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: R9JN8

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 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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2546971.019661
FMO2-HF: Nuclear repulsion 2463421.120277
FMO2-HF: Total energy -83549.899384
FMO2-MP2: Total energy -83796.593874


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.
-1.2981.1971.757-1.642-2.6120.003
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 : 0.038 / 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].
3B95PRO0-0.046-0.0061.976-1.4200.9581.758-1.611-2.5260.003
4B96VAL00.0360.0014.3410.2110.328-0.001-0.031-0.0860.000
5B97ASP-1-0.805-0.8558.0680.0930.0930.0000.0000.0000.000
6B98LEU0-0.038-0.03910.5820.0360.0360.0000.0000.0000.000
7B99ARG10.8710.90112.539-0.052-0.0520.0000.0000.0000.000
8B100GLY0-0.052-0.01116.1850.0040.0040.0000.0000.0000.000
9B101LYS10.8880.94915.2790.0950.0950.0000.0000.0000.000
10B102THR0-0.012-0.00419.042-0.006-0.0060.0000.0000.0000.000
11B103ALA00.0310.00719.935-0.003-0.0030.0000.0000.0000.000
12B104PHE00.0420.03922.0650.0080.0080.0000.0000.0000.000
13B105VAL0-0.015-0.02322.127-0.009-0.0090.0000.0000.0000.000
14B106ALA00.0340.00425.1210.0100.0100.0000.0000.0000.000
15B107GLY00.0340.02227.555-0.011-0.0110.0000.0000.0000.000
16B108VAL0-0.060-0.03725.6300.0030.0030.0000.0000.0000.000
17B109ALA00.0430.02628.1510.0090.0090.0000.0000.0000.000
18B110ASP-1-0.866-0.94428.308-0.133-0.1330.0000.0000.0000.000
19B111SER0-0.003-0.01927.039-0.003-0.0030.0000.0000.0000.000
20B112ASN0-0.122-0.05725.473-0.005-0.0050.0000.0000.0000.000
21B113GLY00.1390.08525.6510.0000.0000.0000.0000.0000.000
22B114TYR0-0.041-0.09321.248-0.014-0.0140.0000.0000.0000.000
23B115GLY00.0420.03021.442-0.017-0.0170.0000.0000.0000.000
24B116TRP00.0410.00622.523-0.009-0.0090.0000.0000.0000.000
25B117ALA0-0.015-0.01219.072-0.006-0.0060.0000.0000.0000.000
26B118ILE00.0560.01917.836-0.022-0.0220.0000.0000.0000.000
27B119CYS0-0.0380.01418.387-0.004-0.0040.0000.0000.0000.000
28B120LYS10.9320.97418.4880.2170.2170.0000.0000.0000.000
29B121LEU00.0080.01112.793-0.004-0.0040.0000.0000.0000.000
30B122LEU00.0120.00014.512-0.030-0.0300.0000.0000.0000.000
31B123ARG10.8960.94515.9230.1310.1310.0000.0000.0000.000
32B124ALA0-0.037-0.00914.0510.0210.0210.0000.0000.0000.000
33B125ALA0-0.035-0.01211.7580.0050.0050.0000.0000.0000.000
34B126GLY0-0.004-0.02212.8050.0380.0380.0000.0000.0000.000
35B127ALA0-0.0170.00815.6740.0310.0310.0000.0000.0000.000
36B128ARG10.9300.98017.6860.0580.0580.0000.0000.0000.000
37B129VAL0-0.027-0.02920.236-0.007-0.0070.0000.0000.0000.000
38B130LEU0-0.016-0.00822.7880.0110.0110.0000.0000.0000.000
39B131VAL00.027-0.00325.800-0.011-0.0110.0000.0000.0000.000
40B132GLY00.0430.03027.8870.0110.0110.0000.0000.0000.000
41B133THR0-0.034-0.01830.538-0.006-0.0060.0000.0000.0000.000
42B134TRP00.0950.04632.4720.0060.0060.0000.0000.0000.000
43B135PRO00.0400.01235.4810.0010.0010.0000.0000.0000.000
44B136PRO0-0.039-0.01038.4760.0020.0020.0000.0000.0000.000
45B137VAL00.0070.00833.2170.0030.0030.0000.0000.0000.000
46B138TYR00.0350.03034.8070.0010.0010.0000.0000.0000.000
47B139SER0-0.030-0.02436.1480.0040.0040.0000.0000.0000.000
48B140ILE0-0.065-0.03835.8310.0040.0040.0000.0000.0000.000
49B141PHE00.0690.03830.1170.0000.0000.0000.0000.0000.000
50B142LYS10.8540.95334.6420.0500.0500.0000.0000.0000.000
51B143LYS10.9170.96835.6850.0580.0580.0000.0000.0000.000
52B176VAL0-0.011-0.02422.0700.0010.0010.0000.0000.0000.000
53B177PHE00.0350.02822.839-0.004-0.0040.0000.0000.0000.000
54B178ASP-1-0.866-0.91923.425-0.095-0.0950.0000.0000.0000.000
55B179LYS10.8410.93726.5510.0680.0680.0000.0000.0000.000
56B180ILE0-0.0200.00728.636-0.007-0.0070.0000.0000.0000.000
57B181TYR0-0.048-0.05430.0040.0060.0060.0000.0000.0000.000
58B182PRO0-0.033-0.00533.591-0.006-0.0060.0000.0000.0000.000
59B183LEU00.023-0.01631.8540.0010.0010.0000.0000.0000.000
60B184ASP-1-0.811-0.88435.205-0.076-0.0760.0000.0000.0000.000
61B185ALA0-0.032-0.02933.4510.0030.0030.0000.0000.0000.000
62B186VAL00.0080.01635.573-0.001-0.0010.0000.0000.0000.000
63B187PHE0-0.012-0.00738.5400.0040.0040.0000.0000.0000.000
64B188ASP-1-0.772-0.87038.627-0.067-0.0670.0000.0000.0000.000
65B189THR0-0.055-0.03140.1760.0020.0020.0000.0000.0000.000
66B190PRO00.0320.00843.008-0.001-0.0010.0000.0000.0000.000
67B191GLN00.0210.00945.504-0.001-0.0010.0000.0000.0000.000
68B192ASP-1-0.804-0.88743.468-0.049-0.0490.0000.0000.0000.000
69B193VAL0-0.095-0.05243.957-0.002-0.0020.0000.0000.0000.000
70B194PRO00.0190.02846.5450.0030.0030.0000.0000.0000.000
71B195PRO00.0550.00649.406-0.001-0.0010.0000.0000.0000.000
72B196GLU-1-0.950-0.98349.346-0.045-0.0450.0000.0000.0000.000
73B197VAL0-0.014-0.00144.437-0.001-0.0010.0000.0000.0000.000
74B198SER0-0.074-0.03246.9290.0000.0000.0000.0000.0000.000
75B199SER0-0.028-0.00848.3730.0000.0000.0000.0000.0000.000
76B200ASN00.0780.03345.9650.0010.0010.0000.0000.0000.000
77B201LYS10.9780.98246.8750.0400.0400.0000.0000.0000.000
78B202ARG10.8000.87642.5190.0490.0490.0000.0000.0000.000
79B203TYR00.0950.01740.699-0.003-0.0030.0000.0000.0000.000
80B204ALA0-0.047-0.00744.2560.0010.0010.0000.0000.0000.000
81B205GLY0-0.023-0.01745.696-0.001-0.0010.0000.0000.0000.000
82B206VAL0-0.061-0.01740.8150.0000.0000.0000.0000.0000.000
83B207GLY0-0.032-0.02241.2710.0000.0000.0000.0000.0000.000
84B208GLY00.0420.02040.696-0.002-0.0020.0000.0000.0000.000
85B209PHE00.0010.00538.491-0.002-0.0020.0000.0000.0000.000
86B210THR0-0.037-0.02538.014-0.004-0.0040.0000.0000.0000.000
87B211ILE00.027-0.00734.226-0.001-0.0010.0000.0000.0000.000
88B212SER0-0.040-0.02935.8250.0000.0000.0000.0000.0000.000
89B213GLU-1-0.834-0.91337.729-0.045-0.0450.0000.0000.0000.000
90B214VAL0-0.0280.00232.7570.0010.0010.0000.0000.0000.000
91B215ALA00.0240.01132.8580.0000.0000.0000.0000.0000.000
92B216GLU-1-0.926-0.96233.822-0.037-0.0370.0000.0000.0000.000
93B217ALA0-0.009-0.00835.2220.0030.0030.0000.0000.0000.000
94B218VAL0-0.034-0.00328.9230.0010.0010.0000.0000.0000.000
95B219ARG10.9430.97031.3920.0420.0420.0000.0000.0000.000
96B220ALA0-0.025-0.00132.8770.0040.0040.0000.0000.0000.000
97B221ASP-1-0.836-0.91931.774-0.045-0.0450.0000.0000.0000.000
98B222VAL0-0.114-0.06927.3050.0020.0020.0000.0000.0000.000
99B223GLY0-0.0200.01028.9040.0030.0030.0000.0000.0000.000
100B224GLN0-0.057-0.05726.2830.0020.0020.0000.0000.0000.000
101B225ILE0-0.066-0.00324.010-0.001-0.0010.0000.0000.0000.000
102B226ASP-1-0.853-0.94419.449-0.068-0.0680.0000.0000.0000.000
103B227ILE0-0.007-0.01216.407-0.015-0.0150.0000.0000.0000.000
104B228LEU00.0310.02820.8510.0110.0110.0000.0000.0000.000
105B229VAL00.0000.00720.508-0.017-0.0170.0000.0000.0000.000
106B230HIS00.0340.03123.5210.0090.0090.0000.0000.0000.000
107B231SER0-0.026-0.01724.732-0.016-0.0160.0000.0000.0000.000
108B232LEU0-0.029-0.01826.7870.0110.0110.0000.0000.0000.000
109B233ALA00.0280.00629.203-0.008-0.0080.0000.0000.0000.000
110B234ASN0-0.038-0.03131.2410.0140.0140.0000.0000.0000.000
111B235GLY00.0410.03233.916-0.002-0.0020.0000.0000.0000.000
112B236PRO00.0100.01135.7430.0000.0000.0000.0000.0000.000
113B237GLU-1-0.889-0.95439.073-0.066-0.0660.0000.0000.0000.000
114B238VAL00.0080.00535.791-0.003-0.0030.0000.0000.0000.000
115B239THR0-0.042-0.01735.637-0.001-0.0010.0000.0000.0000.000
116B240LYS10.8710.94838.3130.0650.0650.0000.0000.0000.000
117B241PRO00.0290.01342.0340.0010.0010.0000.0000.0000.000
118B242LEU00.0770.01943.1010.0020.0020.0000.0000.0000.000
119B243LEU0-0.012-0.00945.7200.0020.0020.0000.0000.0000.000
120B244GLN0-0.0050.00946.2820.0020.0020.0000.0000.0000.000
121B245THR0-0.0040.00644.7180.0000.0000.0000.0000.0000.000
122B246SER00.0100.00647.4520.0030.0030.0000.0000.0000.000
123B247ARG11.0260.99747.5270.0420.0420.0000.0000.0000.000
124B248LYS10.9990.98547.0670.0500.0500.0000.0000.0000.000
125B249GLY0-0.0010.00245.548-0.001-0.0010.0000.0000.0000.000
126B250TYR00.0310.02741.894-0.003-0.0030.0000.0000.0000.000
127B251LEU00.006-0.02242.218-0.003-0.0030.0000.0000.0000.000
128B252ALA0-0.0160.00842.248-0.001-0.0010.0000.0000.0000.000
129B253ALA00.0730.03539.134-0.003-0.0030.0000.0000.0000.000
130B254VAL00.0100.03137.671-0.005-0.0050.0000.0000.0000.000
131B255SER0-0.029-0.01937.211-0.005-0.0050.0000.0000.0000.000
132B256SER00.0390.00936.507-0.004-0.0040.0000.0000.0000.000
133B257SER0-0.093-0.04633.710-0.007-0.0070.0000.0000.0000.000
134B258SER0-0.033-0.02532.505-0.006-0.0060.0000.0000.0000.000
135B259TYR00.0610.03333.307-0.002-0.0020.0000.0000.0000.000
136B260SER00.0590.01234.0880.0000.0000.0000.0000.0000.000
137B261PHE0-0.043-0.01925.952-0.002-0.0020.0000.0000.0000.000
138B262VAL00.0460.03031.144-0.001-0.0010.0000.0000.0000.000
139B263SER0-0.022-0.01133.1620.0030.0030.0000.0000.0000.000
140B264LEU00.0050.00228.8180.0020.0020.0000.0000.0000.000
141B265LEU00.020-0.00827.3180.0010.0010.0000.0000.0000.000
142B266GLN0-0.020-0.01230.2230.0050.0050.0000.0000.0000.000
143B267HIS0-0.024-0.02733.5070.0090.0090.0000.0000.0000.000
144B268PHE00.018-0.01228.5700.0030.0030.0000.0000.0000.000
145B269LEU00.0220.02827.6570.0010.0010.0000.0000.0000.000
146B270PRO0-0.039-0.02329.3820.0040.0040.0000.0000.0000.000
147B271LEU0-0.069-0.00829.3040.0060.0060.0000.0000.0000.000
148B272MET0-0.062-0.02523.509-0.001-0.0010.0000.0000.0000.000
149B273LYS10.8880.95422.1810.0500.0500.0000.0000.0000.000
150B274GLU-1-0.808-0.90723.966-0.040-0.0400.0000.0000.0000.000
151B275GLY0-0.050-0.01720.6910.0070.0070.0000.0000.0000.000
152B276GLY0-0.051-0.01719.419-0.019-0.0190.0000.0000.0000.000
153B277SER0-0.062-0.03517.271-0.004-0.0040.0000.0000.0000.000
154B278ALA00.0450.01020.0880.0000.0000.0000.0000.0000.000
155B279LEU0-0.043-0.01818.731-0.014-0.0140.0000.0000.0000.000
156B280ALA00.0220.01822.2410.0090.0090.0000.0000.0000.000
157B281LEU0-0.029-0.00321.539-0.014-0.0140.0000.0000.0000.000
158B282SER00.0060.00924.5030.0170.0170.0000.0000.0000.000
159B283TYR00.015-0.00425.818-0.011-0.0110.0000.0000.0000.000
160B284ILE0-0.0150.01427.6890.0130.0130.0000.0000.0000.000
161B303ALA00.0130.00630.8900.0000.0000.0000.0000.0000.000
162B304LEU00.027-0.00729.6700.0050.0050.0000.0000.0000.000
163B305GLU-1-0.845-0.92126.436-0.149-0.1490.0000.0000.0000.000
164B306SER0-0.055-0.04328.039-0.002-0.0020.0000.0000.0000.000
165B307ASP-1-0.852-0.91630.783-0.089-0.0890.0000.0000.0000.000
166B308CYS0-0.049-0.00424.4290.0000.0000.0000.0000.0000.000
167B309ARG10.9670.96226.2210.1070.1070.0000.0000.0000.000
168B310THR0-0.036-0.00427.8650.0070.0070.0000.0000.0000.000
169B311LEU00.0360.01028.8750.0040.0040.0000.0000.0000.000
170B312ALA0-0.0180.00325.0620.0010.0010.0000.0000.0000.000
171B313PHE0-0.041-0.01826.7220.0070.0070.0000.0000.0000.000
172B314GLU-1-0.940-0.98029.109-0.060-0.0600.0000.0000.0000.000
173B315ALA00.0270.01127.0120.0070.0070.0000.0000.0000.000
174B316GLY00.0150.01526.1520.0020.0020.0000.0000.0000.000
175B317ARG10.8540.91427.0770.0510.0510.0000.0000.0000.000
176B318ALA0-0.0190.00630.1710.0060.0060.0000.0000.0000.000
177B319ARG10.8580.94627.2240.0460.0460.0000.0000.0000.000
178B320ALA00.0220.01424.0880.0000.0000.0000.0000.0000.000
179B321VAL0-0.047-0.01822.923-0.006-0.0060.0000.0000.0000.000
180B322ARG10.7810.89315.6000.2650.2650.0000.0000.0000.000
181B323VAL00.0320.01721.800-0.004-0.0040.0000.0000.0000.000
182B324ASN0-0.025-0.01618.8550.0080.0080.0000.0000.0000.000
183B325CYS0-0.015-0.01321.8480.0080.0080.0000.0000.0000.000
184B326ILE0-0.0090.01117.705-0.021-0.0210.0000.0000.0000.000
185B327SER00.004-0.00121.6850.0210.0210.0000.0000.0000.000
186B328ALA0-0.006-0.00622.528-0.010-0.0100.0000.0000.0000.000
187B329GLY00.0980.05323.8870.0180.0180.0000.0000.0000.000
188B330PRO0-0.0210.00325.597-0.008-0.0080.0000.0000.0000.000
189B331LEU0-0.0140.03122.886-0.008-0.0080.0000.0000.0000.000
190B363LYS10.7500.86217.3200.3080.3080.0000.0000.0000.000
191B364GLU-1-0.845-0.91520.670-0.228-0.2280.0000.0000.0000.000
192B365LEU00.0010.00820.468-0.026-0.0260.0000.0000.0000.000
193B366GLU-1-0.885-0.95218.535-0.261-0.2610.0000.0000.0000.000
194B367SER0-0.004-0.04319.532-0.017-0.0170.0000.0000.0000.000
195B368ASP-1-0.817-0.90214.427-0.469-0.4690.0000.0000.0000.000
196B369ASP-1-0.810-0.88815.155-0.425-0.4250.0000.0000.0000.000
197B370VAL00.0110.00615.717-0.039-0.0390.0000.0000.0000.000
198B371GLY0-0.001-0.01916.767-0.020-0.0200.0000.0000.0000.000
199B372ARG10.8620.91910.1760.5150.5150.0000.0000.0000.000
200B373ALA0-0.0020.01712.176-0.103-0.1030.0000.0000.0000.000
201B374ALA0-0.027-0.02414.224-0.001-0.0010.0000.0000.0000.000
202B375LEU0-0.012-0.01010.8960.0110.0110.0000.0000.0000.000
203B376PHE0-0.005-0.0018.779-0.007-0.0070.0000.0000.0000.000
204B377LEU00.0280.00311.8230.0310.0310.0000.0000.0000.000
205B378LEU00.0170.00614.9710.0550.0550.0000.0000.0000.000
206B379SER0-0.0210.01410.4760.0090.0090.0000.0000.0000.000
207B380PRO0-0.020-0.03910.7320.0120.0120.0000.0000.0000.000
208B381LEU0-0.0100.0085.8990.0750.0750.0000.0000.0000.000
209B382ALA00.0150.0229.8070.0370.0370.0000.0000.0000.000
210B383ARG10.9710.98212.9570.0430.0430.0000.0000.0000.000
211B384ALA0-0.041-0.02014.4300.0400.0400.0000.0000.0000.000
212B385VAL0-0.019-0.00414.5820.0090.0090.0000.0000.0000.000
213B386THR00.0150.01617.442-0.012-0.0120.0000.0000.0000.000
214B387GLY00.0510.01620.9880.0130.0130.0000.0000.0000.000
215B388ALA0-0.052-0.02419.3330.0070.0070.0000.0000.0000.000
216B389THR00.0450.01721.2740.0010.0010.0000.0000.0000.000
217B390LEU0-0.034-0.02215.427-0.003-0.0030.0000.0000.0000.000
218B391TYR00.0330.00120.121-0.001-0.0010.0000.0000.0000.000
219B392VAL0-0.049-0.00717.702-0.017-0.0170.0000.0000.0000.000
220B393ASP-1-0.773-0.92820.250-0.191-0.1910.0000.0000.0000.000
221B394ASN0-0.048-0.03020.8850.0230.0230.0000.0000.0000.000
222B395GLY00.0240.00622.2670.0090.0090.0000.0000.0000.000
223B396LEU0-0.0480.00623.7630.0150.0150.0000.0000.0000.000
224B397HIS00.015-0.00625.7140.0220.0220.0000.0000.0000.000
225B398ALA0-0.072-0.03525.078-0.008-0.0080.0000.0000.0000.000
226B399MET0-0.0390.00822.9130.0000.0000.0000.0000.0000.000