Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: M36KZ

Calculation Name: 3WVZ-B-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q53FT3

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1683973.316765
FMO2-HF: Nuclear repulsion 1612394.347367
FMO2-HF: Total energy -71578.969397
FMO2-MP2: Total energy -71784.933291


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:-3:ALA )


Summations of interaction energy for fragment #1(B:-3: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.
-55.321-53.0980.212-1.027-1.409-0.005
Interaction energy analysis for fragmet #1(B:-3:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.902
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].
3B-1GLY 0-0.0120.0132.6024.0466.1370.212-1.020-1.284-0.005
4B0SER 00.0060.0014.2591.2281.3600.000-0.007-0.1250.000
5B1MET 00.0110.0207.3410.0510.0510.0000.0000.0000.000
6B2PHE 0-0.003-0.01210.1871.9881.9880.0000.0000.0000.000
7B3GLY 00.0230.00712.825-1.083-1.0830.0000.0000.0000.000
8B4CYS 0-0.052-0.01215.5201.1821.1820.0000.0000.0000.000
9B5LEU 00.0130.00018.289-0.207-0.2070.0000.0000.0000.000
10B6VAL 00.0550.04121.2790.4560.4560.0000.0000.0000.000
11B7ALA 0-0.011-0.01124.395-0.050-0.0500.0000.0000.0000.000
12B8GLY 00.0140.00627.2120.2840.2840.0000.0000.0000.000
13B9ARG 10.7990.90323.70611.66811.6680.0000.0000.0000.000
14B10LEU 00.0130.00220.156-0.044-0.0440.0000.0000.0000.000
15B11VAL 0-0.033-0.01716.2420.0030.0030.0000.0000.0000.000
16B12GLN 00.0030.01216.020-0.668-0.6680.0000.0000.0000.000
17B13THR 00.038-0.00511.333-0.033-0.0330.0000.0000.0000.000
18B14ALA 0-0.039-0.0129.870-1.769-1.7690.0000.0000.0000.000
19B15ALA 00.0000.01010.8261.2741.2740.0000.0000.0000.000
20B16GLN 0-0.0100.00210.545-2.165-2.1650.0000.0000.0000.000
21B17GLN 0-0.031-0.0148.480-0.463-0.4630.0000.0000.0000.000
22B18VAL 0-0.025-0.01011.6190.4810.4810.0000.0000.0000.000
23B19ALA 0-0.027-0.02413.6431.1031.1030.0000.0000.0000.000
24B20GLU -1-0.914-0.95810.201-26.107-26.1070.0000.0000.0000.000
25B21ASP -1-0.894-0.94211.399-18.439-18.4390.0000.0000.0000.000
26B22LYS 10.8130.90613.69315.53015.5300.0000.0000.0000.000
27B23PHE 00.007-0.0049.223-1.008-1.0080.0000.0000.0000.000
28B24VAL 00.0060.00714.2431.2531.2530.0000.0000.0000.000
29B25PHE 0-0.026-0.01813.627-1.049-1.0490.0000.0000.0000.000
30B26ASP -1-0.814-0.89517.342-14.198-14.1980.0000.0000.0000.000
31B27LEU 0-0.060-0.05320.011-0.231-0.2310.0000.0000.0000.000
32B28PRO 00.006-0.00521.9970.5120.5120.0000.0000.0000.000
33B29ASP -1-0.787-0.86925.195-9.987-9.9870.0000.0000.0000.000
34B30TYR 00.0330.00528.4960.0080.0080.0000.0000.0000.000
35B31GLU -1-0.889-0.94929.361-9.472-9.4720.0000.0000.0000.000
36B32SER 0-0.091-0.05530.2840.0920.0920.0000.0000.0000.000
37B33ILE 0-0.048-0.01325.861-0.231-0.2310.0000.0000.0000.000
38B34ASN 00.0090.00429.5270.4320.4320.0000.0000.0000.000
39B35HIS 00.027-0.00628.7740.0660.0660.0000.0000.0000.000
40B36VAL 00.0360.02022.785-0.269-0.2690.0000.0000.0000.000
41B37VAL 0-0.038-0.01622.3530.3000.3000.0000.0000.0000.000
42B38VAL 00.0280.02118.535-0.624-0.6240.0000.0000.0000.000
43B39PHE 0-0.012-0.02516.9180.5400.5400.0000.0000.0000.000
44B40MET 0-0.0180.01315.239-0.548-0.5480.0000.0000.0000.000
45B41LEU 0-0.045-0.02210.5570.7960.7960.0000.0000.0000.000
46B42GLY 0-0.0040.00614.2500.2860.2860.0000.0000.0000.000
47B43THR 0-0.042-0.0199.3490.9220.9220.0000.0000.0000.000
48B44ILE 00.005-0.0046.773-1.491-1.4910.0000.0000.0000.000
49B45PRO 0-0.0180.00111.3751.1821.1820.0000.0000.0000.000
50B46PHE 00.008-0.01413.428-1.042-1.0420.0000.0000.0000.000
51B47PRO 00.0370.01013.6570.3620.3620.0000.0000.0000.000
52B48GLU -1-0.892-0.95516.193-12.894-12.8940.0000.0000.0000.000
53B49GLY 00.0130.00919.8020.0460.0460.0000.0000.0000.000
54B50MET 0-0.0330.00317.7010.6560.6560.0000.0000.0000.000
55B51GLY 0-0.018-0.02719.658-0.055-0.0550.0000.0000.0000.000
56B52GLY 00.0130.00518.898-0.529-0.5290.0000.0000.0000.000
57B53SER 0-0.010-0.01219.5300.6530.6530.0000.0000.0000.000
58B54VAL 0-0.022-0.01220.510-0.562-0.5620.0000.0000.0000.000
59B55TYR 00.021-0.00422.1030.7200.7200.0000.0000.0000.000
60B56PHE 00.019-0.00423.054-0.476-0.4760.0000.0000.0000.000
61B57SER 00.0030.00724.8160.4350.4350.0000.0000.0000.000
62B58TYR 0-0.006-0.00426.701-0.196-0.1960.0000.0000.0000.000
63B59PRO 00.0110.02229.2440.1330.1330.0000.0000.0000.000
64B60ASP -1-0.867-0.93031.901-8.708-8.7080.0000.0000.0000.000
65B61SER 0-0.0010.01434.6310.2950.2950.0000.0000.0000.000
66B62ASN 0-0.045-0.02636.4790.0810.0810.0000.0000.0000.000
67B63GLY 00.0050.00034.9670.0510.0510.0000.0000.0000.000
68B64MET 0-0.051-0.04632.1890.0520.0520.0000.0000.0000.000
69B65PRO 00.0170.02927.7700.0530.0530.0000.0000.0000.000
70B66VAL 00.0070.01129.8650.0120.0120.0000.0000.0000.000
71B67TRP 00.008-0.01021.875-0.239-0.2390.0000.0000.0000.000
72B68GLN 0-0.003-0.00728.0800.6040.6040.0000.0000.0000.000
73B69LEU 0-0.0120.00825.796-0.419-0.4190.0000.0000.0000.000
74B70LEU 0-0.013-0.01524.9360.4280.4280.0000.0000.0000.000
75B71GLY 00.0350.00026.0630.4240.4240.0000.0000.0000.000
76B72PHE 00.0120.02223.601-0.345-0.3450.0000.0000.0000.000
77B73VAL 0-0.029-0.00218.8840.2510.2510.0000.0000.0000.000
78B74THR 00.0380.01120.650-0.296-0.2960.0000.0000.0000.000
79B75ASN 00.0810.02017.956-0.643-0.6430.0000.0000.0000.000
80B76GLY 0-0.0070.00920.4950.0680.0680.0000.0000.0000.000
81B77LYS 10.8670.93823.40812.22512.2250.0000.0000.0000.000
82B78PRO 00.0470.03119.458-0.020-0.0200.0000.0000.0000.000
83B79SER 0-0.020-0.01519.933-0.483-0.4830.0000.0000.0000.000
84B80ALA 0-0.005-0.00222.3240.6040.6040.0000.0000.0000.000
85B81ILE 00.0020.00524.214-0.296-0.2960.0000.0000.0000.000
86B82PHE 0-0.013-0.01423.8350.3460.3460.0000.0000.0000.000
87B83LYS 10.8210.91528.3118.7398.7390.0000.0000.0000.000
88B84ILE 00.0120.00527.121-0.067-0.0670.0000.0000.0000.000
89B85SER 00.0180.02230.8120.2150.2150.0000.0000.0000.000
90B86NME 0-0.0040.00333.8800.0950.0950.0000.0000.0000.000
91B94ACE 00.006-0.00929.7480.0500.0500.0000.0000.0000.000
92B95HIS 0-0.017-0.00825.583-0.048-0.0480.0000.0000.0000.000
93B96PRO 00.0150.02921.422-0.102-0.1020.0000.0000.0000.000
94B97PHE 00.0690.03317.961-0.642-0.6420.0000.0000.0000.000
95B98NME 00.0110.01122.7690.4580.4580.0000.0000.0000.000
96B106ACE 00.0850.00833.0010.0420.0420.0000.0000.0000.000
97B107SER 0-0.049-0.03929.325-0.117-0.1170.0000.0000.0000.000
98B108VAL 0-0.034-0.00623.564-0.151-0.1510.0000.0000.0000.000
99B109ALA 00.0110.02425.6530.1200.1200.0000.0000.0000.000
100B110GLN 0-0.050-0.03520.625-0.214-0.2140.0000.0000.0000.000
101B111ILE 0-0.022-0.00119.1770.5340.5340.0000.0000.0000.000
102B112GLY 00.0080.01218.751-0.771-0.7710.0000.0000.0000.000
103B113ILE 0-0.045-0.02615.5390.6960.6960.0000.0000.0000.000
104B114SER 0-0.009-0.00916.637-0.980-0.9800.0000.0000.0000.000
105B115VAL 0-0.025-0.01414.0600.4180.4180.0000.0000.0000.000
106B116GLU -1-0.856-0.92017.401-12.466-12.4660.0000.0000.0000.000
107B117LEU 00.0700.01520.771-0.206-0.2060.0000.0000.0000.000
108B118LEU 0-0.006-0.02022.5460.3960.3960.0000.0000.0000.000
109B119ASP -1-0.907-0.94824.878-10.351-10.3510.0000.0000.0000.000
110B120SER 0-0.071-0.04425.6700.3690.3690.0000.0000.0000.000
111B121MET 0-0.0140.00523.0300.1070.1070.0000.0000.0000.000
112B122ALA 0-0.046-0.01126.9090.2490.2490.0000.0000.0000.000
113B123GLN 0-0.021-0.00630.1920.4590.4590.0000.0000.0000.000
114B124GLN 0-0.024-0.00126.2780.0050.0050.0000.0000.0000.000
115B125THR 0-0.026-0.02530.9910.1970.1970.0000.0000.0000.000
116B126PRO 0-0.045-0.00229.073-0.002-0.0020.0000.0000.0000.000
117B127VAL 00.0430.01730.9800.2510.2510.0000.0000.0000.000
118B128GLY 00.0300.02829.9390.1890.1890.0000.0000.0000.000
119B129ASN 00.015-0.00331.0210.1990.1990.0000.0000.0000.000
120B130ALA 00.0450.03930.903-0.095-0.0950.0000.0000.0000.000
121B131ALA 0-0.084-0.04431.8350.0390.0390.0000.0000.0000.000
122B132VAL 0-0.030-0.02335.0530.1680.1680.0000.0000.0000.000
123B133SER 00.0190.00233.044-0.112-0.1120.0000.0000.0000.000
124B134SER 00.0470.01432.972-0.248-0.2480.0000.0000.0000.000
125B135VAL 0-0.005-0.00235.3610.2680.2680.0000.0000.0000.000
126B136ASP -1-0.866-0.93537.292-7.958-7.9580.0000.0000.0000.000
127B137SER 0-0.024-0.01539.0660.1930.1930.0000.0000.0000.000
128B138PHE 0-0.0140.00138.4600.2120.2120.0000.0000.0000.000
129B139THR 00.0170.00242.5680.2380.2380.0000.0000.0000.000
130B140GLN 00.022-0.00141.0320.1500.1500.0000.0000.0000.000
131B141PHE 0-0.0040.00644.8520.1700.1700.0000.0000.0000.000
132B142THR 00.0100.00546.7790.1960.1960.0000.0000.0000.000
133B143GLN 0-0.027-0.03446.8720.1250.1250.0000.0000.0000.000
134B144LYS 10.9620.98747.5396.6516.6510.0000.0000.0000.000
135B145MET 0-0.0140.01050.8560.1220.1220.0000.0000.0000.000
136B146LEU 0-0.030-0.02752.5180.1450.1450.0000.0000.0000.000
137B147ASP -1-0.928-0.95153.794-5.606-5.6060.0000.0000.0000.000
138B148ASN 0-0.040-0.01454.9560.1710.1710.0000.0000.0000.000
139B149PHE 00.008-0.00156.7480.1180.1180.0000.0000.0000.000
140B150TYR 0-0.001-0.00958.4900.1350.1350.0000.0000.0000.000
141B151ASN 0-0.0010.00259.1630.1200.1200.0000.0000.0000.000
142B152PHE 0-0.043-0.01061.0020.0950.0950.0000.0000.0000.000
143B153ALA 00.001-0.01962.7960.0950.0950.0000.0000.0000.000
144B154SER 0-0.037-0.01163.9100.1110.1110.0000.0000.0000.000
145B155SER 00.001-0.00565.6210.0730.0730.0000.0000.0000.000
146B156PHE 0-0.045-0.02067.5420.0850.0850.0000.0000.0000.000
147B157ALA 0-0.0370.00367.5520.0340.0340.0000.0000.0000.000
148B158VAL 00.0280.01969.6130.0570.0570.0000.0000.0000.000
149B159SER 0-0.028-0.02272.186-0.022-0.0220.0000.0000.0000.000
150B160GLN 00.048-0.01973.9930.0570.0570.0000.0000.0000.000
151B161ALA 0-0.031-0.01276.5540.0480.0480.0000.0000.0000.000
152B162GLN 0-0.019-0.00774.5060.0130.0130.0000.0000.0000.000
153B163MET 0-0.0340.02073.9140.0140.0140.0000.0000.0000.000
154B164THR 00.0010.00778.5730.0490.0490.0000.0000.0000.000
155B165PRO 0-0.011-0.02580.828-0.029-0.0290.0000.0000.0000.000
156B166SER 00.0580.02779.6750.0420.0420.0000.0000.0000.000
157B167PRO 0-0.039-0.02979.710-0.051-0.0510.0000.0000.0000.000
158B168SER 0-0.035-0.00679.288-0.029-0.0290.0000.0000.0000.000
159B169GLU -1-0.934-0.95174.974-4.281-4.2810.0000.0000.0000.000
160B170MET 0-0.025-0.00871.464-0.001-0.0010.0000.0000.0000.000
161B171PHE 00.0630.02870.710-0.043-0.0430.0000.0000.0000.000
162B172ILE 0-0.019-0.01664.112-0.035-0.0350.0000.0000.0000.000
163B173PRO 0-0.015-0.00565.3840.0020.0020.0000.0000.0000.000
164B174ALA 00.1310.05264.207-0.082-0.0820.0000.0000.0000.000
165B175ASN 0-0.021-0.01561.828-0.111-0.1110.0000.0000.0000.000
166B176VAL 00.001-0.01060.476-0.094-0.0940.0000.0000.0000.000
167B177VAL 00.0240.02356.759-0.109-0.1090.0000.0000.0000.000
168B178LEU 00.0150.00756.156-0.112-0.1120.0000.0000.0000.000
169B179LYS 11.0151.01255.4875.0525.0520.0000.0000.0000.000
170B180TRP 00.0030.02850.543-0.110-0.1100.0000.0000.0000.000
171B181TYR 00.0510.03048.346-0.192-0.1920.0000.0000.0000.000
172B182GLU -1-0.895-0.95050.752-5.835-5.8350.0000.0000.0000.000
173B183ASN 0-0.103-0.08850.790-0.128-0.1280.0000.0000.0000.000
174B184PHE 00.0090.00445.015-0.123-0.1230.0000.0000.0000.000
175B185GLN 00.0290.00746.423-0.073-0.0730.0000.0000.0000.000
176B186ARG 10.9480.98945.5716.0816.0810.0000.0000.0000.000
177B187ARG 10.8940.94944.2896.7736.7730.0000.0000.0000.000
178B188LEU 0-0.007-0.00741.578-0.151-0.1510.0000.0000.0000.000
179B189ALA 00.0040.00541.367-0.205-0.2050.0000.0000.0000.000
180B190GLN 0-0.077-0.02440.657-0.121-0.1210.0000.0000.0000.000
181B191ASN 00.0250.00339.279-0.345-0.3450.0000.0000.0000.000
182B192PRO 00.0940.05536.5070.1890.1890.0000.0000.0000.000
183B193LEU 0-0.050-0.03635.9340.0680.0680.0000.0000.0000.000
184B194PHE 0-0.057-0.03340.2340.1020.1020.0000.0000.0000.000
185B195TRP 0-0.0130.00640.4170.1330.1330.0000.0000.0000.000
186B196LYS 10.9280.97837.8888.0758.0750.0000.0000.0000.000
187B197NME 00.0080.00742.916-0.003-0.0030.0000.0000.0000.000