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: 8924Y

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 OptHSide
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 -1882557.977617
FMO2-HF: Nuclear repulsion 1812180.134934
FMO2-HF: Total energy -70377.842683
FMO2-MP2: Total energy -70578.068993


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.
0.933.3390.318-1.124-1.6040.004
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].
3B3MET0-0.0080.0093.6840.2331.5040.008-0.615-0.6640.002
4B4SER0-0.0160.0062.556-0.0540.9520.295-0.537-0.7650.002
5B5ARG11.0370.9923.4701.2511.3830.0150.028-0.1750.000
6B6ASN0-0.040-0.0256.3540.4540.4540.0000.0000.0000.000
7B7LEU00.0550.0277.0070.2550.2550.0000.0000.0000.000
8B8LEU00.0010.0037.2830.2700.2700.0000.0000.0000.000
9B9ALA0-0.023-0.0109.5690.1930.1930.0000.0000.0000.000
10B10ILE0-0.025-0.00811.3340.1080.1080.0000.0000.0000.000
11B11VAL00.0280.00711.6330.1020.1020.0000.0000.0000.000
12B12HIS0-0.024-0.00613.8210.1430.1430.0000.0000.0000.000
13B13PRO0-0.018-0.01515.3080.0600.0600.0000.0000.0000.000
14B14ILE00.0000.01116.8340.0440.0440.0000.0000.0000.000
15B15LEU00.0110.00913.8650.0390.0390.0000.0000.0000.000
16B16ARG10.8510.89018.0270.2750.2750.0000.0000.0000.000
17B17ASN0-0.0260.00520.7820.0380.0380.0000.0000.0000.000
18B18LEU00.0050.01420.0320.0260.0260.0000.0000.0000.000
19B19MET0-0.0240.02421.7680.0280.0280.0000.0000.0000.000
20B20GLU-1-0.907-0.94023.550-0.180-0.1800.0000.0000.0000.000
21B21GLU-1-0.921-0.95526.002-0.218-0.2180.0000.0000.0000.000
22B22SER0-0.006-0.03524.8910.0160.0160.0000.0000.0000.000
23B23GLY0-0.0110.00027.3280.0150.0150.0000.0000.0000.000
24B24GLU-1-0.773-0.89825.885-0.085-0.0850.0000.0000.0000.000
25B25THR0-0.067-0.04520.903-0.016-0.0160.0000.0000.0000.000
26B26VAL00.0270.03117.618-0.005-0.0050.0000.0000.0000.000
27B27ASN0-0.078-0.04316.2830.0180.0180.0000.0000.0000.000
28B28MET00.0420.04210.546-0.060-0.0600.0000.0000.0000.000
29B29ALA0-0.004-0.01011.5660.0900.0900.0000.0000.0000.000
30B30VAL00.015-0.0016.241-0.195-0.1950.0000.0000.0000.000
31B31LEU00.0190.0029.1140.1860.1860.0000.0000.0000.000
32B32ASP-1-0.773-0.8738.8080.7140.7140.0000.0000.0000.000
33B33GLN00.001-0.0198.952-0.008-0.0080.0000.0000.0000.000
34B34SER0-0.072-0.04010.3710.0230.0230.0000.0000.0000.000
35B35ASP-1-0.904-0.95512.6020.2230.2230.0000.0000.0000.000
36B36HIS0-0.051-0.01813.636-0.058-0.0580.0000.0000.0000.000
37B37GLU-1-0.827-0.92213.7260.1240.1240.0000.0000.0000.000
38B38ALA00.0140.01112.8490.0140.0140.0000.0000.0000.000
39B39ILE0-0.008-0.00710.4540.0640.0640.0000.0000.0000.000
40B40ILE0-0.0230.00111.212-0.114-0.1140.0000.0000.0000.000
41B41ILE0-0.026-0.0307.2440.0810.0810.0000.0000.0000.000
42B42ASP-1-0.813-0.90810.570-0.462-0.4620.0000.0000.0000.000
43B43GLN0-0.030-0.03812.6090.0360.0360.0000.0000.0000.000
44B44VAL00.0170.02916.3550.0140.0140.0000.0000.0000.000
45B45GLN00.007-0.00319.2710.0060.0060.0000.0000.0000.000
46B46CYS0-0.0230.02922.5290.0020.0020.0000.0000.0000.000
47B47THR00.048-0.01025.8630.0110.0110.0000.0000.0000.000
48B48HIS0-0.0390.00428.9450.0140.0140.0000.0000.0000.000
49B49LEU00.0170.00430.2630.0020.0020.0000.0000.0000.000
50B50MET0-0.0050.01631.7840.0070.0070.0000.0000.0000.000
51B51ARG10.8700.91425.4540.0550.0550.0000.0000.0000.000
52B52MET00.0910.06320.6550.0200.0200.0000.0000.0000.000
53B53SER0-0.033-0.02522.329-0.013-0.0130.0000.0000.0000.000
54B54ALA00.0220.03219.2800.0220.0220.0000.0000.0000.000
55B55PRO00.0110.00718.461-0.017-0.0170.0000.0000.0000.000
56B56ILE00.021-0.00412.254-0.007-0.0070.0000.0000.0000.000
57B57GLY0-0.0020.00712.7550.0660.0660.0000.0000.0000.000
58B58GLY0-0.043-0.01213.7720.0350.0350.0000.0000.0000.000
59B59LYS10.8270.90614.361-0.291-0.2910.0000.0000.0000.000
60B60LEU0-0.0010.00116.367-0.021-0.0210.0000.0000.0000.000
61B61PRO00.0280.02817.5970.0090.0090.0000.0000.0000.000
62B62MET0-0.0130.01015.831-0.024-0.0240.0000.0000.0000.000
63B63HIS0-0.046-0.03919.474-0.024-0.0240.0000.0000.0000.000
64B64ALA00.0260.01322.573-0.003-0.0030.0000.0000.0000.000
65B65SER00.0140.02419.311-0.015-0.0150.0000.0000.0000.000
66B66GLY00.0630.02621.069-0.008-0.0080.0000.0000.0000.000
67B67ALA00.0420.02015.283-0.018-0.0180.0000.0000.0000.000
68B68GLY0-0.020-0.00516.966-0.019-0.0190.0000.0000.0000.000
69B69LYS10.8290.87718.0930.0890.0890.0000.0000.0000.000
70B70ALA0-0.033-0.00617.505-0.005-0.0050.0000.0000.0000.000
71B71PHE00.0530.00911.4230.0000.0000.0000.0000.0000.000
72B72LEU00.008-0.00416.4430.0040.0040.0000.0000.0000.000
73B73ALA0-0.0310.00719.4330.0110.0110.0000.0000.0000.000
74B74GLN0-0.055-0.03616.7180.0000.0000.0000.0000.0000.000
75B75LEU0-0.0540.00316.3930.0050.0050.0000.0000.0000.000
76B76SER00.011-0.02320.0670.0120.0120.0000.0000.0000.000
77B77GLU-1-0.865-0.96123.386-0.058-0.0580.0000.0000.0000.000
78B78GLU-1-0.848-0.90825.343-0.004-0.0040.0000.0000.0000.000
79B79GLN00.0340.02018.6960.0070.0070.0000.0000.0000.000
80B80VAL00.0450.03921.6370.0160.0160.0000.0000.0000.000
81B81THR0-0.009-0.01723.0600.0100.0100.0000.0000.0000.000
82B82LYS10.8540.92022.6050.0090.0090.0000.0000.0000.000
83B83LEU00.0330.02717.4770.0210.0210.0000.0000.0000.000
84B84LEU00.0320.01221.6230.0090.0090.0000.0000.0000.000
85B85HIS0-0.038-0.01324.4290.0060.0060.0000.0000.0000.000
86B86ARG10.8440.91819.629-0.103-0.1030.0000.0000.0000.000
87B87LYS10.8160.89717.979-0.155-0.1550.0000.0000.0000.000
88B88GLY0-0.0260.01222.613-0.005-0.0050.0000.0000.0000.000
89B89LEU0-0.002-0.00525.155-0.007-0.0070.0000.0000.0000.000
90B90HIS0-0.0130.00226.9280.0000.0000.0000.0000.0000.000
91B91ALA00.0430.01928.366-0.008-0.0080.0000.0000.0000.000
92B92TYR0-0.041-0.02123.9980.0040.0040.0000.0000.0000.000
93B93THR0-0.012-0.03029.5940.0020.0020.0000.0000.0000.000
94B94HIS0-0.011-0.01532.4620.0010.0010.0000.0000.0000.000
95B95ALA00.0540.03632.310-0.001-0.0010.0000.0000.0000.000
96B96THR0-0.072-0.03727.879-0.003-0.0030.0000.0000.0000.000
97B97LEU00.0080.01427.9640.0050.0050.0000.0000.0000.000
98B98VAL00.0420.00829.1220.0040.0040.0000.0000.0000.000
99B99SER0-0.019-0.00131.3540.0060.0060.0000.0000.0000.000
100B100PRO00.029-0.00429.189-0.007-0.0070.0000.0000.0000.000
101B101VAL0-0.0100.01330.007-0.008-0.0080.0000.0000.0000.000
102B102HIS00.0760.02631.966-0.004-0.0040.0000.0000.0000.000
103B103LEU00.0290.02524.752-0.008-0.0080.0000.0000.0000.000
104B104LYS10.8610.91126.9280.0330.0330.0000.0000.0000.000
105B105GLU-1-0.900-0.93128.546-0.083-0.0830.0000.0000.0000.000
106B106ASP-1-0.752-0.86926.872-0.116-0.1160.0000.0000.0000.000
107B107LEU0-0.044-0.02122.632-0.014-0.0140.0000.0000.0000.000
108B108ALA0-0.031-0.01225.517-0.016-0.0160.0000.0000.0000.000
109B109GLN0-0.037-0.03728.132-0.019-0.0190.0000.0000.0000.000
110B110THR0-0.034-0.01822.563-0.010-0.0100.0000.0000.0000.000
111B111ARG10.8780.93823.2670.1290.1290.0000.0000.0000.000
112B112LYS10.8610.93725.2110.1100.1100.0000.0000.0000.000
113B113ARG10.8050.89226.1970.1320.1320.0000.0000.0000.000
114B114GLY00.0280.02224.261-0.004-0.0040.0000.0000.0000.000
115B115TYR00.0080.00822.262-0.026-0.0260.0000.0000.0000.000
116B116SER0-0.059-0.04720.7560.0190.0190.0000.0000.0000.000
117B117PHE00.028-0.02523.340-0.009-0.0090.0000.0000.0000.000
118B118ASP-1-0.862-0.92324.185-0.068-0.0680.0000.0000.0000.000
119B119ASP-1-0.809-0.88626.077-0.075-0.0750.0000.0000.0000.000
120B120GLU-1-0.781-0.87929.138-0.032-0.0320.0000.0000.0000.000
121B121GLU-1-0.808-0.86127.056-0.063-0.0630.0000.0000.0000.000
122B122HIS0-0.012-0.00422.3440.0110.0110.0000.0000.0000.000
123B123ALA00.004-0.01626.5270.0130.0130.0000.0000.0000.000
124B124LEU00.0260.01529.033-0.008-0.0080.0000.0000.0000.000
125B125GLY0-0.047-0.02631.9200.0020.0020.0000.0000.0000.000
126B126LEU0-0.087-0.02124.698-0.006-0.0060.0000.0000.0000.000
127B127ARG10.7640.83827.7130.0800.0800.0000.0000.0000.000
128B128CYS0-0.044-0.02221.605-0.013-0.0130.0000.0000.0000.000
129B129LEU0-0.0120.01623.1990.0050.0050.0000.0000.0000.000
130B130ALA00.004-0.00718.280-0.017-0.0170.0000.0000.0000.000
131B131ALA00.0250.01818.2740.0250.0250.0000.0000.0000.000
132B132CYS0-0.065-0.01614.464-0.017-0.0170.0000.0000.0000.000
133B133ILE0-0.021-0.00411.4150.0290.0290.0000.0000.0000.000
134B134PHE0-0.030-0.03012.342-0.043-0.0430.0000.0000.0000.000
135B135ASP-1-0.733-0.85110.006-1.000-1.0000.0000.0000.0000.000
136B136GLU-1-0.830-0.90511.288-0.938-0.9380.0000.0000.0000.000
137B137HIS0-0.085-0.03511.5640.2120.2120.0000.0000.0000.000
138B138ARG10.8270.91315.0160.4280.4280.0000.0000.0000.000
139B139GLU-1-0.888-0.94112.602-0.264-0.2640.0000.0000.0000.000
140B140PRO0-0.066-0.02012.313-0.142-0.1420.0000.0000.0000.000
141B141PHE00.013-0.0046.732-0.074-0.0740.0000.0000.0000.000
142B142ALA0-0.015-0.0267.885-0.153-0.1530.0000.0000.0000.000
143B143ALA0-0.008-0.00110.2040.1180.1180.0000.0000.0000.000
144B144ILE00.0210.02013.680-0.003-0.0030.0000.0000.0000.000
145B145SER0-0.016-0.02916.0200.0520.0520.0000.0000.0000.000
146B146ILE00.0330.03119.156-0.008-0.0080.0000.0000.0000.000
147B147SER00.016-0.00121.4380.0130.0130.0000.0000.0000.000
148B148GLY00.0210.00724.1660.0000.0000.0000.0000.0000.000
149B149PRO0-0.001-0.00627.6020.0040.0040.0000.0000.0000.000
150B150ILE00.0960.03131.014-0.007-0.0070.0000.0000.0000.000
151B151SER0-0.069-0.02933.1920.0000.0000.0000.0000.0000.000
152B152ARG10.6760.79929.5860.0840.0840.0000.0000.0000.000
153B153ILE0-0.0190.01427.417-0.006-0.0060.0000.0000.0000.000
154B154THR0-0.010-0.04131.8040.0030.0030.0000.0000.0000.000
155B155ASP-1-0.803-0.89934.184-0.077-0.0770.0000.0000.0000.000
156B156ASP-1-0.927-0.93535.368-0.090-0.0900.0000.0000.0000.000
157B157ARG10.9530.97832.0980.1100.1100.0000.0000.0000.000
158B158VAL0-0.0090.02229.575-0.013-0.0130.0000.0000.0000.000
159B159THR00.012-0.01129.834-0.011-0.0110.0000.0000.0000.000
160B160GLU-1-0.913-0.93830.097-0.164-0.1640.0000.0000.0000.000
161B161PHE00.011-0.01727.299-0.012-0.0120.0000.0000.0000.000
162B162GLY00.002-0.00526.020-0.019-0.0190.0000.0000.0000.000
163B163ALA0-0.025-0.01525.369-0.025-0.0250.0000.0000.0000.000
164B164MET00.0050.01925.393-0.022-0.0220.0000.0000.0000.000
165B165VAL00.0060.00920.088-0.033-0.0330.0000.0000.0000.000
166B166ILE0-0.0360.00120.782-0.046-0.0460.0000.0000.0000.000
167B167LYS10.8210.90021.5010.2590.2590.0000.0000.0000.000
168B168ALA00.0490.02619.371-0.033-0.0330.0000.0000.0000.000
169B169ALA00.019-0.00116.929-0.067-0.0670.0000.0000.0000.000
170B170LYS10.9340.97616.9110.2540.2540.0000.0000.0000.000
171B171GLU-1-0.856-0.92918.538-0.403-0.4030.0000.0000.0000.000
172B172VAL00.0040.00412.688-0.056-0.0560.0000.0000.0000.000
173B173THR0-0.019-0.01413.966-0.125-0.1250.0000.0000.0000.000
174B174LEU0-0.050-0.03514.809-0.051-0.0510.0000.0000.0000.000
175B175ALA0-0.0020.01014.3510.0090.0090.0000.0000.0000.000
176B176TYR0-0.066-0.0527.653-0.136-0.1360.0000.0000.0000.000
177B177GLY0-0.002-0.00412.336-0.008-0.0080.0000.0000.0000.000
178B178GLY0-0.041-0.01115.0190.0610.0610.0000.0000.0000.000
179B179MET0-0.098-0.0337.9080.0440.0440.0000.0000.0000.000