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: 1752Z

Calculation Name: 4X2H-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X2H

Chain ID: B

ChEMBL ID:

UniProt ID: G0SET4

Base Structure: X-ray

Registration Date: 2023-06-22

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1856773.993928
FMO2-HF: Nuclear repulsion 1786523.69595
FMO2-HF: Total energy -70250.297978
FMO2-MP2: Total energy -70455.46709


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:2:LEU)


Summations of interaction energy for fragment #1(B:2: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.
-16.736-11.9541.698-1.358-5.1220.007
Interaction energy analysis for fragmet #1(B:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.019
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].
3B4ARG11.0301.0043.063-9.324-7.0570.158-0.401-2.0240.007
4B5ARG10.9320.9712.887-4.297-3.1080.163-0.387-0.9640.001
5B6TYR00.0240.0192.294-2.199-0.8731.377-0.570-2.134-0.001
6B7ALA0-0.0010.0086.471-0.200-0.2000.0000.0000.0000.000
7B8ALA00.0270.0098.094-0.225-0.2250.0000.0000.0000.000
8B9LYS10.9920.9978.731-0.383-0.3830.0000.0000.0000.000
9B10SER0-0.014-0.00210.483-0.120-0.1200.0000.0000.0000.000
10B11PHE0-0.029-0.02112.289-0.078-0.0780.0000.0000.0000.000
11B12VAL00.0470.02513.421-0.073-0.0730.0000.0000.0000.000
12B13GLU-1-0.967-0.97314.6000.1100.1100.0000.0000.0000.000
13B14TRP0-0.075-0.03516.442-0.035-0.0350.0000.0000.0000.000
14B15TYR00.0770.02218.035-0.037-0.0370.0000.0000.0000.000
15B16TYR00.016-0.05017.795-0.011-0.0110.0000.0000.0000.000
16B17ARG10.9430.98817.904-0.176-0.1760.0000.0000.0000.000
17B18GLN0-0.039-0.02021.764-0.041-0.0410.0000.0000.0000.000
18B19ILE00.0290.03223.634-0.019-0.0190.0000.0000.0000.000
19B20ASN0-0.014-0.00623.836-0.020-0.0200.0000.0000.0000.000
20B21GLU-1-0.907-0.93925.8640.0890.0890.0000.0000.0000.000
21B22ASN0-0.082-0.04328.465-0.004-0.0040.0000.0000.0000.000
22B23LYS10.8460.91526.639-0.107-0.1070.0000.0000.0000.000
23B24PRO0-0.0160.00227.8140.0110.0110.0000.0000.0000.000
24B25VAL00.010-0.01123.4350.0030.0030.0000.0000.0000.000
25B26ALA00.0510.02623.9840.0240.0240.0000.0000.0000.000
26B27SER0-0.060-0.02923.5090.0150.0150.0000.0000.0000.000
27B28GLY0-0.034-0.02320.4660.0030.0030.0000.0000.0000.000
28B29TYR0-0.020-0.01520.3460.0510.0510.0000.0000.0000.000
29B30VAL0-0.014-0.01621.075-0.020-0.0200.0000.0000.0000.000
30B31ASN00.0400.02323.246-0.002-0.0020.0000.0000.0000.000
31B32ASN0-0.0210.00026.020-0.018-0.0180.0000.0000.0000.000
32B33ASN0-0.0050.00121.455-0.007-0.0070.0000.0000.0000.000
33B34ALA00.0270.02424.699-0.002-0.0020.0000.0000.0000.000
34B35THR0-0.026-0.05522.473-0.008-0.0080.0000.0000.0000.000
35B36TYR0-0.043-0.07218.1880.0040.0040.0000.0000.0000.000
36B37THR00.0080.00824.8590.0010.0010.0000.0000.0000.000
37B38LYS10.9110.96128.140-0.087-0.0870.0000.0000.0000.000
38B39ALA0-0.053-0.03226.163-0.007-0.0070.0000.0000.0000.000
39B40GLY00.0190.02428.1540.0020.0020.0000.0000.0000.000
40B41HIS0-0.105-0.07722.7820.0340.0340.0000.0000.0000.000
41B42PRO00.0080.02125.896-0.013-0.0130.0000.0000.0000.000
42B43PRO00.0210.00926.9170.0150.0150.0000.0000.0000.000
43B44ALA00.002-0.00724.4970.0140.0140.0000.0000.0000.000
44B45ASP-1-0.969-0.96524.9750.2690.2690.0000.0000.0000.000
45B46ILE00.0370.01525.1680.0350.0350.0000.0000.0000.000
46B47THR0-0.048-0.01826.743-0.022-0.0220.0000.0000.0000.000
47B48ILE00.0400.01627.2040.0210.0210.0000.0000.0000.000
48B49ASN00.016-0.00628.952-0.004-0.0040.0000.0000.0000.000
49B50GLY0-0.056-0.03930.309-0.013-0.0130.0000.0000.0000.000
50B51ARG10.9070.95732.086-0.167-0.1670.0000.0000.0000.000
51B52VAL00.0160.00731.1770.0120.0120.0000.0000.0000.000
52B53VAL0-0.039-0.02030.528-0.016-0.0160.0000.0000.0000.000
53B54ALA00.0290.02131.0030.0110.0110.0000.0000.0000.000
54B55THR00.010-0.00130.7530.0030.0030.0000.0000.0000.000
55B56PRO00.0270.00326.8870.0020.0020.0000.0000.0000.000
56B57GLU-1-0.802-0.90028.8150.1620.1620.0000.0000.0000.000
57B58GLU-1-0.851-0.91331.7920.1460.1460.0000.0000.0000.000
58B59TRP00.030-0.00825.168-0.009-0.0090.0000.0000.0000.000
59B60ASP-1-0.738-0.88928.5650.1810.1810.0000.0000.0000.000
60B61THR0-0.121-0.05530.737-0.012-0.0120.0000.0000.0000.000
61B62MET00.0160.01732.242-0.003-0.0030.0000.0000.0000.000
62B63LEU0-0.0150.00427.098-0.004-0.0040.0000.0000.0000.000
63B64LYS10.8770.93231.654-0.125-0.1250.0000.0000.0000.000
64B65GLU-1-0.899-0.95434.5010.1180.1180.0000.0000.0000.000
65B66GLN0-0.0180.00631.0040.0000.0000.0000.0000.0000.000
66B67ARG10.8840.94530.145-0.139-0.1390.0000.0000.0000.000
67B68ALA0-0.0200.00235.347-0.010-0.0100.0000.0000.0000.000
68B76SER00.0270.00441.8140.0020.0020.0000.0000.0000.000
69B77THR0-0.030-0.02043.434-0.003-0.0030.0000.0000.0000.000
70B78LEU0-0.0170.00338.3350.0010.0010.0000.0000.0000.000
71B79PRO00.0290.03141.867-0.003-0.0030.0000.0000.0000.000
72B80ILE00.0420.00242.0660.0030.0030.0000.0000.0000.000
73B81GLY00.0070.00139.5410.0000.0000.0000.0000.0000.000
74B82ARG10.8490.92537.237-0.077-0.0770.0000.0000.0000.000
75B83LYS10.8570.92429.410-0.125-0.1250.0000.0000.0000.000
76B84PRO00.0080.00134.7250.0050.0050.0000.0000.0000.000
77B85VAL00.0340.01929.6050.0030.0030.0000.0000.0000.000
78B86ARG10.7190.84226.917-0.147-0.1470.0000.0000.0000.000
79B87TYR0-0.0250.00323.6400.0090.0090.0000.0000.0000.000
80B88ASP-1-0.773-0.85922.9110.1730.1730.0000.0000.0000.000
81B89VAL0-0.043-0.03316.5390.0180.0180.0000.0000.0000.000
82B90ASP-1-0.851-0.92519.2610.2550.2550.0000.0000.0000.000
83B91CYS0-0.088-0.04815.3680.0180.0180.0000.0000.0000.000
84B92PHE00.007-0.0079.2090.0080.0080.0000.0000.0000.000
85B93ASP-1-0.926-0.95010.5221.5521.5520.0000.0000.0000.000
86B94VAL00.0160.0057.1940.0460.0460.0000.0000.0000.000
87B95HIS10.8630.9288.547-0.972-0.9720.0000.0000.0000.000
88B96VAL00.0080.0016.809-0.020-0.0200.0000.0000.0000.000
89B97ILE00.002-0.0039.713-0.117-0.1170.0000.0000.0000.000
90B98ASN00.0460.01412.583-0.152-0.1520.0000.0000.0000.000
91B99ALA0-0.0010.0019.7240.0870.0870.0000.0000.0000.000
92B100ASP-1-0.776-0.87011.1520.1550.1550.0000.0000.0000.000
93B101TYR0-0.0110.00313.886-0.061-0.0610.0000.0000.0000.000
94B102ARG10.9680.96115.858-0.217-0.2170.0000.0000.0000.000
95B103PHE00.0160.02419.026-0.034-0.0340.0000.0000.0000.000
96B104ALA00.0340.00820.8440.0160.0160.0000.0000.0000.000
97B105ALA0-0.0170.00218.731-0.012-0.0120.0000.0000.0000.000
98B106PRO0-0.011-0.00718.937-0.023-0.0230.0000.0000.0000.000
99B107GLN00.0950.04219.9020.0050.0050.0000.0000.0000.000
100B108ARG11.0090.99718.7780.0130.0130.0000.0000.0000.000
101B109MET0-0.051-0.01613.254-0.039-0.0390.0000.0000.0000.000
102B110ILE0-0.041-0.02815.3110.0090.0090.0000.0000.0000.000
103B111GLU-1-0.981-0.97916.852-0.098-0.0980.0000.0000.0000.000
104B112GLN0-0.006-0.00814.616-0.011-0.0110.0000.0000.0000.000
105B113HIS10.7600.87610.4010.1980.1980.0000.0000.0000.000
106B114ALA00.1140.06211.8820.1200.1200.0000.0000.0000.000
107B115PRO00.008-0.01410.9850.0010.0010.0000.0000.0000.000
108B116THR0-0.007-0.0058.2600.3340.3340.0000.0000.0000.000
109B117ASP-1-0.840-0.9196.668-0.936-0.9360.0000.0000.0000.000
110B118GLY0-0.055-0.0215.146-0.149-0.1490.0000.0000.0000.000
111B119VAL00.0430.0556.2070.1520.1520.0000.0000.0000.000
112B120ARG10.7820.8849.068-0.099-0.0990.0000.0000.0000.000
113B121MET0-0.061-0.0236.7510.5940.5940.0000.0000.0000.000
114B122MET00.0290.03110.702-0.105-0.1050.0000.0000.0000.000
115B123MET0-0.080-0.0459.1520.4160.4160.0000.0000.0000.000
116B124ALA00.0460.03312.010-0.220-0.2200.0000.0000.0000.000
117B125LEU0-0.047-0.02511.6230.2340.2340.0000.0000.0000.000
118B126THR00.0100.01213.865-0.164-0.1640.0000.0000.0000.000
119B127VAL00.026-0.00914.8130.0910.0910.0000.0000.0000.000
120B128SER0-0.0010.00717.139-0.044-0.0440.0000.0000.0000.000
121B129GLY00.0730.04119.4620.0140.0140.0000.0000.0000.000
122B130SER0-0.032-0.00122.165-0.017-0.0170.0000.0000.0000.000
123B131VAL0-0.035-0.01225.5780.0050.0050.0000.0000.0000.000
124B132TYR0-0.012-0.01726.846-0.012-0.0120.0000.0000.0000.000
125B133PHE00.011-0.00730.909-0.002-0.0020.0000.0000.0000.000
126B134GLY00.0610.01434.200-0.005-0.0050.0000.0000.0000.000
127B135ALA00.0070.03032.791-0.006-0.0060.0000.0000.0000.000
128B136SER0-0.035-0.07734.768-0.003-0.0030.0000.0000.0000.000
129B137PRO0-0.066-0.04432.0370.0070.0070.0000.0000.0000.000
130B138ARG10.9190.95129.503-0.053-0.0530.0000.0000.0000.000
131B139SER00.0270.04430.5100.0020.0020.0000.0000.0000.000
132B140THR0-0.003-0.01527.7460.0050.0050.0000.0000.0000.000
133B141ASP-1-0.882-0.94931.0000.0960.0960.0000.0000.0000.000
134B142ASP-1-0.743-0.80734.5210.0860.0860.0000.0000.0000.000
135B143TYR0-0.048-0.03133.3670.0000.0000.0000.0000.0000.000
136B144VAL0-0.0190.00635.912-0.004-0.0040.0000.0000.0000.000
137B145ILE0-0.005-0.01034.2920.0010.0010.0000.0000.0000.000
138B146LYS10.9610.99228.345-0.170-0.1700.0000.0000.0000.000
139B147GLN0-0.047-0.01829.9220.0030.0030.0000.0000.0000.000
140B148HIS00.0370.02723.4380.0100.0100.0000.0000.0000.000
141B149PHE0-0.022-0.02320.819-0.009-0.0090.0000.0000.0000.000
142B150ASN00.005-0.01420.6100.0510.0510.0000.0000.0000.000
143B151ASP-1-0.752-0.84119.8390.3460.3460.0000.0000.0000.000
144B152VAL0-0.043-0.02018.2830.0610.0610.0000.0000.0000.000
145B153PHE00.030-0.00616.476-0.053-0.0530.0000.0000.0000.000
146B154ILE00.0010.00616.2860.1160.1160.0000.0000.0000.000
147B155LEU0-0.040-0.01812.748-0.069-0.0690.0000.0000.0000.000
148B156VAL00.0350.02114.6190.1140.1140.0000.0000.0000.000
149B157PRO00.0100.00513.485-0.025-0.0250.0000.0000.0000.000
150B158ASN00.0360.03615.016-0.062-0.0620.0000.0000.0000.000
151B159TRP00.0530.00115.115-0.036-0.0360.0000.0000.0000.000
152B160ASP-1-0.827-0.86518.3730.0800.0800.0000.0000.0000.000
153B161VAL0-0.056-0.02215.425-0.030-0.0300.0000.0000.0000.000
154B162LEU0-0.035-0.02111.308-0.048-0.0480.0000.0000.0000.000
155B163GLU-1-0.834-0.89811.092-0.225-0.2250.0000.0000.0000.000
156B164LYS10.8760.94614.794-0.034-0.0340.0000.0000.0000.000
157B165PRO00.0310.01418.391-0.007-0.0070.0000.0000.0000.000
158B166GLY00.011-0.00319.4790.0160.0160.0000.0000.0000.000
159B167ALA0-0.031-0.00617.9880.0140.0140.0000.0000.0000.000
160B168ARG10.9430.97217.6430.0990.0990.0000.0000.0000.000
161B169SER0-0.0080.00317.6020.0100.0100.0000.0000.0000.000
162B170GLY00.0590.02618.887-0.006-0.0060.0000.0000.0000.000
163B171ARG10.9070.96513.384-0.392-0.3920.0000.0000.0000.000
164B172LYS11.0030.99410.032-0.009-0.0090.0000.0000.0000.000
165B173TYR0-0.027-0.0299.3870.0360.0360.0000.0000.0000.000
166B174LEU0-0.033-0.01114.444-0.026-0.0260.0000.0000.0000.000
167B175ILE00.0010.00017.7980.0740.0740.0000.0000.0000.000
168B176ALA00.0120.00819.329-0.052-0.0520.0000.0000.0000.000
169B177SER0-0.009-0.00620.331-0.033-0.0330.0000.0000.0000.000
170B178HIS0-0.027-0.02020.5190.0450.0450.0000.0000.0000.000
171B179LYS10.9240.97522.270-0.387-0.3870.0000.0000.0000.000
172B180TYR00.0570.02923.0220.0230.0230.0000.0000.0000.000
173B181ARG10.9050.95325.126-0.269-0.2690.0000.0000.0000.000
174B182ALA00.0500.03526.1160.0150.0150.0000.0000.0000.000
175B183TYR00.0000.01126.358-0.010-0.0100.0000.0000.0000.000