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: NN1JQ

Calculation Name: 1TD5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TD5

Chain ID: B

ChEMBL ID:

UniProt ID: P16528

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1885725.07352
FMO2-HF: Nuclear repulsion 1815346.713242
FMO2-HF: Total energy -70378.360278
FMO2-MP2: Total energy -70578.59192


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(B:1:GLY)


Summations of interaction energy for fragment #1(B:1:GLY)
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.
0.9623.1920.206-1.048-1.3870.004
Interaction energy analysis for fragmet #1(B:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.009
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].
3B3MET00.0310.0313.877-0.0181.193-0.003-0.632-0.5750.002
4B4SER0-0.0050.0092.642-0.1770.6600.205-0.411-0.6310.002
5B5ARG11.0120.9813.6581.3821.5640.004-0.005-0.1810.000
6B6ASN0-0.039-0.0096.2020.5620.5620.0000.0000.0000.000
7B7LEU00.0590.0257.1770.2690.2690.0000.0000.0000.000
8B8LEU00.0160.0017.0960.2980.2980.0000.0000.0000.000
9B9ALA0-0.036-0.0209.4620.1970.1970.0000.0000.0000.000
10B10ILE0-0.027-0.01111.4120.1130.1130.0000.0000.0000.000
11B11VAL00.0140.00811.7060.1060.1060.0000.0000.0000.000
12B12HIS0-0.035-0.02613.5520.1170.1170.0000.0000.0000.000
13B13PRO0-0.012-0.01415.0190.0620.0620.0000.0000.0000.000
14B14ILE00.0060.01216.7930.0450.0450.0000.0000.0000.000
15B15LEU0-0.0060.00613.3880.0340.0340.0000.0000.0000.000
16B16ARG10.8430.88117.7400.2460.2460.0000.0000.0000.000
17B17ASN0-0.038-0.01220.5920.0290.0290.0000.0000.0000.000
18B18LEU00.0000.00019.6420.0220.0220.0000.0000.0000.000
19B19MET0-0.0180.03321.6640.0270.0270.0000.0000.0000.000
20B20GLU-1-0.878-0.92023.399-0.160-0.1600.0000.0000.0000.000
21B21GLU-1-0.845-0.91225.610-0.212-0.2120.0000.0000.0000.000
22B22SER0-0.012-0.03124.8220.0150.0150.0000.0000.0000.000
23B23GLY00.0120.00927.2940.0140.0140.0000.0000.0000.000
24B24GLU-1-0.751-0.88925.803-0.059-0.0590.0000.0000.0000.000
25B25THR0-0.082-0.05420.949-0.015-0.0150.0000.0000.0000.000
26B26VAL00.0180.02717.567-0.004-0.0040.0000.0000.0000.000
27B27ASN0-0.066-0.04516.2690.0210.0210.0000.0000.0000.000
28B28MET00.0340.04110.495-0.060-0.0600.0000.0000.0000.000
29B29ALA00.010-0.00811.0630.0950.0950.0000.0000.0000.000
30B30VAL00.012-0.0015.819-0.218-0.2180.0000.0000.0000.000
31B31LEU00.0270.0218.9500.1830.1830.0000.0000.0000.000
32B32ASP-1-0.786-0.8758.6390.8090.8090.0000.0000.0000.000
33B33GLN0-0.013-0.0269.054-0.107-0.1070.0000.0000.0000.000
34B34SER0-0.085-0.05310.2610.0100.0100.0000.0000.0000.000
35B35ASP-1-0.867-0.94012.6080.2550.2550.0000.0000.0000.000
36B36HIS0-0.045-0.02013.722-0.054-0.0540.0000.0000.0000.000
37B37GLU-1-0.808-0.89713.5540.1630.1630.0000.0000.0000.000
38B38ALA00.0360.02112.6120.0280.0280.0000.0000.0000.000
39B39ILE0-0.031-0.01710.1750.0560.0560.0000.0000.0000.000
40B40ILE0-0.0100.00110.849-0.106-0.1060.0000.0000.0000.000
41B41ILE0-0.034-0.0296.8320.1190.1190.0000.0000.0000.000
42B42ASP-1-0.806-0.89110.074-0.386-0.3860.0000.0000.0000.000
43B43GLN0-0.038-0.03312.3020.0200.0200.0000.0000.0000.000
44B44VAL00.0190.02616.1520.0140.0140.0000.0000.0000.000
45B45GLN00.0070.00019.1970.0050.0050.0000.0000.0000.000
46B46CYS0-0.0210.02422.4710.0030.0030.0000.0000.0000.000
47B47THR00.034-0.01025.8790.0120.0120.0000.0000.0000.000
48B48HIS0-0.035-0.00428.9240.0130.0130.0000.0000.0000.000
49B49LEU00.001-0.00729.7200.0030.0030.0000.0000.0000.000
50B50MET00.0020.01930.9870.0090.0090.0000.0000.0000.000
51B51ARG10.8720.92125.0140.0250.0250.0000.0000.0000.000
52B52MET00.0580.05120.2560.0190.0190.0000.0000.0000.000
53B53SER0-0.004-0.01122.052-0.013-0.0130.0000.0000.0000.000
54B54ALA00.0480.04118.5390.0200.0200.0000.0000.0000.000
55B55PRO0-0.0030.00717.709-0.015-0.0150.0000.0000.0000.000
56B56ILE00.0260.00411.727-0.005-0.0050.0000.0000.0000.000
57B57GLY0-0.010-0.00412.2400.0630.0630.0000.0000.0000.000
58B58GLY0-0.035-0.01113.2360.0250.0250.0000.0000.0000.000
59B59LYS10.8140.89914.049-0.363-0.3630.0000.0000.0000.000
60B60LEU00.011-0.00115.984-0.028-0.0280.0000.0000.0000.000
61B61PRO00.0180.02617.4720.0030.0030.0000.0000.0000.000
62B62MET00.0050.01415.717-0.022-0.0220.0000.0000.0000.000
63B63HIS0-0.041-0.02819.491-0.022-0.0220.0000.0000.0000.000
64B64ALA0-0.009-0.00122.455-0.004-0.0040.0000.0000.0000.000
65B65SER00.0050.00319.271-0.017-0.0170.0000.0000.0000.000
66B66GLY00.0490.02320.911-0.009-0.0090.0000.0000.0000.000
67B67ALA00.0380.01915.475-0.018-0.0180.0000.0000.0000.000
68B68GLY0-0.0030.00216.743-0.021-0.0210.0000.0000.0000.000
69B69LYS10.8000.86817.8540.0520.0520.0000.0000.0000.000
70B70ALA0-0.024-0.00117.462-0.008-0.0080.0000.0000.0000.000
71B71PHE00.0310.00011.2440.0050.0050.0000.0000.0000.000
72B72LEU0-0.043-0.02016.3450.0010.0010.0000.0000.0000.000
73B73ALA0-0.0040.00519.2290.0100.0100.0000.0000.0000.000
74B74GLN0-0.044-0.03517.024-0.001-0.0010.0000.0000.0000.000
75B75LEU0-0.0270.01116.2660.0020.0020.0000.0000.0000.000
76B76SER00.019-0.01519.9810.0130.0130.0000.0000.0000.000
77B77GLU-1-0.802-0.92623.240-0.052-0.0520.0000.0000.0000.000
78B78GLU-1-0.821-0.88225.2540.0040.0040.0000.0000.0000.000
79B79GLN00.0730.04618.5290.0060.0060.0000.0000.0000.000
80B80VAL00.0300.02521.6890.0200.0200.0000.0000.0000.000
81B81THR0-0.015-0.01322.7690.0130.0130.0000.0000.0000.000
82B82LYS10.8120.89622.7170.0050.0050.0000.0000.0000.000
83B83LEU00.0390.04217.3270.0220.0220.0000.0000.0000.000
84B84LEU00.0580.01521.1960.0160.0160.0000.0000.0000.000
85B85HIS0-0.022-0.01724.1280.0110.0110.0000.0000.0000.000
86B86ARG10.8020.90119.246-0.120-0.1200.0000.0000.0000.000
87B87LYS10.7790.88917.691-0.195-0.1950.0000.0000.0000.000
88B88GLY0-0.0180.00922.462-0.001-0.0010.0000.0000.0000.000
89B89LEU0-0.022-0.02525.168-0.007-0.0070.0000.0000.0000.000
90B90HIS0-0.0200.00026.529-0.001-0.0010.0000.0000.0000.000
91B91ALA00.0580.02327.987-0.006-0.0060.0000.0000.0000.000
92B92TYR0-0.031-0.01224.0130.0060.0060.0000.0000.0000.000
93B93THR0-0.032-0.03429.4420.0010.0010.0000.0000.0000.000
94B94HIS0-0.015-0.02032.3160.0030.0030.0000.0000.0000.000
95B95ALA00.0510.03731.961-0.002-0.0020.0000.0000.0000.000
96B96THR0-0.052-0.03327.509-0.003-0.0030.0000.0000.0000.000
97B97LEU00.0390.02727.6100.0040.0040.0000.0000.0000.000
98B98VAL0-0.020-0.01729.0370.0030.0030.0000.0000.0000.000
99B99SER0-0.024-0.01631.1940.0050.0050.0000.0000.0000.000
100B100PRO00.026-0.00629.094-0.006-0.0060.0000.0000.0000.000
101B101VAL0-0.0150.00329.789-0.007-0.0070.0000.0000.0000.000
102B102HIS00.0750.03831.797-0.004-0.0040.0000.0000.0000.000
103B103LEU00.0210.02624.467-0.007-0.0070.0000.0000.0000.000
104B104LYS10.8520.91527.0890.0200.0200.0000.0000.0000.000
105B105GLU-1-0.898-0.92828.484-0.072-0.0720.0000.0000.0000.000
106B106ASP-1-0.714-0.84026.744-0.093-0.0930.0000.0000.0000.000
107B107LEU0-0.0240.00622.410-0.014-0.0140.0000.0000.0000.000
108B108ALA0-0.003-0.00825.397-0.018-0.0180.0000.0000.0000.000
109B109GLN0-0.049-0.05227.956-0.019-0.0190.0000.0000.0000.000
110B110THR0-0.028-0.02522.221-0.010-0.0100.0000.0000.0000.000
111B111ARG10.8220.90723.3570.1040.1040.0000.0000.0000.000
112B112LYS10.8590.93925.1520.0950.0950.0000.0000.0000.000
113B113ARG10.7520.86425.7300.1120.1120.0000.0000.0000.000
114B114GLY00.0250.02124.033-0.004-0.0040.0000.0000.0000.000
115B115TYR0-0.040-0.03022.145-0.026-0.0260.0000.0000.0000.000
116B116SER0-0.038-0.03620.8000.0150.0150.0000.0000.0000.000
117B117PHE00.017-0.01723.330-0.009-0.0090.0000.0000.0000.000
118B118ASP-1-0.789-0.89323.859-0.035-0.0350.0000.0000.0000.000
119B119ASP-1-0.804-0.88326.058-0.054-0.0540.0000.0000.0000.000
120B120GLU-1-0.782-0.89029.489-0.011-0.0110.0000.0000.0000.000
121B121GLU-1-0.813-0.86527.008-0.037-0.0370.0000.0000.0000.000
122B122HIS0-0.019-0.01421.9110.0150.0150.0000.0000.0000.000
123B123ALA0-0.006-0.02026.0030.0140.0140.0000.0000.0000.000
124B124LEU00.0410.02228.606-0.008-0.0080.0000.0000.0000.000
125B125GLY0-0.053-0.02631.3800.0020.0020.0000.0000.0000.000
126B126LEU0-0.067-0.02224.407-0.006-0.0060.0000.0000.0000.000
127B127ARG10.7400.81727.7340.0590.0590.0000.0000.0000.000
128B128CYS0-0.074-0.03121.480-0.008-0.0080.0000.0000.0000.000
129B129LEU00.0100.01723.1020.0040.0040.0000.0000.0000.000
130B130ALA0-0.007-0.01018.040-0.015-0.0150.0000.0000.0000.000
131B131ALA00.0200.01818.2800.0220.0220.0000.0000.0000.000
132B132CYS0-0.051-0.00314.391-0.013-0.0130.0000.0000.0000.000
133B133ILE0-0.023-0.00911.6800.0200.0200.0000.0000.0000.000
134B134PHE0-0.025-0.01812.307-0.046-0.0460.0000.0000.0000.000
135B135ASP-1-0.753-0.86510.457-0.975-0.9750.0000.0000.0000.000
136B136GLU-1-0.829-0.90212.117-0.900-0.9000.0000.0000.0000.000
137B137HIS0-0.098-0.04411.9700.2050.2050.0000.0000.0000.000
138B138ARG10.8690.93515.2880.4260.4260.0000.0000.0000.000
139B139GLU-1-0.890-0.93412.470-0.246-0.2460.0000.0000.0000.000
140B140PRO0-0.036-0.02212.461-0.136-0.1360.0000.0000.0000.000
141B141PHE0-0.006-0.0136.753-0.043-0.0430.0000.0000.0000.000
142B142ALA0-0.013-0.0157.940-0.076-0.0760.0000.0000.0000.000
143B143ALA0-0.009-0.00510.0200.1090.1090.0000.0000.0000.000
144B144ILE00.0120.01213.225-0.011-0.0110.0000.0000.0000.000
145B145SER0-0.023-0.03415.7030.0490.0490.0000.0000.0000.000
146B146ILE00.0310.01718.910-0.009-0.0090.0000.0000.0000.000
147B147SER0-0.001-0.00720.6570.0120.0120.0000.0000.0000.000
148B148GLY00.0360.01023.6640.0030.0030.0000.0000.0000.000
149B149PRO0-0.0120.00427.3060.0050.0050.0000.0000.0000.000
150B150ILE00.0730.01930.784-0.007-0.0070.0000.0000.0000.000
151B151SER0-0.055-0.02833.109-0.001-0.0010.0000.0000.0000.000
152B152ARG10.6980.81129.3860.0610.0610.0000.0000.0000.000
153B153ILE0-0.0180.01727.070-0.008-0.0080.0000.0000.0000.000
154B154THR00.014-0.01631.4070.0030.0030.0000.0000.0000.000
155B155ASP-1-0.813-0.90533.997-0.061-0.0610.0000.0000.0000.000
156B156ASP-1-0.910-0.93235.247-0.076-0.0760.0000.0000.0000.000
157B157ARG10.8530.91731.7400.0960.0960.0000.0000.0000.000
158B158VAL00.0250.03029.561-0.011-0.0110.0000.0000.0000.000
159B159THR0-0.018-0.00129.516-0.010-0.0100.0000.0000.0000.000
160B160GLU-1-0.844-0.90329.946-0.139-0.1390.0000.0000.0000.000
161B161PHE00.029-0.00527.036-0.012-0.0120.0000.0000.0000.000
162B162GLY00.0400.01925.852-0.017-0.0170.0000.0000.0000.000
163B163ALA0-0.023-0.01125.354-0.022-0.0220.0000.0000.0000.000
164B164MET0-0.0080.01325.263-0.020-0.0200.0000.0000.0000.000
165B165VAL00.0070.00820.091-0.030-0.0300.0000.0000.0000.000
166B166ILE0-0.0140.00220.723-0.042-0.0420.0000.0000.0000.000
167B167LYS10.7510.88521.6110.2280.2280.0000.0000.0000.000
168B168ALA00.0610.02819.226-0.032-0.0320.0000.0000.0000.000
169B169ALA00.0240.01216.902-0.065-0.0650.0000.0000.0000.000
170B170LYS10.8350.91617.0190.2520.2520.0000.0000.0000.000
171B171GLU-1-0.797-0.89918.857-0.359-0.3590.0000.0000.0000.000
172B172VAL0-0.014-0.01212.662-0.052-0.0520.0000.0000.0000.000
173B173THR0-0.017-0.01514.152-0.139-0.1390.0000.0000.0000.000
174B174LEU0-0.039-0.02315.430-0.037-0.0370.0000.0000.0000.000
175B175ALA0-0.018-0.00314.371-0.001-0.0010.0000.0000.0000.000
176B176TYR0-0.053-0.0528.266-0.135-0.1350.0000.0000.0000.000
177B177GLY00.0010.00212.618-0.018-0.0180.0000.0000.0000.000
178B178GLY0-0.036-0.02015.5330.0340.0340.0000.0000.0000.000
179B179MET0-0.097-0.0288.0360.0050.0050.0000.0000.0000.000