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: N1G9Q

Calculation Name: 3PUF-B-Xray372

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: 2023-06-19

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2049730.046239
FMO2-HF: Nuclear repulsion 1973022.372941
FMO2-HF: Total energy -76707.673297
FMO2-MP2: Total energy -76933.022438


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:13:MET)


Summations of interaction energy for fragment #1(B:13:MET)
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.
-3.4630.0450.805-1.517-2.796-0.008
Interaction energy analysis for fragmet #1(B:13:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.010
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].
3B15GLN0-0.008-0.0132.708-3.506-0.2530.805-1.490-2.568-0.008
4B16HIS0-0.039-0.0393.9921.3181.5730.000-0.027-0.2280.000
5B17VAL00.0350.0286.623-0.194-0.1940.0000.0000.0000.000
6B18PHE00.003-0.0148.3960.1900.1900.0000.0000.0000.000
7B19LEU00.0090.01211.971-0.042-0.0420.0000.0000.0000.000
8B20VAL0-0.012-0.00213.8060.0560.0560.0000.0000.0000.000
9B21SER00.0200.00016.7540.0050.0050.0000.0000.0000.000
10B22GLU-1-0.935-0.96919.483-0.251-0.2510.0000.0000.0000.000
11B23TYR0-0.009-0.00720.849-0.015-0.0150.0000.0000.0000.000
12B24LEU0-0.054-0.00516.512-0.006-0.0060.0000.0000.0000.000
13B35LEU0-0.002-0.01014.4170.0150.0150.0000.0000.0000.000
14B36MET0-0.037-0.00113.109-0.031-0.0310.0000.0000.0000.000
15B37PHE00.0120.0049.275-0.001-0.0010.0000.0000.0000.000
16B38VAL0-0.013-0.01313.3610.0680.0680.0000.0000.0000.000
17B39LYS10.9410.97716.449-0.469-0.4690.0000.0000.0000.000
18B40LEU0-0.009-0.00917.8920.0010.0010.0000.0000.0000.000
19B41VAL00.0310.02321.4840.0160.0160.0000.0000.0000.000
20B42ASN0-0.008-0.00623.266-0.035-0.0350.0000.0000.0000.000
21B43PRO0-0.015-0.01024.9990.0030.0030.0000.0000.0000.000
22B44CYS0-0.0570.00528.2290.0030.0030.0000.0000.0000.000
23B45SER00.0330.00226.3060.0020.0020.0000.0000.0000.000
24B46GLY00.0060.02027.9070.0060.0060.0000.0000.0000.000
25B47GLU-1-0.935-0.96624.0150.2370.2370.0000.0000.0000.000
26B48GLY0-0.037-0.03320.759-0.007-0.0070.0000.0000.0000.000
27B49ALA00.0070.00219.1420.0010.0010.0000.0000.0000.000
28B50ILE0-0.039-0.02212.8930.0140.0140.0000.0000.0000.000
29B51TYR00.0510.02316.376-0.038-0.0380.0000.0000.0000.000
30B52LEU0-0.030-0.00212.9020.0190.0190.0000.0000.0000.000
31B53PHE0-0.0030.00116.143-0.015-0.0150.0000.0000.0000.000
32B54ASN00.029-0.00917.554-0.017-0.0170.0000.0000.0000.000
33B55MET00.0470.00818.9370.0200.0200.0000.0000.0000.000
34B56CYS0-0.0060.00121.3620.0110.0110.0000.0000.0000.000
35B57LEU00.0150.00623.2760.0040.0040.0000.0000.0000.000
36B58GLN0-0.047-0.02124.1350.0140.0140.0000.0000.0000.000
37B59GLN00.0270.02122.480-0.005-0.0050.0000.0000.0000.000
38B60LEU00.0260.00721.4380.0020.0020.0000.0000.0000.000
39B61PHE0-0.022-0.01118.315-0.015-0.0150.0000.0000.0000.000
40B62GLU-1-0.831-0.91019.1890.0400.0400.0000.0000.0000.000
41B63VAL0-0.043-0.02713.304-0.039-0.0390.0000.0000.0000.000
42B64LYS10.9891.00916.7330.0070.0070.0000.0000.0000.000
43B65VAL0-0.044-0.03613.863-0.036-0.0360.0000.0000.0000.000
44B66PHE00.0120.02416.3210.0290.0290.0000.0000.0000.000
45B67LYS10.8510.91716.070-0.063-0.0630.0000.0000.0000.000
46B68GLU-1-0.802-0.89118.283-0.048-0.0480.0000.0000.0000.000
47B69LYS10.9110.93019.432-0.149-0.1490.0000.0000.0000.000
48B70HIS0-0.004-0.00519.781-0.011-0.0110.0000.0000.0000.000
49B71HIS00.0500.03017.270-0.053-0.0530.0000.0000.0000.000
50B72SER0-0.080-0.04013.8840.0490.0490.0000.0000.0000.000
51B73TRP0-0.009-0.01311.202-0.049-0.0490.0000.0000.0000.000
52B74PHE00.0410.01212.126-0.049-0.0490.0000.0000.0000.000
53B75ILE00.0010.0057.8040.0910.0910.0000.0000.0000.000
54B76ASN00.0080.01310.262-0.111-0.1110.0000.0000.0000.000
55B77GLN00.0050.01011.6020.1260.1260.0000.0000.0000.000
56B78SER00.000-0.0077.707-0.286-0.2860.0000.0000.0000.000
57B79VAL00.0460.0179.1140.1670.1670.0000.0000.0000.000
58B80GLN0-0.0230.0036.341-0.768-0.7680.0000.0000.0000.000
59B81SER00.013-0.0179.1360.1230.1230.0000.0000.0000.000
60B82GLY0-0.0140.00610.7540.0620.0620.0000.0000.0000.000
61B83GLY00.1000.04412.4080.0440.0440.0000.0000.0000.000
62B84LEU0-0.096-0.03911.6260.0410.0410.0000.0000.0000.000
63B85LEU00.0280.03912.230-0.131-0.1310.0000.0000.0000.000
64B86HIS00.0250.00210.6410.0850.0850.0000.0000.0000.000
65B87PHE00.0360.01413.858-0.068-0.0680.0000.0000.0000.000
66B88ALA0-0.0010.00715.1200.0430.0430.0000.0000.0000.000
67B89THR00.0450.01717.114-0.021-0.0210.0000.0000.0000.000
68B90PRO0-0.019-0.00820.9430.0200.0200.0000.0000.0000.000
69B91VAL00.0380.02422.5680.0060.0060.0000.0000.0000.000
70B92ASP-1-0.884-0.94025.243-0.003-0.0030.0000.0000.0000.000
71B93PRO00.025-0.01427.2530.0100.0100.0000.0000.0000.000
72B94LEU00.0070.00228.5440.0110.0110.0000.0000.0000.000
73B95PHE00.0210.01728.9220.0050.0050.0000.0000.0000.000
74B96LEU00.0220.00924.0820.0060.0060.0000.0000.0000.000
75B97LEU0-0.008-0.00628.6920.0080.0080.0000.0000.0000.000
76B98LEU00.0020.00031.5760.0030.0030.0000.0000.0000.000
77B99HIS0-0.0060.01530.1210.0080.0080.0000.0000.0000.000
78B100TYR0-0.048-0.05227.4500.0030.0030.0000.0000.0000.000
79B101LEU0-0.0060.00133.325-0.001-0.0010.0000.0000.0000.000
80B102ILE0-0.013-0.01235.517-0.002-0.0020.0000.0000.0000.000
81B103LYS10.9270.96730.747-0.129-0.1290.0000.0000.0000.000
82B104ALA00.0440.02036.7800.0010.0010.0000.0000.0000.000
83B105ASP-1-0.955-0.98639.0030.0550.0550.0000.0000.0000.000
84B106LYS10.8060.90839.628-0.074-0.0740.0000.0000.0000.000
85B107GLU-1-0.975-0.96541.0290.0750.0750.0000.0000.0000.000
86B108GLY00.1100.05343.037-0.001-0.0010.0000.0000.0000.000
87B109LYS10.8180.89445.694-0.047-0.0470.0000.0000.0000.000
88B110PHE0-0.044-0.04244.3300.0010.0010.0000.0000.0000.000
89B111GLN00.1210.09240.5370.0010.0010.0000.0000.0000.000
90B112PRO00.0180.03139.562-0.004-0.0040.0000.0000.0000.000
91B113LEU00.0530.00133.4520.0050.0050.0000.0000.0000.000
92B114ASP-1-0.932-0.97134.1560.0710.0710.0000.0000.0000.000
93B115GLN0-0.002-0.00934.7690.0050.0050.0000.0000.0000.000
94B116VAL0-0.0430.00235.2240.0040.0040.0000.0000.0000.000
95B117VAL0-0.065-0.03529.4720.0060.0060.0000.0000.0000.000
96B118VAL00.0330.02331.0380.0040.0040.0000.0000.0000.000
97B119ASP-1-0.808-0.93227.1220.1760.1760.0000.0000.0000.000
98B120ASN0-0.027-0.01027.4790.0020.0020.0000.0000.0000.000
99B121VAL0-0.0150.01124.5680.0190.0190.0000.0000.0000.000
100B122PHE0-0.033-0.01321.2410.0380.0380.0000.0000.0000.000
101B123PRO00.0640.02022.303-0.023-0.0230.0000.0000.0000.000
102B124ASN0-0.037-0.02419.511-0.034-0.0340.0000.0000.0000.000
103B125CYS00.0080.01522.664-0.021-0.0210.0000.0000.0000.000
104B126ILE00.0620.01825.142-0.016-0.0160.0000.0000.0000.000
105B127LEU0-0.040-0.02420.743-0.014-0.0140.0000.0000.0000.000
106B128LEU0-0.0100.00025.202-0.014-0.0140.0000.0000.0000.000
107B129LEU00.0320.01827.739-0.010-0.0100.0000.0000.0000.000
108B130LYS10.8710.93927.578-0.039-0.0390.0000.0000.0000.000
109B131LEU00.0180.03126.161-0.009-0.0090.0000.0000.0000.000
110B132PRO0-0.0090.00428.3650.0020.0020.0000.0000.0000.000
111B133GLY0-0.020-0.01331.545-0.002-0.0020.0000.0000.0000.000
112B134LEU00.0590.01932.1450.0000.0000.0000.0000.0000.000
113B135GLU-1-0.771-0.83334.7660.0210.0210.0000.0000.0000.000
114B136LYS10.9770.96137.8930.0140.0140.0000.0000.0000.000
115B137LEU0-0.0070.00831.717-0.001-0.0010.0000.0000.0000.000
116B138LEU00.0650.02435.7060.0010.0010.0000.0000.0000.000
117B139HIS0-0.0420.01037.844-0.001-0.0010.0000.0000.0000.000
118B140HIS0-0.060-0.03138.0980.0010.0010.0000.0000.0000.000
119B141VAL00.0310.01736.5690.0000.0000.0000.0000.0000.000
120B142THR0-0.051-0.03839.0200.0050.0050.0000.0000.0000.000
121B143GLU-1-0.914-0.95241.7760.0210.0210.0000.0000.0000.000
122B144GLU-1-0.858-0.95343.3080.0230.0230.0000.0000.0000.000
123B145LYS10.8570.93245.181-0.030-0.0300.0000.0000.0000.000
124B146GLY00.0470.00146.0470.0030.0030.0000.0000.0000.000
125B147ASN0-0.001-0.02047.589-0.003-0.0030.0000.0000.0000.000
126B148PRO00.024-0.00846.6980.0020.0020.0000.0000.0000.000
127B149GLU-1-0.936-0.94847.6250.0160.0160.0000.0000.0000.000
128B150ILE0-0.032-0.01046.3560.0000.0000.0000.0000.0000.000
129B151ASP-1-0.905-0.96942.5950.0280.0280.0000.0000.0000.000
130B152ASN0-0.088-0.05041.321-0.001-0.0010.0000.0000.0000.000
131B153LYN0-0.0430.03842.0060.0010.0010.0000.0000.0000.000
132B154LYS10.8340.91940.837-0.019-0.0190.0000.0000.0000.000
133B155TYR0-0.018-0.01841.0920.0030.0030.0000.0000.0000.000
134B156TYR0-0.003-0.04238.922-0.003-0.0030.0000.0000.0000.000
135B157LYS10.9250.96741.834-0.044-0.0440.0000.0000.0000.000
136B158TYR00.0290.01439.267-0.003-0.0030.0000.0000.0000.000
137B159SER0-0.0010.01641.6680.0000.0000.0000.0000.0000.000
138B160LYS10.9521.00242.125-0.045-0.0450.0000.0000.0000.000
139B161GLU-1-0.909-0.96443.9590.0200.0200.0000.0000.0000.000
140B162LYS10.8790.94443.139-0.023-0.0230.0000.0000.0000.000
141B163THR00.019-0.01538.433-0.002-0.0020.0000.0000.0000.000
142B164LEU00.0110.00940.346-0.001-0.0010.0000.0000.0000.000
143B165LYS10.9580.99742.563-0.017-0.0170.0000.0000.0000.000
144B166TRP0-0.022-0.01133.303-0.003-0.0030.0000.0000.0000.000
145B167LEU00.006-0.01735.908-0.003-0.0030.0000.0000.0000.000
146B168GLU-1-0.889-0.94238.9840.0060.0060.0000.0000.0000.000
147B169LYS10.9120.95239.9670.0000.0000.0000.0000.0000.000
148B170LYS10.8430.92732.3540.0030.0030.0000.0000.0000.000
149B171VAL00.0700.04236.332-0.004-0.0040.0000.0000.0000.000
150B172ASN00.0430.02038.492-0.003-0.0030.0000.0000.0000.000
151B173GLN0-0.0190.00134.754-0.001-0.0010.0000.0000.0000.000
152B174THR0-0.030-0.02133.059-0.004-0.0040.0000.0000.0000.000
153B175VAL00.0470.01635.575-0.005-0.0050.0000.0000.0000.000
154B176ALA0-0.037-0.01338.407-0.003-0.0030.0000.0000.0000.000
155B177ALA00.0110.00633.348-0.005-0.0050.0000.0000.0000.000
156B178LEU00.0040.01034.080-0.007-0.0070.0000.0000.0000.000
157B179LYS10.9590.98335.8210.0210.0210.0000.0000.0000.000
158B180THR0-0.061-0.03835.720-0.002-0.0020.0000.0000.0000.000
159B181ASN0-0.054-0.03631.085-0.012-0.0120.0000.0000.0000.000
160B182ASN0-0.076-0.01633.806-0.007-0.0070.0000.0000.0000.000
161B183VAL00.0030.00632.417-0.001-0.0010.0000.0000.0000.000
162B184ASN0-0.0010.01334.635-0.002-0.0020.0000.0000.0000.000
163B205GLU-1-0.981-1.00545.224-0.009-0.0090.0000.0000.0000.000
164B206GLU-1-0.934-0.97244.5660.0080.0080.0000.0000.0000.000
165B207ASP-1-0.851-0.93542.715-0.010-0.0100.0000.0000.0000.000
166B208TYR00.014-0.01037.0350.0010.0010.0000.0000.0000.000
167B209ILE0-0.0080.00539.3790.0010.0010.0000.0000.0000.000
168B210ARG10.9420.96640.292-0.013-0.0130.0000.0000.0000.000
169B211TYR0-0.0080.01532.3150.0060.0060.0000.0000.0000.000
170B212ALA00.009-0.00635.6600.0020.0020.0000.0000.0000.000
171B213HIS0-0.075-0.03535.6430.0010.0010.0000.0000.0000.000
172B214GLY00.0570.02735.4680.0050.0050.0000.0000.0000.000
173B215LEU0-0.0110.01329.5480.0050.0050.0000.0000.0000.000
174B216ILE0-0.004-0.01631.0610.0040.0040.0000.0000.0000.000
175B217SER0-0.055-0.03632.6570.0060.0060.0000.0000.0000.000
176B218ASP-1-0.906-0.95828.1500.0670.0670.0000.0000.0000.000
177B219TYR0-0.145-0.09425.1070.0050.0050.0000.0000.0000.000
178B220ILE0-0.047-0.02129.7680.0030.0030.0000.0000.0000.000
179B221PRO00.0430.02932.9160.0020.0020.0000.0000.0000.000
180B222LYS10.9010.92634.074-0.071-0.0710.0000.0000.0000.000
181B223GLU-1-0.904-0.96736.4840.0810.0810.0000.0000.0000.000
182B224LEU0-0.033-0.01736.624-0.006-0.0060.0000.0000.0000.000
183B225SER00.0120.01136.639-0.008-0.0080.0000.0000.0000.000
184B226ASP-1-0.767-0.87538.6210.0500.0500.0000.0000.0000.000
185B227ASP-1-0.975-1.00042.0970.0420.0420.0000.0000.0000.000
186B228LEU00.0160.00438.189-0.003-0.0030.0000.0000.0000.000
187B229SER0-0.083-0.02942.259-0.003-0.0030.0000.0000.0000.000
188B230LYS10.9000.95043.796-0.046-0.0460.0000.0000.0000.000
189B231TYR0-0.0300.01044.909-0.002-0.0020.0000.0000.0000.000