Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 43RLN

Calculation Name: 3PUF-B-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: B

ChEMBL ID:

UniProt ID: O75792

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2071927.628294
FMO2-HF: Nuclear repulsion 1994708.438152
FMO2-HF: Total energy -77219.190142
FMO2-MP2: Total energy -77446.214333


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:12:ACE )


Summations of interaction energy for fragment #1(B:12:ACE )
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.
1.432.225-0.006-0.364-0.424-0.001
Interaction energy analysis for fragmet #1(B:12:ACE )
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 : -0.003
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].
3B14ARG 10.8960.9783.8201.5192.314-0.006-0.364-0.424-0.001
4B15GLN 0-0.003-0.0116.554-0.026-0.0260.0000.0000.0000.000
5B16HIS 0-0.040-0.0399.9840.1740.1740.0000.0000.0000.000
6B17VAL 00.0330.02713.201-0.003-0.0030.0000.0000.0000.000
7B18PHE 00.007-0.01215.6700.0190.0190.0000.0000.0000.000
8B19LEU 00.0090.01119.4350.0050.0050.0000.0000.0000.000
9B20VAL 0-0.016-0.00422.1160.0050.0050.0000.0000.0000.000
10B21SER 00.0220.00024.9160.0100.0100.0000.0000.0000.000
11B22GLU -1-0.940-0.97228.078-0.085-0.0850.0000.0000.0000.000
12B23TYR 0-0.003-0.00829.463-0.002-0.0020.0000.0000.0000.000
13B24LEU 0-0.077-0.02025.900-0.003-0.0030.0000.0000.0000.000
14B25NME 00.0180.01923.7400.0000.0000.0000.0000.0000.000
15B34ACE 00.0370.00626.1890.0000.0000.0000.0000.0000.000
16B35LEU 0-0.014-0.01023.2400.0110.0110.0000.0000.0000.000
17B36MET 00.0030.02421.298-0.020-0.0200.0000.0000.0000.000
18B37PHE 00.0110.00417.7870.0130.0130.0000.0000.0000.000
19B38VAL 0-0.013-0.01220.756-0.005-0.0050.0000.0000.0000.000
20B39LYS 10.9380.97519.6410.1180.1180.0000.0000.0000.000
21B40LEU 0-0.002-0.00523.0770.0060.0060.0000.0000.0000.000
22B41VAL 00.0300.02326.356-0.001-0.0010.0000.0000.0000.000
23B42ASN 0-0.011-0.00727.092-0.001-0.0010.0000.0000.0000.000
24B43PRO 0-0.013-0.00829.5010.0050.0050.0000.0000.0000.000
25B44CYS 0-0.0550.00732.7220.0030.0030.0000.0000.0000.000
26B45SER 00.026-0.00229.5560.0010.0010.0000.0000.0000.000
27B46GLY 00.0110.02331.6270.0030.0030.0000.0000.0000.000
28B47GLU -1-0.939-0.96826.445-0.037-0.0370.0000.0000.0000.000
29B48GLY 0-0.036-0.03223.957-0.005-0.0050.0000.0000.0000.000
30B49ALA 00.0070.00123.4700.0020.0020.0000.0000.0000.000
31B50ILE 0-0.041-0.02318.542-0.006-0.0060.0000.0000.0000.000
32B51TYR 00.0530.02421.9410.0070.0070.0000.0000.0000.000
33B52LEU 0-0.038-0.00621.301-0.017-0.0170.0000.0000.0000.000
34B53PHE 0-0.0010.00223.9900.0120.0120.0000.0000.0000.000
35B54ASN 00.017-0.01225.914-0.016-0.0160.0000.0000.0000.000
36B55MET 00.010-0.01427.0770.0070.0070.0000.0000.0000.000
37B56CYS 0-0.015-0.00129.7710.0070.0070.0000.0000.0000.000
38B57LEU 00.0100.00432.0390.0060.0060.0000.0000.0000.000
39B58GLN 0-0.041-0.01732.1620.0070.0070.0000.0000.0000.000
40B59GLN 00.0280.02131.0990.0020.0020.0000.0000.0000.000
41B60LEU 00.0300.00928.982-0.009-0.0090.0000.0000.0000.000
42B61PHE 0-0.026-0.01326.2750.0060.0060.0000.0000.0000.000
43B62GLU -1-0.830-0.90926.063-0.082-0.0820.0000.0000.0000.000
44B63VAL 0-0.041-0.02619.693-0.007-0.0070.0000.0000.0000.000
45B64LYS 10.9901.00923.0820.0730.0730.0000.0000.0000.000
46B65VAL 0-0.046-0.03618.055-0.013-0.0130.0000.0000.0000.000
47B66PHE 00.0090.02220.9170.0110.0110.0000.0000.0000.000
48B67LYS 10.8510.91617.1050.0050.0050.0000.0000.0000.000
49B68GLU -1-0.802-0.89220.760-0.004-0.0040.0000.0000.0000.000
50B69LYS 10.9090.92920.646-0.042-0.0420.0000.0000.0000.000
51B70HIS 0-0.004-0.00520.3940.0020.0020.0000.0000.0000.000
52B71HIS 00.0490.03018.944-0.008-0.0080.0000.0000.0000.000
53B72SER 0-0.079-0.04015.2710.0250.0250.0000.0000.0000.000
54B73TRP 0-0.013-0.01514.304-0.012-0.0120.0000.0000.0000.000
55B74PHE 00.0430.01214.2570.0230.0230.0000.0000.0000.000
56B75ILE 00.0010.00612.393-0.008-0.0080.0000.0000.0000.000
57B76ASN 00.0090.01413.7710.0000.0000.0000.0000.0000.000
58B77GLN 00.0030.01013.9100.0140.0140.0000.0000.0000.000
59B78SER 0-0.001-0.0089.645-0.012-0.0120.0000.0000.0000.000
60B79VAL 00.0450.01710.329-0.011-0.0110.0000.0000.0000.000
61B80GLN 0-0.0230.0038.383-0.100-0.1000.0000.0000.0000.000
62B81SER 00.011-0.0189.888-0.034-0.0340.0000.0000.0000.000
63B82GLY 0-0.0140.00611.877-0.003-0.0030.0000.0000.0000.000
64B83GLY 00.1010.04413.6870.0170.0170.0000.0000.0000.000
65B84LEU 0-0.097-0.03913.8250.0000.0000.0000.0000.0000.000
66B85LEU 00.0270.03816.898-0.022-0.0220.0000.0000.0000.000
67B86HIS 00.0260.00215.599-0.001-0.0010.0000.0000.0000.000
68B87PHE 00.0380.01419.898-0.002-0.0020.0000.0000.0000.000
69B88ALA 0-0.0030.00722.909-0.001-0.0010.0000.0000.0000.000
70B89THR 00.0430.01524.6230.0040.0040.0000.0000.0000.000
71B90PRO 0-0.017-0.00628.376-0.002-0.0020.0000.0000.0000.000
72B91VAL 00.0320.02229.6570.0040.0040.0000.0000.0000.000
73B92ASP -1-0.880-0.93932.435-0.050-0.0500.0000.0000.0000.000
74B93PRO 00.027-0.01334.6380.0000.0000.0000.0000.0000.000
75B94LEU 00.0130.00635.6730.0000.0000.0000.0000.0000.000
76B95PHE 00.0120.01235.1610.0020.0020.0000.0000.0000.000
77B96LEU 00.0220.00730.1800.0020.0020.0000.0000.0000.000
78B97LEU 0-0.001-0.00234.6840.0020.0020.0000.0000.0000.000
79B98LEU 00.0050.00237.8110.0030.0030.0000.0000.0000.000
80B99HIS 0-0.0140.01134.6280.0020.0020.0000.0000.0000.000
81B100TYR 0-0.054-0.05532.3100.0010.0010.0000.0000.0000.000
82B101LEU 00.0100.00938.5190.0030.0030.0000.0000.0000.000
83B102ILE 0-0.021-0.01540.6460.0030.0030.0000.0000.0000.000
84B103LYS 10.9190.96334.9250.0470.0470.0000.0000.0000.000
85B104ALA 00.0520.02441.1400.0020.0020.0000.0000.0000.000
86B105ASP -1-0.946-0.98143.691-0.024-0.0240.0000.0000.0000.000
87B106LYS 10.7930.90143.5770.0280.0280.0000.0000.0000.000
88B107GLU -1-0.979-0.96745.005-0.026-0.0260.0000.0000.0000.000
89B108GLY 00.1050.05047.0640.0020.0020.0000.0000.0000.000
90B109LYS 10.8090.88850.1450.0220.0220.0000.0000.0000.000
91B110PHE 0-0.044-0.04250.0520.0000.0000.0000.0000.0000.000
92B111GLN 00.1130.08845.5600.0000.0000.0000.0000.0000.000
93B112PRO 00.0560.05945.5380.0000.0000.0000.0000.0000.000
94B113LEU 00.048-0.00439.982-0.001-0.0010.0000.0000.0000.000
95B114ASP -1-0.943-0.97740.134-0.045-0.0450.0000.0000.0000.000
96B115GLN 0-0.002-0.00940.2620.0010.0010.0000.0000.0000.000
97B116VAL 0-0.0400.00340.7660.0010.0010.0000.0000.0000.000
98B117VAL 0-0.069-0.03835.310-0.001-0.0010.0000.0000.0000.000
99B118VAL 00.0330.02436.025-0.003-0.0030.0000.0000.0000.000
100B119ASP -1-0.813-0.93631.656-0.056-0.0560.0000.0000.0000.000
101B120ASN 0-0.030-0.01131.696-0.005-0.0050.0000.0000.0000.000
102B121VAL 0-0.0190.00927.403-0.003-0.0030.0000.0000.0000.000
103B122PHE 0-0.037-0.01524.803-0.010-0.0100.0000.0000.0000.000
104B123PRO 00.0620.02026.5900.0000.0000.0000.0000.0000.000
105B124ASN 0-0.041-0.02725.149-0.002-0.0020.0000.0000.0000.000
106B125CYS 00.0090.01528.433-0.001-0.0010.0000.0000.0000.000
107B126ILE 00.0650.02131.0600.0030.0030.0000.0000.0000.000
108B127LEU 0-0.045-0.02727.6760.0020.0020.0000.0000.0000.000
109B128LEU 0-0.013-0.00231.9950.0010.0010.0000.0000.0000.000
110B129LEU 00.0420.02534.7470.0030.0030.0000.0000.0000.000
111B130LYS 10.8740.94135.1730.0670.0670.0000.0000.0000.000
112B131LEU 00.0120.02633.949-0.002-0.0020.0000.0000.0000.000
113B132PRO 0-0.0100.00236.6340.0040.0040.0000.0000.0000.000
114B133GLY 0-0.021-0.01339.8140.0010.0010.0000.0000.0000.000
115B134LEU 00.0480.01239.3720.0010.0010.0000.0000.0000.000
116B135GLU -1-0.798-0.84942.424-0.036-0.0360.0000.0000.0000.000
117B136LYS 10.9740.95945.9190.0410.0410.0000.0000.0000.000
118B137LEU 0-0.029-0.00439.3730.0010.0010.0000.0000.0000.000
119B138LEU 00.0610.02342.3790.0010.0010.0000.0000.0000.000
120B139HIS 0-0.0250.02044.9120.0020.0020.0000.0000.0000.000
121B140HIS 0-0.075-0.03945.2260.0030.0030.0000.0000.0000.000
122B141VAL 00.0160.00642.9530.0010.0010.0000.0000.0000.000
123B142THR 0-0.050-0.03945.3220.0010.0010.0000.0000.0000.000
124B143GLU -1-0.925-0.96048.185-0.025-0.0250.0000.0000.0000.000
125B144GLU -1-0.865-0.95050.196-0.033-0.0330.0000.0000.0000.000
126B145LYS 10.8340.92051.8060.0260.0260.0000.0000.0000.000
127B146GLY 00.0890.02552.682-0.001-0.0010.0000.0000.0000.000
128B147ASN 0-0.0240.00454.4430.0000.0000.0000.0000.0000.000
129B148PRO 00.0760.03054.2320.0000.0000.0000.0000.0000.000
130B149GLU -1-0.955-0.99455.178-0.026-0.0260.0000.0000.0000.000
131B150ILE 0-0.036-0.01953.3150.0000.0000.0000.0000.0000.000
132B151ASP -1-0.949-0.97248.737-0.042-0.0420.0000.0000.0000.000
133B152ASN 0-0.0410.02150.0790.0000.0000.0000.0000.0000.000
134B153LYN 0-0.087-0.02150.9370.0010.0010.0000.0000.0000.000
135B154LYN 0-0.005-0.02647.814-0.001-0.0010.0000.0000.0000.000
136B155TYR -1-0.934-0.97147.679-0.032-0.0320.0000.0000.0000.000
137B156TYR 0-0.042-0.08045.8060.0000.0000.0000.0000.0000.000
138B157LYS 10.9100.95747.7150.0250.0250.0000.0000.0000.000
139B158TYR 00.0160.00744.8480.0010.0010.0000.0000.0000.000
140B159SER 00.0020.01847.3450.0020.0020.0000.0000.0000.000
141B160LYS 10.9470.99846.9020.0210.0210.0000.0000.0000.000
142B161GLU -1-0.914-0.96749.578-0.023-0.0230.0000.0000.0000.000
143B162LYS 10.8800.94649.6420.0290.0290.0000.0000.0000.000
144B163THR 00.026-0.01244.331-0.002-0.0020.0000.0000.0000.000
145B164LEU 00.0040.00546.359-0.001-0.0010.0000.0000.0000.000
146B165LYS 10.9530.99548.2860.0220.0220.0000.0000.0000.000
147B166TRP 0-0.016-0.00739.7080.0000.0000.0000.0000.0000.000
148B167LEU 00.001-0.01941.626-0.001-0.0010.0000.0000.0000.000
149B168GLU -1-0.879-0.94045.013-0.023-0.0230.0000.0000.0000.000
150B169LYS 10.9120.95346.7270.0310.0310.0000.0000.0000.000
151B170LYS 10.8360.92439.3160.0440.0440.0000.0000.0000.000
152B171VAL 00.0690.04142.637-0.001-0.0010.0000.0000.0000.000
153B172ASN 00.0490.02244.4350.0010.0010.0000.0000.0000.000
154B173GLN 0-0.0160.00341.802-0.001-0.0010.0000.0000.0000.000
155B174THR 0-0.035-0.02439.305-0.001-0.0010.0000.0000.0000.000
156B175VAL 00.0410.01541.8340.0000.0000.0000.0000.0000.000
157B176ALA 0-0.020-0.00444.7520.0010.0010.0000.0000.0000.000
158B177ALA 00.0060.00339.9310.0000.0000.0000.0000.0000.000
159B178LEU 00.0020.00939.561-0.001-0.0010.0000.0000.0000.000
160B179LYS 10.9570.98641.7610.0220.0220.0000.0000.0000.000
161B180THR 0-0.065-0.03442.4340.0010.0010.0000.0000.0000.000
162B181ASN 0-0.054-0.03837.657-0.001-0.0010.0000.0000.0000.000
163B182ASN 0-0.101-0.03639.7900.0010.0010.0000.0000.0000.000
164B183VAL 0-0.0010.00637.4720.0000.0000.0000.0000.0000.000
165B184ASN 00.007-0.02139.9200.0020.0020.0000.0000.0000.000
166B185NME 0-0.0140.03042.2210.0000.0000.0000.0000.0000.000
167B204ACE 00.0170.00251.6300.0000.0000.0000.0000.0000.000
168B205GLU -1-1.017-1.02450.572-0.019-0.0190.0000.0000.0000.000
169B206GLU -1-0.907-0.95149.699-0.014-0.0140.0000.0000.0000.000
170B207ASP -1-0.859-0.93747.273-0.017-0.0170.0000.0000.0000.000
171B208TYR 00.039-0.00642.299-0.001-0.0010.0000.0000.0000.000
172B209ILE 00.0050.01644.424-0.002-0.0020.0000.0000.0000.000
173B210ARG 10.9090.95344.4270.0170.0170.0000.0000.0000.000
174B211TYR 0-0.0180.00636.9350.0000.0000.0000.0000.0000.000
175B212ALA 00.014-0.00340.306-0.002-0.0020.0000.0000.0000.000
176B213HIS 0-0.037-0.01740.810-0.002-0.0020.0000.0000.0000.000
177B214GLY 00.0430.01939.690-0.001-0.0010.0000.0000.0000.000
178B215LEU 0-0.0080.01334.606-0.001-0.0010.0000.0000.0000.000
179B216ILE 00.001-0.01436.015-0.003-0.0030.0000.0000.0000.000
180B217SER 0-0.055-0.03437.621-0.001-0.0010.0000.0000.0000.000
181B218ASP -1-0.909-0.95932.608-0.035-0.0350.0000.0000.0000.000
182B219TYR 0-0.141-0.09231.087-0.003-0.0030.0000.0000.0000.000
183B220ILE 0-0.046-0.02034.915-0.001-0.0010.0000.0000.0000.000
184B221PRO 00.0450.02937.1500.0020.0020.0000.0000.0000.000
185B222LYS 10.8960.92238.1130.0180.0180.0000.0000.0000.000
186B223GLU -1-0.904-0.96739.941-0.021-0.0210.0000.0000.0000.000
187B224LEU 0-0.025-0.01341.5990.0010.0010.0000.0000.0000.000
188B225SER 00.0080.00840.7400.0010.0010.0000.0000.0000.000
189B226ASP -1-0.772-0.87742.838-0.016-0.0160.0000.0000.0000.000
190B227ASP -1-0.969-0.99645.919-0.019-0.0190.0000.0000.0000.000
191B228LEU 00.0140.00143.2900.0000.0000.0000.0000.0000.000
192B229SER 0-0.097-0.04046.5330.0010.0010.0000.0000.0000.000
193B230LYS 10.9030.95248.1660.0180.0180.0000.0000.0000.000
194B231TYR 0-0.073-0.02150.0210.0010.0010.0000.0000.0000.000
195B232NME 00.0330.03351.2900.0000.0000.0000.0000.0000.000