FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MV9GZ

Calculation Name: 4P6Z-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P6Z

Chain ID: G

ChEMBL ID:

UniProt ID: Q10567

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 587
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11324463.122566
FMO2-HF: Nuclear repulsion 11086057.326728
FMO2-HF: Total energy -238405.795838
FMO2-MP2: Total energy -239082.59861


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(G:2:PRO)


Summations of interaction energy for fragment #1(G:2: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.
11.481-2.5030.09614.749-0.861-0.003
Interaction energy analysis for fragmet #1(G:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.008
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].
3G4PRO00.0040.0132.56511.688-2.4300.09714.758-0.737-0.003
4G5ILE00.0400.0355.606-0.291-0.2910.0000.0000.0000.000
5G6ARG10.9580.9658.528-0.021-0.0210.0000.0000.0000.000
6G7LEU00.0760.03711.312-0.038-0.0380.0000.0000.0000.000
7G8ARG10.9780.97614.627-0.142-0.1420.0000.0000.0000.000
8G9GLU-1-0.768-0.84812.414-0.084-0.0840.0000.0000.0000.000
9G10LEU00.0340.03013.523-0.038-0.0380.0000.0000.0000.000
10G11ILE0-0.009-0.00714.945-0.028-0.0280.0000.0000.0000.000
11G12ARG10.8130.87116.5640.0300.0300.0000.0000.0000.000
12G13THR0-0.007-0.02115.399-0.028-0.0280.0000.0000.0000.000
13G14ILE00.0370.03217.717-0.011-0.0110.0000.0000.0000.000
14G15ARG10.9080.95419.949-0.059-0.0590.0000.0000.0000.000
15G16THR0-0.073-0.04220.178-0.018-0.0180.0000.0000.0000.000
16G17ALA0-0.039-0.00822.384-0.013-0.0130.0000.0000.0000.000
17G18ARG10.8580.91223.1910.0220.0220.0000.0000.0000.000
18G19THR00.0180.01426.5350.0040.0040.0000.0000.0000.000
19G20GLN00.0860.03726.363-0.002-0.0020.0000.0000.0000.000
20G21ALA00.0150.01026.0280.0150.0150.0000.0000.0000.000
21G22GLU-1-0.725-0.85222.2790.0040.0040.0000.0000.0000.000
22G23GLU-1-0.864-0.91521.7620.1210.1210.0000.0000.0000.000
23G24ARG10.9370.96421.145-0.121-0.1210.0000.0000.0000.000
24G25GLU-1-0.964-0.98520.2490.0950.0950.0000.0000.0000.000
25G26MET0-0.043-0.01317.3790.0400.0400.0000.0000.0000.000
26G27ILE00.002-0.00216.3830.0620.0620.0000.0000.0000.000
27G28GLN00.0210.01116.9890.0590.0590.0000.0000.0000.000
28G29LYS10.9761.00011.494-0.042-0.0420.0000.0000.0000.000
29G30GLU-1-0.829-0.91910.0500.8830.8830.0000.0000.0000.000
30G31CYS0-0.002-0.00612.2870.1430.1430.0000.0000.0000.000
31G32ALA0-0.038-0.00914.0180.0560.0560.0000.0000.0000.000
32G33ALA00.0050.0048.5590.0990.0990.0000.0000.0000.000
33G34ILE0-0.041-0.0149.8490.2590.2590.0000.0000.0000.000
34G35ARG10.9030.96611.512-0.423-0.4230.0000.0000.0000.000
35G36SER0-0.006-0.01110.827-0.082-0.0820.0000.0000.0000.000
36G37SER0-0.0180.0088.1310.0230.0230.0000.0000.0000.000
37G38PHE0-0.001-0.0369.770-0.080-0.0800.0000.0000.0000.000
38G39ARG10.9300.98413.183-0.614-0.6140.0000.0000.0000.000
39G40GLU-1-0.938-0.9708.2212.1962.1960.0000.0000.0000.000
40G41GLU-1-0.841-0.89912.2220.5460.5460.0000.0000.0000.000
41G42ASP-1-0.744-0.8538.1061.6981.6980.0000.0000.0000.000
42G43ASN00.0130.00210.817-0.077-0.0770.0000.0000.0000.000
43G44THR0-0.098-0.0487.839-0.210-0.2100.0000.0000.0000.000
44G45TYR0-0.090-0.0734.504-0.492-0.358-0.001-0.009-0.1240.000
45G46ARG10.8990.9399.486-0.704-0.7040.0000.0000.0000.000
46G47CYS0-0.0070.00712.657-0.092-0.0920.0000.0000.0000.000
47G48ARG10.9020.9307.399-1.145-1.1450.0000.0000.0000.000
48G49ASN00.0540.0218.521-0.136-0.1360.0000.0000.0000.000
49G50VAL00.0710.03912.392-0.074-0.0740.0000.0000.0000.000
50G51ALA0-0.018-0.00715.709-0.058-0.0580.0000.0000.0000.000
51G52LYS10.7500.8699.532-0.950-0.9500.0000.0000.0000.000
52G53LEU00.0070.01615.771-0.043-0.0430.0000.0000.0000.000
53G54LEU00.0110.02717.551-0.039-0.0390.0000.0000.0000.000
54G55TYR0-0.012-0.01318.446-0.038-0.0380.0000.0000.0000.000
55G56MET0-0.010-0.01515.163-0.032-0.0320.0000.0000.0000.000
56G57HIS00.0100.01620.515-0.010-0.0100.0000.0000.0000.000
57G58MET0-0.053-0.02423.118-0.023-0.0230.0000.0000.0000.000
58G59LEU0-0.040-0.01921.766-0.015-0.0150.0000.0000.0000.000
59G60GLY00.0200.02825.322-0.013-0.0130.0000.0000.0000.000
60G61TYR0-0.098-0.07122.1490.0050.0050.0000.0000.0000.000
61G62PRO0-0.021-0.01622.3930.0090.0090.0000.0000.0000.000
62G63ALA00.0610.01020.8490.0250.0250.0000.0000.0000.000
63G64HIS00.0490.03221.8450.0200.0200.0000.0000.0000.000
64G65PHE00.019-0.01317.0160.0090.0090.0000.0000.0000.000
65G66GLY00.0400.01418.5620.0380.0380.0000.0000.0000.000
66G67GLN0-0.001-0.00119.3900.0100.0100.0000.0000.0000.000
67G68LEU00.0040.00520.7820.0010.0010.0000.0000.0000.000
68G69GLU-1-0.775-0.87915.8130.6370.6370.0000.0000.0000.000
69G70CYS0-0.035-0.01419.2780.0120.0120.0000.0000.0000.000
70G71LEU00.0530.02021.138-0.008-0.0080.0000.0000.0000.000
71G72LYS10.7700.87517.263-0.558-0.5580.0000.0000.0000.000
72G73LEU0-0.093-0.03715.8490.0110.0110.0000.0000.0000.000
73G74ILE0-0.0130.00019.805-0.018-0.0180.0000.0000.0000.000
74G75ALA00.0030.00423.152-0.021-0.0210.0000.0000.0000.000
75G76SER0-0.031-0.02318.521-0.008-0.0080.0000.0000.0000.000
76G77GLN00.030-0.00220.794-0.027-0.0270.0000.0000.0000.000
77G78LYS10.8240.91814.816-0.510-0.5100.0000.0000.0000.000
78G79PHE00.0530.01520.5960.0030.0030.0000.0000.0000.000
79G80THR0-0.016-0.03117.318-0.012-0.0120.0000.0000.0000.000
80G81ASP-1-0.773-0.86016.9430.4740.4740.0000.0000.0000.000
81G82LYS10.8950.94119.060-0.233-0.2330.0000.0000.0000.000
82G83ARG10.9050.95822.094-0.192-0.1920.0000.0000.0000.000
83G84ILE0-0.025-0.02417.738-0.014-0.0140.0000.0000.0000.000
84G85GLY00.0610.02820.880-0.001-0.0010.0000.0000.0000.000
85G86TYR0-0.015-0.05521.760-0.010-0.0100.0000.0000.0000.000
86G87LEU0-0.039-0.00822.650-0.013-0.0130.0000.0000.0000.000
87G88GLY00.040-0.01022.345-0.011-0.0110.0000.0000.0000.000
88G89ALA00.003-0.00123.362-0.003-0.0030.0000.0000.0000.000
89G90MET0-0.073-0.02825.963-0.017-0.0170.0000.0000.0000.000
90G91LEU0-0.053-0.01124.384-0.009-0.0090.0000.0000.0000.000
91G92LEU0-0.016-0.01321.392-0.002-0.0020.0000.0000.0000.000
92G93LEU0-0.033-0.00225.579-0.003-0.0030.0000.0000.0000.000
93G94ASP-1-0.754-0.88328.2540.1660.1660.0000.0000.0000.000
94G95GLU-1-0.829-0.92631.8820.1220.1220.0000.0000.0000.000
95G96ARG10.8540.92131.182-0.163-0.1630.0000.0000.0000.000
96G97GLN0-0.053-0.02528.3500.0110.0110.0000.0000.0000.000
97G98ASP-1-0.868-0.91531.7680.1450.1450.0000.0000.0000.000
98G99VAL0-0.008-0.00428.0070.0040.0040.0000.0000.0000.000
99G100HIS00.0530.02530.9850.0150.0150.0000.0000.0000.000
100G101LEU00.0610.02533.0010.0010.0010.0000.0000.0000.000
101G102LEU00.0100.00526.4050.0000.0000.0000.0000.0000.000
102G103MET00.0460.02328.5030.0110.0110.0000.0000.0000.000
103G104THR0-0.0040.00430.312-0.004-0.0040.0000.0000.0000.000
104G105ASN00.002-0.00130.536-0.012-0.0120.0000.0000.0000.000
105G106CYS0-0.055-0.03027.4930.0030.0030.0000.0000.0000.000
106G107ILE00.0390.01629.642-0.003-0.0030.0000.0000.0000.000
107G108LYS10.9140.96631.980-0.122-0.1220.0000.0000.0000.000
108G109ASN0-0.019-0.01330.122-0.015-0.0150.0000.0000.0000.000
109G110ASP-1-0.808-0.87127.7780.1990.1990.0000.0000.0000.000
110G111LEU0-0.009-0.00831.077-0.005-0.0050.0000.0000.0000.000
111G112ASN0-0.092-0.04534.610-0.015-0.0150.0000.0000.0000.000
112G113HIS00.0480.03727.288-0.010-0.0100.0000.0000.0000.000
113G114SER00.0350.02031.548-0.008-0.0080.0000.0000.0000.000
114G115THR0-0.055-0.02628.716-0.007-0.0070.0000.0000.0000.000
115G116GLN00.0930.03831.5880.0030.0030.0000.0000.0000.000
116G117PHE0-0.013-0.02729.1610.0020.0020.0000.0000.0000.000
117G118VAL0-0.0160.00826.9000.0070.0070.0000.0000.0000.000
118G119GLN00.0680.03429.4460.0020.0020.0000.0000.0000.000
119G120GLY0-0.056-0.04132.495-0.003-0.0030.0000.0000.0000.000
120G121LEU0-0.056-0.01225.838-0.002-0.0020.0000.0000.0000.000
121G122ALA00.0720.05329.9170.0020.0020.0000.0000.0000.000
122G123LEU00.0150.00131.591-0.003-0.0030.0000.0000.0000.000
123G124CYS0-0.080-0.03931.680-0.006-0.0060.0000.0000.0000.000
124G125THR00.052-0.00329.5960.0020.0020.0000.0000.0000.000
125G126LEU0-0.012-0.00331.786-0.002-0.0020.0000.0000.0000.000
126G127GLY00.006-0.01634.856-0.004-0.0040.0000.0000.0000.000
127G128CYS0-0.110-0.03933.262-0.006-0.0060.0000.0000.0000.000
128G129MET0-0.006-0.00330.495-0.003-0.0030.0000.0000.0000.000
129G130GLY00.0220.01734.4640.0040.0040.0000.0000.0000.000
130G131SER00.0640.01435.984-0.009-0.0090.0000.0000.0000.000
131G132SER00.0800.03537.7550.0000.0000.0000.0000.0000.000
132G133GLU-1-0.888-0.93839.4730.1070.1070.0000.0000.0000.000
133G134MET0-0.0170.00832.8890.0010.0010.0000.0000.0000.000
134G135CYS0-0.080-0.04438.208-0.002-0.0020.0000.0000.0000.000
135G136ARG10.8230.87640.807-0.085-0.0850.0000.0000.0000.000
136G137ASP-1-0.878-0.93339.2690.1080.1080.0000.0000.0000.000
137G138LEU0-0.060-0.05236.1290.0000.0000.0000.0000.0000.000
138G139ALA00.0210.02840.043-0.002-0.0020.0000.0000.0000.000
139G140GLY00.0450.01643.321-0.003-0.0030.0000.0000.0000.000
140G141GLU-1-0.811-0.89038.8730.0990.0990.0000.0000.0000.000
141G142VAL0-0.012-0.01539.810-0.001-0.0010.0000.0000.0000.000
142G143GLU-1-0.938-0.96441.8740.0660.0660.0000.0000.0000.000
143G144LYS10.8550.91440.131-0.098-0.0980.0000.0000.0000.000
144G145LEU0-0.049-0.03338.488-0.002-0.0020.0000.0000.0000.000
145G146LEU0-0.037-0.00342.267-0.002-0.0020.0000.0000.0000.000
146G147LYS10.9130.95944.964-0.062-0.0620.0000.0000.0000.000
147G148THR00.0170.02041.504-0.003-0.0030.0000.0000.0000.000
148G149SER00.0380.01444.257-0.002-0.0020.0000.0000.0000.000
149G150ASN00.001-0.00338.2620.0000.0000.0000.0000.0000.000
150G151SER00.1070.03042.1180.0020.0020.0000.0000.0000.000
151G152TYR0-0.055-0.02632.5780.0050.0050.0000.0000.0000.000
152G153LEU00.0150.00235.5610.0040.0040.0000.0000.0000.000
153G154ARG10.9330.97938.993-0.061-0.0610.0000.0000.0000.000
154G155LYS10.9370.97638.314-0.079-0.0790.0000.0000.0000.000
155G156LYS10.8740.94833.245-0.115-0.1150.0000.0000.0000.000
156G157ALA00.0390.03639.3570.0020.0020.0000.0000.0000.000
157G158ALA00.0290.01341.4220.0000.0000.0000.0000.0000.000
158G159LEU00.002-0.01540.391-0.001-0.0010.0000.0000.0000.000
159G160CYS0-0.0140.00738.9170.0030.0030.0000.0000.0000.000
160G161ALA00.0340.02240.6340.0010.0010.0000.0000.0000.000
161G162VAL0-0.026-0.00244.042-0.002-0.0020.0000.0000.0000.000
162G163HIS0-0.051-0.01838.475-0.006-0.0060.0000.0000.0000.000
163G164VAL00.0240.00442.1680.0000.0000.0000.0000.0000.000
164G165ILE0-0.0310.00043.308-0.002-0.0020.0000.0000.0000.000
165G166ARG10.7950.88542.646-0.080-0.0800.0000.0000.0000.000
166G167LYS10.7580.88038.819-0.112-0.1120.0000.0000.0000.000
167G168VAL0-0.034-0.02144.2760.0000.0000.0000.0000.0000.000
168G169PRO00.0210.01146.995-0.001-0.0010.0000.0000.0000.000
169G170GLU-1-0.780-0.85950.0760.0700.0700.0000.0000.0000.000
170G171LEU00.0460.01746.244-0.001-0.0010.0000.0000.0000.000
171G172MET0-0.028-0.00450.0430.0000.0000.0000.0000.0000.000
172G173GLU-1-0.910-0.95050.9820.0550.0550.0000.0000.0000.000
173G174MET0-0.0070.00747.168-0.001-0.0010.0000.0000.0000.000
174G175PHE00.008-0.01845.1240.0010.0010.0000.0000.0000.000
175G176LEU00.0040.00250.571-0.001-0.0010.0000.0000.0000.000
176G177PRO0-0.019-0.01152.948-0.002-0.0020.0000.0000.0000.000
177G178ALA0-0.023-0.00649.657-0.002-0.0020.0000.0000.0000.000
178G179THR0-0.051-0.03951.0300.0000.0000.0000.0000.0000.000
179G180LYS10.9210.97752.899-0.048-0.0480.0000.0000.0000.000
180G181ASN0-0.033-0.02654.9540.0000.0000.0000.0000.0000.000
181G182LEU00.0550.03349.9980.0000.0000.0000.0000.0000.000
182G183LEU00.0170.00652.7000.0000.0000.0000.0000.0000.000
183G184ASN0-0.015-0.01255.1080.0000.0000.0000.0000.0000.000
184G185GLU-1-0.858-0.91948.9350.0520.0520.0000.0000.0000.000
185G186LYS10.9190.93951.049-0.042-0.0420.0000.0000.0000.000
186G187ASN00.0090.02344.0120.0010.0010.0000.0000.0000.000
187G188HIS00.0450.00847.0830.0010.0010.0000.0000.0000.000
188G189GLY0-0.0010.01443.8450.0010.0010.0000.0000.0000.000
189G190VAL0-0.018-0.01444.4030.0020.0020.0000.0000.0000.000
190G191LEU00.0140.02546.1550.0010.0010.0000.0000.0000.000
191G192HIS00.0400.03145.5880.0020.0020.0000.0000.0000.000
192G193THR0-0.012-0.02842.5960.0010.0010.0000.0000.0000.000
193G194SER0-0.028-0.01545.9440.0000.0000.0000.0000.0000.000
194G195VAL00.0410.01548.892-0.001-0.0010.0000.0000.0000.000
195G196VAL0-0.057-0.00945.738-0.001-0.0010.0000.0000.0000.000
196G197LEU00.007-0.00847.0650.0000.0000.0000.0000.0000.000
197G198LEU00.0170.01148.924-0.001-0.0010.0000.0000.0000.000
198G199THR0-0.035-0.04251.310-0.002-0.0020.0000.0000.0000.000
199G200GLU-1-0.766-0.87047.6800.0670.0670.0000.0000.0000.000
200G201MET0-0.029-0.01250.675-0.002-0.0020.0000.0000.0000.000
201G202CYS0-0.074-0.03353.206-0.002-0.0020.0000.0000.0000.000
202G203GLU-1-0.856-0.92653.2430.0520.0520.0000.0000.0000.000
203G204ARG10.7730.91248.342-0.065-0.0650.0000.0000.0000.000
204G205SER00.0830.03254.916-0.001-0.0010.0000.0000.0000.000
205G206PRO00.0660.02358.1150.0000.0000.0000.0000.0000.000
206G207ASP-1-0.864-0.93061.0790.0430.0430.0000.0000.0000.000
207G208MET00.014-0.00655.992-0.001-0.0010.0000.0000.0000.000
208G209LEU0-0.0040.01359.249-0.001-0.0010.0000.0000.0000.000
209G210ALA0-0.031-0.01760.871-0.001-0.0010.0000.0000.0000.000
210G211HIS0-0.054-0.03760.274-0.001-0.0010.0000.0000.0000.000
211G212PHE00.027-0.01755.376-0.001-0.0010.0000.0000.0000.000
212G213ARG10.8470.94360.177-0.037-0.0370.0000.0000.0000.000
213G214LYS10.9580.97962.800-0.039-0.0390.0000.0000.0000.000
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