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: NNLMQ

Calculation Name: 3K2N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KG60

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1826191.134412
FMO2-HF: Nuclear repulsion 1757768.977302
FMO2-HF: Total energy -68422.157111
FMO2-MP2: Total energy -68624.831719


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2: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.
-9.545-5.4920.172-1.871-2.3540.012
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.010
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].
3A0ALA00.0330.0292.802-6.107-2.4910.173-1.799-1.9900.012
4A1ALA00.0820.0303.981-2.492-2.1180.000-0.069-0.3050.000
5A2LEU0-0.005-0.0075.036-0.565-0.5650.0000.0000.0000.000
6A3LYS10.9520.9686.955-1.199-1.1990.0000.0000.0000.000
7A4LEU0-0.0030.0318.641-0.212-0.2120.0000.0000.0000.000
8A5MET00.0110.0019.636-0.215-0.2150.0000.0000.0000.000
9A6GLN0-0.004-0.00611.2130.0190.0190.0000.0000.0000.000
10A7TYR0-0.0010.00612.933-0.044-0.0440.0000.0000.0000.000
11A8ILE0-0.007-0.00413.768-0.056-0.0560.0000.0000.0000.000
12A9GLY00.0040.00315.455-0.048-0.0480.0000.0000.0000.000
13A10ASP-1-0.935-0.97617.1550.2090.2090.0000.0000.0000.000
14A11ALA00.014-0.00818.682-0.023-0.0230.0000.0000.0000.000
15A12ILE0-0.042-0.02318.927-0.025-0.0250.0000.0000.0000.000
16A13GLY0-0.056-0.00721.721-0.020-0.0200.0000.0000.0000.000
17A14THR0-0.034-0.00523.188-0.023-0.0230.0000.0000.0000.000
18A15ILE0-0.071-0.03522.774-0.010-0.0100.0000.0000.0000.000
19A16ARG10.9520.98026.073-0.119-0.1190.0000.0000.0000.000
20A17ASP-1-0.821-0.91829.3270.1530.1530.0000.0000.0000.000
21A18PRO00.0440.00827.2170.0150.0150.0000.0000.0000.000
22A19GLN00.0180.00226.6140.0250.0250.0000.0000.0000.000
23A20GLU-1-0.916-0.96226.8980.2180.2180.0000.0000.0000.000
24A21LEU00.0090.03121.6540.0320.0320.0000.0000.0000.000
25A22PHE00.002-0.02222.1470.0390.0390.0000.0000.0000.000
26A23ARG10.9720.99522.132-0.207-0.2070.0000.0000.0000.000
27A24THR0-0.0010.00119.6540.0440.0440.0000.0000.0000.000
28A25VAL0-0.023-0.01816.8610.0670.0670.0000.0000.0000.000
29A26THR0-0.006-0.01017.1230.0780.0780.0000.0000.0000.000
30A27ASP-1-0.940-0.97918.1040.5490.5490.0000.0000.0000.000
31A28LYS10.9530.97914.197-0.552-0.5520.0000.0000.0000.000
32A29LEU0-0.030-0.00713.3130.1920.1920.0000.0000.0000.000
33A30ARG10.8540.92613.386-0.351-0.3510.0000.0000.0000.000
34A31LEU0-0.072-0.02810.2570.0080.0080.0000.0000.0000.000
35A32LEU0-0.060-0.0306.0740.5200.5200.0000.0000.0000.000
36A33PHE0-0.0040.0149.775-0.045-0.0450.0000.0000.0000.000
37A34ALA00.0130.00813.038-0.049-0.0490.0000.0000.0000.000
38A35PHE00.002-0.01316.270-0.061-0.0610.0000.0000.0000.000
39A36ASP-1-0.843-0.92619.6040.3210.3210.0000.0000.0000.000
40A37SER0-0.030-0.01222.967-0.007-0.0070.0000.0000.0000.000
41A38ALA00.0040.00720.8350.0080.0080.0000.0000.0000.000
42A39VAL0-0.0180.00822.791-0.015-0.0150.0000.0000.0000.000
43A40ILE00.0010.00622.2620.0090.0090.0000.0000.0000.000
44A41ILE0-0.0020.00424.817-0.011-0.0110.0000.0000.0000.000
45A42THR00.010-0.00226.7920.0030.0030.0000.0000.0000.000
46A43ILE0-0.038-0.03128.954-0.002-0.0020.0000.0000.0000.000
47A44ASP-1-0.843-0.91731.0140.0550.0550.0000.0000.0000.000
48A45ARG10.8730.92030.563-0.043-0.0430.0000.0000.0000.000
49A46GLU-1-0.924-0.96834.7690.0330.0330.0000.0000.0000.000
50A47ARG10.9390.97838.179-0.051-0.0510.0000.0000.0000.000
51A48ARG10.7860.90336.656-0.044-0.0440.0000.0000.0000.000
52A49GLU-1-0.939-0.98236.1290.0640.0640.0000.0000.0000.000
53A50ALA0-0.039-0.01931.6950.0020.0020.0000.0000.0000.000
54A51SER00.0380.00432.127-0.003-0.0030.0000.0000.0000.000
55A52VAL0-0.044-0.02329.7530.0080.0080.0000.0000.0000.000
56A53PHE0-0.024-0.01125.967-0.005-0.0050.0000.0000.0000.000
57A54PHE0-0.022-0.03323.5040.0040.0040.0000.0000.0000.000
58A55GLU-1-0.923-0.95926.5760.1700.1700.0000.0000.0000.000
59A56MET0-0.041-0.01722.8590.0130.0130.0000.0000.0000.000
60A57LEU00.0220.01425.5230.0230.0230.0000.0000.0000.000
61A58ARG10.9150.96921.689-0.316-0.3160.0000.0000.0000.000
62A59PHE0-0.0110.00027.966-0.008-0.0080.0000.0000.0000.000
63A60GLU-1-0.809-0.92431.7660.1430.1430.0000.0000.0000.000
64A61LEU0-0.0420.00533.053-0.006-0.0060.0000.0000.0000.000
65A62PRO00.0350.00336.109-0.002-0.0020.0000.0000.0000.000
66A63GLU-1-0.886-0.95538.9200.0820.0820.0000.0000.0000.000
67A64GLN00.0620.02740.8160.0020.0020.0000.0000.0000.000
68A65LEU0-0.079-0.03236.799-0.001-0.0010.0000.0000.0000.000
69A66ARG10.9050.96936.243-0.111-0.1110.0000.0000.0000.000
70A67HIS0-0.0360.00437.642-0.001-0.0010.0000.0000.0000.000
71A68GLN00.0130.00134.6420.0000.0000.0000.0000.0000.000
72A69THR00.0650.03834.8890.0050.0050.0000.0000.0000.000
73A70ARG10.8320.91334.956-0.105-0.1050.0000.0000.0000.000
74A71SER00.0620.02736.9240.0000.0000.0000.0000.0000.000
75A72ILE0-0.029-0.02032.7830.0040.0040.0000.0000.0000.000
76A73ALA00.0140.00436.236-0.001-0.0010.0000.0000.0000.000
77A74GLY0-0.039-0.01138.0030.0000.0000.0000.0000.0000.000
78A75THR0-0.058-0.01534.5150.0040.0040.0000.0000.0000.000
79A76TRP00.1030.02327.724-0.001-0.0010.0000.0000.0000.000
80A77LEU0-0.008-0.00127.412-0.001-0.0010.0000.0000.0000.000
81A78GLU-1-0.737-0.85030.0670.0510.0510.0000.0000.0000.000
82A79GLY00.0050.00231.565-0.005-0.0050.0000.0000.0000.000
83A80HIS10.8380.90625.454-0.091-0.0910.0000.0000.0000.000
84A81LEU0-0.0150.00626.7010.0030.0030.0000.0000.0000.000
85A82ASP-1-0.874-0.93227.6210.0280.0280.0000.0000.0000.000
86A83ASP-1-0.864-0.92922.7050.0650.0650.0000.0000.0000.000
87A84ARG10.8660.91220.903-0.009-0.0090.0000.0000.0000.000
88A85THR0-0.0080.00117.7620.0060.0060.0000.0000.0000.000
89A86VAL00.0380.01615.0790.0050.0050.0000.0000.0000.000
90A87THR0-0.028-0.00618.095-0.026-0.0260.0000.0000.0000.000
91A88VAL0-0.031-0.01417.5730.0240.0240.0000.0000.0000.000
92A89ALA00.0090.01420.823-0.018-0.0180.0000.0000.0000.000
93A90SER00.008-0.00124.4590.0130.0130.0000.0000.0000.000
94A91ILE0-0.044-0.03526.870-0.011-0.0110.0000.0000.0000.000
95A92ALA00.0220.00729.495-0.008-0.0080.0000.0000.0000.000
96A93ARG10.8770.93829.777-0.078-0.0780.0000.0000.0000.000
97A94ASP-1-0.791-0.88225.8660.0980.0980.0000.0000.0000.000
98A95ILE0-0.068-0.02628.204-0.005-0.0050.0000.0000.0000.000
99A96PRO00.005-0.01031.307-0.001-0.0010.0000.0000.0000.000
100A97SER0-0.027-0.02134.456-0.002-0.0020.0000.0000.0000.000
101A98PHE0-0.049-0.00633.7840.0000.0000.0000.0000.0000.000
102A99GLY00.1170.04535.779-0.004-0.0040.0000.0000.0000.000
103A100ALA0-0.071-0.03538.8400.0030.0030.0000.0000.0000.000
104A101ASP-1-0.838-0.89440.1360.0600.0600.0000.0000.0000.000
105A102GLY0-0.033-0.02840.2660.0000.0000.0000.0000.0000.000
106A103ALA0-0.056-0.03335.1130.0030.0030.0000.0000.0000.000
107A104PRO00.0670.03436.8100.0050.0050.0000.0000.0000.000
108A105LEU00.0140.00332.1150.0030.0030.0000.0000.0000.000
109A106LEU00.0280.01330.4600.0060.0060.0000.0000.0000.000
110A107TRP00.0160.02933.5550.0040.0040.0000.0000.0000.000
111A108THR00.027-0.00436.1640.0000.0000.0000.0000.0000.000
112A109LEU0-0.026-0.01429.4360.0050.0050.0000.0000.0000.000
113A110HIS00.0050.00632.1390.0100.0100.0000.0000.0000.000
114A111GLU-1-0.924-0.97033.4740.0900.0900.0000.0000.0000.000
115A112LEU0-0.079-0.04032.9930.0000.0000.0000.0000.0000.000
116A113GLY0-0.0450.00232.5300.0050.0050.0000.0000.0000.000
117A114MET0-0.052-0.01326.9420.0130.0130.0000.0000.0000.000
118A115ARG10.8680.92027.019-0.144-0.1440.0000.0000.0000.000
119A116GLN0-0.007-0.00620.6590.0180.0180.0000.0000.0000.000
120A117ILE00.0010.01424.0190.0150.0150.0000.0000.0000.000
121A118VAL0-0.013-0.01817.600-0.010-0.0100.0000.0000.0000.000
122A119LEU0-0.031-0.01021.0480.0020.0020.0000.0000.0000.000
123A120SER0-0.009-0.03216.777-0.020-0.0200.0000.0000.0000.000
124A121PRO00.0400.02019.2370.0060.0060.0000.0000.0000.000
125A122LEU00.0010.01819.6670.0050.0050.0000.0000.0000.000
126A123ARG10.8670.93521.442-0.057-0.0570.0000.0000.0000.000
127A124SER00.0690.02622.8400.0010.0010.0000.0000.0000.000
128A125GLY0-0.0080.00225.324-0.003-0.0030.0000.0000.0000.000
129A126GLY0-0.011-0.00625.845-0.004-0.0040.0000.0000.0000.000
130A127ARG10.9340.97326.991-0.038-0.0380.0000.0000.0000.000
131A128VAL00.0270.00824.8260.0040.0040.0000.0000.0000.000
132A129ILE0-0.031-0.02224.459-0.004-0.0040.0000.0000.0000.000
133A130GLY00.0650.02125.8790.0020.0020.0000.0000.0000.000
134A131PHE0-0.059-0.01822.887-0.006-0.0060.0000.0000.0000.000
135A132LEU00.0180.02317.1240.0030.0030.0000.0000.0000.000
136A133SER0-0.045-0.03020.876-0.007-0.0070.0000.0000.0000.000
137A134PHE00.009-0.00615.7500.0220.0220.0000.0000.0000.000
138A135VAL00.0380.01021.475-0.024-0.0240.0000.0000.0000.000
139A136SER0-0.013-0.02421.7850.0330.0330.0000.0000.0000.000
140A137ALA00.0630.03724.405-0.020-0.0200.0000.0000.0000.000
141A138GLU-1-0.966-0.97723.1250.2190.2190.0000.0000.0000.000
142A139GLU-1-0.950-0.99123.1410.1610.1610.0000.0000.0000.000
143A140LYS10.9070.96717.815-0.363-0.3630.0000.0000.0000.000
144A141LEU00.0240.00116.424-0.022-0.0220.0000.0000.0000.000
145A142TRP00.0120.01212.9380.0990.0990.0000.0000.0000.000
146A143SER0-0.040-0.00511.190-0.103-0.1030.0000.0000.0000.000
147A144ASP-1-0.853-0.95313.2620.0570.0570.0000.0000.0000.000
148A145GLY0-0.021-0.0159.135-0.029-0.0290.0000.0000.0000.000
149A146ASP-1-0.803-0.8998.6180.9570.9570.0000.0000.0000.000
150A147LYS10.9440.96610.199-0.094-0.0940.0000.0000.0000.000
151A148SER00.000-0.0109.4520.0010.0010.0000.0000.0000.000
152A149LEU0-0.0100.0014.386-0.120-0.057-0.001-0.003-0.0590.000
153A150LEU0-0.0060.0078.5920.0230.0230.0000.0000.0000.000
154A151SER00.0260.01412.000-0.053-0.0530.0000.0000.0000.000
155A152GLY0-0.017-0.00110.652-0.033-0.0330.0000.0000.0000.000
156A153VAL00.0410.00110.843-0.028-0.0280.0000.0000.0000.000
157A154SER00.0050.00212.300-0.024-0.0240.0000.0000.0000.000
158A155SER0-0.0380.00214.683-0.044-0.0440.0000.0000.0000.000
159A156SER0-0.036-0.00914.081-0.029-0.0290.0000.0000.0000.000
160A157ILE00.0410.01316.330-0.014-0.0140.0000.0000.0000.000
161A158ALA00.0060.01018.994-0.017-0.0170.0000.0000.0000.000
162A159ILE0-0.0100.01019.592-0.014-0.0140.0000.0000.0000.000
163A160ALA00.0260.03221.012-0.013-0.0130.0000.0000.0000.000
164A161VAL0-0.002-0.01422.870-0.010-0.0100.0000.0000.0000.000
165A162SER0-0.082-0.06424.570-0.016-0.0160.0000.0000.0000.000
166A163ASN00.0020.00725.853-0.018-0.0180.0000.0000.0000.000
167A164ALA00.004-0.00227.379-0.007-0.0070.0000.0000.0000.000
168A165LEU00.0330.00128.228-0.006-0.0060.0000.0000.0000.000
169A166ALA0-0.0100.01030.542-0.007-0.0070.0000.0000.0000.000
170A167TYR0-0.028-0.02531.127-0.003-0.0030.0000.0000.0000.000
171A168GLU-1-0.896-0.94633.4960.0800.0800.0000.0000.0000.000
172A169GLU-1-0.903-0.95634.9810.0440.0440.0000.0000.0000.000
173A170LEU0-0.023-0.01835.409-0.005-0.0050.0000.0000.0000.000
174A171ARG10.9420.98637.323-0.080-0.0800.0000.0000.0000.000
175A172GLN0-0.097-0.05338.159-0.001-0.0010.0000.0000.0000.000
176A173ARG10.8290.92440.306-0.046-0.0460.0000.0000.0000.000
177A174GLU-1-1.004-0.97842.6220.0330.0330.0000.0000.0000.000