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: 5RZ7Z

Calculation Name: 5HYC-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5HYC

Chain ID: B

ChEMBL ID:

UniProt ID: G4NCW2

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -932832.105031
FMO2-HF: Nuclear repulsion 885245.869652
FMO2-HF: Total energy -47586.235379
FMO2-MP2: Total energy -47723.014105


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:3:ALA)


Summations of interaction energy for fragment #1(B:3:ALA)
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.
-6.14-3.1510.001-0.96-2.0290
Interaction energy analysis for fragmet #1(B:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.173 / q_NPA : 0.021
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].
4B4GLN0-0.0780.1133.577-0.1610.4830.012-0.215-0.4400.000
5B5GLY00.039-0.0633.800-1.4300.704-0.022-1.238-0.8740.003
6B6PRO0-0.063-0.0357.1780.5220.5220.0000.0000.0000.000
7B7SER00.0720.0199.829-0.083-0.0830.0000.0000.0000.000
8B7SER0-0.130-0.01811.5360.0390.0390.0000.0000.0000.000
9B8PRO0-0.033-0.10211.9350.0400.0400.0000.0000.0000.000
10B9ILE00.1050.00515.2270.0280.0280.0000.0000.0000.000
11B9ILE0-0.0660.13517.2270.0080.0080.0000.0000.0000.000
12B10PRO00.040-0.03015.4240.0100.0100.0000.0000.0000.000
13B11THR00.1510.04314.600-0.010-0.0100.0000.0000.0000.000
14B11THR0-0.0260.08312.489-0.008-0.0080.0000.0000.0000.000
15B12ASN00.126-0.07615.6770.0220.0220.0000.0000.0000.000
16B12ASN0-0.1120.07918.4800.0230.0230.0000.0000.0000.000
17B13ARG00.078-0.11419.0420.0200.0200.0000.0000.0000.000
18B13ARG10.7751.03919.7520.0570.0570.0000.0000.0000.000
19B14LEU00.031-0.12017.425-0.002-0.0020.0000.0000.0000.000
20B14LEU0-0.0340.11814.7980.0050.0050.0000.0000.0000.000
21B15LYS00.161-0.08818.7850.0030.0030.0000.0000.0000.000
22B15LYS10.8431.06718.725-0.230-0.2300.0000.0000.0000.000
23B16GLN00.043-0.11020.0200.0180.0180.0000.0000.0000.000
24B16GLN0-0.1060.09923.339-0.009-0.0090.0000.0000.0000.000
25B17ILE00.156-0.07322.2710.0040.0040.0000.0000.0000.000
26B17ILE0-0.1150.08520.909-0.004-0.0040.0000.0000.0000.000
27B18ALA00.060-0.08821.274-0.012-0.0120.0000.0000.0000.000
28B18ALA0-0.0750.08620.4990.0060.0060.0000.0000.0000.000
29B19ALA00.088-0.11522.6300.0040.0040.0000.0000.0000.000
30B19ALA0-0.0870.11124.1530.0020.0020.0000.0000.0000.000
31B20ASP00.037-0.14225.0230.0100.0100.0000.0000.0000.000
32B20ASP-1-1.006-0.83926.8500.0200.0200.0000.0000.0000.000
33B21ALA00.175-0.06326.131-0.001-0.0010.0000.0000.0000.000
34B21ALA0-0.0980.08825.322-0.002-0.0020.0000.0000.0000.000
35B22CYS00.000-0.13126.474-0.007-0.0070.0000.0000.0000.000
36B22CYS0-0.1570.07924.6130.0090.0090.0000.0000.0000.000
37B23ASN00.117-0.05527.6760.0020.0020.0000.0000.0000.000
38B23ASN0-0.0850.07229.3520.0070.0070.0000.0000.0000.000
39B24ASP00.137-0.10530.5340.0040.0040.0000.0000.0000.000
40B24ASP-1-1.012-0.82730.7980.0060.0060.0000.0000.0000.000
41B25ALA00.073-0.09530.894-0.004-0.0040.0000.0000.0000.000
42B25ALA0-0.1100.09230.1440.0000.0000.0000.0000.0000.000
43B26ILE0-0.081-0.14531.468-0.004-0.0040.0000.0000.0000.000
44B26ILE0-0.0330.09629.5790.0020.0020.0000.0000.0000.000
45B27GLY00.033-0.09932.7670.0090.0090.0000.0000.0000.000
46B28SER00.0280.01434.0040.0050.0050.0000.0000.0000.000
47B28SER0-0.0660.05138.3070.0000.0000.0000.0000.0000.000
48B29ALA00.063-0.09736.059-0.003-0.0030.0000.0000.0000.000
49B29ALA0-0.0810.09835.1920.0000.0000.0000.0000.0000.000
50B30GLU00.109-0.11236.9890.0060.0060.0000.0000.0000.000
51B30GLU-1-1.036-0.86540.6120.0620.0620.0000.0000.0000.000
52B31PHE00.090-0.05136.5340.0050.0050.0000.0000.0000.000
53B31PHE0-0.1260.06237.850-0.002-0.0020.0000.0000.0000.000
54B32TYR00.146-0.08934.249-0.007-0.0070.0000.0000.0000.000
55B32TYR0-0.1140.07630.6110.0030.0030.0000.0000.0000.000
56B33ASP00.114-0.13135.1200.0010.0010.0000.0000.0000.000
57B33ASP-1-1.007-0.82037.2230.0500.0500.0000.0000.0000.000
58B34HIS00.143-0.09134.526-0.003-0.0030.0000.0000.0000.000
59B34HIS0-0.0350.12032.0650.0050.0050.0000.0000.0000.000
60B35ALA00.112-0.12535.106-0.001-0.0010.0000.0000.0000.000
61B35ALA0-0.1010.14239.145-0.001-0.0010.0000.0000.0000.000
62B36LYS00.017-0.12536.002-0.007-0.0070.0000.0000.0000.000
63B36LYS10.9101.09336.091-0.040-0.0400.0000.0000.0000.000
64B37THR00.051-0.09931.744-0.006-0.0060.0000.0000.0000.000
65B37THR0-0.0650.08830.6540.0000.0000.0000.0000.0000.000
66B38GLU00.091-0.09830.6490.0020.0020.0000.0000.0000.000
67B38GLU-1-1.000-0.83731.3860.0090.0090.0000.0000.0000.000
68B39GLN00.075-0.11031.179-0.007-0.0070.0000.0000.0000.000
69B39GLN0-0.0870.10734.8320.0000.0000.0000.0000.0000.000
70B40TRP00.092-0.12231.477-0.010-0.0100.0000.0000.0000.000
71B40TRP0-0.0700.10930.7270.0030.0030.0000.0000.0000.000
72B41ASN00.148-0.08327.449-0.001-0.0010.0000.0000.0000.000
73B41ASN0-0.0920.10226.0060.0050.0050.0000.0000.0000.000
74B42HIS00.096-0.07027.184-0.008-0.0080.0000.0000.0000.000
75B42HIS0-0.1160.08330.897-0.007-0.0070.0000.0000.0000.000
76B43GLN00.070-0.13328.871-0.014-0.0140.0000.0000.0000.000
77B43GLN0-0.0710.12130.8880.0000.0000.0000.0000.0000.000
78B44ILE00.091-0.09226.474-0.015-0.0150.0000.0000.0000.000
79B44ILE0-0.0900.10124.3320.0010.0010.0000.0000.0000.000
80B45ILE00.070-0.11723.792-0.004-0.0040.0000.0000.0000.000
81B45ILE0-0.0850.10222.9970.0000.0000.0000.0000.0000.000
82B46ASN00.084-0.08124.440-0.020-0.0200.0000.0000.0000.000
83B46ASN0-0.0970.08028.053-0.008-0.0080.0000.0000.0000.000
84B47THR0-0.015-0.10726.871-0.021-0.0210.0000.0000.0000.000
85B47THR00.0200.10026.9640.0000.0000.0000.0000.0000.000
86B48ILE00.101-0.08722.643-0.013-0.0130.0000.0000.0000.000
87B48ILE0-0.0900.10820.5470.0010.0010.0000.0000.0000.000
88B49LEU00.110-0.10921.995-0.021-0.0210.0000.0000.0000.000
89B49LEU0-0.0970.11120.906-0.001-0.0010.0000.0000.0000.000
90B50LYS00.099-0.10423.050-0.029-0.0290.0000.0000.0000.000
91B50LYS10.8351.07827.4970.1030.1030.0000.0000.0000.000
92B51ALA00.083-0.14524.823-0.019-0.0190.0000.0000.0000.000
93B51ALA0-0.0250.13624.0730.0050.0050.0000.0000.0000.000
94B52VAL00.013-0.12520.205-0.001-0.0010.0000.0000.0000.000
95B52VAL0-0.0620.10419.326-0.002-0.0020.0000.0000.0000.000
96B53ILE00.100-0.09521.217-0.042-0.0420.0000.0000.0000.000
97B53ILE0-0.0890.10222.669-0.001-0.0010.0000.0000.0000.000
98B54ALA00.096-0.08923.082-0.028-0.0280.0000.0000.0000.000
99B54ALA0-0.1210.08726.0730.0060.0060.0000.0000.0000.000
100B55GLU00.004-0.13523.126-0.008-0.0080.0000.0000.0000.000
101B55GLU-1-0.880-0.77622.410-0.105-0.1050.0000.0000.0000.000
102B56SER00.036-0.07819.8750.0010.0010.0000.0000.0000.000
103B56SER0-0.0380.07418.982-0.021-0.0210.0000.0000.0000.000
104B57GLN00.041-0.10720.885-0.045-0.0450.0000.0000.0000.000
105B57GLN0-0.1350.07521.631-0.011-0.0110.0000.0000.0000.000
106B58PRO00.012-0.11322.8970.0270.0270.0000.0000.0000.000
107B59SER00.0520.06425.9700.0010.0010.0000.0000.0000.000
108B59SER0-0.0520.06427.0120.0000.0000.0000.0000.0000.000
109B60ASP00.053-0.09229.0240.0170.0170.0000.0000.0000.000
110B60ASP-1-0.830-0.79331.994-0.160-0.1600.0000.0000.0000.000
111B61SER0-0.072-0.13331.005-0.014-0.0140.0000.0000.0000.000
112B61SER0-0.0220.06034.9360.0050.0050.0000.0000.0000.000
113B62THR0-0.051-0.06730.7610.0000.0000.0000.0000.0000.000
114B62THR0-0.1040.03428.719-0.004-0.0040.0000.0000.0000.000
115B63THR00.006-0.08426.938-0.001-0.0010.0000.0000.0000.000
116B63THR0-0.0020.05025.333-0.004-0.0040.0000.0000.0000.000
117B64PRO0-0.020-0.10325.3600.0100.0100.0000.0000.0000.000
118B65PRO00.0610.02923.152-0.016-0.0160.0000.0000.0000.000
119B66GLN00.046-0.00719.8870.0000.0000.0000.0000.0000.000
120B66GLN0-0.0880.09318.9140.0260.0260.0000.0000.0000.000
121B67PHE00.035-0.11817.174-0.094-0.0940.0000.0000.0000.000
122B67PHE0-0.0220.11913.4400.0000.0000.0000.0000.0000.000
123B68LYS00.139-0.08416.6540.0750.0750.0000.0000.0000.000
124B68LYS10.8421.07316.7070.4530.4530.0000.0000.0000.000
125B69PHE00.062-0.10816.017-0.082-0.0820.0000.0000.0000.000
126B69PHE0-0.0700.11316.3090.0000.0000.0000.0000.0000.000
127B70ALA00.112-0.09716.2750.0230.0230.0000.0000.0000.000
128B70ALA0-0.1000.10515.9210.0000.0000.0000.0000.0000.000
129B71VAL00.051-0.12716.609-0.008-0.0080.0000.0000.0000.000
130B71VAL0-0.0630.12718.9360.0000.0000.0000.0000.0000.000
131B72ASN00.097-0.08918.143-0.009-0.0090.0000.0000.0000.000
132B72ASN0-0.1210.07617.6780.0300.0300.0000.0000.0000.000
133B73SER00.064-0.08319.4570.0230.0230.0000.0000.0000.000
134B73SER0-0.0240.08222.6940.0020.0020.0000.0000.0000.000
135B74THR0-0.030-0.12322.065-0.020-0.0200.0000.0000.0000.000
136B74THR0-0.0190.08921.1730.0050.0050.0000.0000.0000.000
137B75ILE00.084-0.10023.5240.0210.0210.0000.0000.0000.000
138B75ILE0-0.0530.13326.876-0.002-0.0020.0000.0000.0000.000
139B76VAL00.050-0.11926.410-0.012-0.0120.0000.0000.0000.000
140B76VAL0-0.0930.10024.3960.0040.0040.0000.0000.0000.000
141B77GLN00.151-0.07127.5880.0040.0040.0000.0000.0000.000
142B77GLN0-0.1390.07131.874-0.009-0.0090.0000.0000.0000.000
143B78HIS00.056-0.15330.3150.0150.0150.0000.0000.0000.000
144B78HIS0-0.1140.10229.133-0.008-0.0080.0000.0000.0000.000
145B79LEU00.021-0.12731.590-0.011-0.0110.0000.0000.0000.000
146B79LEU0-0.1070.08730.6110.0040.0040.0000.0000.0000.000
147B80VAL00.071-0.07933.2650.0020.0020.0000.0000.0000.000
148B80VAL0-0.0600.10737.280-0.001-0.0010.0000.0000.0000.000
149B81PRO00.034-0.08236.3560.0090.0090.0000.0000.0000.000
150B82SER0-0.102-0.07537.404-0.010-0.0100.0000.0000.0000.000
151B82SER00.0720.06638.0390.0020.0020.0000.0000.0000.000
152B112ARG00.1130.02124.4920.0070.0070.0000.0000.0000.000
153B112ARG10.8291.00324.941-0.247-0.2470.0000.0000.0000.000
154B113GLY00.050-0.06925.4190.0130.0130.0000.0000.0000.000
155B114MET00.062-0.03123.565-0.013-0.0130.0000.0000.0000.000
156B114MET0-0.0610.14821.620-0.013-0.0130.0000.0000.0000.000
157B115HIS00.087-0.09119.5750.0010.0010.0000.0000.0000.000
158B115HIS0-0.0710.10215.102-0.047-0.0470.0000.0000.0000.000
159B116SER00.066-0.06717.214-0.024-0.0240.0000.0000.0000.000
160B116SER0-0.0440.07017.199-0.003-0.0030.0000.0000.0000.000
161B117ALA00.047-0.12813.1730.0360.0360.0000.0000.0000.000
162B117ALA0-0.0850.12512.1610.0320.0320.0000.0000.0000.000
163B118THR0-0.063-0.11911.098-0.072-0.0720.0000.0000.0000.000
164B118THR00.0150.07510.011-0.005-0.0050.0000.0000.0000.000
165B119GLY00.026-0.0817.7470.2960.2960.0000.0000.0000.000
166B120ALA00.090-0.0756.712-0.016-0.0160.0000.0000.0000.000
167B120ALA0-0.0660.1646.687-0.041-0.0410.0000.0000.0000.000
168B121PHE00.063-0.0896.394-0.113-0.1130.0000.0000.0000.000
169B121PHE0-0.1120.0868.7210.0170.0170.0000.0000.0000.000
170B122TRP00.062-0.0776.9830.3660.3660.0000.0000.0000.000
171B122TRP0-0.0760.0663.8271.4141.545-0.001-0.035-0.0940.000
172B123ASN00.150-0.0437.901-0.198-0.1980.0000.0000.0000.000
173B123ASN0-0.1560.0528.845-0.324-0.3240.0000.0000.0000.000
174B124ASP00.125-0.1174.0351.4401.450-0.0010.023-0.0320.000
175B124ASP-1-0.940-0.8223.024-7.775-7.7200.0150.515-0.586-0.003
176B125LYS00.080-0.0654.586-1.052-1.037-0.002-0.010-0.0030.000
177B125LYS10.8101.0337.4451.8421.8420.0000.0000.0000.000
178B126THR0-0.032-0.1167.0900.4530.4530.0000.0000.0000.000
179B126THR0-0.0720.01910.9220.0150.0150.0000.0000.0000.000
180B127ASP00.073-0.1178.4840.4030.4030.0000.0000.0000.000
181B127ASP-1-0.794-0.7488.084-1.546-1.5460.0000.0000.0000.000
182B128GLY00.018-0.0886.970-0.843-0.8430.0000.0000.0000.000
183B129MET00.060-0.0188.0740.1110.1110.0000.0000.0000.000
184B129MET0-0.0750.1117.4300.1010.1010.0000.0000.0000.000
185B130TRP00.087-0.0939.4760.1580.1580.0000.0000.0000.000
186B130TRP0-0.0830.11612.136-0.022-0.0220.0000.0000.0000.000
187B131THR00.004-0.08312.153-0.088-0.0880.0000.0000.0000.000
188B131THR0-0.0350.05312.2490.0200.0200.0000.0000.0000.000
189B132TYR00.044-0.11014.5740.0430.0430.0000.0000.0000.000
190B132TYR0-0.0880.09217.762-0.003-0.0030.0000.0000.0000.000
191B133LYS00.126-0.08717.878-0.025-0.0250.0000.0000.0000.000
192B133LYS10.8241.06719.967-0.319-0.3190.0000.0000.0000.000
193B134HIS00.085-0.09220.8000.0090.0090.0000.0000.0000.000
194B134HIS0-0.0840.09924.2110.0070.0070.0000.0000.0000.000
195B135GLU00.128-0.12924.269-0.012-0.0120.0000.0000.0000.000
196B135GLU-1-1.075-0.85724.5140.2830.2830.0000.0000.0000.000
197B136GLY0-0.033-0.10126.092-0.012-0.0120.0000.0000.0000.000
198B137ASP00.1000.00429.8280.0160.0160.0000.0000.0000.000
199B137ASP-1-0.918-0.83932.6480.1160.1160.0000.0000.0000.000
200B138GLU00.136-0.12332.448-0.002-0.0020.0000.0000.0000.000
201B138GLU-1-1.053-0.85835.4340.1270.1270.0000.0000.0000.000
202B139SER0-0.046-0.12035.164-0.001-0.0010.0000.0000.0000.000
203B139SER0-0.0620.06636.521-0.004-0.0040.0000.0000.0000.000
204B140LYS00.153-0.06433.621-0.008-0.0080.0000.0000.0000.000
205B140LYS10.6641.01331.777-0.085-0.0850.0000.0000.0000.000
206B141GLY00.042-0.09234.049-0.006-0.0060.0000.0000.0000.000
207B142MET00.060-0.01730.4690.0010.0010.0000.0000.0000.000
208B142MET0-0.1260.08830.241-0.004-0.0040.0000.0000.0000.000
209B143ASP00.096-0.08126.142-0.008-0.0080.0000.0000.0000.000
210B143ASP-1-0.921-0.80025.1820.2130.2130.0000.0000.0000.000
211B144VAL00.015-0.12124.748-0.007-0.0070.0000.0000.0000.000
212B144VAL0-0.0180.11023.523-0.003-0.0030.0000.0000.0000.000
213B145VAL00.047-0.10420.6300.0150.0150.0000.0000.0000.000
214B145VAL0-0.0860.09118.7070.0070.0070.0000.0000.0000.000
215B146VAL00.096-0.10219.294-0.017-0.0170.0000.0000.0000.000
216B146VAL0-0.0830.11418.703-0.005-0.0050.0000.0000.0000.000
217B147MET00.152-0.13115.3020.0570.0570.0000.0000.0000.000
218B147MET0-0.1220.13213.2280.0270.0270.0000.0000.0000.000
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