01225.392-0.002-0.0020.0000.0000.0000.000
81A129LEU0-0.083-0.05022.687-0.004-0.0040.0000.0000.0000.000
82A130GLY0-0.0020.00026.6920.0020.0020.0000.0000.0000.000
83A131ASP-1-0.903-0.94030.3730.0050.0050.0000.0000.0000.000
84A132SER00.008-0.00432.492-0.003-0.0030.0000.0000.0000.000
85A133ALA00.1540.06334.5680.0020.0020.0000.0000.0000.000
86A134ILE0-0.037-0.01635.6450.0020.0020.0000.0000.0000.000
87A135GLU-1-0.777-0.87634.3010.0130.0130.0000.0000.0000.000
88A136ALA00.0240.02031.3580.0040.0040.0000.0000.0000.000
89A137ARG11.0251.00532.2990.0030.0030.0000.0000.0000.000
90A138ARG10.7810.87234.520-0.011-0.0110.0000.0000.0000.000
91A139LYS10.8510.92430.284-0.007-0.0070.0000.0000.0000.000
92A140ALA00.0730.04730.1900.0050.0050.0000.0000.0000.000
93A141VAL0-0.011-0.00431.1950.0040.0040.0000.0000.0000.000
94A142LYS10.8940.94932.170-0.027-0.0270.0000.0000.0000.000
95A143ASN0-0.021-0.03728.2550.0060.0060.0000.0000.0000.000
96A144ILE00.0520.04029.0250.0060.0060.0000.0000.0000.000
97A145ARG10.8810.93930.754-0.017-0.0170.0000.0000.0000.000
98A146GLY00.0210.01532.0530.0020.0020.0000.0000.0000.000
99A147VAL0-0.006-0.00426.0240.0040.0040.0000.0000.0000.000
100A148ARG11.0251.02729.436-0.023-0.0230.0000.0000.0000.000
101A149ALA0-0.0240.01431.7040.0010.0010.0000.0000.0000.000
102A150LYS10.9130.94628.983-0.069-0.0690.0000.0000.0000.000
103A151ILE00.0320.02926.7620.0030.0030.0000.0000.0000.000
104A152THR00.007-0.01630.5120.0000.0000.0000.0000.0000.000
105A153THR0-0.072-0.03434.026-0.001-0.0010.0000.0000.0000.000
106A154THR0-0.032-0.02829.5200.0020.0020.0000.0000.0000.000
107A155VAL00.0400.01831.1210.0020.0020.0000.0000.0000.000
108A156ASN0-0.024-0.00533.525-0.002-0.0020.0000.0000.0000.000
109A157GLU-1-0.943-0.98135.1750.0640.0640.0000.0000.0000.000
110A158LEU0-0.082-0.04130.8290.0000.0000.0000.0000.0000.000
111A159ASP-1-0.766-0.86634.5660.0520.0520.0000.0000.0000.000
112A160PRO0-0.045-0.01436.409-0.003-0.0030.0000.0000.0000.000
113A161ALA0-0.038-0.02739.716-0.003-0.0030.0000.0000.0000.000
114A162GLY0-0.0110.01636.495-0.003-0.0030.0000.0000.0000.000
115A163ALA0-0.060-0.02137.065-0.002-0.0020.0000.0000.0000.000
116A164ARG10.7860.86031.122-0.069-0.0690.0000.0000.0000.000
117A165LEU0-0.0200.00228.9200.0040.0040.0000.0000.0000.000
118A166CYS0-0.024-0.00530.494-0.007-0.0070.0000.0000.0000.000
119A167VAL0-0.027-0.02029.2760.0060.0060.0000.0000.0000.000
120A168ARG10.8240.90429.162-0.035-0.0350.0000.0000.0000.000
121A169PRO0-0.028-0.00228.6450.0050.0050.0000.0000.0000.000
122A170MET00.0430.01822.446-0.004-0.0040.0000.0000.0000.000
123A171SER0-0.069-0.06527.272-0.005-0.0050.0000.0000.0000.000
124A172GLU-1-0.887-0.95230.3810.0160.0160.0000.0000.0000.000
125A173PHE00.016-0.00726.935-0.002-0.0020.0000.0000.0000.000
126A174GLN00.0150.01329.703-0.006-0.0060.0000.0000.0000.000
127A175SER0-0.095-0.04731.774-0.003-0.0030.0000.0000.0000.000
128A176ASN00.0020.00530.990-0.003-0.0030.0000.0000.0000.000
129A177GLU-1-0.920-0.97032.058-0.021-0.0210.0000.0000.0000.000
130A178ALA00.1050.06029.230-0.004-0.0040.0000.0000.0000.000
131A179TYR0-0.053-0.05725.245-0.006-0.0060.0000.0000.0000.000
132A180ARG10.8920.93327.7790.0120.0120.0000.0000.0000.000
133A181GLU-1-0.942-0.95629.863-0.035-0.0350.0000.0000.0000.000
134A182LEU0-0.005-0.00223.819-0.007-0.0070.0000.0000.0000.000
135A183HIS00.012-0.00124.579-0.010-0.0100.0000.0000.0000.000
136A184ALA0-0.033-0.01526.085-0.007-0.0070.0000.0000.0000.000
137A185ASP-1-0.822-0.89824.871-0.089-0.0890.0000.0000.0000.000
138A186LEU0-0.0040.00219.985-0.011-0.0110.0000.0000.0000.000
139A187LEU0-0.007-0.03323.694-0.010-0.0100.0000.0000.0000.000
140A188THR0-0.041-0.00425.795-0.003-0.0030.0000.0000.0000.000
141A189ARG10.8780.92022.2410.1050.1050.0000.0000.0000.000
142A190LEU0-0.0010.00719.762-0.010-0.0100.0000.0000.0000.000
143A191LYS10.8780.95423.4860.0640.0640.0000.0000.0000.000
144A192ASP-1-0.913-0.98327.096-0.084-0.0840.0000.0000.0000.000
145A193ASP-1-0.874-0.92022.693-0.166-0.1660.0000.0000.0000.000
146A194GLU-1-0.988-1.01122.836-0.141-0.1410.0000.0000.0000.000
147A195ASP-1-0.869-0.92319.669-0.192-0.1920.0000.0000.0000.000
148A196MET0-0.059-0.02718.264-0.023-0.0230.0000.0000.0000.000
149A197ARG10.9240.95717.9940.1140.1140.0000.0000.0000.000
150A198ALA0-0.013-0.00118.430-0.005-0.0050.0000.0000.0000.000
151A199VAL0-0.003-0.00612.550-0.021-0.0210.0000.0000.0000.000
152A200CYS00.0030.00613.766-0.030-0.0300.0000.0000.0000.000
153A201GLN0-0.013-0.01115.0770.0130.0130.0000.0000.0000.000
154A202ASP-1-0.891-0.93411.407-0.430-0.4300.0000.0000.0000.000
155A203LEU0-0.012-0.0058.745-0.016-0.0160.0000.0000.0000.000
156A204VAL00.0090.00211.6290.0220.0220.0000.0000.0000.000
157A205ARG10.8710.93014.3920.2030.2030.0000.0000.0000.000
158A206ARG10.8450.9238.5290.4460.4460.0000.0000.0000.000
159A207PHE00.0750.03011.0970.0480.0480.0000.0000.0000.000
160A208LEU00.0350.00711.8800.0500.0500.0000.0000.0000.000
161A209SER0-0.102-0.03412.0800.0220.0220.0000.0000.0000.000
162A210THR0-0.063-0.0319.7490.0350.0350.0000.0000.0000.000
163A211LYS10.8770.94913.228-0.018-0.0180.0000.0000.0000.000
164A212VAL0-0.0140.00916.469-0.002-0.0020.0000.0000.0000.000
165A213GLY0-0.005-0.02819.7470.0060.0060.0000.0000.0000.000
166A214PRO0-0.0140.01620.6560.0010.0010.0000.0000.0000.000
167A215ARG10.9170.94112.7810.1060.1060.0000.0000.0000.000
168A216GLN0-0.023-0.01419.748-0.002-0.0020.0000.0000.0000.000
169A217GLY0-0.0050.00719.764-0.002-0.0020.0000.0000.0000.000
170A218ALA0-0.003-0.00519.5410.0120.0120.0000.0000.0000.000
171A219THR00.0140.01221.253-0.006-0.0060.0000.0000.0000.000
172A220ALA00.0840.02322.974-0.004-0.0040.0000.0000.0000.000
173A221THR00.0130.01024.232-0.004-0.0040.0000.0000.0000.000
174A222GLN00.028-0.00321.734-0.005-0.0050.0000.0000.0000.000
175A223GLU-1-0.880-0.93019.015-0.141-0.1410.0000.0000.0000.000
176A224GLN00.0030.00720.706-0.010-0.0100.0000.0000.0000.000
177A225VAL00.0450.01823.2960.0030.0030.0000.0000.0000.000
178A226CYS0-0.078-0.02716.9780.0070.0070.0000.0000.0000.000
179A227MET00.0240.00817.9140.0010.0010.0000.0000.0000.000
180A228ASP-1-0.858-0.92020.143-0.057-0.0570.0000.0000.0000.000
181A229TYR0-0.084-0.04619.3950.0100.0100.0000.0000.0000.000
182A230ILE0-0.010-0.01615.1790.0070.0070.0000.0000.0000.000
183A231CYS0-0.029-0.02018.7810.0010.0010.0000.0000.0000.000
184A232ALA00.0350.02721.2140.0050.0050.0000.0000.0000.000
185A233GLU-1-0.846-0.91518.2710.0310.0310.0000.0000.0000.000
186A234ALA0-0.006-0.00718.6660.0090.0090.0000.0000.0000.000
187A235PRO00.0150.00919.6790.0020.0020.0000.0000.0000.000
188A236LEU00.0580.02821.4760.0020.0020.0000.0000.0000.000
189A237PHE0-0.053-0.01515.0480.0150.0150.0000.0000.0000.000
190A238LEU0-0.0210.01417.754-0.006-0.0060.0000.0000.0000.000
191A239ASP-1-0.830-0.95420.106-0.021-0.0210.0000.0000.0000.000
192A240THR00.0240.00921.9250.0010.0010.0000.0000.0000.000
193A241PRO0-0.059-0.00723.4670.0010.0010.0000.0000.0000.000
194A242ALA00.0080.00726.6460.0000.0000.0000.0000.0000.000
195A243ILE0-0.083-0.02424.9540.0010.0010.0000.0000.0000.000
196A244LEU0-0.053-0.04826.7630.0010.0010.0000.0000.0000.000
197A245GLY0-0.0010.02329.8070.0020.0020.0000.0000.0000.000
198A246VAL0-0.080-0.03026.7490.0030.0030.0000.0000.0000.000
199A247PRO00.000-0.00128.674-0.005-0.0050.0000.0000.0000.000
200A248SER0-0.040-0.04723.586-0.004-0.0040.0000.0000.0000.000
201A249SER0-0.021-0.03722.6300.0070.0070.0000.0000.0000.000
202A250LEU00.0090.01416.524-0.004-0.0040.0000.0000.0000.000
203A251ASN0-0.040-0.02917.0090.0220.0220.0000.0000.0000.000
204A252CYS0-0.0030.01416.0070.0430.0430.0000.0000.0000.000
205A253TYR0-0.039-0.05913.809-0.034-0.0340.0000.0000.0000.000
206A254HIS0-0.0070.02114.0950.0730.0730.0000.0000.0000.000
207A255GLN00.0040.00010.6790.0080.0080.0000.0000.0000.000
208A256SER0-0.002-0.0056.8620.0880.0880.0000.0000.0000.000
209A257LEU00.0060.0069.185-0.098-0.0980.0000.0000.0000.000
210A258PRO0-0.005-0.0069.508-0.043-0.0430.0000.0000.0000.000
211A259LEU00.0970.0359.920-0.094-0.0940.0000.0000.0000.000
212A260ALA0-0.030-0.0028.675-0.020-0.0200.0000.0000.0000.000
213A261GLU-1-0.938-0.9746.380-1.162-1.1620.0000.0000.0000.000
214A262MET0-0.027-0.0088.724-0.006-0.0060.0000.0000.0000.000
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