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: 9GY72

Calculation Name: 4P1N-B-Xray322

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: 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 216
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2524598.617799
FMO2-HF: Nuclear repulsion 2436470.551571
FMO2-HF: Total energy -88128.066228
FMO2-MP2: Total energy -88380.12216


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:567:ACE )


Summations of interaction energy for fragment #1(B:567:ACE )
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.
2.6314.1050.847-1.088-1.2350
Interaction energy analysis for fragmet #1(B:567:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.005
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].
3B569SER 0-0.024-0.0163.8711.1872.019-0.004-0.344-0.4840.000
4B570ASN 0-0.038-0.0332.5720.0930.4370.849-0.630-0.5640.000
5B571ILE 00.0480.0344.3800.0820.1790.000-0.021-0.0770.000
6B572THR 00.0150.0025.5100.0810.0810.0000.0000.0000.000
7B573PRO 00.0370.0227.2360.0090.0090.0000.0000.0000.000
8B574PHE 00.0020.0066.5210.0420.0420.0000.0000.0000.000
9B575VAL 00.0210.0139.172-0.042-0.0420.0000.0000.0000.000
10B576GLU -1-0.901-0.96711.4200.0550.0550.0000.0000.0000.000
11B577SER 0-0.029-0.00312.392-0.009-0.0090.0000.0000.0000.000
12B578LEU 00.0280.01212.137-0.017-0.0170.0000.0000.0000.000
13B579SER 00.002-0.00915.228-0.026-0.0260.0000.0000.0000.000
14B580ALA 0-0.0090.00417.082-0.012-0.0120.0000.0000.0000.000
15B581LYS 10.9600.98515.337-0.211-0.2110.0000.0000.0000.000
16B582ALA 0-0.0030.00319.302-0.009-0.0090.0000.0000.0000.000
17B583PHE 0-0.014-0.00121.086-0.007-0.0070.0000.0000.0000.000
18B584VAL 00.0040.01422.930-0.005-0.0050.0000.0000.0000.000
19B585MET 0-0.0110.00624.095-0.004-0.0040.0000.0000.0000.000
20B586TYR 0-0.002-0.04225.160-0.004-0.0040.0000.0000.0000.000
21B587SER 0-0.017-0.03326.872-0.005-0.0050.0000.0000.0000.000
22B588PHE 0-0.069-0.02828.730-0.002-0.0020.0000.0000.0000.000
23B589ALA 00.0620.01229.713-0.002-0.0020.0000.0000.0000.000
24B590GLU -1-0.778-0.85930.7050.0020.0020.0000.0000.0000.000
25B591MET 0-0.061-0.01332.960-0.002-0.0020.0000.0000.0000.000
26B592LYS 10.8510.89834.646-0.028-0.0280.0000.0000.0000.000
27B593PHE 00.0270.01534.893-0.002-0.0020.0000.0000.0000.000
28B594SER 00.027-0.00636.823-0.002-0.0020.0000.0000.0000.000
29B595GLN 0-0.111-0.04138.715-0.001-0.0010.0000.0000.0000.000
30B596ILE 0-0.038-0.01038.9530.0000.0000.0000.0000.0000.000
31B597LEU 0-0.086-0.03038.994-0.002-0.0020.0000.0000.0000.000
32B598NME 00.0020.00542.8520.0010.0010.0000.0000.0000.000
33B653ACE 0-0.011-0.02052.4430.0000.0000.0000.0000.0000.000
34B654ILE 0-0.008-0.01446.5840.0000.0000.0000.0000.0000.000
35B655PRO 00.0170.02349.097-0.001-0.0010.0000.0000.0000.000
36B656ALA 00.0880.04248.8900.0010.0010.0000.0000.0000.000
37B657PRO 00.0350.01547.9840.0000.0000.0000.0000.0000.000
38B658GLU -1-0.936-0.97145.3680.0160.0160.0000.0000.0000.000
39B659LEU 00.0020.00144.1470.0010.0010.0000.0000.0000.000
40B660LYS 10.9040.92943.068-0.014-0.0140.0000.0000.0000.000
41B661LYS 10.9350.98541.110-0.024-0.0240.0000.0000.0000.000
42B662LEU 00.0140.00939.7390.0020.0020.0000.0000.0000.000
43B663CYS 0-0.039-0.02138.3760.0000.0000.0000.0000.0000.000
44B664MET 00.0220.00637.3880.0000.0000.0000.0000.0000.000
45B665GLU -1-0.825-0.90335.6670.0280.0280.0000.0000.0000.000
46B666SER 0-0.006-0.00833.9190.0010.0010.0000.0000.0000.000
47B667LEU 00.0010.00432.7160.0000.0000.0000.0000.0000.000
48B668LEU 00.0380.01631.6890.0010.0010.0000.0000.0000.000
49B669LEU 0-0.0190.00029.2950.0040.0040.0000.0000.0000.000
50B670TYR 0-0.022-0.05027.9980.0020.0020.0000.0000.0000.000
51B671LEU 0-0.028-0.01427.316-0.002-0.0020.0000.0000.0000.000
52B672LYS 10.8520.92523.730-0.061-0.0610.0000.0000.0000.000
53B673SER 0-0.041-0.04523.5190.0060.0060.0000.0000.0000.000
54B674LEU 0-0.003-0.01122.458-0.001-0.0010.0000.0000.0000.000
55B675THR 0-0.027-0.03520.829-0.008-0.0080.0000.0000.0000.000
56B676ILE 0-0.016-0.01518.1180.0040.0040.0000.0000.0000.000
57B677LEU 0-0.017-0.00517.618-0.001-0.0010.0000.0000.0000.000
58B678ALA 00.004-0.01217.817-0.015-0.0150.0000.0000.0000.000
59B679SER 0-0.038-0.01315.292-0.015-0.0150.0000.0000.0000.000
60B680SER 00.0630.02713.4660.0050.0050.0000.0000.0000.000
61B681MET 0-0.021-0.00313.129-0.040-0.0400.0000.0000.0000.000
62B682LYS 10.9570.98314.217-0.050-0.0500.0000.0000.0000.000
63B683LEU 00.0170.0298.257-0.034-0.0340.0000.0000.0000.000
64B684THR 0-0.009-0.0249.411-0.098-0.0980.0000.0000.0000.000
65B685SER 0-0.047-0.02110.860-0.111-0.1110.0000.0000.0000.000
66B686LYS 10.9450.9749.889-0.017-0.0170.0000.0000.0000.000
67B687TRP 0-0.003-0.0134.9340.2760.2760.0000.0000.0000.000
68B688TRP 0-0.036-0.0288.191-0.198-0.1980.0000.0000.0000.000
69B689TYR 0-0.033-0.02111.034-0.015-0.0150.0000.0000.0000.000
70B690GLU -1-0.872-0.9348.569-0.230-0.2300.0000.0000.0000.000
71B691ASN 0-0.083-0.0363.7730.5820.7830.002-0.093-0.1100.000
72B692GLU -1-0.864-0.9348.189-0.458-0.4580.0000.0000.0000.000
73B693SER 00.0430.06111.832-0.072-0.0720.0000.0000.0000.000
74B694LYS 10.7570.8547.0351.0241.0240.0000.0000.0000.000
75B695ASN 0-0.002-0.00110.3650.1330.1330.0000.0000.0000.000
76B696CYS 00.0230.01611.592-0.037-0.0370.0000.0000.0000.000
77B697THR 0-0.036-0.00511.0060.0570.0570.0000.0000.0000.000
78B698LEU 00.0790.02813.4760.0250.0250.0000.0000.0000.000
79B699LYS 10.9360.95914.2720.0240.0240.0000.0000.0000.000
80B700LEU 00.0250.0259.8830.0310.0310.0000.0000.0000.000
81B701ASN 00.0380.00813.5500.0330.0330.0000.0000.0000.000
82B702ILE 0-0.0070.00716.6120.0200.0200.0000.0000.0000.000
83B703LEU 00.0090.00213.5880.0140.0140.0000.0000.0000.000
84B704VAL 00.0330.01514.1570.0190.0190.0000.0000.0000.000
85B705GLN 0-0.059-0.02716.9930.0210.0210.0000.0000.0000.000
86B706TRP 00.0360.02619.4090.0110.0110.0000.0000.0000.000
87B707ILE 0-0.002-0.00415.6000.0100.0100.0000.0000.0000.000
88B708ARG 10.9340.96719.8760.0880.0880.0000.0000.0000.000
89B709ASP -1-0.928-0.96621.836-0.046-0.0460.0000.0000.0000.000
90B710ARG 10.8640.92122.8630.0220.0220.0000.0000.0000.000
91B711PHE 0-0.0130.00421.9650.0060.0060.0000.0000.0000.000
92B712ASN 00.031-0.00324.3390.0040.0040.0000.0000.0000.000
93B713GLU -1-0.727-0.78827.494-0.004-0.0040.0000.0000.0000.000
94B714CYS 0-0.064-0.04126.5690.0060.0060.0000.0000.0000.000
95B715LEU 00.005-0.00127.7430.0040.0040.0000.0000.0000.000
96B716ASP -1-0.910-0.94129.615-0.018-0.0180.0000.0000.0000.000
97B717LYS 10.7760.86332.0320.0030.0030.0000.0000.0000.000
98B718ALA 00.0120.00131.2430.0020.0020.0000.0000.0000.000
99B719GLU -1-0.830-0.91233.152-0.004-0.0040.0000.0000.0000.000
100B720PHE 0-0.041-0.01235.2950.0010.0010.0000.0000.0000.000
101B721LEU 0-0.017-0.01834.7190.0010.0010.0000.0000.0000.000
102B722ARG 10.8580.93332.9500.0020.0020.0000.0000.0000.000
103B723LEU 0-0.0180.00438.1260.0000.0000.0000.0000.0000.000
104B724LYS 10.9550.97040.923-0.004-0.0040.0000.0000.0000.000
105B725LEU 00.012-0.01339.0190.0010.0010.0000.0000.0000.000
106B726HIS 0-0.0050.00440.7300.0010.0010.0000.0000.0000.000
107B727THR 0-0.0190.00344.1720.0000.0000.0000.0000.0000.000
108B728LEU 0-0.024-0.02444.2690.0000.0000.0000.0000.0000.000
109B729ASN 00.0710.05143.3260.0010.0010.0000.0000.0000.000
110B730GLN 0-0.023-0.00547.4720.0000.0000.0000.0000.0000.000
111B731SER 0-0.083-0.04450.137-0.001-0.0010.0000.0000.0000.000
112B732GLU -1-0.951-0.98050.5510.0080.0080.0000.0000.0000.000
113B733ASP -1-0.961-0.98451.8270.0080.0080.0000.0000.0000.000
114B734PRO 00.0510.03949.8570.0010.0010.0000.0000.0000.000
115B735GLN 0-0.096-0.08350.8440.0000.0000.0000.0000.0000.000
116B736VAL 00.0100.01451.1180.0000.0000.0000.0000.0000.000
117B737LEU 0-0.072-0.00645.9760.0010.0010.0000.0000.0000.000
118B738ASP -1-0.992-0.99847.0090.0170.0170.0000.0000.0000.000
119B739ASP -1-0.885-0.94147.5160.0170.0170.0000.0000.0000.000
120B740GLU -1-0.968-0.97145.2940.0170.0170.0000.0000.0000.000
121B741PRO 0-0.033-0.00843.2960.0010.0010.0000.0000.0000.000
122B742THR 00.0280.00238.180-0.001-0.0010.0000.0000.0000.000
123B743ILE 0-0.061-0.02836.2330.0020.0020.0000.0000.0000.000
124B744PHE 00.0480.03233.802-0.001-0.0010.0000.0000.0000.000
125B745VAL 00.023-0.00129.1560.0000.0000.0000.0000.0000.000
126B746GLU -1-0.791-0.91528.9260.0560.0560.0000.0000.0000.000
127B747LYS 10.9080.96730.590-0.036-0.0360.0000.0000.0000.000
128B748LEU 0-0.0010.00032.4000.0000.0000.0000.0000.0000.000
129B749ILE 00.0010.00126.6160.0000.0000.0000.0000.0000.000
130B750TYR 00.0150.00730.0480.0040.0040.0000.0000.0000.000
131B751ASP -1-0.822-0.92631.3030.0460.0460.0000.0000.0000.000
132B752ARG 10.9270.99131.357-0.041-0.0410.0000.0000.0000.000
133B753ALA 00.018-0.00528.6940.0000.0000.0000.0000.0000.000
134B754LEU 00.0290.03330.4420.0020.0020.0000.0000.0000.000
135B755ASP -1-0.862-0.90433.2170.0400.0400.0000.0000.0000.000
136B756ILE 0-0.069-0.02630.202-0.003-0.0030.0000.0000.0000.000
137B757SER 00.038-0.00930.2900.0010.0010.0000.0000.0000.000
138B758ARG 10.8370.91432.819-0.042-0.0420.0000.0000.0000.000
139B759ASN 0-0.012-0.02436.195-0.003-0.0030.0000.0000.0000.000
140B760ALA 0-0.0020.00433.110-0.002-0.0020.0000.0000.0000.000
141B761ALA 00.0420.03035.067-0.001-0.0010.0000.0000.0000.000
142B762ARG 10.8080.88736.799-0.032-0.0320.0000.0000.0000.000
143B763LEU 00.0360.00736.470-0.002-0.0020.0000.0000.0000.000
144B764GLU -1-0.792-0.90034.5670.0570.0570.0000.0000.0000.000
145B765MET 0-0.094-0.04237.921-0.001-0.0010.0000.0000.0000.000
146B766GLU -1-0.863-0.90941.3010.0280.0280.0000.0000.0000.000
147B767GLY 0-0.0230.00041.315-0.002-0.0020.0000.0000.0000.000
148B768GLY 0-0.0070.00739.403-0.001-0.0010.0000.0000.0000.000
149B769ASN 00.008-0.01434.7220.0040.0040.0000.0000.0000.000
150B770TYR 00.1180.03233.1040.0020.0020.0000.0000.0000.000
151B771ASN 00.0770.04130.5420.0070.0070.0000.0000.0000.000
152B772THR 0-0.054-0.01730.3450.0020.0020.0000.0000.0000.000
153B773CYS 0-0.033-0.01431.6760.0020.0020.0000.0000.0000.000
154B774GLU -1-0.854-0.92425.5080.0830.0830.0000.0000.0000.000
155B775LEU 00.0220.00826.1590.0070.0070.0000.0000.0000.000
156B776ALA 00.0040.02327.2440.0030.0030.0000.0000.0000.000
157B777TYR 0-0.005-0.02327.9610.0030.0030.0000.0000.0000.000
158B778ALA 00.0210.01123.1460.0070.0070.0000.0000.0000.000
159B779THR 0-0.040-0.03323.7590.0060.0060.0000.0000.0000.000
160B780SER 0-0.026-0.04325.4560.0010.0010.0000.0000.0000.000
161B781LEU 0-0.020-0.00422.6920.0010.0010.0000.0000.0000.000
162B782TRP 00.0330.01216.5300.0130.0130.0000.0000.0000.000
163B783MET 0-0.086-0.03721.9400.0010.0010.0000.0000.0000.000
164B784LEU 00.020-0.00224.5280.0000.0000.0000.0000.0000.000
165B785GLU -1-0.931-0.97718.7310.1870.1870.0000.0000.0000.000
166B786ILE 0-0.049-0.01420.6420.0070.0070.0000.0000.0000.000
167B787LEU 0-0.032-0.02521.646-0.001-0.0010.0000.0000.0000.000
168B788LEU 0-0.047-0.01721.701-0.002-0.0020.0000.0000.0000.000
169B789ASP -1-0.847-0.90416.2410.2230.2230.0000.0000.0000.000
170B790GLU -1-0.896-0.93818.6920.1180.1180.0000.0000.0000.000
171B791HIS 0-0.095-0.05413.830-0.004-0.0040.0000.0000.0000.000
172B792LEU 0-0.097-0.05617.244-0.020-0.0200.0000.0000.0000.000
173B793SER 0-0.041-0.00920.403-0.017-0.0170.0000.0000.0000.000
174B794SER 00.0070.00523.127-0.008-0.0080.0000.0000.0000.000
175B795ASN 0-0.025-0.03525.110-0.006-0.0060.0000.0000.0000.000
176B796GLU -1-0.784-0.84925.2200.0460.0460.0000.0000.0000.000
177B797VAL 0-0.052-0.01628.426-0.005-0.0050.0000.0000.0000.000
178B798TYR 0-0.070-0.02230.892-0.003-0.0030.0000.0000.0000.000
179B799ASP -1-0.829-0.91430.0610.0220.0220.0000.0000.0000.000
180B800ASP -1-0.884-0.96129.2860.0350.0350.0000.0000.0000.000
181B801GLY 0-0.063-0.01831.433-0.001-0.0010.0000.0000.0000.000
182B802TYR 0-0.112-0.06629.272-0.005-0.0050.0000.0000.0000.000
183B803SER 0-0.055-0.05226.096-0.002-0.0020.0000.0000.0000.000
184B804SER 0-0.0290.02425.6850.0020.0020.0000.0000.0000.000
185B805ASN 00.0140.00624.982-0.005-0.0050.0000.0000.0000.000
186B806ILE 00.0510.03526.1690.0070.0070.0000.0000.0000.000
187B807THR 0-0.030-0.02125.161-0.002-0.0020.0000.0000.0000.000
188B808SER 00.0180.00527.935-0.004-0.0040.0000.0000.0000.000
189B809LEU 0-0.057-0.01227.067-0.002-0.0020.0000.0000.0000.000
190B810ASP -1-0.781-0.85330.5700.0640.0640.0000.0000.0000.000
191B811GLU -1-0.899-0.98228.3620.1040.1040.0000.0000.0000.000
192B812SER 0-0.097-0.07130.9160.0040.0040.0000.0000.0000.000
193B813ASP -1-0.800-0.90531.3240.0640.0640.0000.0000.0000.000
194B814LYS 10.9230.96225.885-0.090-0.0900.0000.0000.0000.000
195B815GLU -1-0.903-0.95927.9660.1100.1100.0000.0000.0000.000
196B816MET 0-0.011-0.00329.9970.0010.0010.0000.0000.0000.000
197B817ILE 00.001-0.00926.2540.0010.0010.0000.0000.0000.000
198B818ARG 10.9530.98123.987-0.123-0.1230.0000.0000.0000.000
199B819LYS 10.8820.95827.032-0.080-0.0800.0000.0000.0000.000
200B820TYR 00.0230.00129.8270.0010.0010.0000.0000.0000.000
201B821VAL 00.0540.03223.132-0.001-0.0010.0000.0000.0000.000
202B822SER 0-0.023-0.00726.2360.0060.0060.0000.0000.0000.000
203B823SER 0-0.088-0.04027.287-0.003-0.0030.0000.0000.0000.000
204B824ILE 00.0340.01727.449-0.003-0.0030.0000.0000.0000.000
205B825ALA 00.0420.02224.366-0.001-0.0010.0000.0000.0000.000
206B826ASN 0-0.062-0.04326.0690.0030.0030.0000.0000.0000.000
207B827ARG 10.8510.93828.777-0.068-0.0680.0000.0000.0000.000
208B828LEU 00.0290.01624.241-0.004-0.0040.0000.0000.0000.000
209B829LYS 10.9560.97323.264-0.149-0.1490.0000.0000.0000.000
210B830ALA 0-0.0030.01227.744-0.004-0.0040.0000.0000.0000.000
211B831LEU 0-0.054-0.02530.412-0.004-0.0040.0000.0000.0000.000
212B832LYS 10.8740.91923.008-0.104-0.1040.0000.0000.0000.000
213B833SER 0-0.031-0.01529.291-0.001-0.0010.0000.0000.0000.000
214B834LYS 10.8320.91831.281-0.056-0.0560.0000.0000.0000.000
215B835MET 0-0.090-0.02729.893-0.005-0.0050.0000.0000.0000.000
216B836SER -1-0.952-0.95029.7030.0550.0550.0000.0000.0000.000