Manual

About

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: JLQM9

Calculation Name: 5U50-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U50

Chain ID: C

ChEMBL ID:

UniProt ID: G9I821

Base Structure: X-ray

Registration Date: 2023-06-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965425.547843
FMO2-HF: Nuclear repulsion 1893197.285185
FMO2-HF: Total energy -72228.262658
FMO2-MP2: Total energy -72439.57597


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:8:PRO)


Summations of interaction energy for fragment #1(C:8:PRO)
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.
-18.04-10.8137.034-5.51-8.75-0.043
Interaction energy analysis for fragmet #1(C:8:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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].
3C10ASP-1-0.862-0.9222.841-2.8070.1510.064-1.283-1.738-0.003
4C11ARG10.9080.9772.740-4.843-3.3660.434-0.530-1.3820.001
5C12ILE0-0.007-0.0094.059-0.886-0.3370.001-0.201-0.3480.000
6C13ASN00.008-0.0066.0280.2190.2190.0000.0000.0000.000
7C14ASP-1-0.880-0.9377.5970.7780.7780.0000.0000.0000.000
8C15PHE0-0.089-0.0358.2840.0050.0050.0000.0000.0000.000
9C16LEU0-0.047-0.0369.892-0.068-0.0680.0000.0000.0000.000
10C17ASP-1-0.870-0.93012.020-0.042-0.0420.0000.0000.0000.000
11C18HIS0-0.087-0.06113.9510.0180.0180.0000.0000.0000.000
12C19LEU00.0460.05613.4270.0250.0250.0000.0000.0000.000
13C20ASN0-0.002-0.02416.461-0.048-0.0480.0000.0000.0000.000
14C21LEU00.0180.00719.0390.0220.0220.0000.0000.0000.000
15C22GLY0-0.040-0.00221.605-0.008-0.0080.0000.0000.0000.000
16C23GLU-1-0.977-0.98225.0100.0630.0630.0000.0000.0000.000
17C24ARG10.8830.94223.644-0.070-0.0700.0000.0000.0000.000
18C25THR00.003-0.00319.1090.0230.0230.0000.0000.0000.000
19C26ILE0-0.026-0.01115.624-0.027-0.0270.0000.0000.0000.000
20C27LYS10.9110.96415.8590.0840.0840.0000.0000.0000.000
21C28GLY00.013-0.00212.802-0.016-0.0160.0000.0000.0000.000
22C29CYS0-0.033-0.01211.3590.0100.0100.0000.0000.0000.000
23C30LEU0-0.021-0.0126.284-0.010-0.0100.0000.0000.0000.000
24C31GLU-1-0.877-0.9289.455-0.588-0.5880.0000.0000.0000.000
25C32ALA00.008-0.0018.3120.0110.0110.0000.0000.0000.000
26C33TYR0-0.005-0.00810.3530.1090.1090.0000.0000.0000.000
27C34SER0-0.018-0.02213.801-0.021-0.0210.0000.0000.0000.000
28C35CYS0-0.058-0.01315.7260.0400.0400.0000.0000.0000.000
29C36LYS10.9810.99819.2850.3180.3180.0000.0000.0000.000
30C37HIS00.0200.00422.0700.0050.0050.0000.0000.0000.000
31C38THR0-0.032-0.03425.4610.0150.0150.0000.0000.0000.000
32C39GLY00.0200.01826.287-0.010-0.0100.0000.0000.0000.000
33C40THR00.0630.01026.2050.0040.0040.0000.0000.0000.000
34C41ASP-1-0.735-0.84522.513-0.266-0.2660.0000.0000.0000.000
35C42LYS10.9341.01126.1080.1600.1600.0000.0000.0000.000
36C43ARG10.9670.97928.5970.1300.1300.0000.0000.0000.000
37C44LEU00.0380.02226.2820.0080.0080.0000.0000.0000.000
38C45SER00.011-0.02926.631-0.001-0.0010.0000.0000.0000.000
39C46ILE0-0.039-0.01928.6590.0060.0060.0000.0000.0000.000
40C47SER00.0210.00632.2040.0090.0090.0000.0000.0000.000
41C48LEU0-0.011-0.00527.0020.0050.0050.0000.0000.0000.000
42C49GLU-1-0.988-0.99631.015-0.154-0.1540.0000.0000.0000.000
43C50HIS0-0.083-0.04932.4380.0120.0120.0000.0000.0000.000
44C51GLU-1-0.861-0.89033.698-0.118-0.1180.0000.0000.0000.000
45C52ILE0-0.071-0.04732.789-0.001-0.0010.0000.0000.0000.000
46C71LEU0-0.019-0.01329.3290.0050.0050.0000.0000.0000.000
47C72LEU0-0.0340.02025.216-0.008-0.0080.0000.0000.0000.000
48C73SER00.0490.02029.1340.0090.0090.0000.0000.0000.000
49C74ARG10.9710.95629.9780.0920.0920.0000.0000.0000.000
50C75SER0-0.016-0.00227.9480.0000.0000.0000.0000.0000.000
51C76SER00.0870.01825.135-0.006-0.0060.0000.0000.0000.000
52C77ARG10.9600.99026.5570.1380.1380.0000.0000.0000.000
53C78LYS10.8890.92826.2260.1880.1880.0000.0000.0000.000
54C79ALA00.0350.01622.500-0.011-0.0110.0000.0000.0000.000
55C80LEU00.0360.02123.318-0.017-0.0170.0000.0000.0000.000
56C81ILE0-0.0100.00824.818-0.007-0.0070.0000.0000.0000.000
57C82TYR00.014-0.01320.512-0.007-0.0070.0000.0000.0000.000
58C83LEU00.0220.04419.465-0.021-0.0210.0000.0000.0000.000
59C84VAL00.0540.01921.587-0.006-0.0060.0000.0000.0000.000
60C85LEU0-0.046-0.01722.1480.0010.0010.0000.0000.0000.000
61C86THR0-0.038-0.04316.616-0.019-0.0190.0000.0000.0000.000
62C87LEU00.0390.02419.610-0.009-0.0090.0000.0000.0000.000
63C88TYR0-0.008-0.00121.8190.0080.0080.0000.0000.0000.000
64C89HIS10.7420.85018.9630.3110.3110.0000.0000.0000.000
65C90MET0-0.0260.00916.453-0.005-0.0050.0000.0000.0000.000
66C91TYR00.0230.00220.0110.0140.0140.0000.0000.0000.000
67C92PRO0-0.006-0.00123.2060.0060.0060.0000.0000.0000.000
68C93ASP-1-0.929-0.96225.859-0.116-0.1160.0000.0000.0000.000
69C94TYR0-0.048-0.02127.4790.0110.0110.0000.0000.0000.000
70C95ASP-1-0.882-0.93329.116-0.115-0.1150.0000.0000.0000.000
71C96PHE0-0.066-0.04324.8010.0030.0030.0000.0000.0000.000
72C97SER0-0.013-0.01529.4690.0050.0050.0000.0000.0000.000
73C98ALA00.020-0.00129.814-0.007-0.0070.0000.0000.0000.000
74C99VAL0-0.008-0.00430.901-0.003-0.0030.0000.0000.0000.000
75C100LYS10.9400.98229.7420.1220.1220.0000.0000.0000.000
76C101ALA00.0170.02026.819-0.003-0.0030.0000.0000.0000.000
77C102HIS0-0.039-0.02627.826-0.012-0.0120.0000.0000.0000.000
78C103GLN0-0.006-0.01030.0920.0040.0040.0000.0000.0000.000
79C104PHE00.006-0.00127.3200.0020.0020.0000.0000.0000.000
80C105PHE0-0.040-0.01021.142-0.009-0.0090.0000.0000.0000.000
81C106THR0-0.022-0.01224.3210.0140.0140.0000.0000.0000.000
82C107GLU-1-0.957-0.98923.002-0.214-0.2140.0000.0000.0000.000
83C108GLU-1-0.854-0.92120.293-0.140-0.1400.0000.0000.0000.000
84C109SER00.000-0.01320.620-0.011-0.0110.0000.0000.0000.000
85C110TRP00.0760.01511.184-0.011-0.0110.0000.0000.0000.000
86C111ASN0-0.011-0.01617.4030.0100.0100.0000.0000.0000.000
87C112THR0-0.0250.01019.8880.0160.0160.0000.0000.0000.000
88C113PHE00.0660.03812.2270.0040.0040.0000.0000.0000.000
89C114LYS10.9370.98016.0530.0830.0830.0000.0000.0000.000
90C115GLN00.0320.00817.0680.0180.0180.0000.0000.0000.000
91C116ILE00.0680.10318.1540.0170.0170.0000.0000.0000.000
92C117PHE00.013-0.00211.9770.0070.0070.0000.0000.0000.000
93C118GLU-1-0.964-0.98816.8630.0150.0150.0000.0000.0000.000
94C119THR0-0.109-0.12418.6720.0140.0140.0000.0000.0000.000
95C120TYR0-0.036-0.01719.6810.0090.0090.0000.0000.0000.000
96C121MET0-0.046-0.00914.3900.0030.0030.0000.0000.0000.000
97C122PHE00.0260.01916.0720.0320.0320.0000.0000.0000.000
98C123GLU-1-0.886-0.96417.8240.1280.1280.0000.0000.0000.000
99C124ALA00.0270.01513.9610.0280.0280.0000.0000.0000.000
100C125SER00.015-0.01312.9760.0590.0590.0000.0000.0000.000
101C126LYS10.8770.94214.037-0.151-0.1510.0000.0000.0000.000
102C127GLU-1-0.891-0.94415.3470.3300.3300.0000.0000.0000.000
103C128TRP0-0.042-0.0145.5010.1460.1460.0000.0000.0000.000
104C129SER0-0.141-0.07812.4400.0900.0900.0000.0000.0000.000
105C130GLU-1-0.867-0.92214.2480.2790.2790.0000.0000.0000.000
106C131THR0-0.043-0.00411.9850.0040.0040.0000.0000.0000.000
107C132TYR0-0.046-0.0377.7790.4770.4770.0000.0000.0000.000
108C133GLY0-0.022-0.00410.745-0.112-0.1120.0000.0000.0000.000
109C134GLY00.0230.00212.625-0.026-0.0260.0000.0000.0000.000
110C135SER0-0.099-0.06212.750-0.073-0.0730.0000.0000.0000.000
111C136SER0-0.040-0.02612.379-0.070-0.0700.0000.0000.0000.000
112C137LEU00.0630.0418.6230.0130.0130.0000.0000.0000.000
113C138LEU00.0170.0138.276-0.061-0.0610.0000.0000.0000.000
114C139GLU-1-0.761-0.8678.8690.2400.2400.0000.0000.0000.000
115C140THR0-0.046-0.0284.530-0.198-0.106-0.001-0.007-0.0830.000
116C141LEU00.0630.0344.119-0.498-0.3330.000-0.046-0.1190.000
117C142TYR0-0.037-0.0186.036-0.265-0.2650.0000.0000.0000.000
118C143LYS10.9690.9844.3990.3620.553-0.001-0.018-0.1720.000
119C144ALA00.0100.0052.104-0.463-0.8252.312-0.691-1.2600.000
120C145LEU0-0.014-0.0193.622-0.343-0.2960.0180.078-0.1430.000
121C146ASP-1-0.919-0.9667.276-0.623-0.6230.0000.0000.0000.000
122C147GLU-1-0.986-0.9862.262-11.834-9.7244.207-2.812-3.505-0.041
123C148VAL0-0.065-0.0194.9980.2050.2050.0000.0000.0000.000
124C149VAL0-0.096-0.0757.7280.2910.2910.0000.0000.0000.000
125C150LYS10.9951.00210.7940.4440.4440.0000.0000.0000.000
126C151LEU00.1050.0429.9640.0710.0710.0000.0000.0000.000
127C152PRO0-0.030-0.00413.7560.0460.0460.0000.0000.0000.000
128C153GLU-1-1.012-1.01216.430-0.284-0.2840.0000.0000.0000.000
129C154CYS0-0.131-0.05414.228-0.026-0.0260.0000.0000.0000.000
130C155GLU-1-0.831-0.86817.043-0.215-0.2150.0000.0000.0000.000
131C156ILE0-0.001-0.00916.320-0.043-0.0430.0000.0000.0000.000
132C157TYR0-0.039-0.02118.3260.0380.0380.0000.0000.0000.000
133C158SER0-0.0030.00618.962-0.028-0.0280.0000.0000.0000.000
134C159TYR0-0.075-0.03921.1220.0050.0050.0000.0000.0000.000
135C160ASN0-0.028-0.02122.8950.0030.0030.0000.0000.0000.000
136C161PRO0-0.016-0.00825.2070.0080.0080.0000.0000.0000.000
137C162ASP-1-0.859-0.92828.293-0.086-0.0860.0000.0000.0000.000
138C163SER0-0.055-0.02631.6560.0050.0050.0000.0000.0000.000
139C164ASP-1-0.861-0.94431.057-0.064-0.0640.0000.0000.0000.000
140C165SER0-0.096-0.05431.3960.0000.0000.0000.0000.0000.000
141C166ASP-1-0.892-0.94026.467-0.149-0.1490.0000.0000.0000.000
142C167PRO00.0120.03024.3440.0030.0030.0000.0000.0000.000
143C168PHE0-0.083-0.03621.520-0.009-0.0090.0000.0000.0000.000
144C169LEU00.0410.00323.012-0.004-0.0040.0000.0000.0000.000
145C170GLU-1-0.751-0.87825.469-0.017-0.0170.0000.0000.0000.000
146C171LYS10.8260.89927.4190.0130.0130.0000.0000.0000.000
147C172GLY0-0.0130.00429.1720.0020.0020.0000.0000.0000.000
148C173ALA0-0.016-0.02425.5880.0060.0060.0000.0000.0000.000
149C174ILE0-0.035-0.00325.072-0.001-0.0010.0000.0000.0000.000
150C175TRP00.031-0.00718.521-0.007-0.0070.0000.0000.0000.000
151C176SER0-0.038-0.02621.440-0.004-0.0040.0000.0000.0000.000
152C177PHE00.0540.03718.7920.0030.0030.0000.0000.0000.000
153C178ASN00.004-0.00817.190-0.048-0.0480.0000.0000.0000.000
154C179PHE00.0200.01315.4560.0220.0220.0000.0000.0000.000
155C180PHE0-0.005-0.00715.218-0.055-0.0550.0000.0000.0000.000
156C181PHE00.0240.01512.1230.0370.0370.0000.0000.0000.000
157C182TYR0-0.017-0.00814.049-0.046-0.0460.0000.0000.0000.000
158C183ASN00.1110.05015.1280.0640.0640.0000.0000.0000.000
159C184ARG10.9150.96017.2240.2340.2340.0000.0000.0000.000
160C185LYS10.9430.95620.2340.2590.2590.0000.0000.0000.000
161C186LEU0-0.0260.00713.6470.0080.0080.0000.0000.0000.000
162C187LYS10.8370.93117.1110.2870.2870.0000.0000.0000.000
163C188ARG10.9820.99011.8200.7610.7610.0000.0000.0000.000
164C189VAL00.0260.00514.6740.0360.0360.0000.0000.0000.000
165C190VAL00.0100.0118.730-0.053-0.0530.0000.0000.0000.000
166C191SER0-0.0120.00111.8500.1150.1150.0000.0000.0000.000
167C192PHE00.015-0.00211.443-0.116-0.1160.0000.0000.0000.000
168C193ARG10.8830.94912.8330.2970.2970.0000.0000.0000.000
169C194PHE00.0380.01214.343-0.003-0.0030.0000.0000.0000.000
170C195SER0-0.001-0.00516.412-0.002-0.0020.0000.0000.0000.000
171C196CYS0-0.0350.00718.9980.0240.0240.0000.0000.0000.000
172C197LEU0-0.0080.00221.630-0.011-0.0110.0000.0000.0000.000
173C198SER00.0340.00924.0990.0180.0180.0000.0000.0000.000
174C199ASN00.0470.02225.465-0.011-0.0110.0000.0000.0000.000
175C200LEU0-0.044-0.01127.960-0.001-0.0010.0000.0000.0000.000