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: 52M8Z

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2758217.938306
FMO2-HF: Nuclear repulsion 2669401.097788
FMO2-HF: Total energy -88816.840517
FMO2-MP2: Total energy -89068.892429


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.
-28.368-15.81723.064-13.85-21.764-0.1
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 : -0.024 / q_NPA : -0.025
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].
3B486GLY00.0490.0023.021-0.7561.6510.218-1.201-1.4240.001
4B487GLY0-0.0250.0062.952-0.5010.2020.119-0.288-0.5340.000
5B488HIS0-0.056-0.0303.713-0.400-0.3280.0060.043-0.1210.000
6B489PRO00.0480.0175.9830.1270.1270.0000.0000.0000.000
7B490GLY00.0000.0147.681-0.117-0.1170.0000.0000.0000.000
8B491ASN0-0.078-0.0468.820-0.035-0.0350.0000.0000.0000.000
9B492SER00.0740.0117.681-0.018-0.0180.0000.0000.0000.000
10B493PRO0-0.0150.0059.739-0.032-0.0320.0000.0000.0000.000
11B494TRP00.0630.0399.902-0.041-0.0410.0000.0000.0000.000
12B495THR0-0.035-0.0136.532-0.052-0.0520.0000.0000.0000.000
13B496VAL0-0.031-0.0119.9130.0250.0250.0000.0000.0000.000
14B497SER0-0.014-0.02210.018-0.056-0.0560.0000.0000.0000.000
15B498LEU0-0.018-0.01611.1990.0700.0700.0000.0000.0000.000
16B499ARG10.8410.89711.9510.0710.0710.0000.0000.0000.000
17B500ASN00.001-0.02215.7840.0370.0370.0000.0000.0000.000
18B501ARG10.8900.93417.9830.1410.1410.0000.0000.0000.000
19B502GLN0-0.042-0.01719.2500.0270.0270.0000.0000.0000.000
20B503GLY00.0410.03018.7070.0060.0060.0000.0000.0000.000
21B504GLN00.0050.00214.4330.0020.0020.0000.0000.0000.000
22B505HIS00.0240.0326.8600.2680.2680.0000.0000.0000.000
23B506PHE0-0.033-0.02711.021-0.030-0.0300.0000.0000.0000.000
24B507CYS0-0.0300.0189.025-0.146-0.1460.0000.0000.0000.000
25B508GLY00.0440.0437.9530.0720.0720.0000.0000.0000.000
26B509GLY00.018-0.0038.8580.0350.0350.0000.0000.0000.000
27B510SER00.0190.01110.7360.0390.0390.0000.0000.0000.000
28B511LEU0-0.043-0.01612.720-0.010-0.0100.0000.0000.0000.000
29B512VAL00.0190.00115.7160.0180.0180.0000.0000.0000.000
30B513LYS10.8700.92318.346-0.005-0.0050.0000.0000.0000.000
31B514GLU-1-0.758-0.86620.5850.0060.0060.0000.0000.0000.000
32B515GLN00.002-0.02522.069-0.006-0.0060.0000.0000.0000.000
33B516TRP00.014-0.00120.922-0.011-0.0110.0000.0000.0000.000
34B517ILE00.0140.01014.6430.0080.0080.0000.0000.0000.000
35B518LEU0-0.0020.01115.437-0.009-0.0090.0000.0000.0000.000
36B519THR00.008-0.01212.458-0.017-0.0170.0000.0000.0000.000
37B520ALA00.0610.03611.9910.0330.0330.0000.0000.0000.000
38B521ARG10.8580.91613.9350.1550.1550.0000.0000.0000.000
39B522GLN00.002-0.02814.0960.0030.0030.0000.0000.0000.000
40B524PHE00.0260.00914.5920.0150.0150.0000.0000.0000.000
41B525SER00.027-0.00218.3760.0030.0030.0000.0000.0000.000
42B526SER0-0.033-0.03221.0780.0150.0150.0000.0000.0000.000
43B527CYS0-0.052-0.04721.942-0.018-0.0180.0000.0000.0000.000
44B528HIS00.0510.03024.7350.0070.0070.0000.0000.0000.000
45B529MET0-0.0200.03118.915-0.002-0.0020.0000.0000.0000.000
46B530PRO00.0410.01624.5800.0060.0060.0000.0000.0000.000
47B531LEU00.015-0.00320.475-0.011-0.0110.0000.0000.0000.000
48B532THR00.0510.01923.8270.0020.0020.0000.0000.0000.000
49B533GLY00.0230.00124.134-0.011-0.0110.0000.0000.0000.000
50B534TYR0-0.0030.02617.790-0.002-0.0020.0000.0000.0000.000
51B535GLU-1-0.802-0.88018.919-0.041-0.0410.0000.0000.0000.000
52B536VAL00.0020.00314.787-0.027-0.0270.0000.0000.0000.000
53B537TRP0-0.060-0.04614.5980.0230.0230.0000.0000.0000.000
54B538LEU00.0460.01613.766-0.010-0.0100.0000.0000.0000.000
55B539GLY00.0820.03814.4210.0010.0010.0000.0000.0000.000
56B540THR0-0.021-0.00213.3580.0250.0250.0000.0000.0000.000
57B541LEU00.0390.01610.687-0.013-0.0130.0000.0000.0000.000
58B542PHE00.0020.01010.1940.1020.1020.0000.0000.0000.000
59B543GLN00.0130.0207.728-0.096-0.0960.0000.0000.0000.000
60B544ASN0-0.020-0.01611.251-0.087-0.0870.0000.0000.0000.000
61B545PRO0-0.0020.02614.5990.0160.0160.0000.0000.0000.000
62B546GLN0-0.003-0.00517.030-0.028-0.0280.0000.0000.0000.000
63B547HIS00.016-0.02219.8530.0080.0080.0000.0000.0000.000
64B548GLY0-0.0110.00222.334-0.003-0.0030.0000.0000.0000.000
65B549GLU-1-0.922-0.95018.3100.0990.0990.0000.0000.0000.000
66B550PRO00.0310.01021.761-0.004-0.0040.0000.0000.0000.000
67B551SER0-0.036-0.03117.866-0.001-0.0010.0000.0000.0000.000
68B552LEU0-0.084-0.02716.723-0.001-0.0010.0000.0000.0000.000
69B553GLN00.0200.01518.360-0.014-0.0140.0000.0000.0000.000
70B554ARG10.8540.90818.3580.0330.0330.0000.0000.0000.000
71B555VAL0-0.028-0.02519.7860.0070.0070.0000.0000.0000.000
72B556PRO00.0590.03620.598-0.013-0.0130.0000.0000.0000.000
73B557VAL0-0.0130.00319.4230.0050.0050.0000.0000.0000.000
74B558ALA00.0260.01922.3000.0020.0020.0000.0000.0000.000
75B559LYS10.9260.95324.1410.0490.0490.0000.0000.0000.000
76B560MET00.0010.02020.745-0.003-0.0030.0000.0000.0000.000
77B561VAL0-0.028-0.01122.4560.0080.0080.0000.0000.0000.000
78B563GLY00.0700.04121.4800.0100.0100.0000.0000.0000.000
79B564PRO00.0040.00322.665-0.005-0.0050.0000.0000.0000.000
80B565SER00.0200.01423.199-0.011-0.0110.0000.0000.0000.000
81B566GLY00.0080.00522.2070.0070.0070.0000.0000.0000.000
82B567SER00.011-0.01020.169-0.003-0.0030.0000.0000.0000.000
83B568GLN0-0.047-0.02116.093-0.026-0.0260.0000.0000.0000.000
84B569LEU00.0370.03615.359-0.024-0.0240.0000.0000.0000.000
85B570VAL0-0.013-0.00917.1240.0040.0040.0000.0000.0000.000
86B571LEU0-0.0010.01617.585-0.003-0.0030.0000.0000.0000.000
87B572LEU0-0.036-0.01516.905-0.004-0.0040.0000.0000.0000.000
88B573LYS10.9250.98420.3110.0400.0400.0000.0000.0000.000
89B574LEU0-0.015-0.00618.826-0.008-0.0080.0000.0000.0000.000
90B575GLU-1-0.931-0.98022.907-0.042-0.0420.0000.0000.0000.000
91B576ARG10.9010.94824.2880.0260.0260.0000.0000.0000.000
92B577SER0-0.015-0.00224.044-0.005-0.0050.0000.0000.0000.000
93B578VAL0-0.0090.01119.3380.0020.0020.0000.0000.0000.000
94B579THR0-0.028-0.01722.5770.0040.0040.0000.0000.0000.000
95B580LEU00.0130.01320.1320.0040.0040.0000.0000.0000.000
96B581ASN00.0410.00820.0790.0070.0070.0000.0000.0000.000
97B582GLN00.0270.01019.7720.0010.0010.0000.0000.0000.000
98B583ARG10.8790.94614.392-0.138-0.1380.0000.0000.0000.000
99B584VAL0-0.029-0.00315.3690.0040.0040.0000.0000.0000.000
100B585ALA00.0250.00915.975-0.005-0.0050.0000.0000.0000.000
101B586LEU0-0.013-0.00316.034-0.003-0.0030.0000.0000.0000.000
102B587ILE0-0.0140.00612.7200.0120.0120.0000.0000.0000.000
103B588CYS0-0.033-0.01416.379-0.016-0.0160.0000.0000.0000.000
104B589LEU00.0290.00817.7960.0040.0040.0000.0000.0000.000
105B590PRO0-0.0030.01418.3240.0010.0010.0000.0000.0000.000
106B591PRO00.006-0.00921.050-0.009-0.0090.0000.0000.0000.000
107B592GLU-1-0.848-0.95523.8430.0040.0040.0000.0000.0000.000
108B593TRP0-0.072-0.03924.6620.0020.0020.0000.0000.0000.000
109B594TYR0-0.0290.00920.1900.0010.0010.0000.0000.0000.000
110B595VAL00.0020.01021.5990.0000.0000.0000.0000.0000.000
111B596VAL0-0.015-0.00616.5070.0030.0030.0000.0000.0000.000
112B597PRO00.0320.02319.687-0.001-0.0010.0000.0000.0000.000
113B598PRO00.012-0.00618.6640.0170.0170.0000.0000.0000.000
114B599GLY0-0.0100.00217.719-0.008-0.0080.0000.0000.0000.000
115B600THR0-0.031-0.02515.5730.0080.0080.0000.0000.0000.000
116B601LYS10.8520.92212.807-0.205-0.2050.0000.0000.0000.000
117B602CYS0-0.038-0.02610.7650.0110.0110.0000.0000.0000.000
118B603GLU-1-0.840-0.9056.6580.4900.4900.0000.0000.0000.000
119B604ILE0-0.050-0.0132.433-0.929-0.2890.872-0.287-1.2250.002
120B605ALA00.020-0.0102.708-0.5730.0610.277-0.291-0.6200.000
121B606GLY0-0.011-0.0052.828-0.794-0.3630.869-0.189-1.112-0.001
122B607TRP0-0.077-0.0423.0630.9131.4040.161-0.031-0.621-0.004
123B608GLY00.0300.0272.9760.5791.0750.054-0.183-0.3670.000
124B609GLU-1-0.917-0.9693.083-0.3401.0480.335-0.723-1.001-0.005
125B610THR0-0.012-0.0131.897-6.147-8.9498.500-3.218-2.480-0.024
126B611LYS10.8750.9343.9711.2751.4250.000-0.025-0.1250.000
127B612GLY00.0250.0147.1890.1740.1740.0000.0000.0000.000
128B613THR0-0.049-0.0376.2870.1600.1600.0000.0000.0000.000
129B614GLY00.0710.0317.3140.1580.1580.0000.0000.0000.000
130B615ASN00.0180.0447.775-0.134-0.1340.0000.0000.0000.000
131B616DAS00.005-0.0014.6010.6350.806-0.001-0.010-0.1600.000
132B617THR0-0.017-0.0286.730-0.308-0.3080.0000.0000.0000.000
133B618VAL0-0.020-0.0067.444-0.206-0.2060.0000.0000.0000.000
134B619LEU0-0.0260.0105.0870.4830.4830.0000.0000.0000.000
135B620ASN0-0.008-0.0112.399-2.254-1.4490.865-0.498-1.1720.001
136B621VAL00.0300.0072.922-2.514-0.6990.347-0.803-1.359-0.008
137B622ALA00.0290.0052.823-0.4380.2900.453-0.282-0.898-0.001
138B623LEU0-0.0080.0074.069-0.278-0.1850.000-0.001-0.0930.000
139B624LEU0-0.029-0.0175.4640.0010.0010.0000.0000.0000.000
140B625ASN00.0310.0039.205-0.065-0.0650.0000.0000.0000.000
141B626VAL00.0290.01812.910-0.004-0.0040.0000.0000.0000.000
142B627ILE00.0060.02014.834-0.009-0.0090.0000.0000.0000.000
143B628SER00.0300.02117.309-0.011-0.0110.0000.0000.0000.000
144B629ASN00.057-0.01019.5370.0130.0130.0000.0000.0000.000
145B630GLN00.0130.00320.700-0.008-0.0080.0000.0000.0000.000
146B631GLU-1-0.897-0.94719.7490.0840.0840.0000.0000.0000.000
147B632CYS0-0.041-0.02213.677-0.026-0.0260.0000.0000.0000.000
148B633ASN00.0100.00318.880-0.017-0.0170.0000.0000.0000.000
149B634ILE00.0490.04221.813-0.009-0.0090.0000.0000.0000.000
150B635LYS10.8680.91717.300-0.064-0.0640.0000.0000.0000.000
151B636HIS0-0.034-0.02114.791-0.036-0.0360.0000.0000.0000.000
152B637ARG10.8960.94120.2710.0150.0150.0000.0000.0000.000
153B638GLY00.0400.02023.661-0.005-0.0050.0000.0000.0000.000
154B639ARG10.8170.92018.3220.0610.0610.0000.0000.0000.000
155B640VAL0-0.047-0.02317.822-0.008-0.0080.0000.0000.0000.000
156B641ARG10.9490.97220.4430.0700.0700.0000.0000.0000.000
157B642GLU-1-0.871-0.95321.0760.0150.0150.0000.0000.0000.000
158B643SER0-0.0150.00020.4740.0060.0060.0000.0000.0000.000
159B644GLU-1-0.866-0.92216.897-0.070-0.0700.0000.0000.0000.000
160B645MET00.0150.02914.0380.0070.0070.0000.0000.0000.000
161B647THR00.0510.0329.9410.0240.0240.0000.0000.0000.000
162B648GLU-1-0.889-0.93712.3300.1740.1740.0000.0000.0000.000
163B649GLY0-0.054-0.02411.3670.0380.0380.0000.0000.0000.000
164B650LEU00.0360.0327.839-0.019-0.0190.0000.0000.0000.000
165B651LEU00.0310.00511.416-0.054-0.0540.0000.0000.0000.000
166B652ALA00.0340.0419.876-0.051-0.0510.0000.0000.0000.000
167B653PRO0-0.010-0.0238.7080.0550.0550.0000.0000.0000.000
168B654VAL00.0420.0254.115-0.155-0.060-0.001-0.014-0.0800.000
169B655GLY0-0.024-0.0203.424-0.788-0.3650.012-0.123-0.3110.001
170B656ALA0-0.0040.0132.453-1.1260.6042.728-1.993-2.465-0.014
171B657CYS0-0.0180.0053.2150.1710.4690.0190.117-0.4340.000
172B658GLU-1-0.747-0.8695.198-1.261-1.160-0.001-0.001-0.0980.000
173B659GLY00.0270.0215.304-0.819-0.8190.0000.0000.0000.000
174B660ASP-1-0.758-0.8832.132-13.764-12.2317.234-3.836-4.930-0.048
175B661TYR0-0.097-0.0825.0500.6210.673-0.001-0.004-0.0470.000
176B662GLY00.013-0.0048.280-0.003-0.0030.0000.0000.0000.000
177B663GLY00.0110.0137.0270.0820.0820.0000.0000.0000.000
178B664PRO00.0090.0047.0760.0250.0250.0000.0000.0000.000
179B665LEU0-0.0200.0047.2140.1050.1050.0000.0000.0000.000
180B666ALA0-0.009-0.0099.290-0.065-0.0650.0000.0000.0000.000
181B668PHE00.0390.03114.027-0.026-0.0260.0000.0000.0000.000
182B669THR00.008-0.00916.2130.0020.0020.0000.0000.0000.000
183B670HIS0-0.001-0.00419.639-0.002-0.0020.0000.0000.0000.000
184B671ASN0-0.038-0.01921.955-0.001-0.0010.0000.0000.0000.000
185B672SER00.0210.01420.006-0.007-0.0070.0000.0000.0000.000
186B673TRP00.0090.01411.5310.0060.0060.0000.0000.0000.000
187B674VAL00.0070.00515.840-0.018-0.0180.0000.0000.0000.000
188B675LEU0-0.027-0.01512.3130.0250.0250.0000.0000.0000.000
189B676GLU-1-0.790-0.93313.9730.0640.0640.0000.0000.0000.000
190B677GLY00.000-0.00412.526-0.016-0.0160.0000.0000.0000.000
191B678ILE0-0.064-0.02110.6370.0090.0090.0000.0000.0000.000
192B679ILE0-0.0190.0024.278-0.0710.026-0.001-0.009-0.0870.000
193B680ILE00.0070.0078.486-0.095-0.0950.0000.0000.0000.000
194B681PRO00.0270.02310.0610.0040.0040.0000.0000.0000.000
195B682ASN0-0.039-0.02010.7790.1370.1370.0000.0000.0000.000
196B683ARG10.9180.96212.5960.0740.0740.0000.0000.0000.000
197B684VAL0-0.051-0.03212.555-0.023-0.0230.0000.0000.0000.000
198B686ALA00.0340.0295.536-0.077-0.0770.0000.0000.0000.000
199B687ARG10.9610.9797.6720.1060.1060.0000.0000.0000.000
200B688SER00.005-0.01611.4540.0490.0490.0000.0000.0000.000
201B689ARG10.9020.94213.041-0.055-0.0550.0000.0000.0000.000
202B690TRP0-0.004-0.01513.110-0.022-0.0220.0000.0000.0000.000
203B691PRO00.0030.01011.8860.0180.0180.0000.0000.0000.000
204B692ALA00.0300.0368.737-0.052-0.0520.0000.0000.0000.000
205B693VAL0-0.005-0.01610.7940.0240.0240.0000.0000.0000.000
206B694PHE00.0440.0227.239-0.038-0.0380.0000.0000.0000.000
207B695THR0-0.015-0.01212.4370.0090.0090.0000.0000.0000.000
208B696ARG10.9110.96214.604-0.024-0.0240.0000.0000.0000.000
209B697VAL00.023-0.00315.119-0.013-0.0130.0000.0000.0000.000
210B698SER0-0.006-0.01417.825-0.009-0.0090.0000.0000.0000.000
211B699VAL0-0.018-0.00620.754-0.002-0.0020.0000.0000.0000.000
212B700PHE0-0.0010.00119.521-0.008-0.0080.0000.0000.0000.000
213B701VAL00.0120.00521.205-0.007-0.0070.0000.0000.0000.000
214B702ASP-1-0.781-0.85223.338-0.013-0.0130.0000.0000.0000.000
215B703TRP00.0090.00420.222-0.002-0.0020.0000.0000.0000.000
216B704ILE00.001-0.00619.443-0.003-0.0030.0000.0000.0000.000
217B705HIS00.0430.00923.620-0.004-0.0040.0000.0000.0000.000
218B706LYS10.8000.89126.4420.0130.0130.0000.0000.0000.000
219B707VAL0-0.077-0.02424.712-0.001-0.0010.0000.0000.0000.000
220B708MET0-0.105-0.04222.9910.0010.0010.0000.0000.0000.000