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: 4NM5N

Calculation Name: 1S9H-C-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2332845.034598
FMO2-HF: Nuclear repulsion 2251816.960104
FMO2-HF: Total energy -81028.074494
FMO2-MP2: Total energy -81266.45766


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.
-20.276-17.2980.019-1.491-1.505-0.008
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 : 1 / q_Mulliken : 0.871 / q_NPA : 0.922
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].
3C225MET 0-0.035-0.0013.7867.2909.528-0.019-1.156-1.063-0.005
4C226GLU -1-0.906-0.9403.777-33.420-33.2050.003-0.052-0.1650.000
5C227LEU 00.0130.0105.5434.0014.0010.0000.0000.0000.000
6C228VAL 00.000-0.0027.0113.4423.4420.0000.0000.0000.000
7C229GLY 00.0370.0149.5662.3372.3370.0000.0000.0000.000
8C230TRP 00.0740.0369.8961.5961.5960.0000.0000.0000.000
9C231LEU 0-0.032-0.02710.5251.8751.8750.0000.0000.0000.000
10C232VAL 00.0010.00212.9971.7061.7060.0000.0000.0000.000
11C233ASP -1-0.890-0.93715.062-16.869-16.8690.0000.0000.0000.000
12C234LYS 10.7240.86615.15316.37116.3710.0000.0000.0000.000
13C235GLY 00.0420.00716.9070.9890.9890.0000.0000.0000.000
14C236ILE 0-0.074-0.02414.0850.6960.6960.0000.0000.0000.000
15C237THR 00.0300.01016.209-0.808-0.8080.0000.0000.0000.000
16C238SER 0-0.016-0.01817.176-0.086-0.0860.0000.0000.0000.000
17C239GLU -1-0.736-0.85013.544-18.950-18.9500.0000.0000.0000.000
18C240LYS 10.9180.97315.65312.26712.2670.0000.0000.0000.000
19C241GLN 00.013-0.00518.0170.1950.1950.0000.0000.0000.000
20C242TRP 0-0.018-0.0187.7590.1610.1610.0000.0000.0000.000
21C243ILE 0-0.016-0.00215.3210.0380.0380.0000.0000.0000.000
22C244GLN 0-0.060-0.04516.5190.3560.3560.0000.0000.0000.000
23C245GLU -1-0.860-0.89117.067-14.247-14.2470.0000.0000.0000.000
24C246ASP -1-0.800-0.89513.909-19.115-19.1150.0000.0000.0000.000
25C247GLN 00.0500.01913.948-0.827-0.8270.0000.0000.0000.000
26C248ALA 00.0090.01014.040-0.827-0.8270.0000.0000.0000.000
27C249SER 0-0.006-0.01610.058-1.815-1.8150.0000.0000.0000.000
28C250TYR 0-0.064-0.0559.170-2.764-2.7640.0000.0000.0000.000
29C251ILE 00.005-0.01610.157-1.358-1.3580.0000.0000.0000.000
30C252SER 0-0.049-0.0208.849-1.663-1.6630.0000.0000.0000.000
31C253PHE 0-0.037-0.0213.212-4.711-4.1210.035-0.270-0.355-0.003
32C254ASN 0-0.047-0.0325.842-4.666-4.6660.0000.0000.0000.000
33C255ALA 00.0510.0528.5352.1472.1470.0000.0000.0000.000
34C256ALA 0-0.067-0.0297.514-2.586-2.5860.0000.0000.0000.000
35C257SER 0-0.084-0.0637.7041.6991.6990.0000.0000.0000.000
36C258ASN 00.0830.0498.464-2.226-2.2260.0000.0000.0000.000
37C259SER 0-0.032-0.0187.5302.2622.2620.0000.0000.0000.000
38C260ARG 10.9300.96510.21418.92918.9290.0000.0000.0000.000
39C261SER 0-0.004-0.00612.1360.3200.3200.0000.0000.0000.000
40C262GLN 00.0390.0044.407-4.256-4.3210.000-0.0130.0780.000
41C263ILE 00.0400.0309.044-0.863-0.8630.0000.0000.0000.000
42C264LYS 10.9140.96410.08317.52517.5250.0000.0000.0000.000
43C265ALA 00.0610.02810.9190.4930.4930.0000.0000.0000.000
44C266ALA 00.0050.0068.4540.3490.3490.0000.0000.0000.000
45C267LEU 00.0130.00010.5331.1911.1910.0000.0000.0000.000
46C268ASP -1-0.884-0.93513.567-16.769-16.7690.0000.0000.0000.000
47C269ASN 0-0.018-0.02711.6202.3262.3260.0000.0000.0000.000
48C270ALA 00.0220.00812.8240.7910.7910.0000.0000.0000.000
49C271GLY 00.0290.00214.6661.0411.0410.0000.0000.0000.000
50C272LYS 10.9140.94117.65614.81714.8170.0000.0000.0000.000
51C273ILE 00.0140.01115.3890.6760.6760.0000.0000.0000.000
52C274MET 0-0.065-0.01117.2050.7680.7680.0000.0000.0000.000
53C275SER 0-0.038-0.01320.4750.7470.7470.0000.0000.0000.000
54C276LEU 00.0220.01622.3250.4370.4370.0000.0000.0000.000
55C277THR 0-0.082-0.03121.0800.1600.1600.0000.0000.0000.000
56C278LYS 10.8760.95119.33915.10715.1070.0000.0000.0000.000
57C279THR 0-0.003-0.02123.9970.5710.5710.0000.0000.0000.000
58C280ALA 00.0460.01526.605-0.234-0.2340.0000.0000.0000.000
59C281PRO 0-0.014-0.02727.929-0.190-0.1900.0000.0000.0000.000
60C282ASP -1-0.832-0.89623.617-12.235-12.2350.0000.0000.0000.000
61C283TYR 0-0.014-0.01019.283-0.192-0.1920.0000.0000.0000.000
62C284LEU 0-0.029-0.02124.8910.0490.0490.0000.0000.0000.000
63C285VAL 0-0.029-0.00128.0530.3630.3630.0000.0000.0000.000
64C286GLY 0-0.0120.00027.112-0.454-0.4540.0000.0000.0000.000
65C287GLN 00.0400.01423.3570.1100.1100.0000.0000.0000.000
66C288NME 00.0120.01526.1280.1660.1660.0000.0000.0000.000
67C294ACE 00.0780.04037.729-0.024-0.0240.0000.0000.0000.000
68C295SER 0-0.051-0.04238.3280.0810.0810.0000.0000.0000.000
69C296ASN 0-0.058-0.04438.0800.1790.1790.0000.0000.0000.000
70C297ARG 10.9300.99836.6238.1928.1920.0000.0000.0000.000
71C298ILE 00.0310.02334.8520.1710.1710.0000.0000.0000.000
72C299TYR 00.0440.03539.1850.1400.1400.0000.0000.0000.000
73C300LYS 10.9790.98141.1637.0467.0460.0000.0000.0000.000
74C301ILE 0-0.066-0.02340.6520.1630.1630.0000.0000.0000.000
75C302LEU 0-0.034-0.03141.6230.1350.1350.0000.0000.0000.000
76C303GLU -1-0.853-0.92744.999-6.508-6.5080.0000.0000.0000.000
77C304LEU 0-0.166-0.06246.5910.1980.1980.0000.0000.0000.000
78C305ASN 0-0.050-0.06449.4720.0250.0250.0000.0000.0000.000
79C306GLY 00.006-0.00251.292-0.010-0.0100.0000.0000.0000.000
80C307TYR 00.0240.07747.3540.0310.0310.0000.0000.0000.000
81C308ASP -1-0.768-0.88948.086-6.662-6.6620.0000.0000.0000.000
82C309PRO 0-0.012-0.00743.245-0.159-0.1590.0000.0000.0000.000
83C310GLN 00.0470.02942.981-0.282-0.2820.0000.0000.0000.000
84C311TYR 00.0310.02943.489-0.149-0.1490.0000.0000.0000.000
85C312ALA 0-0.020-0.02543.763-0.123-0.1230.0000.0000.0000.000
86C313ALA 0-0.005-0.02139.384-0.165-0.1650.0000.0000.0000.000
87C314SER 00.0110.00739.357-0.277-0.2770.0000.0000.0000.000
88C315VAL 0-0.0300.00640.854-0.088-0.0880.0000.0000.0000.000
89C316PHE 0-0.003-0.01237.160-0.168-0.1680.0000.0000.0000.000
90C317LEU 00.0060.02334.984-0.248-0.2480.0000.0000.0000.000
91C318GLY 00.004-0.03036.099-0.182-0.1820.0000.0000.0000.000
92C319TRP 0-0.056-0.02934.561-0.138-0.1380.0000.0000.0000.000
93C320ALA 0-0.038-0.01832.699-0.133-0.1330.0000.0000.0000.000
94C321THR 0-0.102-0.04833.115-0.402-0.4020.0000.0000.0000.000
95C322LYN 00.0930.04234.4180.2010.2010.0000.0000.0000.000
96C323LYS 10.8530.94237.1798.0608.0600.0000.0000.0000.000
97C324PHE 00.0560.04639.7160.1710.1710.0000.0000.0000.000
98C325GLY 00.0880.03642.4080.1230.1230.0000.0000.0000.000
99C326LYS 10.7950.89042.2626.2156.2150.0000.0000.0000.000
100C327ARG 10.7880.91343.0006.6536.6530.0000.0000.0000.000
101C328ASN 00.0220.01437.5690.0950.0950.0000.0000.0000.000
102C329THR 00.0830.00140.6190.1330.1330.0000.0000.0000.000
103C330ILE 0-0.078-0.01237.8600.2080.2080.0000.0000.0000.000
104C331TRP 0-0.050-0.03942.111-0.031-0.0310.0000.0000.0000.000
105C332LEU 0-0.0350.00141.0520.1030.1030.0000.0000.0000.000
106C333PHE 00.0310.00444.991-0.003-0.0030.0000.0000.0000.000
107C334GLY 00.0480.02748.1470.0030.0030.0000.0000.0000.000
108C335PRO 0-0.0060.04246.963-0.180-0.1800.0000.0000.0000.000
109C336ALA 0-0.074-0.04546.9050.0040.0040.0000.0000.0000.000
110C337THR 00.023-0.01343.250-0.013-0.0130.0000.0000.0000.000
111C338THR 0-0.0260.01241.766-0.223-0.2230.0000.0000.0000.000
112C339GLY 00.0970.00240.506-0.189-0.1890.0000.0000.0000.000
113C340LYS 10.9801.00141.3066.6596.6590.0000.0000.0000.000
114C341THR 0-0.031-0.00936.223-0.133-0.1330.0000.0000.0000.000
115C342ASN 0-0.113-0.05437.721-0.073-0.0730.0000.0000.0000.000
116C343ILE 00.1010.02436.392-0.245-0.2450.0000.0000.0000.000
117C344ALA 00.0310.02835.263-0.257-0.2570.0000.0000.0000.000
118C345GLU -1-0.807-0.89132.769-9.424-9.4240.0000.0000.0000.000
119C346ALA 0-0.018-0.00531.550-0.335-0.3350.0000.0000.0000.000
120C347ILE 00.0300.03530.769-0.319-0.3190.0000.0000.0000.000
121C348ALA 0-0.005-0.01030.250-0.274-0.2740.0000.0000.0000.000
122C349HIS 0-0.036-0.02127.412-0.549-0.5490.0000.0000.0000.000
123C350THR 0-0.083-0.05425.995-0.422-0.4220.0000.0000.0000.000
124C351VAL 0-0.047-0.01225.056-0.428-0.4280.0000.0000.0000.000
125C352PRO 00.0080.00621.2740.1010.1010.0000.0000.0000.000
126C353PHE 0-0.022-0.01620.3490.0580.0580.0000.0000.0000.000
127C354TYR 00.022-0.01525.5990.4090.4090.0000.0000.0000.000
128C355GLY 00.020-0.01229.315-0.119-0.1190.0000.0000.0000.000
129C356CYS 0-0.108-0.03032.1300.2100.2100.0000.0000.0000.000
130C357NME 00.0050.03233.3660.1400.1400.0000.0000.0000.000
131C368ACE 00.0210.00532.693-0.005-0.0050.0000.0000.0000.000
132C369CYS 0-0.027-0.02632.9270.1250.1250.0000.0000.0000.000
133C370VAL 00.0290.01929.6440.1200.1200.0000.0000.0000.000
134C371ASP -1-0.853-0.92526.524-11.543-11.5430.0000.0000.0000.000
135C372LYS 10.7720.91626.78010.71510.7150.0000.0000.0000.000
136C373MET 00.0310.02823.6830.0940.0940.0000.0000.0000.000
137C374VAL 00.0280.00729.2540.3150.3150.0000.0000.0000.000
138C375ILE 0-0.0080.00031.830-0.185-0.1850.0000.0000.0000.000
139C376TRP 00.0520.01933.9820.0260.0260.0000.0000.0000.000
140C377TRP 0-0.006-0.00736.3940.0870.0870.0000.0000.0000.000
141C378GLU -1-0.892-0.96638.073-7.922-7.9220.0000.0000.0000.000
142C379NME 0-0.043-0.00341.7150.1740.1740.0000.0000.0000.000
143C408ACE 00.004-0.01037.4020.0570.0570.0000.0000.0000.000
144C409ALA 0-0.036-0.03233.863-0.135-0.1350.0000.0000.0000.000
145C410GLN 0-0.030-0.00333.681-0.005-0.0050.0000.0000.0000.000
146C411ILE 0-0.028-0.00833.470-0.269-0.2690.0000.0000.0000.000
147C412ASP -1-0.819-0.90731.891-9.309-9.3090.0000.0000.0000.000
148C413PRO 0-0.060-0.05334.0790.0880.0880.0000.0000.0000.000
149C414THR 00.0240.01932.130-0.141-0.1410.0000.0000.0000.000
150C415PRO 0-0.015-0.00733.2420.2440.2440.0000.0000.0000.000
151C416VAL 00.0150.00735.5160.2240.2240.0000.0000.0000.000
152C417ILE 0-0.0010.01436.1740.1330.1330.0000.0000.0000.000
153C418VAL 00.0410.01538.991-0.066-0.0660.0000.0000.0000.000
154C419THR 00.0200.01441.1420.0530.0530.0000.0000.0000.000
155C420SER 00.0020.00742.9830.0400.0400.0000.0000.0000.000
156C421ASN 00.013-0.00346.2540.0110.0110.0000.0000.0000.000
157C422THR 00.014-0.00948.6260.1710.1710.0000.0000.0000.000
158C423ASN 0-0.0070.01450.405-0.069-0.0690.0000.0000.0000.000
159C424NME 00.0040.00953.0130.0040.0040.0000.0000.0000.000
160C440ACE 00.0670.02053.2880.0290.0290.0000.0000.0000.000
161C441LEU 0-0.007-0.02247.917-0.115-0.1150.0000.0000.0000.000
162C442GLN 00.1300.06649.434-0.176-0.1760.0000.0000.0000.000
163C443ASP -1-0.891-0.91551.267-6.139-6.1390.0000.0000.0000.000
164C444ARG 10.7790.85746.2506.5076.5070.0000.0000.0000.000
165C445MET 00.0700.06345.148-0.106-0.1060.0000.0000.0000.000
166C446PHE 00.0210.02243.6850.1460.1460.0000.0000.0000.000
167C447LYS 10.8500.93045.7135.9005.9000.0000.0000.0000.000
168C448PHE 00.0370.01743.7210.0810.0810.0000.0000.0000.000
169C449GLU -1-0.852-0.95847.414-5.907-5.9070.0000.0000.0000.000
170C450LEU 00.0230.01143.4690.0540.0540.0000.0000.0000.000
171C451THR 0-0.023-0.00448.090-0.012-0.0120.0000.0000.0000.000
172C452ARG 10.9850.99248.8926.0316.0310.0000.0000.0000.000
173C453ARG 10.8850.91347.0006.3916.3910.0000.0000.0000.000
174C454LEU 0-0.0050.01943.2790.0350.0350.0000.0000.0000.000
175C455ASP -1-0.868-0.92247.213-6.262-6.2620.0000.0000.0000.000
176C456HIS 0-0.067-0.04845.420-0.097-0.0970.0000.0000.0000.000
177C457ASP -1-0.892-0.92643.756-6.773-6.7730.0000.0000.0000.000
178C458PHE 0-0.029-0.01241.329-0.226-0.2260.0000.0000.0000.000
179C459GLY 00.0580.01139.0430.0440.0440.0000.0000.0000.000
180C460LYS 10.7650.87732.9588.8828.8820.0000.0000.0000.000
181C461VAL 00.0270.00133.971-0.020-0.0200.0000.0000.0000.000
182C462THR 0-0.0200.00130.215-0.237-0.2370.0000.0000.0000.000
183C463LYS 11.0431.01025.72210.86810.8680.0000.0000.0000.000
184C464GLN 0-0.004-0.01226.3590.0660.0660.0000.0000.0000.000
185C465GLU -1-0.745-0.89428.915-8.651-8.6510.0000.0000.0000.000
186C466VAL 00.0110.01830.3540.1990.1990.0000.0000.0000.000
187C467LYS 10.8430.90723.98812.07612.0760.0000.0000.0000.000
188C468ASP -1-0.859-0.90929.418-9.316-9.3160.0000.0000.0000.000
189C469PHE 0-0.018-0.00431.8100.2400.2400.0000.0000.0000.000
190C470PHE 00.007-0.02231.8140.1960.1960.0000.0000.0000.000
191C471ARG 10.8360.92230.5449.3579.3570.0000.0000.0000.000
192C472TRP 0-0.0280.00332.7320.1230.1230.0000.0000.0000.000
193C473ALA 00.010-0.00836.2980.1340.1340.0000.0000.0000.000
194C474LYS 10.8920.93731.9179.5809.5800.0000.0000.0000.000
195C475ASP -1-0.919-0.94834.603-9.071-9.0710.0000.0000.0000.000
196C476HIS 0-0.074-0.03637.1000.3150.3150.0000.0000.0000.000
197C477VAL 0-0.043-0.01538.7510.0550.0550.0000.0000.0000.000
198C478VAL 00.0060.00541.5090.1510.1510.0000.0000.0000.000
199C479GLU -1-0.935-0.95544.692-6.985-6.9850.0000.0000.0000.000
200C480VAL 0-0.014-0.01643.7590.0360.0360.0000.0000.0000.000
201C481GLU -1-0.846-0.93146.942-6.191-6.1910.0000.0000.0000.000
202C482HIS 0-0.114-0.07046.384-0.130-0.1300.0000.0000.0000.000
203C483GLU -1-0.973-0.99149.233-5.831-5.8310.0000.0000.0000.000
204C484PHE 0-0.042-0.00449.573-0.095-0.0950.0000.0000.0000.000
205C485TYR 0-0.018-0.02650.7180.1030.1030.0000.0000.0000.000
206C486VAL 00.0250.02746.7200.0220.0220.0000.0000.0000.000
207C487LYS 10.9910.97250.1426.1936.1930.0000.0000.0000.000
208C488LYN 0-0.048-0.00650.7700.1250.1250.0000.0000.0000.000
209C489GLY 0-0.038-0.02352.0600.0140.0140.0000.0000.0000.000
210C490GLY -1-0.896-0.94851.861-6.126-6.1260.0000.0000.0000.000