FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: ZNJZN

Calculation Name: 5D6H-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5D6H

Chain ID: B

ChEMBL ID:

UniProt ID: Q6XBY4

Base Structure: X-ray

Registration Date: 2025-07-10

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -668760.567198
FMO2-HF: Nuclear repulsion 629303.525207
FMO2-HF: Total energy -39457.041991
FMO2-MP2: Total energy -39572.299083


3D Structure Molmil
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:7:HIS)


Summations of interaction energy for fragment #1(B:7:HIS)
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.
-4.348-2.502-0.014-1.068-0.7640.005
Interaction energy analysis for fragmet #1(B:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.124 / q_NPA : 0.040
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].
4B8HIS0-0.0850.0884.8040.3550.3550.0000.0000.0000.000
5B9HIS00.089-0.1133.804-2.950-1.104-0.014-1.068-0.7640.005
6B9HIS0-0.1160.0945.981-0.480-0.4800.0000.0000.0000.000
7B10SER0-0.011-0.1056.2470.6710.6710.0000.0000.0000.000
8B10SER0-0.0520.0807.9440.2460.2460.0000.0000.0000.000
9B11THR0-0.001-0.0918.859-0.026-0.0260.0000.0000.0000.000
10B11THR0-0.0390.07711.4360.0910.0910.0000.0000.0000.000
11B12GLY0-0.005-0.09712.0900.0890.0890.0000.0000.0000.000
12B13CYS00.049-0.05114.6450.0070.0070.0000.0000.0000.000
13B13CYS0-0.2510.20616.0070.0100.0100.0000.0000.0000.000
14B14THR00.051-0.08418.2130.0060.0060.0000.0000.0000.000
15B14THR0-0.0390.08719.0140.0130.0130.0000.0000.0000.000
16B15VAL00.011-0.14120.8740.0150.0150.0000.0000.0000.000
17B15VAL0-0.0610.13022.3010.0010.0010.0000.0000.0000.000
18B16GLY0-0.004-0.06224.2880.0090.0090.0000.0000.0000.000
19B17GLY00.0050.00426.8380.0130.0130.0000.0000.0000.000
20B18SER0-0.092-0.09127.3340.0130.0130.0000.0000.0000.000
21B18SER00.0860.07226.430-0.004-0.0040.0000.0000.0000.000
22B28GLY0-0.004-0.02036.6480.0030.0030.0000.0000.0000.000
23B29THR00.0170.05536.970-0.011-0.0110.0000.0000.0000.000
24B29THR0-0.0700.00538.7270.0030.0030.0000.0000.0000.000
25B30LEU00.135-0.10239.5120.0010.0010.0000.0000.0000.000
26B30LEU0-0.0920.13039.1500.0000.0000.0000.0000.0000.000
27B31ASN00.076-0.05242.1950.0020.0020.0000.0000.0000.000
28B31ASN0-0.0650.08744.071-0.004-0.0040.0000.0000.0000.000
29B32PHE0-0.015-0.10645.7400.0020.0020.0000.0000.0000.000
30B32PHE00.0600.04345.1310.0010.0010.0000.0000.0000.000
31B43LEU00.1510.02460.075-0.001-0.0010.0000.0000.0000.000
32B43LEU0-0.0640.09456.7260.0000.0000.0000.0000.0000.000
33B44THR00.020-0.01260.316-0.002-0.0020.0000.0000.0000.000
34B44THR0-0.026-0.00761.2640.0000.0000.0000.0000.0000.000
35B45ALA00.037-0.09360.3560.0020.0020.0000.0000.0000.000
36B45ALA0-0.0630.07259.522-0.001-0.0010.0000.0000.0000.000
37B46GLU0-0.020-0.13160.0030.0030.0030.0000.0000.0000.000
38B46GLU-1-0.990-0.82358.345-0.069-0.0690.0000.0000.0000.000
39B47VAL00.031-0.11058.633-0.003-0.0030.0000.0000.0000.000
40B47VAL0-0.1130.06659.7990.0000.0000.0000.0000.0000.000
41B48ALA00.191-0.05356.7940.0030.0030.0000.0000.0000.000
42B48ALA0-0.0670.10056.5610.0000.0000.0000.0000.0000.000
43B49SER0-0.035-0.10552.840-0.002-0.0020.0000.0000.0000.000
44B49SER0-0.0850.06951.086-0.001-0.0010.0000.0000.0000.000
45B50ALA00.109-0.09150.7100.0010.0010.0000.0000.0000.000
46B50ALA0-0.0550.10750.6040.0000.0000.0000.0000.0000.000
47B51ALA00.077-0.11546.624-0.002-0.0020.0000.0000.0000.000
48B51ALA0-0.0800.08945.6210.0000.0000.0000.0000.0000.000
49B52THR0-0.102-0.12443.8850.0030.0030.0000.0000.0000.000
50B52THR0-0.0360.07343.1460.0000.0000.0000.0000.0000.000
51B53GLY00.066-0.08039.766-0.001-0.0010.0000.0000.0000.000
52B54GLY00.0490.02137.1210.0040.0040.0000.0000.0000.000
53B55ASN00.0460.01433.2310.0030.0030.0000.0000.0000.000
54B55ASN0-0.1090.05732.399-0.001-0.0010.0000.0000.0000.000
55B56ILE00.087-0.11330.189-0.005-0.0050.0000.0000.0000.000
56B56ILE0-0.0480.13828.9680.0010.0010.0000.0000.0000.000
57B57SER00.021-0.06026.5500.0120.0120.0000.0000.0000.000
58B57SER0-0.0290.05025.556-0.003-0.0030.0000.0000.0000.000
59B58VAL00.083-0.15123.545-0.004-0.0040.0000.0000.0000.000
60B58VAL0-0.0580.14621.712-0.002-0.0020.0000.0000.0000.000
61B59THR00.014-0.09720.4460.0210.0210.0000.0000.0000.000
62B59THR0-0.0270.08718.8010.0210.0210.0000.0000.0000.000
63B60CYS00.150-0.05316.960-0.017-0.0170.0000.0000.0000.000
64B61ASP00.038-0.13313.2850.1240.1240.0000.0000.0000.000
65B61ASP-1-0.839-0.77311.911-1.504-1.5040.0000.0000.0000.000
66B62GLY00.065-0.07110.963-0.229-0.2290.0000.0000.0000.000
67B63THR0-0.0520.00910.3830.1520.1520.0000.0000.0000.000
68B63THR0-0.0520.0348.834-0.080-0.0800.0000.0000.0000.000
69B64ASP00.023-0.15111.5280.1620.1620.0000.0000.0000.000
70B64ASP-1-0.965-0.82412.890-0.631-0.6310.0000.0000.0000.000
71B65PRO0-0.019-0.11014.143-0.062-0.0620.0000.0000.0000.000
72B66VAL00.0400.00117.180-0.022-0.0220.0000.0000.0000.000
73B66VAL0-0.0650.09816.033-0.011-0.0110.0000.0000.0000.000
74B67ASP00.203-0.11718.6230.0230.0230.0000.0000.0000.000
75B67ASP-1-0.983-0.82122.256-0.331-0.3310.0000.0000.0000.000
76B68PHE0-0.018-0.10021.863-0.039-0.0390.0000.0000.0000.000
77B68PHE0-0.0940.07622.5580.0040.0040.0000.0000.0000.000
78B69THR0-0.014-0.06524.3540.0200.0200.0000.0000.0000.000
79B69THR0-0.0670.05327.4400.0100.0100.0000.0000.0000.000
80B70VAL00.144-0.11628.007-0.019-0.0190.0000.0000.0000.000
81B70VAL0-0.0680.12328.9430.0000.0000.0000.0000.0000.000
82B71ALA00.110-0.09830.7500.0120.0120.0000.0000.0000.000
83B71ALA0-0.0840.12333.5590.0000.0000.0000.0000.0000.000
84B72ILE00.061-0.11433.951-0.012-0.0120.0000.0000.0000.000
85B72ILE0-0.0770.09535.4560.0010.0010.0000.0000.0000.000
86B73ASP0-0.103-0.14236.7730.0110.0110.0000.0000.0000.000
87B73ASP-1-0.781-0.87738.187-0.163-0.1630.0000.0000.0000.000
88B93TYR00.1280.02047.730-0.002-0.0020.0000.0000.0000.000
89B93TYR0-0.1770.08149.3610.0010.0010.0000.0000.0000.000
90B94ASN00.123-0.04744.5380.0010.0010.0000.0000.0000.000
91B94ASN0-0.1310.05644.732-0.004-0.0040.0000.0000.0000.000
92B95VAL00.071-0.09840.8300.0040.0040.0000.0000.0000.000
93B95VAL0-0.0420.13338.868-0.001-0.0010.0000.0000.0000.000
94B96TYR00.087-0.10639.492-0.002-0.0020.0000.0000.0000.000
95B96TYR0-0.0980.07840.3670.0020.0020.0000.0000.0000.000
96B97ARG00.181-0.06435.476-0.003-0.0030.0000.0000.0000.000
97B97ARG10.7030.96629.5830.2090.2090.0000.0000.0000.000
98B98ASP00.070-0.11335.757-0.007-0.0070.0000.0000.0000.000
99B98ASP-1-0.922-0.80738.725-0.121-0.1210.0000.0000.0000.000
100B99ALA00.141-0.08838.1730.0020.0020.0000.0000.0000.000
101B99ALA0-0.0620.11838.5560.0000.0000.0000.0000.0000.000
102B100ALA00.001-0.12639.8670.0010.0010.0000.0000.0000.000
103B100ALA0-0.0520.11842.9870.0010.0010.0000.0000.0000.000
104B101ARG0-0.015-0.11441.8310.0040.0040.0000.0000.0000.000
105B101ARG10.8321.04442.6050.1020.1020.0000.0000.0000.000
106B102THR00.039-0.12641.9560.0030.0030.0000.0000.0000.000
107B102THR0-0.0520.07941.7740.0010.0010.0000.0000.0000.000
108B103ASN00.129-0.06938.9800.0040.0040.0000.0000.0000.000
109B103ASN0-0.1200.07336.0830.0010.0010.0000.0000.0000.000
110B104LEU00.125-0.10039.332-0.007-0.0070.0000.0000.0000.000
111B104LEU0-0.1040.10542.0150.0020.0020.0000.0000.0000.000
112B105TYR00.004-0.11637.976-0.002-0.0020.0000.0000.0000.000
113B105TYR0-0.0830.08733.798-0.006-0.0060.0000.0000.0000.000
114B106VAL00.096-0.06938.8150.0030.0030.0000.0000.0000.000
115B106VAL0-0.0960.06939.9830.0010.0010.0000.0000.0000.000
116B107VAL00.132-0.07739.246-0.010-0.0100.0000.0000.0000.000
117B107VAL0-0.0940.10041.6310.0010.0010.0000.0000.0000.000
118B108ASN0-0.019-0.09037.4730.0040.0040.0000.0000.0000.000
119B108ASN0-0.0800.06138.193-0.006-0.0060.0000.0000.0000.000
120B109GLN00.112-0.11436.911-0.005-0.0050.0000.0000.0000.000
121B109GLN0-0.0970.10037.5590.0000.0000.0000.0000.0000.000
122B110PRO0-0.004-0.10931.525-0.003-0.0030.0000.0000.0000.000
123B111GLN00.1200.01332.1920.0120.0120.0000.0000.0000.000
124B111GLN0-0.1030.15032.431-0.002-0.0020.0000.0000.0000.000
125B112GLN00.138-0.10529.060-0.017-0.0170.0000.0000.0000.000
126B112GLN0-0.0520.12326.556-0.018-0.0180.0000.0000.0000.000
127B113PHE00.013-0.10726.8290.0270.0270.0000.0000.0000.000
128B113PHE0-0.0550.08026.0530.0040.0040.0000.0000.0000.000
129B114THR00.064-0.04522.962-0.009-0.0090.0000.0000.0000.000
130B114THR0-0.0070.09521.510-0.004-0.0040.0000.0000.0000.000
131B115THR00.023-0.11020.4410.0360.0360.0000.0000.0000.000
132B115THR0-0.0180.06919.265-0.028-0.0280.0000.0000.0000.000
133B116VAL00.051-0.06518.367-0.011-0.0110.0000.0000.0000.000
134B116VAL0-0.0500.11219.2430.0060.0060.0000.0000.0000.000
135B117SER00.086-0.01716.0830.0050.0050.0000.0000.0000.000
136B117SER0-0.0210.05115.1670.0250.0250.0000.0000.0000.000
137B118GLY00.010-0.11517.2770.0110.0110.0000.0000.0000.000
138B119GLN00.1830.05219.8830.0450.0450.0000.0000.0000.000
139B119GLN0-0.1950.04022.9640.0090.0090.0000.0000.0000.000
140B120ALA00.124-0.06920.689-0.024-0.0240.0000.0000.0000.000
141B120ALA0-0.1050.08922.7240.0080.0080.0000.0000.0000.000
142B121THR0-0.054-0.10322.1590.0150.0150.0000.0000.0000.000
143B121THR00.0070.05623.105-0.003-0.0030.0000.0000.0000.000
144B122ALA00.074-0.08824.882-0.022-0.0220.0000.0000.0000.000
145B122ALA0-0.0860.11029.2230.0050.0050.0000.0000.0000.000
146B123VAL00.039-0.11828.3740.0030.0030.0000.0000.0000.000
147B123VAL0-0.0760.10827.747-0.002-0.0020.0000.0000.0000.000
148B124PRO0-0.028-0.11430.1980.0070.0070.0000.0000.0000.000
149B125ILE00.109-0.00533.5690.0000.0000.0000.0000.0000.000
150B125ILE0-0.0840.12333.6510.0010.0010.0000.0000.0000.000
151B126PHE00.085-0.12336.6440.0010.0010.0000.0000.0000.000
152B126PHE0-0.1430.10636.5030.0020.0020.0000.0000.0000.000
153B127GLY00.098-0.07840.1610.0010.0010.0000.0000.0000.000
154B128ALA00.1070.00143.2610.0020.0020.0000.0000.0000.000
155B128ALA0-0.1030.06545.7760.0010.0010.0000.0000.0000.000
156B129ILE00.071-0.06946.830-0.003-0.0030.0000.0000.0000.000
157B129ILE0-0.0880.15950.1430.0000.0000.0000.0000.0000.000
158B130ALA00.146-0.02950.3620.0010.0010.0000.0000.0000.000
159B130ALA0-0.0630.09952.1970.0000.0000.0000.0000.0000.000
160B131PRO0-0.030-0.17953.2740.0040.0040.0000.0000.0000.000
161B132ASN00.0960.02854.8180.0010.0010.0000.0000.0000.000
162B132ASN0-0.0210.05754.695-0.003-0.0030.0000.0000.0000.000
163B133THR00.035-0.09652.8390.0010.0010.0000.0000.0000.000
164B133THR00.0150.05353.0990.0000.0000.0000.0000.0000.000
165B134GLY0-0.097-0.17849.4160.0000.0000.0000.0000.0000.000
166B135THR0-0.1180.01847.273-0.003-0.0030.0000.0000.0000.000
167B135THR0-0.0230.08648.3060.0000.0000.0000.0000.0000.000
168B136PRO00.113-0.06948.6550.0000.0000.0000.0000.0000.000
169B137LYS00.087-0.00649.8720.0040.0040.0000.0000.0000.000
170B137LYS10.8811.07851.3540.0920.0920.0000.0000.0000.000
171B138ALA00.129-0.12051.869-0.004-0.0040.0000.0000.0000.000
172B138ALA0-0.1220.13853.4100.0000.0000.0000.0000.0000.000
173B139GLN00.010-0.11554.5980.0040.0040.0000.0000.0000.000
174B139GLN0-0.0730.09155.788-0.003-0.0030.0000.0000.0000.000
175B140GLY00.013-0.11054.095-0.003-0.0030.0000.0000.0000.000
176B141ASP00.0750.01753.0890.0040.0040.0000.0000.0000.000
177B141ASP-1-0.942-0.84751.313-0.099-0.0990.0000.0000.0000.000
178B142TYR00.123-0.10551.487-0.003-0.0030.0000.0000.0000.000
179B142TYR0-0.1300.07651.6170.0000.0000.0000.0000.0000.000
180B143LYS00.020-0.10847.589-0.001-0.0010.0000.0000.0000.000
181B143LYS10.8171.04846.6620.1080.1080.0000.0000.0000.000
182B144ASP00.052-0.13845.5970.0040.0040.0000.0000.0000.000
183B144ASP-1-0.916-0.79244.934-0.128-0.1280.0000.0000.0000.000
184B145THR0-0.066-0.11441.832-0.003-0.0030.0000.0000.0000.000
185B145THR0-0.0560.05140.277-0.001-0.0010.0000.0000.0000.000
186B146LEU00.094-0.09139.8340.0040.0040.0000.0000.0000.000
187B146LEU0-0.0750.09939.096-0.001-0.0010.0000.0000.0000.000
188B147LEU00.137-0.10036.546-0.007-0.0070.0000.0000.0000.000
189B147LEU0-0.0850.12334.864-0.001-0.0010.0000.0000.0000.000
190B148VAL00.000-0.12333.5680.0070.0070.0000.0000.0000.000
191B148VAL0-0.0650.10131.749-0.001-0.0010.0000.0000.0000.000
192B149THR00.024-0.11630.817-0.013-0.0130.0000.0000.0000.000
193B149THR0-0.0280.09129.8940.0010.0010.0000.0000.0000.000
194B150VAL00.069-0.11027.0780.0150.0150.0000.0000.0000.000
195B150VAL0-0.0910.12725.286-0.002-0.0020.0000.0000.0000.000
196B151ASN00.068-0.11425.999-0.019-0.0190.0000.0000.0000.000
197B151ASN0-0.1410.06826.767-0.003-0.0030.0000.0000.0000.000
198B152PHE00.025-0.08421.4800.0100.0100.0000.0000.0000.000
199B152PHE00.0640.03620.602-0.013-0.0130.0000.0000.0000.000