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: 52KZZ

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 OptHSide
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 -2545663.096007
FMO2-HF: Nuclear repulsion 2462112.203487
FMO2-HF: Total energy -83550.89252
FMO2-MP2: Total energy -83797.477445


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.
-4.437-0.9620.421-1.478-2.4190.008
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 : 0.006 / 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].
3A95PRO0-0.034-0.0042.847-2.9720.4110.422-1.466-2.3400.008
4A96VAL00.024-0.0075.304-1.090-0.998-0.001-0.012-0.0790.000
5A97ASP-1-0.810-0.8619.0430.4940.4940.0000.0000.0000.000
6A98LEU0-0.013-0.03411.583-0.089-0.0890.0000.0000.0000.000
7A99ARG10.8450.90513.502-0.536-0.5360.0000.0000.0000.000
8A100GLY0-0.029-0.00217.182-0.034-0.0340.0000.0000.0000.000
9A101LYS10.8220.90816.983-0.232-0.2320.0000.0000.0000.000
10A102THR00.0200.01019.9870.0040.0040.0000.0000.0000.000
11A103ALA00.0140.00020.838-0.004-0.0040.0000.0000.0000.000
12A104PHE00.0410.03322.994-0.003-0.0030.0000.0000.0000.000
13A105VAL0-0.018-0.02422.450-0.001-0.0010.0000.0000.0000.000
14A106ALA00.0390.00925.559-0.003-0.0030.0000.0000.0000.000
15A107GLY00.0340.03827.957-0.002-0.0020.0000.0000.0000.000
16A108VAL0-0.037-0.01726.1190.0000.0000.0000.0000.0000.000
17A109ALA00.002-0.00228.718-0.001-0.0010.0000.0000.0000.000
18A110ASP-1-0.860-0.95029.5590.0470.0470.0000.0000.0000.000
19A111SER0-0.006-0.00527.2170.0050.0050.0000.0000.0000.000
20A112ASN0-0.056-0.01825.4650.0100.0100.0000.0000.0000.000
21A113GLY00.1130.06626.032-0.007-0.0070.0000.0000.0000.000
22A114TYR00.009-0.04721.5080.0110.0110.0000.0000.0000.000
23A115GLY00.0320.01821.8490.0110.0110.0000.0000.0000.000
24A116TRP00.0530.02522.7830.0150.0150.0000.0000.0000.000
25A117ALA00.006-0.01219.1050.0150.0150.0000.0000.0000.000
26A118ILE00.0350.01218.0490.0230.0230.0000.0000.0000.000
27A119CYS0-0.034-0.00218.4690.0230.0230.0000.0000.0000.000
28A120LYS10.8290.92517.969-0.109-0.1090.0000.0000.0000.000
29A121LEU0-0.003-0.00212.6090.0320.0320.0000.0000.0000.000
30A122LEU0-0.008-0.00314.3150.0610.0610.0000.0000.0000.000
31A123ARG10.8960.95016.551-0.149-0.1490.0000.0000.0000.000
32A124ALA0-0.070-0.02814.0640.0060.0060.0000.0000.0000.000
33A125ALA0-0.035-0.01312.3200.0420.0420.0000.0000.0000.000
34A126GLY00.012-0.01313.2730.0450.0450.0000.0000.0000.000
35A127ALA00.0010.02816.423-0.030-0.0300.0000.0000.0000.000
36A128ARG10.8650.92118.605-0.137-0.1370.0000.0000.0000.000
37A129VAL0-0.026-0.02020.615-0.004-0.0040.0000.0000.0000.000
38A130LEU00.0210.01723.474-0.009-0.0090.0000.0000.0000.000
39A131VAL00.019-0.00425.8090.0020.0020.0000.0000.0000.000
40A132GLY00.0560.04128.198-0.005-0.0050.0000.0000.0000.000
41A133THR0-0.054-0.04230.7340.0010.0010.0000.0000.0000.000
42A134TRP00.0670.03432.694-0.002-0.0020.0000.0000.0000.000
43A135PRO00.0580.02135.7070.0010.0010.0000.0000.0000.000
44A136PRO0-0.027-0.00738.6060.0010.0010.0000.0000.0000.000
45A137VAL0-0.010-0.00833.6110.0000.0000.0000.0000.0000.000
46A138TYR00.0710.04634.6480.0010.0010.0000.0000.0000.000
47A139SER00.0350.01836.2490.0010.0010.0000.0000.0000.000
48A140ILE0-0.143-0.06337.2830.0000.0000.0000.0000.0000.000
49A141PHE00.0750.02729.7830.0020.0020.0000.0000.0000.000
50A142LYS10.8530.93335.135-0.049-0.0490.0000.0000.0000.000
51A143LYS10.9170.97736.788-0.041-0.0410.0000.0000.0000.000
52A176VAL0-0.007-0.00822.1500.0040.0040.0000.0000.0000.000
53A177PHE00.009-0.00422.5290.0150.0150.0000.0000.0000.000
54A178ASP-1-0.898-0.93225.1400.1220.1220.0000.0000.0000.000
55A179LYS10.8640.95126.794-0.083-0.0830.0000.0000.0000.000
56A180ILE0-0.041-0.00729.0310.0020.0020.0000.0000.0000.000
57A181TYR0-0.036-0.06330.633-0.001-0.0010.0000.0000.0000.000
58A182PRO0-0.0210.00633.7920.0010.0010.0000.0000.0000.000
59A183LEU0-0.009-0.02832.1780.0010.0010.0000.0000.0000.000
60A184ASP-1-0.826-0.91835.5680.0330.0330.0000.0000.0000.000
61A185ALA0-0.015-0.01733.808-0.001-0.0010.0000.0000.0000.000
62A186VAL00.0010.02535.891-0.001-0.0010.0000.0000.0000.000
63A187PHE0-0.019-0.01338.676-0.002-0.0020.0000.0000.0000.000
64A188ASP-1-0.751-0.83838.8040.0330.0330.0000.0000.0000.000
65A189THR0-0.078-0.03440.7270.0020.0020.0000.0000.0000.000
66A190PRO00.0480.01243.649-0.001-0.0010.0000.0000.0000.000
67A191GLN00.0000.00046.2930.0000.0000.0000.0000.0000.000
68A192ASP-1-0.835-0.89744.2850.0240.0240.0000.0000.0000.000
69A193VAL0-0.069-0.02944.3180.0000.0000.0000.0000.0000.000
70A194PRO0-0.0140.01146.9110.0000.0000.0000.0000.0000.000
71A195PRO00.024-0.01249.8320.0010.0010.0000.0000.0000.000
72A196GLU-1-0.875-0.94350.4560.0190.0190.0000.0000.0000.000
73A197VAL00.0010.00144.8930.0010.0010.0000.0000.0000.000
74A198SER0-0.043-0.00947.1020.0020.0020.0000.0000.0000.000
75A199SER0-0.0210.00547.9670.0010.0010.0000.0000.0000.000
76A200ASN00.0330.00047.124-0.001-0.0010.0000.0000.0000.000
77A201LYS10.9590.96746.426-0.022-0.0220.0000.0000.0000.000
78A202ARG10.8850.92942.226-0.032-0.0320.0000.0000.0000.000
79A203TYR00.0520.02041.2730.0020.0020.0000.0000.0000.000
80A204ALA0-0.046-0.01444.6400.0000.0000.0000.0000.0000.000
81A205GLY0-0.038-0.01346.0400.0010.0010.0000.0000.0000.000
82A206VAL0-0.051-0.02941.2430.0010.0010.0000.0000.0000.000
83A207GLY0-0.019-0.01141.4290.0020.0020.0000.0000.0000.000
84A208GLY00.0350.01040.8590.0020.0020.0000.0000.0000.000
85A209PHE0-0.0010.00938.9100.0020.0020.0000.0000.0000.000
86A210THR0-0.035-0.03738.4100.0010.0010.0000.0000.0000.000
87A211ILE00.0290.00135.0550.0040.0040.0000.0000.0000.000
88A212SER0-0.032-0.03836.7050.0030.0030.0000.0000.0000.000
89A213GLU-1-0.817-0.88538.7780.0380.0380.0000.0000.0000.000
90A214VAL0-0.010-0.00733.6510.0030.0030.0000.0000.0000.000
91A215ALA00.0210.01133.8940.0050.0050.0000.0000.0000.000
92A216GLU-1-0.849-0.90734.8580.0500.0500.0000.0000.0000.000
93A217ALA0-0.024-0.01036.0730.0030.0030.0000.0000.0000.000
94A218VAL00.0010.00530.0210.0040.0040.0000.0000.0000.000
95A219ARG10.8850.93432.390-0.047-0.0470.0000.0000.0000.000
96A220ALA0-0.028-0.01333.9310.0020.0020.0000.0000.0000.000
97A221ASP-1-0.830-0.89732.5630.0740.0740.0000.0000.0000.000
98A222VAL0-0.120-0.07228.1430.0070.0070.0000.0000.0000.000
99A223GLY0-0.0240.01230.0000.0040.0040.0000.0000.0000.000
100A224GLN0-0.015-0.03227.4190.0020.0020.0000.0000.0000.000
101A225ILE0-0.044-0.00425.1170.0100.0100.0000.0000.0000.000
102A226ASP-1-0.815-0.89520.3670.1610.1610.0000.0000.0000.000
103A227ILE0-0.005-0.00817.276-0.002-0.0020.0000.0000.0000.000
104A228LEU00.0350.03221.847-0.002-0.0020.0000.0000.0000.000
105A229VAL0-0.009-0.01120.970-0.002-0.0020.0000.0000.0000.000
106A230HIS00.0290.02624.0250.0010.0010.0000.0000.0000.000
107A231SER0-0.063-0.02825.274-0.005-0.0050.0000.0000.0000.000
108A232LEU0-0.029-0.01626.740-0.001-0.0010.0000.0000.0000.000
109A233ALA00.0000.01229.423-0.004-0.0040.0000.0000.0000.000
110A234ASN0-0.029-0.04230.870-0.002-0.0020.0000.0000.0000.000
111A235GLY00.0630.04433.537-0.002-0.0020.0000.0000.0000.000
112A236PRO0-0.037-0.03335.257-0.002-0.0020.0000.0000.0000.000
113A237GLU-1-0.784-0.86239.0810.0050.0050.0000.0000.0000.000
114A238VAL00.012-0.00335.8420.0000.0000.0000.0000.0000.000
115A239THR0-0.0240.01035.572-0.002-0.0020.0000.0000.0000.000
116A240LYS10.8200.90438.335-0.007-0.0070.0000.0000.0000.000
117A241PRO00.0360.01742.0740.0000.0000.0000.0000.0000.000
118A242LEU00.0680.01242.8330.0010.0010.0000.0000.0000.000
119A243LEU0-0.011-0.00545.7350.0010.0010.0000.0000.0000.000
120A244GLN0-0.030-0.00846.9440.0000.0000.0000.0000.0000.000
121A245THR0-0.033-0.00944.9600.0010.0010.0000.0000.0000.000
122A246SER00.000-0.00147.2080.0000.0000.0000.0000.0000.000
123A247ARG11.0210.99947.375-0.005-0.0050.0000.0000.0000.000
124A248LYS10.9950.98947.055-0.011-0.0110.0000.0000.0000.000
125A249GLY0-0.011-0.01245.4030.0010.0010.0000.0000.0000.000
126A250TYR00.0370.02741.3880.0010.0010.0000.0000.0000.000
127A251LEU00.025-0.01142.1140.0000.0000.0000.0000.0000.000
128A252ALA0-0.0090.01142.0720.0010.0010.0000.0000.0000.000
129A253ALA00.0590.03238.9230.0020.0020.0000.0000.0000.000
130A254VAL00.0190.04537.5030.0010.0010.0000.0000.0000.000
131A255SER00.0100.00137.1880.0010.0010.0000.0000.0000.000
132A256SER0-0.018-0.01436.8880.0030.0030.0000.0000.0000.000
133A257SER0-0.074-0.05633.6310.0020.0020.0000.0000.0000.000
134A258SER0-0.008-0.02432.4100.0000.0000.0000.0000.0000.000
135A259TYR00.0390.01533.2700.0020.0020.0000.0000.0000.000
136A260SER00.0600.01134.1970.0010.0010.0000.0000.0000.000
137A261PHE0-0.035-0.01426.3890.0040.0040.0000.0000.0000.000
138A262VAL00.0250.01731.3040.0030.0030.0000.0000.0000.000
139A263SER0-0.029-0.04233.3200.0030.0030.0000.0000.0000.000
140A264LEU0-0.010-0.00829.2120.0020.0020.0000.0000.0000.000
141A265LEU00.012-0.00627.6820.0050.0050.0000.0000.0000.000
142A266GLN0-0.017-0.00830.8700.0020.0020.0000.0000.0000.000
143A267HIS0-0.012-0.02734.1540.0000.0000.0000.0000.0000.000
144A268PHE00.008-0.00229.5360.0030.0030.0000.0000.0000.000
145A269LEU00.0120.02128.4020.0050.0050.0000.0000.0000.000
146A270PRO0-0.070-0.03730.2420.0030.0030.0000.0000.0000.000
147A271LEU0-0.045-0.00530.5060.0000.0000.0000.0000.0000.000
148A272MET0-0.031-0.00524.1750.0060.0060.0000.0000.0000.000
149A273LYS10.8610.93523.085-0.141-0.1410.0000.0000.0000.000
150A274GLU-1-0.786-0.87024.9770.0680.0680.0000.0000.0000.000
151A275GLY0-0.055-0.01821.4650.0100.0100.0000.0000.0000.000
152A276GLY0-0.051-0.01720.2080.0170.0170.0000.0000.0000.000
153A277SER0-0.031-0.03418.765-0.014-0.0140.0000.0000.0000.000
154A278ALA00.014-0.00120.7710.0100.0100.0000.0000.0000.000
155A279LEU0-0.042-0.01318.597-0.009-0.0090.0000.0000.0000.000
156A280ALA00.0300.01722.2130.0060.0060.0000.0000.0000.000
157A281LEU0-0.026-0.01321.798-0.005-0.0050.0000.0000.0000.000
158A282SER00.0210.01324.3090.0010.0010.0000.0000.0000.000
159A283TYR00.007-0.00525.721-0.004-0.0040.0000.0000.0000.000
160A284ILE00.0210.03527.6320.0010.0010.0000.0000.0000.000
161A303ALA00.0220.00131.3420.0010.0010.0000.0000.0000.000
162A304LEU00.0600.03528.932-0.001-0.0010.0000.0000.0000.000
163A305GLU-1-0.870-0.91526.971-0.017-0.0170.0000.0000.0000.000
164A306SER0-0.046-0.02028.654-0.003-0.0030.0000.0000.0000.000
165A307ASP-1-0.817-0.91630.9150.0100.0100.0000.0000.0000.000
166A308CYS0-0.0290.01324.5500.0040.0040.0000.0000.0000.000
167A309ARG10.9850.98226.3880.0180.0180.0000.0000.0000.000
168A310THR0-0.048-0.02728.072-0.001-0.0010.0000.0000.0000.000
169A311LEU00.0210.00428.9140.0020.0020.0000.0000.0000.000
170A312ALA0-0.027-0.00225.2340.0040.0040.0000.0000.0000.000
171A313PHE0-0.027-0.01926.9220.0010.0010.0000.0000.0000.000
172A314GLU-1-0.935-0.97729.4170.0190.0190.0000.0000.0000.000
173A315ALA00.0300.00827.4080.0020.0020.0000.0000.0000.000
174A316GLY00.0140.01626.4760.0050.0050.0000.0000.0000.000
175A317ARG10.8440.91727.370-0.004-0.0040.0000.0000.0000.000
176A318ALA0-0.0240.01630.5350.0010.0010.0000.0000.0000.000
177A319ARG10.8070.86827.951-0.060-0.0600.0000.0000.0000.000
178A320ALA0-0.004-0.00624.3480.0070.0070.0000.0000.0000.000
179A321VAL0-0.042-0.00723.4160.0090.0090.0000.0000.0000.000
180A322ARG10.7930.90016.029-0.091-0.0910.0000.0000.0000.000
181A323VAL00.0300.01822.0200.0100.0100.0000.0000.0000.000
182A324ASN0-0.026-0.02219.140-0.023-0.0230.0000.0000.0000.000
183A325CYS0-0.028-0.01221.9310.0080.0080.0000.0000.0000.000
184A326ILE00.0000.01517.494-0.008-0.0080.0000.0000.0000.000
185A327SER0-0.002-0.00221.6290.0050.0050.0000.0000.0000.000
186A328ALA0-0.012-0.00122.303-0.006-0.0060.0000.0000.0000.000
187A329GLY00.0710.04523.810-0.001-0.0010.0000.0000.0000.000
188A330PRO0-0.028-0.02225.3910.0060.0060.0000.0000.0000.000
189A331LEU0-0.0260.00723.673-0.003-0.0030.0000.0000.0000.000
190A363LYS10.8650.92022.2740.0430.0430.0000.0000.0000.000
191A364GLU-1-0.962-0.97821.098-0.009-0.0090.0000.0000.0000.000
192A365LEU0-0.013-0.00320.700-0.005-0.0050.0000.0000.0000.000
193A366GLU-1-0.807-0.89316.8540.0550.0550.0000.0000.0000.000
194A367SER00.043-0.01419.702-0.001-0.0010.0000.0000.0000.000
195A368ASP-1-0.845-0.92015.5630.1250.1250.0000.0000.0000.000
196A369ASP-1-0.839-0.90515.3030.0060.0060.0000.0000.0000.000
197A370VAL0-0.012-0.01215.718-0.004-0.0040.0000.0000.0000.000
198A371GLY0-0.010-0.01016.7430.0070.0070.0000.0000.0000.000
199A372ARG10.8810.93411.314-0.063-0.0630.0000.0000.0000.000
200A373ALA00.0200.02212.2400.0090.0090.0000.0000.0000.000
201A374ALA0-0.004-0.01314.0480.0010.0010.0000.0000.0000.000
202A375LEU0-0.013-0.01110.8430.0070.0070.0000.0000.0000.000
203A376PHE0-0.004-0.0078.6010.0320.0320.0000.0000.0000.000
204A377LEU00.0400.01311.6510.0050.0050.0000.0000.0000.000
205A378LEU0-0.0110.00914.920-0.004-0.0040.0000.0000.0000.000
206A379SER0-0.0050.00811.2710.0590.0590.0000.0000.0000.000
207A380PRO00.002-0.01811.369-0.061-0.0610.0000.0000.0000.000
208A381LEU0-0.0080.0056.432-0.124-0.1240.0000.0000.0000.000
209A382ALA0-0.0010.0139.987-0.109-0.1090.0000.0000.0000.000
210A383ARG10.9600.98212.194-0.024-0.0240.0000.0000.0000.000
211A384ALA0-0.039-0.01914.7290.0010.0010.0000.0000.0000.000
212A385VAL0-0.028-0.01714.879-0.014-0.0140.0000.0000.0000.000
213A386THR00.0260.01317.6380.0240.0240.0000.0000.0000.000
214A387GLY00.0260.00821.088-0.008-0.0080.0000.0000.0000.000
215A388ALA0-0.044-0.01719.573-0.007-0.0070.0000.0000.0000.000
216A389THR00.0290.00121.6320.0120.0120.0000.0000.0000.000
217A390LEU0-0.028-0.01315.654-0.009-0.0090.0000.0000.0000.000
218A391TYR0-0.004-0.04220.1880.0120.0120.0000.0000.0000.000
219A392VAL0-0.045-0.01717.706-0.009-0.0090.0000.0000.0000.000
220A393ASP-1-0.770-0.91220.280-0.020-0.0200.0000.0000.0000.000
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