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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: 14R7Z

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 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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1328496.620948
FMO2-HF: Nuclear repulsion 1257875.366333
FMO2-HF: Total energy -70621.254615
FMO2-MP2: Total energy -70829.431469


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.
60.89862.5856.254-3.457-4.4830.004
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 : -0.910 / q_NPA : -0.959
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].
3H5SER0-0.018-0.0173.434-5.897-3.3290.089-1.205-1.4520.006
4H6THR00.0010.0051.701-7.643-8.8616.164-2.170-2.775-0.002
5H7GLU-1-0.851-0.9194.01330.25830.5950.001-0.082-0.2560.000
6H8LYS10.9760.9876.715-30.513-30.5130.0000.0000.0000.000
7H9THR0-0.048-0.0206.851-2.383-2.3830.0000.0000.0000.000
8H10VAL00.0210.0217.954-2.567-2.5670.0000.0000.0000.000
9H11GLU-1-0.922-0.96310.03820.16220.1620.0000.0000.0000.000
10H12SER0-0.061-0.03711.775-1.563-1.5630.0000.0000.0000.000
11H13LEU00.023-0.00311.153-1.512-1.5120.0000.0000.0000.000
12H14GLU-1-0.801-0.84914.26013.96013.9600.0000.0000.0000.000
13H15ALA0-0.023-0.00516.204-1.145-1.1450.0000.0000.0000.000
14H16ILE00.0180.00315.681-1.055-1.0550.0000.0000.0000.000
15H17ARG10.7930.84818.155-14.732-14.7320.0000.0000.0000.000
16H18HIS0-0.0040.00119.862-0.487-0.4870.0000.0000.0000.000
17H19ARG10.9290.96721.547-13.036-13.0360.0000.0000.0000.000
18H20ILE00.0230.00820.830-0.549-0.5490.0000.0000.0000.000
19H21ALA0-0.0060.00024.030-0.462-0.4620.0000.0000.0000.000
20H22GLN0-0.015-0.01825.859-0.212-0.2120.0000.0000.0000.000
21H23ILE00.0280.02527.119-0.427-0.4270.0000.0000.0000.000
22H24VAL00.0440.03027.605-0.394-0.3940.0000.0000.0000.000
23H25GLN0-0.021-0.00230.121-0.263-0.2630.0000.0000.0000.000
24H26SER0-0.053-0.03532.192-0.324-0.3240.0000.0000.0000.000
25H27LEU00.0250.00731.291-0.309-0.3090.0000.0000.0000.000
26H28THR0-0.012-0.01033.711-0.263-0.2630.0000.0000.0000.000
27H29HIS0-0.0100.00036.112-0.216-0.2160.0000.0000.0000.000
28H30PHE0-0.004-0.00337.777-0.249-0.2490.0000.0000.0000.000
29H31LEU00.007-0.00337.273-0.216-0.2160.0000.0000.0000.000
30H32ALA00.0070.00840.339-0.195-0.1950.0000.0000.0000.000
31H33ILE0-0.017-0.01842.061-0.211-0.2110.0000.0000.0000.000
32H34LEU0-0.062-0.03042.165-0.187-0.1870.0000.0000.0000.000
33H35HIS00.0120.00642.062-0.210-0.2100.0000.0000.0000.000
34H36GLN0-0.108-0.04545.603-0.194-0.1940.0000.0000.0000.000
35H37SER0-0.055-0.04649.010-0.058-0.0580.0000.0000.0000.000
36H38GLU-1-0.923-0.93550.5625.9425.9420.0000.0000.0000.000
37H39SER00.033-0.01651.800-0.171-0.1710.0000.0000.0000.000
38H40LEU0-0.0560.00048.1080.0650.0650.0000.0000.0000.000
39H41SER00.0650.03247.847-0.065-0.0650.0000.0000.0000.000
40H42PRO00.0020.00449.621-0.030-0.0300.0000.0000.0000.000
41H43TRP00.0920.04346.1370.1470.1470.0000.0000.0000.000
42H44PRO00.015-0.00747.8640.1370.1370.0000.0000.0000.000
43H45THR00.0220.01245.1900.1280.1280.0000.0000.0000.000
44H46ILE00.0250.03344.1560.2030.2030.0000.0000.0000.000
45H47HIS00.0320.02642.9910.1550.1550.0000.0000.0000.000
46H48LYS10.9420.97041.455-6.958-6.9580.0000.0000.0000.000
47H49ASN0-0.047-0.04839.8500.3110.3110.0000.0000.0000.000
48H50PHE00.0440.02738.4120.2040.2040.0000.0000.0000.000
49H51ASN0-0.015-0.01637.5450.2790.2790.0000.0000.0000.000
50H52ILE0-0.043-0.01135.1480.1730.1730.0000.0000.0000.000
51H53LEU00.0310.01833.6380.2720.2720.0000.0000.0000.000
52H54LEU00.0030.01332.7750.3000.3000.0000.0000.0000.000
53H55SER00.0290.00332.0310.2080.2080.0000.0000.0000.000
54H56GLN0-0.028-0.01029.2930.5670.5670.0000.0000.0000.000
55H57ILE00.011-0.00628.1700.4250.4250.0000.0000.0000.000
56H58HIS00.0210.02527.9400.3600.3600.0000.0000.0000.000
57H59SER0-0.046-0.02626.1020.2830.2830.0000.0000.0000.000
58H60LEU0-0.009-0.00823.3770.4950.4950.0000.0000.0000.000
59H61SER00.0480.01923.2100.4060.4060.0000.0000.0000.000
60H62ASN0-0.009-0.00823.7610.3590.3590.0000.0000.0000.000
61H63ASN0-0.041-0.02619.3840.8720.8720.0000.0000.0000.000
62H64LEU00.0130.00219.0010.7300.7300.0000.0000.0000.000
63H65ALA00.0160.00918.9280.6000.6000.0000.0000.0000.000
64H66ALA0-0.033-0.00819.0460.2720.2720.0000.0000.0000.000
65H67HIS0-0.033-0.01914.0890.9690.9690.0000.0000.0000.000
66H68SER00.0180.01415.0620.4820.4820.0000.0000.0000.000
67H69HIS0-0.004-0.00211.8020.3270.3270.0000.0000.0000.000
68H70THR00.017-0.0079.7730.2660.2660.0000.0000.0000.000
69H71LEU00.0040.01410.8151.3721.3720.0000.0000.0000.000
70H72GLN00.0380.02113.2780.5730.5730.0000.0000.0000.000
71H73THR0-0.087-0.01910.362-0.125-0.1250.0000.0000.0000.000
72H74THR0-0.073-0.0498.2972.4812.4810.0000.0000.0000.000
73H75SER00.004-0.00110.891-1.962-1.9620.0000.0000.0000.000
74H76ILE0-0.0040.00112.1371.2221.2220.0000.0000.0000.000
75H77TYR0-0.015-0.00910.211-1.008-1.0080.0000.0000.0000.000
76H78PRO0-0.0070.00315.5100.5250.5250.0000.0000.0000.000
77H79SER00.0500.03715.1600.4840.4840.0000.0000.0000.000
78H80LEU0-0.017-0.03415.793-0.988-0.9880.0000.0000.0000.000
79H81GLU-1-0.923-0.95617.08216.47216.4720.0000.0000.0000.000
80H82PHE0-0.020-0.01019.974-0.699-0.6990.0000.0000.0000.000
81H83PRO00.0250.03521.716-0.142-0.1420.0000.0000.0000.000
82H84VAL0-0.017-0.04722.519-0.500-0.5000.0000.0000.0000.000
83H85LYS10.9030.95925.452-11.463-11.4630.0000.0000.0000.000
84H86GLU-1-0.907-0.95428.9909.7569.7560.0000.0000.0000.000
85H87GLN0-0.037-0.02427.645-0.367-0.3670.0000.0000.0000.000
86H88GLU-1-0.855-0.92126.29911.33311.3330.0000.0000.0000.000
87H89PRO00.0130.00126.8200.2170.2170.0000.0000.0000.000
88H90LEU00.0030.01725.496-0.026-0.0260.0000.0000.0000.000
89H91LEU00.0100.01820.4690.2810.2810.0000.0000.0000.000
90H92THR00.033-0.00923.3630.3020.3020.0000.0000.0000.000
91H93THR0-0.101-0.05525.248-0.057-0.0570.0000.0000.0000.000
92H94LEU0-0.046-0.02621.9480.0510.0510.0000.0000.0000.000
93H95LEU0-0.017-0.00618.4470.3620.3620.0000.0000.0000.000
94H96ARG10.8420.94321.802-9.931-9.9310.0000.0000.0000.000
95H97THR00.0320.00922.4390.1980.1980.0000.0000.0000.000
96H98LYS10.7620.86724.181-9.370-9.3700.0000.0000.0000.000
97H99ALA00.1030.05827.9740.0790.0790.0000.0000.0000.000
98H100LEU00.010-0.01029.940-0.130-0.1300.0000.0000.0000.000
99H101PRO00.0390.01733.223-0.003-0.0030.0000.0000.0000.000
100H102GLU-1-0.886-0.94736.3177.5077.5070.0000.0000.0000.000
101H103VAL0-0.047-0.02631.621-0.076-0.0760.0000.0000.0000.000
102H104GLU-1-0.818-0.88932.3899.1629.1620.0000.0000.0000.000
103H105GLU-1-0.898-0.94635.2077.1367.1360.0000.0000.0000.000
104H106TRP0-0.0160.00433.592-0.029-0.0290.0000.0000.0000.000
105H107GLU-1-0.926-0.95431.5909.3469.3460.0000.0000.0000.000
106H108ALA0-0.015-0.01436.305-0.110-0.1100.0000.0000.0000.000
107H109ASN0-0.053-0.03438.889-0.182-0.1820.0000.0000.0000.000
108H110THR0-0.018-0.02638.139-0.059-0.0590.0000.0000.0000.000
109H111LEU0-0.029-0.01335.320-0.031-0.0310.0000.0000.0000.000
110H112GLN0-0.023-0.00239.757-0.195-0.1950.0000.0000.0000.000
111H113GLU-1-0.933-0.98443.3176.7886.7880.0000.0000.0000.000
112H114TYR0-0.044-0.00640.380-0.119-0.1190.0000.0000.0000.000
113H115GLU-1-0.869-0.94441.2507.4467.4460.0000.0000.0000.000
114H116ALA0-0.093-0.01444.677-0.162-0.1620.0000.0000.0000.000
115H117SER0-0.106-0.04745.738-0.142-0.1420.0000.0000.0000.000
116H118ILE0-0.101-0.06143.806-0.234-0.2340.0000.0000.0000.000
117H127ALA00.0350.00437.176-0.052-0.0520.0000.0000.0000.000
118H128ASN0-0.012-0.01537.6910.1860.1860.0000.0000.0000.000
119H129ASP-1-0.820-0.92340.1877.1027.1020.0000.0000.0000.000
120H130ALA0-0.074-0.03136.839-0.049-0.0490.0000.0000.0000.000
121H131TYR00.0240.01035.2380.1260.1260.0000.0000.0000.000
122H132GLN0-0.032-0.01737.558-0.153-0.1530.0000.0000.0000.000
123H133LYS10.9240.95940.593-7.232-7.2320.0000.0000.0000.000
124H134ASP-1-0.846-0.91935.1428.3718.3710.0000.0000.0000.000
125H135GLN0-0.0050.00138.3740.0500.0500.0000.0000.0000.000
126H136LEU0-0.032-0.01339.706-0.142-0.1420.0000.0000.0000.000
127H137TRP0-0.001-0.00439.132-0.197-0.1970.0000.0000.0000.000
128H138ASP-1-0.823-0.87736.5468.2718.2710.0000.0000.0000.000
129H139GLN00.0400.00639.4310.0530.0530.0000.0000.0000.000
130H140ALA0-0.0120.00742.856-0.140-0.1400.0000.0000.0000.000
131H141ARG10.7970.87536.652-8.213-8.2130.0000.0000.0000.000
132H142ILE0-0.010-0.00739.566-0.015-0.0150.0000.0000.0000.000
133H143ILE00.0250.00942.831-0.114-0.1140.0000.0000.0000.000
134H144PHE0-0.029-0.01344.102-0.108-0.1080.0000.0000.0000.000
135H145MET0-0.052-0.04439.336-0.011-0.0110.0000.0000.0000.000
136H146GLU-1-0.924-0.94344.6976.6516.6510.0000.0000.0000.000
137H147GLU-1-0.828-0.90547.2915.7315.7310.0000.0000.0000.000
138H148ARG10.7610.85545.530-6.837-6.8370.0000.0000.0000.000
139H149GLU-1-0.852-0.90646.6786.5866.5860.0000.0000.0000.000
140H150ASN0-0.065-0.02750.038-0.065-0.0650.0000.0000.0000.000
141H151TYR0-0.113-0.05752.675-0.213-0.2130.0000.0000.0000.000
142H152SER0-0.0080.00253.1080.0990.0990.0000.0000.0000.000
143H153TRP0-0.045-0.01950.845-0.105-0.1050.0000.0000.0000.000
144H154PHE0-0.026-0.01148.7610.0100.0100.0000.0000.0000.000
145H171ARG10.9470.96057.782-5.256-5.2560.0000.0000.0000.000
146H172GLN00.0250.00763.6490.0700.0700.0000.0000.0000.000
147H173LEU00.0520.02766.317-0.041-0.0410.0000.0000.0000.000
148H174GLU-1-0.919-0.96963.6904.8984.8980.0000.0000.0000.000
149H175ILE0-0.0030.00064.619-0.027-0.0270.0000.0000.0000.000
150H176ASP-1-0.876-0.93968.4974.3984.3980.0000.0000.0000.000
151H177ARG10.8130.88270.774-4.362-4.3620.0000.0000.0000.000
152H178ALA00.0050.02069.000-0.033-0.0330.0000.0000.0000.000
153H179THR0-0.030-0.03671.141-0.056-0.0560.0000.0000.0000.000
154H180GLU-1-0.848-0.89173.5314.1194.1190.0000.0000.0000.000
155H181GLU-1-0.904-0.95272.8034.3144.3140.0000.0000.0000.000
156H182GLN0-0.023-0.00672.259-0.081-0.0810.0000.0000.0000.000
157H183ASN0-0.063-0.04075.418-0.088-0.0880.0000.0000.0000.000
158H184ALA00.0810.04278.750-0.060-0.0600.0000.0000.0000.000
159H185ASN0-0.018-0.01575.818-0.075-0.0750.0000.0000.0000.000
160H186GLN0-0.034-0.00679.1220.0110.0110.0000.0000.0000.000
161H187MET00.0070.00580.689-0.044-0.0440.0000.0000.0000.000
162H188LEU0-0.010-0.00781.356-0.064-0.0640.0000.0000.0000.000
163H189THR0-0.048-0.04581.189-0.034-0.0340.0000.0000.0000.000
164H190ASP-1-0.874-0.92483.7493.7373.7370.0000.0000.0000.000
165H191ILE0-0.0040.00586.847-0.063-0.0630.0000.0000.0000.000
166H192LEU00.004-0.00184.175-0.055-0.0550.0000.0000.0000.000
167H193SER0-0.053-0.02888.586-0.049-0.0490.0000.0000.0000.000
168H194PHE0-0.0060.00890.299-0.061-0.0610.0000.0000.0000.000
169H195MET00.0120.00689.461-0.049-0.0490.0000.0000.0000.000
170H196LYS10.9210.98091.311-3.497-3.4970.0000.0000.0000.000
171H197SER0-0.104-0.06993.118-0.026-0.0260.0000.0000.0000.000
172H198GLY00.0500.02694.574-0.040-0.0400.0000.0000.0000.000
173H199LYS10.8940.94590.749-3.540-3.5400.0000.0000.0000.000
174H200ARG11.0051.01591.372-3.242-3.2420.0000.0000.0000.000