FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4978N

Calculation Name: 2ASU-B-Xray372

Preferred Name: Hepatocyte growth factor-like protein

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ASU

Chain ID: B

ChEMBL ID: CHEMBL6042

UniProt ID: P26927

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2757140.305353
FMO2-HF: Nuclear repulsion 2668324.423331
FMO2-HF: Total energy -88815.882022
FMO2-MP2: Total energy -89068.018707


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:484:VAL)


Summations of interaction energy for fragment #1(B:484:VAL)
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.
-25.561-13.22422.464-13.09-21.709-0.08
Interaction energy analysis for fragmet #1(B:484:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.002
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].
3B486GLY00.035-0.0043.001-2.7350.2720.320-1.541-1.7860.004
4B487GLY0-0.0260.0072.739-0.958-0.0800.336-0.447-0.767-0.001
5B488HIS0-0.042-0.0223.4820.0510.0020.0120.195-0.1570.000
6B489PRO00.0480.0175.962-0.197-0.1970.0000.0000.0000.000
7B490GLY00.0030.0127.6890.0460.0460.0000.0000.0000.000
8B491ASN0-0.070-0.0438.772-0.085-0.0850.0000.0000.0000.000
9B492SER00.1180.0667.715-0.007-0.0070.0000.0000.0000.000
10B493PRO00.0010.0039.769-0.061-0.0610.0000.0000.0000.000
11B494TRP00.0660.04110.3200.0320.0320.0000.0000.0000.000
12B495THR0-0.040-0.0246.743-0.031-0.0310.0000.0000.0000.000
13B496VAL0-0.040-0.01210.0470.0450.0450.0000.0000.0000.000
14B497SER0-0.020-0.03210.102-0.088-0.0880.0000.0000.0000.000
15B498LEU0-0.030-0.02011.3120.1370.1370.0000.0000.0000.000
16B499ARG10.8430.89811.9500.3420.3420.0000.0000.0000.000
17B500ASN00.017-0.00415.9230.0330.0330.0000.0000.0000.000
18B501ARG10.8770.92918.1580.1420.1420.0000.0000.0000.000
19B502GLN0-0.031-0.01419.3060.0190.0190.0000.0000.0000.000
20B503GLY00.0450.03518.7090.0120.0120.0000.0000.0000.000
21B504GLN0-0.021-0.01414.460-0.023-0.0230.0000.0000.0000.000
22B505HIS00.0140.0247.2350.2410.2410.0000.0000.0000.000
23B506PHE0-0.034-0.02611.0550.0470.0470.0000.0000.0000.000
24B507CYS0-0.0280.0169.228-0.039-0.0390.0000.0000.0000.000
25B508GLY00.0470.0468.002-0.013-0.0130.0000.0000.0000.000
26B509GLY00.0210.0008.9170.1650.1650.0000.0000.0000.000
27B510SER00.0160.01010.768-0.070-0.0700.0000.0000.0000.000
28B511LEU0-0.032-0.01012.8870.0460.0460.0000.0000.0000.000
29B512VAL00.013-0.00415.8650.0150.0150.0000.0000.0000.000
30B513LYS10.9560.98418.4920.1490.1490.0000.0000.0000.000
31B514GLU-1-0.817-0.91220.736-0.158-0.1580.0000.0000.0000.000
32B515GLN0-0.015-0.01522.151-0.006-0.0060.0000.0000.0000.000
33B516TRP0-0.003-0.01420.9530.0040.0040.0000.0000.0000.000
34B517ILE00.0150.01214.674-0.012-0.0120.0000.0000.0000.000
35B518LEU0-0.0100.00615.5810.0230.0230.0000.0000.0000.000
36B519THR00.010-0.01312.388-0.048-0.0480.0000.0000.0000.000
37B520ALA00.0620.03712.2000.0550.0550.0000.0000.0000.000
38B521ARG10.8820.92914.1470.1920.1920.0000.0000.0000.000
39B522GLN0-0.001-0.03114.046-0.008-0.0080.0000.0000.0000.000
40B524PHE00.0170.00514.6370.0210.0210.0000.0000.0000.000
41B525SER00.029-0.00218.4150.0090.0090.0000.0000.0000.000
42B526SER0-0.031-0.02921.0180.0180.0180.0000.0000.0000.000
43B527CYS0-0.068-0.05422.155-0.033-0.0330.0000.0000.0000.000
44B528HIS00.0450.02624.8690.0010.0010.0000.0000.0000.000
45B529MET0-0.0200.03019.1700.0050.0050.0000.0000.0000.000
46B530PRO00.0450.01324.673-0.003-0.0030.0000.0000.0000.000
47B531LEU00.001-0.00620.825-0.007-0.0070.0000.0000.0000.000
48B532THR00.0620.01924.028-0.006-0.0060.0000.0000.0000.000
49B533GLY00.0250.00324.343-0.001-0.0010.0000.0000.0000.000
50B534TYR0-0.0150.02118.0600.0020.0020.0000.0000.0000.000
51B535GLU-1-0.850-0.92819.033-0.162-0.1620.0000.0000.0000.000
52B536VAL00.0020.00314.988-0.038-0.0380.0000.0000.0000.000
53B537TRP0-0.051-0.03814.6500.0420.0420.0000.0000.0000.000
54B538LEU00.0420.01213.880-0.072-0.0720.0000.0000.0000.000
55B539GLY00.0850.04014.5440.0370.0370.0000.0000.0000.000
56B540THR0-0.0190.00913.3560.0490.0490.0000.0000.0000.000
57B541LEU00.0430.01710.498-0.070-0.0700.0000.0000.0000.000
58B542PHE00.0160.01010.273-0.050-0.0500.0000.0000.0000.000
59B543GLN00.0260.0247.681-0.045-0.0450.0000.0000.0000.000
60B544ASN00.001-0.00310.840-0.072-0.0720.0000.0000.0000.000
61B545PRO0-0.0100.01814.3370.0360.0360.0000.0000.0000.000
62B546GLN00.0010.00216.7700.0130.0130.0000.0000.0000.000
63B547HIS00.002-0.02519.9260.0020.0020.0000.0000.0000.000
64B548GLY0-0.018-0.00222.213-0.006-0.0060.0000.0000.0000.000
65B549GLU-1-0.914-0.94718.525-0.089-0.0890.0000.0000.0000.000
66B550PRO00.0220.00821.906-0.013-0.0130.0000.0000.0000.000
67B551SER0-0.049-0.04417.8920.0040.0040.0000.0000.0000.000
68B552LEU0-0.080-0.02416.789-0.025-0.0250.0000.0000.0000.000
69B553GLN00.0250.01818.4770.0230.0230.0000.0000.0000.000
70B554ARG10.9110.94518.4800.1240.1240.0000.0000.0000.000
71B555VAL0-0.043-0.02319.8940.0250.0250.0000.0000.0000.000
72B556PRO00.0630.04320.703-0.024-0.0240.0000.0000.0000.000
73B557VAL0-0.0110.00119.520-0.004-0.0040.0000.0000.0000.000
74B558ALA00.0310.01922.3830.0130.0130.0000.0000.0000.000
75B559LYS10.9090.94924.1910.1350.1350.0000.0000.0000.000
76B560MET00.0050.02220.839-0.014-0.0140.0000.0000.0000.000
77B561VAL0-0.024-0.00822.5630.0180.0180.0000.0000.0000.000
78B563GLY00.0730.04021.6710.0110.0110.0000.0000.0000.000
79B564PRO0-0.0010.00122.8390.0060.0060.0000.0000.0000.000
80B565SER00.0170.01123.347-0.012-0.0120.0000.0000.0000.000
81B566GLY00.0120.00522.3280.0050.0050.0000.0000.0000.000
82B567SER00.016-0.00520.311-0.010-0.0100.0000.0000.0000.000
83B568GLN0-0.048-0.02316.221-0.031-0.0310.0000.0000.0000.000
84B569LEU00.0350.03715.628-0.040-0.0400.0000.0000.0000.000
85B570VAL0-0.015-0.01017.3250.0300.0300.0000.0000.0000.000
86B571LEU00.0030.01517.791-0.030-0.0300.0000.0000.0000.000
87B572LEU0-0.035-0.01516.9020.0170.0170.0000.0000.0000.000
88B573LYS10.9510.99320.3480.1240.1240.0000.0000.0000.000
89B574LEU0-0.009-0.00319.034-0.002-0.0020.0000.0000.0000.000
90B575GLU-1-0.948-0.98522.977-0.116-0.1160.0000.0000.0000.000
91B576ARG10.9280.96024.6670.1480.1480.0000.0000.0000.000
92B577SER0-0.037-0.01324.121-0.013-0.0130.0000.0000.0000.000
93B578VAL0-0.0070.00419.3860.0080.0080.0000.0000.0000.000
94B579THR0-0.042-0.02322.6540.0120.0120.0000.0000.0000.000
95B580LEU00.0210.00920.328-0.014-0.0140.0000.0000.0000.000
96B581ASN00.0450.01120.1390.0040.0040.0000.0000.0000.000
97B582GLN00.0260.00919.788-0.018-0.0180.0000.0000.0000.000
98B583ARG10.8780.94214.0370.1920.1920.0000.0000.0000.000
99B584VAL0-0.0240.00115.431-0.042-0.0420.0000.0000.0000.000
100B585ALA00.0310.01216.0630.0300.0300.0000.0000.0000.000
101B586LEU00.0070.00716.133-0.031-0.0310.0000.0000.0000.000
102B587ILE0-0.0210.00312.7400.0080.0080.0000.0000.0000.000
103B588CYS0-0.022-0.00916.4770.0090.0090.0000.0000.0000.000
104B589LEU00.008-0.00317.899-0.015-0.0150.0000.0000.0000.000
105B590PRO00.0080.01918.4070.0130.0130.0000.0000.0000.000
106B591PRO00.005-0.00721.148-0.002-0.0020.0000.0000.0000.000
107B592GLU-1-0.864-0.96923.828-0.084-0.0840.0000.0000.0000.000
108B593TRP0-0.039-0.01824.6670.0050.0050.0000.0000.0000.000
109B594TYR0-0.0230.00720.4450.0090.0090.0000.0000.0000.000
110B595VAL00.0040.00521.525-0.007-0.0070.0000.0000.0000.000
111B596VAL0-0.019-0.00616.8140.0060.0060.0000.0000.0000.000
112B597PRO00.0140.01519.8090.0060.0060.0000.0000.0000.000
113B598PRO00.014-0.00918.8430.0020.0020.0000.0000.0000.000
114B599GLY0-0.0020.00617.850-0.001-0.0010.0000.0000.0000.000
115B600THR0-0.041-0.03115.7640.0030.0030.0000.0000.0000.000
116B601LYS10.8860.95512.887-0.037-0.0370.0000.0000.0000.000
117B602CYS0-0.037-0.02410.8820.0090.0090.0000.0000.0000.000
118B603GLU-1-0.911-0.9576.739-0.223-0.2230.0000.0000.0000.000
119B604ILE0-0.045-0.0062.733-0.993-0.1350.538-0.249-1.1470.002
120B605ALA00.017-0.0162.737-0.621-0.0420.235-0.255-0.5600.000
121B606GLY0-0.015-0.0062.915-0.2530.3340.570-0.182-0.975-0.001
122B607TRP0-0.097-0.0533.216-1.498-0.7650.100-0.251-0.581-0.004
123B608GLY00.0160.0213.0481.1921.7050.059-0.178-0.3930.000
124B609GLU-1-0.937-0.9803.3672.9583.8380.283-0.430-0.733-0.001
125B610THR0-0.004-0.0232.7361.7772.4372.058-0.933-1.784-0.003
126B611LYS10.9140.9594.743-1.822-1.702-0.001-0.024-0.0950.000
127B612GLY00.0260.0158.103-0.185-0.1850.0000.0000.0000.000
128B613THR0-0.059-0.0385.892-0.152-0.1520.0000.0000.0000.000
129B614GLY00.0740.0327.200-0.120-0.1200.0000.0000.0000.000
130B615ASN00.0370.0608.1080.1760.1760.0000.0000.0000.000
131B616DAS0-0.010-0.0114.052-0.1860.0040.000-0.027-0.1630.000
132B617THR0-0.042-0.0396.881-0.347-0.3470.0000.0000.0000.000
133B618VAL0-0.0080.0057.217-0.134-0.1340.0000.0000.0000.000
134B619LEU0-0.0250.0075.303-0.010-0.0100.0000.0000.0000.000
135B620ASN0-0.011-0.0112.166-0.684-0.0831.631-0.723-1.5080.001
136B621VAL00.0290.0102.865-3.171-1.2940.421-0.864-1.434-0.009
137B622ALA00.0260.0002.633-0.2520.4640.519-0.291-0.944-0.001
138B623LEU00.0020.0144.074-0.249-0.1530.001-0.005-0.0920.000
139B624LEU0-0.038-0.0215.8200.0750.0750.0000.0000.0000.000
140B625ASN00.026-0.0029.316-0.062-0.0620.0000.0000.0000.000
141B626VAL00.0280.01813.0060.0110.0110.0000.0000.0000.000
142B627ILE00.0070.01915.0120.0090.0090.0000.0000.0000.000
143B628SER00.0340.01717.474-0.014-0.0140.0000.0000.0000.000
144B629ASN00.0760.00619.6940.0080.0080.0000.0000.0000.000
145B630GLN0-0.004-0.00620.9380.0060.0060.0000.0000.0000.000
146B631GLU-1-0.918-0.94819.5730.0410.0410.0000.0000.0000.000
147B632CYS0-0.032-0.01213.939-0.002-0.0020.0000.0000.0000.000
148B633ASN00.0230.00519.0570.0050.0050.0000.0000.0000.000
149B634ILE00.0490.04322.0050.0000.0000.0000.0000.0000.000
150B635LYS10.8650.91117.483-0.088-0.0880.0000.0000.0000.000
151B636HIS0-0.067-0.04215.058-0.006-0.0060.0000.0000.0000.000
152B637ARG10.8810.93520.441-0.031-0.0310.0000.0000.0000.000
153B638GLY00.0430.02123.861-0.003-0.0030.0000.0000.0000.000
154B639ARG10.8460.94018.3700.0120.0120.0000.0000.0000.000
155B640VAL0-0.032-0.01118.195-0.009-0.0090.0000.0000.0000.000
156B641ARG10.9770.97920.4120.0780.0780.0000.0000.0000.000
157B642GLU-1-0.884-0.95521.056-0.049-0.0490.0000.0000.0000.000
158B643SER0-0.027-0.00720.2800.0010.0010.0000.0000.0000.000
159B644GLU-1-0.877-0.92516.821-0.122-0.1220.0000.0000.0000.000
160B645MET0-0.0030.00814.0830.0110.0110.0000.0000.0000.000
161B647THR00.0470.03010.155-0.008-0.0080.0000.0000.0000.000
162B648GLU-1-0.891-0.95812.5130.1130.1130.0000.0000.0000.000
163B649GLY0-0.051-0.01611.4200.0270.0270.0000.0000.0000.000
164B650LEU00.0300.0288.120-0.015-0.0150.0000.0000.0000.000
165B651LEU00.0260.00211.3260.0010.0010.0000.0000.0000.000
166B652ALA00.0320.0269.864-0.009-0.0090.0000.0000.0000.000
167B653PRO0-0.005-0.0218.633-0.011-0.0110.0000.0000.0000.000
168B654VAL00.0450.0304.255-0.0090.085-0.001-0.013-0.0810.000
169B655GLY0-0.025-0.0223.277-0.725-0.3230.012-0.121-0.2940.000
170B656ALA00.0030.0162.445-1.5230.5112.497-2.056-2.475-0.015
171B657CYS0-0.049-0.0133.2390.5600.8690.0190.096-0.4240.000
172B658GLU-1-0.781-0.8995.126-1.193-1.109-0.001-0.002-0.0810.000
173B659GLY00.0260.0174.963-0.350-0.319-0.001-0.001-0.0290.000
174B660ASP-1-0.751-0.8821.890-15.125-18.11912.859-4.781-5.084-0.052
175B661TYR0-0.062-0.0425.2750.4840.530-0.001-0.001-0.0440.000
176B662GLY00.015-0.0038.524-0.015-0.0150.0000.0000.0000.000
177B663GLY00.0060.0127.1970.0840.0840.0000.0000.0000.000
178B664PRO00.0060.0017.2620.1300.1300.0000.0000.0000.000
179B665LEU0-0.0170.0107.333-0.032-0.0320.0000.0000.0000.000
180B666ALA0-0.018-0.0179.3480.0260.0260.0000.0000.0000.000
181B668PHE00.0360.02914.065-0.007-0.0070.0000.0000.0000.000
182B669THR00.016-0.00816.3560.0160.0160.0000.0000.0000.000
183B670HIS0-0.004-0.00219.819-0.010-0.0100.0000.0000.0000.000
184B671ASN0-0.045-0.02522.0560.0000.0000.0000.0000.0000.000
185B672SER00.0220.01520.029-0.004-0.0040.0000.0000.0000.000
186B673TRP00.0140.01911.823-0.001-0.0010.0000.0000.0000.000
187B674VAL00.0080.00315.915-0.010-0.0100.0000.0000.0000.000
188B675LEU0-0.022-0.01112.353-0.008-0.0080.0000.0000.0000.000
189B676GLU-1-0.813-0.94114.069-0.103-0.1030.0000.0000.0000.000
190B677GLY00.003-0.00912.5080.0230.0230.0000.0000.0000.000
191B678ILE0-0.058-0.01710.746-0.037-0.0370.0000.0000.0000.000
192B679ILE0-0.0150.0014.4140.0170.102-0.001-0.006-0.0780.000
193B680ILE0-0.012-0.0048.594-0.060-0.0600.0000.0000.0000.000
194B681PRO00.0430.02610.1640.0100.0100.0000.0000.0000.000
195B682ASN0-0.025-0.01010.9010.1080.1080.0000.0000.0000.000
196B683ARG10.9280.96412.608-0.016-0.0160.0000.0000.0000.000
197B684VAL0-0.052-0.03112.4630.0130.0130.0000.0000.0000.000
198B686ALA00.0420.0335.5790.0530.0530.0000.0000.0000.000
199B687ARG10.9590.9797.676-0.120-0.1200.0000.0000.0000.000
200B688SER00.005-0.00311.458-0.033-0.0330.0000.0000.0000.000
201B689ARG10.9160.94812.929-0.175-0.1750.0000.0000.0000.000
202B690TRP0-0.035-0.02613.133-0.027-0.0270.0000.0000.0000.000
203B691PRO00.0100.01311.9560.0230.0230.0000.0000.0000.000
204B692ALA00.0390.0408.918-0.013-0.0130.0000.0000.0000.000
205B693VAL0-0.001-0.01511.0040.0020.0020.0000.0000.0000.000
206B694PHE00.0360.0197.240-0.045-0.0450.0000.0000.0000.000
207B695THR0-0.027-0.02012.4420.0400.0400.0000.0000.0000.000
208B696ARG10.9290.96914.6370.0590.0590.0000.0000.0000.000
209B697VAL00.0200.00015.1130.0070.0070.0000.0000.0000.000
210B698SER0-0.015-0.01517.8680.0040.0040.0000.0000.0000.000
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212B700PHE0-0.0030.00019.6900.0060.0060.0000.0000.0000.000
213B701VAL00.0090.00421.421-0.007-0.0070.0000.0000.0000.000
214B702ASP-1-0.815-0.89523.410-0.087-0.0870.0000.0000.0000.000
215B703TRP0-0.006-0.00220.669-0.002-0.0020.0000.0000.0000.000
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217B705HIS00.024-0.00423.749-0.004-0.0040.0000.0000.0000.000
218B706LYS10.8400.93526.5550.0840.0840.0000.0000.0000.000
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