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: MNN8Z

Calculation Name: 4R3O-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: G

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 245
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3090591.240081
FMO2-HF: Nuclear repulsion 2994060.10207
FMO2-HF: Total energy -96531.138011
FMO2-MP2: Total energy -96809.653439


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:1:SER)


Summations of interaction energy for fragment #1(G:1: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.
0.2883.5655.147-4.477-3.946-0.003
Interaction energy analysis for fragmet #1(G:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.011
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].
3G3ILE0-0.0170.0083.811-0.8251.560-0.030-1.210-1.144-0.002
4G4GLY00.0540.0386.488-0.347-0.3470.0000.0000.0000.000
5G5THR0-0.061-0.0409.8890.0160.0160.0000.0000.0000.000
6G6GLY00.0380.02412.7870.0280.0280.0000.0000.0000.000
7G7TYR0-0.033-0.02910.2350.0100.0100.0000.0000.0000.000
8G8ASP-1-0.834-0.9039.694-0.125-0.1250.0000.0000.0000.000
9G9LEU0-0.0120.00511.699-0.088-0.0880.0000.0000.0000.000
10G10SER0-0.005-0.00914.937-0.020-0.0200.0000.0000.0000.000
11G11ALA00.014-0.00414.8850.0310.0310.0000.0000.0000.000
12G12SER0-0.063-0.01016.2810.0230.0230.0000.0000.0000.000
13G13THR0-0.030-0.01713.947-0.011-0.0110.0000.0000.0000.000
14G14PHE00.0090.01811.903-0.007-0.0070.0000.0000.0000.000
15G15SER0-0.031-0.0467.055-0.160-0.1600.0000.0000.0000.000
16G16PRO0-0.008-0.0149.1740.0010.0010.0000.0000.0000.000
17G17ASP-1-0.840-0.8844.7712.8282.907-0.001-0.004-0.0740.000
18G18GLY0-0.022-0.0028.4030.0240.0240.0000.0000.0000.000
19G19ARG10.7620.8521.824-3.570-3.0025.178-3.217-2.529-0.001
20G20VAL00.0810.0408.605-0.137-0.1370.0000.0000.0000.000
21G21PHE00.0750.0183.965-0.1850.0230.001-0.043-0.1660.000
22G22GLN00.0130.0139.209-0.191-0.1910.0000.0000.0000.000
23G23VAL00.0500.01711.680-0.084-0.0840.0000.0000.0000.000
24G24GLU-1-0.800-0.8634.8720.6240.661-0.001-0.003-0.0330.000
25G25TYR0-0.108-0.0827.063-0.348-0.3480.0000.0000.0000.000
26G26ALA00.0100.01110.245-0.014-0.0140.0000.0000.0000.000
27G27MET00.005-0.0039.9690.0130.0130.0000.0000.0000.000
28G28LYS10.9550.9825.6932.3762.3760.0000.0000.0000.000
29G29ALA0-0.026-0.01410.6770.0030.0030.0000.0000.0000.000
30G30VAL0-0.033-0.01214.0260.0240.0240.0000.0000.0000.000
31G31GLU-1-0.825-0.89310.482-0.161-0.1610.0000.0000.0000.000
32G32ASN0-0.0240.00013.041-0.011-0.0110.0000.0000.0000.000
33G33SER0-0.0120.01115.6640.0330.0330.0000.0000.0000.000
34G34SER0-0.067-0.04318.763-0.005-0.0050.0000.0000.0000.000
35G35THR00.0330.01619.9960.0010.0010.0000.0000.0000.000
36G36ALA0-0.015-0.00221.5850.0060.0060.0000.0000.0000.000
37G37ILE0-0.004-0.00522.4650.0060.0060.0000.0000.0000.000
38G38GLY00.015-0.00724.740-0.002-0.0020.0000.0000.0000.000
39G39ILE0-0.028-0.01626.4430.0070.0070.0000.0000.0000.000
40G40ARG10.9170.96929.052-0.042-0.0420.0000.0000.0000.000
41G41CYS0-0.046-0.02731.4810.0010.0010.0000.0000.0000.000
42G42LYS10.8220.91134.713-0.006-0.0060.0000.0000.0000.000
43G43ASP-1-0.734-0.84137.8780.0050.0050.0000.0000.0000.000
44G44GLY00.012-0.02636.813-0.002-0.0020.0000.0000.0000.000
45G45VAL0-0.074-0.03730.5840.0030.0030.0000.0000.0000.000
46G46VAL0-0.0030.00732.122-0.003-0.0030.0000.0000.0000.000
47G47PHE0-0.033-0.01727.0850.0010.0010.0000.0000.0000.000
48G48GLY00.0530.01228.405-0.001-0.0010.0000.0000.0000.000
49G49VAL0-0.038-0.02125.663-0.002-0.0020.0000.0000.0000.000
50G50GLU-1-0.727-0.84823.533-0.135-0.1350.0000.0000.0000.000
51G51LYS10.7060.86225.8510.0500.0500.0000.0000.0000.000
52G52LEU00.011-0.00123.4950.0040.0040.0000.0000.0000.000
53G53VAL0-0.0080.00927.7110.0020.0020.0000.0000.0000.000
54G54LEU0-0.014-0.00926.259-0.006-0.0060.0000.0000.0000.000
55G55SER00.014-0.00730.3330.0000.0000.0000.0000.0000.000
56G56LYS10.9480.96834.1060.0950.0950.0000.0000.0000.000
57G57LEU00.0060.00837.1840.0040.0040.0000.0000.0000.000
58G58TYR0-0.075-0.02931.3070.0000.0000.0000.0000.0000.000
59G59GLU-1-0.843-0.92236.810-0.046-0.0460.0000.0000.0000.000
60G60GLU-1-0.922-0.95236.881-0.047-0.0470.0000.0000.0000.000
61G61GLY0-0.016-0.00635.6560.0040.0040.0000.0000.0000.000
62G62SER0-0.009-0.00533.7970.0050.0050.0000.0000.0000.000
63G63ASN0-0.083-0.05529.1910.0000.0000.0000.0000.0000.000
64G64LYS10.9400.97030.0080.0350.0350.0000.0000.0000.000
65G65ARG10.8120.89922.1480.1010.1010.0000.0000.0000.000
66G66LEU00.0250.01727.9340.0040.0040.0000.0000.0000.000
67G67PHE0-0.045-0.03028.047-0.001-0.0010.0000.0000.0000.000
68G68ASN00.0380.02432.2350.0030.0030.0000.0000.0000.000
69G69VAL00.0030.00030.551-0.001-0.0010.0000.0000.0000.000
70G70ASP-1-0.712-0.84933.9420.0170.0170.0000.0000.0000.000
71G71ARG10.8670.93137.086-0.014-0.0140.0000.0000.0000.000
72G72HIS0-0.038-0.02237.166-0.005-0.0050.0000.0000.0000.000
73G73VAL0-0.0160.01532.1790.0020.0020.0000.0000.0000.000
74G74GLY00.0510.03432.732-0.003-0.0030.0000.0000.0000.000
75G75MET0-0.037-0.02425.6970.0070.0070.0000.0000.0000.000
76G76ALA00.0260.02926.307-0.007-0.0070.0000.0000.0000.000
77G77VAL0-0.019-0.00723.4700.0060.0060.0000.0000.0000.000
78G78ALA00.024-0.00419.668-0.009-0.0090.0000.0000.0000.000
79G79GLY00.0360.01918.6700.0050.0050.0000.0000.0000.000
80G80LEU0-0.035-0.01719.2530.0020.0020.0000.0000.0000.000
81G81LEU00.0210.00221.0870.0190.0190.0000.0000.0000.000
82G82ALA0-0.002-0.00924.6790.0120.0120.0000.0000.0000.000
83G83ASP-1-0.660-0.80020.798-0.069-0.0690.0000.0000.0000.000
84G84ALA00.0400.02623.5630.0140.0140.0000.0000.0000.000
85G85ARG10.9240.96224.8680.0630.0630.0000.0000.0000.000
86G86SER0-0.001-0.00125.9560.0080.0080.0000.0000.0000.000
87G87LEU00.0330.00622.2720.0070.0070.0000.0000.0000.000
88G88ALA0-0.018-0.00826.9220.0080.0080.0000.0000.0000.000
89G89ASP-1-0.880-0.93629.673-0.008-0.0080.0000.0000.0000.000
90G90ILE00.0070.01227.4440.0040.0040.0000.0000.0000.000
91G91ALA0-0.007-0.00729.2240.0050.0050.0000.0000.0000.000
92G92ARG10.8250.90331.0940.0110.0110.0000.0000.0000.000
93G93GLU-1-0.918-0.94934.2380.0210.0210.0000.0000.0000.000
94G94GLU-1-0.819-0.87731.8950.0490.0490.0000.0000.0000.000
95G95ALA0-0.002-0.01334.5230.0020.0020.0000.0000.0000.000
96G96SER0-0.043-0.01536.3880.0000.0000.0000.0000.0000.000
97G97ASN00.0430.01236.982-0.001-0.0010.0000.0000.0000.000
98G98PHE00.0100.01137.1780.0010.0010.0000.0000.0000.000
99G99ARG10.8250.87339.294-0.017-0.0170.0000.0000.0000.000
100G100SER0-0.054-0.03342.211-0.001-0.0010.0000.0000.0000.000
101G101ASN0-0.056-0.02540.843-0.001-0.0010.0000.0000.0000.000
102G102PHE0-0.029-0.00739.1930.0010.0010.0000.0000.0000.000
103G103GLY0-0.0020.01344.0890.0000.0000.0000.0000.0000.000
104G104TYR0-0.043-0.02640.525-0.002-0.0020.0000.0000.0000.000
105G105ASN00.0160.00640.1840.0000.0000.0000.0000.0000.000
106G106ILE00.0360.04234.3260.0010.0010.0000.0000.0000.000
107G107PRO00.0410.02735.381-0.002-0.0020.0000.0000.0000.000
108G108LEU0-0.004-0.00330.3410.0020.0020.0000.0000.0000.000
109G109LYS10.8880.93829.844-0.053-0.0530.0000.0000.0000.000
110G110HIS00.0510.03529.7410.0080.0080.0000.0000.0000.000
111G111LEU00.003-0.00230.5940.0030.0030.0000.0000.0000.000
112G112ALA0-0.020-0.01626.4390.0000.0000.0000.0000.0000.000
113G113ASP-1-0.885-0.94026.3840.1000.1000.0000.0000.0000.000
114G114ARG10.7690.86026.894-0.052-0.0520.0000.0000.0000.000
115G115VAL00.0150.00025.5070.0020.0020.0000.0000.0000.000
116G116ALA0-0.0110.00322.753-0.002-0.0020.0000.0000.0000.000
117G117MET00.0150.00722.7570.0160.0160.0000.0000.0000.000
118G118TYR0-0.016-0.00724.5860.0050.0050.0000.0000.0000.000
119G119VAL0-0.028-0.02019.535-0.005-0.0050.0000.0000.0000.000
120G120HIS00.0420.02518.892-0.004-0.0040.0000.0000.0000.000
121G121ALA0-0.0010.01420.7390.0130.0130.0000.0000.0000.000
122G122TYR0-0.065-0.03820.878-0.007-0.0070.0000.0000.0000.000
123G123THR0-0.131-0.07716.388-0.001-0.0010.0000.0000.0000.000
124G124LEU00.0170.01817.4190.0310.0310.0000.0000.0000.000
125G125TYR00.0060.00019.8680.0110.0110.0000.0000.0000.000
126G126SER00.0010.00020.286-0.009-0.0090.0000.0000.0000.000
127G127ALA0-0.028-0.01421.272-0.017-0.0170.0000.0000.0000.000
128G128VAL0-0.0120.00522.055-0.013-0.0130.0000.0000.0000.000
129G129ARG10.7640.85218.6830.0760.0760.0000.0000.0000.000
130G130PRO00.0590.02115.147-0.002-0.0020.0000.0000.0000.000
131G131PHE00.0410.02717.980-0.035-0.0350.0000.0000.0000.000
132G132GLY00.0230.01216.636-0.001-0.0010.0000.0000.0000.000
133G133CYS0-0.094-0.05617.693-0.020-0.0200.0000.0000.0000.000
134G134SER00.0860.04816.4360.0170.0170.0000.0000.0000.000
135G135PHE0-0.033-0.02619.079-0.018-0.0180.0000.0000.0000.000
136G136MET0-0.0210.01322.5750.0130.0130.0000.0000.0000.000
137G137LEU00.0240.01624.838-0.008-0.0080.0000.0000.0000.000
138G138GLY00.0240.00928.2240.0060.0060.0000.0000.0000.000
139G139SER0-0.057-0.05931.054-0.002-0.0020.0000.0000.0000.000
140G140TYR0-0.019-0.03134.4970.0020.0020.0000.0000.0000.000
141G141SER0-0.025-0.00837.582-0.002-0.0020.0000.0000.0000.000
142G142VAL00.0650.02640.4750.0010.0010.0000.0000.0000.000
143G143ASN0-0.015-0.00742.6300.0000.0000.0000.0000.0000.000
144G144ASP-1-0.854-0.90536.5430.0450.0450.0000.0000.0000.000
145G145GLY00.0180.02637.4000.0030.0030.0000.0000.0000.000
146G146ALA0-0.0090.00034.935-0.001-0.0010.0000.0000.0000.000
147G147GLN0-0.095-0.07431.4900.0100.0100.0000.0000.0000.000
148G148LEU00.0380.01026.513-0.006-0.0060.0000.0000.0000.000
149G149TYR0-0.0020.00425.5460.0040.0040.0000.0000.0000.000
150G150MET0-0.066-0.02617.252-0.018-0.0180.0000.0000.0000.000
151G151ILE00.0290.02020.4020.0200.0200.0000.0000.0000.000
152G152ASP-1-0.779-0.86815.1810.1830.1830.0000.0000.0000.000
153G153PRO0-0.007-0.01914.3360.0150.0150.0000.0000.0000.000
154G154SER0-0.065-0.06313.7530.0120.0120.0000.0000.0000.000
155G155GLY00.008-0.00115.7220.0090.0090.0000.0000.0000.000
156G156VAL0-0.043-0.00116.074-0.005-0.0050.0000.0000.0000.000
157G157SER00.0510.01018.887-0.027-0.0270.0000.0000.0000.000
158G158TYR0-0.011-0.00118.0470.0000.0000.0000.0000.0000.000
159G159GLY00.0170.01022.699-0.016-0.0160.0000.0000.0000.000
160G160TYR0-0.026-0.02419.2740.0070.0070.0000.0000.0000.000
161G161TRP0-0.001-0.02225.550-0.007-0.0070.0000.0000.0000.000
162G162GLY00.0470.01825.704-0.010-0.0100.0000.0000.0000.000
163G163CYS0-0.075-0.01821.0010.0110.0110.0000.0000.0000.000
164G164ALA00.0570.01820.322-0.013-0.0130.0000.0000.0000.000
165G165ILE0-0.006-0.00517.5070.0160.0160.0000.0000.0000.000
166G166GLY00.0310.02416.654-0.002-0.0020.0000.0000.0000.000
167G167LYS10.8680.92016.0160.2580.2580.0000.0000.0000.000
168G168ALA00.0100.02515.979-0.012-0.0120.0000.0000.0000.000
169G169ARG10.8530.90610.8220.0290.0290.0000.0000.0000.000
170G170GLN00.0570.00715.3910.0330.0330.0000.0000.0000.000
171G171ALA00.0380.03017.4130.0110.0110.0000.0000.0000.000
172G172ALA00.0770.04420.3870.0120.0120.0000.0000.0000.000
173G173LYS10.8570.91717.710-0.040-0.0400.0000.0000.0000.000
174G174THR0-0.019-0.01320.4910.0040.0040.0000.0000.0000.000
175G175GLU-1-0.827-0.90622.993-0.053-0.0530.0000.0000.0000.000
176G176ILE0-0.011-0.00823.6620.0050.0050.0000.0000.0000.000
177G177GLU-1-0.943-0.96421.8780.0330.0330.0000.0000.0000.000
178G178LYS10.7980.89726.5980.0500.0500.0000.0000.0000.000
179G179LEU0-0.045-0.01329.5890.0000.0000.0000.0000.0000.000
180G180GLN00.0040.00031.0750.0090.0090.0000.0000.0000.000
181G181MET00.0520.00328.4210.0020.0020.0000.0000.0000.000
182G182LYS10.9070.95730.386-0.041-0.0410.0000.0000.0000.000
183G183GLU-1-0.836-0.91734.9630.0160.0160.0000.0000.0000.000
184G184MET0-0.0470.01035.443-0.002-0.0020.0000.0000.0000.000
185G185THR0-0.002-0.02638.0590.0020.0020.0000.0000.0000.000
186G186CYS0-0.001-0.03036.739-0.003-0.0030.0000.0000.0000.000
187G187ARG10.8240.90237.6930.0120.0120.0000.0000.0000.000
188G188ASP-1-0.857-0.91138.515-0.010-0.0100.0000.0000.0000.000
189G189ILE0-0.030-0.01332.843-0.003-0.0030.0000.0000.0000.000
190G190VAL00.0170.01334.142-0.004-0.0040.0000.0000.0000.000
191G191LYS10.8880.94234.5110.0170.0170.0000.0000.0000.000
192G192GLU-1-0.717-0.82632.355-0.034-0.0340.0000.0000.0000.000
193G193VAL0-0.0170.00429.437-0.004-0.0040.0000.0000.0000.000
194G194ALA00.016-0.00229.989-0.007-0.0070.0000.0000.0000.000
195G195LYS10.8410.90331.4270.0280.0280.0000.0000.0000.000
196G196ILE00.0160.01025.942-0.007-0.0070.0000.0000.0000.000
197G197ILE0-0.043-0.01725.799-0.010-0.0100.0000.0000.0000.000
198G198TYR0-0.047-0.05827.330-0.012-0.0120.0000.0000.0000.000
199G199ILE0-0.049-0.01126.231-0.007-0.0070.0000.0000.0000.000
200G200VAL0-0.035-0.01822.076-0.010-0.0100.0000.0000.0000.000
201G201HIS10.7600.87823.5250.1060.1060.0000.0000.0000.000
202G202ASP-1-0.765-0.87022.685-0.205-0.2050.0000.0000.0000.000
203G203GLU-1-0.866-0.92925.177-0.118-0.1180.0000.0000.0000.000
204G204VAL00.0000.00626.1550.0040.0040.0000.0000.0000.000
205G205LYS10.7880.87719.3750.2380.2380.0000.0000.0000.000
206G206ASP-1-0.863-0.93422.899-0.208-0.2080.0000.0000.0000.000
207G207LYS10.7760.89025.8660.1580.1580.0000.0000.0000.000
208G208ALA00.0540.02929.6360.0030.0030.0000.0000.0000.000
209G209PHE0-0.044-0.03428.947-0.007-0.0070.0000.0000.0000.000
210G210GLU-1-0.764-0.86830.760-0.055-0.0550.0000.0000.0000.000
211G211LEU00.0140.00730.506-0.003-0.0030.0000.0000.0000.000
212G212GLU-1-0.786-0.88230.466-0.048-0.0480.0000.0000.0000.000
213G213LEU00.008-0.01531.4670.0000.0000.0000.0000.0000.000
214G214SER0-0.003-0.02832.649-0.001-0.0010.0000.0000.0000.000
215G215TRP00.0200.01334.2280.0010.0010.0000.0000.0000.000
216G216VAL00.010-0.01034.1670.0000.0000.0000.0000.0000.000
217G217GLY00.0260.00536.7470.0030.0030.0000.0000.0000.000
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