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: 2236R

Calculation Name: 1S9H-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1S9H

Chain ID: C

ChEMBL ID:

UniProt ID: P03132

Base Structure: X-ray

Registration Date: 2023-06-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2298403.455199
FMO2-HF: Nuclear repulsion 2218057.32825
FMO2-HF: Total energy -80346.126949
FMO2-MP2: Total energy -80582.173453


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(C:223:ALA)


Summations of interaction energy for fragment #1(C:223:ALA)
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.
-0.6923.0420.064-1.936-1.8610.002
Interaction energy analysis for fragmet #1(C:223:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.022
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].
3C225MET0-0.078-0.0423.786-1.0171.853-0.029-1.602-1.2390.005
4C226GLU-1-0.881-0.9273.8030.5250.7540.003-0.041-0.1900.000
5C227LEU0-0.015-0.0055.5490.1940.1940.0000.0000.0000.000
6C228VAL00.0090.0047.0650.0560.0560.0000.0000.0000.000
7C229GLY00.0370.0169.5740.0440.0440.0000.0000.0000.000
8C230TRP00.0550.0219.7990.0140.0140.0000.0000.0000.000
9C231LEU0-0.038-0.02910.607-0.005-0.0050.0000.0000.0000.000
10C232VAL00.0190.01013.0470.0020.0020.0000.0000.0000.000
11C233ASP-1-0.876-0.91315.1060.0930.0930.0000.0000.0000.000
12C234LYS10.7580.86714.339-0.156-0.1560.0000.0000.0000.000
13C235GLY00.0310.00916.956-0.005-0.0050.0000.0000.0000.000
14C236ILE0-0.107-0.04014.334-0.006-0.0060.0000.0000.0000.000
15C237THR00.0420.00816.272-0.031-0.0310.0000.0000.0000.000
16C238SER0-0.011-0.01317.173-0.018-0.0180.0000.0000.0000.000
17C239GLU-1-0.726-0.83313.969-0.139-0.1390.0000.0000.0000.000
18C240LYS10.8990.94915.7080.0440.0440.0000.0000.0000.000
19C241GLN0-0.009-0.01718.1810.0180.0180.0000.0000.0000.000
20C242TRP00.001-0.0087.850-0.035-0.0350.0000.0000.0000.000
21C243ILE0-0.010-0.00115.2600.0320.0320.0000.0000.0000.000
22C244GLN0-0.020-0.01416.5360.0050.0050.0000.0000.0000.000
23C245GLU-1-0.886-0.89717.1240.1110.1110.0000.0000.0000.000
24C246ASP-1-0.864-0.93914.1670.2970.2970.0000.0000.0000.000
25C247GLN00.0520.02713.9400.0080.0080.0000.0000.0000.000
26C248ALA00.0070.01214.0210.0020.0020.0000.0000.0000.000
27C249SER00.0200.00310.0790.0330.0330.0000.0000.0000.000
28C250TYR0-0.041-0.0429.1520.0570.0570.0000.0000.0000.000
29C251ILE00.008-0.01410.150-0.025-0.0250.0000.0000.0000.000
30C252SER0-0.045-0.0209.1530.0390.0390.0000.0000.0000.000
31C253PHE0-0.026-0.0163.091-0.6010.0710.091-0.284-0.479-0.003
32C254ASN0-0.054-0.0315.829-0.193-0.1930.0000.0000.0000.000
33C255ALA00.0540.0518.529-0.095-0.0950.0000.0000.0000.000
34C256ALA0-0.065-0.0317.589-0.019-0.0190.0000.0000.0000.000
35C257SER0-0.060-0.0467.654-0.098-0.0980.0000.0000.0000.000
36C258ASN00.0560.0378.4970.0360.0360.0000.0000.0000.000
37C259SER0-0.022-0.0048.369-0.056-0.0560.0000.0000.0000.000
38C260ARG10.9010.92910.3090.2460.2460.0000.0000.0000.000
39C261SER00.002-0.00212.2300.0130.0130.0000.0000.0000.000
40C262GLN00.0500.0154.476-0.569-0.606-0.001-0.0090.0470.000
41C263ILE00.0290.0219.076-0.027-0.0270.0000.0000.0000.000
42C264LYS10.8340.89710.1660.3530.3530.0000.0000.0000.000
43C265ALA00.0510.01811.0710.0350.0350.0000.0000.0000.000
44C266ALA00.0230.0168.5330.0230.0230.0000.0000.0000.000
45C267LEU00.0190.00310.6300.0810.0810.0000.0000.0000.000
46C268ASP-1-0.846-0.88613.655-0.282-0.2820.0000.0000.0000.000
47C269ASN0-0.007-0.00811.7940.0930.0930.0000.0000.0000.000
48C270ALA00.0100.00312.8670.0410.0410.0000.0000.0000.000
49C271GLY00.014-0.00614.7490.0370.0370.0000.0000.0000.000
50C272LYS10.8350.91417.7470.1800.1800.0000.0000.0000.000
51C273ILE00.0340.00915.3100.0160.0160.0000.0000.0000.000
52C274MET0-0.0550.00317.1260.0340.0340.0000.0000.0000.000
53C275SER0-0.045-0.02820.5500.0060.0060.0000.0000.0000.000
54C276LEU0-0.0050.01022.3480.0040.0040.0000.0000.0000.000
55C277THR0-0.065-0.02521.267-0.001-0.0010.0000.0000.0000.000
56C278LYS10.8150.91420.0030.0280.0280.0000.0000.0000.000
57C279THR0-0.005-0.01523.995-0.002-0.0020.0000.0000.0000.000
58C280ALA00.0410.01726.6610.0060.0060.0000.0000.0000.000
59C281PRO00.010-0.02027.9780.0070.0070.0000.0000.0000.000
60C282ASP-1-0.821-0.88423.544-0.007-0.0070.0000.0000.0000.000
61C283TYR0-0.016-0.03119.1150.0000.0000.0000.0000.0000.000
62C284LEU0-0.036-0.02224.9310.0080.0080.0000.0000.0000.000
63C285VAL0-0.037-0.01028.0820.0030.0030.0000.0000.0000.000
64C286GLY0-0.0030.00927.1340.0050.0050.0000.0000.0000.000
65C287GLN00.0600.03423.368-0.002-0.0020.0000.0000.0000.000
66C295SER00.0530.01238.3700.0010.0010.0000.0000.0000.000
67C296ASN0-0.083-0.05837.959-0.003-0.0030.0000.0000.0000.000
68C297ARG10.9060.96335.932-0.038-0.0380.0000.0000.0000.000
69C298ILE00.0380.02634.906-0.001-0.0010.0000.0000.0000.000
70C299TYR00.0130.00939.206-0.002-0.0020.0000.0000.0000.000
71C300LYS10.9390.96941.179-0.027-0.0270.0000.0000.0000.000
72C301ILE0-0.073-0.02240.949-0.002-0.0020.0000.0000.0000.000
73C302LEU0-0.017-0.02141.520-0.002-0.0020.0000.0000.0000.000
74C303GLU-1-0.829-0.91845.0230.0230.0230.0000.0000.0000.000
75C304LEU0-0.123-0.04446.551-0.001-0.0010.0000.0000.0000.000
76C305ASN0-0.051-0.07049.4980.0010.0010.0000.0000.0000.000
77C306GLY00.0150.00551.317-0.001-0.0010.0000.0000.0000.000
78C307TYR00.0100.06847.378-0.001-0.0010.0000.0000.0000.000
79C308ASP-1-0.820-0.91747.7790.0180.0180.0000.0000.0000.000
80C309PRO00.0180.00843.279-0.001-0.0010.0000.0000.0000.000
81C310GLN00.0540.03943.0050.0020.0020.0000.0000.0000.000
82C311TYR0-0.033-0.05043.514-0.001-0.0010.0000.0000.0000.000
83C312ALA0-0.006-0.01843.927-0.001-0.0010.0000.0000.0000.000
84C313ALA0-0.006-0.01539.319-0.002-0.0020.0000.0000.0000.000
85C314SER0-0.002-0.00639.3890.0000.0000.0000.0000.0000.000
86C315VAL0-0.025-0.00540.893-0.002-0.0020.0000.0000.0000.000
87C316PHE0-0.010-0.00737.140-0.003-0.0030.0000.0000.0000.000
88C317LEU00.0220.02734.989-0.003-0.0030.0000.0000.0000.000
89C318GLY00.013-0.01136.137-0.002-0.0020.0000.0000.0000.000
90C319TRP0-0.076-0.04334.494-0.002-0.0020.0000.0000.0000.000
91C320ALA0-0.036-0.01632.700-0.003-0.0030.0000.0000.0000.000
92C321THR0-0.088-0.04433.169-0.002-0.0020.0000.0000.0000.000
93C322LYN00.011-0.01133.8960.0000.0000.0000.0000.0000.000
94C323LYS10.8130.89537.178-0.002-0.0020.0000.0000.0000.000
95C324PHE00.0480.04439.7150.0000.0000.0000.0000.0000.000
96C325GLY00.0790.03742.412-0.001-0.0010.0000.0000.0000.000
97C326LYS10.7720.88342.2610.0120.0120.0000.0000.0000.000
98C327ARG10.7210.86743.4940.0090.0090.0000.0000.0000.000
99C328ASN00.0060.00837.6530.0020.0020.0000.0000.0000.000
100C329THR00.1120.01840.681-0.001-0.0010.0000.0000.0000.000
101C330ILE0-0.090-0.01738.0250.0010.0010.0000.0000.0000.000
102C331TRP0-0.053-0.03142.1640.0010.0010.0000.0000.0000.000
103C332LEU0-0.022-0.00140.7670.0020.0020.0000.0000.0000.000
104C333PHE00.009-0.00145.039-0.001-0.0010.0000.0000.0000.000
105C334GLY00.0250.01948.1940.0000.0000.0000.0000.0000.000
106C335PRO0-0.010-0.00447.0040.0000.0000.0000.0000.0000.000
107C336ALA0-0.059-0.03746.9080.0000.0000.0000.0000.0000.000
108C337THR00.0510.00443.1960.0020.0020.0000.0000.0000.000
109C338THR00.0060.03041.8020.0000.0000.0000.0000.0000.000
110C339GLY00.048-0.03339.5390.0010.0010.0000.0000.0000.000
111C340LYS10.7860.86740.4610.0070.0070.0000.0000.0000.000
112C341THR00.1200.06437.4270.0000.0000.0000.0000.0000.000
113C342ASN0-0.0620.03637.570-0.001-0.0010.0000.0000.0000.000
114C343ILE00.1000.01936.4250.0030.0030.0000.0000.0000.000
115C344ALA00.0350.02735.3010.0010.0010.0000.0000.0000.000
116C345GLU-1-0.829-0.90932.7410.0070.0070.0000.0000.0000.000
117C346ALA0-0.046-0.02731.5750.0000.0000.0000.0000.0000.000
118C347ILE00.0280.02430.8040.0040.0040.0000.0000.0000.000
119C348ALA0-0.012-0.01030.297-0.002-0.0020.0000.0000.0000.000
120C349HIS0-0.014-0.01127.477-0.006-0.0060.0000.0000.0000.000
121C350THR0-0.061-0.03426.0380.0060.0060.0000.0000.0000.000
122C351VAL0-0.034-0.00525.0980.0030.0030.0000.0000.0000.000
123C352PRO00.0220.01621.216-0.004-0.0040.0000.0000.0000.000
124C353PHE0-0.032-0.01320.471-0.006-0.0060.0000.0000.0000.000
125C354TYR00.008-0.02125.6690.0020.0020.0000.0000.0000.000
126C355GLY0-0.015-0.01929.384-0.006-0.0060.0000.0000.0000.000
127C356CYS0-0.0480.02131.5700.0020.0020.0000.0000.0000.000
128C369CYS0-0.014-0.01833.0100.0000.0000.0000.0000.0000.000
129C370VAL00.0390.01729.7900.0020.0020.0000.0000.0000.000
130C371ASP-1-0.796-0.89426.262-0.112-0.1120.0000.0000.0000.000
131C372LYS10.7920.91127.1730.0810.0810.0000.0000.0000.000
132C373MET00.0300.02623.4090.0050.0050.0000.0000.0000.000
133C374VAL00.0270.00529.3230.0050.0050.0000.0000.0000.000
134C375ILE00.0000.00531.897-0.003-0.0030.0000.0000.0000.000
135C376TRP00.0470.01033.8210.0040.0040.0000.0000.0000.000
136C377TRP00.0150.00336.458-0.002-0.0020.0000.0000.0000.000
137C378GLU-1-0.825-0.89738.147-0.010-0.0100.0000.0000.0000.000
138C409ALA0-0.040-0.03433.9640.0020.0020.0000.0000.0000.000
139C410GLN0-0.018-0.01133.776-0.003-0.0030.0000.0000.0000.000
140C411ILE0-0.046-0.02233.561-0.004-0.0040.0000.0000.0000.000
141C412ASP-1-0.823-0.90632.056-0.058-0.0580.0000.0000.0000.000
142C413PRO0-0.023-0.02934.1610.0030.0030.0000.0000.0000.000
143C414THR00.0240.03032.2420.0000.0000.0000.0000.0000.000
144C415PRO0-0.034-0.01933.2640.0010.0010.0000.0000.0000.000
145C416VAL00.0130.00835.5810.0010.0010.0000.0000.0000.000
146C417ILE00.0080.02236.2320.0030.0030.0000.0000.0000.000
147C418VAL00.0150.00139.049-0.001-0.0010.0000.0000.0000.000
148C419THR00.0250.04841.1960.0030.0030.0000.0000.0000.000
149C420SER0-0.040-0.01943.037-0.001-0.0010.0000.0000.0000.000
150C421ASN00.002-0.01046.3090.0010.0010.0000.0000.0000.000
151C422THR0-0.002-0.01448.9380.0010.0010.0000.0000.0000.000
152C423ASN00.0330.03850.4670.0000.0000.0000.0000.0000.000
153C441LEU00.029-0.01048.0740.0000.0000.0000.0000.0000.000
154C442GLN00.0910.04549.5010.0000.0000.0000.0000.0000.000
155C443ASP-1-0.821-0.89251.331-0.010-0.0100.0000.0000.0000.000
156C444ARG10.8620.90146.0260.0210.0210.0000.0000.0000.000
157C445MET00.0750.07445.185-0.001-0.0010.0000.0000.0000.000
158C446PHE0-0.0010.00443.2460.0010.0010.0000.0000.0000.000
159C447LYS10.8460.93245.7650.0030.0030.0000.0000.0000.000
160C448PHE00.0350.02143.5830.0010.0010.0000.0000.0000.000
161C449GLU-1-0.853-0.95047.457-0.001-0.0010.0000.0000.0000.000
162C450LEU00.004-0.00643.4470.0010.0010.0000.0000.0000.000
163C451THR0-0.029-0.00948.1270.0000.0000.0000.0000.0000.000
164C452ARG10.9810.98449.030-0.011-0.0110.0000.0000.0000.000
165C453ARG10.9010.92647.078-0.011-0.0110.0000.0000.0000.000
166C454LEU0-0.0030.02143.1570.0010.0010.0000.0000.0000.000
167C455ASP-1-0.877-0.93347.2310.0160.0160.0000.0000.0000.000
168C456HIS0-0.053-0.03245.445-0.002-0.0020.0000.0000.0000.000
169C457ASP-1-0.898-0.93443.7630.0260.0260.0000.0000.0000.000
170C458PHE0-0.029-0.01441.3340.0020.0020.0000.0000.0000.000
171C459GLY00.0560.01339.053-0.001-0.0010.0000.0000.0000.000
172C460LYS10.6830.84632.969-0.014-0.0140.0000.0000.0000.000
173C461VAL00.033-0.01034.0790.0030.0030.0000.0000.0000.000
174C462THR0-0.008-0.00529.9110.0030.0030.0000.0000.0000.000
175C463LYS11.0491.01624.852-0.060-0.0600.0000.0000.0000.000
176C464GLN00.0250.00826.649-0.002-0.0020.0000.0000.0000.000
177C465GLU-1-0.738-0.86628.9240.0410.0410.0000.0000.0000.000
178C466VAL00.0040.01530.416-0.002-0.0020.0000.0000.0000.000
179C467LYS10.8470.90824.003-0.054-0.0540.0000.0000.0000.000
180C468ASP-1-0.860-0.90529.4390.0570.0570.0000.0000.0000.000
181C469PHE0-0.020-0.00831.821-0.001-0.0010.0000.0000.0000.000
182C470PHE00.008-0.02431.832-0.002-0.0020.0000.0000.0000.000
183C471ARG10.8230.90730.525-0.056-0.0560.0000.0000.0000.000
184C472TRP00.0020.01732.749-0.002-0.0020.0000.0000.0000.000
185C473ALA00.003-0.01136.318-0.001-0.0010.0000.0000.0000.000
186C474LYS10.8970.94031.810-0.022-0.0220.0000.0000.0000.000
187C475ASP-1-0.919-0.94534.4220.0480.0480.0000.0000.0000.000
188C476HIS0-0.054-0.03237.1020.0010.0010.0000.0000.0000.000
189C477VAL0-0.037-0.00538.831-0.002-0.0020.0000.0000.0000.000
190C478VAL00.0130.00841.5110.0010.0010.0000.0000.0000.000
191C479GLU-1-0.859-0.90344.6930.0030.0030.0000.0000.0000.000
192C480VAL0-0.007-0.01543.9350.0010.0010.0000.0000.0000.000
193C481GLU-1-0.796-0.86546.9430.0040.0040.0000.0000.0000.000
194C482HIS0-0.088-0.06246.286-0.002-0.0020.0000.0000.0000.000
195C483GLU-1-0.951-0.97749.258-0.001-0.0010.0000.0000.0000.000
196C484PHE0-0.044-0.00549.9490.0010.0010.0000.0000.0000.000
197C485TYR0-0.001-0.01950.7610.0000.0000.0000.0000.0000.000
198C486VAL00.0310.01946.8060.0000.0000.0000.0000.0000.000
199C487LYS10.9990.98650.185-0.009-0.0090.0000.0000.0000.000
200C488LYN0-0.0100.03250.8000.0000.0000.0000.0000.0000.000
201C489GLY00.0260.01652.0940.0010.0010.0000.0000.0000.000
202C490GLY0-0.038-0.02951.8360.0010.0010.0000.0000.0000.000