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: VK9M1

Calculation Name: 2R39-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2R39

Chain ID: A

ChEMBL ID:

UniProt ID: Q87KC5

Base Structure: X-ray

Registration Date: 2025-07-09

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -864494.030467
FMO2-HF: Nuclear repulsion 820952.545548
FMO2-HF: Total energy -43541.48492
FMO2-MP2: Total energy -43669.47765


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:377:VAL)


Summations of interaction energy for fragment #1(A:377:VAL)
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.
0.0871.455-0.007-0.653-0.7080.004
Interaction energy analysis for fragmet #1(A:377:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : 0.020
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].
4A378ASP-1-1.005-0.8274.5013.1733.5860.000-0.134-0.2790.000
5A379PRO00.001-0.0853.815-2.514-1.559-0.007-0.519-0.4290.004
6A380ALA00.081-0.0086.4820.1050.1050.0000.0000.0000.000
7A380ALA0-0.0030.1289.8730.0690.0690.0000.0000.0000.000
8A381GLY0-0.071-0.1377.4520.2260.2260.0000.0000.0000.000
9A382MET00.1440.0019.407-0.116-0.1160.0000.0000.0000.000
10A382MET0-0.0900.13513.125-0.018-0.0180.0000.0000.0000.000
11A383SER0-0.065-0.08812.4380.1360.1360.0000.0000.0000.000
12A383SER0-0.0310.06013.801-0.003-0.0030.0000.0000.0000.000
13A384VAL00.063-0.12214.961-0.062-0.0620.0000.0000.0000.000
14A384VAL0-0.0410.12417.3390.0030.0030.0000.0000.0000.000
15A385ILE00.065-0.09618.6470.0430.0430.0000.0000.0000.000
16A385ILE0-0.0560.10120.037-0.002-0.0020.0000.0000.0000.000
17A386ARG00.154-0.07121.713-0.023-0.0230.0000.0000.0000.000
18A386ARG10.7571.03924.588-0.092-0.0920.0000.0000.0000.000
19A387ASP00.019-0.14824.8990.0130.0130.0000.0000.0000.000
20A387ASP-1-0.910-0.76027.2230.0190.0190.0000.0000.0000.000
21A388ARG00.169-0.07027.7490.0080.0080.0000.0000.0000.000
22A388ARG10.8381.06228.980-0.077-0.0770.0000.0000.0000.000
23A389ASN00.089-0.07929.9080.0060.0060.0000.0000.0000.000
24A389ASN0-0.1430.05533.0070.0020.0020.0000.0000.0000.000
25A390GLN00.094-0.09732.758-0.009-0.0090.0000.0000.0000.000
26A390GLN0-0.1500.09129.028-0.003-0.0030.0000.0000.0000.000
27A391LEU00.106-0.09933.6080.0040.0040.0000.0000.0000.000
28A391LEU0-0.0800.10035.824-0.001-0.0010.0000.0000.0000.000
29A392PHE0-0.040-0.11035.599-0.003-0.0030.0000.0000.0000.000
30A392PHE0-0.1100.05634.5010.0010.0010.0000.0000.0000.000
31A393ARG00.081-0.11837.0550.0030.0030.0000.0000.0000.000
32A393ARG10.8581.04536.9490.0030.0030.0000.0000.0000.000
33A394VAL00.268-0.12938.660-0.003-0.0030.0000.0000.0000.000
34A394VAL0-0.2430.05940.7250.0010.0010.0000.0000.0000.000
35A395ASN00.2900.26638.103-0.001-0.0010.0000.0000.0000.000
36A395ASN0-0.046-0.04736.306-0.003-0.0030.0000.0000.0000.000
37A396SER0-0.118-0.15938.7210.0000.0000.0000.0000.0000.000
38A396SER0-0.0240.07937.672-0.002-0.0020.0000.0000.0000.000
39A397ALA00.028-0.19139.171-0.004-0.0040.0000.0000.0000.000
40A397ALA0-0.1480.11838.6240.0010.0010.0000.0000.0000.000
41A398GLY0-0.021-0.06140.6050.0010.0010.0000.0000.0000.000
42A399GLU00.106-0.03937.5940.0040.0040.0000.0000.0000.000
43A399GLU-1-0.804-0.66636.3120.0180.0180.0000.0000.0000.000
44A400VAL00.066-0.05937.171-0.006-0.0060.0000.0000.0000.000
45A400VAL0-0.0950.05935.6150.0020.0020.0000.0000.0000.000
46A401GLU00.196-0.09933.7560.0040.0040.0000.0000.0000.000
47A401GLU-1-0.953-0.79032.8310.0040.0040.0000.0000.0000.000
48A402ASN00.036-0.13630.1720.0030.0030.0000.0000.0000.000
49A402ASN0-0.0880.06529.2480.0140.0140.0000.0000.0000.000
50A403THR0-0.031-0.07128.850-0.002-0.0020.0000.0000.0000.000
51A403THR0-0.0640.03329.0580.0010.0010.0000.0000.0000.000
52A404TYR00.070-0.10024.4810.0150.0150.0000.0000.0000.000
53A404TYR0-0.0540.07223.4390.0030.0030.0000.0000.0000.000
54A405THR00.049-0.06722.806-0.015-0.0150.0000.0000.0000.000
55A405THR0-0.0470.07921.366-0.006-0.0060.0000.0000.0000.000
56A406LEU00.020-0.11719.0180.0360.0360.0000.0000.0000.000
57A406LEU0-0.0100.12118.399-0.002-0.0020.0000.0000.0000.000
58A407LYS00.154-0.05916.592-0.034-0.0340.0000.0000.0000.000
59A407LYS10.8111.04414.9060.1090.1090.0000.0000.0000.000
60A408VAL00.027-0.10713.9050.0670.0670.0000.0000.0000.000
61A408VAL0-0.0140.12013.7730.0050.0050.0000.0000.0000.000
62A409ILE00.040-0.08311.5760.0330.0330.0000.0000.0000.000
63A409ILE0-0.1200.0719.6770.0220.0220.0000.0000.0000.000
64A410ASN00.216-0.07910.763-0.032-0.0320.0000.0000.0000.000
65A410ASN0-0.1220.12211.091-0.266-0.2660.0000.0000.0000.000
66A411LYS00.001-0.1236.6300.3690.3690.0000.0000.0000.000
67A411LYS10.8221.0545.1610.8790.8790.0000.0000.0000.000
68A412THR00.036-0.0626.985-0.919-0.9190.0000.0000.0000.000
69A412THR0-0.0490.0337.8060.1140.1140.0000.0000.0000.000
70A413GLN00.076-0.0869.0430.1860.1860.0000.0000.0000.000
71A413GLN0-0.1060.07210.141-0.164-0.1640.0000.0000.0000.000
72A414GLN00.058-0.12111.9920.1610.1610.0000.0000.0000.000
73A414GLN0-0.0480.09913.7530.0090.0090.0000.0000.0000.000
74A415VAL00.111-0.07113.768-0.135-0.1350.0000.0000.0000.000
75A415VAL0-0.0340.11018.0690.0070.0070.0000.0000.0000.000
76A416GLN00.001-0.10914.3080.0080.0080.0000.0000.0000.000
77A416GLN0-0.0800.09612.2150.1000.1000.0000.0000.0000.000
78A417GLU00.124-0.10515.7380.0260.0260.0000.0000.0000.000
79A417GLU-1-1.029-0.87119.107-0.240-0.2400.0000.0000.0000.000
80A418TYR00.003-0.10216.465-0.014-0.0140.0000.0000.0000.000
81A418TYR0-0.0850.07511.5800.0090.0090.0000.0000.0000.000
82A419ASN00.100-0.09817.3660.0030.0030.0000.0000.0000.000
83A419ASN0-0.0460.11119.917-0.017-0.0170.0000.0000.0000.000
84A420LEU00.044-0.08318.4600.0060.0060.0000.0000.0000.000
85A420LEU0-0.1170.06617.6260.0000.0000.0000.0000.0000.000
86A421ASP00.104-0.08120.305-0.016-0.0160.0000.0000.0000.000
87A421ASP-1-0.991-0.86221.1970.0110.0110.0000.0000.0000.000
88A422VAL00.086-0.09421.3820.0160.0160.0000.0000.0000.000
89A422VAL0-0.0580.09123.7400.0000.0000.0000.0000.0000.000
90A423LYS0-0.009-0.09623.251-0.015-0.0150.0000.0000.0000.000
91A423LYS10.8811.07421.449-0.225-0.2250.0000.0000.0000.000
92A424GLY00.040-0.12524.7500.0150.0150.0000.0000.0000.000
93A425LEU00.041-0.01127.3020.0050.0050.0000.0000.0000.000
94A425LEU0-0.0480.11428.6290.0000.0000.0000.0000.0000.000
95A426ASN00.046-0.06630.321-0.002-0.0020.0000.0000.0000.000
96A426ASN0-0.1110.04932.7390.0060.0060.0000.0000.0000.000
97A427ASP00.068-0.11533.349-0.004-0.0040.0000.0000.0000.000
98A427ASP-1-0.915-0.83136.1090.0420.0420.0000.0000.0000.000
99A428VAL00.029-0.09431.1700.0050.0050.0000.0000.0000.000
100A428VAL0-0.0760.05729.3570.0030.0030.0000.0000.0000.000
101A429SER00.001-0.10632.633-0.003-0.0030.0000.0000.0000.000
102A429SER0-0.0750.01333.901-0.002-0.0020.0000.0000.0000.000
103A430TRP00.128-0.10128.7080.0100.0100.0000.0000.0000.000
104A430TRP0-0.0980.09522.3300.0120.0120.0000.0000.0000.000
105A431TYR0-0.023-0.15329.234-0.008-0.0080.0000.0000.0000.000
106A431TYR0-0.1420.11730.923-0.004-0.0040.0000.0000.0000.000
107A432GLY00.107-0.08427.1930.0020.0020.0000.0000.0000.000
108A433LYS00.014-0.03624.0020.0060.0060.0000.0000.0000.000
109A433LYS10.9121.09423.2160.1610.1610.0000.0000.0000.000
110A434GLN00.125-0.08623.8100.0100.0100.0000.0000.0000.000
111A434GLN0-0.0660.12324.849-0.007-0.0070.0000.0000.0000.000
112A435THR00.056-0.08921.8260.0040.0040.0000.0000.0000.000
113A435THR0-0.0150.09822.0440.0100.0100.0000.0000.0000.000
114A436ILE0-0.078-0.11720.4840.0160.0160.0000.0000.0000.000
115A436ILE0-0.0630.06417.5820.0030.0030.0000.0000.0000.000
116A437GLN00.114-0.08619.466-0.014-0.0140.0000.0000.0000.000
117A437GLN0-0.0680.10320.783-0.006-0.0060.0000.0000.0000.000
118A438VAL00.083-0.07716.1920.0550.0550.0000.0000.0000.000
119A438VAL0-0.1220.07714.9790.0000.0000.0000.0000.0000.000
120A439GLU00.126-0.09416.139-0.085-0.0850.0000.0000.0000.000
121A439GLU-1-0.958-0.84317.749-0.533-0.5330.0000.0000.0000.000
122A440PRO0-0.015-0.09812.998-0.065-0.0650.0000.0000.0000.000
123A441GLY0-0.014-0.00311.5840.0860.0860.0000.0000.0000.000
124A442GLU00.075-0.04712.5640.0830.0830.0000.0000.0000.000
125A442GLU-1-0.944-0.79116.073-0.454-0.4540.0000.0000.0000.000
126A443VAL00.046-0.12014.348-0.068-0.0680.0000.0000.0000.000
127A443VAL0-0.1210.07713.8270.0180.0180.0000.0000.0000.000
128A444LEU00.030-0.13315.9590.0360.0360.0000.0000.0000.000
129A444LEU0-0.0290.14117.9130.0170.0170.0000.0000.0000.000
130A445ASN00.131-0.07418.0460.0190.0190.0000.0000.0000.000
131A445ASN0-0.1420.05820.8910.0080.0080.0000.0000.0000.000
132A446LEU0-0.034-0.14820.733-0.004-0.0040.0000.0000.0000.000
133A446LEU0-0.0660.11419.4800.0020.0020.0000.0000.0000.000
134A447PRO00.028-0.09622.4480.0230.0230.0000.0000.0000.000
135A448MET00.0850.00025.528-0.015-0.0150.0000.0000.0000.000
136A448MET0-0.1010.10023.9760.0020.0020.0000.0000.0000.000
137A449SER0-0.023-0.08126.8640.0110.0110.0000.0000.0000.000
138A449SER0-0.0520.04030.503-0.002-0.0020.0000.0000.0000.000
139A450LEU00.070-0.12229.093-0.010-0.0100.0000.0000.0000.000
140A450LEU0-0.0830.10325.9400.0030.0030.0000.0000.0000.000
141A451GLY00.034-0.08129.9800.0020.0020.0000.0000.0000.000
142A452ALA00.1220.03933.376-0.001-0.0010.0000.0000.0000.000
143A452ALA0-0.0370.10233.2190.0020.0020.0000.0000.0000.000
144A453ASP00.128-0.13035.069-0.002-0.0020.0000.0000.0000.000
145A453ASP-1-0.920-0.77338.7520.0410.0410.0000.0000.0000.000
146A454PRO0-0.077-0.15538.1820.0070.0070.0000.0000.0000.000
147A455ASP00.126-0.00939.3810.0080.0080.0000.0000.0000.000
148A455ASP-1-0.990-0.82942.5820.0430.0430.0000.0000.0000.000
149A456LYS00.011-0.09938.6750.0020.0020.0000.0000.0000.000
150A456LYS10.8611.06038.069-0.047-0.0470.0000.0000.0000.000
151A457LEU00.030-0.11035.7460.0060.0060.0000.0000.0000.000
152A457LEU0-0.1260.07033.8690.0000.0000.0000.0000.0000.000
153A458ASN00.135-0.04335.410-0.004-0.0040.0000.0000.0000.000
154A458ASN0-0.1150.05733.916-0.006-0.0060.0000.0000.0000.000
155A459SER00.040-0.08135.779-0.004-0.0040.0000.0000.0000.000
156A459SER0-0.0240.05634.5920.0010.0010.0000.0000.0000.000
157A460ALA00.079-0.10435.594-0.002-0.0020.0000.0000.0000.000
158A460ALA0-0.0870.11236.685-0.001-0.0010.0000.0000.0000.000
159A461ILE00.028-0.10332.214-0.008-0.0080.0000.0000.0000.000
160A461ILE0-0.0590.09530.1880.0010.0010.0000.0000.0000.000
161A462THR0-0.010-0.09830.2970.0080.0080.0000.0000.0000.000
162A462THR00.0170.11129.039-0.004-0.0040.0000.0000.0000.000
163A463THR00.030-0.08326.331-0.008-0.0080.0000.0000.0000.000
164A463THR0-0.0390.06724.379-0.005-0.0050.0000.0000.0000.000
165A464ILE00.035-0.07924.642-0.001-0.0010.0000.0000.0000.000
166A464ILE0-0.0630.09123.826-0.004-0.0040.0000.0000.0000.000
167A465GLN00.058-0.18120.4750.0230.0230.0000.0000.0000.000
168A465GLN0-0.0090.16218.614-0.026-0.0260.0000.0000.0000.000
169A466PHE00.097-0.05619.588-0.022-0.0220.0000.0000.0000.000
170A466PHE0-0.1030.09518.894-0.002-0.0020.0000.0000.0000.000
171A467ILE00.099-0.11116.8660.0580.0580.0000.0000.0000.000
172A467ILE0-0.0930.11016.7580.0020.0020.0000.0000.0000.000
173A468LEU00.102-0.10614.684-0.032-0.0320.0000.0000.0000.000
174A468LEU0-0.1170.08212.541-0.009-0.0090.0000.0000.0000.000
175A469THR00.065-0.07814.6400.0500.0500.0000.0000.0000.000
176A469THR0-0.0690.06516.7100.0200.0200.0000.0000.0000.000
177A470ASP00.129-0.08513.0050.0030.0030.0000.0000.0000.000
178A470ASP-1-0.884-0.79611.786-0.812-0.8120.0000.0000.0000.000
179A471LYS00.146-0.04813.688-0.011-0.0110.0000.0000.0000.000
180A471LYS10.8771.04617.8460.1890.1890.0000.0000.0000.000
181A472SER0-0.005-0.08715.3740.0580.0580.0000.0000.0000.000
182A472SER0-0.0290.07114.382-0.037-0.0370.0000.0000.0000.000
183A473ASN0-0.011-0.07410.5560.0170.0170.0000.0000.0000.000
184A473ASN0-0.1320.0189.572-0.185-0.1850.0000.0000.0000.000
185A474GLU00.112-0.09210.633-0.014-0.0140.0000.0000.0000.000
186A474GLU-1-1.065-0.88512.613-0.011-0.0110.0000.0000.0000.000
187A475PHE00.075-0.08910.1520.1700.1700.0000.0000.0000.000
188A475PHE0-0.0950.0727.480-0.238-0.2380.0000.0000.0000.000
189A476THR0-0.024-0.10111.306-0.131-0.1310.0000.0000.0000.000
190A476THR0-0.0580.02514.1940.0160.0160.0000.0000.0000.000
191A477ILE00.109-0.07911.4240.1690.1690.0000.0000.0000.000
192A477ILE0-0.0930.0849.571-0.022-0.0220.0000.0000.0000.000
193A478GLU00.054-0.09712.245-0.134-0.1340.0000.0000.0000.000
194A478GLU-1-0.924-0.78314.2660.5270.5270.0000.0000.0000.000
195A479VAL00.052-0.11614.3670.1200.1200.0000.0000.0000.000
196A479VAL0-0.1010.09814.024-0.010-0.0100.0000.0000.0000.000
197A480GLU00.149-0.11416.403-0.066-0.0660.0000.0000.0000.000
198A480GLU-1-0.962-0.79019.4070.3450.3450.0000.0000.0000.000
199A481SER0-0.028-0.07919.6890.0070.0070.0000.0000.0000.000
200A481SER0-0.0090.06521.410-0.012-0.0120.0000.0000.0000.000
201A482ARG00.076-0.12222.5560.0140.0140.0000.0000.0000.000
202A482ARG10.7450.99223.657-0.242-0.2420.0000.0000.0000.000
203A483PHE00.154-0.04826.366-0.010-0.0100.0000.0000.0000.000
204A483PHE0-0.0800.10928.7500.0020.0020.0000.0000.0000.000
205A484ILE00.042-0.09929.3490.0070.0070.0000.0000.0000.000
206A484ILE0-0.1370.07029.4300.0010.0010.0000.0000.0000.000
207A485LYS00.151-0.07932.397-0.009-0.0090.0000.0000.0000.000
208A485LYS10.7971.05136.328-0.072-0.0720.0000.0000.0000.000
209A486LYS00.119-0.07936.0490.0050.0050.0000.0000.0000.000
210A486LYS10.8701.07039.368-0.040-0.0400.0000.0000.0000.000
211A487LEU0-0.073-0.12138.7080.0040.0040.0000.0000.0000.000
212A487LEU00.0530.03041.832-0.001-0.0010.0000.0000.0000.000