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: M373Z

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2518681.378376
FMO2-HF: Nuclear repulsion 2430873.490294
FMO2-HF: Total energy -87807.888082
FMO2-MP2: Total energy -88059.085589


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.
-72.577-84.26948.363-19.526-17.1460.149
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 : -0.774 / q_NPA : -0.863
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].
3B570ASN00.018-0.0092.083-7.438-6.6926.297-3.300-3.743-0.009
4B571ILE00.0440.0353.815-7.280-6.5600.005-0.211-0.5150.001
5B572THR0-0.031-0.0165.431-4.799-4.7990.0000.0000.0000.000
6B573PRO00.0280.0087.185-2.833-2.8330.0000.0000.0000.000
7B574PHE00.0060.0138.164-2.214-2.2140.0000.0000.0000.000
8B575VAL00.0500.0289.540-2.214-2.2140.0000.0000.0000.000
9B576GLU-1-0.825-0.88711.67620.66520.6650.0000.0000.0000.000
10B577SER0-0.038-0.00313.650-1.582-1.5820.0000.0000.0000.000
11B578LEU00.0320.00912.941-1.227-1.2270.0000.0000.0000.000
12B579SER0-0.011-0.02415.213-1.090-1.0900.0000.0000.0000.000
13B580ALA0-0.034-0.00917.557-0.975-0.9750.0000.0000.0000.000
14B581LYS10.8200.90817.362-16.743-16.7430.0000.0000.0000.000
15B582ALA00.0230.01519.948-0.724-0.7240.0000.0000.0000.000
16B583PHE0-0.013-0.00621.463-0.628-0.6280.0000.0000.0000.000
17B584VAL0-0.0170.00323.418-0.665-0.6650.0000.0000.0000.000
18B585MET0-0.0070.00724.776-0.707-0.7070.0000.0000.0000.000
19B586TYR00.001-0.02925.484-0.364-0.3640.0000.0000.0000.000
20B587SER0-0.031-0.02727.175-0.490-0.4900.0000.0000.0000.000
21B588PHE0-0.056-0.03429.359-0.524-0.5240.0000.0000.0000.000
22B589ALA00.0520.02229.917-0.390-0.3900.0000.0000.0000.000
23B590GLU-1-0.743-0.83330.2209.7229.7220.0000.0000.0000.000
24B591MET0-0.068-0.00632.905-0.444-0.4440.0000.0000.0000.000
25B592LYS10.8550.91534.888-8.406-8.4060.0000.0000.0000.000
26B593PHE00.0330.01334.846-0.284-0.2840.0000.0000.0000.000
27B594SER0-0.025-0.03236.447-0.221-0.2210.0000.0000.0000.000
28B595GLN0-0.088-0.05138.790-0.325-0.3250.0000.0000.0000.000
29B596ILE0-0.035-0.00138.547-0.217-0.2170.0000.0000.0000.000
30B597LEU0-0.061-0.01438.541-0.170-0.1700.0000.0000.0000.000
31B654ILE0-0.019-0.02146.510-0.021-0.0210.0000.0000.0000.000
32B655PRO00.0280.01249.783-0.033-0.0330.0000.0000.0000.000
33B656ALA00.0860.05549.2430.1450.1450.0000.0000.0000.000
34B657PRO00.0390.01948.2060.1470.1470.0000.0000.0000.000
35B658GLU-1-0.946-0.97746.3436.8106.8100.0000.0000.0000.000
36B659LEU00.0120.00044.0640.2250.2250.0000.0000.0000.000
37B660LYS10.8590.91943.519-6.642-6.6420.0000.0000.0000.000
38B661LYS10.9000.94541.840-7.242-7.2420.0000.0000.0000.000
39B662LEU0-0.017-0.00740.5030.2560.2560.0000.0000.0000.000
40B663CYS0-0.055-0.03838.9080.2620.2620.0000.0000.0000.000
41B664MET00.0460.02237.7990.2970.2970.0000.0000.0000.000
42B665GLU-1-0.811-0.88836.4088.1648.1640.0000.0000.0000.000
43B666SER0-0.013-0.01134.5760.2910.2910.0000.0000.0000.000
44B667LEU00.0100.01032.9700.3550.3550.0000.0000.0000.000
45B668LEU00.0300.01432.0830.3910.3910.0000.0000.0000.000
46B669LEU0-0.0040.00430.0220.4090.4090.0000.0000.0000.000
47B670TYR0-0.033-0.04228.4240.4310.4310.0000.0000.0000.000
48B671LEU0-0.0100.00127.4670.4870.4870.0000.0000.0000.000
49B672LYS10.8280.90325.262-11.132-11.1320.0000.0000.0000.000
50B673SER0-0.031-0.04524.1650.6440.6440.0000.0000.0000.000
51B674LEU0-0.025-0.01522.7230.7840.7840.0000.0000.0000.000
52B675THR0-0.016-0.02421.9960.8220.8220.0000.0000.0000.000
53B676ILE0-0.014-0.00618.7890.8800.8800.0000.0000.0000.000
54B677LEU0-0.032-0.01217.9221.2451.2450.0000.0000.0000.000
55B678ALA00.0170.00217.4231.1471.1470.0000.0000.0000.000
56B679SER0-0.0130.00316.4001.2841.2840.0000.0000.0000.000
57B680SER00.0300.01113.3712.1222.1220.0000.0000.0000.000
58B681MET0-0.0040.00512.5262.3492.3490.0000.0000.0000.000
59B682LYS10.9540.97813.300-14.456-14.4560.0000.0000.0000.000
60B683LEU00.0020.0118.5541.2981.2980.0000.0000.0000.000
61B684THR0-0.010-0.0278.5663.6633.6630.0000.0000.0000.000
62B685SER0-0.035-0.0259.0542.5002.5000.0000.0000.0000.000
63B686LYS10.8370.90610.053-26.197-26.1970.0000.0000.0000.000
64B687TRP0-0.016-0.0301.780-23.256-26.03912.054-4.919-4.3520.047
65B688TRP0-0.007-0.0086.1293.6963.6960.0000.0000.0000.000
66B689TYR0-0.030-0.0227.586-1.459-1.4590.0000.0000.0000.000
67B690GLU-1-0.876-0.8977.96525.71525.7150.0000.0000.0000.000
68B691ASN0-0.080-0.0691.732-24.976-31.76917.174-5.962-4.4200.052
69B692GLU-1-0.860-0.8964.85237.47137.484-0.001-0.004-0.0070.000
70B693SER0-0.002-0.0206.1054.2604.2600.0000.0000.0000.000
71B694LYS10.8420.9216.391-39.310-39.3100.0000.0000.0000.000
72B695ASN0-0.012-0.0251.780-33.575-37.16112.835-5.129-4.1200.058
73B696CYS0-0.036-0.0055.1552.0702.061-0.001-0.0010.0110.000
74B697THR00.0040.0106.882-3.858-3.8580.0000.0000.0000.000
75B698LEU00.0400.0168.695-1.570-1.5700.0000.0000.0000.000
76B699LYS10.8430.89611.879-23.085-23.0850.0000.0000.0000.000
77B700LEU00.0540.0297.273-1.516-1.5160.0000.0000.0000.000
78B701ASN0-0.002-0.00411.354-2.781-2.7810.0000.0000.0000.000
79B702ILE00.0200.00813.404-1.223-1.2230.0000.0000.0000.000
80B703LEU0-0.0040.00512.624-1.046-1.0460.0000.0000.0000.000
81B704VAL00.0440.01912.019-1.043-1.0430.0000.0000.0000.000
82B705GLN0-0.039-0.01115.011-2.117-2.1170.0000.0000.0000.000
83B706TRP00.0330.01518.421-0.814-0.8140.0000.0000.0000.000
84B707ILE0-0.001-0.00614.759-0.813-0.8130.0000.0000.0000.000
85B708ARG10.8640.90318.739-15.995-15.9950.0000.0000.0000.000
86B709ASP-1-0.894-0.92620.45313.33113.3310.0000.0000.0000.000
87B710ARG10.8580.92122.098-13.616-13.6160.0000.0000.0000.000
88B711PHE0-0.0240.00121.420-0.487-0.4870.0000.0000.0000.000
89B712ASN00.0450.00023.488-0.384-0.3840.0000.0000.0000.000
90B713GLU-1-0.754-0.82026.30510.91010.9100.0000.0000.0000.000
91B714CYS0-0.054-0.04026.029-0.424-0.4240.0000.0000.0000.000
92B715LEU0-0.0030.01126.656-0.336-0.3360.0000.0000.0000.000
93B716ASP-1-0.889-0.94129.14110.01710.0170.0000.0000.0000.000
94B717LYS10.7610.85730.928-10.539-10.5390.0000.0000.0000.000
95B718ALA00.0260.01131.239-0.337-0.3370.0000.0000.0000.000
96B719GLU-1-0.829-0.88032.6689.2319.2310.0000.0000.0000.000
97B720PHE0-0.033-0.01235.072-0.370-0.3700.0000.0000.0000.000
98B721LEU0-0.009-0.00934.848-0.304-0.3040.0000.0000.0000.000
99B722ARG10.8560.89132.836-9.523-9.5230.0000.0000.0000.000
100B723LEU0-0.0110.00438.341-0.221-0.2210.0000.0000.0000.000
101B724LYS10.9310.97840.935-7.673-7.6730.0000.0000.0000.000
102B725LEU00.021-0.00439.004-0.192-0.1920.0000.0000.0000.000
103B726HIS0-0.0100.00040.786-0.257-0.2570.0000.0000.0000.000
104B727THR0-0.027-0.02344.318-0.185-0.1850.0000.0000.0000.000
105B728LEU0-0.0060.00144.581-0.147-0.1470.0000.0000.0000.000
106B729ASN00.0220.00043.988-0.221-0.2210.0000.0000.0000.000
107B730GLN0-0.058-0.01947.864-0.041-0.0410.0000.0000.0000.000
108B731SER0-0.090-0.03950.395-0.143-0.1430.0000.0000.0000.000
109B732GLU-1-0.937-0.98249.9586.1106.1100.0000.0000.0000.000
110B733ASP-1-0.938-0.97252.6125.8815.8810.0000.0000.0000.000
111B734PRO0-0.036-0.02053.4590.0620.0620.0000.0000.0000.000
112B735GLN0-0.082-0.04754.451-0.081-0.0810.0000.0000.0000.000
113B736VAL00.0130.01951.6720.0980.0980.0000.0000.0000.000
114B737LEU0-0.038-0.03446.3130.1040.1040.0000.0000.0000.000
115B738ASP-1-0.957-0.97247.7746.5246.5240.0000.0000.0000.000
116B739ASP-1-0.869-0.93549.0555.9905.9900.0000.0000.0000.000
117B740GLU-1-0.868-0.91146.0876.8716.8710.0000.0000.0000.000
118B741PRO0-0.065-0.02144.9810.1050.1050.0000.0000.0000.000
119B742THR00.019-0.00239.5230.0780.0780.0000.0000.0000.000
120B743ILE0-0.031-0.01837.5170.0770.0770.0000.0000.0000.000
121B744PHE00.0380.02935.6700.1600.1600.0000.0000.0000.000
122B745VAL00.0160.00930.666-0.035-0.0350.0000.0000.0000.000
123B746GLU-1-0.750-0.89030.8659.6659.6650.0000.0000.0000.000
124B747LYS10.8360.90132.070-7.893-7.8930.0000.0000.0000.000
125B748LEU00.0050.00933.945-0.051-0.0510.0000.0000.0000.000
126B749ILE0-0.005-0.00228.067-0.006-0.0060.0000.0000.0000.000
127B750TYR00.0480.01831.5860.0850.0850.0000.0000.0000.000
128B751ASP-1-0.811-0.89233.0198.0678.0670.0000.0000.0000.000
129B752ARG10.8840.93533.111-8.934-8.9340.0000.0000.0000.000
130B753ALA00.0480.02830.2810.0200.0200.0000.0000.0000.000
131B754LEU00.0150.02031.9470.0160.0160.0000.0000.0000.000
132B755ASP-1-0.858-0.89234.7697.9347.9340.0000.0000.0000.000
133B756ILE0-0.012-0.00131.419-0.172-0.1720.0000.0000.0000.000
134B757SER00.035-0.01031.534-0.023-0.0230.0000.0000.0000.000
135B758ARG10.7900.87933.971-7.875-7.8750.0000.0000.0000.000
136B759ASN00.0220.01137.416-0.296-0.2960.0000.0000.0000.000
137B760ALA00.0110.01733.652-0.114-0.1140.0000.0000.0000.000
138B761ALA00.0480.02235.684-0.065-0.0650.0000.0000.0000.000
139B762ARG10.7820.86337.476-7.001-7.0010.0000.0000.0000.000
140B763LEU00.0360.01236.320-0.138-0.1380.0000.0000.0000.000
141B764GLU-1-0.733-0.82134.9358.5468.5460.0000.0000.0000.000
142B765MET0-0.077-0.04038.271-0.070-0.0700.0000.0000.0000.000
143B766GLU-1-0.828-0.87841.6766.7726.7720.0000.0000.0000.000
144B767GLY0-0.040-0.00641.054-0.089-0.0890.0000.0000.0000.000
145B768GLY00.0220.01439.8110.0170.0170.0000.0000.0000.000
146B769ASN0-0.001-0.01234.3180.3080.3080.0000.0000.0000.000
147B770TYR00.1050.03233.2710.1590.1590.0000.0000.0000.000
148B771ASN00.0330.02329.717-0.063-0.0630.0000.0000.0000.000
149B772THR00.006-0.00330.2390.2920.2920.0000.0000.0000.000
150B773CYS0-0.058-0.01432.0530.0680.0680.0000.0000.0000.000
151B774GLU-1-0.778-0.88425.60711.41311.4130.0000.0000.0000.000
152B775LEU00.0110.01227.0390.2820.2820.0000.0000.0000.000
153B776ALA00.0090.02227.8720.2380.2380.0000.0000.0000.000
154B777TYR0-0.009-0.04528.7570.0080.0080.0000.0000.0000.000
155B778ALA00.0140.00023.8520.1640.1640.0000.0000.0000.000
156B779THR0-0.027-0.02024.7610.4150.4150.0000.0000.0000.000
157B780SER0-0.013-0.02926.7290.1240.1240.0000.0000.0000.000
158B781LEU0-0.038-0.01223.956-0.016-0.0160.0000.0000.0000.000
159B782TRP00.0540.02317.3610.4630.4630.0000.0000.0000.000
160B783MET0-0.053-0.01923.4010.0810.0810.0000.0000.0000.000
161B784LEU0-0.002-0.01126.470-0.085-0.0850.0000.0000.0000.000
162B785GLU-1-0.856-0.93519.33814.84814.8480.0000.0000.0000.000
163B786ILE0-0.051-0.01722.2260.2280.2280.0000.0000.0000.000
164B787LEU0-0.026-0.00723.682-0.107-0.1070.0000.0000.0000.000
165B788LEU0-0.058-0.03524.071-0.339-0.3390.0000.0000.0000.000
166B789ASP-1-0.805-0.89218.52316.18116.1810.0000.0000.0000.000
167B790GLU-1-0.852-0.91021.37911.49811.4980.0000.0000.0000.000
168B791HIS0-0.088-0.04416.8170.2170.2170.0000.0000.0000.000
169B792LEU0-0.088-0.04618.4910.1470.1470.0000.0000.0000.000
170B793SER00.0000.00122.163-0.549-0.5490.0000.0000.0000.000
171B794SER0-0.016-0.00924.987-0.352-0.3520.0000.0000.0000.000
172B795ASN0-0.042-0.04426.7950.1980.1980.0000.0000.0000.000
173B796GLU-1-0.794-0.87126.51611.36311.3630.0000.0000.0000.000
174B797VAL0-0.051-0.02929.415-0.092-0.0920.0000.0000.0000.000
175B798TYR0-0.065-0.02532.138-0.396-0.3960.0000.0000.0000.000
176B799ASP-1-0.776-0.89930.10610.46310.4630.0000.0000.0000.000
177B800ASP-1-0.874-0.92730.8229.5929.5920.0000.0000.0000.000
178B801GLY0-0.059-0.01032.913-0.299-0.2990.0000.0000.0000.000
179B802TYR0-0.090-0.05430.602-0.138-0.1380.0000.0000.0000.000
180B803SER0-0.080-0.03526.6110.4290.4290.0000.0000.0000.000
181B804SER0-0.063-0.04826.7090.6430.6430.0000.0000.0000.000
182B805ASN00.0230.01225.599-0.667-0.6670.0000.0000.0000.000
183B806ILE00.0270.02127.6200.2770.2770.0000.0000.0000.000
184B807THR0-0.070-0.04226.936-0.097-0.0970.0000.0000.0000.000
185B808SER00.0180.00729.599-0.298-0.2980.0000.0000.0000.000
186B809LEU0-0.049-0.00329.422-0.248-0.2480.0000.0000.0000.000
187B810ASP-1-0.756-0.85032.3578.5118.5110.0000.0000.0000.000
188B811GLU-1-0.788-0.90130.10310.32310.3230.0000.0000.0000.000
189B812SER0-0.096-0.07233.1360.0340.0340.0000.0000.0000.000
190B813ASP-1-0.809-0.90333.4948.6468.6460.0000.0000.0000.000
191B814LYS10.8760.93628.188-10.202-10.2020.0000.0000.0000.000
192B815GLU-1-0.820-0.89530.2789.6679.6670.0000.0000.0000.000
193B816MET0-0.027-0.00632.237-0.092-0.0920.0000.0000.0000.000
194B817ILE00.0170.00028.4380.0280.0280.0000.0000.0000.000
195B818ARG10.8390.89526.904-10.212-10.2120.0000.0000.0000.000
196B819LYS10.8120.91329.282-8.806-8.8060.0000.0000.0000.000
197B820TYR00.0390.02231.776-0.021-0.0210.0000.0000.0000.000
198B821VAL00.0640.03624.9930.0110.0110.0000.0000.0000.000
199B822SER0-0.022-0.02327.9010.1840.1840.0000.0000.0000.000
200B823SER0-0.098-0.05328.963-0.093-0.0930.0000.0000.0000.000
201B824ILE00.0250.00828.620-0.108-0.1080.0000.0000.0000.000
202B825ALA00.0500.03125.5880.0930.0930.0000.0000.0000.000
203B826ASN0-0.019-0.01527.2660.3620.3620.0000.0000.0000.000
204B827ARG10.8120.90029.880-8.794-8.7940.0000.0000.0000.000
205B828LEU00.0400.02324.954-0.135-0.1350.0000.0000.0000.000
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