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: G5NZ1

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1881480.065702
FMO2-HF: Nuclear repulsion 1811103.34546
FMO2-HF: Total energy -70376.720241
FMO2-MP2: Total energy -70577.027853


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.
-0.491.5780.138-0.851-1.3550.002
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 : 0.003 / q_NPA : -0.016
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].
3B3MET0-0.0090.0163.6520.5011.3710.009-0.349-0.5300.000
4B4SER00.0030.0152.9691.6452.6790.121-0.467-0.6880.002
5B5ARG11.0280.9853.805-1.378-1.2140.008-0.035-0.1370.000
6B6ASN0-0.023-0.0246.351-0.135-0.1350.0000.0000.0000.000
7B7LEU00.0580.0317.037-0.037-0.0370.0000.0000.0000.000
8B8LEU0-0.0020.0038.0390.0090.0090.0000.0000.0000.000
9B9ALA0-0.032-0.01310.192-0.055-0.0550.0000.0000.0000.000
10B10ILE0-0.026-0.01011.374-0.024-0.0240.0000.0000.0000.000
11B11VAL00.0250.00612.201-0.006-0.0060.0000.0000.0000.000
12B12HIS0-0.0020.00314.332-0.018-0.0180.0000.0000.0000.000
13B13PRO0-0.029-0.02515.9610.0020.0020.0000.0000.0000.000
14B14ILE00.0200.02917.2980.0000.0000.0000.0000.0000.000
15B15LEU00.0090.00314.5390.0020.0020.0000.0000.0000.000
16B16ARG10.8970.94618.791-0.071-0.0710.0000.0000.0000.000
17B17ASN00.0330.03221.6180.0010.0010.0000.0000.0000.000
18B18LEU00.0050.02020.217-0.002-0.0020.0000.0000.0000.000
19B19MET0-0.052-0.00422.4900.0040.0040.0000.0000.0000.000
20B20GLU-1-0.958-0.99624.2100.0440.0440.0000.0000.0000.000
21B21GLU-1-0.942-0.97426.705-0.008-0.0080.0000.0000.0000.000
22B22SER0-0.029-0.03425.2950.0000.0000.0000.0000.0000.000
23B23GLY00.0110.00827.866-0.001-0.0010.0000.0000.0000.000
24B24GLU-1-0.767-0.87226.0250.0750.0750.0000.0000.0000.000
25B25THR0-0.071-0.05021.164-0.002-0.0020.0000.0000.0000.000
26B26VAL00.0280.03617.982-0.006-0.0060.0000.0000.0000.000
27B27ASN0-0.080-0.04416.1460.0100.0100.0000.0000.0000.000
28B28MET00.0430.04210.828-0.082-0.0820.0000.0000.0000.000
29B29ALA00.003-0.01011.5880.0970.0970.0000.0000.0000.000
30B30VAL00.0130.0006.293-0.113-0.1130.0000.0000.0000.000
31B31LEU00.020-0.0049.1180.0640.0640.0000.0000.0000.000
32B32ASP-1-0.815-0.9058.8050.5540.5540.0000.0000.0000.000
33B33GLN00.035-0.0118.791-0.025-0.0250.0000.0000.0000.000
34B34SER0-0.093-0.03010.277-0.061-0.0610.0000.0000.0000.000
35B35ASP-1-0.961-0.98112.5990.2580.2580.0000.0000.0000.000
36B36HIS0-0.062-0.02913.752-0.029-0.0290.0000.0000.0000.000
37B37GLU-1-0.911-0.98613.7250.1890.1890.0000.0000.0000.000
38B38ALA0-0.0070.00412.8490.0400.0400.0000.0000.0000.000
39B39ILE0-0.011-0.00710.4170.0040.0040.0000.0000.0000.000
40B40ILE0-0.035-0.00511.2160.0380.0380.0000.0000.0000.000
41B41ILE0-0.031-0.0277.6420.0920.0920.0000.0000.0000.000
42B42ASP-1-0.829-0.92410.9240.4940.4940.0000.0000.0000.000
43B43GLN0-0.009-0.02513.389-0.062-0.0620.0000.0000.0000.000
44B44VAL00.0150.03017.0870.0080.0080.0000.0000.0000.000
45B45GLN00.0250.02120.200-0.032-0.0320.0000.0000.0000.000
46B46CYS0-0.0100.03423.331-0.009-0.0090.0000.0000.0000.000
47B47THR00.050-0.03026.6230.0070.0070.0000.0000.0000.000
48B48HIS0-0.0450.01829.843-0.006-0.0060.0000.0000.0000.000
49B49LEU00.0340.01130.9360.0080.0080.0000.0000.0000.000
50B50MET0-0.0130.01432.2290.0060.0060.0000.0000.0000.000
51B51ARG10.8500.89126.220-0.131-0.1310.0000.0000.0000.000
52B52MET00.0840.06220.5080.0000.0000.0000.0000.0000.000
53B53SER0-0.027-0.02822.7190.0030.0030.0000.0000.0000.000
54B54ALA00.0100.02519.305-0.005-0.0050.0000.0000.0000.000
55B55PRO0-0.012-0.00618.8200.0090.0090.0000.0000.0000.000
56B56ILE00.0350.00412.9380.0060.0060.0000.0000.0000.000
57B57GLY0-0.0090.00212.7570.0070.0070.0000.0000.0000.000
58B58GLY0-0.042-0.01313.789-0.039-0.0390.0000.0000.0000.000
59B59LYS10.8930.95814.561-0.307-0.3070.0000.0000.0000.000
60B60LEU00.0020.00216.010-0.035-0.0350.0000.0000.0000.000
61B61PRO00.0270.02417.5980.0030.0030.0000.0000.0000.000
62B62MET0-0.0050.00015.9590.0040.0040.0000.0000.0000.000
63B63HIS0-0.055-0.04019.483-0.010-0.0100.0000.0000.0000.000
64B64ALA00.0390.02222.581-0.008-0.0080.0000.0000.0000.000
65B65SER00.0180.03019.3310.0020.0020.0000.0000.0000.000
66B66GLY00.0750.02321.073-0.012-0.0120.0000.0000.0000.000
67B67ALA00.0440.02115.290-0.018-0.0180.0000.0000.0000.000
68B68GLY0-0.019-0.00316.970-0.019-0.0190.0000.0000.0000.000
69B69LYS10.8100.86618.095-0.052-0.0520.0000.0000.0000.000
70B70ALA0-0.032-0.00817.454-0.019-0.0190.0000.0000.0000.000
71B71PHE00.0550.00411.240-0.018-0.0180.0000.0000.0000.000
72B72LEU00.009-0.00416.445-0.023-0.0230.0000.0000.0000.000
73B73ALA0-0.0350.00519.434-0.009-0.0090.0000.0000.0000.000
74B74GLN0-0.023-0.00916.729-0.020-0.0200.0000.0000.0000.000
75B75LEU0-0.0560.00216.633-0.013-0.0130.0000.0000.0000.000
76B76SER0-0.008-0.01620.0680.0100.0100.0000.0000.0000.000
77B77GLU-1-0.873-0.97023.386-0.019-0.0190.0000.0000.0000.000
78B78GLU-1-0.927-0.96025.401-0.027-0.0270.0000.0000.0000.000
79B79GLN0-0.009-0.02819.2340.0120.0120.0000.0000.0000.000
80B80VAL00.0580.05021.6360.0120.0120.0000.0000.0000.000
81B81THR0-0.001-0.01223.0600.0120.0120.0000.0000.0000.000
82B82LYS10.9100.96422.0790.0390.0390.0000.0000.0000.000
83B83LEU00.0120.01817.3510.0070.0070.0000.0000.0000.000
84B84LEU00.0080.00221.6220.0120.0120.0000.0000.0000.000
85B85HIS0-0.026-0.00824.4280.0070.0070.0000.0000.0000.000
86B86ARG10.9050.96319.872-0.049-0.0490.0000.0000.0000.000
87B87LYS10.9090.94418.521-0.124-0.1240.0000.0000.0000.000
88B88GLY0-0.0240.01422.6120.0040.0040.0000.0000.0000.000
89B89LEU0-0.001-0.00125.1550.0010.0010.0000.0000.0000.000
90B90HIS00.0000.00826.966-0.007-0.0070.0000.0000.0000.000
91B91ALA00.0360.01528.3670.0000.0000.0000.0000.0000.000
92B92TYR0-0.036-0.02223.6500.0010.0010.0000.0000.0000.000
93B93THR0-0.014-0.03629.5960.0000.0000.0000.0000.0000.000
94B94HIS0-0.020-0.01632.464-0.003-0.0030.0000.0000.0000.000
95B95ALA00.0620.03832.316-0.004-0.0040.0000.0000.0000.000
96B96THR0-0.081-0.04027.885-0.002-0.0020.0000.0000.0000.000
97B97LEU00.0240.01927.641-0.004-0.0040.0000.0000.0000.000
98B98VAL00.0430.00829.1240.0030.0030.0000.0000.0000.000
99B99SER00.0000.01431.355-0.002-0.0020.0000.0000.0000.000
100B100PRO00.021-0.01029.179-0.002-0.0020.0000.0000.0000.000
101B101VAL0-0.0060.01130.008-0.004-0.0040.0000.0000.0000.000
102B102HIS00.0590.01631.968-0.001-0.0010.0000.0000.0000.000
103B103LEU00.0280.02724.770-0.002-0.0020.0000.0000.0000.000
104B104LYS10.9160.93927.3280.0000.0000.0000.0000.0000.000
105B105GLU-1-0.948-0.95828.547-0.008-0.0080.0000.0000.0000.000
106B106ASP-1-0.791-0.89926.8090.0090.0090.0000.0000.0000.000
107B107LEU0-0.045-0.02022.649-0.004-0.0040.0000.0000.0000.000
108B108ALA0-0.026-0.00425.519-0.010-0.0100.0000.0000.0000.000
109B109GLN0-0.011-0.02128.135-0.010-0.0100.0000.0000.0000.000
110B110THR0-0.039-0.02422.6720.0010.0010.0000.0000.0000.000
111B111ARG10.8790.92523.2270.0460.0460.0000.0000.0000.000
112B112LYS10.8670.94125.2150.0310.0310.0000.0000.0000.000
113B113ARG10.8750.95226.7280.0010.0010.0000.0000.0000.000
114B114GLY00.0390.02624.2650.0000.0000.0000.0000.0000.000
115B115TYR00.0080.00722.268-0.008-0.0080.0000.0000.0000.000
116B116SER0-0.065-0.05920.7570.0000.0000.0000.0000.0000.000
117B117PHE00.019-0.02823.3440.0020.0020.0000.0000.0000.000
118B118ASP-1-0.864-0.90924.2710.0740.0740.0000.0000.0000.000
119B119ASP-1-0.831-0.92626.0810.0410.0410.0000.0000.0000.000
120B120GLU-1-0.795-0.87929.0990.0500.0500.0000.0000.0000.000
121B121GLU-1-0.826-0.87127.0670.0410.0410.0000.0000.0000.000
122B122HIS0-0.027-0.00522.6420.0170.0170.0000.0000.0000.000
123B123ALA00.001-0.02026.5300.0070.0070.0000.0000.0000.000
124B124LEU00.0280.01529.036-0.004-0.0040.0000.0000.0000.000
125B125GLY0-0.039-0.02631.9240.0050.0050.0000.0000.0000.000
126B126LEU0-0.092-0.01924.7480.0020.0020.0000.0000.0000.000
127B127ARG10.7770.86327.681-0.039-0.0390.0000.0000.0000.000
128B128CYS0-0.043-0.01421.5900.0090.0090.0000.0000.0000.000
129B129LEU00.0060.01623.210-0.011-0.0110.0000.0000.0000.000
130B130ALA00.001-0.01118.3460.0130.0130.0000.0000.0000.000
131B131ALA00.0280.01918.282-0.011-0.0110.0000.0000.0000.000
132B132CYS0-0.069-0.02114.5560.0170.0170.0000.0000.0000.000
133B133ILE0-0.0190.00211.2150.0090.0090.0000.0000.0000.000
134B134PHE0-0.024-0.03012.346-0.025-0.0250.0000.0000.0000.000
135B135ASP-1-0.768-0.8699.947-0.750-0.7500.0000.0000.0000.000
136B136GLU-1-0.851-0.93111.092-0.823-0.8230.0000.0000.0000.000
137B137HIS0-0.047-0.02411.7770.1250.1250.0000.0000.0000.000
138B138ARG10.8290.90915.0090.2920.2920.0000.0000.0000.000
139B139GLU-1-0.910-0.94612.617-0.270-0.2700.0000.0000.0000.000
140B140PRO0-0.070-0.02112.315-0.073-0.0730.0000.0000.0000.000
141B141PHE00.0280.0016.788-0.062-0.0620.0000.0000.0000.000
142B142ALA0-0.014-0.0257.8890.0710.0710.0000.0000.0000.000
143B143ALA0-0.021-0.00710.209-0.029-0.0290.0000.0000.0000.000
144B144ILE00.0340.02513.6850.0620.0620.0000.0000.0000.000
145B145SER0-0.011-0.02716.025-0.014-0.0140.0000.0000.0000.000
146B146ILE00.0430.04019.1620.0150.0150.0000.0000.0000.000
147B147SER0-0.006-0.01521.529-0.003-0.0030.0000.0000.0000.000
148B148GLY00.0090.00124.1720.0070.0070.0000.0000.0000.000
149B149PRO00.012-0.00527.608-0.001-0.0010.0000.0000.0000.000
150B150ILE00.1040.02931.019-0.004-0.0040.0000.0000.0000.000
151B151SER0-0.067-0.02133.197-0.003-0.0030.0000.0000.0000.000
152B152ARG10.6460.77029.674-0.070-0.0700.0000.0000.0000.000
153B153ILE0-0.0100.02027.506-0.005-0.0050.0000.0000.0000.000
154B154THR0-0.007-0.04631.8090.0010.0010.0000.0000.0000.000
155B155ASP-1-0.822-0.90534.1890.0220.0220.0000.0000.0000.000
156B156ASP-1-0.906-0.91735.3730.0160.0160.0000.0000.0000.000
157B157ARG10.9500.97432.267-0.025-0.0250.0000.0000.0000.000
158B158VAL0-0.0010.02829.530-0.001-0.0010.0000.0000.0000.000
159B159THR0-0.018-0.02329.8390.0000.0000.0000.0000.0000.000
160B160GLU-1-0.917-0.94530.102-0.009-0.0090.0000.0000.0000.000
161B161PHE00.044-0.01327.338-0.002-0.0020.0000.0000.0000.000
162B162GLY0-0.015-0.01126.0320.0000.0000.0000.0000.0000.000
163B163ALA0-0.023-0.01525.375-0.008-0.0080.0000.0000.0000.000
164B164MET0-0.0020.03525.643-0.008-0.0080.0000.0000.0000.000
165B165VAL00.0140.01320.252-0.005-0.0050.0000.0000.0000.000
166B166ILE0-0.0460.00120.788-0.016-0.0160.0000.0000.0000.000
167B167LYS10.8540.93521.5060.0150.0150.0000.0000.0000.000
168B168ALA00.0640.03019.525-0.016-0.0160.0000.0000.0000.000
169B169ALA00.0240.00316.932-0.017-0.0170.0000.0000.0000.000
170B170LYS10.9280.97116.9170.0550.0550.0000.0000.0000.000
171B171GLU-1-0.905-0.96718.538-0.099-0.0990.0000.0000.0000.000
172B172VAL00.0050.01012.695-0.023-0.0230.0000.0000.0000.000
173B173THR0-0.010-0.01313.963-0.074-0.0740.0000.0000.0000.000
174B174LEU0-0.060-0.04014.809-0.059-0.0590.0000.0000.0000.000
175B175ALA00.0020.01214.367-0.015-0.0150.0000.0000.0000.000
176B176TYR0-0.080-0.0467.657-0.103-0.1030.0000.0000.0000.000
177B177GLY0-0.003-0.00312.321-0.054-0.0540.0000.0000.0000.000
178B178GLY0-0.044-0.01015.0190.0150.0150.0000.0000.0000.000
179B179MET0-0.080-0.0277.7420.0540.0540.0000.0000.0000.000