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

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FMODB ID: 9G6G2

Calculation Name: 4P1N-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P1N

Chain ID: B

ChEMBL ID:

UniProt ID: W0TA43

Base Structure: X-ray

Registration Date: 2023-06-20

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2510258.459634
FMO2-HF: Nuclear repulsion 2422451.589454
FMO2-HF: Total energy -87806.87018
FMO2-MP2: Total energy -88058.057731


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:568:ASP)


Summations of interaction energy for fragment #1(B:568:ASP)
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.
-70.088-76.03743.427-19.924-17.5520.166
Interaction energy analysis for fragmet #1(B:568:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.788 / q_NPA : -0.865
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].
3B570ASN00.003-0.0192.407-8.139-4.4612.103-2.671-3.1110.001
4B571ILE00.0580.0363.660-7.419-6.4860.017-0.328-0.6210.002
5B572THR00.0190.0035.435-4.101-4.1010.0000.0000.0000.000
6B573PRO00.0220.0136.954-2.851-2.8510.0000.0000.0000.000
7B574PHE00.0080.0118.263-2.180-2.1800.0000.0000.0000.000
8B575VAL00.0340.0249.195-2.242-2.2420.0000.0000.0000.000
9B576GLU-1-0.829-0.90411.35719.85019.8500.0000.0000.0000.000
10B577SER0-0.034-0.00213.196-1.629-1.6290.0000.0000.0000.000
11B578LEU00.0360.01612.882-1.219-1.2190.0000.0000.0000.000
12B579SER0-0.008-0.02114.847-1.081-1.0810.0000.0000.0000.000
13B580ALA0-0.021-0.00417.343-0.975-0.9750.0000.0000.0000.000
14B581LYS10.8850.94617.444-16.417-16.4170.0000.0000.0000.000
15B582ALA00.0020.00819.797-0.692-0.6920.0000.0000.0000.000
16B583PHE0-0.020-0.00421.245-0.685-0.6850.0000.0000.0000.000
17B584VAL0-0.0030.00223.199-0.646-0.6460.0000.0000.0000.000
18B585MET00.0030.01424.727-0.720-0.7200.0000.0000.0000.000
19B586TYR0-0.019-0.03525.304-0.368-0.3680.0000.0000.0000.000
20B587SER0-0.015-0.02326.955-0.473-0.4730.0000.0000.0000.000
21B588PHE0-0.065-0.03029.158-0.512-0.5120.0000.0000.0000.000
22B589ALA00.0580.01130.034-0.375-0.3750.0000.0000.0000.000
23B590GLU-1-0.758-0.83430.1529.5929.5920.0000.0000.0000.000
24B591MET0-0.054-0.00132.804-0.395-0.3950.0000.0000.0000.000
25B592LYS10.8560.91434.912-8.434-8.4340.0000.0000.0000.000
26B593PHE00.0410.01734.728-0.266-0.2660.0000.0000.0000.000
27B594SER0-0.003-0.02536.148-0.230-0.2300.0000.0000.0000.000
28B595GLN0-0.131-0.06238.480-0.331-0.3310.0000.0000.0000.000
29B596ILE0-0.047-0.01738.708-0.213-0.2130.0000.0000.0000.000
30B597LEU0-0.064-0.01338.016-0.194-0.1940.0000.0000.0000.000
31B654ILE0-0.033-0.02846.236-0.016-0.0160.0000.0000.0000.000
32B655PRO00.0330.01749.628-0.025-0.0250.0000.0000.0000.000
33B656ALA00.0990.04649.2240.1440.1440.0000.0000.0000.000
34B657PRO00.0270.00848.4230.1330.1330.0000.0000.0000.000
35B658GLU-1-0.950-0.97146.1956.7636.7630.0000.0000.0000.000
36B659LEU00.0160.00643.8770.2290.2290.0000.0000.0000.000
37B660LYS10.8700.92343.385-6.665-6.6650.0000.0000.0000.000
38B661LYS10.8920.94341.775-7.225-7.2250.0000.0000.0000.000
39B662LEU00.006-0.00140.3030.2570.2570.0000.0000.0000.000
40B663CYS0-0.046-0.02838.7650.2580.2580.0000.0000.0000.000
41B664MET00.0450.01737.7190.3150.3150.0000.0000.0000.000
42B665GLU-1-0.806-0.86936.4538.1358.1350.0000.0000.0000.000
43B666SER0-0.002-0.00434.5060.2970.2970.0000.0000.0000.000
44B667LEU0-0.0030.00532.8590.3680.3680.0000.0000.0000.000
45B668LEU00.0520.02132.0240.3790.3790.0000.0000.0000.000
46B669LEU0-0.018-0.00130.0620.4030.4030.0000.0000.0000.000
47B670TYR0-0.029-0.05128.4630.4200.4200.0000.0000.0000.000
48B671LEU0-0.021-0.01127.4180.4860.4860.0000.0000.0000.000
49B672LYS10.8240.91225.184-11.222-11.2220.0000.0000.0000.000
50B673SER0-0.044-0.05224.0900.6680.6680.0000.0000.0000.000
51B674LEU0-0.005-0.00822.5990.7910.7910.0000.0000.0000.000
52B675THR0-0.017-0.01221.9810.7760.7760.0000.0000.0000.000
53B676ILE0-0.019-0.01318.7770.8830.8830.0000.0000.0000.000
54B677LEU0-0.026-0.01117.9391.1941.1940.0000.0000.0000.000
55B678ALA00.001-0.00817.3711.1201.1200.0000.0000.0000.000
56B679SER0-0.021-0.00716.5371.3941.3940.0000.0000.0000.000
57B680SER00.0390.01613.4702.0442.0440.0000.0000.0000.000
58B681MET00.0000.01212.4612.3092.3090.0000.0000.0000.000
59B682LYS10.9670.98713.031-14.377-14.3770.0000.0000.0000.000
60B683LEU00.0160.0308.8821.4071.4070.0000.0000.0000.000
61B684THR0-0.005-0.0278.3753.8393.8390.0000.0000.0000.000
62B685SER0-0.041-0.0198.8752.3522.3520.0000.0000.0000.000
63B686LYS10.8740.94010.159-24.674-24.6740.0000.0000.0000.000
64B687TRP0-0.044-0.0321.882-24.037-23.7319.769-5.163-4.9120.037
65B688TRP0-0.018-0.0185.7355.7675.7670.0000.0000.0000.000
66B689TYR0-0.036-0.0327.5370.3780.3780.0000.0000.0000.000
67B690GLU-1-0.890-0.9418.03326.34926.3490.0000.0000.0000.000
68B691ASN0-0.087-0.0571.734-27.260-33.28016.670-5.960-4.6900.061
69B692GLU-1-0.824-0.8824.74438.97839.010-0.001-0.006-0.0250.000
70B693SER0-0.021-0.0265.7904.7634.7630.0000.0000.0000.000
71B694LYS10.8210.9076.217-39.872-39.8720.0000.0000.0000.000
72B695ASN0-0.024-0.0291.738-35.309-40.18614.870-5.795-4.1970.065
73B696CYS0-0.034-0.0045.1681.5311.530-0.001-0.0010.0040.000
74B697THR0-0.026-0.0077.248-4.185-4.1850.0000.0000.0000.000
75B698LEU00.0630.0219.156-1.286-1.2860.0000.0000.0000.000
76B699LYS10.8280.89211.686-22.024-22.0240.0000.0000.0000.000
77B700LEU00.0660.0316.826-1.662-1.6620.0000.0000.0000.000
78B701ASN00.0240.01310.881-2.596-2.5960.0000.0000.0000.000
79B702ILE00.0180.01113.423-1.221-1.2210.0000.0000.0000.000
80B703LEU0-0.006-0.00412.129-0.995-0.9950.0000.0000.0000.000
81B704VAL00.0440.02111.678-1.051-1.0510.0000.0000.0000.000
82B705GLN0-0.033-0.00914.775-2.016-2.0160.0000.0000.0000.000
83B706TRP00.0250.01318.020-0.772-0.7720.0000.0000.0000.000
84B707ILE00.002-0.00314.488-0.790-0.7900.0000.0000.0000.000
85B708ARG10.8640.90518.364-16.024-16.0240.0000.0000.0000.000
86B709ASP-1-0.886-0.92419.99913.33513.3350.0000.0000.0000.000
87B710ARG10.8540.91721.848-13.411-13.4110.0000.0000.0000.000
88B711PHE0-0.0240.00321.188-0.516-0.5160.0000.0000.0000.000
89B712ASN00.033-0.00323.254-0.368-0.3680.0000.0000.0000.000
90B713GLU-1-0.704-0.79126.01310.79010.7900.0000.0000.0000.000
91B714CYS0-0.060-0.04325.807-0.421-0.4210.0000.0000.0000.000
92B715LEU0-0.0040.00026.423-0.385-0.3850.0000.0000.0000.000
93B716ASP-1-0.905-0.94028.7859.9589.9580.0000.0000.0000.000
94B717LYS10.7600.84630.817-10.422-10.4220.0000.0000.0000.000
95B718ALA00.0090.00230.928-0.350-0.3500.0000.0000.0000.000
96B719GLU-1-0.815-0.87532.2969.2009.2000.0000.0000.0000.000
97B720PHE0-0.033-0.01034.658-0.388-0.3880.0000.0000.0000.000
98B721LEU0-0.018-0.01934.625-0.296-0.2960.0000.0000.0000.000
99B722ARG10.8360.88932.543-9.539-9.5390.0000.0000.0000.000
100B723LEU0-0.0210.00437.965-0.222-0.2220.0000.0000.0000.000
101B724LYS10.9490.97140.510-7.613-7.6130.0000.0000.0000.000
102B725LEU00.017-0.01039.203-0.201-0.2010.0000.0000.0000.000
103B726HIS0-0.0040.00140.552-0.280-0.2800.0000.0000.0000.000
104B727THR0-0.022-0.00444.128-0.187-0.1870.0000.0000.0000.000
105B728LEU0-0.008-0.00344.441-0.152-0.1520.0000.0000.0000.000
106B729ASN00.0240.00543.811-0.190-0.1900.0000.0000.0000.000
107B730GLN0-0.056-0.01347.778-0.060-0.0600.0000.0000.0000.000
108B731SER0-0.089-0.05050.167-0.152-0.1520.0000.0000.0000.000
109B732GLU-1-0.978-0.99150.3096.0496.0490.0000.0000.0000.000
110B733ASP-1-0.942-1.04452.1925.9155.9150.0000.0000.0000.000
111B734PRO00.0800.14353.3940.0430.0430.0000.0000.0000.000
112B735GLN0-0.126-0.09454.633-0.086-0.0860.0000.0000.0000.000
113B736VAL0-0.035-0.00852.2270.0690.0690.0000.0000.0000.000
114B737LEU0-0.012-0.01646.5440.1140.1140.0000.0000.0000.000
115B738ASP-1-0.971-0.98548.1336.4696.4690.0000.0000.0000.000
116B739ASP-1-0.886-0.94948.9496.0126.0120.0000.0000.0000.000
117B740GLU-1-0.885-0.91246.1696.8816.8810.0000.0000.0000.000
118B741PRO0-0.034-0.01244.8950.0800.0800.0000.0000.0000.000
119B742THR00.0200.00439.8830.0770.0770.0000.0000.0000.000
120B743ILE0-0.046-0.02137.5540.0590.0590.0000.0000.0000.000
121B744PHE00.0420.03035.6240.1060.1060.0000.0000.0000.000
122B745VAL00.0240.00330.488-0.055-0.0550.0000.0000.0000.000
123B746GLU-1-0.767-0.89930.9229.6449.6440.0000.0000.0000.000
124B747LYS10.8330.90232.256-7.828-7.8280.0000.0000.0000.000
125B748LEU00.0110.00733.891-0.062-0.0620.0000.0000.0000.000
126B749ILE0-0.002-0.00227.9250.0060.0060.0000.0000.0000.000
127B750TYR00.0240.01331.4820.0720.0720.0000.0000.0000.000
128B751ASP-1-0.781-0.88432.9438.0288.0280.0000.0000.0000.000
129B752ARG10.9380.98932.651-9.000-9.0000.0000.0000.0000.000
130B753ALA00.0280.00230.150-0.014-0.0140.0000.0000.0000.000
131B754LEU00.0300.02731.8250.0170.0170.0000.0000.0000.000
132B755ASP-1-0.851-0.90334.7247.7667.7660.0000.0000.0000.000
133B756ILE0-0.072-0.02531.261-0.157-0.1570.0000.0000.0000.000
134B757SER00.039-0.00931.6720.0090.0090.0000.0000.0000.000
135B758ARG10.7870.89134.094-7.815-7.8150.0000.0000.0000.000
136B759ASN00.003-0.01837.357-0.274-0.2740.0000.0000.0000.000
137B760ALA00.0150.01934.060-0.115-0.1150.0000.0000.0000.000
138B761ALA00.0540.03436.021-0.066-0.0660.0000.0000.0000.000
139B762ARG10.7890.86537.846-6.924-6.9240.0000.0000.0000.000
140B763LEU00.0370.01136.735-0.119-0.1190.0000.0000.0000.000
141B764GLU-1-0.753-0.83835.4208.4088.4080.0000.0000.0000.000
142B765MET0-0.088-0.04538.646-0.071-0.0710.0000.0000.0000.000
143B766GLU-1-0.828-0.87542.0976.6896.6890.0000.0000.0000.000
144B767GLY0-0.037-0.00641.766-0.081-0.0810.0000.0000.0000.000
145B768GLY00.0010.01039.8840.0320.0320.0000.0000.0000.000
146B769ASN00.0220.00934.7930.2980.2980.0000.0000.0000.000
147B770TYR00.0970.02233.5020.1400.1400.0000.0000.0000.000
148B771ASN00.0420.02330.078-0.067-0.0670.0000.0000.0000.000
149B772THR0-0.011-0.01530.6850.2500.2500.0000.0000.0000.000
150B773CYS0-0.041-0.01232.2420.0880.0880.0000.0000.0000.000
151B774GLU-1-0.805-0.88625.71011.34411.3440.0000.0000.0000.000
152B775LEU00.0210.01126.9460.3010.3010.0000.0000.0000.000
153B776ALA00.0050.02528.0260.2320.2320.0000.0000.0000.000
154B777TYR0-0.001-0.03628.9950.0490.0490.0000.0000.0000.000
155B778ALA00.0290.01324.0180.1660.1660.0000.0000.0000.000
156B779THR0-0.037-0.02924.8840.4290.4290.0000.0000.0000.000
157B780SER0-0.014-0.03126.6140.1320.1320.0000.0000.0000.000
158B781LEU0-0.027-0.00724.182-0.036-0.0360.0000.0000.0000.000
159B782TRP00.0280.00817.4600.4900.4900.0000.0000.0000.000
160B783MET0-0.058-0.02323.2530.1000.1000.0000.0000.0000.000
161B784LEU00.014-0.00526.081-0.018-0.0180.0000.0000.0000.000
162B785GLU-1-0.868-0.94119.63114.40414.4040.0000.0000.0000.000
163B786ILE0-0.043-0.01222.0580.2830.2830.0000.0000.0000.000
164B787LEU0-0.025-0.01623.3130.0250.0250.0000.0000.0000.000
165B788LEU0-0.055-0.02423.842-0.281-0.2810.0000.0000.0000.000
166B789ASP-1-0.846-0.90418.25016.05616.0560.0000.0000.0000.000
167B790GLU-1-0.899-0.94820.86711.73511.7350.0000.0000.0000.000
168B791HIS0-0.100-0.05216.2710.2470.2470.0000.0000.0000.000
169B792LEU0-0.084-0.05418.5560.1750.1750.0000.0000.0000.000
170B793SER0-0.042-0.00622.087-0.589-0.5890.0000.0000.0000.000
171B794SER0-0.009-0.00124.901-0.323-0.3230.0000.0000.0000.000
172B795ASN0-0.026-0.03526.8370.1770.1770.0000.0000.0000.000
173B796GLU-1-0.775-0.86626.53211.31611.3160.0000.0000.0000.000
174B797VAL0-0.046-0.01629.512-0.079-0.0790.0000.0000.0000.000
175B798TYR0-0.077-0.02732.255-0.370-0.3700.0000.0000.0000.000
176B799ASP-1-0.801-0.91330.42910.40310.4030.0000.0000.0000.000
177B800ASP-1-0.860-0.92630.5129.6999.6990.0000.0000.0000.000
178B801GLY0-0.072-0.02132.755-0.301-0.3010.0000.0000.0000.000
179B802TYR0-0.095-0.06030.475-0.117-0.1170.0000.0000.0000.000
180B803SER0-0.068-0.02927.0460.4300.4300.0000.0000.0000.000
181B804SER0-0.038-0.02826.9050.6640.6640.0000.0000.0000.000
182B805ASN00.0050.01126.054-0.660-0.6600.0000.0000.0000.000
183B806ILE00.0320.02327.7510.2660.2660.0000.0000.0000.000
184B807THR0-0.029-0.01927.054-0.011-0.0110.0000.0000.0000.000
185B808SER00.0310.01029.820-0.290-0.2900.0000.0000.0000.000
186B809LEU0-0.054-0.00829.189-0.235-0.2350.0000.0000.0000.000
187B810ASP-1-0.772-0.86732.6868.3558.3550.0000.0000.0000.000
188B811GLU-1-0.791-0.90130.52210.09310.0930.0000.0000.0000.000
189B812SER0-0.091-0.06633.2940.0710.0710.0000.0000.0000.000
190B813ASP-1-0.806-0.89533.4148.5618.5610.0000.0000.0000.000
191B814LYS10.8920.93428.114-9.973-9.9730.0000.0000.0000.000
192B815GLU-1-0.833-0.90030.2449.5409.5400.0000.0000.0000.000
193B816MET0-0.018-0.00932.352-0.012-0.0120.0000.0000.0000.000
194B817ILE00.014-0.00428.3650.0240.0240.0000.0000.0000.000
195B818ARG10.8550.91126.934-10.068-10.0680.0000.0000.0000.000
196B819LYS10.8340.92229.213-8.631-8.6310.0000.0000.0000.000
197B820TYR00.0260.00431.731-0.011-0.0110.0000.0000.0000.000
198B821VAL00.0520.03025.0410.0270.0270.0000.0000.0000.000
199B822SER0-0.040-0.01827.9180.1910.1910.0000.0000.0000.000
200B823SER0-0.079-0.03829.070-0.072-0.0720.0000.0000.0000.000
201B824ILE00.0260.01128.817-0.097-0.0970.0000.0000.0000.000
202B825ALA00.0510.02725.7140.0500.0500.0000.0000.0000.000
203B826ASN0-0.037-0.02727.4410.3020.3020.0000.0000.0000.000
204B827ARG10.8300.90530.080-8.675-8.6750.0000.0000.0000.000
205B828LEU00.0350.01825.242-0.132-0.1320.0000.0000.0000.000
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