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

tag_button

FMODB ID: 66V9Z

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 OptAll
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 -2297763.50311
FMO2-HF: Nuclear repulsion 2217415.793683
FMO2-HF: Total energy -80347.709427
FMO2-MP2: Total energy -80583.511273


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.
0.4443.4170.041-1.386-1.6280.003
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 : 0.081 / q_NPA : 0.035
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].
3C225MET0-0.045-0.0483.898-0.1211.946-0.009-1.120-0.9380.004
4C226GLU-1-0.885-0.9303.7490.1150.4630.007-0.075-0.2800.000
5C227LEU0-0.037-0.0145.2790.3180.388-0.001-0.002-0.0670.000
6C228VAL00.0150.0087.1500.1690.1690.0000.0000.0000.000
7C229GLY00.0350.0169.5520.1030.1030.0000.0000.0000.000
8C230TRP00.0390.0159.6400.0570.0570.0000.0000.0000.000
9C231LEU0-0.029-0.02210.6090.0430.0430.0000.0000.0000.000
10C232VAL00.0030.00512.9660.0330.0330.0000.0000.0000.000
11C233ASP-1-0.874-0.92314.913-0.057-0.0570.0000.0000.0000.000
12C234LYS10.7320.85514.149-0.030-0.0300.0000.0000.0000.000
13C235GLY00.0190.01016.9260.0100.0100.0000.0000.0000.000
14C236ILE0-0.099-0.04514.3410.0050.0050.0000.0000.0000.000
15C237THR00.0270.01416.149-0.038-0.0380.0000.0000.0000.000
16C238SER0-0.023-0.02317.094-0.012-0.0120.0000.0000.0000.000
17C239GLU-1-0.691-0.80514.230-0.134-0.1340.0000.0000.0000.000
18C240LYS10.9060.95515.8880.0680.0680.0000.0000.0000.000
19C241GLN00.002-0.01118.6340.0200.0200.0000.0000.0000.000
20C242TRP00.0190.0078.034-0.027-0.0270.0000.0000.0000.000
21C243ILE0-0.010-0.00615.6690.0280.0280.0000.0000.0000.000
22C244GLN0-0.014-0.01117.0140.0080.0080.0000.0000.0000.000
23C245GLU-1-0.864-0.90117.5500.0330.0330.0000.0000.0000.000
24C246ASP-1-0.786-0.88314.1070.1590.1590.0000.0000.0000.000
25C247GLN00.0260.01814.0600.0020.0020.0000.0000.0000.000
26C248ALA00.0010.01114.2230.0120.0120.0000.0000.0000.000
27C249SER00.027-0.0129.9480.0350.0350.0000.0000.0000.000
28C250TYR0-0.065-0.0469.2270.0580.0580.0000.0000.0000.000
29C251ILE00.013-0.00810.2280.0010.0010.0000.0000.0000.000
30C252SER0-0.035-0.0158.9670.0640.0640.0000.0000.0000.000
31C253PHE0-0.023-0.0183.192-0.3300.1770.045-0.184-0.368-0.001
32C254ASN0-0.032-0.0225.813-0.064-0.0640.0000.0000.0000.000
33C255ALA00.0310.0288.628-0.071-0.0710.0000.0000.0000.000
34C256ALA0-0.029-0.0168.0020.0480.0480.0000.0000.0000.000
35C257SER0-0.022-0.0147.625-0.098-0.0980.0000.0000.0000.000
36C258ASN00.0440.0378.3220.0010.0010.0000.0000.0000.000
37C259SER0-0.031-0.0278.126-0.070-0.0700.0000.0000.0000.000
38C260ARG10.8320.87910.1820.1370.1370.0000.0000.0000.000
39C261SER00.0070.01112.3340.0050.0050.0000.0000.0000.000
40C262GLN00.0460.0184.765-0.512-0.531-0.001-0.0050.0250.000
41C263ILE00.0250.0189.545-0.073-0.0730.0000.0000.0000.000
42C264LYS10.8330.89610.5170.3170.3170.0000.0000.0000.000
43C265ALA00.0440.01911.0910.0170.0170.0000.0000.0000.000
44C266ALA00.0260.0198.507-0.014-0.0140.0000.0000.0000.000
45C267LEU00.0160.00510.6050.0710.0710.0000.0000.0000.000
46C268ASP-1-0.845-0.89213.760-0.303-0.3030.0000.0000.0000.000
47C269ASN0-0.042-0.02912.6170.0830.0830.0000.0000.0000.000
48C270ALA00.0240.01713.1990.0410.0410.0000.0000.0000.000
49C271GLY00.031-0.00215.1050.0430.0430.0000.0000.0000.000
50C272LYS10.8160.91018.2650.2320.2320.0000.0000.0000.000
51C273ILE00.0390.01615.1940.0220.0220.0000.0000.0000.000
52C274MET0-0.0350.00717.0560.0400.0400.0000.0000.0000.000
53C275SER0-0.088-0.07820.3520.0110.0110.0000.0000.0000.000
54C276LEU0-0.032-0.01022.5340.0100.0100.0000.0000.0000.000
55C277THR0-0.045-0.02621.0380.0010.0010.0000.0000.0000.000
56C278LYS10.8370.93219.7500.1150.1150.0000.0000.0000.000
57C279THR0-0.020-0.02723.8030.0040.0040.0000.0000.0000.000
58C280ALA00.0580.01226.3060.0020.0020.0000.0000.0000.000
59C281PRO00.006-0.01428.0680.0050.0050.0000.0000.0000.000
60C282ASP-1-0.821-0.87023.236-0.079-0.0790.0000.0000.0000.000
61C283TYR0-0.017-0.02719.0080.0010.0010.0000.0000.0000.000
62C284LEU0-0.012-0.00825.0010.0100.0100.0000.0000.0000.000
63C285VAL0-0.015-0.00528.1410.0070.0070.0000.0000.0000.000
64C286GLY0-0.011-0.00226.883-0.001-0.0010.0000.0000.0000.000
65C287GLN00.0490.03023.4120.0030.0030.0000.0000.0000.000
66C295SER00.0470.01138.5890.0000.0000.0000.0000.0000.000
67C296ASN0-0.015-0.01338.201-0.002-0.0020.0000.0000.0000.000
68C297ARG10.8850.93235.976-0.013-0.0130.0000.0000.0000.000
69C298ILE00.0130.01434.9950.0000.0000.0000.0000.0000.000
70C299TYR0-0.003-0.00639.095-0.001-0.0010.0000.0000.0000.000
71C300LYS10.8100.90241.152-0.005-0.0050.0000.0000.0000.000
72C301ILE0-0.030-0.01441.0440.0000.0000.0000.0000.0000.000
73C302LEU00.007-0.00441.326-0.001-0.0010.0000.0000.0000.000
74C303GLU-1-0.748-0.84544.9990.0040.0040.0000.0000.0000.000
75C304LEU0-0.074-0.02146.5170.0000.0000.0000.0000.0000.000
76C305ASN0-0.086-0.08549.4720.0000.0000.0000.0000.0000.000
77C306GLY00.0200.02451.1610.0000.0000.0000.0000.0000.000
78C307TYR00.0090.02547.7060.0000.0000.0000.0000.0000.000
79C308ASP-1-0.813-0.91447.532-0.004-0.0040.0000.0000.0000.000
80C309PRO00.0270.01043.772-0.002-0.0020.0000.0000.0000.000
81C310GLN00.0450.02942.8020.0000.0000.0000.0000.0000.000
82C311TYR0-0.021-0.03142.933-0.002-0.0020.0000.0000.0000.000
83C312ALA00.004-0.00243.830-0.002-0.0020.0000.0000.0000.000
84C313ALA00.0160.00039.093-0.003-0.0030.0000.0000.0000.000
85C314SER00.000-0.00239.057-0.002-0.0020.0000.0000.0000.000
86C315VAL0-0.032-0.01140.464-0.003-0.0030.0000.0000.0000.000
87C316PHE0-0.015-0.01537.197-0.003-0.0030.0000.0000.0000.000
88C317LEU00.0080.01035.007-0.004-0.0040.0000.0000.0000.000
89C318GLY0-0.023-0.02335.981-0.004-0.0040.0000.0000.0000.000
90C319TRP0-0.059-0.02734.803-0.002-0.0020.0000.0000.0000.000
91C320ALA0-0.002-0.00332.694-0.004-0.0040.0000.0000.0000.000
92C321THR0-0.059-0.03833.234-0.006-0.0060.0000.0000.0000.000
93C322LYN00.004-0.01333.8880.0020.0020.0000.0000.0000.000
94C323LYS10.8220.90937.0400.0250.0250.0000.0000.0000.000
95C324PHE00.0410.02539.6160.0020.0020.0000.0000.0000.000
96C325GLY00.0210.01441.2980.0010.0010.0000.0000.0000.000
97C326LYS10.7910.88541.9250.0280.0280.0000.0000.0000.000
98C327ARG10.7340.85543.8630.0260.0260.0000.0000.0000.000
99C328ASN0-0.019-0.00237.4430.0040.0040.0000.0000.0000.000
100C329THR00.023-0.01040.998-0.001-0.0010.0000.0000.0000.000
101C330ILE0-0.0380.01238.1500.0020.0020.0000.0000.0000.000
102C331TRP0-0.063-0.03142.1840.0000.0000.0000.0000.0000.000
103C332LEU00.0210.01540.6070.0020.0020.0000.0000.0000.000
104C333PHE00.0080.03844.8480.0000.0000.0000.0000.0000.000
105C334GLY00.0230.00948.2310.0000.0000.0000.0000.0000.000
106C335PRO0-0.010-0.01047.2280.0000.0000.0000.0000.0000.000
107C336ALA0-0.052-0.01947.1800.0000.0000.0000.0000.0000.000
108C337THR00.012-0.02542.9410.0010.0010.0000.0000.0000.000
109C338THR0-0.063-0.02441.755-0.001-0.0010.0000.0000.0000.000
110C339GLY00.0690.01639.6910.0000.0000.0000.0000.0000.000
111C340LYS10.7630.86840.6370.0230.0230.0000.0000.0000.000
112C341THR00.0900.03937.3730.0000.0000.0000.0000.0000.000
113C342ASN0-0.0220.00437.537-0.003-0.0030.0000.0000.0000.000
114C343ILE00.0990.03736.2420.0000.0000.0000.0000.0000.000
115C344ALA00.0300.02235.429-0.001-0.0010.0000.0000.0000.000
116C345GLU-1-0.820-0.89433.023-0.020-0.0200.0000.0000.0000.000
117C346ALA0-0.022-0.01031.577-0.002-0.0020.0000.0000.0000.000
118C347ILE00.0100.01130.564-0.001-0.0010.0000.0000.0000.000
119C348ALA00.0080.00230.206-0.004-0.0040.0000.0000.0000.000
120C349HIS0-0.015-0.01127.578-0.010-0.0100.0000.0000.0000.000
121C350THR0-0.047-0.02626.1210.0040.0040.0000.0000.0000.000
122C351VAL0-0.034-0.01325.226-0.002-0.0020.0000.0000.0000.000
123C352PRO00.0110.01320.9150.0010.0010.0000.0000.0000.000
124C353PHE0-0.0200.00020.644-0.006-0.0060.0000.0000.0000.000
125C354TYR0-0.005-0.01125.5820.0030.0030.0000.0000.0000.000
126C355GLY00.002-0.00629.290-0.005-0.0050.0000.0000.0000.000
127C356CYS0-0.093-0.01432.2800.0050.0050.0000.0000.0000.000
128C369CYS0-0.012-0.02233.2040.0000.0000.0000.0000.0000.000
129C370VAL00.0480.03229.9650.0020.0020.0000.0000.0000.000
130C371ASP-1-0.773-0.86325.826-0.155-0.1550.0000.0000.0000.000
131C372LYS10.8040.92127.0070.1050.1050.0000.0000.0000.000
132C373MET00.0230.01923.0500.0070.0070.0000.0000.0000.000
133C374VAL00.0260.00829.1130.0070.0070.0000.0000.0000.000
134C375ILE00.0140.00431.807-0.005-0.0050.0000.0000.0000.000
135C376TRP00.030-0.00134.3660.0030.0030.0000.0000.0000.000
136C377TRP00.0050.00536.835-0.001-0.0010.0000.0000.0000.000
137C378GLU-1-0.795-0.88838.653-0.026-0.0260.0000.0000.0000.000
138C409ALA0-0.027-0.03133.8310.0020.0020.0000.0000.0000.000
139C410GLN0-0.036-0.02033.684-0.003-0.0030.0000.0000.0000.000
140C411ILE0-0.031-0.02634.014-0.004-0.0040.0000.0000.0000.000
141C412ASP-1-0.815-0.89132.311-0.088-0.0880.0000.0000.0000.000
142C413PRO0-0.013-0.02534.4530.0030.0030.0000.0000.0000.000
143C414THR00.0330.04432.7460.0000.0000.0000.0000.0000.000
144C415PRO00.000-0.00433.3050.0030.0030.0000.0000.0000.000
145C416VAL0-0.0190.00835.9030.0030.0030.0000.0000.0000.000
146C417ILE00.0120.01736.2660.0030.0030.0000.0000.0000.000
147C418VAL00.0190.00139.041-0.002-0.0020.0000.0000.0000.000
148C419THR0-0.0160.00241.8320.0020.0020.0000.0000.0000.000
149C420SER00.0280.00343.495-0.001-0.0010.0000.0000.0000.000
150C421ASN00.018-0.00846.8690.0010.0010.0000.0000.0000.000
151C422THR0-0.0150.00449.4190.0010.0010.0000.0000.0000.000
152C423ASN00.0130.00951.155-0.001-0.0010.0000.0000.0000.000
153C441LEU00.027-0.01148.4570.0000.0000.0000.0000.0000.000
154C442GLN00.0900.04449.590-0.002-0.0020.0000.0000.0000.000
155C443ASP-1-0.814-0.88850.889-0.026-0.0260.0000.0000.0000.000
156C444ARG10.8830.91746.2330.0370.0370.0000.0000.0000.000
157C445MET00.0110.05045.442-0.001-0.0010.0000.0000.0000.000
158C446PHE00.0300.00842.9790.0020.0020.0000.0000.0000.000
159C447LYS10.8140.90746.1590.0160.0160.0000.0000.0000.000
160C448PHE00.0230.01443.8180.0010.0010.0000.0000.0000.000
161C449GLU-1-0.784-0.90547.697-0.016-0.0160.0000.0000.0000.000
162C450LEU00.0080.00943.3530.0010.0010.0000.0000.0000.000
163C451THR0-0.049-0.03347.9590.0000.0000.0000.0000.0000.000
164C452ARG10.9350.96649.2180.0040.0040.0000.0000.0000.000
165C453ARG10.9040.92747.1490.0030.0030.0000.0000.0000.000
166C454LEU0-0.0070.01843.2390.0010.0010.0000.0000.0000.000
167C455ASP-1-0.849-0.91747.3520.0030.0030.0000.0000.0000.000
168C456HIS0-0.036-0.02845.513-0.002-0.0020.0000.0000.0000.000
169C457ASP-1-0.884-0.92943.8470.0110.0110.0000.0000.0000.000
170C458PHE0-0.058-0.02241.5910.0010.0010.0000.0000.0000.000
171C459GLY00.0520.01139.412-0.001-0.0010.0000.0000.0000.000
172C460LYS10.6830.84933.0390.0110.0110.0000.0000.0000.000
173C461VAL00.0410.00034.2180.0030.0030.0000.0000.0000.000
174C462THR0-0.031-0.02830.0700.0010.0010.0000.0000.0000.000
175C463LYS10.9680.98122.620-0.015-0.0150.0000.0000.0000.000
176C464GLN00.0510.02627.013-0.005-0.0050.0000.0000.0000.000
177C465GLU-1-0.786-0.87728.9940.0120.0120.0000.0000.0000.000
178C466VAL0-0.0070.00030.380-0.001-0.0010.0000.0000.0000.000
179C467LYS10.8500.91924.2520.0120.0120.0000.0000.0000.000
180C468ASP-1-0.866-0.90529.7330.0160.0160.0000.0000.0000.000
181C469PHE00.0130.01132.1450.0000.0000.0000.0000.0000.000
182C470PHE00.025-0.01031.769-0.002-0.0020.0000.0000.0000.000
183C471ARG10.7790.87430.644-0.016-0.0160.0000.0000.0000.000
184C472TRP0-0.049-0.02732.462-0.001-0.0010.0000.0000.0000.000
185C473ALA00.018-0.00235.8560.0000.0000.0000.0000.0000.000
186C474LYS10.8980.93831.7000.0230.0230.0000.0000.0000.000
187C475ASP-1-0.856-0.91133.8250.0080.0080.0000.0000.0000.000
188C476HIS0-0.096-0.04036.4320.0030.0030.0000.0000.0000.000
189C477VAL0-0.0100.00238.412-0.001-0.0010.0000.0000.0000.000
190C478VAL0-0.0110.00941.0220.0020.0020.0000.0000.0000.000
191C479GLU-1-0.821-0.89243.930-0.022-0.0220.0000.0000.0000.000
192C480VAL0-0.024-0.02144.1120.0010.0010.0000.0000.0000.000
193C481GLU-1-0.768-0.86147.058-0.014-0.0140.0000.0000.0000.000
194C482HIS0-0.058-0.02946.052-0.002-0.0020.0000.0000.0000.000
195C483GLU-1-0.913-0.95149.115-0.016-0.0160.0000.0000.0000.000
196C484PHE0-0.017-0.01449.543-0.001-0.0010.0000.0000.0000.000
197C485TYR00.011-0.01650.7680.0010.0010.0000.0000.0000.000
198C486VAL0-0.0190.00347.1230.0010.0010.0000.0000.0000.000
199C487LYS10.9761.00549.9600.0090.0090.0000.0000.0000.000
200C488LYN0-0.057-0.01451.6500.0010.0010.0000.0000.0000.000
201C489GLY00.0320.02452.4830.0010.0010.0000.0000.0000.000
202C490GLY0-0.036-0.03251.8390.0000.0000.0000.0000.0000.000