FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 494RN

Calculation Name: 2PTG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTG

Chain ID: A

ChEMBL ID:

UniProt ID: Q0VIP6

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2547290.713751
FMO2-HF: Nuclear repulsion 2463741.262628
FMO2-HF: Total energy -83549.451123
FMO2-MP2: Total energy -83796.23529


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:93:PRO)


Summations of interaction energy for fragment #1(A:93:PRO)
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.
-5.618-1.8480.562-1.624-2.7080.012
Interaction energy analysis for fragmet #1(A:93:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.007
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].
3A95PRO0-0.040-0.0082.809-4.008-0.3370.563-1.612-2.6220.012
4A96VAL00.026-0.0025.304-1.001-0.902-0.001-0.012-0.0860.000
5A97ASP-1-0.822-0.8878.8540.4760.4760.0000.0000.0000.000
6A98LEU0-0.012-0.04111.225-0.069-0.0690.0000.0000.0000.000
7A99ARG10.8530.92613.299-0.534-0.5340.0000.0000.0000.000
8A100GLY0-0.027-0.00116.601-0.035-0.0350.0000.0000.0000.000
9A101LYS10.9130.95416.046-0.324-0.3240.0000.0000.0000.000
10A102THR0-0.022-0.00919.891-0.005-0.0050.0000.0000.0000.000
11A103ALA00.014-0.00420.374-0.001-0.0010.0000.0000.0000.000
12A104PHE00.0350.03522.528-0.006-0.0060.0000.0000.0000.000
13A105VAL0-0.011-0.02221.8930.0000.0000.0000.0000.0000.000
14A106ALA00.0290.00725.066-0.004-0.0040.0000.0000.0000.000
15A107GLY00.0230.03027.450-0.002-0.0020.0000.0000.0000.000
16A108VAL0-0.031-0.02525.656-0.001-0.0010.0000.0000.0000.000
17A109ALA0-0.008-0.00628.257-0.001-0.0010.0000.0000.0000.000
18A110ASP-1-0.855-0.95029.2550.0310.0310.0000.0000.0000.000
19A111SER0-0.015-0.01226.8470.0050.0050.0000.0000.0000.000
20A112ASN0-0.058-0.01625.1040.0080.0080.0000.0000.0000.000
21A113GLY00.1050.06225.628-0.006-0.0060.0000.0000.0000.000
22A114TYR0-0.021-0.07821.2770.0080.0080.0000.0000.0000.000
23A115GLY00.0370.01921.3870.0100.0100.0000.0000.0000.000
24A116TRP00.0510.02222.3250.0140.0140.0000.0000.0000.000
25A117ALA0-0.008-0.03318.7060.0130.0130.0000.0000.0000.000
26A118ILE00.0570.01717.5860.0190.0190.0000.0000.0000.000
27A119CYS0-0.0230.00918.0150.0240.0240.0000.0000.0000.000
28A120LYS10.9170.99717.857-0.063-0.0630.0000.0000.0000.000
29A121LEU00.0070.00312.4610.0270.0270.0000.0000.0000.000
30A122LEU0-0.006-0.00513.9020.0580.0580.0000.0000.0000.000
31A123ARG10.8670.93416.158-0.126-0.1260.0000.0000.0000.000
32A124ALA0-0.065-0.02513.7340.0060.0060.0000.0000.0000.000
33A125ALA0-0.037-0.01511.8450.0320.0320.0000.0000.0000.000
34A126GLY00.016-0.00912.9260.0570.0570.0000.0000.0000.000
35A127ALA00.0060.02615.800-0.024-0.0240.0000.0000.0000.000
36A128ARG10.9300.97418.156-0.147-0.1470.0000.0000.0000.000
37A129VAL0-0.011-0.01320.290-0.002-0.0020.0000.0000.0000.000
38A130LEU00.0170.01623.061-0.010-0.0100.0000.0000.0000.000
39A131VAL00.026-0.00125.3610.0010.0010.0000.0000.0000.000
40A132GLY00.0490.03427.747-0.004-0.0040.0000.0000.0000.000
41A133THR0-0.045-0.03630.257-0.001-0.0010.0000.0000.0000.000
42A134TRP00.0960.04632.233-0.001-0.0010.0000.0000.0000.000
43A135PRO00.0670.02635.2380.0010.0010.0000.0000.0000.000
44A136PRO0-0.043-0.01738.1490.0010.0010.0000.0000.0000.000
45A137VAL0-0.008-0.00432.8290.0000.0000.0000.0000.0000.000
46A138TYR00.0560.05034.4110.0000.0000.0000.0000.0000.000
47A139SER0-0.015-0.01435.8280.0010.0010.0000.0000.0000.000
48A140ILE0-0.137-0.06436.8840.0000.0000.0000.0000.0000.000
49A141PHE00.0830.02929.4470.0010.0010.0000.0000.0000.000
50A142LYS10.8770.95034.764-0.041-0.0410.0000.0000.0000.000
51A143LYS10.9220.98236.418-0.035-0.0350.0000.0000.0000.000
52A176VAL00.0140.00621.8290.0050.0050.0000.0000.0000.000
53A177PHE00.012-0.00722.1700.0150.0150.0000.0000.0000.000
54A178ASP-1-0.976-0.98724.7710.1140.1140.0000.0000.0000.000
55A179LYS10.8870.97326.441-0.080-0.0800.0000.0000.0000.000
56A180ILE0-0.040-0.00328.6180.0020.0020.0000.0000.0000.000
57A181TYR0-0.025-0.03830.155-0.001-0.0010.0000.0000.0000.000
58A182PRO0-0.030-0.00633.3380.0010.0010.0000.0000.0000.000
59A183LEU00.007-0.02131.7660.0010.0010.0000.0000.0000.000
60A184ASP-1-0.824-0.90635.0780.0300.0300.0000.0000.0000.000
61A185ALA0-0.021-0.02333.331-0.001-0.0010.0000.0000.0000.000
62A186VAL00.0020.02235.462-0.001-0.0010.0000.0000.0000.000
63A187PHE0-0.017-0.01238.384-0.002-0.0020.0000.0000.0000.000
64A188ASP-1-0.763-0.85038.7600.0350.0350.0000.0000.0000.000
65A189THR0-0.091-0.04340.3490.0020.0020.0000.0000.0000.000
66A190PRO00.0330.00843.147-0.002-0.0020.0000.0000.0000.000
67A191GLN00.0180.00945.786-0.001-0.0010.0000.0000.0000.000
68A192ASP-1-0.825-0.90243.6320.0260.0260.0000.0000.0000.000
69A193VAL0-0.085-0.03643.821-0.001-0.0010.0000.0000.0000.000
70A194PRO0-0.0200.01146.3020.0000.0000.0000.0000.0000.000
71A195PRO00.028-0.01249.3320.0010.0010.0000.0000.0000.000
72A196GLU-1-0.859-0.93549.7750.0180.0180.0000.0000.0000.000
73A197VAL0-0.017-0.01544.4440.0000.0000.0000.0000.0000.000
74A198SER0-0.052-0.01246.6200.0020.0020.0000.0000.0000.000
75A199SER0-0.021-0.00347.4930.0010.0010.0000.0000.0000.000
76A200ASN00.0650.04646.648-0.001-0.0010.0000.0000.0000.000
77A201LYS10.9630.95346.004-0.018-0.0180.0000.0000.0000.000
78A202ARG10.8770.92341.757-0.026-0.0260.0000.0000.0000.000
79A203TYR00.0470.01240.7220.0020.0020.0000.0000.0000.000
80A204ALA0-0.053-0.01944.1830.0010.0010.0000.0000.0000.000
81A205GLY0-0.039-0.01245.6070.0010.0010.0000.0000.0000.000
82A206VAL0-0.054-0.02640.8700.0010.0010.0000.0000.0000.000
83A207GLY0-0.013-0.01240.9920.0020.0020.0000.0000.0000.000
84A208GLY00.0410.01640.4000.0020.0020.0000.0000.0000.000
85A209PHE0-0.0060.01038.4290.0020.0020.0000.0000.0000.000
86A210THR0-0.011-0.01937.9140.0010.0010.0000.0000.0000.000
87A211ILE00.023-0.00734.3840.0040.0040.0000.0000.0000.000
88A212SER0-0.017-0.03236.1990.0040.0040.0000.0000.0000.000
89A213GLU-1-0.832-0.89638.3140.0390.0390.0000.0000.0000.000
90A214VAL0-0.033-0.00233.0480.0030.0030.0000.0000.0000.000
91A215ALA00.0240.00533.4290.0050.0050.0000.0000.0000.000
92A216GLU-1-0.947-0.96734.4820.0540.0540.0000.0000.0000.000
93A217ALA0-0.008-0.00735.4610.0030.0030.0000.0000.0000.000
94A218VAL0-0.029-0.00229.5510.0040.0040.0000.0000.0000.000
95A219ARG10.9700.98532.156-0.054-0.0540.0000.0000.0000.000
96A220ALA0-0.030-0.00833.8270.0030.0030.0000.0000.0000.000
97A221ASP-1-0.833-0.92932.5610.0720.0720.0000.0000.0000.000
98A222VAL0-0.120-0.06828.0900.0070.0070.0000.0000.0000.000
99A223GLY0-0.0290.00429.9080.0060.0060.0000.0000.0000.000
100A224GLN0-0.020-0.03927.4170.0040.0040.0000.0000.0000.000
101A225ILE0-0.059-0.00124.8880.0090.0090.0000.0000.0000.000
102A226ASP-1-0.843-0.92020.4390.1910.1910.0000.0000.0000.000
103A227ILE0-0.010-0.01317.2130.0020.0020.0000.0000.0000.000
104A228LEU00.0350.03221.592-0.005-0.0050.0000.0000.0000.000
105A229VAL0-0.010-0.00720.485-0.001-0.0010.0000.0000.0000.000
106A230HIS00.0220.02423.6140.0000.0000.0000.0000.0000.000
107A231SER0-0.030-0.00625.105-0.005-0.0050.0000.0000.0000.000
108A232LEU0-0.031-0.01526.425-0.001-0.0010.0000.0000.0000.000
109A233ALA00.0080.00529.433-0.004-0.0040.0000.0000.0000.000
110A234ASN0-0.051-0.04730.772-0.001-0.0010.0000.0000.0000.000
111A235GLY00.0780.04733.550-0.002-0.0020.0000.0000.0000.000
112A236PRO0-0.045-0.02935.277-0.001-0.0010.0000.0000.0000.000
113A237GLU-1-0.833-0.91739.0980.0040.0040.0000.0000.0000.000
114A238VAL00.0020.00135.6170.0000.0000.0000.0000.0000.000
115A239THR0-0.041-0.00735.612-0.002-0.0020.0000.0000.0000.000
116A240LYS10.8740.94438.324-0.005-0.0050.0000.0000.0000.000
117A241PRO00.0320.01842.0640.0000.0000.0000.0000.0000.000
118A242LEU00.0770.01443.1520.0010.0010.0000.0000.0000.000
119A243LEU00.003-0.00245.7090.0010.0010.0000.0000.0000.000
120A244GLN0-0.026-0.00746.3380.0000.0000.0000.0000.0000.000
121A245THR0-0.0290.00844.9960.0010.0010.0000.0000.0000.000
122A246SER00.0030.00047.2000.0000.0000.0000.0000.0000.000
123A247ARG11.0391.00647.371-0.006-0.0060.0000.0000.0000.000
124A248LYS10.9910.98347.052-0.009-0.0090.0000.0000.0000.000
125A249GLY0-0.036-0.02245.4150.0010.0010.0000.0000.0000.000
126A250TYR00.0530.03541.9480.0000.0000.0000.0000.0000.000
127A251LEU00.004-0.01842.1090.0000.0000.0000.0000.0000.000
128A252ALA0-0.0100.01042.0760.0010.0010.0000.0000.0000.000
129A253ALA00.0650.03738.7530.0020.0020.0000.0000.0000.000
130A254VAL00.0210.03237.5070.0010.0010.0000.0000.0000.000
131A255SER0-0.035-0.02237.1890.0020.0020.0000.0000.0000.000
132A256SER00.016-0.00536.5670.0030.0030.0000.0000.0000.000
133A257SER0-0.078-0.03533.7330.0020.0020.0000.0000.0000.000
134A258SER0-0.012-0.02732.4140.0000.0000.0000.0000.0000.000
135A259TYR00.0560.02433.2700.0030.0030.0000.0000.0000.000
136A260SER00.0680.02033.9770.0020.0020.0000.0000.0000.000
137A261PHE0-0.029-0.01626.1880.0040.0040.0000.0000.0000.000
138A262VAL00.0270.01931.2890.0040.0040.0000.0000.0000.000
139A263SER0-0.037-0.03833.3200.0040.0040.0000.0000.0000.000
140A264LEU00.002-0.00328.9010.0030.0030.0000.0000.0000.000
141A265LEU00.0300.00027.7820.0060.0060.0000.0000.0000.000
142A266GLN0-0.030-0.01430.8360.0030.0030.0000.0000.0000.000
143A267HIS0-0.026-0.03434.1540.0010.0010.0000.0000.0000.000
144A268PHE00.0180.00429.3330.0030.0030.0000.0000.0000.000
145A269LEU00.0100.02028.3830.0070.0070.0000.0000.0000.000
146A270PRO0-0.073-0.03630.2420.0050.0050.0000.0000.0000.000
147A271LEU0-0.044-0.01030.4530.0010.0010.0000.0000.0000.000
148A272MET0-0.032-0.01024.4740.0050.0050.0000.0000.0000.000
149A273LYS10.8880.96022.929-0.162-0.1620.0000.0000.0000.000
150A274GLU-1-0.817-0.90825.0430.0910.0910.0000.0000.0000.000
151A275GLY0-0.064-0.02221.5760.0130.0130.0000.0000.0000.000
152A276GLY0-0.042-0.01120.2080.0210.0210.0000.0000.0000.000
153A277SER0-0.038-0.03818.778-0.007-0.0070.0000.0000.0000.000
154A278ALA00.0160.00120.7710.0060.0060.0000.0000.0000.000
155A279LEU0-0.039-0.00818.577-0.007-0.0070.0000.0000.0000.000
156A280ALA00.0190.01022.2230.0040.0040.0000.0000.0000.000
157A281LEU0-0.035-0.00621.598-0.006-0.0060.0000.0000.0000.000
158A282SER00.0460.02124.3270.0020.0020.0000.0000.0000.000
159A283TYR00.016-0.00725.776-0.005-0.0050.0000.0000.0000.000
160A284ILE00.0140.02427.6510.0020.0020.0000.0000.0000.000
161A303ALA00.0350.00731.2890.0010.0010.0000.0000.0000.000
162A304LEU00.0520.02729.0670.0000.0000.0000.0000.0000.000
163A305GLU-1-0.880-0.92626.872-0.011-0.0110.0000.0000.0000.000
164A306SER0-0.051-0.01928.602-0.001-0.0010.0000.0000.0000.000
165A307ASP-1-0.836-0.93230.9290.0180.0180.0000.0000.0000.000
166A308CYS0-0.0300.01224.4910.0060.0060.0000.0000.0000.000
167A309ARG10.9890.98126.4730.0080.0080.0000.0000.0000.000
168A310THR0-0.031-0.00528.0120.0010.0010.0000.0000.0000.000
169A311LEU00.011-0.00328.8900.0030.0030.0000.0000.0000.000
170A312ALA0-0.0210.00225.3120.0060.0060.0000.0000.0000.000
171A313PHE0-0.038-0.01626.9220.0040.0040.0000.0000.0000.000
172A314GLU-1-0.932-0.97829.4100.0310.0310.0000.0000.0000.000
173A315ALA00.0360.01027.4020.0020.0020.0000.0000.0000.000
174A316GLY00.0160.01626.4770.0070.0070.0000.0000.0000.000
175A317ARG10.8370.90927.370-0.026-0.0260.0000.0000.0000.000
176A318ALA0-0.0270.01230.4750.0010.0010.0000.0000.0000.000
177A319ARG10.8400.91827.816-0.082-0.0820.0000.0000.0000.000
178A320ALA0-0.006-0.00924.3300.0100.0100.0000.0000.0000.000
179A321VAL0-0.034-0.00523.4230.0130.0130.0000.0000.0000.000
180A322ARG10.7770.89216.087-0.139-0.1390.0000.0000.0000.000
181A323VAL00.0360.01522.0200.0070.0070.0000.0000.0000.000
182A324ASN0-0.029-0.01518.961-0.021-0.0210.0000.0000.0000.000
183A325CYS0-0.012-0.00621.9050.0060.0060.0000.0000.0000.000
184A326ILE0-0.0110.01417.569-0.008-0.0080.0000.0000.0000.000
185A327SER0-0.013-0.00421.6200.0060.0060.0000.0000.0000.000
186A328ALA00.0040.00222.423-0.007-0.0070.0000.0000.0000.000
187A329GLY00.0710.04223.8150.0010.0010.0000.0000.0000.000
188A330PRO0-0.036-0.00525.4140.0050.0050.0000.0000.0000.000
189A331LEU0-0.0100.02323.229-0.003-0.0030.0000.0000.0000.000
190A363LYS10.8350.88822.2830.0570.0570.0000.0000.0000.000
191A364GLU-1-0.925-0.93920.874-0.038-0.0380.0000.0000.0000.000
192A365LEU00.0020.01120.915-0.006-0.0060.0000.0000.0000.000
193A366GLU-1-0.843-0.92217.326-0.001-0.0010.0000.0000.0000.000
194A367SER00.046-0.02119.3970.0010.0010.0000.0000.0000.000
195A368ASP-1-0.947-0.97715.1450.0680.0680.0000.0000.0000.000
196A369ASP-1-0.888-0.93314.980-0.043-0.0430.0000.0000.0000.000
197A370VAL0-0.022-0.01515.750-0.002-0.0020.0000.0000.0000.000
198A371GLY0-0.008-0.01416.3120.0110.0110.0000.0000.0000.000
199A372ARG10.9440.97710.700-0.005-0.0050.0000.0000.0000.000
200A373ALA00.0230.02512.2060.0140.0140.0000.0000.0000.000
201A374ALA0-0.009-0.01414.0610.0110.0110.0000.0000.0000.000
202A375LEU0-0.023-0.01610.3910.0140.0140.0000.0000.0000.000
203A376PHE0-0.009-0.0088.7750.0430.0430.0000.0000.0000.000
204A377LEU00.0290.00711.6660.0250.0250.0000.0000.0000.000
205A378LEU0-0.0040.00414.9110.0060.0060.0000.0000.0000.000
206A379SER00.0040.01611.2210.0750.0750.0000.0000.0000.000
207A380PRO0-0.016-0.02811.523-0.060-0.0600.0000.0000.0000.000
208A381LEU0-0.0070.0086.483-0.099-0.0990.0000.0000.0000.000
209A382ALA00.0060.0169.987-0.110-0.1100.0000.0000.0000.000
210A383ARG10.9640.98012.385-0.177-0.1770.0000.0000.0000.000
211A384ALA0-0.038-0.01914.722-0.008-0.0080.0000.0000.0000.000
212A385VAL0-0.017-0.00914.865-0.021-0.0210.0000.0000.0000.000
213A386THR00.0080.01617.6210.0230.0230.0000.0000.0000.000
214A387GLY00.0470.01221.088-0.008-0.0080.0000.0000.0000.000
215A388ALA0-0.054-0.02819.524-0.008-0.0080.0000.0000.0000.000
216A389THR00.0400.00721.5700.0120.0120.0000.0000.0000.000
217A390LEU0-0.028-0.01415.376-0.009-0.0090.0000.0000.0000.000
218A391TYR00.001-0.03120.1420.0110.0110.0000.0000.0000.000
219A392VAL0-0.040-0.01117.765-0.010-0.0100.0000.0000.0000.000
220A393ASP-1-0.749-0.90120.267-0.029-0.0290.0000.0000.0000.000
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