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: 7GVLK

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299524.756879
FMO2-HF: Nuclear repulsion 2219180.3142
FMO2-HF: Total energy -80344.442679
FMO2-MP2: Total energy -80580.679105


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.
-0.1793.2410.017-1.788-1.650.002
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 : 0.050 / q_NPA : 0.023
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].
3C225MET0-0.085-0.0333.786-0.8511.917-0.028-1.555-1.1860.004
4C226GLU-1-0.896-0.9363.7620.6370.8560.003-0.040-0.1810.000
5C227LEU00.0110.0095.5460.1800.1800.0000.0000.0000.000
6C228VAL0-0.005-0.0077.0150.0720.0720.0000.0000.0000.000
7C229GLY00.0350.0129.5480.0430.0430.0000.0000.0000.000
8C230TRP00.0860.0399.8940.0120.0120.0000.0000.0000.000
9C231LEU0-0.034-0.02910.534-0.009-0.0090.0000.0000.0000.000
10C232VAL00.0020.00212.9990.0010.0010.0000.0000.0000.000
11C233ASP-1-0.898-0.94115.0630.1120.1120.0000.0000.0000.000
12C234LYS10.7550.87114.424-0.149-0.1490.0000.0000.0000.000
13C235GLY00.0330.00816.911-0.006-0.0060.0000.0000.0000.000
14C236ILE0-0.080-0.02814.234-0.008-0.0080.0000.0000.0000.000
15C237THR00.0290.00916.215-0.033-0.0330.0000.0000.0000.000
16C238SER0-0.016-0.01717.183-0.018-0.0180.0000.0000.0000.000
17C239GLU-1-0.737-0.84913.550-0.171-0.1710.0000.0000.0000.000
18C240LYS10.9180.97215.6580.0580.0580.0000.0000.0000.000
19C241GLN00.009-0.00818.0140.0270.0270.0000.0000.0000.000
20C242TRP0-0.015-0.0157.760-0.036-0.0360.0000.0000.0000.000
21C243ILE0-0.019-0.00215.3190.0340.0340.0000.0000.0000.000
22C244GLN0-0.063-0.04816.5160.0110.0110.0000.0000.0000.000
23C245GLU-1-0.875-0.88716.9990.1070.1070.0000.0000.0000.000
24C246ASP-1-0.829-0.91313.8960.2860.2860.0000.0000.0000.000
25C247GLN00.0540.02113.939-0.001-0.0010.0000.0000.0000.000
26C248ALA00.0050.00814.029-0.004-0.0040.0000.0000.0000.000
27C249SER0-0.003-0.01410.0470.0270.0270.0000.0000.0000.000
28C250TYR0-0.065-0.0569.1590.0340.0340.0000.0000.0000.000
29C251ILE00.004-0.01810.150-0.036-0.0360.0000.0000.0000.000
30C252SER0-0.051-0.0228.8730.0300.0300.0000.0000.0000.000
31C253PHE0-0.016-0.0123.205-0.4460.0450.043-0.182-0.353-0.002
32C254ASN0-0.043-0.0295.836-0.230-0.2300.0000.0000.0000.000
33C255ALA00.0420.0468.530-0.084-0.0840.0000.0000.0000.000
34C256ALA0-0.060-0.0267.520-0.034-0.0340.0000.0000.0000.000
35C257SER0-0.081-0.0627.708-0.074-0.0740.0000.0000.0000.000
36C258ASN00.0780.0478.4680.0050.0050.0000.0000.0000.000
37C259SER0-0.026-0.0147.5160.0730.0730.0000.0000.0000.000
38C260ARG10.9220.96110.2150.2780.2780.0000.0000.0000.000
39C261SER0-0.008-0.00812.1340.0100.0100.0000.0000.0000.000
40C262GLN00.0510.0114.387-0.641-0.699-0.001-0.0110.0700.000
41C263ILE00.0410.0319.061-0.030-0.0300.0000.0000.0000.000
42C264LYS10.9060.95910.0970.3770.3770.0000.0000.0000.000
43C265ALA00.0620.02810.9390.0350.0350.0000.0000.0000.000
44C266ALA00.0090.0118.4690.0250.0250.0000.0000.0000.000
45C267LEU00.014-0.00210.5490.0910.0910.0000.0000.0000.000
46C268ASP-1-0.891-0.93813.580-0.308-0.3080.0000.0000.0000.000
47C269ASN0-0.013-0.02411.6380.1020.1020.0000.0000.0000.000
48C270ALA00.0170.00912.8340.0460.0460.0000.0000.0000.000
49C271GLY00.027-0.00114.6780.0400.0400.0000.0000.0000.000
50C272LYS10.9140.94117.6710.2180.2180.0000.0000.0000.000
51C273ILE00.0140.01115.3710.0180.0180.0000.0000.0000.000
52C274MET0-0.066-0.01117.2140.0350.0350.0000.0000.0000.000
53C275SER0-0.036-0.01420.4850.0130.0130.0000.0000.0000.000
54C276LEU00.0260.01722.3070.0020.0020.0000.0000.0000.000
55C277THR0-0.084-0.03121.0630.0060.0060.0000.0000.0000.000
56C278LYS10.8770.95319.3230.0450.0450.0000.0000.0000.000
57C279THR0-0.007-0.02223.979-0.003-0.0030.0000.0000.0000.000
58C280ALA00.0400.01326.6090.0060.0060.0000.0000.0000.000
59C281PRO0-0.013-0.03027.9320.0070.0070.0000.0000.0000.000
60C282ASP-1-0.832-0.89623.599-0.004-0.0040.0000.0000.0000.000
61C283TYR0-0.010-0.00719.2870.0010.0010.0000.0000.0000.000
62C284LEU0-0.033-0.02424.8920.0070.0070.0000.0000.0000.000
63C285VAL0-0.031-0.00328.0480.0030.0030.0000.0000.0000.000
64C286GLY0-0.0060.00427.1090.0050.0050.0000.0000.0000.000
65C287GLN00.0530.03023.335-0.002-0.0020.0000.0000.0000.000
66C295SER00.0510.01638.321-0.001-0.0010.0000.0000.0000.000
67C296ASN0-0.077-0.05638.071-0.004-0.0040.0000.0000.0000.000
68C297ARG10.9240.99336.617-0.035-0.0350.0000.0000.0000.000
69C298ILE00.0310.02234.850-0.001-0.0010.0000.0000.0000.000
70C299TYR00.0520.03839.181-0.002-0.0020.0000.0000.0000.000
71C300LYS10.9690.97741.158-0.028-0.0280.0000.0000.0000.000
72C301ILE0-0.060-0.02040.649-0.002-0.0020.0000.0000.0000.000
73C302LEU0-0.034-0.03041.622-0.002-0.0020.0000.0000.0000.000
74C303GLU-1-0.858-0.93044.9960.0220.0220.0000.0000.0000.000
75C304LEU0-0.162-0.05946.590-0.001-0.0010.0000.0000.0000.000
76C305ASN0-0.043-0.05949.4690.0010.0010.0000.0000.0000.000
77C306GLY00.0110.00051.289-0.001-0.0010.0000.0000.0000.000
78C307TYR00.0110.06947.352-0.001-0.0010.0000.0000.0000.000
79C308ASP-1-0.832-0.92348.0820.0200.0200.0000.0000.0000.000
80C309PRO00.0180.01143.241-0.001-0.0010.0000.0000.0000.000
81C310GLN00.0620.03842.9780.0020.0020.0000.0000.0000.000
82C311TYR0-0.040-0.06043.487-0.001-0.0010.0000.0000.0000.000
83C312ALA0-0.010-0.02043.761-0.001-0.0010.0000.0000.0000.000
84C313ALA00.002-0.01639.382-0.002-0.0020.0000.0000.0000.000
85C314SER00.0080.00539.3560.0000.0000.0000.0000.0000.000
86C315VAL0-0.0270.00740.855-0.002-0.0020.0000.0000.0000.000
87C316PHE0-0.007-0.01237.161-0.003-0.0030.0000.0000.0000.000
88C317LEU00.0100.02534.966-0.003-0.0030.0000.0000.0000.000
89C318GLY00.003-0.03036.101-0.002-0.0020.0000.0000.0000.000
90C319TRP0-0.060-0.03234.564-0.002-0.0020.0000.0000.0000.000
91C320ALA0-0.036-0.01632.701-0.003-0.0030.0000.0000.0000.000
92C321THR0-0.095-0.04433.119-0.002-0.0020.0000.0000.0000.000
93C322LYN00.0960.04434.3990.0000.0000.0000.0000.0000.000
94C323LYS10.8540.94237.161-0.005-0.0050.0000.0000.0000.000
95C324PHE00.0540.04539.6990.0000.0000.0000.0000.0000.000
96C325GLY00.0860.03542.389-0.001-0.0010.0000.0000.0000.000
97C326LYS10.8040.91142.2430.0120.0120.0000.0000.0000.000
98C327ARG10.7880.91143.0070.0080.0080.0000.0000.0000.000
99C328ASN00.0230.01437.5760.0030.0030.0000.0000.0000.000
100C329THR00.0790.00040.625-0.002-0.0020.0000.0000.0000.000
101C330ILE0-0.076-0.01237.8620.0010.0010.0000.0000.0000.000
102C331TRP0-0.048-0.03842.1140.0010.0010.0000.0000.0000.000
103C332LEU0-0.0270.00541.0460.0020.0020.0000.0000.0000.000
104C333PHE00.007-0.00144.993-0.001-0.0010.0000.0000.0000.000
105C334GLY00.0240.01448.149-0.001-0.0010.0000.0000.0000.000
106C335PRO0-0.013-0.00146.9630.0000.0000.0000.0000.0000.000
107C336ALA0-0.057-0.03246.9050.0000.0000.0000.0000.0000.000
108C337THR00.028-0.01043.2490.0020.0020.0000.0000.0000.000
109C338THR00.0090.02541.7660.0000.0000.0000.0000.0000.000
110C339GLY00.035-0.04139.4940.0010.0010.0000.0000.0000.000
111C340LYS10.8040.87340.3740.0100.0100.0000.0000.0000.000
112C341THR00.1400.05737.5120.0010.0010.0000.0000.0000.000
113C342ASN0-0.1010.02037.4220.0000.0000.0000.0000.0000.000
114C343ILE00.1320.03636.3910.0020.0020.0000.0000.0000.000
115C344ALA00.0290.02435.2620.0010.0010.0000.0000.0000.000
116C345GLU-1-0.821-0.90732.5890.0030.0030.0000.0000.0000.000
117C346ALA0-0.068-0.03731.5450.0000.0000.0000.0000.0000.000
118C347ILE00.0390.04330.7680.0040.0040.0000.0000.0000.000
119C348ALA0-0.008-0.00930.252-0.002-0.0020.0000.0000.0000.000
120C349HIS0-0.032-0.02527.412-0.006-0.0060.0000.0000.0000.000
121C350THR0-0.075-0.04825.9960.0050.0050.0000.0000.0000.000
122C351VAL0-0.045-0.01025.0570.0040.0040.0000.0000.0000.000
123C352PRO00.0170.01121.280-0.004-0.0040.0000.0000.0000.000
124C353PHE0-0.014-0.01120.360-0.008-0.0080.0000.0000.0000.000
125C354TYR00.019-0.01525.6070.0040.0040.0000.0000.0000.000
126C355GLY0-0.008-0.01629.322-0.006-0.0060.0000.0000.0000.000
127C356CYS0-0.0570.01831.6030.0020.0020.0000.0000.0000.000
128C369CYS0-0.021-0.02332.943-0.001-0.0010.0000.0000.0000.000
129C370VAL00.0300.01329.6540.0030.0030.0000.0000.0000.000
130C371ASP-1-0.847-0.92126.536-0.106-0.1060.0000.0000.0000.000
131C372LYS10.7710.91227.0230.0870.0870.0000.0000.0000.000
132C373MET00.0270.02723.6900.0040.0040.0000.0000.0000.000
133C374VAL00.0260.00529.2620.0060.0060.0000.0000.0000.000
134C375ILE0-0.0040.00231.836-0.004-0.0040.0000.0000.0000.000
135C376TRP00.0300.00633.9820.0040.0040.0000.0000.0000.000
136C377TRP00.0110.00436.400-0.002-0.0020.0000.0000.0000.000
137C378GLU-1-0.844-0.91538.077-0.014-0.0140.0000.0000.0000.000
138C409ALA0-0.049-0.03133.8600.0000.0000.0000.0000.0000.000
139C410GLN0-0.010-0.01133.696-0.003-0.0030.0000.0000.0000.000
140C411ILE0-0.034-0.01233.484-0.004-0.0040.0000.0000.0000.000
141C412ASP-1-0.817-0.90531.902-0.058-0.0580.0000.0000.0000.000
142C413PRO0-0.063-0.05534.0900.0030.0030.0000.0000.0000.000
143C414THR00.0370.02532.4160.0020.0020.0000.0000.0000.000
144C415PRO0-0.020-0.01033.2490.0010.0010.0000.0000.0000.000
145C416VAL00.0140.00535.5220.0010.0010.0000.0000.0000.000
146C417ILE00.0000.01436.1780.0030.0030.0000.0000.0000.000
147C418VAL00.0500.01838.996-0.002-0.0020.0000.0000.0000.000
148C419THR0-0.0220.03441.1470.0030.0030.0000.0000.0000.000
149C420SER0-0.0030.00142.986-0.001-0.0010.0000.0000.0000.000
150C421ASN00.0180.00546.2580.0010.0010.0000.0000.0000.000
151C422THR0-0.003-0.01348.8320.0010.0010.0000.0000.0000.000
152C423ASN00.0220.03150.4100.0000.0000.0000.0000.0000.000
153C441LEU00.021-0.01247.9350.0000.0000.0000.0000.0000.000
154C442GLN00.1070.04649.4410.0000.0000.0000.0000.0000.000
155C443ASP-1-0.900-0.94251.273-0.009-0.0090.0000.0000.0000.000
156C444ARG10.8390.88745.9730.0210.0210.0000.0000.0000.000
157C445MET00.0680.06345.154-0.001-0.0010.0000.0000.0000.000
158C446PHE00.0220.02343.6880.0010.0010.0000.0000.0000.000
159C447LYS10.8510.93245.7160.0020.0020.0000.0000.0000.000
160C448PHE00.0350.01643.7250.0020.0020.0000.0000.0000.000
161C449GLU-1-0.851-0.95747.415-0.001-0.0010.0000.0000.0000.000
162C450LEU00.0110.00643.4690.0010.0010.0000.0000.0000.000
163C451THR0-0.014-0.00148.090-0.001-0.0010.0000.0000.0000.000
164C452ARG10.9790.98748.890-0.011-0.0110.0000.0000.0000.000
165C453ARG10.8970.92046.985-0.009-0.0090.0000.0000.0000.000
166C454LEU0-0.0110.01643.2750.0010.0010.0000.0000.0000.000
167C455ASP-1-0.866-0.92047.2090.0150.0150.0000.0000.0000.000
168C456HIS0-0.058-0.04345.414-0.002-0.0020.0000.0000.0000.000
169C457ASP-1-0.891-0.92743.7490.0240.0240.0000.0000.0000.000
170C458PHE0-0.028-0.01541.2720.0020.0020.0000.0000.0000.000
171C459GLY00.0630.01539.037-0.002-0.0020.0000.0000.0000.000
172C460LYS10.7160.87732.747-0.011-0.0110.0000.0000.0000.000
173C461VAL00.020-0.01533.9630.0030.0030.0000.0000.0000.000
174C462THR00.0000.00630.2090.0040.0040.0000.0000.0000.000
175C463LYS11.0451.01425.717-0.051-0.0510.0000.0000.0000.000
176C464GLN00.005-0.00926.344-0.002-0.0020.0000.0000.0000.000
177C465GLU-1-0.747-0.89528.9090.0410.0410.0000.0000.0000.000
178C466VAL00.0120.01630.352-0.002-0.0020.0000.0000.0000.000
179C467LYS10.8470.91023.965-0.055-0.0550.0000.0000.0000.000
180C468ASP-1-0.854-0.90729.4140.0590.0590.0000.0000.0000.000
181C469PHE0-0.020-0.00531.804-0.001-0.0010.0000.0000.0000.000
182C470PHE00.005-0.02331.812-0.002-0.0020.0000.0000.0000.000
183C471ARG10.8390.92530.470-0.059-0.0590.0000.0000.0000.000
184C472TRP0-0.0180.00732.728-0.002-0.0020.0000.0000.0000.000
185C473ALA00.010-0.01036.295-0.001-0.0010.0000.0000.0000.000
186C474LYS10.8870.93531.864-0.026-0.0260.0000.0000.0000.000
187C475ASP-1-0.917-0.94734.5900.0520.0520.0000.0000.0000.000
188C476HIS0-0.073-0.03537.0860.0010.0010.0000.0000.0000.000
189C477VAL0-0.039-0.01338.736-0.002-0.0020.0000.0000.0000.000
190C478VAL0-0.006-0.00141.4930.0010.0010.0000.0000.0000.000
191C479GLU-1-0.924-0.94944.6750.0050.0050.0000.0000.0000.000
192C480VAL0-0.014-0.01743.7520.0000.0000.0000.0000.0000.000
193C481GLU-1-0.814-0.86846.9240.0060.0060.0000.0000.0000.000
194C482HIS0-0.089-0.05746.367-0.002-0.0020.0000.0000.0000.000
195C483GLU-1-0.980-0.99349.237-0.001-0.0010.0000.0000.0000.000
196C484PHE0-0.0210.00649.5770.0000.0000.0000.0000.0000.000
197C485TYR0-0.021-0.02550.7160.0000.0000.0000.0000.0000.000
198C486VAL00.0370.03446.7220.0010.0010.0000.0000.0000.000
199C487LYS11.0140.98650.143-0.010-0.0100.0000.0000.0000.000
200C488LYN0-0.0260.01250.7830.0000.0000.0000.0000.0000.000
201C489GLY00.0150.01052.0590.0010.0010.0000.0000.0000.000
202C490GLY0-0.043-0.03351.8640.0010.0010.0000.0000.0000.000