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: YZMN2

Calculation Name: 4PJQ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PJQ

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2117781.242837
FMO2-HF: Nuclear repulsion 2037617.858238
FMO2-HF: Total energy -80163.384599
FMO2-MP2: Total energy -80397.704736


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:88:ARG)


Summations of interaction energy for fragment #1(B:88:ARG)
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.
-300.64-290.48511.046-10.19-11.011-0.128
Interaction energy analysis for fragmet #1(B:88:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.918
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].
3B90GLU-1-0.842-0.9263.610-26.750-24.8410.005-0.796-1.1180.000
4B91GLU-1-0.837-0.9202.091-125.234-117.70911.040-9.052-9.513-0.128
5B92ALA0-0.047-0.0253.9243.7534.4740.001-0.342-0.3800.000
6B93LEU00.0150.0005.4593.7523.7520.0000.0000.0000.000
7B94GLU-1-0.933-0.9487.498-30.025-30.0250.0000.0000.0000.000
8B95LEU0-0.007-0.0197.1341.9971.9970.0000.0000.0000.000
9B96PHE0-0.023-0.0079.3552.4852.4850.0000.0000.0000.000
10B97GLU-1-0.869-0.95711.344-15.903-15.9030.0000.0000.0000.000
11B98GLU-1-0.973-0.97912.070-22.958-22.9580.0000.0000.0000.000
12B99MET0-0.065-0.03013.2740.8250.8250.0000.0000.0000.000
13B100LYS10.8700.93814.96217.84717.8470.0000.0000.0000.000
14B101GLU-1-0.981-0.97117.021-15.106-15.1060.0000.0000.0000.000
15B102LYS10.8660.93616.86618.34718.3470.0000.0000.0000.000
16B103GLY0-0.023-0.00420.1330.4280.4280.0000.0000.0000.000
17B104ILE0-0.062-0.02417.5140.5160.5160.0000.0000.0000.000
18B105VAL0-0.012-0.00618.794-0.442-0.4420.0000.0000.0000.000
19B106PRO0-0.015-0.02315.108-0.115-0.1150.0000.0000.0000.000
20B107ASP-1-0.823-0.89415.946-14.762-14.7620.0000.0000.0000.000
21B108VAL00.031-0.01516.254-0.604-0.6040.0000.0000.0000.000
22B109VAL0-0.0040.00112.908-0.463-0.4630.0000.0000.0000.000
23B110THR00.0030.00411.054-0.862-0.8620.0000.0000.0000.000
24B111TYR00.0300.00411.591-1.199-1.1990.0000.0000.0000.000
25B112THR00.0240.02013.440-0.282-0.2820.0000.0000.0000.000
26B113THR0-0.065-0.0417.600-0.549-0.5490.0000.0000.0000.000
27B114LEU0-0.024-0.0107.942-1.398-1.3980.0000.0000.0000.000
28B115ILE00.0200.02110.004-0.117-0.1170.0000.0000.0000.000
29B116SER0-0.007-0.00510.8540.5830.5830.0000.0000.0000.000
30B117GLY0-0.080-0.0357.3880.0110.0110.0000.0000.0000.000
31B118LEU00.024-0.0078.113-0.044-0.0440.0000.0000.0000.000
32B119GLY00.0270.02410.3220.9550.9550.0000.0000.0000.000
33B120LYS10.8870.9277.38824.57524.5750.0000.0000.0000.000
34B121ALA0-0.062-0.0218.1020.3550.3550.0000.0000.0000.000
35B122GLY00.0020.0149.9870.4350.4350.0000.0000.0000.000
36B123ARG10.7250.8308.53421.55021.5500.0000.0000.0000.000
37B124LEU00.0220.00013.689-0.297-0.2970.0000.0000.0000.000
38B125GLU-1-0.839-0.93716.315-12.055-12.0550.0000.0000.0000.000
39B126GLU-1-0.727-0.82113.146-18.233-18.2330.0000.0000.0000.000
40B127ALA0-0.025-0.01114.091-0.194-0.1940.0000.0000.0000.000
41B128LEU00.007-0.00515.4720.2090.2090.0000.0000.0000.000
42B129GLU-1-0.940-0.95617.605-14.143-14.1430.0000.0000.0000.000
43B130LEU0-0.044-0.03112.7890.1060.1060.0000.0000.0000.000
44B131PHE0-0.011-0.00717.2910.0780.0780.0000.0000.0000.000
45B132GLU-1-0.855-0.94919.574-11.057-11.0570.0000.0000.0000.000
46B133GLU-1-0.913-0.95018.524-14.503-14.5030.0000.0000.0000.000
47B134MET0-0.074-0.01818.4000.1710.1710.0000.0000.0000.000
48B135LYS10.8870.93720.74410.96510.9650.0000.0000.0000.000
49B136GLU-1-0.991-0.97724.121-10.763-10.7630.0000.0000.0000.000
50B137LYS10.8800.94420.81113.22013.2200.0000.0000.0000.000
51B138GLY0-0.026-0.00524.6380.0170.0170.0000.0000.0000.000
52B139ILE0-0.048-0.01519.6990.0710.0710.0000.0000.0000.000
53B140VAL00.001-0.01323.0210.1730.1730.0000.0000.0000.000
54B141PRO0-0.021-0.00820.525-0.289-0.2890.0000.0000.0000.000
55B142ASP-1-0.827-0.92318.811-14.023-14.0230.0000.0000.0000.000
56B143VAL00.0610.00621.179-0.144-0.1440.0000.0000.0000.000
57B144VAL0-0.0010.00715.6510.0410.0410.0000.0000.0000.000
58B145THR00.0150.01817.181-0.523-0.5230.0000.0000.0000.000
59B146TYR00.015-0.00618.194-0.076-0.0760.0000.0000.0000.000
60B147THR0-0.0070.00119.619-0.075-0.0750.0000.0000.0000.000
61B148THR0-0.029-0.01214.260-0.208-0.2080.0000.0000.0000.000
62B149LEU0-0.004-0.00516.935-0.032-0.0320.0000.0000.0000.000
63B150ILE00.0250.02818.9260.2470.2470.0000.0000.0000.000
64B151SER0-0.025-0.01518.3050.4390.4390.0000.0000.0000.000
65B152GLY00.003-0.00617.7880.1330.1330.0000.0000.0000.000
66B153LEU00.0170.00918.4710.1330.1330.0000.0000.0000.000
67B154GLY00.0090.00521.8080.3850.3850.0000.0000.0000.000
68B155LYS10.8200.90719.02412.17112.1710.0000.0000.0000.000
69B156ALA0-0.021-0.00420.3830.1810.1810.0000.0000.0000.000
70B157GLY0-0.038-0.00621.9470.2610.2610.0000.0000.0000.000
71B158ARG10.8330.92623.04011.53011.5300.0000.0000.0000.000
72B159LEU00.001-0.00726.186-0.152-0.1520.0000.0000.0000.000
73B160GLU-1-0.860-0.94028.369-8.319-8.3190.0000.0000.0000.000
74B161GLU-1-0.819-0.91225.760-10.368-10.3680.0000.0000.0000.000
75B162ALA0-0.030-0.01224.957-0.148-0.1480.0000.0000.0000.000
76B163LEU0-0.025-0.01826.157-0.061-0.0610.0000.0000.0000.000
77B164GLU-1-0.912-0.94728.630-9.161-9.1610.0000.0000.0000.000
78B165LEU00.002-0.01522.594-0.050-0.0500.0000.0000.0000.000
79B166PHE0-0.029-0.02226.790-0.141-0.1410.0000.0000.0000.000
80B167GLU-1-0.900-0.95828.339-8.343-8.3430.0000.0000.0000.000
81B168GLU-1-0.797-0.89226.698-10.348-10.3480.0000.0000.0000.000
82B169MET0-0.086-0.03124.634-0.110-0.1100.0000.0000.0000.000
83B170LYS10.8480.91728.1338.5068.5060.0000.0000.0000.000
84B171GLU-1-0.965-0.96531.539-8.457-8.4570.0000.0000.0000.000
85B172LYS10.8190.92125.41610.94510.9450.0000.0000.0000.000
86B173GLY0-0.027-0.01130.396-0.141-0.1410.0000.0000.0000.000
87B174ILE0-0.069-0.02825.145-0.124-0.1240.0000.0000.0000.000
88B175VAL0-0.024-0.01628.8260.1920.1920.0000.0000.0000.000
89B176PRO0-0.008-0.00426.362-0.381-0.3810.0000.0000.0000.000
90B177ASP-1-0.848-0.93623.113-11.599-11.5990.0000.0000.0000.000
91B178VAL00.0390.00425.2720.0650.0650.0000.0000.0000.000
92B179VAL00.0130.01320.7970.1670.1670.0000.0000.0000.000
93B180THR00.0190.00824.177-0.048-0.0480.0000.0000.0000.000
94B181TYR00.008-0.01825.1580.0880.0880.0000.0000.0000.000
95B182THR0-0.028-0.00526.1480.3300.3300.0000.0000.0000.000
96B183THR0-0.058-0.03023.3470.0630.0630.0000.0000.0000.000
97B184LEU00.0170.00925.9480.1460.1460.0000.0000.0000.000
98B185ILE00.0300.02128.6590.2450.2450.0000.0000.0000.000
99B186SER0-0.045-0.01927.8940.2160.2160.0000.0000.0000.000
100B187GLY0-0.026-0.01528.8460.1660.1660.0000.0000.0000.000
101B188LEU00.0380.01329.7130.1720.1720.0000.0000.0000.000
102B189GLY00.0120.01333.1180.2410.2410.0000.0000.0000.000
103B190LYS10.9070.95428.8049.4319.4310.0000.0000.0000.000
104B191ALA0-0.067-0.03032.8990.1140.1140.0000.0000.0000.000
105B192GLY0-0.028-0.01534.6430.1660.1660.0000.0000.0000.000
106B193ARG10.8410.92133.9628.1718.1710.0000.0000.0000.000
107B194LEU0-0.017-0.02437.621-0.096-0.0960.0000.0000.0000.000
108B195GLU-1-0.900-0.96339.488-6.513-6.5130.0000.0000.0000.000
109B196GLU-1-0.772-0.87136.752-7.657-7.6570.0000.0000.0000.000
110B197ALA0-0.022-0.01135.346-0.136-0.1360.0000.0000.0000.000
111B198LEU0-0.036-0.02436.308-0.092-0.0920.0000.0000.0000.000
112B199GLU-1-0.922-0.95038.385-7.186-7.1860.0000.0000.0000.000
113B200LEU00.006-0.00631.895-0.107-0.1070.0000.0000.0000.000
114B201PHE0-0.042-0.02934.948-0.186-0.1860.0000.0000.0000.000
115B202GLU-1-0.905-0.95936.266-7.069-7.0690.0000.0000.0000.000
116B203GLU-1-0.778-0.86634.087-8.400-8.4000.0000.0000.0000.000
117B204MET0-0.046-0.03031.148-0.146-0.1460.0000.0000.0000.000
118B205LYS10.8400.92634.5207.3287.3280.0000.0000.0000.000
119B206GLU-1-0.967-0.97737.236-7.183-7.1830.0000.0000.0000.000
120B207LYS10.8220.91833.3678.3038.3030.0000.0000.0000.000
121B208GLY0-0.0060.00634.601-0.178-0.1780.0000.0000.0000.000
122B209ILE0-0.052-0.01629.430-0.235-0.2350.0000.0000.0000.000
123B210VAL0-0.039-0.02331.7710.2620.2620.0000.0000.0000.000
124B211PRO0-0.021-0.00931.008-0.288-0.2880.0000.0000.0000.000
125B212ASP-1-0.843-0.92026.916-10.241-10.2410.0000.0000.0000.000
126B213VAL00.0440.00130.1980.2450.2450.0000.0000.0000.000
127B214VAL00.0060.00327.3960.2150.2150.0000.0000.0000.000
128B215THR00.0420.04630.7590.0890.0890.0000.0000.0000.000
129B216TYR00.0540.01432.5000.1440.1440.0000.0000.0000.000
130B217THR0-0.026-0.00933.1380.1800.1800.0000.0000.0000.000
131B218THR0-0.061-0.05332.3580.1570.1570.0000.0000.0000.000
132B219LEU00.0100.00534.8980.1810.1810.0000.0000.0000.000
133B220ILE00.0360.02837.6650.2070.2070.0000.0000.0000.000
134B221SER0-0.051-0.02237.4720.2650.2650.0000.0000.0000.000
135B222GLY00.003-0.00638.6450.1550.1550.0000.0000.0000.000
136B223LEU00.0370.00739.9040.1450.1450.0000.0000.0000.000
137B224GLY0-0.0120.00042.5840.1690.1690.0000.0000.0000.000
138B225LYS10.7970.88640.3047.1867.1860.0000.0000.0000.000
139B226ALA0-0.0150.00744.0370.1000.1000.0000.0000.0000.000
140B227GLY0-0.033-0.00745.7460.1170.1170.0000.0000.0000.000
141B228ARG10.8150.90245.0706.4956.4950.0000.0000.0000.000
142B229LEU0-0.008-0.01546.923-0.101-0.1010.0000.0000.0000.000
143B230GLU-1-0.785-0.88948.134-5.718-5.7180.0000.0000.0000.000
144B231GLU-1-0.758-0.85145.489-6.267-6.2670.0000.0000.0000.000
145B232ALA0-0.027-0.01543.580-0.128-0.1280.0000.0000.0000.000
146B233LEU0-0.002-0.01044.135-0.126-0.1260.0000.0000.0000.000
147B234GLU-1-0.911-0.94646.111-6.219-6.2190.0000.0000.0000.000
148B235LEU0-0.003-0.00839.736-0.126-0.1260.0000.0000.0000.000
149B236PHE0-0.033-0.02341.519-0.207-0.2070.0000.0000.0000.000
150B237GLU-1-0.886-0.95542.831-6.392-6.3920.0000.0000.0000.000
151B238GLU-1-0.799-0.88740.604-7.255-7.2550.0000.0000.0000.000
152B239MET0-0.080-0.04336.607-0.120-0.1200.0000.0000.0000.000
153B240LYS10.8600.93339.5716.3516.3510.0000.0000.0000.000
154B241GLU-1-0.965-0.97141.970-6.544-6.5440.0000.0000.0000.000
155B242LYS10.8210.91937.9297.3847.3840.0000.0000.0000.000
156B243GLY0-0.016-0.00237.757-0.210-0.2100.0000.0000.0000.000
157B244ILE0-0.047-0.01134.104-0.244-0.2440.0000.0000.0000.000
158B245VAL0-0.025-0.01635.8120.2220.2220.0000.0000.0000.000
159B246PRO0-0.0030.00635.906-0.208-0.2080.0000.0000.0000.000
160B247ASP-1-0.829-0.92633.894-8.251-8.2510.0000.0000.0000.000
161B248VAL00.042-0.00436.3660.1760.1760.0000.0000.0000.000
162B249VAL0-0.0040.00234.9940.2150.2150.0000.0000.0000.000
163B250THR00.0230.00837.5100.1430.1430.0000.0000.0000.000
164B251TYR00.0370.01339.7920.1060.1060.0000.0000.0000.000
165B252THR0-0.0090.00341.1730.2280.2280.0000.0000.0000.000
166B253THR0-0.058-0.03440.2780.1560.1560.0000.0000.0000.000
167B254LEU00.0110.01142.9920.1450.1450.0000.0000.0000.000
168B255ILE00.0300.03145.4740.1570.1570.0000.0000.0000.000
169B256SER0-0.029-0.02845.7970.1630.1630.0000.0000.0000.000
170B257GLY0-0.033-0.01347.0060.1200.1200.0000.0000.0000.000
171B258LEU00.0500.02448.4240.1150.1150.0000.0000.0000.000
172B259GLY0-0.0070.00050.9960.1280.1280.0000.0000.0000.000
173B260LYS10.8430.90648.2176.0516.0510.0000.0000.0000.000
174B261ALA0-0.0090.00852.5070.0830.0830.0000.0000.0000.000
175B262GLY0-0.030-0.00454.2010.0910.0910.0000.0000.0000.000
176B263ARG10.7440.85653.2035.6555.6550.0000.0000.0000.000
177B264LEU0-0.011-0.01454.715-0.089-0.0890.0000.0000.0000.000
178B265GLU-1-0.886-0.95455.600-5.163-5.1630.0000.0000.0000.000
179B266GLU-1-0.768-0.87853.095-5.587-5.5870.0000.0000.0000.000
180B267ALA0-0.014-0.01051.081-0.114-0.1140.0000.0000.0000.000
181B268LEU0-0.042-0.02451.271-0.107-0.1070.0000.0000.0000.000
182B269GLU-1-0.905-0.94652.764-5.600-5.6000.0000.0000.0000.000
183B270LEU00.0330.01046.560-0.115-0.1150.0000.0000.0000.000
184B271PHE0-0.058-0.04047.932-0.147-0.1470.0000.0000.0000.000
185B272GLU-1-0.889-0.96148.811-5.809-5.8090.0000.0000.0000.000
186B273GLU-1-0.825-0.90946.205-6.493-6.4930.0000.0000.0000.000
187B274MET0-0.073-0.04042.907-0.116-0.1160.0000.0000.0000.000
188B275LYS10.8620.93144.8085.7315.7310.0000.0000.0000.000
189B276GLU-1-0.951-0.96146.870-6.098-6.0980.0000.0000.0000.000
190B277LYS10.8530.93441.9846.7696.7690.0000.0000.0000.000
191B278GLY0-0.0180.00142.015-0.179-0.1790.0000.0000.0000.000
192B279ILE0-0.041-0.01039.320-0.168-0.1680.0000.0000.0000.000
193B280VAL0-0.032-0.02040.7060.1790.1790.0000.0000.0000.000
194B281PRO0-0.010-0.00341.966-0.085-0.0850.0000.0000.0000.000
195B282ASP-1-0.838-0.90641.015-7.187-7.1870.0000.0000.0000.000
196B283VAL0-0.019-0.03544.0550.1580.1580.0000.0000.0000.000
197B284VAL00.0340.00844.1300.1580.1580.0000.0000.0000.000
198B285THR00.0520.03745.3730.1210.1210.0000.0000.0000.000
199B286TYR00.0470.02547.9060.1760.1760.0000.0000.0000.000
200B287THR0-0.056-0.02849.7650.1410.1410.0000.0000.0000.000
201B288THR0-0.018-0.01349.5540.1280.1280.0000.0000.0000.000
202B289LEU00.0310.01851.3040.1240.1240.0000.0000.0000.000
203B290ILE00.0010.00453.8150.1170.1170.0000.0000.0000.000
204B291SER0-0.067-0.02955.0460.1320.1320.0000.0000.0000.000
205B292GLY0-0.022-0.01356.1650.1010.1010.0000.0000.0000.000
206B293LEU00.0340.00757.6510.0870.0870.0000.0000.0000.000
207B294GLY0-0.0030.00459.6730.0930.0930.0000.0000.0000.000
208B295LYS10.8560.92356.9615.2745.2740.0000.0000.0000.000
209B296ALA0-0.0070.01262.3930.0720.0720.0000.0000.0000.000
210B297GLY0-0.044-0.01063.8890.0630.0630.0000.0000.0000.000