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: LZNL9

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973252.553368
FMO2-HF: Nuclear repulsion 1901021.937959
FMO2-HF: Total energy -72230.615409
FMO2-MP2: Total energy -72441.855932


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.
-23.849-13.1775.771-6.633-9.812-0.047
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 : -0.013 / 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-1-0.850-0.9242.177-12.783-8.0022.978-3.644-4.115-0.040
4C11ARG10.9130.9642.420-6.073-4.0361.354-1.230-2.1620.007
5C12ILE0-0.0010.0044.074-1.229-0.6800.004-0.177-0.3750.000
6C13ASN00.0200.0015.8860.1610.1610.0000.0000.0000.000
7C14ASP-1-0.926-0.9677.3251.1021.1020.0000.0000.0000.000
8C15PHE0-0.061-0.0278.5560.0170.0170.0000.0000.0000.000
9C16LEU0-0.009-0.0049.898-0.097-0.0970.0000.0000.0000.000
10C17ASP-1-0.806-0.89811.942-0.088-0.0880.0000.0000.0000.000
11C18HIS0-0.040-0.02613.9300.0170.0170.0000.0000.0000.000
12C19LEU00.0410.04313.3450.0240.0240.0000.0000.0000.000
13C20ASN0-0.001-0.01816.503-0.041-0.0410.0000.0000.0000.000
14C21LEU00.0190.01218.7650.0260.0260.0000.0000.0000.000
15C22GLY0-0.015-0.00321.558-0.011-0.0110.0000.0000.0000.000
16C23GLU-1-0.927-0.97125.1970.0600.0600.0000.0000.0000.000
17C24ARG10.7000.81223.125-0.085-0.0850.0000.0000.0000.000
18C25THR0-0.010-0.01219.5700.0250.0250.0000.0000.0000.000
19C26ILE0-0.014-0.00415.773-0.028-0.0280.0000.0000.0000.000
20C27LYS10.7790.87515.9180.0830.0830.0000.0000.0000.000
21C28GLY00.007-0.00413.146-0.009-0.0090.0000.0000.0000.000
22C29CYS0-0.091-0.04510.953-0.001-0.0010.0000.0000.0000.000
23C30LEU0-0.0130.0046.093-0.001-0.0010.0000.0000.0000.000
24C31GLU-1-0.820-0.9108.910-0.688-0.6880.0000.0000.0000.000
25C32ALA00.0000.0008.6040.0760.0760.0000.0000.0000.000
26C33TYR0-0.010-0.03110.6870.0910.0910.0000.0000.0000.000
27C34SER00.011-0.00114.2330.0010.0010.0000.0000.0000.000
28C35CYS0-0.046-0.00315.8320.0420.0420.0000.0000.0000.000
29C36LYS10.9740.98719.3180.3300.3300.0000.0000.0000.000
30C37HIS00.0390.00721.9710.0010.0010.0000.0000.0000.000
31C38THR0-0.026-0.02325.5390.0150.0150.0000.0000.0000.000
32C39GLY00.0370.01826.377-0.010-0.0100.0000.0000.0000.000
33C40THR00.0520.00725.4210.0070.0070.0000.0000.0000.000
34C41ASP-1-0.741-0.82722.124-0.277-0.2770.0000.0000.0000.000
35C42LYS10.9150.99525.7020.1610.1610.0000.0000.0000.000
36C43ARG10.9810.98428.3820.1290.1290.0000.0000.0000.000
37C44LEU00.0510.03226.3740.0080.0080.0000.0000.0000.000
38C45SER00.021-0.01526.3350.0000.0000.0000.0000.0000.000
39C46ILE0-0.046-0.02428.3440.0060.0060.0000.0000.0000.000
40C47SER00.0170.00432.0750.0080.0080.0000.0000.0000.000
41C48LEU00.0070.00826.9250.0060.0060.0000.0000.0000.000
42C49GLU-1-0.894-0.93230.565-0.147-0.1470.0000.0000.0000.000
43C50HIS0-0.060-0.04532.1380.0120.0120.0000.0000.0000.000
44C51GLU-1-0.800-0.83132.992-0.121-0.1210.0000.0000.0000.000
45C52ILE0-0.030-0.02333.2340.0000.0000.0000.0000.0000.000
46C71LEU00.0040.01529.3430.0050.0050.0000.0000.0000.000
47C72LEU0-0.039-0.01325.104-0.008-0.0080.0000.0000.0000.000
48C73SER0-0.015-0.00528.2520.0130.0130.0000.0000.0000.000
49C74ARG10.9550.94930.1280.0910.0910.0000.0000.0000.000
50C75SER0-0.001-0.01028.0480.0000.0000.0000.0000.0000.000
51C76SER00.0750.03325.736-0.007-0.0070.0000.0000.0000.000
52C77ARG10.7610.88726.4240.1280.1280.0000.0000.0000.000
53C78LYS10.9270.94325.6370.1710.1710.0000.0000.0000.000
54C79ALA00.0350.02322.158-0.011-0.0110.0000.0000.0000.000
55C80LEU00.0300.02023.058-0.018-0.0180.0000.0000.0000.000
56C81ILE0-0.0200.00325.047-0.004-0.0040.0000.0000.0000.000
57C82TYR00.027-0.00520.423-0.003-0.0030.0000.0000.0000.000
58C83LEU00.0090.03419.209-0.028-0.0280.0000.0000.0000.000
59C84VAL00.0640.02521.458-0.007-0.0070.0000.0000.0000.000
60C85LEU0-0.077-0.04021.8910.0030.0030.0000.0000.0000.000
61C86THR0-0.031-0.03816.745-0.025-0.0250.0000.0000.0000.000
62C87LEU00.0480.04219.694-0.013-0.0130.0000.0000.0000.000
63C88TYR0-0.038-0.02822.0000.0040.0040.0000.0000.0000.000
64C89HIS10.6890.81119.1970.3040.3040.0000.0000.0000.000
65C90MET0-0.0050.03115.8250.0030.0030.0000.0000.0000.000
66C91TYR00.0350.01219.7620.0120.0120.0000.0000.0000.000
67C92PRO0-0.034-0.01622.7910.0060.0060.0000.0000.0000.000
68C93ASP-1-0.945-0.97125.591-0.138-0.1380.0000.0000.0000.000
69C94TYR0-0.054-0.06327.4930.0160.0160.0000.0000.0000.000
70C95ASP-1-0.885-0.92728.939-0.120-0.1200.0000.0000.0000.000
71C96PHE0-0.058-0.03024.7760.0020.0020.0000.0000.0000.000
72C97SER0-0.035-0.03229.1860.0040.0040.0000.0000.0000.000
73C98ALA00.009-0.01529.674-0.006-0.0060.0000.0000.0000.000
74C99VAL0-0.019-0.01930.747-0.002-0.0020.0000.0000.0000.000
75C100LYS10.8610.95029.7800.1290.1290.0000.0000.0000.000
76C101ALA00.0310.02226.871-0.002-0.0020.0000.0000.0000.000
77C102HIS0-0.051-0.03427.994-0.012-0.0120.0000.0000.0000.000
78C103GLN0-0.037-0.02830.0830.0070.0070.0000.0000.0000.000
79C104PHE00.0280.02227.3980.0030.0030.0000.0000.0000.000
80C105PHE0-0.037-0.01221.081-0.010-0.0100.0000.0000.0000.000
81C106THR00.0140.00524.4460.0180.0180.0000.0000.0000.000
82C107GLU-1-0.866-0.91823.481-0.190-0.1900.0000.0000.0000.000
83C108GLU-1-0.814-0.85420.452-0.149-0.1490.0000.0000.0000.000
84C109SER0-0.013-0.02620.088-0.004-0.0040.0000.0000.0000.000
85C110TRP00.0570.01310.843-0.008-0.0080.0000.0000.0000.000
86C111ASN00.011-0.00517.4140.0090.0090.0000.0000.0000.000
87C112THR0-0.0320.00219.9450.0170.0170.0000.0000.0000.000
88C113PHE00.0390.02212.3670.0020.0020.0000.0000.0000.000
89C114LYS10.7870.88315.8270.0650.0650.0000.0000.0000.000
90C115GLN00.0280.00917.1250.0120.0120.0000.0000.0000.000
91C116ILE00.0080.02519.1560.0170.0170.0000.0000.0000.000
92C117PHE00.012-0.00611.7300.0060.0060.0000.0000.0000.000
93C118GLU-1-0.814-0.91217.054-0.007-0.0070.0000.0000.0000.000
94C119THR0-0.062-0.02819.1530.0200.0200.0000.0000.0000.000
95C120TYR0-0.040-0.02619.8890.0090.0090.0000.0000.0000.000
96C121MET0-0.0010.00813.2910.0100.0100.0000.0000.0000.000
97C122PHE00.0160.03415.9690.0380.0380.0000.0000.0000.000
98C123GLU-1-0.796-0.86017.7690.1090.1090.0000.0000.0000.000
99C124ALA00.0420.01314.1980.0270.0270.0000.0000.0000.000
100C125SER0-0.040-0.04113.3690.0510.0510.0000.0000.0000.000
101C126LYS10.7640.87314.444-0.164-0.1640.0000.0000.0000.000
102C127GLU-1-0.777-0.87415.2890.2700.2700.0000.0000.0000.000
103C128TRP0-0.041-0.0045.0410.1340.1340.0000.0000.0000.000
104C129SER0-0.116-0.07512.5100.0800.0800.0000.0000.0000.000
105C130GLU-1-0.851-0.91014.4550.2460.2460.0000.0000.0000.000
106C131THR0-0.066-0.03111.917-0.005-0.0050.0000.0000.0000.000
107C132TYR0-0.047-0.0228.7840.4240.4240.0000.0000.0000.000
108C133GLY0-0.0160.00010.881-0.107-0.1070.0000.0000.0000.000
109C134GLY00.0320.01512.689-0.024-0.0240.0000.0000.0000.000
110C135SER0-0.096-0.07612.180-0.062-0.0620.0000.0000.0000.000
111C136SER0-0.051-0.03412.110-0.059-0.0590.0000.0000.0000.000
112C137LEU00.0590.0497.831-0.026-0.0260.0000.0000.0000.000
113C138LEU00.0280.0118.227-0.067-0.0670.0000.0000.0000.000
114C139GLU-1-0.754-0.8578.7630.2900.2900.0000.0000.0000.000
115C140THR0-0.055-0.0344.345-0.143-0.021-0.001-0.011-0.1100.000
116C141LEU00.0540.0254.194-0.575-0.440-0.001-0.034-0.1000.000
117C142TYR0-0.036-0.0186.354-0.192-0.1920.0000.0000.0000.000
118C143LYS10.8620.9173.9120.2580.5440.001-0.042-0.2450.000
119C144ALA00.0060.0052.408-0.774-0.2930.730-0.326-0.8860.000
120C145LEU0-0.019-0.0083.697-0.293-0.2310.0110.051-0.1240.000
121C146ASP-1-0.859-0.9317.469-0.499-0.4990.0000.0000.0000.000
122C147GLU-1-0.887-0.9322.783-5.288-3.0690.695-1.220-1.695-0.014
123C148VAL0-0.034-0.0025.2900.0210.0210.0000.0000.0000.000
124C149VAL0-0.087-0.0738.0380.2060.2060.0000.0000.0000.000
125C150LYS10.8750.92311.2510.3540.3540.0000.0000.0000.000
126C151LEU00.0920.03510.7750.0550.0550.0000.0000.0000.000
127C152PRO0-0.056-0.01713.6740.0380.0380.0000.0000.0000.000
128C153GLU-1-0.888-0.92916.449-0.264-0.2640.0000.0000.0000.000
129C154CYS0-0.107-0.03614.421-0.038-0.0380.0000.0000.0000.000
130C155GLU-1-0.753-0.82417.025-0.214-0.2140.0000.0000.0000.000
131C156ILE0-0.005-0.01316.392-0.042-0.0420.0000.0000.0000.000
132C157TYR0-0.042-0.04718.3410.0370.0370.0000.0000.0000.000
133C158SER0-0.008-0.02018.887-0.028-0.0280.0000.0000.0000.000
134C159TYR0-0.067-0.08021.1870.0050.0050.0000.0000.0000.000
135C160ASN0-0.027-0.02023.137-0.001-0.0010.0000.0000.0000.000
136C161PRO0-0.0050.00425.5120.0080.0080.0000.0000.0000.000
137C162ASP-1-0.864-0.93328.553-0.089-0.0890.0000.0000.0000.000
138C163SER0-0.049-0.02531.9900.0060.0060.0000.0000.0000.000
139C164ASP-1-0.884-0.95631.004-0.072-0.0720.0000.0000.0000.000
140C165SER0-0.061-0.03031.1720.0010.0010.0000.0000.0000.000
141C166ASP-1-0.738-0.82227.138-0.153-0.1530.0000.0000.0000.000
142C167PRO0-0.0210.02324.0720.0010.0010.0000.0000.0000.000
143C168PHE0-0.043-0.04221.075-0.019-0.0190.0000.0000.0000.000
144C169LEU00.0090.00622.911-0.005-0.0050.0000.0000.0000.000
145C170GLU-1-0.738-0.87225.098-0.026-0.0260.0000.0000.0000.000
146C171LYS10.8230.90327.0620.0210.0210.0000.0000.0000.000
147C172GLY00.0050.01228.8880.0030.0030.0000.0000.0000.000
148C173ALA0-0.033-0.02525.0850.0070.0070.0000.0000.0000.000
149C174ILE0-0.0240.00025.154-0.002-0.0020.0000.0000.0000.000
150C175TRP00.0450.01318.359-0.007-0.0070.0000.0000.0000.000
151C176SER0-0.029-0.01421.191-0.005-0.0050.0000.0000.0000.000
152C177PHE00.0380.04118.8650.0040.0040.0000.0000.0000.000
153C178ASN0-0.010-0.01218.005-0.055-0.0550.0000.0000.0000.000
154C179PHE00.0450.01815.7850.0230.0230.0000.0000.0000.000
155C180PHE0-0.012-0.01415.140-0.062-0.0620.0000.0000.0000.000
156C181PHE00.0300.02312.5920.0430.0430.0000.0000.0000.000
157C182TYR0-0.008-0.01314.364-0.041-0.0410.0000.0000.0000.000
158C183ASN00.0740.04315.9230.0420.0420.0000.0000.0000.000
159C184ARG10.7750.84617.6340.2100.2100.0000.0000.0000.000
160C185LYS10.9130.94820.1210.2240.2240.0000.0000.0000.000
161C186LEU00.0040.00613.6210.0080.0080.0000.0000.0000.000
162C187LYS10.8240.92716.6730.2690.2690.0000.0000.0000.000
163C188ARG10.8910.95211.2130.7080.7080.0000.0000.0000.000
164C189VAL00.0120.00814.7800.0450.0450.0000.0000.0000.000
165C190VAL0-0.016-0.0058.669-0.078-0.0780.0000.0000.0000.000
166C191SER00.0190.01411.8860.1150.1150.0000.0000.0000.000
167C192PHE00.023-0.01210.878-0.144-0.1440.0000.0000.0000.000
168C193ARG10.8750.94512.9540.3590.3590.0000.0000.0000.000
169C194PHE00.023-0.00214.059-0.015-0.0150.0000.0000.0000.000
170C195SER0-0.001-0.01916.235-0.001-0.0010.0000.0000.0000.000
171C196CYS0-0.0370.00818.8190.0220.0220.0000.0000.0000.000
172C197LEU00.001-0.00421.517-0.011-0.0110.0000.0000.0000.000
173C198SER00.0490.02123.9750.0180.0180.0000.0000.0000.000
174C199ASN00.0160.03024.816-0.012-0.0120.0000.0000.0000.000
175C200LEU0-0.040-0.01927.5070.0000.0000.0000.0000.0000.000