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: YN7K2

Calculation Name: 1JPE-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JPE

Chain ID: A

ChEMBL ID:

UniProt ID: P36655

Base Structure: X-ray

Registration Date: 2025-07-08

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 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -940490.467818
FMO2-HF: Nuclear repulsion 894619.408888
FMO2-HF: Total energy -45871.05893
FMO2-MP2: Total energy -46006.322544


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(A:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-1.4620.8680.008-0.924-1.4170.002
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.159 / q_NPA : 0.044
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].
4A11PHE0-0.0980.1054.421-0.0710.2740.000-0.149-0.1960.000
5A12VAL00.010-0.1203.7900.5511.892-0.006-0.669-0.6660.002
6A12VAL0-0.0540.1113.458-0.0590.1100.016-0.038-0.1470.000
7A13PRO00.065-0.0515.303-0.290-0.291-0.002-0.0030.0040.000
8A14ALA00.1760.0269.081-0.312-0.3120.0000.0000.0000.000
9A14ALA0-0.0260.12611.6530.0240.0240.0000.0000.0000.000
10A15ASP00.030-0.10510.934-0.166-0.1660.0000.0000.0000.000
11A15ASP-1-0.921-0.80013.751-0.133-0.1330.0000.0000.0000.000
12A16GLN00.060-0.1129.6250.0380.0380.0000.0000.0000.000
13A16GLN0-0.1040.0648.4800.2090.2090.0000.0000.0000.000
14A17ALA00.093-0.0968.803-0.065-0.0650.0000.0000.0000.000
15A17ALA0-0.0730.1057.844-0.057-0.0570.0000.0000.0000.000
16A18PHE00.006-0.0959.514-0.094-0.0940.0000.0000.0000.000
17A18PHE0-0.1270.07211.112-0.005-0.0050.0000.0000.0000.000
18A19ALA00.197-0.06413.2060.1050.1050.0000.0000.0000.000
19A19ALA0-0.1420.09214.7420.0050.0050.0000.0000.0000.000
20A20PHE00.110-0.07615.668-0.022-0.0220.0000.0000.0000.000
21A20PHE0-0.1030.06918.5760.0120.0120.0000.0000.0000.000
22A21ASP00.046-0.13319.0380.0270.0270.0000.0000.0000.000
23A21ASP-1-0.948-0.81921.436-0.176-0.1760.0000.0000.0000.000
24A22PHE00.014-0.09822.433-0.024-0.0240.0000.0000.0000.000
25A22PHE0-0.0600.07524.9350.0050.0050.0000.0000.0000.000
26A23GLN00.159-0.08626.0290.0110.0110.0000.0000.0000.000
27A23GLN0-0.1040.10228.233-0.003-0.0030.0000.0000.0000.000
28A24GLN00.103-0.10829.247-0.010-0.0100.0000.0000.0000.000
29A24GLN0-0.1150.10432.1430.0020.0020.0000.0000.0000.000
30A25ASN00.035-0.10232.6810.0070.0070.0000.0000.0000.000
31A25ASN0-0.1000.08335.2420.0040.0040.0000.0000.0000.000
32A26GLN00.140-0.04835.976-0.002-0.0020.0000.0000.0000.000
33A26GLN0-0.1640.03239.5690.0050.0050.0000.0000.0000.000
34A27HIS00.189-0.03137.198-0.001-0.0010.0000.0000.0000.000
35A27HIS10.7750.98439.3380.0800.0800.0000.0000.0000.000
36A28ASP00.086-0.09335.261-0.001-0.0010.0000.0000.0000.000
37A28ASP-1-1.015-0.83634.622-0.116-0.1160.0000.0000.0000.000
38A29LEU00.168-0.08731.7910.0050.0050.0000.0000.0000.000
39A29LEU0-0.1030.11029.4610.0010.0010.0000.0000.0000.000
40A30ASN00.054-0.10028.690-0.004-0.0040.0000.0000.0000.000
41A30ASN0-0.1060.08526.578-0.012-0.0120.0000.0000.0000.000
42A31LEU00.065-0.10825.2500.0100.0100.0000.0000.0000.000
43A31LEU0-0.0680.10824.3910.0000.0000.0000.0000.0000.000
44A32THR00.029-0.08222.218-0.011-0.0110.0000.0000.0000.000
45A32THR0-0.0060.06920.470-0.002-0.0020.0000.0000.0000.000
46A33TRP00.014-0.10518.0950.0300.0300.0000.0000.0000.000
47A33TRP0-0.0610.09317.0080.0060.0060.0000.0000.0000.000
48A34GLN00.101-0.07316.303-0.010-0.0100.0000.0000.0000.000
49A34GLN0-0.1120.06215.632-0.008-0.0080.0000.0000.0000.000
50A35ILE00.071-0.10512.9790.0010.0010.0000.0000.0000.000
51A35ILE0-0.1390.08912.1080.0160.0160.0000.0000.0000.000
52A36LYS00.142-0.0679.1010.1090.1090.0000.0000.0000.000
53A36LYS10.8151.0486.1922.4052.4050.0000.0000.0000.000
54A37ASP00.079-0.12110.061-0.087-0.0870.0000.0000.0000.000
55A37ASP-1-0.980-0.8379.761-1.505-1.5050.0000.0000.0000.000
56A38GLY0-0.015-0.1007.369-0.561-0.5610.0000.0000.0000.000
57A39TYR00.045-0.0047.550-0.499-0.4990.0000.0000.0000.000
58A39TYR0-0.1210.0643.508-0.590-0.4060.0020.017-0.2030.000
59A40TYR00.055-0.1029.4170.1640.1640.0000.0000.0000.000
60A40TYR0-0.0930.09111.8500.0080.0080.0000.0000.0000.000
61A41LEU00.077-0.12213.047-0.033-0.0330.0000.0000.0000.000
62A41LEU0-0.0760.10514.8700.0160.0160.0000.0000.0000.000
63A42TYR00.102-0.08515.914-0.008-0.0080.0000.0000.0000.000
64A42TYR0-0.1030.05116.0030.0090.0090.0000.0000.0000.000
65A43ARG00.155-0.06818.6420.0280.0280.0000.0000.0000.000
66A43ARG10.7581.02322.3680.2730.2730.0000.0000.0000.000
67A44LYS0-0.020-0.16221.9650.0220.0220.0000.0000.0000.000
68A44LYS10.9021.08923.3830.2220.2220.0000.0000.0000.000
69A45GLN00.051-0.09520.6350.0360.0360.0000.0000.0000.000
70A45GLN0-0.0550.11519.4850.0110.0110.0000.0000.0000.000
71A46ILE00.105-0.09722.0450.0110.0110.0000.0000.0000.000
72A46ILE0-0.1080.10220.794-0.001-0.0010.0000.0000.0000.000
73A47ARG00.087-0.11623.2030.0090.0090.0000.0000.0000.000
74A47ARG10.7451.02325.8270.1200.1200.0000.0000.0000.000
75A48ILE00.002-0.13625.949-0.001-0.0010.0000.0000.0000.000
76A48ILE0-0.0430.13026.369-0.001-0.0010.0000.0000.0000.000
77A49THR00.025-0.12428.3880.0010.0010.0000.0000.0000.000
78A49THR0-0.0470.09630.505-0.004-0.0040.0000.0000.0000.000
79A50PRO0-0.006-0.06731.2590.0010.0010.0000.0000.0000.000
80A51GLU00.063-0.02333.7800.0020.0020.0000.0000.0000.000
81A51GLU-1-0.864-0.78232.011-0.071-0.0710.0000.0000.0000.000
82A52HIS00.049-0.10535.629-0.001-0.0010.0000.0000.0000.000
83A52HIS0-0.0780.10437.801-0.001-0.0010.0000.0000.0000.000
84A53ALA00.208-0.08837.3500.0040.0040.0000.0000.0000.000
85A53ALA0-0.0230.11636.432-0.001-0.0010.0000.0000.0000.000
86A54LYS0-0.003-0.09738.331-0.001-0.0010.0000.0000.0000.000
87A54LYS10.8611.04540.6970.0590.0590.0000.0000.0000.000
88A55ILE00.025-0.13835.3810.0040.0040.0000.0000.0000.000
89A55ILE0-0.0090.13332.8570.0000.0000.0000.0000.0000.000
90A56ALA00.081-0.07936.8260.0050.0050.0000.0000.0000.000
91A56ALA0-0.0630.09236.6290.0000.0000.0000.0000.0000.000
92A57ASP00.056-0.12435.235-0.003-0.0030.0000.0000.0000.000
93A57ASP-1-0.989-0.84935.624-0.111-0.1110.0000.0000.0000.000
94A58VAL00.033-0.12430.9680.0000.0000.0000.0000.0000.000
95A58VAL0-0.0580.12828.997-0.002-0.0020.0000.0000.0000.000
96A59GLN00.111-0.10831.2470.0000.0000.0000.0000.0000.000
97A59GLN0-0.1310.09731.005-0.009-0.0090.0000.0000.0000.000
98A60LEU00.069-0.12326.812-0.004-0.0040.0000.0000.0000.000
99A60LEU0-0.0890.11325.124-0.001-0.0010.0000.0000.0000.000
100A61PRO0-0.011-0.08924.3940.0100.0100.0000.0000.0000.000
101A62GLN00.1580.01225.689-0.014-0.0140.0000.0000.0000.000
102A62GLN0-0.1870.07225.5440.0110.0110.0000.0000.0000.000
103A63GLY00.000-0.10722.301-0.012-0.0120.0000.0000.0000.000
104A64VAL00.039-0.01920.9160.0480.0480.0000.0000.0000.000
105A64VAL0-0.0540.12118.886-0.003-0.0030.0000.0000.0000.000
106A65TRP00.097-0.07320.925-0.023-0.0230.0000.0000.0000.000
107A65TRP0-0.1200.06523.3190.0100.0100.0000.0000.0000.000
108A66HIS00.074-0.10617.8590.0020.0020.0000.0000.0000.000
109A66HIS0-0.0490.10514.086-0.014-0.0140.0000.0000.0000.000
110A67GLU00.123-0.12518.2090.0410.0410.0000.0000.0000.000
111A67GLU-1-1.060-0.86319.748-0.320-0.3200.0000.0000.0000.000
112A68ASP00.011-0.07015.635-0.055-0.0550.0000.0000.0000.000
113A68ASP-1-0.801-0.79714.862-0.543-0.5430.0000.0000.0000.000
114A69GLU00.083-0.12415.7180.0440.0440.0000.0000.0000.000
115A69GLU-1-0.939-0.82814.318-0.498-0.4980.0000.0000.0000.000
116A70PHE00.010-0.07516.4370.0650.0650.0000.0000.0000.000
117A70PHE0-0.1190.04211.7770.0110.0110.0000.0000.0000.000
118A71TYR00.033-0.11017.4700.0500.0500.0000.0000.0000.000
119A71TYR0-0.1340.07317.7510.0180.0180.0000.0000.0000.000
120A72GLY00.063-0.06219.6620.0240.0240.0000.0000.0000.000
121A73LYS00.1560.03020.271-0.050-0.0500.0000.0000.0000.000
122A73LYS10.8121.05123.7480.2700.2700.0000.0000.0000.000
123A74SER0-0.063-0.12820.8710.0430.0430.0000.0000.0000.000
124A74SER00.0090.08919.8360.0060.0060.0000.0000.0000.000
125A75GLU00.158-0.09020.967-0.039-0.0390.0000.0000.0000.000
126A75GLU-1-0.927-0.76822.899-0.297-0.2970.0000.0000.0000.000
127A76ILE0-0.008-0.14617.5570.0400.0400.0000.0000.0000.000
128A76ILE0-0.0630.12215.480-0.012-0.0120.0000.0000.0000.000
129A77TYR00.048-0.11717.5470.0320.0320.0000.0000.0000.000
130A77TYR0-0.0890.05918.0210.0140.0140.0000.0000.0000.000
131A78ARG00.089-0.09514.774-0.069-0.0690.0000.0000.0000.000
132A78ARG10.7970.99611.3711.2001.2000.0000.0000.0000.000
133A79ASP00.169-0.06614.3220.0740.0740.0000.0000.0000.000
134A79ASP-1-1.032-0.84615.371-0.782-0.7820.0000.0000.0000.000
135A80ARG00.112-0.11015.774-0.012-0.0120.0000.0000.0000.000
136A80ARG10.8471.05718.4770.4070.4070.0000.0000.0000.000
137A81LEU00.028-0.11018.1980.0070.0070.0000.0000.0000.000
138A81LEU0-0.0730.12319.562-0.002-0.0020.0000.0000.0000.000
139A82THR0-0.023-0.08120.6170.0050.0050.0000.0000.0000.000
140A82THR0-0.0380.05124.006-0.007-0.0070.0000.0000.0000.000
141A83LEU00.142-0.10824.047-0.001-0.0010.0000.0000.0000.000
142A83LEU0-0.1040.11524.873-0.002-0.0020.0000.0000.0000.000
143A84PRO0-0.047-0.10526.4440.0090.0090.0000.0000.0000.000
144A85VAL00.083-0.00729.976-0.004-0.0040.0000.0000.0000.000
145A85VAL0-0.0480.10429.1960.0010.0010.0000.0000.0000.000
146A86THR00.047-0.07231.9240.0030.0030.0000.0000.0000.000
147A86THR0-0.0270.08136.383-0.002-0.0020.0000.0000.0000.000
148A87ILE00.097-0.11135.6780.0010.0010.0000.0000.0000.000
149A87ILE0-0.0650.13733.7790.0010.0010.0000.0000.0000.000
150A88ASN00.143-0.05837.1480.0030.0030.0000.0000.0000.000
151A88ASN0-0.1220.06740.342-0.001-0.0010.0000.0000.0000.000
152A89GLN00.132-0.09540.0130.0040.0040.0000.0000.0000.000
153A89GLN0-0.1300.06442.145-0.001-0.0010.0000.0000.0000.000
154A90ALA00.095-0.10538.645-0.003-0.0030.0000.0000.0000.000
155A90ALA0-0.0590.14237.999-0.001-0.0010.0000.0000.0000.000
156A91SER00.017-0.03039.8850.0010.0010.0000.0000.0000.000
157A91SER0-0.0440.04840.9370.0020.0020.0000.0000.0000.000
158A92ALA00.137-0.11739.723-0.005-0.0050.0000.0000.0000.000
159A92ALA0-0.0740.12641.5340.0010.0010.0000.0000.0000.000
160A93GLY0-0.070-0.12137.0560.0040.0040.0000.0000.0000.000
161A94ALA00.1040.00836.3150.0040.0040.0000.0000.0000.000
162A94ALA0-0.0520.11736.761-0.001-0.0010.0000.0000.0000.000
163A95THR0-0.062-0.10232.287-0.002-0.0020.0000.0000.0000.000
164A95THR0-0.0230.06131.2000.0040.0040.0000.0000.0000.000
165A96LEU00.117-0.08630.3980.0040.0040.0000.0000.0000.000
166A96LEU0-0.1060.10528.975-0.002-0.0020.0000.0000.0000.000
167A97THR00.043-0.07127.546-0.005-0.0050.0000.0000.0000.000
168A97THR0-0.0560.06226.5630.0030.0030.0000.0000.0000.000
169A98VAL00.077-0.10424.6120.0010.0010.0000.0000.0000.000
170A98VAL0-0.0720.11722.826-0.004-0.0040.0000.0000.0000.000
171A99THR00.008-0.06622.0970.0010.0010.0000.0000.0000.000
172A99THR00.0020.06921.6840.0140.0140.0000.0000.0000.000
173A100TYR00.080-0.05519.4620.0070.0070.0000.0000.0000.000
174A100TYR0-0.0280.10016.0300.0120.0120.0000.0000.0000.000
175A101GLN00.121-0.11316.4190.0260.0260.0000.0000.0000.000
176A101GLN0-0.0850.10315.7600.0160.0160.0000.0000.0000.000
177A102GLY00.033-0.08813.3560.0080.0080.0000.0000.0000.000
178A103CYS00.009-0.06410.8240.1110.1110.0000.0000.0000.000
179A103CYS0-0.1020.28211.2560.0790.0790.0000.0000.0000.000
180A104ALA00.140-0.0736.5450.1640.1640.0000.0000.0000.000
181A104ALA0-0.0860.0995.696-0.271-0.2710.0000.0000.0000.000
182A105ASP00.100-0.1017.8410.3110.3110.0000.0000.0000.000
183A105ASP-1-0.847-0.7658.216-1.623-1.6230.0000.0000.0000.000
184A106ALA00.030-0.1264.8310.6270.669-0.002-0.007-0.0330.000
185A106ALA0-0.0960.1064.381-0.537-0.495-0.001-0.026-0.0160.000
186A107GLY0-0.033-0.1016.3280.4760.4760.0000.0000.0000.000
187A108PHE00.0260.0037.7720.3420.3420.0000.0000.0000.000
188A108PHE0-0.0600.0873.587-0.0310.1770.001-0.049-0.1600.000
189A109CYS00.060-0.1508.782-0.361-0.3610.0000.0000.0000.000
190A110TYR00.031-0.10511.2560.1820.1820.0000.0000.0000.000
191A110TYR0-0.0770.0616.715-0.295-0.2950.0000.0000.0000.000
192A111PRO0-0.014-0.08212.033-0.011-0.0110.0000.0000.0000.000
193A112PRO00.009-0.01715.599-0.047-0.0470.0000.0000.0000.000
194A113GLH0-0.054-0.03215.2870.0220.0220.0000.0000.0000.000
195A114THR00.0240.00118.505-0.034-0.0340.0000.0000.0000.000
196A114THR0-0.0370.04822.9570.0080.0080.0000.0000.0000.000
197A115LYS00.008-0.13121.7980.0260.0260.0000.0000.0000.000
198A115LYS10.8271.06017.6050.1520.1520.0000.0000.0000.000
199A116THR00.060-0.07423.060-0.012-0.0120.0000.0000.0000.000
200A116THR0-0.0600.07127.1340.0010.0010.0000.0000.0000.000
201A117VAL00.072-0.12726.7240.0090.0090.0000.0000.0000.000
202A117VAL0-0.0660.12326.132-0.003-0.0030.0000.0000.0000.000
203A118PRO0-0.046-0.09728.2350.0040.0040.0000.0000.0000.000
204A119LEU00.109-0.02631.473-0.007-0.0070.0000.0000.0000.000
205A119LEU0-0.1010.11432.053-0.002-0.0020.0000.0000.0000.000
206A120SER0-0.009-0.09034.0130.0080.0080.0000.0000.0000.000
207A120SER0-0.0350.07034.8950.0010.0010.0000.0000.0000.000
208A121GLU00.143-0.11536.730-0.006-0.0060.0000.0000.0000.000
209A121GLU-1-1.036-0.85141.022-0.039-0.0390.0000.0000.0000.000
210A122VAL0-0.019-0.14340.172-0.001-0.0010.0000.0000.0000.000
211A122VAL0-0.1190.09638.717-0.001-0.0010.0000.0000.0000.000
212A123VAL00.120-0.11441.5970.0000.0000.0000.0000.0000.000
213A123VAL0-0.0580.12945.6790.0000.0000.0000.0000.0000.000
214A124ALA00.095-0.07744.545-0.004-0.0040.0000.0000.0000.000
215A124ALA0-0.1170.06445.7050.0000.0000.0000.0000.0000.000
216A125ASN0-0.063-0.11645.0980.0000.0000.0000.0000.0000.000
217A125ASN00.0290.02848.0890.0000.0000.0000.0000.0000.000