Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: GN161

Calculation Name: 4H63-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H63

Chain ID: H

ChEMBL ID:

UniProt ID: Q9P6Q0

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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1332054.220896
FMO2-HF: Nuclear repulsion 1261432.05503
FMO2-HF: Total energy -70622.165866
FMO2-MP2: Total energy -70830.251963


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(H:3:ASP)


Summations of interaction energy for fragment #1(H:3: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.
56.91762.6031.623-2.863-4.4440.008
Interaction energy analysis for fragmet #1(H:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.881 / q_NPA : -0.944
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].
3H5SER0-0.047-0.0232.803-9.520-6.0710.521-1.793-2.1770.004
4H6THR0-0.009-0.0152.233-8.650-6.6571.103-1.031-2.0640.004
5H7GLU-1-0.850-0.9144.63631.60831.852-0.001-0.039-0.2030.000
6H8LYS11.0021.0006.903-31.188-31.1880.0000.0000.0000.000
7H9THR0-0.065-0.0357.286-2.244-2.2440.0000.0000.0000.000
8H10VAL00.0270.0198.542-2.380-2.3800.0000.0000.0000.000
9H11GLU-1-0.917-0.96010.75620.18920.1890.0000.0000.0000.000
10H12SER0-0.052-0.03012.088-1.567-1.5670.0000.0000.0000.000
11H13LEU00.017-0.00511.702-1.449-1.4490.0000.0000.0000.000
12H14GLU-1-0.801-0.86014.88714.09814.0980.0000.0000.0000.000
13H15ALA0-0.044-0.01516.793-1.159-1.1590.0000.0000.0000.000
14H16ILE00.0270.01216.163-1.044-1.0440.0000.0000.0000.000
15H17ARG10.8100.87418.785-14.706-14.7060.0000.0000.0000.000
16H18HIS00.0050.00420.577-0.454-0.4540.0000.0000.0000.000
17H19ARG10.9050.95521.575-13.084-13.0840.0000.0000.0000.000
18H20ILE00.0280.01521.260-0.567-0.5670.0000.0000.0000.000
19H21ALA0-0.005-0.00424.715-0.462-0.4620.0000.0000.0000.000
20H22GLN0-0.017-0.01226.537-0.156-0.1560.0000.0000.0000.000
21H23ILE00.0220.01627.643-0.432-0.4320.0000.0000.0000.000
22H24VAL00.0460.03728.355-0.413-0.4130.0000.0000.0000.000
23H25GLN0-0.0160.00530.746-0.264-0.2640.0000.0000.0000.000
24H26SER0-0.051-0.04132.681-0.336-0.3360.0000.0000.0000.000
25H27LEU00.014-0.00131.750-0.299-0.2990.0000.0000.0000.000
26H28THR0-0.015-0.02234.265-0.281-0.2810.0000.0000.0000.000
27H29HIS0-0.0090.00736.663-0.199-0.1990.0000.0000.0000.000
28H30PHE0-0.001-0.00438.355-0.252-0.2520.0000.0000.0000.000
29H31LEU0-0.001-0.00637.728-0.209-0.2090.0000.0000.0000.000
30H32ALA00.0110.01240.768-0.186-0.1860.0000.0000.0000.000
31H33ILE0-0.021-0.01842.591-0.208-0.2080.0000.0000.0000.000
32H34LEU0-0.037-0.02142.825-0.180-0.1800.0000.0000.0000.000
33H35HIS00.0130.00442.404-0.227-0.2270.0000.0000.0000.000
34H36GLN0-0.094-0.04446.060-0.199-0.1990.0000.0000.0000.000
35H37SER0-0.029-0.01949.460-0.072-0.0720.0000.0000.0000.000
36H38GLU-1-0.942-0.94051.3475.8615.8610.0000.0000.0000.000
37H39SER0-0.015-0.02652.226-0.137-0.1370.0000.0000.0000.000
38H40LEU0-0.024-0.00148.8550.1190.1190.0000.0000.0000.000
39H41SER00.0460.01548.488-0.062-0.0620.0000.0000.0000.000
40H42PRO0-0.004-0.00750.537-0.002-0.0020.0000.0000.0000.000
41H43TRP00.0850.03945.9930.1440.1440.0000.0000.0000.000
42H44PRO00.0200.00248.0240.1360.1360.0000.0000.0000.000
43H45THR00.0160.00845.9060.1310.1310.0000.0000.0000.000
44H46ILE00.0180.02744.6800.2000.2000.0000.0000.0000.000
45H47HIS00.0200.02543.3520.1360.1360.0000.0000.0000.000
46H48LYS10.9730.98641.743-6.941-6.9410.0000.0000.0000.000
47H49ASN0-0.040-0.03740.0960.3120.3120.0000.0000.0000.000
48H50PHE00.0570.02238.6400.2160.2160.0000.0000.0000.000
49H51ASN0-0.021-0.01338.0320.2480.2480.0000.0000.0000.000
50H52ILE0-0.035-0.01335.4110.1870.1870.0000.0000.0000.000
51H53LEU00.0210.00634.1250.2670.2670.0000.0000.0000.000
52H54LEU00.0070.01833.2450.2930.2930.0000.0000.0000.000
53H55SER00.0270.00732.4060.2010.2010.0000.0000.0000.000
54H56GLN0-0.043-0.01229.7870.5860.5860.0000.0000.0000.000
55H57ILE00.0300.00628.6120.4170.4170.0000.0000.0000.000
56H58HIS00.0370.03128.2740.3320.3320.0000.0000.0000.000
57H59SER0-0.045-0.03326.7620.3180.3180.0000.0000.0000.000
58H60LEU0-0.018-0.00923.8290.4920.4920.0000.0000.0000.000
59H61SER00.0370.00923.4380.4310.4310.0000.0000.0000.000
60H62ASN0-0.027-0.02123.7580.4370.4370.0000.0000.0000.000
61H63ASN0-0.035-0.01519.8730.6900.6900.0000.0000.0000.000
62H64LEU00.0400.02219.2610.7360.7360.0000.0000.0000.000
63H65ALA00.0070.00218.8950.6170.6170.0000.0000.0000.000
64H66ALA0-0.045-0.02319.3210.3530.3530.0000.0000.0000.000
65H67HIS0-0.022-0.01914.4531.0401.0400.0000.0000.0000.000
66H68SER0-0.012-0.00114.8700.6500.6500.0000.0000.0000.000
67H69HIS00.0160.00311.1840.2660.2660.0000.0000.0000.000
68H70THR00.0220.0049.5030.4140.4140.0000.0000.0000.000
69H71LEU00.0170.01210.8961.2221.2220.0000.0000.0000.000
70H72GLN00.0290.02513.3630.3200.3200.0000.0000.0000.000
71H73THR0-0.099-0.0309.4910.1450.1450.0000.0000.0000.000
72H74THR0-0.059-0.0368.5892.2112.2110.0000.0000.0000.000
73H75SER0-0.013-0.02410.906-1.803-1.8030.0000.0000.0000.000
74H76ILE0-0.0110.00212.3841.2831.2830.0000.0000.0000.000
75H77TYR0-0.0010.00210.696-1.065-1.0650.0000.0000.0000.000
76H78PRO0-0.0080.00416.2400.5020.5020.0000.0000.0000.000
77H79SER00.015-0.02115.5550.3580.3580.0000.0000.0000.000
78H80LEU0-0.014-0.03316.408-0.936-0.9360.0000.0000.0000.000
79H81GLU-1-0.894-0.91017.16716.70216.7020.0000.0000.0000.000
80H82PHE0-0.0010.00720.491-0.705-0.7050.0000.0000.0000.000
81H83PRO00.0300.03122.210-0.114-0.1140.0000.0000.0000.000
82H84VAL0-0.006-0.03523.262-0.499-0.4990.0000.0000.0000.000
83H85LYS10.9250.95426.181-11.558-11.5580.0000.0000.0000.000
84H86GLU-1-0.903-0.93529.3899.7429.7420.0000.0000.0000.000
85H87GLN0-0.043-0.04027.999-0.304-0.3040.0000.0000.0000.000
86H88GLU-1-0.891-0.94426.76811.25411.2540.0000.0000.0000.000
87H89PRO00.0090.01627.2800.2050.2050.0000.0000.0000.000
88H90LEU00.0000.01226.4370.0200.0200.0000.0000.0000.000
89H91LEU00.0130.02020.8250.2790.2790.0000.0000.0000.000
90H92THR00.019-0.01423.8100.2760.2760.0000.0000.0000.000
91H93THR0-0.098-0.05225.795-0.189-0.1890.0000.0000.0000.000
92H94LEU0-0.033-0.02522.3850.0170.0170.0000.0000.0000.000
93H95LEU0-0.0290.00118.8420.4460.4460.0000.0000.0000.000
94H96ARG10.8420.91122.196-9.861-9.8610.0000.0000.0000.000
95H97THR0-0.005-0.00522.3690.0530.0530.0000.0000.0000.000
96H98LYS10.7800.88224.177-9.349-9.3490.0000.0000.0000.000
97H99ALA00.0980.05728.012-0.025-0.0250.0000.0000.0000.000
98H100LEU00.0220.01130.146-0.086-0.0860.0000.0000.0000.000
99H101PRO00.0290.00933.6060.0080.0080.0000.0000.0000.000
100H102GLU-1-0.888-0.94736.6817.5267.5260.0000.0000.0000.000
101H103VAL0-0.053-0.01831.993-0.070-0.0700.0000.0000.0000.000
102H104GLU-1-0.777-0.87332.2679.0979.0970.0000.0000.0000.000
103H105GLU-1-0.902-0.94435.2487.0507.0500.0000.0000.0000.000
104H106TRP0-0.0150.00133.876-0.024-0.0240.0000.0000.0000.000
105H107GLU-1-0.922-0.95231.8629.2689.2680.0000.0000.0000.000
106H108ALA0-0.021-0.01336.315-0.095-0.0950.0000.0000.0000.000
107H109ASN0-0.067-0.04138.829-0.199-0.1990.0000.0000.0000.000
108H110THR00.009-0.01138.084-0.046-0.0460.0000.0000.0000.000
109H111LEU0-0.029-0.00835.276-0.049-0.0490.0000.0000.0000.000
110H112GLN0-0.023-0.00539.615-0.265-0.2650.0000.0000.0000.000
111H113GLU-1-0.941-0.98243.1836.7836.7830.0000.0000.0000.000
112H114TYR0-0.034-0.00340.116-0.121-0.1210.0000.0000.0000.000
113H115GLU-1-0.873-0.94540.9357.3457.3450.0000.0000.0000.000
114H116ALA0-0.070-0.01544.224-0.160-0.1600.0000.0000.0000.000
115H117SER0-0.126-0.06645.257-0.138-0.1380.0000.0000.0000.000
116H118ILE0-0.118-0.06543.344-0.212-0.2120.0000.0000.0000.000
117H127ALA00.0470.00836.013-0.037-0.0370.0000.0000.0000.000
118H128ASN0-0.025-0.01937.3570.2180.2180.0000.0000.0000.000
119H129ASP-1-0.819-0.90739.4797.1227.1220.0000.0000.0000.000
120H130ALA0-0.063-0.01436.395-0.113-0.1130.0000.0000.0000.000
121H131TYR00.0610.01334.5730.0050.0050.0000.0000.0000.000
122H132GLN0-0.042-0.03337.030-0.168-0.1680.0000.0000.0000.000
123H133LYS10.9050.95640.314-7.347-7.3470.0000.0000.0000.000
124H134ASP-1-0.853-0.92835.5678.2458.2450.0000.0000.0000.000
125H135GLN00.0180.01737.9190.1050.1050.0000.0000.0000.000
126H136LEU0-0.017-0.01039.118-0.118-0.1180.0000.0000.0000.000
127H137TRP0-0.016-0.00638.568-0.201-0.2010.0000.0000.0000.000
128H138ASP-1-0.843-0.88336.0948.2388.2380.0000.0000.0000.000
129H139GLN00.025-0.00438.9520.0120.0120.0000.0000.0000.000
130H140ALA0-0.0060.00842.419-0.137-0.1370.0000.0000.0000.000
131H141ARG10.7950.86936.225-8.188-8.1880.0000.0000.0000.000
132H142ILE0-0.016-0.00639.453-0.042-0.0420.0000.0000.0000.000
133H143ILE00.0470.01942.631-0.099-0.0990.0000.0000.0000.000
134H144PHE0-0.037-0.01343.821-0.116-0.1160.0000.0000.0000.000
135H145MET0-0.063-0.04739.1640.0130.0130.0000.0000.0000.000
136H146GLU-1-0.938-0.96644.4806.6346.6340.0000.0000.0000.000
137H147GLU-1-0.824-0.88547.1365.7235.7230.0000.0000.0000.000
138H148ARG10.7640.85545.452-6.793-6.7930.0000.0000.0000.000
139H149GLU-1-0.825-0.88646.2896.5966.5960.0000.0000.0000.000
140H150ASN0-0.073-0.03549.795-0.081-0.0810.0000.0000.0000.000
141H151TYR0-0.108-0.06652.562-0.217-0.2170.0000.0000.0000.000
142H152SER0-0.020-0.00453.0910.0910.0910.0000.0000.0000.000
143H153TRP0-0.039-0.02050.790-0.070-0.0700.0000.0000.0000.000
144H154PHE0-0.034-0.01548.688-0.036-0.0360.0000.0000.0000.000
145H171ARG10.8840.90758.902-5.185-5.1850.0000.0000.0000.000
146H172GLN00.0400.01964.1030.0470.0470.0000.0000.0000.000
147H173LEU00.0530.03066.657-0.028-0.0280.0000.0000.0000.000
148H174GLU-1-0.858-0.91463.6124.9314.9310.0000.0000.0000.000
149H175ILE0-0.012-0.00364.625-0.024-0.0240.0000.0000.0000.000
150H176ASP-1-0.867-0.93568.4684.4124.4120.0000.0000.0000.000
151H177ARG10.7880.85270.776-4.358-4.3580.0000.0000.0000.000
152H178ALA00.0290.02469.118-0.042-0.0420.0000.0000.0000.000
153H179THR0-0.077-0.04971.264-0.055-0.0550.0000.0000.0000.000
154H180GLU-1-0.858-0.89373.8344.0934.0930.0000.0000.0000.000
155H181GLU-1-0.841-0.91572.9214.3184.3180.0000.0000.0000.000
156H182GLN00.0080.01572.802-0.070-0.0700.0000.0000.0000.000
157H183ASN0-0.075-0.04875.429-0.094-0.0940.0000.0000.0000.000
158H184ALA00.0420.02878.745-0.060-0.0600.0000.0000.0000.000
159H185ASN0-0.034-0.03176.376-0.063-0.0630.0000.0000.0000.000
160H186GLN0-0.043-0.01379.2070.0170.0170.0000.0000.0000.000
161H187MET00.0270.00980.804-0.047-0.0470.0000.0000.0000.000
162H188LEU0-0.020-0.01381.555-0.065-0.0650.0000.0000.0000.000
163H189THR0-0.029-0.03381.137-0.035-0.0350.0000.0000.0000.000
164H190ASP-1-0.857-0.91083.7723.7493.7490.0000.0000.0000.000
165H191ILE0-0.0120.00386.647-0.064-0.0640.0000.0000.0000.000
166H192LEU00.002-0.00184.371-0.059-0.0590.0000.0000.0000.000
167H193SER0-0.057-0.03688.651-0.045-0.0450.0000.0000.0000.000
168H194PHE00.0060.01790.363-0.061-0.0610.0000.0000.0000.000
169H195MET0-0.017-0.01689.495-0.051-0.0510.0000.0000.0000.000
170H196LYS10.9410.98391.105-3.489-3.4890.0000.0000.0000.000
171H197SER0-0.107-0.07293.204-0.013-0.0130.0000.0000.0000.000
172H198GLY00.0330.02395.496-0.020-0.0200.0000.0000.0000.000
173H199LYS10.9280.96791.016-3.528-3.5280.0000.0000.0000.000
174H200ARG10.9841.00491.313-3.268-3.2680.0000.0000.0000.000