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: 37QRL

Calculation Name: 3R4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R4U

Chain ID: A

ChEMBL ID:

UniProt ID: P18640

Base Structure: X-ray

Registration Date: 2023-09-26

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 428
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8024758.344564
FMO2-HF: Nuclear repulsion 7850541.308173
FMO2-HF: Total energy -174217.036391
FMO2-MP2: Total energy -174726.807312


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:864:SER)


Summations of interaction energy for fragment #1(A:864: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.
-9.324-3.6260.691-2.682-3.7080.018
Interaction energy analysis for fragmet #1(A:864:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.037
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].
3A866ALA0-0.0400.0012.591-7.416-3.0180.490-2.216-2.6730.016
4A867ASN00.0910.0314.433-0.843-0.5010.001-0.051-0.2910.000
5A868ILE0-0.055-0.0095.2920.0950.0950.0000.0000.0000.000
6A869ASN0-0.003-0.0407.235-0.212-0.2120.0000.0000.0000.000
7A870ASP-1-0.866-0.9018.9320.0370.0370.0000.0000.0000.000
8A871SER0-0.061-0.02210.929-0.061-0.0610.0000.0000.0000.000
9A872LYS10.8690.94611.422-0.882-0.8820.0000.0000.0000.000
10A873ILE00.012-0.00514.145-0.012-0.0120.0000.0000.0000.000
11A874LEU0-0.033-0.01017.233-0.021-0.0210.0000.0000.0000.000
12A875SER0-0.030-0.02515.0680.0850.0850.0000.0000.0000.000
13A876LEU00.0180.03517.0230.0020.0020.0000.0000.0000.000
14A877GLN0-0.073-0.06614.3370.0310.0310.0000.0000.0000.000
15A878ASN00.0500.04619.579-0.044-0.0440.0000.0000.0000.000
16A879ARG10.8940.93715.309-0.528-0.5280.0000.0000.0000.000
17A880LYS10.9040.94021.836-0.345-0.3450.0000.0000.0000.000
18A881ASN00.0200.00624.804-0.014-0.0140.0000.0000.0000.000
19A882THR00.0670.04625.339-0.025-0.0250.0000.0000.0000.000
20A883LEU00.0050.01823.8620.0380.0380.0000.0000.0000.000
21A884VAL00.010-0.00520.700-0.018-0.0180.0000.0000.0000.000
22A885ASP-1-0.686-0.83919.5730.3570.3570.0000.0000.0000.000
23A886THR0-0.094-0.06316.050-0.007-0.0070.0000.0000.0000.000
24A887SER0-0.058-0.03915.4960.0410.0410.0000.0000.0000.000
25A888GLY00.0050.01316.1160.0010.0010.0000.0000.0000.000
26A889TYR0-0.024-0.02016.980-0.056-0.0560.0000.0000.0000.000
27A890ASN0-0.095-0.03721.054-0.004-0.0040.0000.0000.0000.000
28A891ALA00.0130.00122.903-0.020-0.0200.0000.0000.0000.000
29A892GLU-1-0.952-0.97124.9080.1370.1370.0000.0000.0000.000
30A893VAL0-0.038-0.02824.3810.0050.0050.0000.0000.0000.000
31A894SER0-0.033-0.00727.714-0.008-0.0080.0000.0000.0000.000
32A895GLU-1-0.934-0.98029.8540.2040.2040.0000.0000.0000.000
33A896GLU-1-0.948-0.97132.3040.1060.1060.0000.0000.0000.000
34A897GLY00.0320.01335.1270.0050.0050.0000.0000.0000.000
35A898ASP-1-0.948-0.98335.6750.1520.1520.0000.0000.0000.000
36A899VAL0-0.011-0.00329.6350.0090.0090.0000.0000.0000.000
37A900GLN0-0.076-0.03531.1550.0070.0070.0000.0000.0000.000
38A901LEU00.0340.01726.2520.0190.0190.0000.0000.0000.000
39A902ASN0-0.045-0.01624.851-0.024-0.0240.0000.0000.0000.000
40A903PRO00.016-0.00124.9610.0240.0240.0000.0000.0000.000
41A904ILE0-0.085-0.04523.7260.0130.0130.0000.0000.0000.000
42A905PHE00.0100.03515.5540.0030.0030.0000.0000.0000.000
43A906PRO0-0.009-0.03718.931-0.026-0.0260.0000.0000.0000.000
44A907PHE0-0.080-0.04618.3750.0400.0400.0000.0000.0000.000
45A908ASP-1-0.838-0.91721.9030.3060.3060.0000.0000.0000.000
46A909PHE00.0500.02623.280-0.013-0.0130.0000.0000.0000.000
47A910LYS10.9060.94626.201-0.169-0.1690.0000.0000.0000.000
48A911LEU00.0150.02229.185-0.008-0.0080.0000.0000.0000.000
49A912GLY00.0640.02531.7760.0030.0030.0000.0000.0000.000
50A913SER00.014-0.00435.1110.0000.0000.0000.0000.0000.000
51A914SER0-0.007-0.00937.325-0.008-0.0080.0000.0000.0000.000
52A915GLY00.0340.02140.2770.0030.0030.0000.0000.0000.000
53A916GLU-1-0.968-0.99441.5410.0830.0830.0000.0000.0000.000
54A917ASP-1-0.953-0.96340.7980.1110.1110.0000.0000.0000.000
55A918ARG10.9060.97836.540-0.104-0.1040.0000.0000.0000.000
56A919GLY00.0130.01033.936-0.001-0.0010.0000.0000.0000.000
57A920LYS10.9230.96432.673-0.115-0.1150.0000.0000.0000.000
58A921VAL0-0.003-0.00126.6060.0030.0030.0000.0000.0000.000
59A922ILE0-0.013-0.00629.4530.0010.0010.0000.0000.0000.000
60A923VAL00.002-0.00224.0010.0080.0080.0000.0000.0000.000
61A924THR00.002-0.00327.376-0.011-0.0110.0000.0000.0000.000
62A925GLN00.014-0.01122.536-0.005-0.0050.0000.0000.0000.000
63A926ASN00.0410.00625.183-0.022-0.0220.0000.0000.0000.000
64A927GLU-1-0.869-0.96026.4540.0720.0720.0000.0000.0000.000
65A928ASN00.0050.00126.810-0.010-0.0100.0000.0000.0000.000
66A929ILE0-0.0110.00421.339-0.010-0.0100.0000.0000.0000.000
67A930VAL00.0020.04723.1160.0020.0020.0000.0000.0000.000
68A931TYR0-0.026-0.00625.082-0.008-0.0080.0000.0000.0000.000
69A932ASN0-0.017-0.01923.919-0.017-0.0170.0000.0000.0000.000
70A933SER0-0.038-0.04820.687-0.011-0.0110.0000.0000.0000.000
71A934MET0-0.030-0.02322.279-0.002-0.0020.0000.0000.0000.000
72A935TYR0-0.0140.00724.0450.0000.0000.0000.0000.0000.000
73A936GLU-1-0.928-0.94422.862-0.038-0.0380.0000.0000.0000.000
74A937SER0-0.018-0.03218.830-0.007-0.0070.0000.0000.0000.000
75A938PHE0-0.0420.00518.3720.0050.0050.0000.0000.0000.000
76A939SER0-0.007-0.04015.277-0.014-0.0140.0000.0000.0000.000
77A940ILE0-0.0050.01917.3450.0250.0250.0000.0000.0000.000
78A941SER00.016-0.00214.6730.0160.0160.0000.0000.0000.000
79A942PHE00.0070.00916.9220.0120.0120.0000.0000.0000.000
80A943TRP0-0.0320.01214.274-0.045-0.0450.0000.0000.0000.000
81A944ILE00.0510.01219.259-0.020-0.0200.0000.0000.0000.000
82A945ARG10.8750.94723.017-0.221-0.2210.0000.0000.0000.000
83A946ILE00.0530.03425.850-0.006-0.0060.0000.0000.0000.000
84A947ASN0-0.068-0.00329.492-0.003-0.0030.0000.0000.0000.000
85A948LYS10.9180.96932.563-0.115-0.1150.0000.0000.0000.000
86A949TRP00.036-0.00727.6620.0000.0000.0000.0000.0000.000
87A950VAL00.0370.00433.6420.0010.0010.0000.0000.0000.000
88A951SER00.0240.00436.4560.0010.0010.0000.0000.0000.000
89A952ASN00.0000.00337.4760.0020.0020.0000.0000.0000.000
90A953LEU0-0.0220.00734.354-0.003-0.0030.0000.0000.0000.000
91A954PRO00.0390.01838.355-0.002-0.0020.0000.0000.0000.000
92A955GLY00.0320.01637.0210.0060.0060.0000.0000.0000.000
93A956TYR00.013-0.00134.476-0.004-0.0040.0000.0000.0000.000
94A957THR00.0290.02332.4500.0040.0040.0000.0000.0000.000
95A958ILE0-0.066-0.03727.6860.0020.0020.0000.0000.0000.000
96A959ILE0-0.010-0.01024.3730.0100.0100.0000.0000.0000.000
97A960ASP-1-0.821-0.91128.3860.1090.1090.0000.0000.0000.000
98A961SER0-0.013-0.00727.8430.0040.0040.0000.0000.0000.000
99A962VAL0-0.0060.00829.938-0.009-0.0090.0000.0000.0000.000
100A963LYS10.9420.96233.246-0.078-0.0780.0000.0000.0000.000
101A964ASN0-0.054-0.03335.745-0.003-0.0030.0000.0000.0000.000
102A965ASN00.0250.00038.1080.0010.0010.0000.0000.0000.000
103A966SER00.0470.03834.413-0.003-0.0030.0000.0000.0000.000
104A967GLY00.0480.03530.8110.0050.0050.0000.0000.0000.000
105A968TRP0-0.020-0.01024.537-0.001-0.0010.0000.0000.0000.000
106A969SER0-0.016-0.02729.0360.0070.0070.0000.0000.0000.000
107A970ILE00.0140.00924.1360.0030.0030.0000.0000.0000.000
108A971GLY00.0570.02928.6090.0000.0000.0000.0000.0000.000
109A972ILE0-0.045-0.02129.9140.0080.0080.0000.0000.0000.000
110A973ILE00.0520.02132.295-0.007-0.0070.0000.0000.0000.000
111A974SER0-0.0120.01334.630-0.001-0.0010.0000.0000.0000.000
112A975ASN0-0.040-0.02733.0070.0030.0030.0000.0000.0000.000
113A976PHE00.003-0.00930.9200.0060.0060.0000.0000.0000.000
114A977LEU0-0.042-0.01225.0110.0050.0050.0000.0000.0000.000
115A978VAL0-0.004-0.02228.039-0.001-0.0010.0000.0000.0000.000
116A979PHE0-0.0020.00524.7760.0100.0100.0000.0000.0000.000
117A980THR00.022-0.00927.328-0.008-0.0080.0000.0000.0000.000
118A981LEU0-0.010-0.00226.4010.0060.0060.0000.0000.0000.000
119A982LYS10.9290.97129.930-0.075-0.0750.0000.0000.0000.000
120A983GLN00.0090.02933.4490.0010.0010.0000.0000.0000.000
121A984ASN00.031-0.00934.860-0.001-0.0010.0000.0000.0000.000
122A985GLU-1-0.969-0.99138.2170.0490.0490.0000.0000.0000.000
123A986ASP-1-0.904-0.93040.9610.0410.0410.0000.0000.0000.000
124A987SER0-0.104-0.07137.169-0.002-0.0020.0000.0000.0000.000
125A988GLU-1-0.860-0.93334.2290.0750.0750.0000.0000.0000.000
126A989GLN0-0.023-0.02030.132-0.008-0.0080.0000.0000.0000.000
127A990SER00.0140.00729.8700.0090.0090.0000.0000.0000.000
128A991ILE0-0.0170.00323.941-0.006-0.0060.0000.0000.0000.000
129A992ASN0-0.048-0.03227.5280.0120.0120.0000.0000.0000.000
130A993PHE00.0380.02624.7670.0030.0030.0000.0000.0000.000
131A994SER00.0300.01826.867-0.003-0.0030.0000.0000.0000.000
132A995TYR0-0.055-0.02328.901-0.001-0.0010.0000.0000.0000.000
133A996ASP-1-0.813-0.90229.8160.0960.0960.0000.0000.0000.000
134A997ILE00.0500.01731.9750.0050.0050.0000.0000.0000.000
135A998SER0-0.093-0.03735.275-0.001-0.0010.0000.0000.0000.000
136A999ASN0-0.012-0.00831.449-0.005-0.0050.0000.0000.0000.000
137A1000ASN0-0.104-0.08330.4550.0190.0190.0000.0000.0000.000
138A1001ALA00.0490.04134.0640.0000.0000.0000.0000.0000.000
139A1002PRO0-0.032-0.02135.463-0.001-0.0010.0000.0000.0000.000
140A1003GLY00.0440.04134.5800.0020.0020.0000.0000.0000.000
141A1004TYR0-0.0020.00424.5340.0030.0030.0000.0000.0000.000
142A1005ASN0-0.008-0.01729.5940.0090.0090.0000.0000.0000.000
143A1006LYS10.8450.93525.223-0.192-0.1920.0000.0000.0000.000
144A1007TRP0-0.019-0.01021.3260.0030.0030.0000.0000.0000.000
145A1008PHE0-0.035-0.00120.7940.0010.0010.0000.0000.0000.000
146A1009PHE00.0520.01813.1920.0130.0130.0000.0000.0000.000
147A1010VAL00.0550.03818.310-0.023-0.0230.0000.0000.0000.000
148A1011THR0-0.050-0.04414.3460.0710.0710.0000.0000.0000.000
149A1012VAL00.0210.02317.485-0.028-0.0280.0000.0000.0000.000
150A1013THR0-0.045-0.01615.6440.0200.0200.0000.0000.0000.000
151A1014ASN00.0840.02118.872-0.009-0.0090.0000.0000.0000.000
152A1015ASN00.0300.02720.6490.0010.0010.0000.0000.0000.000
153A1016MET00.0350.03222.5830.0000.0000.0000.0000.0000.000
154A1017MET0-0.016-0.00325.053-0.004-0.0040.0000.0000.0000.000
155A1018GLY0-0.057-0.03323.701-0.012-0.0120.0000.0000.0000.000
156A1019ASN0-0.038-0.02522.5210.0100.0100.0000.0000.0000.000
157A1020MET00.0520.05522.6480.0040.0040.0000.0000.0000.000
158A1021LYS10.9240.95118.190-0.016-0.0160.0000.0000.0000.000
159A1022ILE00.0350.02520.6330.0190.0190.0000.0000.0000.000
160A1023TYR0-0.010-0.02315.981-0.020-0.0200.0000.0000.0000.000
161A1024ILE00.0250.01418.9410.0200.0200.0000.0000.0000.000
162A1025ASN0-0.069-0.05216.8070.0230.0230.0000.0000.0000.000
163A1026GLY00.0290.02614.2510.0140.0140.0000.0000.0000.000
164A1027LYS10.9010.95514.898-0.271-0.2710.0000.0000.0000.000
165A1028LEU0-0.015-0.00517.8530.0040.0040.0000.0000.0000.000
166A1029ILE0-0.070-0.02919.588-0.006-0.0060.0000.0000.0000.000
167A1030ASP-1-0.795-0.90522.9540.0720.0720.0000.0000.0000.000
168A1031THR0-0.043-0.03622.9470.0040.0040.0000.0000.0000.000
169A1032ILE0-0.0150.01324.754-0.007-0.0070.0000.0000.0000.000
170A1033LYS10.8670.92826.5100.0030.0030.0000.0000.0000.000
171A1034VAL0-0.0150.00425.7130.0060.0060.0000.0000.0000.000
172A1035LYS10.8790.95428.680-0.049-0.0490.0000.0000.0000.000
173A1036GLU-1-0.888-0.95231.5840.0020.0020.0000.0000.0000.000
174A1037LEU0-0.028-0.01929.7980.0050.0050.0000.0000.0000.000
175A1038THR00.022-0.00433.5810.0030.0030.0000.0000.0000.000
176A1039GLY00.002-0.00135.1960.0020.0020.0000.0000.0000.000
177A1040ILE0-0.0490.00330.0930.0030.0030.0000.0000.0000.000
178A1041ASN0-0.011-0.01832.779-0.007-0.0070.0000.0000.0000.000
179A1042PHE0-0.018-0.02327.4870.0080.0080.0000.0000.0000.000
180A1043SER0-0.0050.00730.089-0.005-0.0050.0000.0000.0000.000
181A1044LYS10.9620.99028.090-0.090-0.0900.0000.0000.0000.000
182A1045THR0-0.026-0.00928.3130.0070.0070.0000.0000.0000.000
183A1046ILE0-0.0160.00024.040-0.003-0.0030.0000.0000.0000.000
184A1047THR00.003-0.00728.1450.0050.0050.0000.0000.0000.000
185A1048PHE0-0.038-0.01823.3210.0030.0030.0000.0000.0000.000
186A1049GLU-1-0.815-0.92829.2430.1190.1190.0000.0000.0000.000
187A1050ILE0-0.063-0.01132.038-0.001-0.0010.0000.0000.0000.000
188A1051ASN00.009-0.00734.097-0.007-0.0070.0000.0000.0000.000
189A1052LYS10.9270.96336.945-0.086-0.0860.0000.0000.0000.000
190A1053ILE00.0000.00236.620-0.002-0.0020.0000.0000.0000.000
191A1054PRO0-0.012-0.01540.543-0.001-0.0010.0000.0000.0000.000
192A1055ASP-1-0.915-0.95843.7400.0660.0660.0000.0000.0000.000
193A1056THR0-0.0150.00541.7990.0010.0010.0000.0000.0000.000
194A1057GLY0-0.007-0.01644.097-0.003-0.0030.0000.0000.0000.000
195A1058LEU0-0.030-0.01346.789-0.003-0.0030.0000.0000.0000.000
196A1059ILE00.0400.01947.7600.0030.0030.0000.0000.0000.000
197A1060THR0-0.026-0.01348.2410.0020.0020.0000.0000.0000.000
198A1061SER0-0.094-0.04646.2810.0010.0010.0000.0000.0000.000
199A1062ASP-1-0.859-0.92845.4080.0860.0860.0000.0000.0000.000
200A1063SER0-0.101-0.06842.489-0.002-0.0020.0000.0000.0000.000
201A1064ASP-1-0.890-0.92340.8520.0970.0970.0000.0000.0000.000
202A1065ASN0-0.019-0.01036.7620.0020.0020.0000.0000.0000.000
203A1066ILE0-0.066-0.02133.5420.0020.0020.0000.0000.0000.000
204A1067ASN0-0.029-0.03031.792-0.001-0.0010.0000.0000.0000.000
205A1068MET00.0120.01327.3660.0040.0040.0000.0000.0000.000
206A1069TRP0-0.074-0.04025.371-0.009-0.0090.0000.0000.0000.000
207A1070ILE00.0420.01522.0150.0120.0120.0000.0000.0000.000
208A1071ARG10.8480.91014.766-0.653-0.6530.0000.0000.0000.000
209A1072ASP-1-0.828-0.90714.9100.7220.7220.0000.0000.0000.000
210A1073PHE00.0570.03916.6410.0190.0190.0000.0000.0000.000
211A1074TYR0-0.101-0.06011.5210.0810.0810.0000.0000.0000.000
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