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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 9GN52

Calculation Name: 3X2R-D-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3X2R

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0F6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1707328.812594
FMO2-HF: Nuclear repulsion 1633627.720136
FMO2-HF: Total energy -73701.092457
FMO2-MP2: Total energy -73916.796794


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(D:47:ACE )


Summations of interaction energy for fragment #1(D:47:ACE )
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.
0.2051.6270.034-0.636-0.819-0.002
Interaction energy analysis for fragmet #1(D:47:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.018
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].
3D49ILE 00.0590.0573.8890.9471.574-0.005-0.248-0.3740.000
4D50PHE 0-0.029-0.0146.780-0.054-0.0540.0000.0000.0000.000
5D51VAL 00.0530.03510.1010.0780.0780.0000.0000.0000.000
6D52SER 0-0.030-0.02912.8570.0030.0030.0000.0000.0000.000
7D53VAL 00.0070.00516.5550.0080.0080.0000.0000.0000.000
8D54TYR 00.0140.00819.2440.0010.0010.0000.0000.0000.000
9D55ASN 00.011-0.00922.9320.0030.0030.0000.0000.0000.000
10D56ILE 0-0.0050.02222.554-0.003-0.0030.0000.0000.0000.000
11D57GLN 0-0.037-0.01425.5110.0010.0010.0000.0000.0000.000
12D58ASP -1-0.836-0.92429.230-0.076-0.0760.0000.0000.0000.000
13D59GLU -1-0.919-0.96930.992-0.069-0.0690.0000.0000.0000.000
14D60THR 00.0040.00633.5700.0050.0050.0000.0000.0000.000
15D61GLY 0-0.0150.00035.5390.0040.0040.0000.0000.0000.000
16D62GLN 0-0.044-0.02437.9810.0060.0060.0000.0000.0000.000
17D63PHE 0-0.002-0.01839.204-0.003-0.0030.0000.0000.0000.000
18D64LYS 10.8880.95239.8580.0600.0600.0000.0000.0000.000
19D65PRO 00.0450.03443.2850.0020.0020.0000.0000.0000.000
20D66TYR 00.0240.02046.880-0.001-0.0010.0000.0000.0000.000
21D67PRO 00.004-0.03448.9760.0000.0000.0000.0000.0000.000
22D68ALA 0-0.062-0.00745.0650.0000.0000.0000.0000.0000.000
23D69SER 00.0530.03045.5130.0020.0020.0000.0000.0000.000
24D70ASN 00.0700.04145.275-0.002-0.0020.0000.0000.0000.000
25D71PHE 0-0.008-0.01143.4320.0000.0000.0000.0000.0000.000
26D72SER 0-0.100-0.05740.990-0.003-0.0030.0000.0000.0000.000
27D73THR 00.0710.04235.8750.0030.0030.0000.0000.0000.000
28D74ALA 0-0.038-0.02138.2310.0000.0000.0000.0000.0000.000
29D75VAL 00.0180.00231.956-0.003-0.0030.0000.0000.0000.000
30D76PRO 0-0.035-0.00730.4070.0010.0010.0000.0000.0000.000
31D77GLN 00.0630.01831.176-0.001-0.0010.0000.0000.0000.000
32D78SER 00.0070.00427.332-0.002-0.0020.0000.0000.0000.000
33D79ALA 00.0340.02424.755-0.014-0.0140.0000.0000.0000.000
34D80THR 00.006-0.00322.0380.0070.0070.0000.0000.0000.000
35D81ALA 00.0160.02421.995-0.005-0.0050.0000.0000.0000.000
36D82MET 0-0.001-0.00120.883-0.023-0.0230.0000.0000.0000.000
37D83LEU 00.0540.04117.775-0.020-0.0200.0000.0000.0000.000
38D84VAL 00.0230.00916.934-0.043-0.0430.0000.0000.0000.000
39D85THR 00.024-0.02416.244-0.048-0.0480.0000.0000.0000.000
40D86ALA 00.0540.04816.812-0.031-0.0310.0000.0000.0000.000
41D87LEU 0-0.010-0.01213.028-0.054-0.0540.0000.0000.0000.000
42D88LYS 10.9110.95511.5400.4190.4190.0000.0000.0000.000
43D89ASP -1-0.927-0.97112.260-0.457-0.4570.0000.0000.0000.000
44D90SER 0-0.0190.00212.1470.0140.0140.0000.0000.0000.000
45D91ARG 10.7280.8907.9440.4410.4410.0000.0000.0000.000
46D92TRP 00.061-0.0063.689-0.985-0.1900.039-0.388-0.445-0.002
47D93PHE 00.0730.0306.2270.2530.2530.0000.0000.0000.000
48D94ILE 0-0.124-0.0587.5260.0130.0130.0000.0000.0000.000
49D95PRO 00.0490.02410.0690.1020.1020.0000.0000.0000.000
50D96LEU 0-0.034-0.02312.6790.0170.0170.0000.0000.0000.000
51D97GLU -1-0.912-0.96115.456-0.124-0.1240.0000.0000.0000.000
52D98ARG 10.8410.92317.0600.1470.1470.0000.0000.0000.000
53D99GLN 00.0920.08021.7140.0010.0010.0000.0000.0000.000
54D100GLY 0-0.005-0.00624.3810.0100.0100.0000.0000.0000.000
55D101LEU 0-0.003-0.01122.8220.0020.0020.0000.0000.0000.000
56D102GLN 00.0360.01724.9080.0040.0040.0000.0000.0000.000
57D103ASN 00.0490.00827.4720.0110.0110.0000.0000.0000.000
58D104LEU 00.0540.04620.7170.0060.0060.0000.0000.0000.000
59D105LEU 0-0.014-0.02425.2530.0070.0070.0000.0000.0000.000
60D106ASN 0-0.031-0.02527.2490.0100.0100.0000.0000.0000.000
61D107GLU -1-0.853-0.92026.718-0.058-0.0580.0000.0000.0000.000
62D108ARG 10.9150.95421.3480.0640.0640.0000.0000.0000.000
63D109LYS 10.8670.94427.4930.0490.0490.0000.0000.0000.000
64D110ILE 00.0420.03331.0990.0050.0050.0000.0000.0000.000
65D111ILE 0-0.030-0.01625.8600.0030.0030.0000.0000.0000.000
66D112ARG 10.9110.94826.4390.0340.0340.0000.0000.0000.000
67D113ALA 00.0250.01930.8740.0030.0030.0000.0000.0000.000
68D114ALA 0-0.027-0.01232.5750.0020.0020.0000.0000.0000.000
69D115GLN 0-0.087-0.04027.5180.0040.0040.0000.0000.0000.000
70D116GLU -1-0.969-0.97333.256-0.010-0.0100.0000.0000.0000.000
71D117NME 0-0.0210.00036.1970.0010.0010.0000.0000.0000.000
72D128ACE 00.0240.00219.5400.0000.0000.0000.0000.0000.000
73D129GLN 00.0210.00220.439-0.001-0.0010.0000.0000.0000.000
74D130SER 0-0.020-0.00919.799-0.001-0.0010.0000.0000.0000.000
75D131LEU 0-0.028-0.02518.741-0.009-0.0090.0000.0000.0000.000
76D132THR 0-0.0120.01112.8790.0090.0090.0000.0000.0000.000
77D133ALA 00.0650.02415.164-0.019-0.0190.0000.0000.0000.000
78D134ALA 0-0.012-0.01813.089-0.021-0.0210.0000.0000.0000.000
79D135ASN 00.0310.01212.2680.0080.0080.0000.0000.0000.000
80D136ILE 00.0020.01311.5680.0090.0090.0000.0000.0000.000
81D137MET 00.0130.00014.361-0.032-0.0320.0000.0000.0000.000
82D138VAL 0-0.046-0.01115.4410.0010.0010.0000.0000.0000.000
83D139GLU -1-0.895-0.96118.109-0.100-0.1000.0000.0000.0000.000
84D140GLY 0-0.028-0.01621.814-0.009-0.0090.0000.0000.0000.000
85D141SER 0-0.031-0.03324.522-0.002-0.0020.0000.0000.0000.000
86D142ILE 0-0.032-0.02627.000-0.005-0.0050.0000.0000.0000.000
87D143ILE 00.0130.00429.1450.0060.0060.0000.0000.0000.000
88D144GLY 00.0180.01131.1550.0060.0060.0000.0000.0000.000
89D145TYR 0-0.141-0.14333.392-0.006-0.0060.0000.0000.0000.000
90D146GLU -1-0.915-0.95436.041-0.049-0.0490.0000.0000.0000.000
91D147SER 00.1020.05339.107-0.002-0.0020.0000.0000.0000.000
92D148ASN 00.008-0.01941.9110.0000.0000.0000.0000.0000.000
93D149VAL 0-0.0120.01639.171-0.001-0.0010.0000.0000.0000.000
94D150LYS 10.8740.95141.8700.0420.0420.0000.0000.0000.000
95D151SER 00.011-0.00543.303-0.001-0.0010.0000.0000.0000.000
96D152GLY 0-0.036-0.01245.9410.0020.0020.0000.0000.0000.000
97D153GLY 00.0320.01048.610-0.002-0.0020.0000.0000.0000.000
98D154VAL 0-0.065-0.01450.8160.0020.0020.0000.0000.0000.000
99D155GLY 00.0870.02753.941-0.001-0.0010.0000.0000.0000.000
100D156ALA 0-0.065-0.01856.6780.0010.0010.0000.0000.0000.000
101D157ARG 10.9670.98160.1350.0210.0210.0000.0000.0000.000
102D158TYR 00.0010.01863.0280.0010.0010.0000.0000.0000.000
103D159PHE 00.0210.04165.8510.0000.0000.0000.0000.0000.000
104D160GLY 00.010-0.03767.4270.0000.0000.0000.0000.0000.000
105D161ILE 0-0.038-0.02261.2840.0000.0000.0000.0000.0000.000
106D162GLY 0-0.005-0.00761.3390.0000.0000.0000.0000.0000.000
107D163ALA 0-0.005-0.00856.0650.0000.0000.0000.0000.0000.000
108D164ASP -1-0.923-0.96754.773-0.030-0.0300.0000.0000.0000.000
109D165THR 0-0.035-0.01148.955-0.001-0.0010.0000.0000.0000.000
110D166GLN 00.0460.01249.4180.0000.0000.0000.0000.0000.000
111D167TYR 0-0.010-0.00543.069-0.002-0.0020.0000.0000.0000.000
112D168GLN 00.016-0.00143.5590.0010.0010.0000.0000.0000.000
113D169LEU 0-0.055-0.02538.877-0.002-0.0020.0000.0000.0000.000
114D170ASP -1-0.712-0.78737.540-0.055-0.0550.0000.0000.0000.000
115D171GLN 0-0.062-0.03734.3300.0000.0000.0000.0000.0000.000
116D172ILE 0-0.006-0.00230.2130.0000.0000.0000.0000.0000.000
117D173ALA 0-0.031-0.01929.671-0.004-0.0040.0000.0000.0000.000
118D174VAL 0-0.027-0.00924.2560.0010.0010.0000.0000.0000.000
119D175ASN 00.007-0.02325.2350.0000.0000.0000.0000.0000.000
120D176LEU 0-0.0110.00619.167-0.007-0.0070.0000.0000.0000.000
121D177ARG 10.9730.96720.8570.1020.1020.0000.0000.0000.000
122D178VAL 0-0.0010.02314.590-0.017-0.0170.0000.0000.0000.000
123D179VAL 00.0270.01617.7310.0230.0230.0000.0000.0000.000
124D180ASN 00.0050.00016.642-0.014-0.0140.0000.0000.0000.000
125D181VAL 0-0.014-0.00516.8730.0030.0030.0000.0000.0000.000
126D182SER 0-0.059-0.02417.2120.0150.0150.0000.0000.0000.000
127D183THR 00.004-0.01719.6610.0000.0000.0000.0000.0000.000
128D184GLY 00.0000.01421.2340.0000.0000.0000.0000.0000.000
129D185GLU -1-0.964-0.96921.411-0.007-0.0070.0000.0000.0000.000
130D186ILE 0-0.003-0.01520.665-0.010-0.0100.0000.0000.0000.000
131D187LEU 0-0.041-0.01515.4620.0080.0080.0000.0000.0000.000
132D188SER 00.0190.00417.1430.0020.0020.0000.0000.0000.000
133D189SER 0-0.041-0.02619.954-0.004-0.0040.0000.0000.0000.000
134D190VAL 00.0320.02620.4220.0080.0080.0000.0000.0000.000
135D191ASN 00.0340.03123.379-0.010-0.0100.0000.0000.0000.000
136D192THR 0-0.052-0.01323.0810.0050.0050.0000.0000.0000.000
137D193SER 00.029-0.02426.3390.0040.0040.0000.0000.0000.000
138D194LYS 10.8470.98025.2650.1220.1220.0000.0000.0000.000
139D195THR 00.010-0.00430.3330.0030.0030.0000.0000.0000.000
140D196ILE 0-0.028-0.02733.550-0.004-0.0040.0000.0000.0000.000
141D197LEU 00.0010.01635.7480.0040.0040.0000.0000.0000.000
142D198SER 00.0200.01438.454-0.001-0.0010.0000.0000.0000.000
143D199TYR 0-0.014-0.01940.5370.0030.0030.0000.0000.0000.000
144D200GLU -1-0.885-0.94044.562-0.040-0.0400.0000.0000.0000.000
145D201VAL 0-0.037-0.02147.4940.0010.0010.0000.0000.0000.000
146D202GLN 00.0230.01150.159-0.001-0.0010.0000.0000.0000.000
147D203ALA 0-0.012-0.00853.7200.0010.0010.0000.0000.0000.000
148D204GLY 00.0510.03156.6780.0000.0000.0000.0000.0000.000
149D205VAL 0-0.080-0.04560.1580.0010.0010.0000.0000.0000.000
150D206PHE 00.0340.03063.7540.0000.0000.0000.0000.0000.000
151D207ARG 10.8420.91667.0350.0190.0190.0000.0000.0000.000
152D208PHE 00.0620.02470.1530.0000.0000.0000.0000.0000.000
153D209ILE 0-0.044-0.01972.8580.0000.0000.0000.0000.0000.000
154D210ASP -1-0.824-0.88676.292-0.015-0.0150.0000.0000.0000.000
155D211TYR 0-0.076-0.06179.0960.0000.0000.0000.0000.0000.000
156D212GLN 0-0.0010.01477.7100.0000.0000.0000.0000.0000.000
157D213ARG 10.8570.89875.7410.0150.0150.0000.0000.0000.000
158D214LEU 00.0110.01471.4440.0000.0000.0000.0000.0000.000
159D215LEU 0-0.024-0.00366.4990.0000.0000.0000.0000.0000.000
160D216GLU -1-0.887-0.95765.143-0.023-0.0230.0000.0000.0000.000
161D217GLY 0-0.0120.00162.2570.0000.0000.0000.0000.0000.000
162D218GLU -1-0.922-0.95958.115-0.027-0.0270.0000.0000.0000.000
163D219VAL 0-0.039-0.01654.016-0.001-0.0010.0000.0000.0000.000
164D220GLY 00.0520.01252.2350.0010.0010.0000.0000.0000.000
165D221TYR 0-0.073-0.02242.002-0.001-0.0010.0000.0000.0000.000
166D222THR 00.0220.01046.0340.0000.0000.0000.0000.0000.000
167D223SER 0-0.030-0.00139.825-0.002-0.0020.0000.0000.0000.000
168D224ASN 00.0390.00039.9760.0020.0020.0000.0000.0000.000
169D225GLU -1-0.917-0.95334.415-0.080-0.0800.0000.0000.0000.000
170D226PRO 00.005-0.00732.6170.0000.0000.0000.0000.0000.000
171D227VAL 00.0790.05232.323-0.008-0.0080.0000.0000.0000.000
172D228MET 00.001-0.01329.170-0.006-0.0060.0000.0000.0000.000
173D229LEU 0-0.005-0.00528.179-0.010-0.0100.0000.0000.0000.000
174D230CYS 00.0040.02027.739-0.008-0.0080.0000.0000.0000.000
175D231LEU 00.0320.01626.298-0.005-0.0050.0000.0000.0000.000
176D232MET 00.0330.00923.014-0.015-0.0150.0000.0000.0000.000
177D233SER 00.0030.01623.346-0.012-0.0120.0000.0000.0000.000
178D234ALA 00.0090.00423.710-0.009-0.0090.0000.0000.0000.000
179D235ILE 00.0050.00720.596-0.006-0.0060.0000.0000.0000.000
180D236GLU -1-0.919-0.95819.367-0.224-0.2240.0000.0000.0000.000
181D237THR 0-0.034-0.05818.921-0.011-0.0110.0000.0000.0000.000
182D238GLY 00.0280.01420.0990.0010.0010.0000.0000.0000.000
183D239VAL 00.016-0.00514.542-0.006-0.0060.0000.0000.0000.000
184D240ILE 0-0.032-0.01015.350-0.026-0.0260.0000.0000.0000.000
185D241PHE 0-0.041-0.02416.1520.0050.0050.0000.0000.0000.000
186D242LEU 00.0050.01215.4760.0100.0100.0000.0000.0000.000
187D243ILE 0-0.024-0.00610.745-0.008-0.0080.0000.0000.0000.000
188D244ASN 0-0.004-0.02412.7640.0050.0050.0000.0000.0000.000
189D245ASP -1-0.905-0.94215.216-0.077-0.0770.0000.0000.0000.000
190D246GLY 0-0.023-0.01212.4910.0240.0240.0000.0000.0000.000
191D247ILE 0-0.070-0.03411.1830.0420.0420.0000.0000.0000.000
192D248ASP -1-0.969-0.97512.7740.0000.0000.0000.0000.0000.000
193D249ARG 10.8550.96713.8810.0630.0630.0000.0000.0000.000
194D250GLY 0-0.027-0.01911.8780.0220.0220.0000.0000.0000.000
195D251NME 0-0.013-0.0238.730-0.033-0.0330.0000.0000.0000.000