FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: KK7Y3

Calculation Name: 5HYC-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

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 OptHSide
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 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -932300.935084
FMO2-HF: Nuclear repulsion 884712.37715
FMO2-HF: Total energy -47588.557934
FMO2-MP2: Total energy -47725.309048


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: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.
-11.282-6.9661.277-2.145-3.449-0.018
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 : 0.167 / q_NPA : 0.027
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].
4B4GLN0-0.0490.1113.429-0.3490.3170.034-0.208-0.4930.000
5B5GLY00.024-0.0643.800-1.7860.713-0.024-1.454-1.0220.005
6B6PRO0-0.062-0.0367.1780.4820.4820.0000.0000.0000.000
7B7SER00.0990.0229.852-0.083-0.0830.0000.0000.0000.000
8B7SER0-0.0620.04711.3790.0240.0240.0000.0000.0000.000
9B8PRO0-0.069-0.10811.9460.0470.0470.0000.0000.0000.000
10B9ILE00.086-0.00715.2470.0300.0300.0000.0000.0000.000
11B9ILE0-0.0760.13617.2210.0070.0070.0000.0000.0000.000
12B10PRO00.010-0.08115.4320.0090.0090.0000.0000.0000.000
13B11THR00.1400.04014.619-0.011-0.0110.0000.0000.0000.000
14B11THR0-0.0250.08512.494-0.012-0.0120.0000.0000.0000.000
15B12ASN00.109-0.05915.6800.0200.0200.0000.0000.0000.000
16B12ASN0-0.1080.06718.4490.0220.0220.0000.0000.0000.000
17B13ARG00.093-0.08919.0640.0200.0200.0000.0000.0000.000
18B13ARG10.7500.98619.9120.0670.0670.0000.0000.0000.000
19B14LEU00.044-0.11617.4240.0000.0000.0000.0000.0000.000
20B14LEU0-0.0310.10914.8010.0040.0040.0000.0000.0000.000
21B15LYS00.145-0.07718.7900.0010.0010.0000.0000.0000.000
22B15LYS10.8321.05218.676-0.187-0.1870.0000.0000.0000.000
23B16GLN00.036-0.11720.0120.0170.0170.0000.0000.0000.000
24B16GLN0-0.0810.08723.311-0.007-0.0070.0000.0000.0000.000
25B17ILE00.132-0.04522.2700.0060.0060.0000.0000.0000.000
26B17ILE0-0.1200.07121.084-0.004-0.0040.0000.0000.0000.000
27B18ALA00.086-0.08821.248-0.011-0.0110.0000.0000.0000.000
28B18ALA0-0.0770.08920.4850.0040.0040.0000.0000.0000.000
29B19ALA00.082-0.09222.6150.0030.0030.0000.0000.0000.000
30B19ALA0-0.0710.09124.1140.0020.0020.0000.0000.0000.000
31B20ASP00.025-0.12925.0090.0100.0100.0000.0000.0000.000
32B20ASP-1-0.998-0.84326.9760.0090.0090.0000.0000.0000.000
33B21ALA00.177-0.06626.1110.0000.0000.0000.0000.0000.000
34B21ALA0-0.0930.07825.266-0.003-0.0030.0000.0000.0000.000
35B22CYS00.047-0.12326.462-0.006-0.0060.0000.0000.0000.000
36B22CYS0-0.1750.06724.6640.0070.0070.0000.0000.0000.000
37B23ASN00.076-0.07127.6300.0020.0020.0000.0000.0000.000
38B23ASN0-0.0830.07229.1100.0080.0080.0000.0000.0000.000
39B24ASP00.127-0.07830.5130.0050.0050.0000.0000.0000.000
40B24ASP-1-1.019-0.84030.810-0.006-0.0060.0000.0000.0000.000
41B25ALA00.095-0.08930.809-0.003-0.0030.0000.0000.0000.000
42B25ALA0-0.1150.08230.0230.0000.0000.0000.0000.0000.000
43B26ILE0-0.068-0.14431.375-0.003-0.0030.0000.0000.0000.000
44B26ILE0-0.0530.09529.1630.0020.0020.0000.0000.0000.000
45B27GLY00.054-0.09932.6540.0080.0080.0000.0000.0000.000
46B28SER00.0340.00733.9840.0060.0060.0000.0000.0000.000
47B28SER0-0.0590.05437.9050.0000.0000.0000.0000.0000.000
48B29ALA00.044-0.08435.913-0.002-0.0020.0000.0000.0000.000
49B29ALA0-0.0750.09135.0200.0000.0000.0000.0000.0000.000
50B30GLU00.118-0.09636.8440.0050.0050.0000.0000.0000.000
51B30GLU-1-1.030-0.86840.4610.0500.0500.0000.0000.0000.000
52B31PHE00.087-0.04536.3860.0050.0050.0000.0000.0000.000
53B31PHE0-0.1300.05337.795-0.002-0.0020.0000.0000.0000.000
54B32TYR00.160-0.10234.184-0.007-0.0070.0000.0000.0000.000
55B32TYR0-0.1130.08130.4910.0030.0030.0000.0000.0000.000
56B33ASP00.111-0.10634.9800.0010.0010.0000.0000.0000.000
57B33ASP-1-0.951-0.79437.1020.0360.0360.0000.0000.0000.000
58B34HIS00.144-0.08034.422-0.003-0.0030.0000.0000.0000.000
59B34HIS0-0.0340.12032.0130.0060.0060.0000.0000.0000.000
60B35ALA00.081-0.09435.024-0.002-0.0020.0000.0000.0000.000
61B35ALA0-0.0820.10839.1080.0000.0000.0000.0000.0000.000
62B36LYS00.032-0.12335.925-0.007-0.0070.0000.0000.0000.000
63B36LYS10.8321.03836.051-0.030-0.0300.0000.0000.0000.000
64B37THR00.050-0.11031.668-0.006-0.0060.0000.0000.0000.000
65B37THR0-0.0660.08430.5800.0000.0000.0000.0000.0000.000
66B38GLU00.080-0.09730.5830.0010.0010.0000.0000.0000.000
67B38GLU-1-0.993-0.83831.273-0.005-0.0050.0000.0000.0000.000
68B39GLN00.082-0.09731.142-0.008-0.0080.0000.0000.0000.000
69B39GLN0-0.0880.09834.8450.0000.0000.0000.0000.0000.000
70B40TRP00.061-0.10531.410-0.009-0.0090.0000.0000.0000.000
71B40TRP0-0.0770.09530.7020.0030.0030.0000.0000.0000.000
72B41ASN00.170-0.07627.370-0.002-0.0020.0000.0000.0000.000
73B41ASN0-0.1340.07925.2590.0050.0050.0000.0000.0000.000
74B42HIS00.102-0.05927.150-0.009-0.0090.0000.0000.0000.000
75B42HIS0-0.1030.08130.866-0.005-0.0050.0000.0000.0000.000
76B43GLN00.074-0.12028.858-0.014-0.0140.0000.0000.0000.000
77B43GLN0-0.0660.11930.8830.0020.0020.0000.0000.0000.000
78B44ILE00.099-0.08926.423-0.014-0.0140.0000.0000.0000.000
79B44ILE0-0.0810.10624.2640.0010.0010.0000.0000.0000.000
80B45ILE00.085-0.10923.772-0.005-0.0050.0000.0000.0000.000
81B45ILE0-0.1040.10122.9840.0000.0000.0000.0000.0000.000
82B46ASN00.080-0.08324.441-0.020-0.0200.0000.0000.0000.000
83B46ASN0-0.1040.07428.049-0.007-0.0070.0000.0000.0000.000
84B47THR00.005-0.10226.886-0.020-0.0200.0000.0000.0000.000
85B47THR0-0.0050.09027.1620.0010.0010.0000.0000.0000.000
86B48ILE00.126-0.07722.613-0.012-0.0120.0000.0000.0000.000
87B48ILE0-0.1090.10120.5170.0010.0010.0000.0000.0000.000
88B49LEU00.105-0.09322.028-0.020-0.0200.0000.0000.0000.000
89B49LEU0-0.0930.10321.101-0.001-0.0010.0000.0000.0000.000
90B50LYS00.096-0.10523.077-0.027-0.0270.0000.0000.0000.000
91B50LYS10.8271.06027.4710.1190.1190.0000.0000.0000.000
92B51ALA00.061-0.13124.825-0.017-0.0170.0000.0000.0000.000
93B51ALA0-0.0170.12724.0620.0040.0040.0000.0000.0000.000
94B52VAL00.021-0.12120.1780.0000.0000.0000.0000.0000.000
95B52VAL0-0.0590.10818.985-0.002-0.0020.0000.0000.0000.000
96B53ILE00.126-0.04721.218-0.039-0.0390.0000.0000.0000.000
97B53ILE0-0.0830.09222.4740.0000.0000.0000.0000.0000.000
98B54ALA00.084-0.07523.082-0.023-0.0230.0000.0000.0000.000
99B54ALA0-0.1380.06126.1110.0060.0060.0000.0000.0000.000
100B55GLU00.013-0.10423.210-0.007-0.0070.0000.0000.0000.000
101B55GLU-1-0.857-0.76222.538-0.107-0.1070.0000.0000.0000.000
102B56SER00.080-0.09419.8490.0020.0020.0000.0000.0000.000
103B56SER0-0.0790.04719.123-0.017-0.0170.0000.0000.0000.000
104B57GLN00.018-0.11320.887-0.044-0.0440.0000.0000.0000.000
105B57GLN0-0.1060.09021.618-0.026-0.0260.0000.0000.0000.000
106B58PRO00.003-0.12022.9140.0250.0250.0000.0000.0000.000
107B59SER00.0430.06425.9700.0000.0000.0000.0000.0000.000
108B59SER0-0.0490.06327.165-0.001-0.0010.0000.0000.0000.000
109B60ASP00.060-0.09329.1180.0150.0150.0000.0000.0000.000
110B60ASP-1-0.827-0.79132.165-0.154-0.1540.0000.0000.0000.000
111B61SER0-0.079-0.13230.982-0.015-0.0150.0000.0000.0000.000
112B61SER0-0.0240.06134.9350.0050.0050.0000.0000.0000.000
113B62THR0-0.048-0.06830.9420.0000.0000.0000.0000.0000.000
114B62THR0-0.0980.03428.889-0.004-0.0040.0000.0000.0000.000
115B63THR00.076-0.09126.973-0.001-0.0010.0000.0000.0000.000
116B63THR0-0.0290.06825.343-0.003-0.0030.0000.0000.0000.000
117B64PRO0-0.050-0.10625.3390.0090.0090.0000.0000.0000.000
118B65PRO00.0340.01023.089-0.012-0.0120.0000.0000.0000.000
119B66GLN00.0710.03320.0040.0010.0010.0000.0000.0000.000
120B66GLN0-0.1040.07918.5600.0330.0330.0000.0000.0000.000
121B67PHE00.028-0.11517.172-0.090-0.0900.0000.0000.0000.000
122B67PHE0-0.0250.10613.5330.0000.0000.0000.0000.0000.000
123B68LYS00.142-0.08316.8300.0730.0730.0000.0000.0000.000
124B68LYS10.8351.05816.7890.4730.4730.0000.0000.0000.000
125B69PHE00.054-0.09816.147-0.081-0.0810.0000.0000.0000.000
126B69PHE0-0.0600.10716.235-0.002-0.0020.0000.0000.0000.000
127B70ALA00.119-0.09016.3370.0270.0270.0000.0000.0000.000
128B70ALA0-0.1060.10015.972-0.001-0.0010.0000.0000.0000.000
129B71VAL00.061-0.11716.637-0.013-0.0130.0000.0000.0000.000
130B71VAL0-0.0830.11518.8160.0000.0000.0000.0000.0000.000
131B72ASN00.102-0.07118.110-0.004-0.0040.0000.0000.0000.000
132B72ASN0-0.1280.06217.6200.0240.0240.0000.0000.0000.000
133B73SER00.082-0.08319.3950.0190.0190.0000.0000.0000.000
134B73SER0-0.0240.07622.5950.0020.0020.0000.0000.0000.000
135B74THR0-0.016-0.09821.997-0.018-0.0180.0000.0000.0000.000
136B74THR0-0.0350.08321.1870.0050.0050.0000.0000.0000.000
137B75ILE00.089-0.08723.4250.0190.0190.0000.0000.0000.000
138B75ILE0-0.0480.11726.900-0.002-0.0020.0000.0000.0000.000
139B76VAL00.069-0.12526.271-0.011-0.0110.0000.0000.0000.000
140B76VAL0-0.0960.10424.1990.0030.0030.0000.0000.0000.000
141B77GLN00.155-0.07027.4430.0040.0040.0000.0000.0000.000
142B77GLN0-0.1150.08031.765-0.008-0.0080.0000.0000.0000.000
143B78HIS00.039-0.14930.1450.0130.0130.0000.0000.0000.000
144B78HIS0-0.1240.09528.937-0.006-0.0060.0000.0000.0000.000
145B79LEU00.021-0.11631.336-0.011-0.0110.0000.0000.0000.000
146B79LEU0-0.0990.08230.1230.0030.0030.0000.0000.0000.000
147B80VAL00.092-0.08333.0710.0020.0020.0000.0000.0000.000
148B80VAL0-0.0800.11136.997-0.001-0.0010.0000.0000.0000.000
149B81PRO00.024-0.08836.1450.0080.0080.0000.0000.0000.000
150B82SER0-0.080-0.07037.186-0.009-0.0090.0000.0000.0000.000
151B82SER00.0530.06137.4190.0030.0030.0000.0000.0000.000
152B112ARG00.1270.06723.9660.0050.0050.0000.0000.0000.000
153B112ARG10.8361.00025.343-0.213-0.2130.0000.0000.0000.000
154B113GLY00.043-0.10125.1980.0110.0110.0000.0000.0000.000
155B114MET00.047-0.01423.377-0.010-0.0100.0000.0000.0000.000
156B114MET0-0.0630.12821.308-0.012-0.0120.0000.0000.0000.000
157B115HIS00.093-0.09219.4120.0010.0010.0000.0000.0000.000
158B115HIS0-0.0750.10114.913-0.036-0.0360.0000.0000.0000.000
159B116SER00.059-0.06617.052-0.020-0.0200.0000.0000.0000.000
160B116SER0-0.0430.06517.048-0.004-0.0040.0000.0000.0000.000
161B117ALA00.034-0.10713.0030.0320.0320.0000.0000.0000.000
162B117ALA0-0.0650.10312.0340.0290.0290.0000.0000.0000.000
163B118THR0-0.071-0.10310.995-0.057-0.0570.0000.0000.0000.000
164B118THR00.0130.04510.3290.0020.0020.0000.0000.0000.000
165B119GLY00.040-0.0777.6890.2390.2390.0000.0000.0000.000
166B120ALA00.035-0.0246.7320.0220.0220.0000.0000.0000.000
167B120ALA0-0.0390.1096.754-0.036-0.0360.0000.0000.0000.000
168B121PHE00.106-0.0736.520-0.146-0.1460.0000.0000.0000.000
169B121PHE0-0.1310.0818.7390.0130.0130.0000.0000.0000.000
170B122TRP00.088-0.0647.0410.3690.3690.0000.0000.0000.000
171B122TRP0-0.0900.0563.9281.2541.361-0.001-0.030-0.0760.000
172B123ASN00.187-0.0437.680-0.203-0.2030.0000.0000.0000.000
173B123ASN0-0.1850.0439.494-0.206-0.2060.0000.0000.0000.000
174B124ASP00.123-0.1074.1261.3641.393-0.0010.003-0.0300.000
175B124ASP-1-0.911-0.8222.389-12.401-11.4051.271-0.448-1.819-0.023
176B125LYS00.071-0.0594.676-0.848-0.829-0.002-0.008-0.0090.000
177B125LYS10.7971.0307.4481.8041.8040.0000.0000.0000.000
178B126THR0-0.047-0.1327.1780.4320.4320.0000.0000.0000.000
179B126THR0-0.0670.01511.0780.0040.0040.0000.0000.0000.000
180B127ASP00.077-0.0858.4750.3810.3810.0000.0000.0000.000
181B127ASP-1-0.834-0.7668.396-1.503-1.5030.0000.0000.0000.000
182B128GLY00.046-0.0866.970-0.793-0.7930.0000.0000.0000.000
183B129MET00.0810.0028.0670.1130.1130.0000.0000.0000.000
184B129MET0-0.1010.0927.5400.0770.0770.0000.0000.0000.000
185B130TRP00.111-0.0849.4580.1410.1410.0000.0000.0000.000
186B130TRP0-0.0950.10912.044-0.021-0.0210.0000.0000.0000.000
187B131THR0-0.004-0.07712.134-0.081-0.0810.0000.0000.0000.000
188B131THR0-0.0360.05112.4120.0220.0220.0000.0000.0000.000
189B132TYR00.052-0.10714.4390.0420.0420.0000.0000.0000.000
190B132TYR0-0.0960.06717.711-0.001-0.0010.0000.0000.0000.000
191B133LYS00.110-0.08517.855-0.026-0.0260.0000.0000.0000.000
192B133LYS10.6590.96119.753-0.242-0.2420.0000.0000.0000.000
193B134HIS00.062-0.09720.7510.0100.0100.0000.0000.0000.000
194B134HIS0-0.0740.11024.1450.0040.0040.0000.0000.0000.000
195B135GLU00.132-0.10624.245-0.012-0.0120.0000.0000.0000.000
196B135GLU-1-0.987-0.81424.3670.2540.2540.0000.0000.0000.000
197B136GLY0-0.014-0.10226.066-0.010-0.0100.0000.0000.0000.000
198B137ASP00.0650.00929.7820.0150.0150.0000.0000.0000.000
199B137ASP-1-0.875-0.81332.6870.0990.0990.0000.0000.0000.000
200B138GLU00.133-0.10132.422-0.002-0.0020.0000.0000.0000.000
201B138GLU-1-1.048-0.87735.3740.1140.1140.0000.0000.0000.000
202B139SER0-0.029-0.11935.054-0.001-0.0010.0000.0000.0000.000
203B139SER0-0.0900.03436.641-0.003-0.0030.0000.0000.0000.000
204B140LYS00.132-0.07333.512-0.007-0.0070.0000.0000.0000.000
205B140LYS10.6971.00731.889-0.066-0.0660.0000.0000.0000.000
206B141GLY00.029-0.09433.850-0.006-0.0060.0000.0000.0000.000
207B142MET00.056-0.01330.2950.0010.0010.0000.0000.0000.000
208B142MET0-0.1180.08930.008-0.004-0.0040.0000.0000.0000.000
209B143ASP00.097-0.07725.959-0.005-0.0050.0000.0000.0000.000
210B143ASP-1-0.853-0.77724.9190.1930.1930.0000.0000.0000.000
211B144VAL00.014-0.11124.607-0.006-0.0060.0000.0000.0000.000
212B144VAL0-0.0360.11023.533-0.002-0.0020.0000.0000.0000.000
213B145VAL00.076-0.10720.4950.0140.0140.0000.0000.0000.000
214B145VAL0-0.0910.09918.4410.0060.0060.0000.0000.0000.000
215B146VAL00.103-0.09819.192-0.016-0.0160.0000.0000.0000.000
216B146VAL0-0.0970.10218.669-0.004-0.0040.0000.0000.0000.000
217B147MET00.150-0.10615.2800.0510.0510.0000.0000.0000.000
218B147MET0-0.1210.12013.2200.0220.0220.0000.0000.0000.000
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