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: YNRM2

Calculation Name: 2E7V-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2E7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VHK8

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -977527.880864
FMO2-HF: Nuclear repulsion 929753.812758
FMO2-HF: Total energy -47774.068106
FMO2-MP2: Total energy -47913.742717


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:45:LYS)


Summations of interaction energy for fragment #1(A:45: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.
-19.809-34.48910.15510.506-5.9850.037
Interaction energy analysis for fragmet #1(A:45:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.140 / q_NPA : 0.004
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].
4A46LYS10.7941.0514.0701.0401.3920.002-0.142-0.2120.000
5A47ALA00.166-0.0903.819-2.584-0.854-0.020-1.059-0.6510.002
6A47ALA0-0.0790.1077.3710.1450.1450.0000.0000.0000.000
7A48TYR0-0.012-0.1266.9550.4650.4650.0000.0000.0000.000
8A48TYR0-0.0870.0708.9390.0090.0090.0000.0000.0000.000
9A49PHE00.085-0.0939.766-0.143-0.1430.0000.0000.0000.000
10A49PHE0-0.0390.12112.322-0.058-0.0580.0000.0000.0000.000
11A50TYR00.032-0.08513.3040.0620.0620.0000.0000.0000.000
12A50TYR0-0.1000.04111.654-0.068-0.0680.0000.0000.0000.000
13A51HIS00.075-0.07416.094-0.057-0.0570.0000.0000.0000.000
14A51HIS0-0.0460.09918.9400.0110.0110.0000.0000.0000.000
15A52SER0-0.028-0.07519.6790.0080.0080.0000.0000.0000.000
16A52SER00.0050.04121.197-0.010-0.0100.0000.0000.0000.000
17A53SER00.023-0.06222.891-0.025-0.0250.0000.0000.0000.000
18A53SER0-0.0530.05427.1830.0060.0060.0000.0000.0000.000
19A54PHE00.059-0.12826.4760.0150.0150.0000.0000.0000.000
20A54PHE0-0.1090.08721.860-0.018-0.0180.0000.0000.0000.000
21A55GLN00.088-0.07727.591-0.001-0.0010.0000.0000.0000.000
22A55GLN0-0.0200.13130.2900.0170.0170.0000.0000.0000.000
23A56ILE00.077-0.09930.802-0.010-0.0100.0000.0000.0000.000
24A56ILE0-0.1410.07428.489-0.005-0.0050.0000.0000.0000.000
25A57LEU00.065-0.12132.0650.0130.0130.0000.0000.0000.000
26A57LEU0-0.0720.11132.7440.0000.0000.0000.0000.0000.000
27A58ASN00.083-0.06334.788-0.007-0.0070.0000.0000.0000.000
28A58ASN0-0.1360.04836.7780.0070.0070.0000.0000.0000.000
29A59VAL00.111-0.10536.3410.0080.0080.0000.0000.0000.000
30A59VAL0-0.0950.08534.745-0.003-0.0030.0000.0000.0000.000
31A60GLU00.126-0.11137.684-0.007-0.0070.0000.0000.0000.000
32A60GLU-1-1.005-0.82341.721-0.148-0.1480.0000.0000.0000.000
33A61TYR00.106-0.11938.343-0.006-0.0060.0000.0000.0000.000
34A61TYR0-0.1910.02635.427-0.005-0.0050.0000.0000.0000.000
35A62THR00.032-0.08239.2000.0090.0090.0000.0000.0000.000
36A62THR0-0.0270.08940.093-0.001-0.0010.0000.0000.0000.000
37A63GLU00.137-0.09939.825-0.011-0.0110.0000.0000.0000.000
38A63GLU-1-0.967-0.82642.971-0.159-0.1590.0000.0000.0000.000
39A64ALA00.076-0.12439.785-0.005-0.0050.0000.0000.0000.000
40A64ALA0-0.0270.15139.2630.0000.0000.0000.0000.0000.000
41A65LEU0-0.039-0.14436.004-0.008-0.0080.0000.0000.0000.000
42A65LEU0-0.0470.13434.854-0.003-0.0030.0000.0000.0000.000
43A66ASN00.127-0.09635.310-0.016-0.0160.0000.0000.0000.000
44A66ASN0-0.0420.15038.807-0.007-0.0070.0000.0000.0000.000
45A67SER0-0.037-0.10135.905-0.007-0.0070.0000.0000.0000.000
46A67SER0-0.0630.07736.863-0.002-0.0020.0000.0000.0000.000
47A68PRO00.047-0.10030.7190.0000.0000.0000.0000.0000.000
48A69ALA00.083-0.03132.521-0.017-0.0170.0000.0000.0000.000
49A69ALA0-0.0720.11435.3640.0030.0030.0000.0000.0000.000
50A70THR0-0.045-0.09734.8490.0050.0050.0000.0000.0000.000
51A70THR0-0.0360.05736.689-0.004-0.0040.0000.0000.0000.000
52A71HIS00.136-0.05934.939-0.017-0.0170.0000.0000.0000.000
53A71HIS0-0.0420.11637.1740.0010.0010.0000.0000.0000.000
54A72GLU00.025-0.13735.128-0.014-0.0140.0000.0000.0000.000
55A72GLU-1-0.854-0.79937.294-0.183-0.1830.0000.0000.0000.000
56A73TYR00.152-0.07133.499-0.009-0.0090.0000.0000.0000.000
57A73TYR0-0.1070.11628.880-0.002-0.0020.0000.0000.0000.000
58A74ARG00.033-0.09930.520-0.022-0.0220.0000.0000.0000.000
59A74ARG10.8341.04030.7310.2650.2650.0000.0000.0000.000
60A75THR00.060-0.07630.153-0.027-0.0270.0000.0000.0000.000
61A75THR0-0.0290.07233.7410.0040.0040.0000.0000.0000.000
62A76LEU00.088-0.10631.133-0.011-0.0110.0000.0000.0000.000
63A76LEU0-0.0610.13231.0830.0010.0010.0000.0000.0000.000
64A77SER0-0.018-0.12328.058-0.012-0.0120.0000.0000.0000.000
65A77SER0-0.0260.07827.195-0.008-0.0080.0000.0000.0000.000
66A78GLU00.140-0.09026.387-0.042-0.0420.0000.0000.0000.000
67A78GLU-1-1.026-0.84427.013-0.310-0.3100.0000.0000.0000.000
68A79ARG00.058-0.13426.434-0.027-0.0270.0000.0000.0000.000
69A79ARG10.8461.09528.9300.3000.3000.0000.0000.0000.000
70A80ILE00.071-0.09426.575-0.008-0.0080.0000.0000.0000.000
71A80ILE0-0.0550.09724.869-0.003-0.0030.0000.0000.0000.000
72A81GLU00.041-0.14522.643-0.026-0.0260.0000.0000.0000.000
73A81GLU-1-0.885-0.78122.244-0.502-0.5020.0000.0000.0000.000
74A82ALA00.099-0.10121.978-0.075-0.0750.0000.0000.0000.000
75A82ALA0-0.0390.13625.4950.0080.0080.0000.0000.0000.000
76A83MET00.061-0.10423.391-0.022-0.0220.0000.0000.0000.000
77A83MET0-0.1050.11525.6880.0070.0070.0000.0000.0000.000
78A84ILE00.131-0.06421.1820.0040.0040.0000.0000.0000.000
79A84ILE0-0.0810.08219.011-0.018-0.0180.0000.0000.0000.000
80A85THR0-0.012-0.10518.596-0.059-0.0590.0000.0000.0000.000
81A85THR0-0.0970.00818.143-0.041-0.0410.0000.0000.0000.000
82A86ASP00.079-0.14819.105-0.071-0.0710.0000.0000.0000.000
83A86ASP-1-0.971-0.79723.283-0.408-0.4080.0000.0000.0000.000
84A87GLU00.057-0.12621.1760.0060.0060.0000.0000.0000.000
85A87GLU-1-0.871-0.76221.094-0.399-0.3990.0000.0000.0000.000
86A88PHE00.042-0.11116.5000.0300.0300.0000.0000.0000.000
87A88PHE0-0.0930.07215.480-0.052-0.0520.0000.0000.0000.000
88A89ARG00.014-0.13516.534-0.075-0.0750.0000.0000.0000.000
89A89ARG10.9101.11013.2550.9390.9390.0000.0000.0000.000
90A90GLY0-0.001-0.07417.8230.0230.0230.0000.0000.0000.000
91A91SER0-0.005-0.00317.8400.0680.0680.0000.0000.0000.000
92A91SER0-0.0010.07216.649-0.033-0.0330.0000.0000.0000.000
93A92SER00.020-0.07015.914-0.032-0.0320.0000.0000.0000.000
94A92SER0-0.0190.07315.7620.0150.0150.0000.0000.0000.000
95A93LEU00.004-0.12712.388-0.019-0.0190.0000.0000.0000.000
96A93LEU0-0.0850.10811.267-0.031-0.0310.0000.0000.0000.000
97A94LYS00.106-0.09712.351-0.226-0.2260.0000.0000.0000.000
98A94LYS10.8561.07513.9690.5320.5320.0000.0000.0000.000
99A95SER0-0.011-0.10610.390-0.026-0.0260.0000.0000.0000.000
100A95SER0-0.0040.0969.780-0.018-0.0180.0000.0000.0000.000
101A96GLU0-0.030-0.1647.709-0.455-0.4550.0000.0000.0000.000
102A96GLU-1-0.830-0.7877.319-1.433-1.4330.0000.0000.0000.000
103A97PHE00.140-0.0798.690-0.564-0.5640.0000.0000.0000.000
104A97PHE0-0.0210.14213.0100.0020.0020.0000.0000.0000.000
105A98ILE00.002-0.09610.9750.0500.0500.0000.0000.0000.000
106A98ILE0-0.1850.0167.764-0.121-0.1210.0000.0000.0000.000
107A99ARG00.107-0.09911.7210.1310.1310.0000.0000.0000.000
108A99ARG10.8991.07613.1611.1251.1250.0000.0000.0000.000
109A100THR0-0.037-0.10715.160-0.144-0.1440.0000.0000.0000.000
110A100THR0-0.0060.06717.6790.0200.0200.0000.0000.0000.000
111A101HIS00.047-0.06417.9200.0120.0120.0000.0000.0000.000
112A101HIS0-0.1010.07118.3320.0160.0160.0000.0000.0000.000
113A102VAL00.095-0.11421.053-0.047-0.0470.0000.0000.0000.000
114A102VAL0-0.0410.13724.5430.0020.0020.0000.0000.0000.000
115A103VAL00.063-0.11724.1430.0090.0090.0000.0000.0000.000
116A103VAL0-0.1400.09422.262-0.005-0.0050.0000.0000.0000.000
117A104LYS00.039-0.11524.7590.0180.0180.0000.0000.0000.000
118A104LYS10.8351.06028.2250.2830.2830.0000.0000.0000.000
119A105LEU00.080-0.10628.351-0.022-0.0220.0000.0000.0000.000
120A105LEU0-0.0190.15829.4140.0010.0010.0000.0000.0000.000
121A106ARG00.046-0.10331.0140.0120.0120.0000.0000.0000.000
122A106ARG10.6630.91228.9720.2960.2960.0000.0000.0000.000
123A107LYS00.175-0.06633.240-0.006-0.0060.0000.0000.0000.000
124A107LYS10.8271.05337.7590.1860.1860.0000.0000.0000.000
125A108GLU00.004-0.16536.1330.0040.0040.0000.0000.0000.000
126A108GLU-1-0.911-0.79833.319-0.244-0.2440.0000.0000.0000.000
127A109GLY0-0.003-0.09437.2780.0010.0010.0000.0000.0000.000
128A110THR0-0.001-0.01840.8150.0000.0000.0000.0000.0000.000
129A110THR00.0250.10242.679-0.001-0.0010.0000.0000.0000.000
130A111GLY00.053-0.04637.9070.0010.0010.0000.0000.0000.000
131A112VAL00.104-0.00734.5860.0040.0040.0000.0000.0000.000
132A112VAL0-0.0640.10732.510-0.002-0.0020.0000.0000.0000.000
133A113VAL00.076-0.11831.266-0.002-0.0020.0000.0000.0000.000
134A113VAL0-0.1020.12729.693-0.002-0.0020.0000.0000.0000.000
135A114ALA00.109-0.09027.9510.0100.0100.0000.0000.0000.000
136A114ALA0-0.0680.10927.329-0.003-0.0030.0000.0000.0000.000
137A115ASP00.106-0.08525.548-0.013-0.0130.0000.0000.0000.000
138A115ASP-1-0.877-0.75325.228-0.350-0.3500.0000.0000.0000.000
139A116VAL00.066-0.11622.4060.0010.0010.0000.0000.0000.000
140A116VAL0-0.0260.13420.361-0.005-0.0050.0000.0000.0000.000
141A117VAL00.077-0.10618.771-0.005-0.0050.0000.0000.0000.000
142A117VAL0-0.0520.09816.735-0.023-0.0230.0000.0000.0000.000
143A118MET00.085-0.10615.9190.0140.0140.0000.0000.0000.000
144A118MET0-0.0720.12215.414-0.017-0.0170.0000.0000.0000.000
145A119LYS00.118-0.07512.238-0.032-0.0320.0000.0000.0000.000
146A119LYS10.8161.0439.4682.0092.0090.0000.0000.0000.000
147A120PHE00.029-0.1019.3040.1010.1010.0000.0000.0000.000
148A120PHE0-0.0260.1169.033-0.017-0.0170.0000.0000.0000.000
149A121ARG00.059-0.0915.382-0.203-0.193-0.002-0.003-0.0060.000
150A121ARG10.8341.0404.5412.7912.887-0.001-0.033-0.0640.000
151A122SER00.056-0.1013.857-0.0140.1350.0200.012-0.1810.000
152A122SER0-0.0650.0445.7560.3810.415-0.001-0.005-0.0270.000
153A123SER00.049-0.0032.7419.323-5.100-0.10615.174-0.6460.001
154A123SER00.0320.1006.598-0.210-0.2100.0000.0000.0000.000
155A124LYS00.121-0.0532.9130.5380.3160.2140.526-0.517-0.001
156A124LYS10.8791.0692.167-31.202-33.3849.947-4.103-3.6630.035
157A125ARG00.085-0.1093.299-0.373-0.5970.1020.139-0.0180.000
158A125ARG10.9471.0977.583-1.586-1.5860.0000.0000.0000.000
159A126ASN00.123-0.0976.275-0.524-0.5240.0000.0000.0000.000
160A126ASN0-0.0650.0938.756-0.174-0.1740.0000.0000.0000.000
161A127ASN00.108-0.0848.8900.1610.1610.0000.0000.0000.000
162A127ASN0-0.0370.15012.587-0.047-0.0470.0000.0000.0000.000
163A128ARG00.134-0.04711.637-0.148-0.1480.0000.0000.0000.000
164A128ARG10.9161.09712.8140.5370.5370.0000.0000.0000.000
165A129LYS0-0.014-0.15013.077-0.062-0.0620.0000.0000.0000.000
166A129LYS10.9471.06816.6790.4890.4890.0000.0000.0000.000
167A130VAL00.182-0.07613.5010.0180.0180.0000.0000.0000.000
168A130VAL0-0.0600.12912.562-0.001-0.0010.0000.0000.0000.000
169A131MET00.120-0.08211.5120.0860.0860.0000.0000.0000.000
170A131MET0-0.0660.1198.641-0.042-0.0420.0000.0000.0000.000
171A132LYS00.113-0.07412.532-0.024-0.0240.0000.0000.0000.000
172A132LYS10.8321.05716.1930.4780.4780.0000.0000.0000.000
173A133THR00.029-0.06015.9540.0000.0000.0000.0000.0000.000
174A133THR0-0.0450.04816.3470.0250.0250.0000.0000.0000.000
175A134ARG00.062-0.07514.7910.0800.0800.0000.0000.0000.000
176A134ARG10.7750.9889.6701.0301.0300.0000.0000.0000.000
177A135ILE00.113-0.06215.7140.0370.0370.0000.0000.0000.000
178A135ILE0-0.0920.07813.241-0.018-0.0180.0000.0000.0000.000
179A136GLN00.100-0.08416.7280.0170.0170.0000.0000.0000.000
180A136GLN0-0.0570.09719.7110.0030.0030.0000.0000.0000.000
181A137SER0-0.057-0.11319.5330.0380.0380.0000.0000.0000.000
182A137SER0-0.0090.07619.5320.0210.0210.0000.0000.0000.000
183A138VAL00.116-0.06219.1550.0550.0550.0000.0000.0000.000
184A138VAL0-0.0800.08817.348-0.010-0.0100.0000.0000.0000.000
185A139LEU00.071-0.09020.4580.0260.0260.0000.0000.0000.000
186A139LEU0-0.0850.07619.910-0.010-0.0100.0000.0000.0000.000
187A140ARG00.158-0.04822.3390.0190.0190.0000.0000.0000.000
188A140ARG10.7951.04422.7620.3240.3240.0000.0000.0000.000
189A141ARG00.048-0.08324.1390.0290.0290.0000.0000.0000.000
190A141ARG10.6740.94221.2920.4060.4060.0000.0000.0000.000
191A142LEU00.041-0.10025.3470.0220.0220.0000.0000.0000.000
192A142LEU0-0.0750.09123.302-0.010-0.0100.0000.0000.0000.000
193A143SER00.038-0.07426.8450.0100.0100.0000.0000.0000.000
194A143SER0-0.1050.02128.0920.0070.0070.0000.0000.0000.000
195A144SER0-0.007-0.08829.228-0.002-0.0020.0000.0000.0000.000
196A144SER00.0320.10332.0810.0050.0050.0000.0000.0000.000
197A145SER0-0.027-0.09232.4840.0140.0140.0000.0000.0000.000
198A145SER0-0.0150.07933.501-0.001-0.0010.0000.0000.0000.000
199A146GLY0-0.037-0.10730.4380.0100.0100.0000.0000.0000.000
200A147ASN00.024-0.04729.710-0.014-0.0140.0000.0000.0000.000
201A147ASN0-0.0530.10131.252-0.004-0.0040.0000.0000.0000.000
202A148LEU00.057-0.06126.699-0.005-0.0050.0000.0000.0000.000
203A148LEU0-0.1010.08523.805-0.010-0.0100.0000.0000.0000.000
204A149GLU00.035-0.14427.475-0.004-0.0040.0000.0000.0000.000
205A149GLU-1-0.812-0.74829.846-0.236-0.2360.0000.0000.0000.000
206A150ILE00.111-0.10227.628-0.016-0.0160.0000.0000.0000.000
207A150ILE0-0.0620.09124.675-0.005-0.0050.0000.0000.0000.000
208A151ALA00.047-0.11428.8520.0040.0040.0000.0000.0000.000
209A151ALA0-0.0440.14432.4980.0030.0030.0000.0000.0000.000
210A152PRO0-0.040-0.12731.008-0.004-0.0040.0000.0000.0000.000
211A153SER00.1010.02932.152-0.003-0.0030.0000.0000.0000.000
212A153SER0-0.0220.08136.2470.0020.0020.0000.0000.0000.000
213A154ASN00.037-0.07635.347-0.002-0.0020.0000.0000.0000.000
214A154ASN0-0.0770.07833.070-0.005-0.0050.0000.0000.0000.000
215A155GLU00.106-0.10236.6180.0030.0030.0000.0000.0000.000
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