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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: 437GN

Calculation Name: 3X2R-D-Xray372

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: 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:


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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1694412.080839
FMO2-HF: Nuclear repulsion 1621050.662403
FMO2-HF: Total energy -73361.418436
FMO2-MP2: Total energy -73575.87992


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:48:LYS)


Summations of interaction energy for fragment #1(D:48:LYS)
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.
-33.459-27.4777.048-4.179-8.85-0.014
Interaction energy analysis for fragmet #1(D:48:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.991 / q_NPA : 0.987
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].
3D50PHE0-0.009-0.0153.877-1.5940.117-0.015-0.800-0.8960.004
4D51VAL00.0220.0216.4482.2832.2830.0000.0000.0000.000
5D52SER00.0050.0038.908-0.439-0.4390.0000.0000.0000.000
6D53VAL00.0170.00612.2740.3980.3980.0000.0000.0000.000
7D54TYR00.002-0.00214.746-0.119-0.1190.0000.0000.0000.000
8D55ASN0-0.001-0.02118.2560.3850.3850.0000.0000.0000.000
9D56ILE0-0.0020.00117.869-0.318-0.3180.0000.0000.0000.000
10D57GLN0-0.070-0.02620.7910.0840.0840.0000.0000.0000.000
11D58ASP-1-0.830-0.92724.526-10.378-10.3780.0000.0000.0000.000
12D59GLU-1-0.827-0.89126.790-10.655-10.6550.0000.0000.0000.000
13D60THR00.0040.00529.5760.4100.4100.0000.0000.0000.000
14D61GLY0-0.0100.00331.7110.2790.2790.0000.0000.0000.000
15D62GLN0-0.021-0.00233.7960.4800.4800.0000.0000.0000.000
16D63PHE0-0.009-0.01434.614-0.286-0.2860.0000.0000.0000.000
17D64LYS10.8070.89933.4719.1449.1440.0000.0000.0000.000
18D65PRO00.0330.02738.6440.1230.1230.0000.0000.0000.000
19D66TYR00.0380.01942.364-0.037-0.0370.0000.0000.0000.000
20D67PRO00.005-0.02044.8330.0030.0030.0000.0000.0000.000
21D68ALA0-0.048-0.00140.193-0.001-0.0010.0000.0000.0000.000
22D69SER00.0260.00740.4620.1380.1380.0000.0000.0000.000
23D70ASN00.0610.03340.133-0.109-0.1090.0000.0000.0000.000
24D71PHE00.001-0.00138.486-0.069-0.0690.0000.0000.0000.000
25D72SER0-0.083-0.04335.902-0.264-0.2640.0000.0000.0000.000
26D73THR00.0440.00931.1800.2090.2090.0000.0000.0000.000
27D74ALA0-0.018-0.00233.567-0.031-0.0310.0000.0000.0000.000
28D75VAL00.0480.02427.260-0.081-0.0810.0000.0000.0000.000
29D76PRO00.009-0.00225.9040.0680.0680.0000.0000.0000.000
30D77GLN00.0350.01726.023-0.180-0.1800.0000.0000.0000.000
31D78SER0-0.024-0.02522.456-0.099-0.0990.0000.0000.0000.000
32D79ALA00.0680.02620.259-0.806-0.8060.0000.0000.0000.000
33D80THR00.0380.03617.2400.1290.1290.0000.0000.0000.000
34D81ALA00.0050.00216.155-1.142-1.1420.0000.0000.0000.000
35D82MET00.0020.02315.877-0.943-0.9430.0000.0000.0000.000
36D83LEU00.0110.02413.067-0.692-0.6920.0000.0000.0000.000
37D84VAL00.0190.00311.543-1.635-1.6350.0000.0000.0000.000
38D85THR00.015-0.00611.030-1.964-1.9640.0000.0000.0000.000
39D86ALA00.0470.03311.626-1.657-1.6570.0000.0000.0000.000
40D87LEU00.0100.0128.404-1.181-1.1810.0000.0000.0000.000
41D88LYS10.8940.9506.22334.22734.2270.0000.0000.0000.000
42D89ASP-1-0.846-0.9317.074-31.078-31.0780.0000.0000.0000.000
43D90SER0-0.042-0.0169.062-0.263-0.2630.0000.0000.0000.000
44D91ARG10.7310.8653.99533.80934.1080.000-0.034-0.2650.000
45D92TRP00.0260.0052.245-2.492-0.9183.811-2.184-3.2010.000
46D93PHE00.0620.0232.8661.2792.3370.937-0.242-1.752-0.012
47D94ILE0-0.101-0.0542.197-9.296-7.9992.316-0.904-2.709-0.006
48D95PRO00.0520.0334.4982.5792.622-0.001-0.015-0.0270.000
49D96LEU0-0.099-0.0398.075-1.379-1.3790.0000.0000.0000.000
50D97GLU-1-0.837-0.91810.228-15.834-15.8340.0000.0000.0000.000
51D98ARG10.8410.89312.76119.88519.8850.0000.0000.0000.000
52D99GLN00.0240.03416.7620.5650.5650.0000.0000.0000.000
53D100GLY00.0200.00618.9560.7360.7360.0000.0000.0000.000
54D101LEU0-0.002-0.01018.1500.1090.1090.0000.0000.0000.000
55D102GLN00.0410.01519.987-0.274-0.2740.0000.0000.0000.000
56D103ASN00.0210.01022.1100.6730.6730.0000.0000.0000.000
57D104LEU00.0200.01915.8630.1050.1050.0000.0000.0000.000
58D105LEU00.008-0.01120.5810.0520.0520.0000.0000.0000.000
59D106ASN00.0100.02622.9680.6030.6030.0000.0000.0000.000
60D107GLU-1-0.833-0.91322.084-12.658-12.6580.0000.0000.0000.000
61D108ARG10.8320.91216.90516.74616.7460.0000.0000.0000.000
62D109LYS10.8120.89623.40211.81911.8190.0000.0000.0000.000
63D110ILE00.0380.02726.7290.3270.3270.0000.0000.0000.000
64D111ILE00.004-0.00621.2740.1660.1660.0000.0000.0000.000
65D112ARG10.8830.95524.10812.19312.1930.0000.0000.0000.000
66D113ALA00.0440.01927.3070.2700.2700.0000.0000.0000.000
67D114ALA0-0.026-0.00727.8990.3130.3130.0000.0000.0000.000
68D115GLN0-0.051-0.01823.196-0.080-0.0800.0000.0000.0000.000
69D116GLU-1-0.997-0.99729.004-9.980-9.9800.0000.0000.0000.000
70D129GLN00.0370.00419.103-0.530-0.5300.0000.0000.0000.000
71D130SER00.0070.00516.9170.6500.6500.0000.0000.0000.000
72D131LEU0-0.006-0.01414.408-0.601-0.6010.0000.0000.0000.000
73D132THR00.0250.0279.6351.2621.2620.0000.0000.0000.000
74D133ALA00.0500.03112.2590.3710.3710.0000.0000.0000.000
75D134ALA0-0.014-0.02010.294-2.081-2.0810.0000.0000.0000.000
76D135ASN00.0430.03210.4992.0682.0680.0000.0000.0000.000
77D136ILE00.0210.0307.8260.8780.8780.0000.0000.0000.000
78D137MET0-0.017-0.01711.738-1.009-1.0090.0000.0000.0000.000
79D138VAL0-0.010-0.00311.6290.1960.1960.0000.0000.0000.000
80D139GLU-1-0.849-0.90514.414-12.917-12.9170.0000.0000.0000.000
81D140GLY00.001-0.01018.097-0.248-0.2480.0000.0000.0000.000
82D141SER0-0.053-0.05020.7160.0580.0580.0000.0000.0000.000
83D142ILE0-0.008-0.00923.539-0.203-0.2030.0000.0000.0000.000
84D143ILE0-0.002-0.00425.5630.3390.3390.0000.0000.0000.000
85D144GLY00.0370.01627.5680.3790.3790.0000.0000.0000.000
86D145TYR0-0.103-0.07729.410-0.335-0.3350.0000.0000.0000.000
87D146GLU-1-0.882-0.91432.131-8.300-8.3000.0000.0000.0000.000
88D147SER00.0320.01035.321-0.101-0.1010.0000.0000.0000.000
89D148ASN0-0.016-0.02038.1960.1420.1420.0000.0000.0000.000
90D149VAL0-0.014-0.00235.832-0.040-0.0400.0000.0000.0000.000
91D150LYS10.9000.96638.6397.6247.6240.0000.0000.0000.000
92D151SER0-0.034-0.04039.887-0.110-0.1100.0000.0000.0000.000
93D152GLY0-0.008-0.00642.6200.1260.1260.0000.0000.0000.000
94D153GLY00.0480.01945.459-0.148-0.1480.0000.0000.0000.000
95D154VAL0-0.076-0.02447.6940.1260.1260.0000.0000.0000.000
96D155GLY00.0700.02550.779-0.086-0.0860.0000.0000.0000.000
97D156ALA0-0.057-0.01353.5210.0980.0980.0000.0000.0000.000
98D157ARG10.9290.94957.0215.2065.2060.0000.0000.0000.000
99D158TYR00.0100.02059.9080.0780.0780.0000.0000.0000.000
100D159PHE00.0600.03463.063-0.039-0.0390.0000.0000.0000.000
101D160GLY00.022-0.01263.9870.0440.0440.0000.0000.0000.000
102D161ILE0-0.0270.00057.893-0.027-0.0270.0000.0000.0000.000
103D162GLY0-0.002-0.01457.6900.0710.0710.0000.0000.0000.000
104D163ALA0-0.0090.00452.420-0.042-0.0420.0000.0000.0000.000
105D164ASP-1-0.841-0.91750.376-6.236-6.2360.0000.0000.0000.000
106D165THR0-0.043-0.02345.393-0.134-0.1340.0000.0000.0000.000
107D166GLN00.0250.01045.8350.0710.0710.0000.0000.0000.000
108D167TYR00.0210.01139.918-0.189-0.1890.0000.0000.0000.000
109D168GLN00.0260.02339.6000.1770.1770.0000.0000.0000.000
110D169LEU0-0.059-0.01935.378-0.203-0.2030.0000.0000.0000.000
111D170ASP-1-0.745-0.84833.948-8.463-8.4630.0000.0000.0000.000
112D171GLN0-0.113-0.07531.038-0.370-0.3700.0000.0000.0000.000
113D172ILE0-0.016-0.00525.9790.0700.0700.0000.0000.0000.000
114D173ALA0-0.004-0.00526.494-0.145-0.1450.0000.0000.0000.000
115D174VAL0-0.043-0.02620.899-0.002-0.0020.0000.0000.0000.000
116D175ASN00.0030.00422.309-0.078-0.0780.0000.0000.0000.000
117D176LEU00.008-0.00415.486-0.361-0.3610.0000.0000.0000.000
118D177ARG10.8300.89417.53112.96712.9670.0000.0000.0000.000
119D178VAL00.0170.01512.337-0.790-0.7900.0000.0000.0000.000
120D179VAL0-0.014-0.01215.0030.7870.7870.0000.0000.0000.000
121D180ASN00.0360.01215.099-1.627-1.6270.0000.0000.0000.000
122D181VAL0-0.034-0.02114.6650.7560.7560.0000.0000.0000.000
123D182SER0-0.041-0.03415.9350.6380.6380.0000.0000.0000.000
124D183THR0-0.087-0.08118.3120.3960.3960.0000.0000.0000.000
125D184GLY0-0.0030.01119.7870.5680.5680.0000.0000.0000.000
126D185GLU-1-0.878-0.90219.745-12.336-12.3360.0000.0000.0000.000
127D186ILE0-0.009-0.02418.587-0.757-0.7570.0000.0000.0000.000
128D187LEU0-0.028-0.00413.8170.2310.2310.0000.0000.0000.000
129D188SER00.0600.03414.7300.0650.0650.0000.0000.0000.000
130D189SER0-0.042-0.03017.723-0.073-0.0730.0000.0000.0000.000
131D190VAL00.0000.01218.1740.4340.4340.0000.0000.0000.000
132D191ASN00.0310.02220.597-0.449-0.4490.0000.0000.0000.000
133D192THR0-0.048-0.02720.0800.0940.0940.0000.0000.0000.000
134D193SER00.0460.01423.1590.1620.1620.0000.0000.0000.000
135D194LYS10.8330.93621.56712.77412.7740.0000.0000.0000.000
136D195THR00.0490.02727.1290.0700.0700.0000.0000.0000.000
137D196ILE0-0.003-0.01929.762-0.375-0.3750.0000.0000.0000.000
138D197LEU0-0.0310.00532.0340.2860.2860.0000.0000.0000.000
139D198SER00.0450.03034.867-0.073-0.0730.0000.0000.0000.000
140D199TYR0-0.031-0.03036.5960.1940.1940.0000.0000.0000.000
141D200GLU-1-0.882-0.93340.880-7.211-7.2110.0000.0000.0000.000
142D201VAL0-0.037-0.01243.8760.0850.0850.0000.0000.0000.000
143D202GLN0-0.007-0.00946.531-0.044-0.0440.0000.0000.0000.000
144D203ALA0-0.013-0.01949.9690.0620.0620.0000.0000.0000.000
145D204GLY00.0600.03953.044-0.039-0.0390.0000.0000.0000.000
146D205VAL0-0.093-0.05156.2990.0740.0740.0000.0000.0000.000
147D206PHE00.0410.02858.9750.0360.0360.0000.0000.0000.000
148D207ARG10.8050.90263.2264.9544.9540.0000.0000.0000.000
149D208PHE00.0320.02666.475-0.019-0.0190.0000.0000.0000.000
150D209ILE0-0.055-0.03668.124-0.022-0.0220.0000.0000.0000.000
151D210ASP-1-0.848-0.94372.223-4.347-4.3470.0000.0000.0000.000
152D211TYR0-0.0450.00774.6850.0800.0800.0000.0000.0000.000
153D212GLN00.004-0.02773.100-0.123-0.1230.0000.0000.0000.000
154D213ARG10.8830.95267.9684.6914.6910.0000.0000.0000.000
155D214LEU00.0530.04666.7190.0380.0380.0000.0000.0000.000
156D215LEU0-0.025-0.02462.587-0.008-0.0080.0000.0000.0000.000
157D216GLU-1-0.919-0.96560.843-5.212-5.2120.0000.0000.0000.000
158D217GLY0-0.002-0.00157.935-0.005-0.0050.0000.0000.0000.000
159D218GLU-1-0.930-0.96553.780-5.773-5.7730.0000.0000.0000.000
160D219VAL0-0.036-0.02249.928-0.055-0.0550.0000.0000.0000.000
161D220GLY00.0440.01247.9790.0680.0680.0000.0000.0000.000
162D221TYR0-0.063-0.02137.537-0.046-0.0460.0000.0000.0000.000
163D222THR00.0130.00340.9330.1180.1180.0000.0000.0000.000
164D223SER0-0.072-0.03835.327-0.130-0.1300.0000.0000.0000.000
165D224ASN00.015-0.01635.9110.2040.2040.0000.0000.0000.000
166D225GLU-1-0.873-0.90530.949-9.711-9.7110.0000.0000.0000.000
167D226PRO00.008-0.01327.933-0.031-0.0310.0000.0000.0000.000
168D227VAL00.0840.04128.155-0.433-0.4330.0000.0000.0000.000
169D228MET0-0.018-0.01124.391-0.288-0.2880.0000.0000.0000.000
170D229LEU00.0150.00323.119-0.567-0.5670.0000.0000.0000.000
171D230CYS0-0.0080.00323.719-0.437-0.4370.0000.0000.0000.000
172D231LEU00.0010.00922.071-0.239-0.2390.0000.0000.0000.000
173D232MET0-0.014-0.00318.183-0.594-0.5940.0000.0000.0000.000
174D233SER00.020-0.00819.403-0.414-0.4140.0000.0000.0000.000
175D234ALA0-0.034-0.01120.615-0.142-0.1420.0000.0000.0000.000
176D235ILE00.0330.01616.304-0.316-0.3160.0000.0000.0000.000
177D236GLU-1-0.876-0.92515.778-16.197-16.1970.0000.0000.0000.000
178D237THR0-0.039-0.02615.744-0.352-0.3520.0000.0000.0000.000
179D238GLY00.0400.02617.3290.0660.0660.0000.0000.0000.000
180D239VAL0-0.001-0.01610.884-0.319-0.3190.0000.0000.0000.000
181D240ILE0-0.011-0.00712.467-0.629-0.6290.0000.0000.0000.000
182D241PHE0-0.028-0.02214.0480.0880.0880.0000.0000.0000.000
183D242LEU0-0.022-0.00712.7890.1510.1510.0000.0000.0000.000
184D243ILE0-0.036-0.0088.695-0.644-0.6440.0000.0000.0000.000
185D244ASN0-0.018-0.01811.238-0.609-0.6090.0000.0000.0000.000
186D245ASP-1-0.846-0.90314.426-13.693-13.6930.0000.0000.0000.000
187D246GLY00.0280.01411.6900.2050.2050.0000.0000.0000.000
188D247ILE0-0.081-0.04611.134-0.490-0.4900.0000.0000.0000.000
189D248ASP-1-0.881-0.92712.798-14.031-14.0310.0000.0000.0000.000
190D249ARG10.7200.84513.88714.80914.8090.0000.0000.0000.000
191D250GLY0-0.039-0.0119.9530.4290.4290.0000.0000.0000.000