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: 43M2N

Calculation Name: 2WD5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CU62

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2143200.024291
FMO2-HF: Nuclear repulsion 2064543.462671
FMO2-HF: Total energy -78656.56162
FMO2-MP2: Total energy -78882.472396


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:492:LYS)


Summations of interaction energy for fragment #1(B:492:LYS)
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.
38.10341.1250.072-1.027-2.0670
Interaction energy analysis for fragmet #1(B:492:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.026 / q_NPA : 0.991
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].
3B494GLN0-0.034-0.0153.0660.6582.4540.004-0.768-1.0320.001
4B495LEU00.0370.0193.2353.4934.2900.066-0.199-0.665-0.001
5B496LEU00.0890.0475.7023.2953.2950.0000.0000.0000.000
6B497ARG10.8030.8717.82424.24824.2480.0000.0000.0000.000
7B498ALA00.0140.0108.7092.0842.0840.0000.0000.0000.000
8B499ALA00.0300.02910.2901.6331.6330.0000.0000.0000.000
9B500THR0-0.077-0.02011.8701.4401.4400.0000.0000.0000.000
10B501GLY00.0630.03113.6791.1561.1560.0000.0000.0000.000
11B502LYS10.9720.96215.61814.01014.0100.0000.0000.0000.000
12B503ALA00.0130.00916.7820.1230.1230.0000.0000.0000.000
13B504ILE00.0330.03017.2000.3550.3550.0000.0000.0000.000
14B505LEU0-0.028-0.02112.167-0.110-0.1100.0000.0000.0000.000
15B506ASN00.0070.00415.848-0.551-0.5510.0000.0000.0000.000
16B507GLY00.0870.07218.8540.2530.2530.0000.0000.0000.000
17B508ILE0-0.011-0.00715.0060.1710.1710.0000.0000.0000.000
18B509ASP-1-0.771-0.86314.333-18.403-18.4030.0000.0000.0000.000
19B510SER0-0.033-0.01017.1240.2140.2140.0000.0000.0000.000
20B511ILE00.0240.01319.9260.4760.4760.0000.0000.0000.000
21B512ASN00.0260.01116.2750.6500.6500.0000.0000.0000.000
22B513LYS10.8420.91119.26514.09814.0980.0000.0000.0000.000
23B514VAL00.0160.01922.1370.3540.3540.0000.0000.0000.000
24B515LEU0-0.0130.00221.0030.3940.3940.0000.0000.0000.000
25B516GLU-1-0.838-0.89720.052-14.212-14.2120.0000.0000.0000.000
26B517HIS0-0.034-0.01523.4840.1970.1970.0000.0000.0000.000
27B518PHE00.023-0.00326.9430.4030.4030.0000.0000.0000.000
28B519ARG10.8300.88020.64113.90613.9060.0000.0000.0000.000
29B520ARG10.8980.95423.32712.49012.4900.0000.0000.0000.000
30B521LYS10.8790.93027.77410.29610.2960.0000.0000.0000.000
31B522GLY00.0300.04130.3570.3150.3150.0000.0000.0000.000
32B523ILE0-0.021-0.00631.7650.2430.2430.0000.0000.0000.000
33B524ASN0-0.007-0.02231.308-0.068-0.0680.0000.0000.0000.000
34B525GLN00.0560.02630.348-0.269-0.2690.0000.0000.0000.000
35B526HIS0-0.028-0.01530.055-0.302-0.3020.0000.0000.0000.000
36B527VAL0-0.011-0.00227.020-0.133-0.1330.0000.0000.0000.000
37B528GLN0-0.009-0.01822.628-0.654-0.6540.0000.0000.0000.000
38B529ASN00.0070.00725.473-0.648-0.6480.0000.0000.0000.000
39B530GLY00.0400.03927.9070.0120.0120.0000.0000.0000.000
40B531TYR0-0.052-0.05219.855-0.045-0.0450.0000.0000.0000.000
41B532HIS00.0070.00222.307-0.583-0.5830.0000.0000.0000.000
42B533GLY00.0520.04818.945-0.524-0.5240.0000.0000.0000.000
43B534ILE0-0.029-0.01414.4690.6150.6150.0000.0000.0000.000
44B535VAL00.0260.01218.461-0.351-0.3510.0000.0000.0000.000
45B536MET0-0.050-0.01612.436-0.150-0.1500.0000.0000.0000.000
46B537ASN0-0.006-0.01212.167-0.674-0.6740.0000.0000.0000.000
47B538ASN0-0.051-0.03515.5670.1480.1480.0000.0000.0000.000
48B539PHE0-0.029-0.01318.0600.6670.6670.0000.0000.0000.000
49B540GLU-1-0.814-0.88215.743-17.453-17.4530.0000.0000.0000.000
50B541CYS0-0.011-0.00518.1710.7030.7030.0000.0000.0000.000
51B542GLU-1-0.867-0.92618.460-14.043-14.0430.0000.0000.0000.000
52B543PRO00.0380.00116.3620.2470.2470.0000.0000.0000.000
53B544ALA0-0.024-0.00118.5300.0830.0830.0000.0000.0000.000
54B545PHE00.022-0.00721.3530.4760.4760.0000.0000.0000.000
55B546TYR00.0030.00413.9110.3000.3000.0000.0000.0000.000
56B547THR00.0440.02519.253-0.229-0.2290.0000.0000.0000.000
57B548CYS00.0580.04521.2990.0890.0890.0000.0000.0000.000
58B549VAL00.0310.01420.9240.2360.2360.0000.0000.0000.000
59B550GLU-1-0.758-0.88416.474-15.698-15.6980.0000.0000.0000.000
60B551VAL0-0.047-0.02120.582-0.072-0.0720.0000.0000.0000.000
61B552THR0-0.0060.01323.6340.4760.4760.0000.0000.0000.000
62B553ALA0-0.038-0.01521.7130.1940.1940.0000.0000.0000.000
63B554GLY00.0410.01322.4980.1780.1780.0000.0000.0000.000
64B555ASN0-0.013-0.02320.665-1.189-1.1890.0000.0000.0000.000
65B556ARG10.9850.99421.8209.7469.7460.0000.0000.0000.000
66B557LEU00.0090.01716.4270.0370.0370.0000.0000.0000.000
67B558PHE00.007-0.01914.666-0.605-0.6050.0000.0000.0000.000
68B559TYR00.0120.01119.7100.2920.2920.0000.0000.0000.000
69B560HIS00.0230.02719.775-0.532-0.5320.0000.0000.0000.000
70B561ILE00.0320.02021.7150.6160.6160.0000.0000.0000.000
71B562VAL0-0.026-0.00924.464-0.318-0.3180.0000.0000.0000.000
72B563ASP-1-0.774-0.88527.269-9.925-9.9250.0000.0000.0000.000
73B564SER0-0.025-0.02530.4380.2300.2300.0000.0000.0000.000
74B565ASP-1-0.742-0.87631.937-8.400-8.4000.0000.0000.0000.000
75B566GLU-1-0.790-0.86733.925-8.428-8.4280.0000.0000.0000.000
76B567VAL0-0.0430.01328.374-0.077-0.0770.0000.0000.0000.000
77B568SER0-0.011-0.02929.677-0.279-0.2790.0000.0000.0000.000
78B569THR0-0.026-0.04030.753-0.221-0.2210.0000.0000.0000.000
79B570LYS10.8570.92431.8628.4258.4250.0000.0000.0000.000
80B571ILE00.0170.00525.961-0.111-0.1110.0000.0000.0000.000
81B572LEU00.0400.01129.067-0.118-0.1180.0000.0000.0000.000
82B573MET0-0.0140.01030.4240.0800.0800.0000.0000.0000.000
83B574GLU-1-0.764-0.87029.838-9.082-9.0820.0000.0000.0000.000
84B575PHE0-0.009-0.01023.357-0.119-0.1190.0000.0000.0000.000
85B576ASN0-0.030-0.02128.340-0.102-0.1020.0000.0000.0000.000
86B577LYS10.8120.90631.2889.0289.0280.0000.0000.0000.000
87B578MET0-0.071-0.04127.805-0.045-0.0450.0000.0000.0000.000
88B579ASN0-0.041-0.01328.8780.0490.0490.0000.0000.0000.000
89B580LEU0-0.0290.00023.955-0.293-0.2930.0000.0000.0000.000
90B581PRO0-0.039-0.03021.9790.1850.1850.0000.0000.0000.000
91B582GLY00.0350.03423.112-0.285-0.2850.0000.0000.0000.000
92B583GLU-1-0.932-0.98122.763-10.718-10.7180.0000.0000.0000.000
93B584VAL0-0.026-0.01722.925-0.571-0.5710.0000.0000.0000.000
94B585THR0-0.024-0.01424.9200.4200.4200.0000.0000.0000.000
95B586PHE00.0230.00925.348-0.438-0.4380.0000.0000.0000.000
96B587LEU0-0.004-0.00124.9530.2580.2580.0000.0000.0000.000
97B588PRO00.0120.01528.310-0.152-0.1520.0000.0000.0000.000
98B589LEU00.0090.00427.9680.2860.2860.0000.0000.0000.000
99B590ASN0-0.048-0.04331.8310.0830.0830.0000.0000.0000.000
100B591LYS10.8800.94334.4547.8987.8980.0000.0000.0000.000
101B592LEU0-0.0270.00529.8030.1150.1150.0000.0000.0000.000
102B593ASP-1-0.898-0.94434.502-7.392-7.3920.0000.0000.0000.000
103B594VAL0-0.043-0.02232.983-0.151-0.1510.0000.0000.0000.000
104B595ARG10.9190.95936.4107.2387.2380.0000.0000.0000.000
105B596ASP-1-0.866-0.92837.810-7.554-7.5540.0000.0000.0000.000
106B597THR0-0.068-0.04837.6380.1230.1230.0000.0000.0000.000
107B598ALA00.0170.02438.791-0.161-0.1610.0000.0000.0000.000
108B599TYR0-0.030-0.05533.888-0.014-0.0140.0000.0000.0000.000
109B600PRO00.0040.00439.1830.0980.0980.0000.0000.0000.000
110B601GLU-1-0.936-0.94940.104-6.878-6.8780.0000.0000.0000.000
111B602THR0-0.078-0.05838.8460.1590.1590.0000.0000.0000.000
112B603ASN00.010-0.00739.369-0.263-0.2630.0000.0000.0000.000
113B604ASP-1-0.878-0.92637.993-7.452-7.4520.0000.0000.0000.000
114B605ALA00.0320.01434.768-0.175-0.1750.0000.0000.0000.000
115B606ILE00.0070.01129.6120.0990.0990.0000.0000.0000.000
116B607PRO00.0490.02432.195-0.188-0.1880.0000.0000.0000.000
117B608MET0-0.0030.04326.359-0.295-0.2950.0000.0000.0000.000
118B609ILE00.025-0.00127.336-0.330-0.3300.0000.0000.0000.000
119B610SER0-0.059-0.02927.824-0.189-0.1890.0000.0000.0000.000
120B611LYS10.8620.92225.4289.8309.8300.0000.0000.0000.000
121B612LEU0-0.0350.00921.778-0.531-0.5310.0000.0000.0000.000
122B613ARG10.8860.94319.38713.85713.8570.0000.0000.0000.000
123B614TYR00.009-0.02621.572-0.681-0.6810.0000.0000.0000.000
124B615ASN00.0230.01623.3420.6940.6940.0000.0000.0000.000
125B616PRO00.0740.02324.9810.0980.0980.0000.0000.0000.000
126B617ARG10.8730.94325.56711.15611.1560.0000.0000.0000.000
127B618PHE0-0.002-0.02022.5430.1550.1550.0000.0000.0000.000
128B619ASP-1-0.765-0.85027.372-9.228-9.2280.0000.0000.0000.000
129B620LYS10.9150.95429.6188.2528.2520.0000.0000.0000.000
130B621ALA00.0080.00426.2950.0660.0660.0000.0000.0000.000
131B622PHE00.011-0.00321.419-0.120-0.1200.0000.0000.0000.000
132B623LYS10.8730.90926.9298.8248.8240.0000.0000.0000.000
133B624HIS00.0010.00429.2430.2260.2260.0000.0000.0000.000
134B625VAL0-0.090-0.03524.2870.0150.0150.0000.0000.0000.000
135B626PHE00.030-0.00222.178-0.105-0.1050.0000.0000.0000.000
136B627GLY0-0.0010.00728.3070.1250.1250.0000.0000.0000.000
137B628LYS10.8070.93431.6798.2948.2940.0000.0000.0000.000
138B629THR00.003-0.00528.9950.1330.1330.0000.0000.0000.000
139B630LEU00.0030.00131.896-0.069-0.0690.0000.0000.0000.000
140B631ILE00.0240.01226.835-0.086-0.0860.0000.0000.0000.000
141B632CYS0-0.036-0.02230.8520.2260.2260.0000.0000.0000.000
142B633ARG10.8940.94632.7887.5967.5960.0000.0000.0000.000
143B634SER0-0.008-0.03734.776-0.051-0.0510.0000.0000.0000.000
144B635MET00.0710.04333.8430.0580.0580.0000.0000.0000.000
145B636GLU-1-0.848-0.88536.011-7.293-7.2930.0000.0000.0000.000
146B637VAL00.0610.02937.7360.1130.1130.0000.0000.0000.000
147B638SER0-0.029-0.04134.9500.0030.0030.0000.0000.0000.000
148B639THR0-0.019-0.01837.2100.0770.0770.0000.0000.0000.000
149B640GLN0-0.033-0.00640.0890.2740.2740.0000.0000.0000.000
150B641LEU00.0430.00037.7550.1120.1120.0000.0000.0000.000
151B642ALA0-0.033-0.01437.5260.0730.0730.0000.0000.0000.000
152B643ARG10.8750.93139.5436.7876.7870.0000.0000.0000.000
153B644ALA0-0.0020.01543.2800.1540.1540.0000.0000.0000.000
154B645PHE00.0220.00541.0890.0910.0910.0000.0000.0000.000
155B646THR00.0040.00940.754-0.056-0.0560.0000.0000.0000.000
156B647MET0-0.043-0.02936.610-0.148-0.1480.0000.0000.0000.000
157B648ASP-1-0.744-0.82033.287-8.193-8.1930.0000.0000.0000.000
158B649CYS0-0.042-0.00933.573-0.106-0.1060.0000.0000.0000.000
159B650ILE0-0.0150.00526.675-0.040-0.0400.0000.0000.0000.000
160B651THR00.0380.03830.056-0.035-0.0350.0000.0000.0000.000
161B652LEU00.002-0.01026.107-0.272-0.2720.0000.0000.0000.000
162B653GLU-1-0.884-0.96125.130-10.398-10.3980.0000.0000.0000.000
163B654GLY0-0.004-0.00125.809-0.273-0.2730.0000.0000.0000.000
164B655ASP-1-0.914-0.95726.758-9.367-9.3670.0000.0000.0000.000
165B656GLN0-0.027-0.03627.2960.1500.1500.0000.0000.0000.000
166B657VAL0-0.018-0.01131.8830.1560.1560.0000.0000.0000.000
167B658SER0-0.017-0.01735.0830.0210.0210.0000.0000.0000.000
168B659HIS0-0.070-0.06036.1280.3180.3180.0000.0000.0000.000
169B660ARG10.9160.94438.9187.4187.4180.0000.0000.0000.000
170B661GLY00.0260.01740.0010.1130.1130.0000.0000.0000.000
171B662ALA0-0.023-0.00136.4140.0010.0010.0000.0000.0000.000
172B663LEU00.0380.01735.564-0.074-0.0740.0000.0000.0000.000
173B664THR0-0.068-0.04229.229-0.125-0.1250.0000.0000.0000.000
174B665GLY00.0800.04629.716-0.044-0.0440.0000.0000.0000.000
175B666GLY0-0.023-0.00628.4480.1330.1330.0000.0000.0000.000
176B667TYR0-0.058-0.04321.5190.0920.0920.0000.0000.0000.000
177B668TYR0-0.020-0.01222.349-0.423-0.4230.0000.0000.0000.000
178B669ASP-1-0.799-0.87417.962-14.453-14.4530.0000.0000.0000.000
179B670THR00.0040.00015.635-0.512-0.5120.0000.0000.0000.000
180B671ARG10.8470.90713.05317.33417.3340.0000.0000.0000.000
181B672LYS10.7590.89214.82713.56513.5650.0000.0000.0000.000
182B673SER00.0530.00514.586-0.529-0.5290.0000.0000.0000.000
183B674ARG10.8520.91512.40114.35914.3590.0000.0000.0000.000
184B675LEU0-0.031-0.02211.868-1.234-1.2340.0000.0000.0000.000
185B676GLU-1-0.873-0.91911.445-18.956-18.9560.0000.0000.0000.000
186B677LEU00.0460.0117.210-1.557-1.5570.0000.0000.0000.000
187B678GLN0-0.026-0.0087.343-2.795-2.7950.0000.0000.0000.000
188B679LYS10.9200.9549.16817.40817.4080.0000.0000.0000.000
189B680ASP-1-0.861-0.9225.723-27.604-27.6040.0000.0000.0000.000
190B681VAL0-0.082-0.0513.556-3.614-3.3410.004-0.048-0.2280.000
191B682ARG10.8470.9135.32017.80917.859-0.0010.000-0.0490.000
192B683LYS10.8180.9027.97325.84825.8480.0000.0000.0000.000
193B684ALA0-0.075-0.0144.393-0.797-0.691-0.001-0.012-0.0930.000
194B685GLU-1-1.002-0.9986.466-22.764-22.7640.0000.0000.0000.000