FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: MR6ZZ

Calculation Name: 4U3Q-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: B

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -743962.272391
FMO2-HF: Nuclear repulsion 704299.882644
FMO2-HF: Total energy -39662.389746
FMO2-MP2: Total energy -39775.748832


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:10:LYS)


Summations of interaction energy for fragment #1(B:10:LYS)
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.
-13.94-7.3771.66-3.767-4.456-0.009
Interaction energy analysis for fragmet #1(B:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.169 / q_NPA : 0.048
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].
4B11ALA0-0.0740.0984.8710.0940.278-0.001-0.084-0.0980.000
5B12LYS00.044-0.1143.068-3.368-1.3930.053-1.042-0.9860.005
6B12LYS10.8531.0862.917-1.363-1.0090.057-0.164-0.2470.001
7B13ALA00.109-0.1192.847-0.833-0.3770.067-0.042-0.4810.000
8B13ALA0-0.0620.1212.929-0.0870.1870.263-0.292-0.2450.000
9B14GLU00.097-0.1074.0410.1680.456-0.001-0.162-0.1250.000
10B14GLU-1-0.987-0.8434.155-4.803-4.6290.001-0.100-0.076-0.001
11B15LYS00.098-0.0586.0200.1300.1300.0000.0000.0000.000
12B15LYS10.8751.0597.966-0.354-0.3540.0000.0000.0000.000
13B16VAL00.047-0.0977.612-0.018-0.0180.0000.0000.0000.000
14B16VAL0-0.0900.0947.7280.0150.0150.0000.0000.0000.000
15B17GLU00.119-0.1318.1590.0710.0710.0000.0000.0000.000
16B17GLU-1-0.945-0.8107.827-0.566-0.5660.0000.0000.0000.000
17B18CYS00.085-0.1129.8740.0230.0230.0000.0000.0000.000
18B18CYS0-0.1530.0719.876-0.013-0.0130.0000.0000.0000.000
19B19ALA00.085-0.08911.952-0.007-0.0070.0000.0000.0000.000
20B19ALA0-0.0870.09912.7490.0170.0170.0000.0000.0000.000
21B20LEU00.017-0.11213.0300.0220.0220.0000.0000.0000.000
22B20LEU0-0.0650.10111.4780.0040.0040.0000.0000.0000.000
23B21LYS00.111-0.06513.9320.0220.0220.0000.0000.0000.000
24B21LYS10.7371.00911.5440.3640.3640.0000.0000.0000.000
25B22GLY0-0.069-0.14815.451-0.009-0.0090.0000.0000.0000.000
26B23GLY0-0.0100.00418.3590.0100.0100.0000.0000.0000.000
27B24ILE00.0960.00119.919-0.001-0.0010.0000.0000.0000.000
28B24ILE0-0.0930.09523.6590.0000.0000.0000.0000.0000.000
29B25PHE00.036-0.11821.3580.0000.0000.0000.0000.0000.000
30B25PHE0-0.0760.09117.1480.0030.0030.0000.0000.0000.000
31B26ARG00.134-0.06222.741-0.003-0.0030.0000.0000.0000.000
32B26ARG10.7300.95926.989-0.038-0.0380.0000.0000.0000.000
33B27GLY0-0.016-0.11325.5110.0090.0090.0000.0000.0000.000
34B28THR00.0230.03326.970-0.006-0.0060.0000.0000.0000.000
35B28THR0-0.0520.07130.7830.0000.0000.0000.0000.0000.000
36B29LEU00.112-0.09227.2380.0050.0050.0000.0000.0000.000
37B29LEU0-0.0750.10824.0260.0010.0010.0000.0000.0000.000
38B30PRO00.015-0.08727.308-0.007-0.0070.0000.0000.0000.000
39B31ALA00.102-0.01029.8960.0030.0030.0000.0000.0000.000
40B31ALA0-0.0840.12432.760-0.001-0.0010.0000.0000.0000.000
41B32ALA00.086-0.09632.559-0.002-0.0020.0000.0000.0000.000
42B32ALA0-0.0700.10835.295-0.001-0.0010.0000.0000.0000.000
43B33ASP0-0.036-0.12032.361-0.004-0.0040.0000.0000.0000.000
44B33ASP-1-0.912-0.83430.6120.0960.0960.0000.0000.0000.000
45B34CYS00.207-0.07833.2520.0020.0020.0000.0000.0000.000
46B34CYS0-0.1870.03836.754-0.001-0.0010.0000.0000.0000.000
47B35PRO0-0.057-0.11435.7180.0010.0010.0000.0000.0000.000
48B36GLY00.010-0.00532.631-0.002-0.0020.0000.0000.0000.000
49B37ILE00.1130.00131.271-0.004-0.0040.0000.0000.0000.000
50B37ILE0-0.1070.11330.2450.0000.0000.0000.0000.0000.000
51B38ASP00.152-0.05930.0260.0070.0070.0000.0000.0000.000
52B38ASP-1-0.884-0.76831.0700.0390.0390.0000.0000.0000.000
53B39THR0-0.025-0.11727.317-0.008-0.0080.0000.0000.0000.000
54B39THR0-0.0390.05925.3970.0010.0010.0000.0000.0000.000
55B40THR00.054-0.07225.7720.0090.0090.0000.0000.0000.000
56B40THR0-0.0550.06825.752-0.002-0.0020.0000.0000.0000.000
57B41VAL00.047-0.10521.653-0.006-0.0060.0000.0000.0000.000
58B41VAL0-0.0470.12219.7500.0010.0010.0000.0000.0000.000
59B42THR00.016-0.09621.1940.0070.0070.0000.0000.0000.000
60B42THR0-0.0240.06721.473-0.001-0.0010.0000.0000.0000.000
61B43PHE00.077-0.05216.697-0.004-0.0040.0000.0000.0000.000
62B43PHE0-0.0760.10015.7090.0080.0080.0000.0000.0000.000
63B44ASN00.161-0.07517.693-0.010-0.0100.0000.0000.0000.000
64B44ASN0-0.1180.07019.6340.0110.0110.0000.0000.0000.000
65B45ALA00.136-0.09016.378-0.008-0.0080.0000.0000.0000.000
66B45ALA0-0.0510.10717.5230.0010.0010.0000.0000.0000.000
67B46ASP0-0.009-0.12115.963-0.048-0.0480.0000.0000.0000.000
68B46ASP-1-0.824-0.77519.199-0.127-0.1270.0000.0000.0000.000
69B47GLY00.023-0.06614.953-0.025-0.0250.0000.0000.0000.000
70B48THR00.0090.01715.7730.0210.0210.0000.0000.0000.000
71B48THR0-0.0780.01320.0640.0100.0100.0000.0000.0000.000
72B49ALA00.095-0.11218.618-0.007-0.0070.0000.0000.0000.000
73B49ALA0-0.0460.10818.3370.0030.0030.0000.0000.0000.000
74B50GLN00.028-0.09520.316-0.005-0.0050.0000.0000.0000.000
75B50GLN0-0.0840.08123.677-0.004-0.0040.0000.0000.0000.000
76B51LYS00.113-0.07922.8130.0040.0040.0000.0000.0000.000
77B51LYS10.7290.97823.649-0.057-0.0570.0000.0000.0000.000
78B52VAL00.067-0.09925.138-0.006-0.0060.0000.0000.0000.000
79B52VAL0-0.0830.09227.6780.0000.0000.0000.0000.0000.000
80B53GLU00.067-0.11228.6690.0050.0050.0000.0000.0000.000
81B53GLU-1-0.862-0.76227.6870.0430.0430.0000.0000.0000.000
82B54LEU0-0.073-0.12330.839-0.003-0.0030.0000.0000.0000.000
83B54LEU00.0590.03133.5680.0000.0000.0000.0000.0000.000
84B64PRO00.024-0.02233.9330.0010.0010.0000.0000.0000.000
85B65LEU00.0600.01232.669-0.006-0.0060.0000.0000.0000.000
86B65LEU0-0.0440.12731.9850.0000.0000.0000.0000.0000.000
87B66THR00.023-0.09629.6720.0050.0050.0000.0000.0000.000
88B66THR0-0.0620.07029.331-0.001-0.0010.0000.0000.0000.000
89B67TYR00.038-0.12726.581-0.004-0.0040.0000.0000.0000.000
90B67TYR0-0.1230.07325.778-0.001-0.0010.0000.0000.0000.000
91B68ARG00.120-0.09224.7530.0000.0000.0000.0000.0000.000
92B68ARG10.7561.02522.3980.0650.0650.0000.0000.0000.000
93B69GLY00.021-0.10121.6310.0070.0070.0000.0000.0000.000
94B70THR0-0.0370.01718.121-0.009-0.0090.0000.0000.0000.000
95B70THR0-0.0130.05817.1540.0060.0060.0000.0000.0000.000
96B71TRP00.050-0.08414.9220.0250.0250.0000.0000.0000.000
97B71TRP0-0.0990.08211.1940.0060.0060.0000.0000.0000.000
98B72MET00.095-0.05910.794-0.048-0.0480.0000.0000.0000.000
99B72MET0-0.1140.0809.660-0.006-0.0060.0000.0000.0000.000
100B73VAL00.080-0.1297.6920.0420.0420.0000.0000.0000.000
101B73VAL0-0.0660.1346.7570.0020.0020.0000.0000.0000.000
102B74ARG00.077-0.1096.669-0.127-0.1270.0000.0000.0000.000
103B74ARG10.7260.9757.243-0.383-0.3830.0000.0000.0000.000
104B75GLU00.106-0.0912.7190.1320.3950.274-0.065-0.4720.001
105B75GLU-1-0.924-0.8212.493-2.519-1.5480.527-0.785-0.713-0.001
106B76ASP00.001-0.1192.745-1.3520.2720.420-1.031-1.013-0.014
107B76ASP-1-0.828-0.7797.0350.6750.6750.0000.0000.0000.000
108B77GLY0-0.054-0.1575.2620.0950.0950.0000.0000.0000.000
109B78ILE00.057-0.0066.204-0.122-0.1220.0000.0000.0000.000
110B78ILE0-0.0830.1019.594-0.008-0.0080.0000.0000.0000.000
111B79VAL00.038-0.1289.2540.0020.0020.0000.0000.0000.000
112B79VAL0-0.0620.11011.032-0.008-0.0080.0000.0000.0000.000
113B80GLU00.075-0.10011.6930.0230.0230.0000.0000.0000.000
114B80GLU-1-0.875-0.81112.1640.1500.1500.0000.0000.0000.000
115B81LEU00.128-0.08314.210-0.037-0.0370.0000.0000.0000.000
116B81LEU0-0.1130.11117.0980.0010.0010.0000.0000.0000.000
117B82SER0-0.022-0.10517.3280.0170.0170.0000.0000.0000.000
118B82SER0-0.0560.07817.2850.0000.0000.0000.0000.0000.000
119B83LEU00.094-0.10419.668-0.018-0.0180.0000.0000.0000.000
120B83LEU0-0.0420.11321.3520.0000.0000.0000.0000.0000.000
121B84VAL00.056-0.07323.1800.0030.0030.0000.0000.0000.000
122B84VAL0-0.0890.09824.052-0.001-0.0010.0000.0000.0000.000
123B85SER0-0.090-0.18926.1650.0090.0090.0000.0000.0000.000
124B85SER00.0820.07729.458-0.002-0.0020.0000.0000.0000.000
125B95LYS00.1020.02019.230-0.009-0.0090.0000.0000.0000.000
126B95LYS10.8221.02515.892-0.017-0.0170.0000.0000.0000.000
127B96GLU00.008-0.14219.6430.0110.0110.0000.0000.0000.000
128B96GLU-1-0.815-0.74419.9750.0680.0680.0000.0000.0000.000
129B97LEU00.087-0.11915.714-0.016-0.0160.0000.0000.0000.000
130B97LEU0-0.1170.10114.2220.0070.0070.0000.0000.0000.000
131B98TYR00.042-0.10014.594-0.004-0.0040.0000.0000.0000.000
132B98TYR0-0.1060.05415.280-0.006-0.0060.0000.0000.0000.000
133B99GLU00.221-0.08812.6800.0320.0320.0000.0000.0000.000
134B99GLU-1-0.953-0.78713.1000.3680.3680.0000.0000.0000.000
135B100LEU00.092-0.10612.103-0.054-0.0540.0000.0000.0000.000
136B100LEU0-0.0850.11811.6040.0070.0070.0000.0000.0000.000
137B101ILE00.030-0.08413.1200.0850.0850.0000.0000.0000.000
138B101ILE0-0.0830.07716.806-0.006-0.0060.0000.0000.0000.000
139B102ASP00.030-0.09015.8270.0380.0380.0000.0000.0000.000
140B102ASP-1-0.829-0.79318.2030.1620.1620.0000.0000.0000.000
141B103SER00.016-0.08615.698-0.001-0.0010.0000.0000.0000.000
142B103SER0-0.0240.05516.7750.0110.0110.0000.0000.0000.000
143B104ASN00.077-0.05616.710-0.032-0.0320.0000.0000.0000.000
144B104ASN0-0.1270.05320.4950.0030.0030.0000.0000.0000.000
145B105SER00.116-0.07117.665-0.024-0.0240.0000.0000.0000.000
146B105SER0-0.0310.04218.558-0.004-0.0040.0000.0000.0000.000
147B106VAL0-0.026-0.07216.4970.0350.0350.0000.0000.0000.000
148B106VAL0-0.0340.10915.124-0.001-0.0010.0000.0000.0000.000
149B107ARG00.164-0.08416.876-0.027-0.0270.0000.0000.0000.000
150B107ARG10.7080.99717.019-0.270-0.2700.0000.0000.0000.000
151B108TYR00.086-0.09917.4880.0260.0260.0000.0000.0000.000
152B108TYR0-0.0810.11320.122-0.002-0.0020.0000.0000.0000.000
153B109MET00.039-0.14317.278-0.008-0.0080.0000.0000.0000.000
154B109MET0-0.0970.12213.8520.0090.0090.0000.0000.0000.000
155B110GLY0-0.012-0.09218.6630.0000.0000.0000.0000.0000.000
156B111ALA00.1010.00419.7690.0000.0000.0000.0000.0000.000
157B111ALA0-0.0310.12721.696-0.004-0.0040.0000.0000.0000.000
158B112PRO0-0.054-0.14117.2710.0190.0190.0000.0000.0000.000
159B113GLY00.0090.00818.715-0.016-0.0160.0000.0000.0000.000
160B114ALA00.062-0.00820.7180.0020.0020.0000.0000.0000.000
161B114ALA0-0.0860.12422.963-0.004-0.0040.0000.0000.0000.000
162B115GLY00.040-0.08819.705-0.003-0.0030.0000.0000.0000.000
163B116LYS00.019-0.02120.408-0.011-0.0110.0000.0000.0000.000
164B116LYS10.8541.08021.741-0.127-0.1270.0000.0000.0000.000
165B117PRO00.033-0.11920.7230.0120.0120.0000.0000.0000.000
166B118SER00.0620.03921.7300.0110.0110.0000.0000.0000.000
167B118SER0-0.0110.08525.858-0.001-0.0010.0000.0000.0000.000
168B119LYS00.152-0.05923.449-0.002-0.0020.0000.0000.0000.000
169B119LYS10.8511.05524.033-0.187-0.1870.0000.0000.0000.000
170B120GLU00.046-0.12924.4540.0060.0060.0000.0000.0000.000
171B120GLU-1-0.973-0.83628.5100.1280.1280.0000.0000.0000.000
172B121MET00.107-0.10526.879-0.007-0.0070.0000.0000.0000.000
173B121MET0-0.0970.12226.7550.0010.0010.0000.0000.0000.000
174B122ALA00.079-0.11322.678-0.013-0.0130.0000.0000.0000.000
175B122ALA0-0.0950.09821.7520.0050.0050.0000.0000.0000.000
176B123PRO0-0.026-0.13223.2640.0020.0020.0000.0000.0000.000
177B124PHE00.0900.00825.041-0.002-0.0020.0000.0000.0000.000
178B124PHE0-0.0760.10427.848-0.001-0.0010.0000.0000.0000.000
179B125TYR00.085-0.05723.442-0.014-0.0140.0000.0000.0000.000
180B125TYR0-0.1250.06522.6860.0030.0030.0000.0000.0000.000
181B126VAL00.106-0.10521.4640.0090.0090.0000.0000.0000.000
182B126VAL0-0.0990.08521.0270.0030.0030.0000.0000.0000.000
183B127LEU00.044-0.11221.239-0.012-0.0120.0000.0000.0000.000
184B127LEU0-0.0800.10021.061-0.002-0.0020.0000.0000.0000.000
185B128LYS00.121-0.08020.9900.0160.0160.0000.0000.0000.000
186B128LYS10.7571.00421.907-0.139-0.1390.0000.0000.0000.000
187B129LYS00.118-0.11021.266-0.011-0.0110.0000.0000.0000.000
188B129LYS10.7371.02517.376-0.014-0.0140.0000.0000.0000.000
189B130THR0-0.162-0.17422.445-0.001-0.0010.0000.0000.0000.000
190B130THR00.0760.06025.9140.0010.0010.0000.0000.0000.000