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

tag_button

FMODB ID: J28L9

Calculation Name: 2DP9-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2DP9

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM30

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
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 -1080040.714163
FMO2-HF: Nuclear repulsion 1030148.409354
FMO2-HF: Total energy -49892.304809
FMO2-MP2: Total energy -50039.467428


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:-2:MET)


Summations of interaction energy for fragment #1(A:-2:MET)
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.
-8.283-3.7842.135-2.009-4.622-0.004
Interaction energy analysis for fragmet #1(A:-2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.075 / 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].
4A-1ASP-1-0.997-0.8364.087-0.6960.1880.008-0.412-0.4790.000
5A0TYR0-0.013-0.1423.807-3.293-2.026-0.004-0.665-0.5970.003
6A0TYR0-0.0020.1343.397-1.404-0.5550.1880.038-1.075-0.005
7A1MET00.134-0.0974.9900.9270.992-0.002-0.003-0.0600.000
8A1MET0-0.1140.0969.656-0.041-0.0410.0000.0000.0000.000
9A2GLU0-0.016-0.1398.1490.2900.2900.0000.0000.0000.000
10A2GLU-1-0.933-0.8256.894-0.792-0.7920.0000.0000.0000.000
11A3ARG00.052-0.1177.7350.1700.1700.0000.0000.0000.000
12A3ARG10.8911.0945.694-2.817-2.8170.0000.0000.0000.000
13A4PRO0-0.008-0.0978.700-0.202-0.2020.0000.0000.0000.000
14A5LYS00.088-0.00211.5210.0910.0910.0000.0000.0000.000
15A5LYS10.8981.07215.0160.0120.0120.0000.0000.0000.000
16A6LEU00.011-0.14314.7420.0260.0260.0000.0000.0000.000
17A6LEU0-0.0430.13916.270-0.005-0.0050.0000.0000.0000.000
18A7GLY00.028-0.07314.3820.0470.0470.0000.0000.0000.000
19A8LEU00.090-0.06015.731-0.056-0.0560.0000.0000.0000.000
20A8LEU0-0.0740.15716.311-0.007-0.0070.0000.0000.0000.000
21A9ILE00.090-0.08116.9360.0710.0710.0000.0000.0000.000
22A9ILE0-0.1480.05420.563-0.004-0.0040.0000.0000.0000.000
23A10VAL00.040-0.14017.636-0.069-0.0690.0000.0000.0000.000
24A10VAL0-0.0210.15516.385-0.001-0.0010.0000.0000.0000.000
25A11ARG00.053-0.09118.9270.0550.0550.0000.0000.0000.000
26A11ARG10.8981.06722.569-0.264-0.2640.0000.0000.0000.000
27A12GLU00.043-0.09219.348-0.002-0.0020.0000.0000.0000.000
28A12GLU-1-0.832-0.78117.3750.5770.5770.0000.0000.0000.000
29A13PRO0-0.011-0.12219.679-0.034-0.0340.0000.0000.0000.000
30A14TYR00.127-0.00717.8790.0460.0460.0000.0000.0000.000
31A14TYR0-0.0550.10318.724-0.008-0.0080.0000.0000.0000.000
32A15ALA00.114-0.06715.449-0.020-0.0200.0000.0000.0000.000
33A15ALA0-0.0580.08915.5360.0080.0080.0000.0000.0000.000
34A16SER00.002-0.10713.5810.0850.0850.0000.0000.0000.000
35A16SER0-0.0220.07315.2210.0340.0340.0000.0000.0000.000
36A17LEU00.080-0.08513.0490.1050.1050.0000.0000.0000.000
37A17LEU0-0.0890.09716.188-0.011-0.0110.0000.0000.0000.000
38A18ILE00.081-0.08312.600-0.040-0.0400.0000.0000.0000.000
39A18ILE0-0.1130.07311.0680.0000.0000.0000.0000.0000.000
40A19VAL00.052-0.0638.883-0.155-0.1550.0000.0000.0000.000
41A19VAL0-0.1200.0658.9020.0060.0060.0000.0000.0000.000
42A20ASP00.080-0.0838.1060.3960.3960.0000.0000.0000.000
43A20ASP-1-0.933-0.81611.1151.1151.1150.0000.0000.0000.000
44A21GLY0-0.002-0.1169.637-0.088-0.0880.0000.0000.0000.000
45A22ARG00.050-0.01810.206-0.157-0.1570.0000.0000.0000.000
46A22ARG10.8611.05614.037-0.297-0.2970.0000.0000.0000.000
47A23LYS00.158-0.03813.495-0.060-0.0600.0000.0000.0000.000
48A23LYS10.5970.94814.991-0.108-0.1080.0000.0000.0000.000
49A24VAL00.067-0.12313.7480.0600.0600.0000.0000.0000.000
50A24VAL0-0.0050.14712.774-0.008-0.0080.0000.0000.0000.000
51A25TRP00.077-0.09514.743-0.051-0.0510.0000.0000.0000.000
52A25TRP0-0.0660.11017.7890.0150.0150.0000.0000.0000.000
53A26GLU00.107-0.08517.7090.0430.0430.0000.0000.0000.000
54A26GLU-1-0.900-0.81016.7690.1710.1710.0000.0000.0000.000
55A27ILE00.044-0.14018.610-0.031-0.0310.0000.0000.0000.000
56A27ILE0-0.0430.14422.0330.0030.0030.0000.0000.0000.000
57A28ARG00.026-0.12422.4020.0300.0300.0000.0000.0000.000
58A28ARG10.7511.02619.921-0.148-0.1480.0000.0000.0000.000
59A29ARG00.145-0.08524.236-0.016-0.0160.0000.0000.0000.000
60A29ARG10.8011.03027.993-0.058-0.0580.0000.0000.0000.000
61A30ARG00.001-0.10126.073-0.007-0.0070.0000.0000.0000.000
62A30ARG10.8931.07126.8550.0020.0020.0000.0000.0000.000
63A31LYS00.097-0.07924.4460.0090.0090.0000.0000.0000.000
64A31LYS10.9131.08225.2840.0660.0660.0000.0000.0000.000
65A32THR00.021-0.09621.9820.0180.0180.0000.0000.0000.000
66A32THR0-0.0260.06820.128-0.005-0.0050.0000.0000.0000.000
67A33ARG00.064-0.10522.285-0.021-0.0210.0000.0000.0000.000
68A33ARG10.7611.00523.2360.1060.1060.0000.0000.0000.000
69A34HIS00.128-0.07618.919-0.039-0.0390.0000.0000.0000.000
70A34HIS0-0.1030.09514.4740.0170.0170.0000.0000.0000.000
71A35ARG00.029-0.13416.2730.0190.0190.0000.0000.0000.000
72A35ARG10.8031.05416.6060.2390.2390.0000.0000.0000.000
73A36GLY00.000-0.07912.4870.0130.0130.0000.0000.0000.000
74A37PRO00.0400.0248.7070.0960.0960.0000.0000.0000.000
75A38LEU00.099-0.05210.4600.0490.0490.0000.0000.0000.000
76A38LEU0-0.1320.12312.708-0.006-0.0060.0000.0000.0000.000
77A39GLY0-0.008-0.09211.0300.1080.1080.0000.0000.0000.000
78A40ILE00.081-0.04611.720-0.187-0.1870.0000.0000.0000.000
79A40ILE0-0.0660.14511.237-0.005-0.0050.0000.0000.0000.000
80A41VAL00.144-0.10213.3860.1540.1540.0000.0000.0000.000
81A41VAL0-0.1530.08516.050-0.013-0.0130.0000.0000.0000.000
82A42SER00.031-0.11516.415-0.097-0.0970.0000.0000.0000.000
83A42SER00.0160.12216.889-0.021-0.0210.0000.0000.0000.000
84A43GLY0-0.037-0.10318.2430.0340.0340.0000.0000.0000.000
85A44GLY0-0.095-0.06120.847-0.005-0.0050.0000.0000.0000.000
86A45ARG00.058-0.02717.748-0.039-0.0390.0000.0000.0000.000
87A45ARG10.9021.10216.981-0.566-0.5660.0000.0000.0000.000
88A46LEU00.156-0.08614.168-0.063-0.0630.0000.0000.0000.000
89A46LEU0-0.1040.12312.090-0.030-0.0300.0000.0000.0000.000
90A47ILE00.003-0.12912.3410.1400.1400.0000.0000.0000.000
91A47ILE0-0.0790.09812.047-0.024-0.0240.0000.0000.0000.000
92A48GLY00.102-0.0688.4340.3330.3330.0000.0000.0000.000
93A49GLN00.033-0.0147.464-0.333-0.3330.0000.0000.0000.000
94A49GLN00.0060.1495.9930.4680.4680.0000.0000.0000.000
95A50ALA00.099-0.0737.2790.2470.2470.0000.0000.0000.000
96A50ALA0-0.0460.1129.5760.0030.0030.0000.0000.0000.000
97A51ASP00.084-0.1158.7750.1950.1950.0000.0000.0000.000
98A51ASP-1-0.922-0.8028.099-1.441-1.4410.0000.0000.0000.000
99A52LEU00.123-0.09110.278-0.008-0.0080.0000.0000.0000.000
100A52LEU0-0.1750.08714.6280.0240.0240.0000.0000.0000.000
101A53VAL0-0.045-0.18314.0740.0120.0120.0000.0000.0000.000
102A53VAL0-0.0260.17312.7870.0060.0060.0000.0000.0000.000
103A54GLY00.012-0.11515.476-0.004-0.0040.0000.0000.0000.000
104A55VAL00.0600.00918.8570.0160.0160.0000.0000.0000.000
105A55VAL0-0.1360.05420.6620.0060.0060.0000.0000.0000.000
106A56GLU00.105-0.09521.586-0.010-0.0100.0000.0000.0000.000
107A56GLU-1-0.989-0.84021.714-0.204-0.2040.0000.0000.0000.000
108A57GLY00.007-0.08023.9070.0240.0240.0000.0000.0000.000
109A58PRO0-0.099-0.07627.305-0.011-0.0110.0000.0000.0000.000
110A59PHE00.0790.01028.614-0.009-0.0090.0000.0000.0000.000
111A59PHE0-0.0810.08024.696-0.001-0.0010.0000.0000.0000.000
112A60SER0-0.009-0.07029.8300.0090.0090.0000.0000.0000.000
113A60SER00.0360.09733.4740.0020.0020.0000.0000.0000.000
114A61VAL00.118-0.12330.587-0.005-0.0050.0000.0000.0000.000
115A61VAL0-0.0760.10230.8320.0020.0020.0000.0000.0000.000
116A62GLU00.051-0.12630.7710.0020.0020.0000.0000.0000.000
117A62GLU-1-0.889-0.80734.524-0.004-0.0040.0000.0000.0000.000
118A63GLU00.075-0.11430.8960.0000.0000.0000.0000.0000.000
119A63GLU-1-0.936-0.80830.367-0.057-0.0570.0000.0000.0000.000
120A64LEU00.045-0.09926.983-0.016-0.0160.0000.0000.0000.000
121A64LEU0-0.0600.09424.8570.0020.0020.0000.0000.0000.000
122A65LEU00.041-0.09526.636-0.003-0.0030.0000.0000.0000.000
123A65LEU0-0.0500.11528.7550.0020.0020.0000.0000.0000.000
124A66ALA00.073-0.10628.6020.0080.0080.0000.0000.0000.000
125A66ALA0-0.0750.11828.923-0.002-0.0020.0000.0000.0000.000
126A67HIS0-0.003-0.08124.368-0.012-0.0120.0000.0000.0000.000
127A67HIS0-0.1220.04223.320-0.011-0.0110.0000.0000.0000.000
128A68GLN00.200-0.09823.1650.0000.0000.0000.0000.0000.000
129A68GLN0-0.0580.11524.674-0.012-0.0120.0000.0000.0000.000
130A69GLU00.028-0.14521.5830.0320.0320.0000.0000.0000.000
131A69GLU-1-0.862-0.79620.903-0.080-0.0800.0000.0000.0000.000
132A70LYS00.046-0.10518.7080.0110.0110.0000.0000.0000.000
133A70LYS10.8191.07119.4680.1780.1780.0000.0000.0000.000
134A71HIS00.028-0.09518.2200.0070.0070.0000.0000.0000.000
135A71HIS0-0.0630.08421.2170.0190.0190.0000.0000.0000.000
136A72LEU00.047-0.10720.3540.0280.0280.0000.0000.0000.000
137A72LEU0-0.0950.09617.9230.0150.0150.0000.0000.0000.000
138A73ALA00.135-0.10521.7160.0320.0320.0000.0000.0000.000
139A73ALA0-0.1090.09423.284-0.001-0.0010.0000.0000.0000.000
140A74GLU00.140-0.09624.242-0.019-0.0190.0000.0000.0000.000
141A74GLU-1-1.036-0.84526.9030.0930.0930.0000.0000.0000.000
142A75GLU00.142-0.12727.7260.0020.0020.0000.0000.0000.000
143A75GLU-1-0.865-0.73631.0970.0270.0270.0000.0000.0000.000
144A76ALA00.086-0.10930.576-0.006-0.0060.0000.0000.0000.000
145A76ALA0-0.0580.11932.0120.0010.0010.0000.0000.0000.000
146A77PHE00.022-0.13028.695-0.005-0.0050.0000.0000.0000.000
147A77PHE0-0.0800.08626.9020.0030.0030.0000.0000.0000.000
148A78LEU00.058-0.11228.6350.0060.0060.0000.0000.0000.000
149A78LEU0-0.0540.12725.882-0.001-0.0010.0000.0000.0000.000
150A79ARG00.099-0.08429.397-0.003-0.0030.0000.0000.0000.000
151A79ARG10.7530.99333.203-0.020-0.0200.0000.0000.0000.000
152A80ALA00.079-0.10432.876-0.007-0.0070.0000.0000.0000.000
153A80ALA0-0.0740.11332.4670.0020.0020.0000.0000.0000.000
154A81TYR00.032-0.11829.3980.0020.0020.0000.0000.0000.000
155A81TYR0-0.1150.07225.9480.0010.0010.0000.0000.0000.000
156A82ALA00.110-0.12330.8820.0040.0040.0000.0000.0000.000
157A82ALA0-0.0300.13430.881-0.001-0.0010.0000.0000.0000.000
158A83LYS0-0.081-0.13331.809-0.004-0.0040.0000.0000.0000.000
159A83LYS10.8461.06034.121-0.061-0.0610.0000.0000.0000.000
160A84ASP00.080-0.08535.453-0.001-0.0010.0000.0000.0000.000
161A84ASP-1-0.978-0.85138.2920.0090.0090.0000.0000.0000.000
162A85GLU00.039-0.13534.634-0.006-0.0060.0000.0000.0000.000
163A85GLU-1-1.032-0.84933.8650.0240.0240.0000.0000.0000.000
164A86PRO0-0.010-0.13032.1820.0010.0010.0000.0000.0000.000
165A87LEU00.000-0.03328.1020.0080.0080.0000.0000.0000.000
166A87LEU0-0.0470.12227.0380.0040.0040.0000.0000.0000.000
167A88TYR00.091-0.07125.377-0.012-0.0120.0000.0000.0000.000
168A88TYR0-0.0970.07024.705-0.006-0.0060.0000.0000.0000.000
169A89ALA00.147-0.10721.8070.0300.0300.0000.0000.0000.000
170A89ALA0-0.0650.13421.180-0.002-0.0020.0000.0000.0000.000
171A90TRP00.056-0.10218.669-0.039-0.0390.0000.0000.0000.000
172A90TRP0-0.1320.04017.8290.0170.0170.0000.0000.0000.000
173A91VAL00.129-0.11016.8340.0580.0580.0000.0000.0000.000
174A91VAL0-0.0900.12115.709-0.002-0.0020.0000.0000.0000.000
175A92LEU00.056-0.11812.779-0.056-0.0560.0000.0000.0000.000
176A92LEU0-0.1020.07411.8230.0370.0370.0000.0000.0000.000
177A93GLU00.082-0.10110.2520.1210.1210.0000.0000.0000.000
178A93GLU-1-0.925-0.83210.361-1.130-1.1300.0000.0000.0000.000
179A94ASN0-0.002-0.1196.1770.2970.2970.0000.0000.0000.000
180A94ASN0-0.0960.0765.641-0.472-0.4720.0000.0000.0000.000
181A95ALA00.170-0.1025.202-0.126-0.1260.0000.0000.0000.000
182A95ALA0-0.0800.1108.0540.0100.0100.0000.0000.0000.000
183A96PHE00.036-0.0733.640-0.920-0.8380.023-0.001-0.1040.000
184A96PHE0-0.0610.0812.9771.0642.4191.924-0.965-2.314-0.002
185A97ARG00.118-0.1035.087-0.146-0.149-0.002-0.0010.0070.000
186A97ARG10.6860.9848.500-1.454-1.4540.0000.0000.0000.000
187A98TYR00.080-0.1136.9191.0851.0850.0000.0000.0000.000
188A98TYR0-0.1540.0416.199-0.445-0.4450.0000.0000.0000.000
189A99GLU00.060-0.1128.085-0.610-0.6100.0000.0000.0000.000
190A99GLU-1-0.936-0.8107.4974.0924.0920.0000.0000.0000.000
191A100LYS00.007-0.14610.016-0.402-0.4020.0000.0000.0000.000
192A100LYS10.8661.07613.274-1.139-1.1390.0000.0000.0000.000
193A101PRO00.022-0.07412.3870.0720.0720.0000.0000.0000.000
194A102LEU00.037-0.03213.927-0.103-0.1030.0000.0000.0000.000
195A102LEU0-0.0170.14511.482-0.051-0.0510.0000.0000.0000.000
196A103HIS00.127-0.08215.378-0.035-0.0350.0000.0000.0000.000
197A103HIS0-0.0860.08420.0360.0100.0100.0000.0000.0000.000
198A104VAL00.073-0.12718.5300.0100.0100.0000.0000.0000.000
199A104VAL0-0.0830.13717.464-0.008-0.0080.0000.0000.0000.000
200A105PRO00.032-0.06419.832-0.028-0.0280.0000.0000.0000.000
201A106ARG00.081-0.00423.3520.0000.0000.0000.0000.0000.000
202A106ARG10.9321.09924.670-0.305-0.3050.0000.0000.0000.000
203A107ARG00.034-0.09325.879-0.009-0.0090.0000.0000.0000.000
204A107ARG10.9311.08327.092-0.200-0.2000.0000.0000.0000.000
205A108PRO0-0.016-0.11028.5140.0090.0090.0000.0000.0000.000
206A109GLY00.0720.02228.924-0.008-0.0080.0000.0000.0000.000
207A110ARG00.1070.01324.953-0.004-0.0040.0000.0000.0000.000
208A110ARG10.7370.99622.862-0.318-0.3180.0000.0000.0000.000
209A111VAL00.096-0.11924.505-0.013-0.0130.0000.0000.0000.000
210A111VAL0-0.0310.14623.9320.0000.0000.0000.0000.0000.000
211A112MET00.016-0.11023.2860.0260.0260.0000.0000.0000.000
212A112MET0-0.1000.07922.7880.0120.0120.0000.0000.0000.000
213A113PHE00.074-0.11223.598-0.009-0.0090.0000.0000.0000.000
214A113PHE0-0.0440.12421.887-0.002-0.0020.0000.0000.0000.000
215A114VAL00.066-0.12024.4780.0110.0110.0000.0000.0000.000
216A114VAL0-0.0460.11828.2120.0000.0000.0000.0000.0000.000
217A115ASP00.127-0.08324.242-0.006-0.0060.0000.0000.0000.000
218A115ASP-1-0.873-0.74323.394-0.023-0.0230.0000.0000.0000.000
219A116LEU0-0.008-0.14024.9720.0010.0010.0000.0000.0000.000
220A116LEU0-0.0400.12327.636-0.001-0.0010.0000.0000.0000.000
221A117SER00.068-0.09324.477-0.005-0.0050.0000.0000.0000.000
222A117SER0-0.0530.07323.765-0.008-0.0080.0000.0000.0000.000
223A118GLU00.026-0.10425.928-0.019-0.0190.0000.0000.0000.000
224A118GLU-1-0.912-0.82126.246-0.080-0.0800.0000.0000.0000.000
225A119VAL00.008-0.13228.5410.0010.0010.0000.0000.0000.000
226A119VAL0-0.0440.13430.3380.0020.0020.0000.0000.0000.000
227A120ARG00.017-0.12031.566-0.010-0.0100.0000.0000.0000.000
228A120ARG10.8801.07234.3620.0530.0530.0000.0000.0000.000
229A121TRP00.008-0.09133.8540.0090.0090.0000.0000.0000.000
230A121TRP00.0500.03430.0720.0020.0020.0000.0000.0000.000