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: 7Y34K

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 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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -742389.07948
FMO2-HF: Nuclear repulsion 702728.216325
FMO2-HF: Total energy -39660.863156
FMO2-MP2: Total energy -39774.191434


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.
-8.113-3.0880.392-2.525-2.8930.004
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 : 0.039
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].
4B11ALA0-0.0730.1144.8340.0720.282-0.001-0.100-0.1080.000
5B12LYS00.051-0.1243.067-3.645-1.3460.040-1.258-1.0810.006
6B12LYS10.8911.1033.502-0.922-0.7730.004-0.042-0.1110.000
7B13ALA00.120-0.1402.925-0.709-0.2920.030-0.092-0.3550.000
8B13ALA0-0.0360.1543.181-0.1660.0920.067-0.148-0.1780.000
9B14GLU00.131-0.1134.2590.3080.429-0.001-0.052-0.0680.000
10B14GLU-1-0.997-0.8104.284-2.588-2.520-0.001-0.016-0.0510.000
11B15LYS00.115-0.0616.1010.1440.1440.0000.0000.0000.000
12B15LYS10.8541.0528.419-0.226-0.2260.0000.0000.0000.000
13B16VAL00.017-0.1197.8710.0080.0080.0000.0000.0000.000
14B16VAL0-0.0680.0977.9440.0180.0180.0000.0000.0000.000
15B17GLU00.104-0.1248.2830.0890.0890.0000.0000.0000.000
16B17GLU-1-1.032-0.8486.738-0.733-0.7330.0000.0000.0000.000
17B18CYS00.033-0.1409.8760.0410.0410.0000.0000.0000.000
18B18CYS0-0.1380.0679.797-0.007-0.0070.0000.0000.0000.000
19B19ALA00.087-0.09312.1220.0000.0000.0000.0000.0000.000
20B19ALA0-0.0810.10413.2800.0130.0130.0000.0000.0000.000
21B20LEU00.003-0.13313.3480.0270.0270.0000.0000.0000.000
22B20LEU0-0.0780.11912.1090.0040.0040.0000.0000.0000.000
23B21LYS00.116-0.07614.1070.0240.0240.0000.0000.0000.000
24B21LYS10.8451.06912.0930.3470.3470.0000.0000.0000.000
25B22GLY0-0.089-0.14215.813-0.006-0.0060.0000.0000.0000.000
26B23GLY0-0.047-0.02018.5090.0110.0110.0000.0000.0000.000
27B24ILE00.112-0.00320.032-0.001-0.0010.0000.0000.0000.000
28B24ILE0-0.1080.09623.984-0.001-0.0010.0000.0000.0000.000
29B25PHE00.082-0.11121.418-0.001-0.0010.0000.0000.0000.000
30B25PHE0-0.1040.09217.5820.0020.0020.0000.0000.0000.000
31B26ARG00.154-0.09222.743-0.002-0.0020.0000.0000.0000.000
32B26ARG10.7290.97327.029-0.025-0.0250.0000.0000.0000.000
33B27GLY0-0.046-0.11725.6890.0070.0070.0000.0000.0000.000
34B28THR00.0410.01427.050-0.005-0.0050.0000.0000.0000.000
35B28THR0-0.0540.08131.003-0.001-0.0010.0000.0000.0000.000
36B29LEU00.089-0.08527.3790.0050.0050.0000.0000.0000.000
37B29LEU0-0.0900.10324.5710.0020.0020.0000.0000.0000.000
38B30PRO00.021-0.08727.733-0.006-0.0060.0000.0000.0000.000
39B31ALA00.085-0.02330.5120.0020.0020.0000.0000.0000.000
40B31ALA0-0.0750.13533.677-0.001-0.0010.0000.0000.0000.000
41B32ALA00.100-0.09532.561-0.002-0.0020.0000.0000.0000.000
42B32ALA0-0.0770.10434.943-0.001-0.0010.0000.0000.0000.000
43B33ASP00.000-0.12232.746-0.004-0.0040.0000.0000.0000.000
44B33ASP-1-0.953-0.83731.4990.0810.0810.0000.0000.0000.000
45B34CYS00.200-0.07833.9350.0010.0010.0000.0000.0000.000
46B34CYS0-0.1920.03837.322-0.001-0.0010.0000.0000.0000.000
47B35PRO0-0.096-0.12836.1740.0010.0010.0000.0000.0000.000
48B36GLY00.0080.00333.117-0.001-0.0010.0000.0000.0000.000
49B37ILE00.113-0.02431.464-0.005-0.0050.0000.0000.0000.000
50B37ILE0-0.0980.12630.4530.0000.0000.0000.0000.0000.000
51B38ASP00.137-0.08330.2110.0060.0060.0000.0000.0000.000
52B38ASP-1-0.903-0.76431.0360.0280.0280.0000.0000.0000.000
53B39THR0-0.027-0.09927.321-0.006-0.0060.0000.0000.0000.000
54B39THR0-0.0350.06325.5580.0010.0010.0000.0000.0000.000
55B40THR00.025-0.08625.9150.0050.0050.0000.0000.0000.000
56B40THR0-0.0570.06025.656-0.002-0.0020.0000.0000.0000.000
57B41VAL00.044-0.12521.778-0.003-0.0030.0000.0000.0000.000
58B41VAL0-0.0410.14019.9120.0010.0010.0000.0000.0000.000
59B42THR00.072-0.08621.6350.0050.0050.0000.0000.0000.000
60B42THR0-0.0700.06621.8920.0020.0020.0000.0000.0000.000
61B43PHE00.102-0.06617.1030.0000.0000.0000.0000.0000.000
62B43PHE0-0.0840.10515.9740.0060.0060.0000.0000.0000.000
63B44ASN00.159-0.07618.159-0.012-0.0120.0000.0000.0000.000
64B44ASN0-0.1140.06819.8530.0060.0060.0000.0000.0000.000
65B45ALA00.128-0.08916.210-0.005-0.0050.0000.0000.0000.000
66B45ALA0-0.0520.10716.914-0.001-0.0010.0000.0000.0000.000
67B46ASP0-0.028-0.15016.038-0.043-0.0430.0000.0000.0000.000
68B46ASP-1-0.842-0.75219.499-0.125-0.1250.0000.0000.0000.000
69B47GLY0-0.006-0.08815.077-0.015-0.0150.0000.0000.0000.000
70B48THR00.0430.02115.9790.0190.0190.0000.0000.0000.000
71B48THR0-0.1000.00920.0770.0080.0080.0000.0000.0000.000
72B49ALA00.082-0.12418.710-0.009-0.0090.0000.0000.0000.000
73B49ALA0-0.0570.12618.6140.0020.0020.0000.0000.0000.000
74B50GLN00.010-0.10920.5510.0000.0000.0000.0000.0000.000
75B50GLN0-0.0810.08824.426-0.004-0.0040.0000.0000.0000.000
76B51LYS00.102-0.10323.3720.0010.0010.0000.0000.0000.000
77B51LYS10.7851.05323.630-0.043-0.0430.0000.0000.0000.000
78B52VAL00.078-0.09525.410-0.004-0.0040.0000.0000.0000.000
79B52VAL0-0.0810.09727.814-0.001-0.0010.0000.0000.0000.000
80B53GLU00.064-0.11028.7930.0040.0040.0000.0000.0000.000
81B53GLU-1-0.887-0.80228.0780.0340.0340.0000.0000.0000.000
82B54LEU0-0.048-0.11830.813-0.003-0.0030.0000.0000.0000.000
83B54LEU00.0670.03533.3710.0000.0000.0000.0000.0000.000
84B64PRO00.026-0.01734.3460.0010.0010.0000.0000.0000.000
85B65LEU0-0.004-0.03832.829-0.005-0.0050.0000.0000.0000.000
86B65LEU0-0.0460.13532.2050.0000.0000.0000.0000.0000.000
87B66THR00.061-0.07729.8600.0040.0040.0000.0000.0000.000
88B66THR0-0.0410.07429.104-0.002-0.0020.0000.0000.0000.000
89B67TYR00.030-0.11926.716-0.002-0.0020.0000.0000.0000.000
90B67TYR0-0.1130.10625.9960.0000.0000.0000.0000.0000.000
91B68ARG00.099-0.13424.772-0.002-0.0020.0000.0000.0000.000
92B68ARG10.8301.08424.0270.0610.0610.0000.0000.0000.000
93B69GLY00.010-0.09921.8300.0060.0060.0000.0000.0000.000
94B70THR00.0160.04217.906-0.007-0.0070.0000.0000.0000.000
95B70THR0-0.0330.04716.9440.0060.0060.0000.0000.0000.000
96B71TRP00.063-0.09315.0200.0240.0240.0000.0000.0000.000
97B71TRP0-0.1060.07911.3110.0000.0000.0000.0000.0000.000
98B72MET00.055-0.08811.090-0.042-0.0420.0000.0000.0000.000
99B72MET0-0.1120.1069.461-0.001-0.0010.0000.0000.0000.000
100B73VAL00.138-0.1227.8120.0580.0580.0000.0000.0000.000
101B73VAL0-0.0830.1386.525-0.003-0.0030.0000.0000.0000.000
102B74ARG00.083-0.0796.848-0.097-0.0970.0000.0000.0000.000
103B74ARG10.7290.9967.442-0.311-0.3110.0000.0000.0000.000
104B75GLU00.114-0.1322.845-0.428-0.0340.104-0.189-0.3090.000
105B75GLU-1-1.000-0.8232.827-0.615-0.0920.136-0.294-0.3650.001
106B76ASP0-0.027-0.1463.4680.5451.1310.014-0.334-0.267-0.003
107B76ASP-1-0.810-0.7747.5870.5700.5700.0000.0000.0000.000
108B77GLY0-0.068-0.1335.8360.0870.0870.0000.0000.0000.000
109B78ILE00.084-0.0146.705-0.133-0.1330.0000.0000.0000.000
110B78ILE0-0.0940.0959.863-0.010-0.0100.0000.0000.0000.000
111B79VAL00.020-0.1219.548-0.013-0.0130.0000.0000.0000.000
112B79VAL0-0.0740.10611.359-0.008-0.0080.0000.0000.0000.000
113B80GLU00.107-0.11211.9690.0190.0190.0000.0000.0000.000
114B80GLU-1-0.954-0.83812.6990.1010.1010.0000.0000.0000.000
115B81LEU00.104-0.10714.185-0.034-0.0340.0000.0000.0000.000
116B81LEU0-0.1330.11717.2660.0000.0000.0000.0000.0000.000
117B82SER00.012-0.09017.5310.0170.0170.0000.0000.0000.000
118B82SER0-0.0590.06617.8140.0020.0020.0000.0000.0000.000
119B83LEU00.071-0.10120.089-0.015-0.0150.0000.0000.0000.000
120B83LEU0-0.0520.11721.469-0.001-0.0010.0000.0000.0000.000
121B84VAL00.071-0.09023.5570.0050.0050.0000.0000.0000.000
122B84VAL0-0.0970.07524.584-0.001-0.0010.0000.0000.0000.000
123B85SER0-0.056-0.14926.6730.0060.0060.0000.0000.0000.000
124B85SER00.0740.07629.784-0.002-0.0020.0000.0000.0000.000
125B95LYS00.1090.02519.366-0.008-0.0080.0000.0000.0000.000
126B95LYS10.8411.03816.871-0.024-0.0240.0000.0000.0000.000
127B96GLU0-0.014-0.16019.0310.0100.0100.0000.0000.0000.000
128B96GLU-1-0.875-0.79219.7950.0520.0520.0000.0000.0000.000
129B97LEU00.145-0.10415.532-0.017-0.0170.0000.0000.0000.000
130B97LEU0-0.1340.08714.3000.0080.0080.0000.0000.0000.000
131B98TYR00.062-0.10514.559-0.002-0.0020.0000.0000.0000.000
132B98TYR0-0.1280.07415.192-0.007-0.0070.0000.0000.0000.000
133B99GLU00.183-0.10512.8620.0200.0200.0000.0000.0000.000
134B99GLU-1-0.958-0.81212.6750.3860.3860.0000.0000.0000.000
135B100LEU00.103-0.11012.377-0.052-0.0520.0000.0000.0000.000
136B100LEU0-0.1290.11211.7410.0040.0040.0000.0000.0000.000
137B101ILE00.050-0.07413.5650.0680.0680.0000.0000.0000.000
138B101ILE0-0.1100.05717.543-0.004-0.0040.0000.0000.0000.000
139B102ASP00.030-0.10215.7740.0420.0420.0000.0000.0000.000
140B102ASP-1-0.874-0.80418.3210.1270.1270.0000.0000.0000.000
141B103SER00.031-0.08115.831-0.001-0.0010.0000.0000.0000.000
142B103SER0-0.0540.04916.6900.0080.0080.0000.0000.0000.000
143B104ASN00.096-0.06116.859-0.029-0.0290.0000.0000.0000.000
144B104ASN0-0.1290.04820.7640.0060.0060.0000.0000.0000.000
145B105SER00.068-0.04318.408-0.021-0.0210.0000.0000.0000.000
146B105SER0-0.0580.02119.402-0.004-0.0040.0000.0000.0000.000
147B106VAL00.033-0.09716.9280.0270.0270.0000.0000.0000.000
148B106VAL0-0.0340.13115.565-0.001-0.0010.0000.0000.0000.000
149B107ARG00.178-0.08217.125-0.023-0.0230.0000.0000.0000.000
150B107ARG10.7611.03317.033-0.239-0.2390.0000.0000.0000.000
151B108TYR00.078-0.09617.7220.0220.0220.0000.0000.0000.000
152B108TYR0-0.0670.11620.259-0.001-0.0010.0000.0000.0000.000
153B109MET00.000-0.14817.628-0.006-0.0060.0000.0000.0000.000
154B109MET0-0.0940.12814.5500.0110.0110.0000.0000.0000.000
155B110GLY00.017-0.09119.0390.0010.0010.0000.0000.0000.000
156B111ALA00.1090.01019.6650.0000.0000.0000.0000.0000.000
157B111ALA0-0.0200.13221.684-0.003-0.0030.0000.0000.0000.000
158B112PRO0-0.047-0.13117.2460.0200.0200.0000.0000.0000.000
159B113GLY00.0100.01018.505-0.014-0.0140.0000.0000.0000.000
160B114ALA00.051-0.01820.446-0.002-0.0020.0000.0000.0000.000
161B114ALA0-0.0910.12122.664-0.004-0.0040.0000.0000.0000.000
162B115GLY00.025-0.09419.685-0.005-0.0050.0000.0000.0000.000
163B116LYS00.025-0.02520.441-0.008-0.0080.0000.0000.0000.000
164B116LYS10.8881.09622.335-0.116-0.1160.0000.0000.0000.000
165B117PRO00.027-0.11520.9990.0050.0050.0000.0000.0000.000
166B118SER00.0920.04322.0020.0080.0080.0000.0000.0000.000
167B118SER0-0.0220.08626.091-0.002-0.0020.0000.0000.0000.000
168B119LYS00.159-0.06424.0200.0000.0000.0000.0000.0000.000
169B119LYS10.8521.06424.352-0.157-0.1570.0000.0000.0000.000
170B120GLU00.026-0.15225.0280.0030.0030.0000.0000.0000.000
171B120GLU-1-0.949-0.81929.2600.1080.1080.0000.0000.0000.000
172B121MET00.093-0.11127.103-0.008-0.0080.0000.0000.0000.000
173B121MET0-0.0900.12626.7410.0010.0010.0000.0000.0000.000
174B122ALA00.075-0.11523.167-0.010-0.0100.0000.0000.0000.000
175B122ALA0-0.0860.10022.2080.0040.0040.0000.0000.0000.000
176B123PRO0-0.049-0.13123.7430.0000.0000.0000.0000.0000.000
177B124PHE00.069-0.01225.456-0.004-0.0040.0000.0000.0000.000
178B124PHE0-0.0630.12628.013-0.001-0.0010.0000.0000.0000.000
179B125TYR00.117-0.07223.466-0.012-0.0120.0000.0000.0000.000
180B125TYR0-0.1210.07322.6620.0030.0030.0000.0000.0000.000
181B126VAL00.118-0.09121.7550.0070.0070.0000.0000.0000.000
182B126VAL0-0.1170.07721.3600.0020.0020.0000.0000.0000.000
183B127LEU00.028-0.12421.444-0.009-0.0090.0000.0000.0000.000
184B127LEU0-0.0870.11720.779-0.002-0.0020.0000.0000.0000.000
185B128LYS00.150-0.10221.3290.0080.0080.0000.0000.0000.000
186B128LYS10.8571.08023.575-0.088-0.0880.0000.0000.0000.000
187B129LYS00.115-0.06821.660-0.007-0.0070.0000.0000.0000.000
188B129LYS10.8411.06918.9370.0360.0360.0000.0000.0000.000
189B130THR0-0.164-0.18622.7700.0000.0000.0000.0000.0000.000
190B130THR00.0720.06825.8020.0010.0010.0000.0000.0000.000