FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QY37Y

Calculation Name: 2PTG-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTG

Chain ID: B

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:


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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2547118.365491
FMO2-HF: Nuclear repulsion 2463567.190781
FMO2-HF: Total energy -83551.17471
FMO2-MP2: Total energy -83797.724596


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(B:93:PRO)


Summations of interaction energy for fragment #1(B: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.
-2.4230.6560.705-1.428-2.3560.002
Interaction energy analysis for fragmet #1(B:93:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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].
3B95PRO0-0.0320.0012.305-2.2080.7790.706-1.407-2.2860.002
4B96VAL00.026-0.0074.4310.0900.182-0.001-0.021-0.0700.000
5B97ASP-1-0.811-0.8658.1230.2470.2470.0000.0000.0000.000
6B98LEU0-0.025-0.03510.6860.0250.0250.0000.0000.0000.000
7B99ARG10.8850.92212.749-0.216-0.2160.0000.0000.0000.000
8B100GLY0-0.050-0.00916.275-0.008-0.0080.0000.0000.0000.000
9B101LYS10.8200.90415.852-0.026-0.0260.0000.0000.0000.000
10B102THR0-0.0030.00019.172-0.011-0.0110.0000.0000.0000.000
11B103ALA00.0310.01219.988-0.001-0.0010.0000.0000.0000.000
12B104PHE00.0420.03222.1150.0040.0040.0000.0000.0000.000
13B105VAL0-0.015-0.02322.212-0.008-0.0080.0000.0000.0000.000
14B106ALA00.0380.00625.1010.0080.0080.0000.0000.0000.000
15B107GLY00.0300.02027.690-0.010-0.0100.0000.0000.0000.000
16B108VAL0-0.053-0.03225.9000.0010.0010.0000.0000.0000.000
17B109ALA00.0440.02928.5280.0090.0090.0000.0000.0000.000
18B110ASP-1-0.862-0.94429.148-0.114-0.1140.0000.0000.0000.000
19B111SER0-0.012-0.02027.359-0.001-0.0010.0000.0000.0000.000
20B112ASN0-0.106-0.04625.771-0.006-0.0060.0000.0000.0000.000
21B113GLY00.1440.07926.0040.0000.0000.0000.0000.0000.000
22B114TYR0-0.001-0.04321.565-0.013-0.0130.0000.0000.0000.000
23B115GLY00.0450.03321.824-0.013-0.0130.0000.0000.0000.000
24B116TRP00.0480.01322.895-0.004-0.0040.0000.0000.0000.000
25B117ALA0-0.014-0.01719.267-0.003-0.0030.0000.0000.0000.000
26B118ILE00.0570.02218.214-0.018-0.0180.0000.0000.0000.000
27B119CYS0-0.0520.00018.5410.0030.0030.0000.0000.0000.000
28B120LYS10.9390.98418.8450.2020.2020.0000.0000.0000.000
29B121LEU00.0100.01112.8720.0020.0020.0000.0000.0000.000
30B122LEU00.003-0.00314.491-0.015-0.0150.0000.0000.0000.000
31B123ARG10.8570.91915.8850.0910.0910.0000.0000.0000.000
32B124ALA0-0.033-0.00514.3020.0240.0240.0000.0000.0000.000
33B125ALA0-0.037-0.01111.7960.0110.0110.0000.0000.0000.000
34B126GLY0-0.008-0.02612.7570.0590.0590.0000.0000.0000.000
35B127ALA0-0.0140.01815.6720.0260.0260.0000.0000.0000.000
36B128ARG10.9520.97717.7170.0050.0050.0000.0000.0000.000
37B129VAL0-0.032-0.02620.193-0.005-0.0050.0000.0000.0000.000
38B130LEU0-0.022-0.00722.7770.0060.0060.0000.0000.0000.000
39B131VAL00.0270.00225.685-0.009-0.0090.0000.0000.0000.000
40B132GLY00.0530.03927.8490.0090.0090.0000.0000.0000.000
41B133THR0-0.058-0.03830.602-0.007-0.0070.0000.0000.0000.000
42B134TRP00.0710.03832.5750.0050.0050.0000.0000.0000.000
43B135PRO00.0310.00735.7110.0000.0000.0000.0000.0000.000
44B136PRO0-0.0200.00038.5870.0010.0010.0000.0000.0000.000
45B137VAL00.0100.00533.9260.0030.0030.0000.0000.0000.000
46B138TYR00.0830.05034.6590.0010.0010.0000.0000.0000.000
47B139SER0-0.028-0.01736.2940.0040.0040.0000.0000.0000.000
48B140ILE0-0.071-0.03436.1080.0040.0040.0000.0000.0000.000
49B141PHE00.0820.04430.1080.0010.0010.0000.0000.0000.000
50B142LYS10.8200.93334.8450.0340.0340.0000.0000.0000.000
51B143LYS10.9090.95635.9400.0440.0440.0000.0000.0000.000
52B176VAL0-0.045-0.04122.1060.0010.0010.0000.0000.0000.000
53B177PHE00.0230.01422.7570.0010.0010.0000.0000.0000.000
54B178ASP-1-0.825-0.88923.368-0.046-0.0460.0000.0000.0000.000
55B179LYS10.8290.92026.5180.0350.0350.0000.0000.0000.000
56B180ILE0-0.0290.00028.606-0.006-0.0060.0000.0000.0000.000
57B181TYR0-0.052-0.07629.8580.0050.0050.0000.0000.0000.000
58B182PRO0-0.0270.00433.551-0.006-0.0060.0000.0000.0000.000
59B183LEU00.004-0.02431.7540.0020.0020.0000.0000.0000.000
60B184ASP-1-0.814-0.90835.244-0.059-0.0590.0000.0000.0000.000
61B185ALA0-0.027-0.02433.4430.0030.0030.0000.0000.0000.000
62B186VAL00.0080.02235.561-0.001-0.0010.0000.0000.0000.000
63B187PHE0-0.006-0.00638.5840.0030.0030.0000.0000.0000.000
64B188ASP-1-0.761-0.84038.359-0.046-0.0460.0000.0000.0000.000
65B189THR0-0.065-0.03840.2160.0030.0030.0000.0000.0000.000
66B190PRO00.0700.02943.055-0.001-0.0010.0000.0000.0000.000
67B191GLN0-0.0070.00045.5340.0000.0000.0000.0000.0000.000
68B192ASP-1-0.815-0.88043.912-0.033-0.0330.0000.0000.0000.000
69B193VAL0-0.079-0.04343.938-0.002-0.0020.0000.0000.0000.000
70B194PRO00.0320.03346.5380.0020.0020.0000.0000.0000.000
71B195PRO00.049-0.00649.430-0.001-0.0010.0000.0000.0000.000
72B196GLU-1-0.963-0.98249.652-0.034-0.0340.0000.0000.0000.000
73B197VAL0-0.022-0.01344.554-0.001-0.0010.0000.0000.0000.000
74B198SER0-0.065-0.01947.0140.0000.0000.0000.0000.0000.000
75B199SER0-0.029-0.00848.3640.0000.0000.0000.0000.0000.000
76B200ASN00.0700.02346.8470.0000.0000.0000.0000.0000.000
77B201LYS10.9941.00147.1080.0310.0310.0000.0000.0000.000
78B202ARG10.7980.87142.8340.0370.0370.0000.0000.0000.000
79B203TYR00.1010.04241.166-0.002-0.0020.0000.0000.0000.000
80B204ALA0-0.045-0.00644.3350.0020.0020.0000.0000.0000.000
81B205GLY0-0.020-0.01545.659-0.001-0.0010.0000.0000.0000.000
82B206VAL0-0.066-0.02340.7120.0000.0000.0000.0000.0000.000
83B207GLY0-0.037-0.02141.2450.0000.0000.0000.0000.0000.000
84B208GLY00.0390.01540.690-0.002-0.0020.0000.0000.0000.000
85B209PHE0-0.0020.00138.486-0.001-0.0010.0000.0000.0000.000
86B210THR0-0.049-0.04838.011-0.004-0.0040.0000.0000.0000.000
87B211ILE00.0300.00134.4500.0000.0000.0000.0000.0000.000
88B212SER0-0.031-0.03735.8820.0020.0020.0000.0000.0000.000
89B213GLU-1-0.828-0.89437.805-0.028-0.0280.0000.0000.0000.000
90B214VAL0-0.008-0.00332.9400.0010.0010.0000.0000.0000.000
91B215ALA00.0260.01832.9300.0010.0010.0000.0000.0000.000
92B216GLU-1-0.838-0.88933.915-0.012-0.0120.0000.0000.0000.000
93B217ALA0-0.019-0.00935.3460.0030.0030.0000.0000.0000.000
94B218VAL0-0.0110.00129.0560.0020.0020.0000.0000.0000.000
95B219ARG10.8410.89231.4870.0170.0170.0000.0000.0000.000
96B220ALA0-0.0150.00032.9930.0050.0050.0000.0000.0000.000
97B221ASP-1-0.819-0.87331.590-0.018-0.0180.0000.0000.0000.000
98B222VAL0-0.116-0.07727.1830.0030.0030.0000.0000.0000.000
99B223GLY0-0.0180.01429.0410.0060.0060.0000.0000.0000.000
100B224GLN0-0.055-0.05326.5020.0020.0020.0000.0000.0000.000
101B225ILE0-0.046-0.00124.1750.0010.0010.0000.0000.0000.000
102B226ASP-1-0.825-0.90719.5420.0160.0160.0000.0000.0000.000
103B227ILE00.002-0.00816.313-0.009-0.0090.0000.0000.0000.000
104B228LEU00.0300.03120.9460.0070.0070.0000.0000.0000.000
105B229VAL00.0050.00520.464-0.015-0.0150.0000.0000.0000.000
106B230HIS00.0340.02623.5260.0070.0070.0000.0000.0000.000
107B231SER0-0.039-0.01225.466-0.016-0.0160.0000.0000.0000.000
108B232LEU0-0.031-0.02027.1070.0090.0090.0000.0000.0000.000
109B233ALA00.0230.00829.289-0.008-0.0080.0000.0000.0000.000
110B234ASN0-0.029-0.03931.4250.0110.0110.0000.0000.0000.000
111B235GLY00.0450.03733.843-0.003-0.0030.0000.0000.0000.000
112B236PRO00.0250.01135.7410.0000.0000.0000.0000.0000.000
113B237GLU-1-0.811-0.90139.000-0.055-0.0550.0000.0000.0000.000
114B238VAL0-0.003-0.00135.733-0.003-0.0030.0000.0000.0000.000
115B239THR0-0.027-0.00835.400-0.002-0.0020.0000.0000.0000.000
116B240LYS10.7730.88838.2660.0550.0550.0000.0000.0000.000
117B241PRO00.0440.01341.9850.0010.0010.0000.0000.0000.000
118B242LEU00.0580.01542.6520.0020.0020.0000.0000.0000.000
119B243LEU0-0.013-0.01045.6880.0020.0020.0000.0000.0000.000
120B244GLN0-0.0130.00846.4840.0010.0010.0000.0000.0000.000
121B245THR00.0000.00644.6350.0000.0000.0000.0000.0000.000
122B246SER00.0190.01547.4190.0030.0030.0000.0000.0000.000
123B247ARG11.0220.99347.4730.0330.0330.0000.0000.0000.000
124B248LYS10.9910.98747.0130.0390.0390.0000.0000.0000.000
125B249GLY00.0300.01645.481-0.001-0.0010.0000.0000.0000.000
126B250TYR00.0090.01441.161-0.002-0.0020.0000.0000.0000.000
127B251LEU00.020-0.01642.165-0.002-0.0020.0000.0000.0000.000
128B252ALA0-0.0090.01142.188-0.001-0.0010.0000.0000.0000.000
129B253ALA00.0610.02939.127-0.002-0.0020.0000.0000.0000.000
130B254VAL00.0140.03937.609-0.004-0.0040.0000.0000.0000.000
131B255SER00.0130.00237.155-0.002-0.0020.0000.0000.0000.000
132B256SER0-0.007-0.00936.557-0.003-0.0030.0000.0000.0000.000
133B257SER0-0.077-0.04133.647-0.005-0.0050.0000.0000.0000.000
134B258SER0-0.027-0.02632.447-0.005-0.0050.0000.0000.0000.000
135B259TYR00.0430.02633.254-0.001-0.0010.0000.0000.0000.000
136B260SER00.043-0.00234.1370.0010.0010.0000.0000.0000.000
137B261PHE0-0.038-0.01526.1610.0000.0000.0000.0000.0000.000
138B262VAL00.0430.03031.1980.0010.0010.0000.0000.0000.000
139B263SER0-0.018-0.03733.2260.0040.0040.0000.0000.0000.000
140B264LEU0-0.007-0.00328.8310.0030.0030.0000.0000.0000.000
141B265LEU00.007-0.01427.4820.0030.0030.0000.0000.0000.000
142B266GLN0-0.018-0.00830.3130.0060.0060.0000.0000.0000.000
143B267HIS0-0.018-0.02333.6190.0080.0080.0000.0000.0000.000
144B268PHE00.006-0.01228.5990.0030.0030.0000.0000.0000.000
145B269LEU00.0210.03027.9850.0040.0040.0000.0000.0000.000
146B270PRO0-0.016-0.01529.5500.0060.0060.0000.0000.0000.000
147B271LEU0-0.062-0.01629.6490.0070.0070.0000.0000.0000.000
148B272MET0-0.065-0.03023.4660.0000.0000.0000.0000.0000.000
149B273LYS10.8560.92922.141-0.012-0.0120.0000.0000.0000.000
150B274GLU-1-0.773-0.87024.1740.0030.0030.0000.0000.0000.000
151B275GLY0-0.056-0.01920.9390.0120.0120.0000.0000.0000.000
152B276GLY0-0.052-0.01919.633-0.009-0.0090.0000.0000.0000.000
153B277SER0-0.050-0.03317.520-0.005-0.0050.0000.0000.0000.000
154B278ALA00.0400.00820.225-0.002-0.0020.0000.0000.0000.000
155B279LEU0-0.046-0.02318.763-0.013-0.0130.0000.0000.0000.000
156B280ALA00.0280.02022.2720.0070.0070.0000.0000.0000.000
157B281LEU0-0.017-0.00421.566-0.014-0.0140.0000.0000.0000.000
158B282SER00.0020.00924.4620.0140.0140.0000.0000.0000.000
159B283TYR00.009-0.00925.807-0.011-0.0110.0000.0000.0000.000
160B284ILE0-0.0100.01427.6310.0110.0110.0000.0000.0000.000
161B303ALA00.0600.03630.7980.0010.0010.0000.0000.0000.000
162B304LEU0-0.021-0.03429.6380.0050.0050.0000.0000.0000.000
163B305GLU-1-0.825-0.88326.834-0.126-0.1260.0000.0000.0000.000
164B306SER0-0.013-0.01828.046-0.001-0.0010.0000.0000.0000.000
165B307ASP-1-0.873-0.90930.791-0.067-0.0670.0000.0000.0000.000
166B308CYS0-0.0280.00524.4130.0030.0030.0000.0000.0000.000
167B309ARG10.9630.95226.1460.0870.0870.0000.0000.0000.000
168B310THR0-0.044-0.02527.8760.0070.0070.0000.0000.0000.000
169B311LEU00.0370.01428.8120.0050.0050.0000.0000.0000.000
170B312ALA0-0.0140.00425.0140.0030.0030.0000.0000.0000.000
171B313PHE0-0.032-0.01526.7220.0090.0090.0000.0000.0000.000
172B314GLU-1-0.941-0.97829.131-0.035-0.0350.0000.0000.0000.000
173B315ALA00.0250.01027.1620.0070.0070.0000.0000.0000.000
174B316GLY00.0150.01526.1830.0050.0050.0000.0000.0000.000
175B317ARG10.8400.90927.0940.0210.0210.0000.0000.0000.000
176B318ALA0-0.0170.00530.2510.0060.0060.0000.0000.0000.000
177B319ARG10.8420.92127.5570.0030.0030.0000.0000.0000.000
178B320ALA00.0130.00824.1950.0040.0040.0000.0000.0000.000
179B321VAL0-0.052-0.01923.1130.0010.0010.0000.0000.0000.000
180B322ARG10.7880.90115.5370.1610.1610.0000.0000.0000.000
181B323VAL00.0230.01521.920-0.004-0.0040.0000.0000.0000.000
182B324ASN0-0.027-0.02119.073-0.002-0.0020.0000.0000.0000.000
183B325CYS0-0.017-0.01021.8230.0070.0070.0000.0000.0000.000
184B326ILE0-0.0080.01117.541-0.019-0.0190.0000.0000.0000.000
185B327SER0-0.015-0.00921.6350.0190.0190.0000.0000.0000.000
186B328ALA0-0.003-0.00122.402-0.010-0.0100.0000.0000.0000.000
187B329GLY00.0930.05123.8210.0170.0170.0000.0000.0000.000
188B330PRO0-0.034-0.02625.597-0.006-0.0060.0000.0000.0000.000
189B331LEU0-0.0180.01823.422-0.008-0.0080.0000.0000.0000.000
190B363LYS10.7870.86717.2080.3090.3090.0000.0000.0000.000
191B364GLU-1-0.884-0.93820.585-0.238-0.2380.0000.0000.0000.000
192B365LEU00.0120.01720.458-0.023-0.0230.0000.0000.0000.000
193B366GLU-1-0.787-0.88619.134-0.225-0.2250.0000.0000.0000.000
194B367SER0-0.045-0.04119.865-0.019-0.0190.0000.0000.0000.000
195B368ASP-1-0.842-0.92114.960-0.434-0.4340.0000.0000.0000.000
196B369ASP-1-0.817-0.88915.502-0.406-0.4060.0000.0000.0000.000
197B370VAL00.0280.01415.818-0.034-0.0340.0000.0000.0000.000
198B371GLY00.003-0.01316.972-0.014-0.0140.0000.0000.0000.000
199B372ARG10.8320.89910.6520.4990.4990.0000.0000.0000.000
200B373ALA0-0.0100.00912.340-0.088-0.0880.0000.0000.0000.000
201B374ALA0-0.018-0.02014.1480.0080.0080.0000.0000.0000.000
202B375LEU0-0.006-0.00611.0710.0190.0190.0000.0000.0000.000
203B376PHE00.0030.0039.1290.0100.0100.0000.0000.0000.000
204B377LEU00.0350.01311.7530.0480.0480.0000.0000.0000.000
205B378LEU00.0120.01014.9280.0580.0580.0000.0000.0000.000
206B379SER0-0.0310.00010.7000.0260.0260.0000.0000.0000.000
207B380PRO0-0.002-0.02810.828-0.005-0.0050.0000.0000.0000.000
208B381LEU0-0.0150.0016.1810.0610.0610.0000.0000.0000.000
209B382ALA00.0080.0229.8510.0130.0130.0000.0000.0000.000
210B383ARG10.9660.98412.650-0.113-0.1130.0000.0000.0000.000
211B384ALA0-0.040-0.02014.4490.0260.0260.0000.0000.0000.000
212B385VAL0-0.029-0.01414.699-0.002-0.0020.0000.0000.0000.000
213B386THR00.0330.01517.466-0.005-0.0050.0000.0000.0000.000
214B387GLY00.0330.01221.0050.0090.0090.0000.0000.0000.000
215B388ALA0-0.050-0.01819.3130.0030.0030.0000.0000.0000.000
216B389THR00.0390.00921.2850.0010.0010.0000.0000.0000.000
217B390LEU0-0.030-0.01615.609-0.005-0.0050.0000.0000.0000.000
218B391TYR00.006-0.04220.108-0.001-0.0010.0000.0000.0000.000
219B392VAL0-0.049-0.01717.652-0.018-0.0180.0000.0000.0000.000
220B393ASP-1-0.793-0.93220.202-0.177-0.1770.0000.0000.0000.000
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