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: NN21Q

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3016290.198991
FMO2-HF: Nuclear repulsion 2923642.921051
FMO2-HF: Total energy -92647.27794
FMO2-MP2: Total energy -92916.738136


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.
-28.253-17.5416.073-6.09-10.695-0.02
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 : -0.035 / q_NPA : -0.022
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].
3A5ARG10.7520.8322.4150.6944.8292.153-2.150-4.138-0.010
4A6THR00.0020.0054.5170.4730.531-0.001-0.020-0.0370.000
5A7LEU0-0.020-0.0038.1540.1360.1360.0000.0000.0000.000
6A8HIS00.0330.01810.2780.1580.1580.0000.0000.0000.000
7A9HIS0-0.040-0.04713.6090.0440.0440.0000.0000.0000.000
8A10PHE00.0780.02116.0920.0360.0360.0000.0000.0000.000
9A11PRO00.0270.00919.6190.0030.0030.0000.0000.0000.000
10A12LEU0-0.0200.01020.6400.0040.0040.0000.0000.0000.000
11A13ASP-1-0.742-0.83219.454-0.368-0.3680.0000.0000.0000.000
12A14PRO00.008-0.00220.428-0.040-0.0400.0000.0000.0000.000
13A15ALA00.0290.01318.289-0.026-0.0260.0000.0000.0000.000
14A16SER0-0.015-0.05815.891-0.073-0.0730.0000.0000.0000.000
15A17ARG10.7710.86515.6690.3030.3030.0000.0000.0000.000
16A18GLN0-0.004-0.01616.629-0.034-0.0340.0000.0000.0000.000
17A19VAL0-0.0060.00510.714-0.032-0.0320.0000.0000.0000.000
18A20ARG10.7930.86412.1660.5300.5300.0000.0000.0000.000
19A21LEU0-0.0180.00513.819-0.038-0.0380.0000.0000.0000.000
20A22ALA0-0.009-0.01512.434-0.003-0.0030.0000.0000.0000.000
21A23LEU0-0.008-0.0037.072-0.024-0.0240.0000.0000.0000.000
22A24GLY00.0370.02210.433-0.041-0.0410.0000.0000.0000.000
23A25GLU-1-0.802-0.87213.179-0.354-0.3540.0000.0000.0000.000
24A26LYS10.7530.8549.9770.5700.5700.0000.0000.0000.000
25A27ARG10.8500.9249.9380.3790.3790.0000.0000.0000.000
26A28LEU0-0.0010.0195.392-0.149-0.1490.0000.0000.0000.000
27A29PRO0-0.013-0.0176.2530.1370.1370.0000.0000.0000.000
28A30PHE0-0.026-0.0206.260-0.691-0.6910.0000.0000.0000.000
29A31VAL00.0200.0257.9820.3550.3550.0000.0000.0000.000
30A32GLU-1-0.790-0.87910.117-0.788-0.7880.0000.0000.0000.000
31A33MET0-0.010-0.00512.8370.0740.0740.0000.0000.0000.000
32A34GLN0-0.040-0.02915.0800.0690.0690.0000.0000.0000.000
33A35VAL00.0200.01017.7250.0390.0390.0000.0000.0000.000
34A36ARG10.8100.87519.8680.2620.2620.0000.0000.0000.000
35A37TYR00.021-0.00421.2100.0280.0280.0000.0000.0000.000
36A38TRP00.0160.01023.1910.0100.0100.0000.0000.0000.000
37A39GLU-1-0.863-0.90126.616-0.199-0.1990.0000.0000.0000.000
38A40MET0-0.041-0.01425.0050.0130.0130.0000.0000.0000.000
39A41PRO00.0260.02222.0480.0120.0120.0000.0000.0000.000
40A42PRO00.023-0.01122.643-0.017-0.0170.0000.0000.0000.000
41A43GLU-1-0.934-0.95518.757-0.316-0.3160.0000.0000.0000.000
42A44PHE00.0140.01415.689-0.016-0.0160.0000.0000.0000.000
43A45THR00.017-0.00218.538-0.016-0.0160.0000.0000.0000.000
44A46SER0-0.104-0.05718.9410.0190.0190.0000.0000.0000.000
45A47LEU0-0.026-0.00113.3580.0080.0080.0000.0000.0000.000
46A48ASN0-0.006-0.04815.5130.0200.0200.0000.0000.0000.000
47A49PRO00.0000.01317.8810.0050.0050.0000.0000.0000.000
48A50SER0-0.062-0.04620.0380.0150.0150.0000.0000.0000.000
49A51GLY00.0050.00121.4680.0090.0090.0000.0000.0000.000
50A52MET0-0.030-0.00620.570-0.008-0.0080.0000.0000.0000.000
51A53PRO0-0.0550.00716.978-0.033-0.0330.0000.0000.0000.000
52A54PRO0-0.013-0.01613.4980.0300.0300.0000.0000.0000.000
53A55VAL00.003-0.02012.0140.0450.0450.0000.0000.0000.000
54A56LEU0-0.028-0.0015.925-0.030-0.0300.0000.0000.0000.000
55A57VAL00.0020.0017.3620.1570.1570.0000.0000.0000.000
56A58GLU-1-0.758-0.8582.392-5.796-4.4521.382-0.951-1.776-0.009
57A59THR0-0.008-0.0223.1770.3390.9010.041-0.164-0.438-0.001
58A60LYS10.9850.9862.316-20.086-16.0342.495-2.650-3.8970.001
59A61HIS0-0.005-0.0074.132-0.217-0.0770.001-0.028-0.1130.000
60A62GLN00.0080.0027.635-0.119-0.1190.0000.0000.0000.000
61A63ARG10.9130.9768.073-1.101-1.1010.0000.0000.0000.000
62A64ASN00.0480.0246.799-0.101-0.1010.0000.0000.0000.000
63A65LEU0-0.016-0.0025.4290.2490.2490.0000.0000.0000.000
64A66VAL00.0100.0137.115-0.327-0.3270.0000.0000.0000.000
65A67ILE0-0.0090.0056.2630.1490.1490.0000.0000.0000.000
66A68CYS0-0.004-0.00610.500-0.103-0.1030.0000.0000.0000.000
67A69GLU-1-0.758-0.85513.882-0.234-0.2340.0000.0000.0000.000
68A70THR0-0.004-0.02014.301-0.027-0.0270.0000.0000.0000.000
69A71ARG10.9200.95614.7310.1200.1200.0000.0000.0000.000
70A72ALA00.0100.01712.8840.0410.0410.0000.0000.0000.000
71A73ILE0-0.009-0.0049.212-0.029-0.0290.0000.0000.0000.000
72A74LEU0-0.003-0.0089.934-0.102-0.1020.0000.0000.0000.000
73A75GLU-1-0.792-0.86212.120-0.189-0.1890.0000.0000.0000.000
74A76HIS0-0.009-0.0074.3830.4380.494-0.001-0.005-0.0500.000
75A77ILE00.0140.0187.2020.0260.0260.0000.0000.0000.000
76A78GLU-1-0.779-0.8978.611-0.187-0.1870.0000.0000.0000.000
77A79GLU-1-1.003-1.00811.1580.0730.0730.0000.0000.0000.000
78A80THR0-0.082-0.0515.5190.0150.0150.0000.0000.0000.000
79A81GLU-1-0.804-0.8713.966-2.187-1.8220.003-0.122-0.246-0.001
80A82THR0-0.017-0.0177.896-0.030-0.0300.0000.0000.0000.000
81A83GLU-1-0.925-0.93410.947-0.212-0.2120.0000.0000.0000.000
82A84PRO00.0260.01911.925-0.099-0.0990.0000.0000.0000.000
83A85PRO0-0.0090.00214.295-0.053-0.0530.0000.0000.0000.000
84A86LEU0-0.010-0.01514.0840.0050.0050.0000.0000.0000.000
85A87LEU0-0.0190.00317.0730.0080.0080.0000.0000.0000.000
86A88GLY00.0100.00319.0320.0130.0130.0000.0000.0000.000
87A89ARG10.9190.94420.447-0.023-0.0230.0000.0000.0000.000
88A90ASP-1-0.800-0.88722.330-0.012-0.0120.0000.0000.0000.000
89A91PRO00.019-0.00624.629-0.014-0.0140.0000.0000.0000.000
90A92ALA00.0140.01025.651-0.010-0.0100.0000.0000.0000.000
91A93GLU-1-0.761-0.85824.332-0.078-0.0780.0000.0000.0000.000
92A94ARG10.8210.91116.0520.0600.0600.0000.0000.0000.000
93A95ALA00.0090.01022.649-0.016-0.0160.0000.0000.0000.000
94A96GLU-1-0.741-0.82725.240-0.107-0.1070.0000.0000.0000.000
95A97ALA00.0120.00321.648-0.012-0.0120.0000.0000.0000.000
96A98ARG10.8170.87216.7910.0910.0910.0000.0000.0000.000
97A99ARG10.7910.87722.3870.0940.0940.0000.0000.0000.000
98A100LEU0-0.016-0.01925.198-0.005-0.0050.0000.0000.0000.000
99A101LEU00.0300.01718.482-0.006-0.0060.0000.0000.0000.000
100A102GLN0-0.0090.01122.5890.0000.0000.0000.0000.0000.000
101A103TRP0-0.037-0.02324.6060.0110.0110.0000.0000.0000.000
102A104PHE00.0180.00224.5150.0050.0050.0000.0000.0000.000
103A105ASP-1-0.755-0.85120.343-0.299-0.2990.0000.0000.0000.000
104A106ARG10.8670.93524.0650.1380.1380.0000.0000.0000.000
105A107LYS10.8140.90827.3750.1120.1120.0000.0000.0000.000
106A108PHE00.019-0.00128.1330.0050.0050.0000.0000.0000.000
107A109ASP-1-0.800-0.90126.528-0.200-0.2000.0000.0000.0000.000
108A110ASN0-0.046-0.03228.6520.0130.0130.0000.0000.0000.000
109A111GLU-1-0.831-0.87831.586-0.104-0.1040.0000.0000.0000.000
110A112VAL0-0.029-0.01331.6300.0060.0060.0000.0000.0000.000
111A113ASN0-0.026-0.02926.6090.0050.0050.0000.0000.0000.000
112A114GLY00.0190.01030.700-0.001-0.0010.0000.0000.0000.000
113A115PHE0-0.057-0.01532.7430.0110.0110.0000.0000.0000.000
114A116LEU0-0.018-0.02833.2350.0000.0000.0000.0000.0000.000
115A117LEU0-0.0140.00727.290-0.004-0.0040.0000.0000.0000.000
116A118HIS00.007-0.00431.3570.0070.0070.0000.0000.0000.000
117A119GLU-1-0.761-0.88033.079-0.122-0.1220.0000.0000.0000.000
118A120LYS10.7850.88634.0650.1680.1680.0000.0000.0000.000
119A121MET0-0.0190.00726.328-0.005-0.0050.0000.0000.0000.000
120A122GLU-1-0.854-0.92029.163-0.193-0.1930.0000.0000.0000.000
121A123LYS10.8470.90631.5060.1230.1230.0000.0000.0000.000
122A124ARG10.8920.95133.6770.1730.1730.0000.0000.0000.000
123A125LEU0-0.048-0.01927.8020.0040.0040.0000.0000.0000.000
124A126LEU00.0220.00330.9270.0040.0040.0000.0000.0000.000
125A127ARG10.8760.93733.7960.1450.1450.0000.0000.0000.000
126A128MET00.0010.01335.8850.0050.0050.0000.0000.0000.000
127A129GLY0-0.0060.01138.7390.0070.0070.0000.0000.0000.000
128A130ALA0-0.018-0.01439.760-0.006-0.0060.0000.0000.0000.000
129A131PRO00.0310.01438.8920.0020.0020.0000.0000.0000.000
130A132ASP-1-0.840-0.90440.675-0.090-0.0900.0000.0000.0000.000
131A133LEU0-0.005-0.02542.149-0.003-0.0030.0000.0000.0000.000
132A134ALA0-0.040-0.00744.6880.0020.0020.0000.0000.0000.000
133A135ALA00.0500.02239.519-0.001-0.0010.0000.0000.0000.000
134A136LEU00.0300.00737.761-0.004-0.0040.0000.0000.0000.000
135A137ARG10.8520.91940.1450.0860.0860.0000.0000.0000.000
136A138GLN00.0330.02938.8040.0040.0040.0000.0000.0000.000
137A139GLY00.0600.02136.986-0.001-0.0010.0000.0000.0000.000
138A140ARG10.8170.88336.9250.1220.1220.0000.0000.0000.000
139A141GLU-1-0.888-0.93939.020-0.098-0.0980.0000.0000.0000.000
140A142ALA00.0100.01036.2660.0020.0020.0000.0000.0000.000
141A143LEU00.000-0.00132.977-0.002-0.0020.0000.0000.0000.000
142A144ARG10.9020.95035.7540.1090.1090.0000.0000.0000.000
143A145MET0-0.0090.00338.1920.0040.0040.0000.0000.0000.000
144A146HIS0-0.013-0.01731.976-0.003-0.0030.0000.0000.0000.000
145A147LEU0-0.030-0.01033.030-0.004-0.0040.0000.0000.0000.000
146A148GLY00.0380.01335.0760.0010.0010.0000.0000.0000.000
147A149TYR00.0080.01731.1980.0030.0030.0000.0000.0000.000
148A150ILE00.0270.01029.8430.0020.0020.0000.0000.0000.000
149A151GLU-1-0.752-0.84932.897-0.115-0.1150.0000.0000.0000.000
150A152SER0-0.067-0.04435.8730.0050.0050.0000.0000.0000.000
151A153LEU0-0.021-0.00530.7090.0040.0040.0000.0000.0000.000
152A154LEU0-0.015-0.01029.5510.0010.0010.0000.0000.0000.000
153A155GLN0-0.087-0.04833.5740.0060.0060.0000.0000.0000.000
154A156THR0-0.093-0.05335.6180.0070.0070.0000.0000.0000.000
155A157ARG10.7740.86929.8420.1060.1060.0000.0000.0000.000
156A158ASP-1-0.911-0.94629.623-0.105-0.1050.0000.0000.0000.000
157A159TRP0-0.037-0.03025.897-0.022-0.0220.0000.0000.0000.000
158A160LEU00.0190.01125.8850.0150.0150.0000.0000.0000.000
159A161ALA0-0.0040.00224.5430.0140.0140.0000.0000.0000.000
160A162GLY0-0.013-0.00426.5180.0160.0160.0000.0000.0000.000
161A163ARG10.8760.90125.4890.0480.0480.0000.0000.0000.000
162A164ARG10.8540.93019.5750.1580.1580.0000.0000.0000.000
163A165MET0-0.0260.01719.5630.0020.0020.0000.0000.0000.000
164A166SER0-0.044-0.04619.840-0.002-0.0020.0000.0000.0000.000
165A167LEU00.0710.01314.436-0.016-0.0160.0000.0000.0000.000
166A168ALA00.0060.01318.592-0.009-0.0090.0000.0000.0000.000
167A169ASP-1-0.763-0.85422.229-0.200-0.2000.0000.0000.0000.000
168A170PHE00.037-0.00216.1270.0030.0030.0000.0000.0000.000
169A171ALA00.0380.02320.421-0.014-0.0140.0000.0000.0000.000
170A172ALA00.0050.00921.5330.0030.0030.0000.0000.0000.000
171A173ALA00.001-0.00423.0830.0080.0080.0000.0000.0000.000
172A174ALA0-0.0080.00920.4080.0000.0000.0000.0000.0000.000
173A175HIS00.009-0.01122.5020.0120.0120.0000.0000.0000.000
174A176LEU0-0.004-0.00425.3220.0100.0100.0000.0000.0000.000
175A177SER0-0.009-0.00524.0440.0000.0000.0000.0000.0000.000
176A178VAL00.0110.01124.4170.0020.0020.0000.0000.0000.000
177A179ILE00.0300.00626.9350.0140.0140.0000.0000.0000.000
178A180ASP-1-0.818-0.87329.069-0.200-0.2000.0000.0000.0000.000
179A181TYR0-0.038-0.02926.9900.0020.0020.0000.0000.0000.000
180A182PHE0-0.008-0.01928.6400.0110.0110.0000.0000.0000.000
181A183GLY00.0090.01232.5610.0130.0130.0000.0000.0000.000
182A184ASP-1-0.811-0.88634.133-0.137-0.1370.0000.0000.0000.000
183A185VAL0-0.0040.00631.6000.0080.0080.0000.0000.0000.000
184A186PRO0-0.0330.00435.0650.0010.0010.0000.0000.0000.000
185A187TRP00.023-0.03829.9950.0100.0100.0000.0000.0000.000
186A188LYS10.8020.88336.7830.1060.1060.0000.0000.0000.000
187A189ASP-1-0.807-0.87639.974-0.099-0.0990.0000.0000.0000.000
188A190PHE0-0.020-0.00336.7210.0050.0050.0000.0000.0000.000
189A191GLN00.0360.01636.683-0.011-0.0110.0000.0000.0000.000
190A192ALA00.0050.00835.265-0.006-0.0060.0000.0000.0000.000
191A193ALA00.0270.00032.402-0.010-0.0100.0000.0000.0000.000
192A194LYS10.9280.96731.9040.1250.1250.0000.0000.0000.000
193A195THR0-0.036-0.03232.563-0.010-0.0100.0000.0000.0000.000
194A196TRP0-0.086-0.05925.603-0.010-0.0100.0000.0000.0000.000
195A197TYR0-0.023-0.03926.199-0.023-0.0230.0000.0000.0000.000
196A198MET0-0.0100.00627.885-0.016-0.0160.0000.0000.0000.000
197A199LYS10.9150.96827.4160.1400.1400.0000.0000.0000.000
198A200LEU0-0.028-0.01622.738-0.017-0.0170.0000.0000.0000.000
199A201LYS10.8330.93323.7220.1990.1990.0000.0000.0000.000
200A202SER00.0190.00325.173-0.012-0.0120.0000.0000.0000.000
201A203ARG10.7370.84119.4050.3260.3260.0000.0000.0000.000
202A204PRO0-0.041-0.03918.086-0.012-0.0120.0000.0000.0000.000
203A205CYS0-0.042-0.01816.505-0.011-0.0110.0000.0000.0000.000
204A206PHE00.0920.03817.531-0.032-0.0320.0000.0000.0000.000
205A207ARG10.9510.98920.4730.3850.3850.0000.0000.0000.000
206A208PRO00.004-0.00916.3650.0260.0260.0000.0000.0000.000
207A209ILE00.0370.02617.5590.0190.0190.0000.0000.0000.000
208A210LEU0-0.0530.00620.6780.0340.0340.0000.0000.0000.000
209A211ALA00.0260.01721.8590.0290.0290.0000.0000.0000.000
210A212ASP-1-0.794-0.84320.480-0.474-0.4740.0000.0000.0000.000
211A213ARG10.8020.86023.2570.3190.3190.0000.0000.0000.000
212A214TRP00.0450.02222.606-0.024-0.0240.0000.0000.0000.000
213A215PRO00.0250.00527.2880.0210.0210.0000.0000.0000.000
214A216GLY0-0.050-0.02230.3340.0030.0030.0000.0000.0000.000
215A217LEU0-0.033-0.00828.8600.0110.0110.0000.0000.0000.000
216A218ALA00.0110.01830.758-0.015-0.0150.0000.0000.0000.000
217A219PRO00.0130.01529.8550.0070.0070.0000.0000.0000.000
218A220ALA0-0.015-0.01132.0620.0110.0110.0000.0000.0000.000
219A221ALA0-0.021-0.02633.360-0.009-0.0090.0000.0000.0000.000
220A222HIS00.0080.01133.3030.0030.0030.0000.0000.0000.000
221A223TYR0-0.084-0.05024.200-0.005-0.0050.0000.0000.0000.000
222A224ASP-1-0.822-0.91627.452-0.270-0.2700.0000.0000.0000.000
223A225ASP-1-0.871-0.91129.072-0.190-0.1900.0000.0000.0000.000
224A226LEU0-0.037-0.03427.326-0.005-0.0050.0000.0000.0000.000
225A227ASP-1-0.917-0.96031.165-0.150-0.1500.0000.0000.0000.000
226A228PHE0-0.040-0.01431.4930.0110.0110.0000.0000.0000.000