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: 1NKLZ

Calculation Name: 4ANN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ANN

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G185

Base Structure: X-ray

Registration Date: 2023-09-23

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1928099.082277
FMO2-HF: Nuclear repulsion 1856964.71832
FMO2-HF: Total energy -71134.363957
FMO2-MP2: Total energy -71345.445197


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:30:LEU)


Summations of interaction energy for fragment #1(A:30:LEU)
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.
-7.329-2.3646.246-4.43-6.781-0.012
Interaction energy analysis for fragmet #1(A:30:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.036
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].
3A32MET0-0.066-0.0222.787-1.0511.2880.030-1.099-1.2700.001
4A33ARG10.8610.9303.407-1.527-0.8490.014-0.410-0.282-0.003
5A34GLU-1-0.834-0.8846.2200.2290.2290.0000.0000.0000.000
6A35ILE0-0.022-0.0089.183-0.045-0.0450.0000.0000.0000.000
7A36PRO00.0390.01312.5650.0490.0490.0000.0000.0000.000
8A37LYS10.8140.92215.4640.0710.0710.0000.0000.0000.000
9A38SER0-0.039-0.02018.704-0.004-0.0040.0000.0000.0000.000
10A39SER0-0.080-0.04716.535-0.004-0.0040.0000.0000.0000.000
11A40ILE00.0050.00816.569-0.011-0.0110.0000.0000.0000.000
12A41LYS10.8990.94320.3900.1140.1140.0000.0000.0000.000
13A42PRO00.0390.01323.824-0.006-0.0060.0000.0000.0000.000
14A43GLU-1-0.832-0.91525.554-0.095-0.0950.0000.0000.0000.000
15A44HIS0-0.013-0.02222.761-0.007-0.0070.0000.0000.0000.000
16A45PHE00.0440.02821.400-0.015-0.0150.0000.0000.0000.000
17A46HIS0-0.070-0.04021.632-0.012-0.0120.0000.0000.0000.000
18A47LEU0-0.006-0.00221.9770.0000.0000.0000.0000.0000.000
19A48MET00.0070.00917.185-0.030-0.0300.0000.0000.0000.000
20A49TYR00.0530.03117.252-0.033-0.0330.0000.0000.0000.000
21A50LEU0-0.034-0.00918.771-0.014-0.0140.0000.0000.0000.000
22A51LEU0-0.026-0.01913.185-0.013-0.0130.0000.0000.0000.000
23A52GLU-1-0.838-0.90513.897-0.308-0.3080.0000.0000.0000.000
24A53GLN0-0.063-0.02615.8680.0330.0330.0000.0000.0000.000
25A54HIS0-0.031-0.02216.962-0.004-0.0040.0000.0000.0000.000
26A55SER00.008-0.01016.6820.0330.0330.0000.0000.0000.000
27A56PRO0-0.0130.00416.612-0.034-0.0340.0000.0000.0000.000
28A57TYR0-0.059-0.05216.3390.0180.0180.0000.0000.0000.000
29A58PHE0-0.039-0.02911.598-0.004-0.0040.0000.0000.0000.000
30A59ILE00.0090.0237.6740.0590.0590.0000.0000.0000.000
31A60ASP-1-0.864-0.91010.786-0.368-0.3680.0000.0000.0000.000
32A61ALA00.0350.00710.908-0.129-0.1290.0000.0000.0000.000
33A62GLU-1-0.895-0.94911.941-0.316-0.3160.0000.0000.0000.000
34A63LEU0-0.049-0.02612.239-0.040-0.0400.0000.0000.0000.000
35A64THR0-0.048-0.03012.6150.0810.0810.0000.0000.0000.000
36A65GLU-1-0.871-0.93714.661-0.130-0.1300.0000.0000.0000.000
37A66LEU0-0.0010.01713.2800.0330.0330.0000.0000.0000.000
38A67ARG10.8170.88017.476-0.036-0.0360.0000.0000.0000.000
39A68ASP-1-0.806-0.90118.022-0.014-0.0140.0000.0000.0000.000
40A69SER0-0.056-0.04913.422-0.007-0.0070.0000.0000.0000.000
41A70PHE00.0270.01114.1480.0290.0290.0000.0000.0000.000
42A71GLN0-0.032-0.0459.6470.0230.0230.0000.0000.0000.000
43A72ILE0-0.0120.0128.5620.0970.0970.0000.0000.0000.000
44A73HIS0-0.0080.0017.597-0.087-0.0870.0000.0000.0000.000
45A74TYR00.0420.0134.9610.1970.1970.0000.0000.0000.000
46A75ASP-1-0.818-0.8868.363-0.290-0.2900.0000.0000.0000.000
47A76ILE0-0.042-0.0264.361-0.185-0.035-0.001-0.017-0.1320.000
48A77ASN0-0.015-0.0138.5980.1310.1310.0000.0000.0000.000
49A78ASP-1-0.864-0.94911.516-0.160-0.1600.0000.0000.0000.000
50A79ASN0-0.152-0.08013.8630.0700.0700.0000.0000.0000.000
51A80HIS0-0.0090.01310.5110.0310.0310.0000.0000.0000.000
52A81THR0-0.016-0.00510.199-0.026-0.0260.0000.0000.0000.000
53A82PRO00.0360.0136.365-0.022-0.0220.0000.0000.0000.000
54A83PHE00.0220.0098.3630.0990.0990.0000.0000.0000.000
55A84ASP-1-0.792-0.9008.5860.0040.0040.0000.0000.0000.000
56A85ASN0-0.013-0.01110.0880.0250.0250.0000.0000.0000.000
57A86ILE0-0.0010.00412.4740.0250.0250.0000.0000.0000.000
58A87LYS10.7790.90412.1670.0380.0380.0000.0000.0000.000
59A88SER0-0.041-0.01216.3310.0060.0060.0000.0000.0000.000
60A89PHE0-0.0140.00816.1270.0060.0060.0000.0000.0000.000
61A90THR00.004-0.01820.1240.0040.0040.0000.0000.0000.000
62A91LYS10.8970.93523.1230.0420.0420.0000.0000.0000.000
63A92ASN00.0390.03124.453-0.001-0.0010.0000.0000.0000.000
64A93GLU-1-0.763-0.85821.179-0.102-0.1020.0000.0000.0000.000
65A94LYS10.8000.89918.8530.0460.0460.0000.0000.0000.000
66A95LEU0-0.013-0.00120.028-0.010-0.0100.0000.0000.0000.000
67A96ARG10.8110.88221.7220.1100.1100.0000.0000.0000.000
68A97TYR00.0000.00815.7380.0000.0000.0000.0000.0000.000
69A98LEU00.000-0.00516.791-0.015-0.0150.0000.0000.0000.000
70A99LEU0-0.0170.00019.021-0.008-0.0080.0000.0000.0000.000
71A100ASN0-0.038-0.02819.4090.0050.0050.0000.0000.0000.000
72A101ILE0-0.0120.00214.948-0.015-0.0150.0000.0000.0000.000
73A102LYS10.8870.95417.4460.0950.0950.0000.0000.0000.000
74A103ASN00.0190.00919.1030.0170.0170.0000.0000.0000.000
75A104LEU00.006-0.00913.262-0.004-0.0040.0000.0000.0000.000
76A105GLU-1-0.918-0.96917.560-0.153-0.1530.0000.0000.0000.000
77A106GLU-1-0.755-0.82320.395-0.156-0.1560.0000.0000.0000.000
78A107VAL00.0020.00715.9320.0080.0080.0000.0000.0000.000
79A108ASN0-0.020-0.00619.265-0.004-0.0040.0000.0000.0000.000
80A109ARG10.7350.85821.4660.1770.1770.0000.0000.0000.000
81A110THR0-0.048-0.03820.5690.0020.0020.0000.0000.0000.000
82A111ARG10.8770.92321.5460.1870.1870.0000.0000.0000.000
83A112TYR0-0.046-0.02716.3640.0090.0090.0000.0000.0000.000
84A113THR0-0.050-0.03115.3660.0180.0180.0000.0000.0000.000
85A114PHE00.0440.01012.039-0.046-0.0460.0000.0000.0000.000
86A115VAL00.0140.0158.5830.0580.0580.0000.0000.0000.000
87A116LEU00.0010.01310.160-0.040-0.0400.0000.0000.0000.000
88A117ALA00.0740.0176.9740.0620.0620.0000.0000.0000.000
89A118PRO00.0210.0017.479-0.090-0.0900.0000.0000.0000.000
90A119ASP-1-0.833-0.9242.223-2.138-0.6862.349-1.451-2.350-0.017
91A120GLU-1-0.795-0.8563.563-2.291-1.6730.018-0.277-0.359-0.002
92A121LEU0-0.044-0.0025.893-0.018-0.0180.0000.0000.0000.000
93A122PHE00.008-0.0024.398-0.1000.020-0.001-0.004-0.1140.000
94A123PHE0-0.008-0.01610.0030.0530.0530.0000.0000.0000.000
95A124THR00.019-0.00613.615-0.007-0.0070.0000.0000.0000.000
96A125ARG10.8910.92716.2170.1750.1750.0000.0000.0000.000
97A126ASP-1-0.859-0.89618.611-0.152-0.1520.0000.0000.0000.000
98A127GLY00.0090.00217.5130.0170.0170.0000.0000.0000.000
99A128LEU0-0.0160.01018.3730.0050.0050.0000.0000.0000.000
100A129PRO0-0.041-0.00414.706-0.021-0.0210.0000.0000.0000.000
101A130ILE0-0.026-0.00911.1200.0170.0170.0000.0000.0000.000
102A131ALA00.0210.0079.934-0.028-0.0280.0000.0000.0000.000
103A132LYS10.8060.9051.9770.369-0.0233.837-1.172-2.2740.009
104A133THR0-0.072-0.0655.534-0.132-0.1320.0000.0000.0000.000
105A134ARG10.8140.8978.0860.7180.7180.0000.0000.0000.000
106A135GLY0-0.007-0.00211.845-0.040-0.0400.0000.0000.0000.000
107A136LEU0-0.045-0.02414.3640.0250.0250.0000.0000.0000.000
108A137GLN00.0660.03018.1860.0200.0200.0000.0000.0000.000
109A138ASN0-0.078-0.05420.9950.0080.0080.0000.0000.0000.000
110A139VAL0-0.037-0.01319.3960.0170.0170.0000.0000.0000.000
111A140VAL00.009-0.00314.6650.0070.0070.0000.0000.0000.000
112A141ASP-1-0.811-0.88713.493-0.266-0.2660.0000.0000.0000.000
113A142PRO00.0060.00911.134-0.059-0.0590.0000.0000.0000.000
114A143LEU00.0160.01613.5720.0120.0120.0000.0000.0000.000
115A144PRO0-0.0120.00615.792-0.017-0.0170.0000.0000.0000.000
116A145VAL00.0180.01215.0190.0200.0200.0000.0000.0000.000
117A146SER00.000-0.00618.0020.0040.0040.0000.0000.0000.000
118A147GLU-1-0.897-0.95420.169-0.106-0.1060.0000.0000.0000.000
119A148ALA00.0300.01021.600-0.002-0.0020.0000.0000.0000.000
120A149GLU-1-0.797-0.86615.638-0.138-0.1380.0000.0000.0000.000
121A150PHE00.007-0.00315.847-0.006-0.0060.0000.0000.0000.000
122A151LEU00.0110.00617.566-0.004-0.0040.0000.0000.0000.000
123A152THR0-0.015-0.01717.9920.0080.0080.0000.0000.0000.000
124A153ARG10.8220.89010.7460.1920.1920.0000.0000.0000.000
125A154TYR0-0.009-0.02715.236-0.003-0.0030.0000.0000.0000.000
126A155LYS10.7870.88317.2680.0800.0800.0000.0000.0000.000
127A156ALA00.0310.02315.2410.0080.0080.0000.0000.0000.000
128A157LEU00.0240.01310.9660.0130.0130.0000.0000.0000.000
129A158VAL00.0090.00114.9760.0090.0090.0000.0000.0000.000
130A159ILE0-0.028-0.01418.5770.0100.0100.0000.0000.0000.000
131A160CYS0-0.045-0.01414.1300.0120.0120.0000.0000.0000.000
132A161ALA00.0330.01915.9440.0090.0090.0000.0000.0000.000
133A162PHE0-0.028-0.02316.7470.0090.0090.0000.0000.0000.000
134A163ASN0-0.100-0.05519.1640.0150.0150.0000.0000.0000.000
135A164GLU-1-0.838-0.93016.1920.0110.0110.0000.0000.0000.000
136A165LYS10.8530.92215.499-0.002-0.0020.0000.0000.0000.000
137A166GLN0-0.068-0.02717.3130.0140.0140.0000.0000.0000.000
138A167SER0-0.029-0.00712.835-0.004-0.0040.0000.0000.0000.000
139A168PHE00.054-0.00610.446-0.014-0.0140.0000.0000.0000.000
140A169ASP-1-0.810-0.9109.964-0.011-0.0110.0000.0000.0000.000
141A170ALA0-0.004-0.00513.088-0.006-0.0060.0000.0000.0000.000
142A171LEU0-0.071-0.02916.168-0.002-0.0020.0000.0000.0000.000
143A172VAL0-0.029-0.01613.947-0.005-0.0050.0000.0000.0000.000
144A173GLU-1-0.978-0.98214.146-0.021-0.0210.0000.0000.0000.000
145A174GLY0-0.0050.01117.8700.0080.0080.0000.0000.0000.000
146A175ASN0-0.052-0.03821.122-0.010-0.0100.0000.0000.0000.000
147A176LEU00.0670.03020.3880.0050.0050.0000.0000.0000.000
148A177GLU-1-0.903-0.96223.541-0.042-0.0420.0000.0000.0000.000
149A178LEU0-0.098-0.04126.7760.0040.0040.0000.0000.0000.000
150A179HIS00.0010.00822.9680.0060.0060.0000.0000.0000.000
151A180LYS10.8020.88925.6840.0150.0150.0000.0000.0000.000
152A181GLY00.0640.03025.6280.0030.0030.0000.0000.0000.000
153A182THR0-0.044-0.01225.624-0.001-0.0010.0000.0000.0000.000
154A183PRO00.0530.00527.715-0.003-0.0030.0000.0000.0000.000
155A184PHE00.0100.01822.570-0.001-0.0010.0000.0000.0000.000
156A185GLU-1-0.700-0.83922.588-0.028-0.0280.0000.0000.0000.000
157A186THR0-0.015-0.00724.848-0.002-0.0020.0000.0000.0000.000
158A187LYS10.8150.88627.6800.0340.0340.0000.0000.0000.000
159A188VAL0-0.0050.01221.572-0.004-0.0040.0000.0000.0000.000
160A189ILE0-0.011-0.01023.123-0.005-0.0050.0000.0000.0000.000
161A190GLU-1-0.783-0.87525.043-0.040-0.0400.0000.0000.0000.000
162A191ALA0-0.0160.01125.6220.0000.0000.0000.0000.0000.000
163A192ALA00.0210.01026.506-0.005-0.0050.0000.0000.0000.000
164A193THR00.0240.00726.951-0.002-0.0020.0000.0000.0000.000
165A194LEU00.0760.04221.4760.0030.0030.0000.0000.0000.000
166A195ASP-1-0.866-0.92324.870-0.096-0.0960.0000.0000.0000.000
167A196LEU0-0.051-0.01827.8690.0030.0030.0000.0000.0000.000
168A197LEU0-0.0060.00121.1470.0040.0040.0000.0000.0000.000
169A198THR00.000-0.01225.140-0.004-0.0040.0000.0000.0000.000
170A199ALA00.0460.02226.0030.0020.0020.0000.0000.0000.000
171A200PHE00.0010.00926.0650.0040.0040.0000.0000.0000.000
172A201LEU0-0.006-0.01221.7300.0040.0040.0000.0000.0000.000
173A202ASP-1-0.861-0.94726.151-0.081-0.0810.0000.0000.0000.000
174A203GLU-1-0.973-0.99528.959-0.048-0.0480.0000.0000.0000.000
175A204GLN0-0.090-0.03026.6160.0080.0080.0000.0000.0000.000
176A205TYR0-0.105-0.03526.0500.0060.0060.0000.0000.0000.000