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: 85G8Y

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1858126.594482
FMO2-HF: Nuclear repulsion 1787875.456185
FMO2-HF: Total energy -70251.138297
FMO2-MP2: Total energy -70456.395383


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.
-11.583-7.8041.228-1.195-3.8110.006
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 : 0.045 / q_NPA : 0.013
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].
3B4ARG10.9770.9643.170-7.493-5.6010.090-0.460-1.5220.005
4B5ARG10.9460.9803.243-2.621-1.7930.036-0.258-0.6050.001
5B6TYR00.0350.0212.488-1.375-0.3161.102-0.477-1.6840.000
6B7ALA00.0090.0126.763-0.084-0.0840.0000.0000.0000.000
7B8ALA00.0370.0148.565-0.132-0.1320.0000.0000.0000.000
8B9LYS10.8950.9409.285-0.264-0.2640.0000.0000.0000.000
9B10SER0-0.032-0.01410.710-0.075-0.0750.0000.0000.0000.000
10B11PHE0-0.018-0.01112.476-0.049-0.0490.0000.0000.0000.000
11B12VAL00.0440.02213.830-0.056-0.0560.0000.0000.0000.000
12B13GLU-1-0.837-0.89415.1380.0710.0710.0000.0000.0000.000
13B14TRP0-0.040-0.00516.980-0.030-0.0300.0000.0000.0000.000
14B15TYR00.0790.02718.582-0.028-0.0280.0000.0000.0000.000
15B16TYR00.037-0.03317.996-0.007-0.0070.0000.0000.0000.000
16B17ARG10.8270.93218.310-0.125-0.1250.0000.0000.0000.000
17B18GLN0-0.027-0.02221.910-0.031-0.0310.0000.0000.0000.000
18B19ILE00.0380.02324.027-0.014-0.0140.0000.0000.0000.000
19B20ASN0-0.047-0.03224.065-0.020-0.0200.0000.0000.0000.000
20B21GLU-1-0.845-0.92725.0270.0740.0740.0000.0000.0000.000
21B22ASN0-0.048-0.01928.615-0.005-0.0050.0000.0000.0000.000
22B23LYS10.8290.92825.840-0.083-0.0830.0000.0000.0000.000
23B24PRO0-0.009-0.00127.9040.0070.0070.0000.0000.0000.000
24B25VAL0-0.002-0.02023.5970.0030.0030.0000.0000.0000.000
25B26ALA00.0330.01024.1570.0170.0170.0000.0000.0000.000
26B27SER0-0.031-0.01323.9590.0100.0100.0000.0000.0000.000
27B28GLY0-0.028-0.01920.6120.0000.0000.0000.0000.0000.000
28B29TYR0-0.007-0.01520.4300.0390.0390.0000.0000.0000.000
29B30VAL00.002-0.01221.177-0.020-0.0200.0000.0000.0000.000
30B31ASN00.0100.01223.338-0.001-0.0010.0000.0000.0000.000
31B32ASN0-0.031-0.00725.618-0.021-0.0210.0000.0000.0000.000
32B33ASN0-0.010-0.00221.151-0.011-0.0110.0000.0000.0000.000
33B34ALA00.0400.03524.7080.0010.0010.0000.0000.0000.000
34B35THR0-0.003-0.02422.490-0.004-0.0040.0000.0000.0000.000
35B36TYR0-0.030-0.04518.1430.0060.0060.0000.0000.0000.000
36B37THR00.0170.00724.8350.0020.0020.0000.0000.0000.000
37B38LYS10.9100.95928.210-0.063-0.0630.0000.0000.0000.000
38B39ALA0-0.049-0.02925.910-0.006-0.0060.0000.0000.0000.000
39B40GLY00.0140.01727.9260.0050.0050.0000.0000.0000.000
40B41HIS0-0.084-0.05722.6050.0270.0270.0000.0000.0000.000
41B42PRO00.0120.01925.857-0.010-0.0100.0000.0000.0000.000
42B43PRO00.016-0.00226.7640.0120.0120.0000.0000.0000.000
43B44ALA0-0.011-0.00924.2550.0110.0110.0000.0000.0000.000
44B45ASP-1-0.838-0.90624.7930.2490.2490.0000.0000.0000.000
45B46ILE00.0190.02625.2090.0270.0270.0000.0000.0000.000
46B47THR0-0.040-0.02926.799-0.012-0.0120.0000.0000.0000.000
47B48ILE00.0360.02227.2370.0170.0170.0000.0000.0000.000
48B49ASN00.012-0.00528.932-0.004-0.0040.0000.0000.0000.000
49B50GLY0-0.029-0.00630.715-0.009-0.0090.0000.0000.0000.000
50B51ARG10.8860.93732.474-0.130-0.1300.0000.0000.0000.000
51B52VAL00.0220.00631.3510.0110.0110.0000.0000.0000.000
52B53VAL0-0.051-0.02130.424-0.011-0.0110.0000.0000.0000.000
53B54ALA00.0100.01531.1740.0090.0090.0000.0000.0000.000
54B55THR0-0.034-0.05130.7980.0020.0020.0000.0000.0000.000
55B56PRO00.0280.00926.8200.0040.0040.0000.0000.0000.000
56B57GLU-1-0.770-0.86028.7770.1330.1330.0000.0000.0000.000
57B58GLU-1-0.777-0.84631.7210.1240.1240.0000.0000.0000.000
58B59TRP00.0390.00425.041-0.007-0.0070.0000.0000.0000.000
59B60ASP-1-0.718-0.87628.7760.1400.1400.0000.0000.0000.000
60B61THR0-0.128-0.06930.714-0.011-0.0110.0000.0000.0000.000
61B62MET00.0350.03432.172-0.002-0.0020.0000.0000.0000.000
62B63LEU0-0.0160.00027.070-0.004-0.0040.0000.0000.0000.000
63B64LYS10.8560.92331.664-0.104-0.1040.0000.0000.0000.000
64B65GLU-1-0.900-0.94534.6770.0990.0990.0000.0000.0000.000
65B66GLN0-0.0010.02230.568-0.001-0.0010.0000.0000.0000.000
66B67ARG10.8170.90930.596-0.113-0.1130.0000.0000.0000.000
67B68ALA0-0.045-0.02135.330-0.011-0.0110.0000.0000.0000.000
68B76SER00.0470.02342.0810.0010.0010.0000.0000.0000.000
69B77THR0-0.028-0.03143.627-0.003-0.0030.0000.0000.0000.000
70B78LEU0-0.0230.00438.9350.0020.0020.0000.0000.0000.000
71B79PRO00.0240.02642.409-0.003-0.0030.0000.0000.0000.000
72B80ILE00.034-0.00342.4330.0030.0030.0000.0000.0000.000
73B81GLY00.0040.00339.9230.0000.0000.0000.0000.0000.000
74B82ARG10.7880.90337.619-0.065-0.0650.0000.0000.0000.000
75B83LYS10.8290.90329.982-0.104-0.1040.0000.0000.0000.000
76B84PRO00.0110.00335.0750.0040.0040.0000.0000.0000.000
77B85VAL00.0390.02729.9670.0030.0030.0000.0000.0000.000
78B86ARG10.6820.81227.380-0.118-0.1180.0000.0000.0000.000
79B87TYR0-0.007-0.01524.1420.0090.0090.0000.0000.0000.000
80B88ASP-1-0.764-0.83723.0910.1410.1410.0000.0000.0000.000
81B89VAL0-0.039-0.03016.8320.0130.0130.0000.0000.0000.000
82B90ASP-1-0.795-0.87519.2100.2050.2050.0000.0000.0000.000
83B91CYS0-0.073-0.03515.8080.0170.0170.0000.0000.0000.000
84B92PHE00.021-0.0069.815-0.001-0.0010.0000.0000.0000.000
85B93ASP-1-0.851-0.9229.7011.5601.5600.0000.0000.0000.000
86B94VAL0-0.019-0.0057.199-0.057-0.0570.0000.0000.0000.000
87B95HIS10.8710.9378.498-0.685-0.6850.0000.0000.0000.000
88B96VAL00.011-0.0036.531-0.118-0.1180.0000.0000.0000.000
89B97ILE0-0.021-0.0139.570-0.075-0.0750.0000.0000.0000.000
90B98ASN00.0330.01512.556-0.118-0.1180.0000.0000.0000.000
91B99ALA00.0210.0159.3310.0720.0720.0000.0000.0000.000
92B100ASP-1-0.759-0.84410.8060.0650.0650.0000.0000.0000.000
93B101TYR0-0.002-0.00513.616-0.042-0.0420.0000.0000.0000.000
94B102ARG10.9000.91115.587-0.173-0.1730.0000.0000.0000.000
95B103PHE00.0420.03518.757-0.026-0.0260.0000.0000.0000.000
96B104ALA00.0270.00520.4320.0110.0110.0000.0000.0000.000
97B105ALA0-0.0090.01219.029-0.011-0.0110.0000.0000.0000.000
98B106PRO0-0.009-0.00619.575-0.015-0.0150.0000.0000.0000.000
99B107GLN00.0120.00320.1460.0070.0070.0000.0000.0000.000
100B108ARG11.0141.00018.5250.0280.0280.0000.0000.0000.000
101B109MET0-0.044-0.01414.450-0.032-0.0320.0000.0000.0000.000
102B110ILE0-0.026-0.02815.1860.0050.0050.0000.0000.0000.000
103B111GLU-1-0.917-0.94716.623-0.085-0.0850.0000.0000.0000.000
104B112GLN0-0.020-0.00914.707-0.007-0.0070.0000.0000.0000.000
105B113HIS10.7420.83910.6440.2610.2610.0000.0000.0000.000
106B114ALA00.1230.07712.1780.1090.1090.0000.0000.0000.000
107B115PRO0-0.009-0.02610.802-0.017-0.0170.0000.0000.0000.000
108B116THR0-0.001-0.0037.8390.2840.2840.0000.0000.0000.000
109B117ASP-1-0.830-0.8936.322-0.803-0.8030.0000.0000.0000.000
110B118GLY0-0.015-0.0074.922-0.186-0.1860.0000.0000.0000.000
111B119VAL00.0360.0285.9580.2130.2130.0000.0000.0000.000
112B120ARG10.7680.8769.069-0.019-0.0190.0000.0000.0000.000
113B121MET0-0.042-0.0166.1740.5810.5810.0000.0000.0000.000
114B122MET00.0380.03510.049-0.092-0.0920.0000.0000.0000.000
115B123MET0-0.073-0.0409.1050.3790.3790.0000.0000.0000.000
116B124ALA00.0680.05612.132-0.171-0.1710.0000.0000.0000.000
117B125LEU0-0.054-0.02711.9370.2360.2360.0000.0000.0000.000
118B126THR0-0.025-0.00513.893-0.118-0.1180.0000.0000.0000.000
119B127VAL00.010-0.01514.8800.0720.0720.0000.0000.0000.000
120B128SER00.0160.00317.262-0.044-0.0440.0000.0000.0000.000
121B129GLY0-0.010-0.00119.6440.0090.0090.0000.0000.0000.000
122B130SER0-0.017-0.01022.317-0.015-0.0150.0000.0000.0000.000
123B131VAL0-0.035-0.01025.8200.0000.0000.0000.0000.0000.000
124B132TYR00.003-0.00126.876-0.008-0.0080.0000.0000.0000.000
125B133PHE00.017-0.00431.285-0.001-0.0010.0000.0000.0000.000
126B134GLY00.0620.00834.538-0.004-0.0040.0000.0000.0000.000
127B135ALA00.0140.03133.251-0.005-0.0050.0000.0000.0000.000
128B136SER0-0.024-0.05835.369-0.003-0.0030.0000.0000.0000.000
129B137PRO0-0.046-0.03732.4200.0050.0050.0000.0000.0000.000
130B138ARG10.9150.95030.028-0.043-0.0430.0000.0000.0000.000
131B139SER00.0170.02531.0690.0010.0010.0000.0000.0000.000
132B140THR0-0.033-0.04128.2450.0090.0090.0000.0000.0000.000
133B141ASP-1-0.815-0.88131.2490.0840.0840.0000.0000.0000.000
134B142ASP-1-0.736-0.82734.7480.0680.0680.0000.0000.0000.000
135B143TYR0-0.017-0.01533.445-0.001-0.0010.0000.0000.0000.000
136B144VAL0-0.0130.01036.398-0.003-0.0030.0000.0000.0000.000
137B145ILE0-0.006-0.00934.6580.0010.0010.0000.0000.0000.000
138B146LYS10.9080.95827.426-0.148-0.1480.0000.0000.0000.000
139B147GLN0-0.063-0.02430.2650.0020.0020.0000.0000.0000.000
140B148HIS00.0350.02323.2270.0070.0070.0000.0000.0000.000
141B149PHE0-0.027-0.02321.341-0.010-0.0100.0000.0000.0000.000
142B150ASN00.0230.01320.2090.0360.0360.0000.0000.0000.000
143B151ASP-1-0.754-0.84420.0560.2740.2740.0000.0000.0000.000
144B152VAL0-0.030-0.02018.4370.0530.0530.0000.0000.0000.000
145B153PHE00.017-0.00816.660-0.050-0.0500.0000.0000.0000.000
146B154ILE00.0130.01216.4240.0940.0940.0000.0000.0000.000
147B155LEU0-0.033-0.01112.884-0.070-0.0700.0000.0000.0000.000
148B156VAL00.0280.01314.6570.0900.0900.0000.0000.0000.000
149B157PRO00.0280.00712.821-0.027-0.0270.0000.0000.0000.000
150B158ASN00.0080.01814.699-0.049-0.0490.0000.0000.0000.000
151B159TRP00.040-0.00614.991-0.036-0.0360.0000.0000.0000.000
152B160ASP-1-0.774-0.84918.2990.0340.0340.0000.0000.0000.000
153B161VAL0-0.096-0.05015.755-0.018-0.0180.0000.0000.0000.000
154B162LEU0-0.047-0.01511.189-0.034-0.0340.0000.0000.0000.000
155B163GLU-1-0.860-0.90911.610-0.251-0.2510.0000.0000.0000.000
156B164LYS10.8220.91515.094-0.023-0.0230.0000.0000.0000.000
157B165PRO00.0410.01518.512-0.006-0.0060.0000.0000.0000.000
158B166GLY00.0110.00019.8280.0150.0150.0000.0000.0000.000
159B167ALA0-0.0160.00318.2350.0090.0090.0000.0000.0000.000
160B168ARG10.9390.96717.5170.0760.0760.0000.0000.0000.000
161B169SER00.0210.00817.0580.0050.0050.0000.0000.0000.000
162B170GLY00.0440.02018.447-0.006-0.0060.0000.0000.0000.000
163B171ARG10.8800.93813.025-0.325-0.3250.0000.0000.0000.000
164B172LYS10.9520.98411.570-0.013-0.0130.0000.0000.0000.000
165B173TYR0-0.007-0.0219.1990.0280.0280.0000.0000.0000.000
166B174LEU0-0.0140.00414.246-0.018-0.0180.0000.0000.0000.000
167B175ILE00.0020.00217.7860.0540.0540.0000.0000.0000.000
168B176ALA00.0380.02119.390-0.043-0.0430.0000.0000.0000.000
169B177SER0-0.027-0.02020.475-0.019-0.0190.0000.0000.0000.000
170B178HIS0-0.053-0.03520.6010.0340.0340.0000.0000.0000.000
171B179LYS10.8260.91022.356-0.298-0.2980.0000.0000.0000.000
172B180TYR00.0310.01523.0540.0200.0200.0000.0000.0000.000
173B181ARG10.8920.93025.199-0.217-0.2170.0000.0000.0000.000
174B182ALA00.0370.02526.2440.0120.0120.0000.0000.0000.000
175B183TYR00.0320.02726.382-0.005-0.0050.0000.0000.0000.000