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: 5JG8Z

Calculation Name: 4Y4Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y4Q

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0M3

Base Structure: X-ray

Registration Date: 2023-09-23

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 -1898964.658305
FMO2-HF: Nuclear repulsion 1829383.698358
FMO2-HF: Total energy -69580.959947
FMO2-MP2: Total energy -69785.65153


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(B:76:SER)


Summations of interaction energy for fragment #1(B:76:SER)
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.
-23.733-18.77713.473-8.932-9.495-0.065
Interaction energy analysis for fragmet #1(B:76:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.022
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].
3B78PHE0-0.022-0.0133.870-0.9430.696-0.013-0.730-0.8960.002
4B79SER00.025-0.0015.663-0.585-0.5850.0000.0000.0000.000
5B80LYS10.7750.8438.918-0.700-0.7000.0000.0000.0000.000
6B81LEU00.0120.0266.726-0.090-0.0900.0000.0000.0000.000
7B82GLN0-0.001-0.0158.614-0.042-0.0420.0000.0000.0000.000
8B83GLU-1-0.823-0.88111.3350.4880.4880.0000.0000.0000.000
9B84LEU0-0.089-0.03713.155-0.041-0.0410.0000.0000.0000.000
10B85ASN0-0.047-0.02912.629-0.030-0.0300.0000.0000.0000.000
11B86PRO00.0000.00112.9200.0130.0130.0000.0000.0000.000
12B87GLU-1-0.831-0.90914.4030.1630.1630.0000.0000.0000.000
13B88VAL0-0.040-0.0118.364-0.006-0.0060.0000.0000.0000.000
14B89LEU0-0.0100.0039.9610.0190.0190.0000.0000.0000.000
15B90GLY0-0.015-0.0226.245-0.053-0.0530.0000.0000.0000.000
16B91TRP0-0.044-0.0293.688-1.043-0.3720.034-0.283-0.4220.002
17B92ILE0-0.0050.0005.7290.1510.1510.0000.0000.0000.000
18B93ASN0-0.046-0.0365.846-0.255-0.2550.0000.0000.0000.000
19B94VAL00.0490.0237.690-0.120-0.1200.0000.0000.0000.000
20B95TYR00.0070.0196.3610.1790.1790.0000.0000.0000.000
21B96GLY0-0.019-0.01111.5230.0800.0800.0000.0000.0000.000
22B97THR0-0.058-0.03313.0400.0760.0760.0000.0000.0000.000
23B98ASN0-0.087-0.07012.827-0.043-0.0430.0000.0000.0000.000
24B99ILE0-0.021-0.00511.2890.0340.0340.0000.0000.0000.000
25B100ASP-1-0.824-0.8956.370-0.368-0.3680.0000.0000.0000.000
26B101TYR00.0120.0108.209-0.086-0.0860.0000.0000.0000.000
27B102PRO00.0220.0257.9820.2810.2810.0000.0000.0000.000
28B103LEU0-0.042-0.0167.800-0.074-0.0740.0000.0000.0000.000
29B104VAL00.0400.01110.671-0.008-0.0080.0000.0000.0000.000
30B105GLN0-0.072-0.04413.876-0.008-0.0080.0000.0000.0000.000
31B106ALA00.0480.04917.0470.0030.0030.0000.0000.0000.000
32B107LYS10.8060.88419.834-0.075-0.0750.0000.0000.0000.000
33B108ASP-1-0.903-0.94923.6730.0380.0380.0000.0000.0000.000
34B109ASN0-0.011-0.01224.6540.0040.0040.0000.0000.0000.000
35B110GLU-1-0.931-0.95322.5820.0340.0340.0000.0000.0000.000
36B120GLU-1-0.956-0.98318.9340.0880.0880.0000.0000.0000.000
37B121PHE00.0200.00012.794-0.004-0.0040.0000.0000.0000.000
38B122ALA0-0.007-0.00117.060-0.011-0.0110.0000.0000.0000.000
39B123ALA0-0.0150.00416.536-0.014-0.0140.0000.0000.0000.000
40B124THR0-0.052-0.04112.0170.0130.0130.0000.0000.0000.000
41B125GLY00.0510.03113.837-0.005-0.0050.0000.0000.0000.000
42B126ALA0-0.014-0.02413.1000.0170.0170.0000.0000.0000.000
43B127ILE0-0.0330.00012.331-0.027-0.0270.0000.0000.0000.000
44B128PHE00.0020.00013.8900.0290.0290.0000.0000.0000.000
45B129LEU0-0.001-0.00812.528-0.013-0.0130.0000.0000.0000.000
46B130ASP-1-0.740-0.83316.6510.0200.0200.0000.0000.0000.000
47B131ALA0-0.014-0.00519.7880.0050.0050.0000.0000.0000.000
48B132ARG10.7780.86421.905-0.011-0.0110.0000.0000.0000.000
49B133ASN0-0.026-0.01817.966-0.004-0.0040.0000.0000.0000.000
50B134ASN0-0.007-0.02217.4110.0220.0220.0000.0000.0000.000
51B135PRO0-0.009-0.01114.665-0.002-0.0020.0000.0000.0000.000
52B136LYS10.7760.87412.643-0.034-0.0340.0000.0000.0000.000
53B137PHE00.0470.01510.641-0.018-0.0180.0000.0000.0000.000
54B138GLU-1-0.833-0.88214.2450.0050.0050.0000.0000.0000.000
55B139ASP-1-0.815-0.88317.0600.0060.0060.0000.0000.0000.000
56B140PHE0-0.0120.00118.382-0.006-0.0060.0000.0000.0000.000
57B141ASN00.0190.00419.802-0.009-0.0090.0000.0000.0000.000
58B142THR0-0.012-0.00715.0860.0140.0140.0000.0000.0000.000
59B143ILE00.0050.01217.985-0.009-0.0090.0000.0000.0000.000
60B144ILE0-0.030-0.01913.0120.0170.0170.0000.0000.0000.000
61B145TYR0-0.013-0.02817.045-0.018-0.0180.0000.0000.0000.000
62B146GLY00.0480.01917.4620.0190.0190.0000.0000.0000.000
63B147HIS0-0.0160.00218.336-0.019-0.0190.0000.0000.0000.000
64B148HIS0-0.004-0.01321.433-0.001-0.0010.0000.0000.0000.000
65B149VAL00.001-0.00522.4270.0040.0040.0000.0000.0000.000
66B150GLU-1-0.884-0.92524.796-0.010-0.0100.0000.0000.0000.000
67B151ASN0-0.078-0.05725.501-0.005-0.0050.0000.0000.0000.000
68B152GLY0-0.014-0.01422.919-0.001-0.0010.0000.0000.0000.000
69B153VAL00.0180.01217.470-0.007-0.0070.0000.0000.0000.000
70B154MET0-0.013-0.00118.489-0.004-0.0040.0000.0000.0000.000
71B155PHE00.0120.02414.9340.0000.0000.0000.0000.0000.000
72B156GLY00.0240.00618.352-0.007-0.0070.0000.0000.0000.000
73B157ASP-1-0.761-0.86916.734-0.156-0.1560.0000.0000.0000.000
74B158VAL00.0200.01016.854-0.011-0.0110.0000.0000.0000.000
75B159ALA00.0380.02419.106-0.003-0.0030.0000.0000.0000.000
76B160LYS10.8140.90019.6590.1280.1280.0000.0000.0000.000
77B161PHE0-0.041-0.01816.105-0.005-0.0050.0000.0000.0000.000
78B162ALA00.0850.04222.1240.0010.0010.0000.0000.0000.000
79B163ASP-1-0.875-0.93325.122-0.106-0.1060.0000.0000.0000.000
80B164GLN0-0.036-0.01624.9500.0000.0000.0000.0000.0000.000
81B165GLU-1-0.893-0.94925.056-0.134-0.1340.0000.0000.0000.000
82B166PHE0-0.054-0.03818.296-0.023-0.0230.0000.0000.0000.000
83B167PHE00.0280.01120.404-0.021-0.0210.0000.0000.0000.000
84B168ASP-1-0.872-0.91820.690-0.154-0.1540.0000.0000.0000.000
85B169GLN0-0.129-0.06420.334-0.027-0.0270.0000.0000.0000.000
86B170HIS10.7910.90415.6880.2280.2280.0000.0000.0000.000
87B171ARG10.8890.93516.4050.2280.2280.0000.0000.0000.000
88B172TYR0-0.061-0.04712.3550.0130.0130.0000.0000.0000.000
89B173GLY00.0440.0119.3810.0300.0300.0000.0000.0000.000
90B174SER0-0.076-0.0244.1260.3240.367-0.001-0.008-0.0340.000
91B175ILE00.0270.0126.0090.5030.5030.0000.0000.0000.000
92B176TYR0-0.027-0.0082.184-2.490-1.8686.980-3.973-3.628-0.015
93B177TYR00.0850.0414.1540.1110.1710.000-0.0650.0050.000
94B178ASN0-0.015-0.0187.238-0.074-0.0740.0000.0000.0000.000
95B179GLY00.0170.0197.104-0.009-0.0090.0000.0000.0000.000
96B180VAL0-0.073-0.0276.6030.0780.0780.0000.0000.0000.000
97B181GLU-1-0.813-0.9022.021-18.929-17.0086.473-3.873-4.520-0.054
98B182LYS10.7820.8825.5120.5810.5810.0000.0000.0000.000
99B183GLY00.0510.0337.367-0.149-0.1490.0000.0000.0000.000
100B184LEU0-0.013-0.0089.3350.1530.1530.0000.0000.0000.000
101B185GLU-1-0.787-0.87511.463-0.296-0.2960.0000.0000.0000.000
102B186ILE00.0100.01314.6610.0380.0380.0000.0000.0000.000
103B187PHE00.010-0.01016.862-0.010-0.0100.0000.0000.0000.000
104B188GLU-1-0.826-0.94420.230-0.065-0.0650.0000.0000.0000.000
105B189MET0-0.039-0.00220.734-0.005-0.0050.0000.0000.0000.000
106B190LEU00.0400.02223.0690.0020.0020.0000.0000.0000.000
107B191GLU-1-0.885-0.96525.263-0.034-0.0340.0000.0000.0000.000
108B192VAL00.0100.01527.1140.0000.0000.0000.0000.0000.000
109B193ASP-1-0.784-0.88829.297-0.012-0.0120.0000.0000.0000.000
110B194ALA0-0.029-0.01928.5040.0000.0000.0000.0000.0000.000
111B195TYR0-0.075-0.03529.4260.0040.0040.0000.0000.0000.000
112B196ASP-1-0.779-0.87930.232-0.024-0.0240.0000.0000.0000.000
113B197PHE0-0.032-0.03629.7350.0000.0000.0000.0000.0000.000
114B198ASN0-0.100-0.04330.4400.0010.0010.0000.0000.0000.000
115B199ILE00.0040.01425.508-0.003-0.0030.0000.0000.0000.000
116B200TYR0-0.018-0.01723.5670.0000.0000.0000.0000.0000.000
117B201ASP-1-0.926-0.96626.3050.0000.0000.0000.0000.0000.000
118B202PRO0-0.0030.01221.887-0.005-0.0050.0000.0000.0000.000
119B203GLY00.0170.00822.2150.0020.0020.0000.0000.0000.000
120B204ILE0-0.0290.00223.2880.0010.0010.0000.0000.0000.000
121B205GLN0-0.022-0.02125.224-0.004-0.0040.0000.0000.0000.000
122B206GLY0-0.030-0.01427.5990.0020.0020.0000.0000.0000.000
123B207GLU-1-0.879-0.94329.150-0.041-0.0410.0000.0000.0000.000
124B208ASP-1-0.878-0.94930.212-0.030-0.0300.0000.0000.0000.000
125B209ARG10.8520.92630.5230.0140.0140.0000.0000.0000.000
126B210GLN0-0.014-0.01224.901-0.001-0.0010.0000.0000.0000.000
127B211GLN0-0.018-0.01927.652-0.006-0.0060.0000.0000.0000.000
128B212ALA00.0160.00729.663-0.002-0.0020.0000.0000.0000.000
129B213TYR0-0.044-0.02923.853-0.002-0.0020.0000.0000.0000.000
130B214LEU00.0060.00024.145-0.002-0.0020.0000.0000.0000.000
131B215ASP-1-0.853-0.92627.213-0.054-0.0540.0000.0000.0000.000
132B216HIS0-0.034-0.01529.864-0.002-0.0020.0000.0000.0000.000
133B217LEU00.0140.02123.0770.0000.0000.0000.0000.0000.000
134B218LEU00.0330.02325.104-0.003-0.0030.0000.0000.0000.000
135B219SER0-0.169-0.08228.165-0.002-0.0020.0000.0000.0000.000
136B220VAL0-0.019-0.01428.7610.0010.0010.0000.0000.0000.000
137B221ALA0-0.040-0.00226.9740.0000.0000.0000.0000.0000.000
138B222MET0-0.066-0.02327.2600.0010.0010.0000.0000.0000.000
139B223HIS0-0.045-0.02124.939-0.003-0.0030.0000.0000.0000.000
140B224LYS10.8810.91724.2170.0730.0730.0000.0000.0000.000
141B225ARG10.7330.85519.5950.1690.1690.0000.0000.0000.000
142B226ASP-1-0.929-0.95524.122-0.098-0.0980.0000.0000.0000.000
143B227ILE0-0.031-0.02019.551-0.012-0.0120.0000.0000.0000.000
144B228SER0-0.009-0.00522.7980.0130.0130.0000.0000.0000.000
145B229LEU0-0.0220.00620.331-0.014-0.0140.0000.0000.0000.000
146B230SER00.010-0.00623.4720.0100.0100.0000.0000.0000.000
147B231PRO00.0260.00023.823-0.004-0.0040.0000.0000.0000.000
148B232SER0-0.035-0.01123.7180.0060.0060.0000.0000.0000.000
149B233ASP-1-0.864-0.88919.845-0.132-0.1320.0000.0000.0000.000
150B234ARG10.8700.91313.2170.1130.1130.0000.0000.0000.000
151B235ILE0-0.021-0.00417.158-0.025-0.0250.0000.0000.0000.000
152B236ILE0-0.008-0.00912.2930.0220.0220.0000.0000.0000.000
153B237LEU00.0210.02216.440-0.016-0.0160.0000.0000.0000.000
154B238LEU00.0010.00313.6600.0190.0190.0000.0000.0000.000
155B239SER00.0000.00317.232-0.014-0.0140.0000.0000.0000.000
156B240THR00.004-0.02519.7740.0090.0090.0000.0000.0000.000
157B241CYS0-0.020-0.01421.756-0.002-0.0020.0000.0000.0000.000
158B242PHE0-0.0120.00325.246-0.006-0.0060.0000.0000.0000.000
159B243LEU00.003-0.01126.5280.0030.0030.0000.0000.0000.000
160B244ASP-1-0.927-0.95429.642-0.039-0.0390.0000.0000.0000.000
161B245VAL0-0.026-0.00931.7340.0010.0010.0000.0000.0000.000
162B246THR0-0.039-0.02532.3000.0020.0020.0000.0000.0000.000
163B247ASN0-0.044-0.04131.3990.0020.0020.0000.0000.0000.000
164B248GLY00.0940.05130.3810.0010.0010.0000.0000.0000.000
165B249ARG10.8020.90725.1510.0140.0140.0000.0000.0000.000
166B250HIS00.0380.03423.104-0.006-0.0060.0000.0000.0000.000
167B251ILE0-0.020-0.01620.7090.0090.0090.0000.0000.0000.000
168B252VAL00.0070.01516.732-0.009-0.0090.0000.0000.0000.000
169B253VAL00.0160.00018.2730.0140.0140.0000.0000.0000.000
170B254ALA00.0120.00614.233-0.022-0.0220.0000.0000.0000.000
171B255LYS10.8300.90416.2090.1840.1840.0000.0000.0000.000
172B256ILE0-0.002-0.00211.589-0.043-0.0430.0000.0000.0000.000
173B257THR0-0.018-0.00912.2930.0040.0040.0000.0000.0000.000
174B258ASP-1-0.803-0.88911.692-0.376-0.3760.0000.0000.0000.000
175B259THR0-0.074-0.0419.224-0.143-0.1430.0000.0000.0000.000