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: 49NYN

Calculation Name: 5WWO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WWO

Chain ID: B

ChEMBL ID:

UniProt ID: P38333

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 254
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3377355.506697
FMO2-HF: Nuclear repulsion 3276725.121505
FMO2-HF: Total energy -100630.385192
FMO2-MP2: Total energy -100932.252194


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:205:ALA)


Summations of interaction energy for fragment #1(B:205:ALA)
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.
-0.6361.0740.113-0.846-0.9770.004
Interaction energy analysis for fragmet #1(B:205:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.000
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].
3B207PRO00.0470.0043.764-1.804-0.446-0.007-0.738-0.6130.004
4B208GLU-1-0.816-0.9095.572-0.772-0.7720.0000.0000.0000.000
5B209LYS10.9240.9496.3020.6680.6680.0000.0000.0000.000
6B210VAL00.0130.0097.8780.1290.1290.0000.0000.0000.000
7B211ILE00.0330.0212.800-0.1640.1880.120-0.108-0.3640.000
8B212LYS10.9650.9897.4290.6030.6030.0000.0000.0000.000
9B213ALA00.0050.00910.4170.0650.0650.0000.0000.0000.000
10B214TYR0-0.013-0.04110.5200.0420.0420.0000.0000.0000.000
11B215THR00.0670.0369.8530.0490.0490.0000.0000.0000.000
12B216THR0-0.043-0.01012.3700.0070.0070.0000.0000.0000.000
13B217VAL0-0.050-0.03515.2410.0150.0150.0000.0000.0000.000
14B218GLY00.0520.02015.1100.0070.0070.0000.0000.0000.000
15B219SER0-0.0130.00516.3050.0050.0050.0000.0000.0000.000
16B220ILE0-0.014-0.00418.3450.0010.0010.0000.0000.0000.000
17B221LEU0-0.084-0.04817.4390.0010.0010.0000.0000.0000.000
18B222LYS11.0001.01719.333-0.010-0.0100.0000.0000.0000.000
19B223THR0-0.006-0.00422.242-0.002-0.0020.0000.0000.0000.000
20B224TRP0-0.052-0.01924.2620.0000.0000.0000.0000.0000.000
21B225THR00.0460.02526.1170.0060.0060.0000.0000.0000.000
22B226HIS0-0.028-0.02929.055-0.001-0.0010.0000.0000.0000.000
23B227GLY00.0400.03929.578-0.003-0.0030.0000.0000.0000.000
24B228LYS10.9200.95127.098-0.027-0.0270.0000.0000.0000.000
25B229LEU00.0650.05122.455-0.004-0.0040.0000.0000.0000.000
26B230PRO00.0380.01320.021-0.004-0.0040.0000.0000.0000.000
27B231LYS10.9820.97621.1750.0030.0030.0000.0000.0000.000
28B232LEU00.0640.03315.3320.0120.0120.0000.0000.0000.000
29B233PHE00.0450.02916.7020.0230.0230.0000.0000.0000.000
30B234LYS10.9340.95418.135-0.051-0.0510.0000.0000.0000.000
31B235VAL00.0420.03716.3790.0050.0050.0000.0000.0000.000
32B236ILE0-0.0020.04313.7890.0170.0170.0000.0000.0000.000
33B237PRO0-0.043-0.02115.9280.0430.0430.0000.0000.0000.000
34B238SER0-0.056-0.04418.2330.0030.0030.0000.0000.0000.000
35B239LEU0-0.0070.00512.3780.0010.0010.0000.0000.0000.000
36B240ARG10.9920.97214.021-0.391-0.3910.0000.0000.0000.000
37B241ASN00.0020.0087.849-0.178-0.1780.0000.0000.0000.000
38B242TRP00.014-0.00210.1510.0850.0850.0000.0000.0000.000
39B243GLN00.004-0.00511.231-0.057-0.0570.0000.0000.0000.000
40B244ASP-1-0.845-0.9216.0812.2762.2760.0000.0000.0000.000
41B245VAL0-0.055-0.0247.441-0.087-0.0870.0000.0000.0000.000
42B246ILE0-0.013-0.0069.320-0.115-0.1150.0000.0000.0000.000
43B247TYR00.0330.0178.419-0.096-0.0960.0000.0000.0000.000
44B248VAL0-0.0110.0136.264-0.047-0.0470.0000.0000.0000.000
45B249THR0-0.162-0.1049.332-0.129-0.1290.0000.0000.0000.000
46B250ASN0-0.021-0.03412.561-0.015-0.0150.0000.0000.0000.000
47B251PRO00.0480.00413.467-0.029-0.0290.0000.0000.0000.000
48B252GLU-1-0.913-0.94916.7540.1570.1570.0000.0000.0000.000
49B253GLU-1-0.870-0.91418.5440.0290.0290.0000.0000.0000.000
50B254TRP0-0.072-0.02616.003-0.010-0.0100.0000.0000.0000.000
51B255SER00.0420.00921.0620.0020.0020.0000.0000.0000.000
52B256PRO00.023-0.01424.5250.0110.0110.0000.0000.0000.000
53B257HIS00.0170.00626.8980.0090.0090.0000.0000.0000.000
54B258VAL00.0180.01721.0910.0030.0030.0000.0000.0000.000
55B259VAL00.0520.05022.5710.0120.0120.0000.0000.0000.000
56B260TYR0-0.068-0.01223.9260.0100.0100.0000.0000.0000.000
57B261GLU-1-0.894-0.96425.4220.0910.0910.0000.0000.0000.000
58B262ALA0-0.0070.00620.5410.0050.0050.0000.0000.0000.000
59B263THR0-0.005-0.01222.5750.0170.0170.0000.0000.0000.000
60B264LYS10.8890.94124.285-0.081-0.0810.0000.0000.0000.000
61B265LEU0-0.0330.00521.092-0.001-0.0010.0000.0000.0000.000
62B266PHE00.0630.02016.6950.0040.0040.0000.0000.0000.000
63B267VAL0-0.010-0.00422.1150.0090.0090.0000.0000.0000.000
64B268SER0-0.097-0.06624.884-0.004-0.0040.0000.0000.0000.000
65B269ASN0-0.026-0.02223.063-0.013-0.0130.0000.0000.0000.000
66B270LEU00.0060.04118.4740.0080.0080.0000.0000.0000.000
67B271THR00.0440.00922.230-0.018-0.0180.0000.0000.0000.000
68B272ALA00.012-0.01123.6250.0080.0080.0000.0000.0000.000
69B273LYS10.9890.99221.046-0.307-0.3070.0000.0000.0000.000
70B274GLU-1-0.765-0.88317.2240.4580.4580.0000.0000.0000.000
71B275SER00.0400.01619.7490.0040.0040.0000.0000.0000.000
72B276GLN00.0000.00322.393-0.009-0.0090.0000.0000.0000.000
73B277LYS10.8370.91816.677-0.473-0.4730.0000.0000.0000.000
74B278PHE00.0490.02918.0410.0050.0050.0000.0000.0000.000
75B279ILE0-0.069-0.04219.207-0.013-0.0130.0000.0000.0000.000
76B280ASN0-0.040-0.02320.0760.0080.0080.0000.0000.0000.000
77B281LEU00.0120.02513.955-0.007-0.0070.0000.0000.0000.000
78B282ILE00.0330.02216.341-0.012-0.0120.0000.0000.0000.000
79B283LEU0-0.078-0.04019.556-0.024-0.0240.0000.0000.0000.000
80B284LEU0-0.023-0.02523.127-0.019-0.0190.0000.0000.0000.000
81B285GLU-1-0.846-0.90718.8460.1960.1960.0000.0000.0000.000
82B286ARG10.9050.95422.052-0.134-0.1340.0000.0000.0000.000
83B287PHE0-0.073-0.06423.747-0.018-0.0180.0000.0000.0000.000
84B288ARG10.8350.89525.502-0.141-0.1410.0000.0000.0000.000
85B289ASP-1-0.789-0.87422.2450.1270.1270.0000.0000.0000.000
86B290ASN0-0.097-0.05725.932-0.012-0.0120.0000.0000.0000.000
87B291ILE0-0.035-0.01128.316-0.009-0.0090.0000.0000.0000.000
88B292GLU-1-0.905-0.94728.7040.0610.0610.0000.0000.0000.000
89B293THR0-0.056-0.03727.238-0.007-0.0070.0000.0000.0000.000
90B294SER0-0.052-0.01430.422-0.006-0.0060.0000.0000.0000.000
91B295GLU-1-0.898-0.95833.0370.0330.0330.0000.0000.0000.000
92B296ASP-1-0.867-0.89636.5630.0460.0460.0000.0000.0000.000
93B297HIS10.7760.88533.717-0.056-0.0560.0000.0000.0000.000
94B298SER0-0.055-0.05135.3760.0040.0040.0000.0000.0000.000
95B299LEU00.0010.00229.7860.0030.0030.0000.0000.0000.000
96B300ASN00.0770.03430.293-0.001-0.0010.0000.0000.0000.000
97B301TYR00.0570.01232.0940.0060.0060.0000.0000.0000.000
98B302HIS00.013-0.01529.7330.0050.0050.0000.0000.0000.000
99B303ILE00.0530.03626.6390.0060.0060.0000.0000.0000.000
100B304TYR0-0.011-0.07929.2640.0070.0070.0000.0000.0000.000
101B305ARG10.8930.95331.932-0.068-0.0680.0000.0000.0000.000
102B306ALA00.0030.00826.8230.0020.0020.0000.0000.0000.000
103B307VAL00.0400.02428.7530.0070.0070.0000.0000.0000.000
104B308LYS10.9660.98530.006-0.068-0.0680.0000.0000.0000.000
105B309LYS10.8690.93429.564-0.091-0.0910.0000.0000.0000.000
106B310SER00.012-0.00327.2400.0040.0040.0000.0000.0000.000
107B311LEU00.0250.01929.0760.0050.0050.0000.0000.0000.000
108B312TYR0-0.036-0.01332.170-0.005-0.0050.0000.0000.0000.000
109B313LYS10.8410.92625.965-0.171-0.1710.0000.0000.0000.000
110B314PRO00.0460.02729.6260.0100.0100.0000.0000.0000.000
111B315SER0-0.013-0.01229.5100.0040.0040.0000.0000.0000.000
112B316ALA0-0.017-0.00225.3270.0060.0060.0000.0000.0000.000
113B317PHE00.0480.03126.4270.0100.0100.0000.0000.0000.000
114B318PHE00.019-0.00528.5880.0000.0000.0000.0000.0000.000
115B319LYS10.9280.96426.476-0.174-0.1740.0000.0000.0000.000
116B320GLY00.0020.00224.0100.0110.0110.0000.0000.0000.000
117B321PHE00.0200.00224.2920.0080.0080.0000.0000.0000.000
118B322LEU0-0.020-0.00726.820-0.004-0.0040.0000.0000.0000.000
119B323PHE00.014-0.00728.847-0.007-0.0070.0000.0000.0000.000
120B324PRO00.0570.02724.817-0.005-0.0050.0000.0000.0000.000
121B325LEU00.0210.02226.996-0.004-0.0040.0000.0000.0000.000
122B326VAL0-0.079-0.04928.788-0.008-0.0080.0000.0000.0000.000
123B327GLU-1-0.896-0.93829.0830.1360.1360.0000.0000.0000.000
124B328THR0-0.0240.00925.3900.0040.0040.0000.0000.0000.000
125B329GLY00.0210.01228.572-0.002-0.0020.0000.0000.0000.000
126B330CYS0-0.0410.00331.478-0.005-0.0050.0000.0000.0000.000
127B331ASN00.0730.04632.322-0.007-0.0070.0000.0000.0000.000
128B332VAL00.058-0.00635.0920.0020.0020.0000.0000.0000.000
129B333ARG10.9340.99235.723-0.055-0.0550.0000.0000.0000.000
130B334GLU-1-0.719-0.86829.8260.1030.1030.0000.0000.0000.000
131B335ALA00.0240.00133.8810.0030.0030.0000.0000.0000.000
132B336THR0-0.057-0.03135.992-0.001-0.0010.0000.0000.0000.000
133B337ILE0-0.0040.01334.094-0.001-0.0010.0000.0000.0000.000
134B338ALA00.0140.01532.5500.0000.0000.0000.0000.0000.000
135B339GLY00.0160.00034.4930.0010.0010.0000.0000.0000.000
136B340SER0-0.059-0.03837.766-0.002-0.0020.0000.0000.0000.000
137B341VAL0-0.014-0.00333.959-0.002-0.0020.0000.0000.0000.000
138B342LEU00.018-0.00235.615-0.001-0.0010.0000.0000.0000.000
139B343ALA00.002-0.00837.439-0.001-0.0010.0000.0000.0000.000
140B344LYN00.0190.08839.678-0.001-0.0010.0000.0000.0000.000
141B345VAL0-0.032-0.00236.087-0.002-0.0020.0000.0000.0000.000
142B346SER0-0.055-0.02139.2170.0010.0010.0000.0000.0000.000
143B347VAL00.0320.00536.6620.0050.0050.0000.0000.0000.000
144B348PRO00.0140.00837.161-0.003-0.0030.0000.0000.0000.000
145B349ALA00.0990.04039.5560.0040.0040.0000.0000.0000.000
146B350LEU00.0440.02837.4830.0000.0000.0000.0000.0000.000
147B351HIS00.008-0.00633.9780.0050.0050.0000.0000.0000.000
148B352SER0-0.010-0.00137.0560.0030.0030.0000.0000.0000.000
149B353SER00.0000.00039.2270.0000.0000.0000.0000.0000.000
150B354ALA00.0380.02036.7440.0000.0000.0000.0000.0000.000
151B355ALA0-0.013-0.01035.2620.0030.0030.0000.0000.0000.000
152B356LEU0-0.006-0.00836.4770.0000.0000.0000.0000.0000.000
153B357SER0-0.004-0.01839.461-0.001-0.0010.0000.0000.0000.000
154B358TYR0-0.095-0.04730.829-0.002-0.0020.0000.0000.0000.000
155B359LEU00.014-0.00734.7630.0000.0000.0000.0000.0000.000
156B360LEU0-0.0100.00437.610-0.003-0.0030.0000.0000.0000.000
157B361ARG10.8610.93038.595-0.090-0.0900.0000.0000.0000.000
158B362LEU00.0310.04433.8650.0010.0010.0000.0000.0000.000
159B363PRO00.0310.02836.371-0.006-0.0060.0000.0000.0000.000
160B364PHE0-0.014-0.01339.0330.0000.0000.0000.0000.0000.000
161B365SER00.0480.01637.7300.0000.0000.0000.0000.0000.000
162B366PRO00.004-0.00540.2970.0010.0010.0000.0000.0000.000
163B367PRO00.0370.01036.289-0.001-0.0010.0000.0000.0000.000
164B368THR00.1020.04536.6320.0030.0030.0000.0000.0000.000
165B369THR0-0.045-0.01737.944-0.001-0.0010.0000.0000.0000.000
166B370VAL0-0.021-0.00438.849-0.002-0.0020.0000.0000.0000.000
167B371PHE00.0050.00434.0130.0000.0000.0000.0000.0000.000
168B372ILE00.0260.02339.002-0.001-0.0010.0000.0000.0000.000
169B373LYS10.8660.92741.559-0.056-0.0560.0000.0000.0000.000
170B374ILE0-0.044-0.00839.918-0.002-0.0020.0000.0000.0000.000
171B375LEU0-0.009-0.01337.781-0.001-0.0010.0000.0000.0000.000
172B376LEU0-0.0070.00242.038-0.002-0.0020.0000.0000.0000.000
173B377ASP-1-0.842-0.92945.1850.0530.0530.0000.0000.0000.000
174B378LYS10.7670.90740.618-0.074-0.0740.0000.0000.0000.000
175B379LYS10.8870.95545.406-0.049-0.0490.0000.0000.0000.000
176B380TYR00.0380.02441.5650.0000.0000.0000.0000.0000.000
177B381ALA00.0170.02447.082-0.001-0.0010.0000.0000.0000.000
178B382LEU0-0.023-0.01344.7910.0040.0040.0000.0000.0000.000
179B383PRO00.0380.02144.027-0.003-0.0030.0000.0000.0000.000
180B384TYR00.0890.02647.3320.0000.0000.0000.0000.0000.000
181B385GLN00.0220.02943.996-0.001-0.0010.0000.0000.0000.000
182B386THR00.0090.00142.7420.0000.0000.0000.0000.0000.000
183B387VAL00.0010.00145.3280.0000.0000.0000.0000.0000.000
184B388ASP-1-0.806-0.89448.2120.0540.0540.0000.0000.0000.000
185B389ASP-1-0.800-0.90543.1880.0750.0750.0000.0000.0000.000
186B390CYS0-0.072-0.03045.9000.0000.0000.0000.0000.0000.000
187B391VAL00.0080.00947.289-0.002-0.0020.0000.0000.0000.000
188B392TYR00.023-0.00346.686-0.001-0.0010.0000.0000.0000.000
189B393TYR0-0.040-0.01442.8840.0000.0000.0000.0000.0000.000
190B394PHE0-0.002-0.02046.637-0.001-0.0010.0000.0000.0000.000
191B395MET00.0600.03249.735-0.001-0.0010.0000.0000.0000.000
192B396ARG10.7930.90741.582-0.070-0.0700.0000.0000.0000.000
193B397PHE0-0.077-0.03945.1420.0000.0000.0000.0000.0000.000
194B398ARG10.8980.94550.597-0.045-0.0450.0000.0000.0000.000
195B399ILE0-0.037-0.02653.3910.0010.0010.0000.0000.0000.000
196B400LEU0-0.035-0.00851.4300.0000.0000.0000.0000.0000.000
197B401ASP-1-0.940-0.95655.8950.0330.0330.0000.0000.0000.000
198B402ASP-1-0.962-0.97755.5790.0370.0370.0000.0000.0000.000
199B411ARG11.0361.01745.702-0.050-0.0500.0000.0000.0000.000
200B412VAL00.0460.01751.1950.0000.0000.0000.0000.0000.000
201B413LEU0-0.036-0.00148.0560.0020.0020.0000.0000.0000.000
202B414PRO00.0460.01945.395-0.002-0.0020.0000.0000.0000.000
203B415VAL00.0720.01848.5540.0010.0010.0000.0000.0000.000
204B416ILE0-0.020-0.01143.738-0.001-0.0010.0000.0000.0000.000
205B417TRP00.0350.01646.1820.0010.0010.0000.0000.0000.000
206B418HIS00.0230.01947.7540.0000.0000.0000.0000.0000.000
207B419LYS10.9720.97749.053-0.043-0.0430.0000.0000.0000.000
208B420ALA00.0030.02046.3670.0000.0000.0000.0000.0000.000
209B421PHE00.0250.01648.2350.0000.0000.0000.0000.0000.000
210B422LEU0-0.005-0.00651.1310.0000.0000.0000.0000.0000.000
211B423THR0-0.036-0.03048.530-0.001-0.0010.0000.0000.0000.000
212B424PHE0-0.024-0.01649.3220.0000.0000.0000.0000.0000.000
213B425ALA00.0280.01251.0780.0000.0000.0000.0000.0000.000
214B426GLN0-0.011-0.00854.1360.0010.0010.0000.0000.0000.000
215B427ARG10.8250.91550.600-0.051-0.0510.0000.0000.0000.000
216B428TYR0-0.007-0.03748.0970.0000.0000.0000.0000.0000.000
217B429LYS10.9240.99653.634-0.038-0.0380.0000.0000.0000.000
218B430ASN00.020-0.00657.101-0.002-0.0020.0000.0000.0000.000
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