Manual

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: 89N2Y

Calculation Name: 5NR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NR1

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptHSide
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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3007040.456338
FMO2-HF: Nuclear repulsion 2914393.428679
FMO2-HF: Total energy -92647.027659
FMO2-MP2: Total energy -92916.439407


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:3:VAL)


Summations of interaction energy for fragment #1(A:3:VAL)
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.
-19.394-9.6775.992-5.616-10.095-0.027
Interaction energy analysis for fragmet #1(A:3:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / 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].
3A5ARG10.7790.8582.4500.0494.3311.641-2.186-3.738-0.008
4A6THR00.0080.0104.3040.3750.4560.000-0.029-0.0520.000
5A7LEU0-0.037-0.0157.8510.1110.1110.0000.0000.0000.000
6A8HIS00.0360.01410.2970.1220.1220.0000.0000.0000.000
7A9HIS0-0.032-0.04913.5020.0650.0650.0000.0000.0000.000
8A10PHE00.0590.02616.1350.0210.0210.0000.0000.0000.000
9A11PRO00.0450.01319.6110.0020.0020.0000.0000.0000.000
10A12LEU0-0.049-0.00920.569-0.001-0.0010.0000.0000.0000.000
11A13ASP-1-0.744-0.84019.531-0.316-0.3160.0000.0000.0000.000
12A14PRO00.0220.01020.471-0.035-0.0350.0000.0000.0000.000
13A15ALA00.0330.01618.639-0.020-0.0200.0000.0000.0000.000
14A16SER00.002-0.05916.008-0.058-0.0580.0000.0000.0000.000
15A17ARG10.7830.86015.7230.2700.2700.0000.0000.0000.000
16A18GLN0-0.024-0.01317.203-0.024-0.0240.0000.0000.0000.000
17A19VAL0-0.014-0.00111.097-0.018-0.0180.0000.0000.0000.000
18A20ARG10.8070.88812.4930.4870.4870.0000.0000.0000.000
19A21LEU0-0.017-0.00413.980-0.043-0.0430.0000.0000.0000.000
20A22ALA00.003-0.00112.7790.0090.0090.0000.0000.0000.000
21A23LEU0-0.0040.0037.4740.0020.0020.0000.0000.0000.000
22A24GLY00.0340.01910.857-0.058-0.0580.0000.0000.0000.000
23A25GLU-1-0.815-0.87013.361-0.312-0.3120.0000.0000.0000.000
24A26LYS10.7430.84210.1360.4300.4300.0000.0000.0000.000
25A27ARG10.9010.96210.3460.3880.3880.0000.0000.0000.000
26A28LEU00.0020.0135.634-0.168-0.1680.0000.0000.0000.000
27A29PRO0-0.022-0.0216.2330.1290.1290.0000.0000.0000.000
28A30PHE0-0.029-0.0156.547-0.646-0.6460.0000.0000.0000.000
29A31VAL00.0210.0198.1100.3330.3330.0000.0000.0000.000
30A32GLU-1-0.812-0.89510.126-0.692-0.6920.0000.0000.0000.000
31A33MET0-0.0060.00412.7940.0620.0620.0000.0000.0000.000
32A34GLN0-0.037-0.03014.9710.0570.0570.0000.0000.0000.000
33A35VAL00.0220.00917.8090.0260.0260.0000.0000.0000.000
34A36ARG10.8080.88719.8010.2440.2440.0000.0000.0000.000
35A37TYR00.0470.01521.1110.0230.0230.0000.0000.0000.000
36A38TRP00.0400.02723.0640.0100.0100.0000.0000.0000.000
37A39GLU-1-0.886-0.93026.128-0.184-0.1840.0000.0000.0000.000
38A40MET0-0.060-0.03124.8330.0130.0130.0000.0000.0000.000
39A41PRO00.0240.02321.7620.0110.0110.0000.0000.0000.000
40A42PRO00.0450.01022.575-0.014-0.0140.0000.0000.0000.000
41A43GLU-1-0.925-0.96718.628-0.282-0.2820.0000.0000.0000.000
42A44PHE0-0.0020.00215.487-0.022-0.0220.0000.0000.0000.000
43A45THR00.0130.00118.566-0.013-0.0130.0000.0000.0000.000
44A46SER0-0.102-0.04618.9320.0200.0200.0000.0000.0000.000
45A47LEU0-0.030-0.00713.1060.0060.0060.0000.0000.0000.000
46A48ASN0-0.032-0.05915.7420.0300.0300.0000.0000.0000.000
47A49PRO00.0090.01617.8660.0030.0030.0000.0000.0000.000
48A50SER0-0.062-0.04620.0140.0110.0110.0000.0000.0000.000
49A51GLY0-0.001-0.00621.1730.0070.0070.0000.0000.0000.000
50A52MET0-0.023-0.00420.536-0.010-0.0100.0000.0000.0000.000
51A53PRO0-0.0650.01316.737-0.027-0.0270.0000.0000.0000.000
52A54PRO00.002-0.01013.4740.0280.0280.0000.0000.0000.000
53A55VAL00.009-0.01711.4880.0410.0410.0000.0000.0000.000
54A56LEU0-0.028-0.0075.907-0.055-0.0550.0000.0000.0000.000
55A57VAL0-0.009-0.0057.0080.1560.1560.0000.0000.0000.000
56A58GLU-1-0.777-0.8702.300-4.697-3.7592.078-1.056-1.961-0.007
57A59THR00.018-0.0023.0360.1250.7520.168-0.118-0.677-0.002
58A60LYS10.9840.9802.291-12.715-9.2422.106-2.175-3.404-0.010
59A61HIS0-0.010-0.0104.177-0.551-0.4010.001-0.037-0.1140.000
60A62GLN00.0220.0127.152-0.179-0.1790.0000.0000.0000.000
61A63ARG10.9120.9667.728-0.909-0.9090.0000.0000.0000.000
62A64ASN00.0380.0196.249-0.009-0.0090.0000.0000.0000.000
63A65LEU0-0.0110.0065.7260.1800.1800.0000.0000.0000.000
64A66VAL00.0090.0017.101-0.281-0.2810.0000.0000.0000.000
65A67ILE0-0.0010.0116.1330.1250.1250.0000.0000.0000.000
66A68CYS00.0080.00110.290-0.102-0.1020.0000.0000.0000.000
67A69GLU-1-0.774-0.85413.731-0.188-0.1880.0000.0000.0000.000
68A70THR00.0290.01414.326-0.009-0.0090.0000.0000.0000.000
69A71ARG10.9300.96815.1140.1000.1000.0000.0000.0000.000
70A72ALA00.0240.01112.8920.0250.0250.0000.0000.0000.000
71A73ILE0-0.015-0.0049.563-0.009-0.0090.0000.0000.0000.000
72A74LEU0-0.010-0.01510.477-0.056-0.0560.0000.0000.0000.000
73A75GLU-1-0.788-0.86312.665-0.100-0.1000.0000.0000.0000.000
74A76HIS00.0210.0144.6210.3070.351-0.001-0.002-0.0400.000
75A77ILE00.0060.0067.6640.0440.0440.0000.0000.0000.000
76A78GLU-1-0.774-0.8829.055-0.115-0.1150.0000.0000.0000.000
77A79GLU-1-1.037-1.01510.9870.1510.1510.0000.0000.0000.000
78A80THR0-0.083-0.0485.7940.0410.0410.0000.0000.0000.000
79A81GLU-1-0.818-0.8854.498-0.819-0.697-0.001-0.013-0.1090.000
80A82THR0-0.012-0.0158.663-0.069-0.0690.0000.0000.0000.000
81A83GLU-1-1.000-0.98111.474-0.109-0.1090.0000.0000.0000.000
82A84PRO00.0030.01012.424-0.076-0.0760.0000.0000.0000.000
83A85PRO00.0040.00214.613-0.046-0.0460.0000.0000.0000.000
84A86LEU0-0.011-0.01414.562-0.006-0.0060.0000.0000.0000.000
85A87LEU0-0.031-0.00717.4030.0080.0080.0000.0000.0000.000
86A88GLY00.0070.00719.3460.0160.0160.0000.0000.0000.000
87A89ARG10.9330.95621.014-0.038-0.0380.0000.0000.0000.000
88A90ASP-1-0.840-0.90722.8080.0050.0050.0000.0000.0000.000
89A91PRO00.026-0.00425.165-0.012-0.0120.0000.0000.0000.000
90A92ALA00.0260.01226.206-0.009-0.0090.0000.0000.0000.000
91A93GLU-1-0.761-0.86924.956-0.049-0.0490.0000.0000.0000.000
92A94ARG10.8700.93017.0100.0050.0050.0000.0000.0000.000
93A95ALA0-0.004-0.00123.448-0.013-0.0130.0000.0000.0000.000
94A96GLU-1-0.746-0.81925.937-0.082-0.0820.0000.0000.0000.000
95A97ALA00.022-0.00422.137-0.011-0.0110.0000.0000.0000.000
96A98ARG10.8180.86917.8250.0470.0470.0000.0000.0000.000
97A99ARG10.7980.88123.0030.0710.0710.0000.0000.0000.000
98A100LEU0-0.005-0.00925.500-0.004-0.0040.0000.0000.0000.000
99A101LEU00.0390.01918.917-0.006-0.0060.0000.0000.0000.000
100A102GLN0-0.0090.00822.994-0.002-0.0020.0000.0000.0000.000
101A103TRP0-0.040-0.02325.1830.0070.0070.0000.0000.0000.000
102A104PHE00.005-0.01224.9340.0040.0040.0000.0000.0000.000
103A105ASP-1-0.781-0.88620.912-0.240-0.2400.0000.0000.0000.000
104A106ARG10.8640.93224.6210.1090.1090.0000.0000.0000.000
105A107LYS10.8380.92227.8260.0910.0910.0000.0000.0000.000
106A108PHE00.007-0.00228.5390.0040.0040.0000.0000.0000.000
107A109ASP-1-0.843-0.91026.801-0.178-0.1780.0000.0000.0000.000
108A110ASN0-0.035-0.04028.8720.0070.0070.0000.0000.0000.000
109A111GLU-1-0.842-0.88531.938-0.088-0.0880.0000.0000.0000.000
110A112VAL0-0.019-0.01132.0600.0050.0050.0000.0000.0000.000
111A113ASN0-0.036-0.04127.1140.0050.0050.0000.0000.0000.000
112A114GLY00.0340.02631.131-0.002-0.0020.0000.0000.0000.000
113A115PHE0-0.046-0.01333.0260.0080.0080.0000.0000.0000.000
114A116LEU0-0.028-0.03533.5280.0000.0000.0000.0000.0000.000
115A117LEU0-0.016-0.00627.627-0.003-0.0030.0000.0000.0000.000
116A118HIS0-0.026-0.01331.6790.0040.0040.0000.0000.0000.000
117A119GLU-1-0.745-0.87433.296-0.106-0.1060.0000.0000.0000.000
118A120LYS10.7970.89534.3770.1470.1470.0000.0000.0000.000
119A121MET0-0.0080.00426.620-0.004-0.0040.0000.0000.0000.000
120A122GLU-1-0.859-0.91829.270-0.170-0.1700.0000.0000.0000.000
121A123LYS10.8850.93331.6210.1080.1080.0000.0000.0000.000
122A124ARG10.8870.95033.6730.1540.1540.0000.0000.0000.000
123A125LEU0-0.060-0.02127.8740.0030.0030.0000.0000.0000.000
124A126LEU00.0180.01030.8140.0000.0000.0000.0000.0000.000
125A127ARG10.8590.92933.8330.1320.1320.0000.0000.0000.000
126A128MET00.0110.00836.1040.0050.0050.0000.0000.0000.000
127A129GLY0-0.029-0.00138.7800.0060.0060.0000.0000.0000.000
128A130ALA0-0.018-0.01039.556-0.006-0.0060.0000.0000.0000.000
129A131PRO00.0290.00738.8800.0020.0020.0000.0000.0000.000
130A132ASP-1-0.838-0.90640.759-0.079-0.0790.0000.0000.0000.000
131A133LEU00.004-0.03042.188-0.002-0.0020.0000.0000.0000.000
132A134ALA0-0.054-0.02544.1280.0000.0000.0000.0000.0000.000
133A135ALA00.0560.03539.7650.0000.0000.0000.0000.0000.000
134A136LEU00.003-0.00237.931-0.003-0.0030.0000.0000.0000.000
135A137ARG10.8960.94340.3360.0750.0750.0000.0000.0000.000
136A138GLN00.0180.02739.3840.0040.0040.0000.0000.0000.000
137A139GLY00.0550.01737.529-0.001-0.0010.0000.0000.0000.000
138A140ARG10.8080.87937.4200.1100.1100.0000.0000.0000.000
139A141GLU-1-0.893-0.94039.328-0.083-0.0830.0000.0000.0000.000
140A142ALA00.0240.01436.7890.0010.0010.0000.0000.0000.000
141A143LEU0-0.010-0.00433.250-0.001-0.0010.0000.0000.0000.000
142A144ARG10.9130.95236.1440.0960.0960.0000.0000.0000.000
143A145MET0-0.0120.00538.5910.0040.0040.0000.0000.0000.000
144A146HIS0-0.007-0.01632.608-0.002-0.0020.0000.0000.0000.000
145A147LEU0-0.022-0.01233.311-0.002-0.0020.0000.0000.0000.000
146A148GLY00.0370.01635.4340.0010.0010.0000.0000.0000.000
147A149TYR00.0140.02231.8490.0030.0030.0000.0000.0000.000
148A150ILE00.0210.00930.4320.0020.0020.0000.0000.0000.000
149A151GLU-1-0.759-0.86033.464-0.097-0.0970.0000.0000.0000.000
150A152SER0-0.077-0.04636.2760.0050.0050.0000.0000.0000.000
151A153LEU0-0.027-0.02231.4000.0040.0040.0000.0000.0000.000
152A154LEU0-0.014-0.01230.0860.0020.0020.0000.0000.0000.000
153A155GLN0-0.086-0.03934.0670.0050.0050.0000.0000.0000.000
154A156THR0-0.085-0.04136.2280.0060.0060.0000.0000.0000.000
155A157ARG10.7800.87130.7250.0820.0820.0000.0000.0000.000
156A158ASP-1-0.931-0.94830.115-0.082-0.0820.0000.0000.0000.000
157A159TRP0-0.041-0.03626.250-0.020-0.0200.0000.0000.0000.000
158A160LEU00.0160.00826.4130.0120.0120.0000.0000.0000.000
159A161ALA0-0.016-0.00725.3870.0110.0110.0000.0000.0000.000
160A162GLY0-0.0070.00127.4590.0130.0130.0000.0000.0000.000
161A163ARG10.8960.92625.6390.0290.0290.0000.0000.0000.000
162A164ARG10.8770.94920.0140.1050.1050.0000.0000.0000.000
163A165MET0-0.0200.01519.8860.0000.0000.0000.0000.0000.000
164A166SER0-0.038-0.02920.4020.0040.0040.0000.0000.0000.000
165A167LEU00.0650.00615.167-0.015-0.0150.0000.0000.0000.000
166A168ALA00.0030.01819.333-0.008-0.0080.0000.0000.0000.000
167A169ASP-1-0.746-0.86922.965-0.165-0.1650.0000.0000.0000.000
168A170PHE00.0480.00616.5760.0000.0000.0000.0000.0000.000
169A171ALA00.0320.02921.025-0.014-0.0140.0000.0000.0000.000
170A172ALA00.0070.00522.0120.0010.0010.0000.0000.0000.000
171A173ALA0-0.006-0.01223.4060.0040.0040.0000.0000.0000.000
172A174ALA0-0.0010.00520.647-0.003-0.0030.0000.0000.0000.000
173A175HIS00.0080.00322.6800.0050.0050.0000.0000.0000.000
174A176LEU0-0.015-0.01325.5670.0080.0080.0000.0000.0000.000
175A177SER00.0040.00824.128-0.001-0.0010.0000.0000.0000.000
176A178VAL0-0.0010.00124.3210.0010.0010.0000.0000.0000.000
177A179ILE00.0220.00126.9190.0120.0120.0000.0000.0000.000
178A180ASP-1-0.817-0.88929.253-0.177-0.1770.0000.0000.0000.000
179A181TYR0-0.027-0.01626.7530.0020.0020.0000.0000.0000.000
180A182PHE0-0.033-0.02528.7770.0090.0090.0000.0000.0000.000
181A183GLY00.0130.00132.8990.0120.0120.0000.0000.0000.000
182A184ASP-1-0.812-0.88034.181-0.122-0.1220.0000.0000.0000.000
183A185VAL00.0120.01131.6690.0060.0060.0000.0000.0000.000
184A186PRO0-0.043-0.00235.1170.0000.0000.0000.0000.0000.000
185A187TRP00.057-0.01629.9860.0100.0100.0000.0000.0000.000
186A188LYS10.8090.88336.8540.0950.0950.0000.0000.0000.000
187A189ASP-1-0.849-0.90640.094-0.086-0.0860.0000.0000.0000.000
188A190PHE0-0.0140.01437.0840.0040.0040.0000.0000.0000.000
189A191GLN00.0360.01537.190-0.010-0.0100.0000.0000.0000.000
190A192ALA00.0120.00435.760-0.005-0.0050.0000.0000.0000.000
191A193ALA00.0220.00032.993-0.008-0.0080.0000.0000.0000.000
192A194LYS10.9080.95532.5050.1090.1090.0000.0000.0000.000
193A195THR0-0.045-0.03333.017-0.009-0.0090.0000.0000.0000.000
194A196TRP0-0.061-0.03726.278-0.011-0.0110.0000.0000.0000.000
195A197TYR0-0.014-0.01826.463-0.021-0.0210.0000.0000.0000.000
196A198MET00.0160.01228.289-0.014-0.0140.0000.0000.0000.000
197A199LYS10.9170.96727.8330.1150.1150.0000.0000.0000.000
198A200LEU0-0.013-0.01623.064-0.016-0.0160.0000.0000.0000.000
199A201LYS10.8120.92723.8340.1780.1780.0000.0000.0000.000
200A202SER00.007-0.00425.367-0.012-0.0120.0000.0000.0000.000
201A203ARG10.7380.84119.6320.2740.2740.0000.0000.0000.000
202A204PRO0-0.010-0.02418.386-0.014-0.0140.0000.0000.0000.000
203A205CYS0-0.053-0.01616.673-0.013-0.0130.0000.0000.0000.000
204A206PHE00.0780.02917.761-0.032-0.0320.0000.0000.0000.000
205A207ARG10.9420.98220.5020.3680.3680.0000.0000.0000.000
206A208PRO00.019-0.00516.6750.0250.0250.0000.0000.0000.000
207A209ILE00.0350.02817.9360.0170.0170.0000.0000.0000.000
208A210LEU0-0.0350.01320.9460.0270.0270.0000.0000.0000.000
209A211ALA00.0260.01722.0890.0260.0260.0000.0000.0000.000
210A212ASP-1-0.813-0.85920.613-0.426-0.4260.0000.0000.0000.000
211A213ARG10.8190.88123.4510.2920.2920.0000.0000.0000.000
212A214TRP00.0260.01522.533-0.022-0.0220.0000.0000.0000.000
213A215PRO00.0400.01227.0170.0180.0180.0000.0000.0000.000
214A216GLY0-0.037-0.01230.1280.0040.0040.0000.0000.0000.000
215A217LEU0-0.050-0.02328.6970.0110.0110.0000.0000.0000.000
216A218ALA00.0000.01830.654-0.014-0.0140.0000.0000.0000.000
217A219PRO00.0210.01929.5740.0080.0080.0000.0000.0000.000
218A220ALA0-0.017-0.01431.9160.0100.0100.0000.0000.0000.000
219A221ALA00.003-0.01133.218-0.008-0.0080.0000.0000.0000.000
220A222HIS00.003-0.00133.3490.0020.0020.0000.0000.0000.000
221A223TYR0-0.083-0.04024.366-0.006-0.0060.0000.0000.0000.000
222A224ASP-1-0.842-0.92827.854-0.242-0.2420.0000.0000.0000.000
223A225ASP-1-0.863-0.90829.263-0.173-0.1730.0000.0000.0000.000
224A226LEU0-0.060-0.05227.311-0.003-0.0030.0000.0000.0000.000
225A227ASP-1-0.921-0.95531.204-0.134-0.1340.0000.0000.0000.000
226A228PHE0-0.021-0.00131.8080.0090.0090.0000.0000.0000.000