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: ZV3GN

Calculation Name: 4FHR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FHR

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WY63

Base Structure: X-ray

Registration Date: 2023-09-24

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303479.011458
FMO2-HF: Nuclear repulsion 2220659.565932
FMO2-HF: Total energy -82819.445526
FMO2-MP2: Total energy -83062.071857


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:113:HIS)


Summations of interaction energy for fragment #1(B:113:HIS)
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.
-0.00699999999999922.3080.034-0.918-1.4310.006
Interaction energy analysis for fragmet #1(B:113:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.032
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].
3B115ASP-1-0.834-0.9113.768-3.073-1.624-0.007-0.532-0.9100.003
4B116PRO00.0380.0015.0830.5730.5730.0000.0000.0000.000
5B117VAL00.0500.0238.0320.1800.1800.0000.0000.0000.000
6B118GLN00.0150.0138.8090.2250.2250.0000.0000.0000.000
7B119LEU00.0140.0038.0720.0980.0980.0000.0000.0000.000
8B120VAL00.0140.01511.1450.0350.0350.0000.0000.0000.000
9B121ASN0-0.074-0.04513.7130.0140.0140.0000.0000.0000.000
10B122PHE0-0.029-0.01413.7210.0250.0250.0000.0000.0000.000
11B123LEU0-0.001-0.02613.281-0.011-0.0110.0000.0000.0000.000
12B124GLN0-0.0160.00816.649-0.037-0.0370.0000.0000.0000.000
13B125SER0-0.033-0.01419.317-0.035-0.0350.0000.0000.0000.000
14B126GLU-1-0.987-0.98118.1820.4250.4250.0000.0000.0000.000
15B127HIS00.0220.01421.373-0.016-0.0160.0000.0000.0000.000
16B128PRO00.0890.02421.7830.0320.0320.0000.0000.0000.000
17B129GLN00.0280.02321.787-0.009-0.0090.0000.0000.0000.000
18B130THR0-0.017-0.00918.3130.0210.0210.0000.0000.0000.000
19B131ILE00.0260.01716.9620.0670.0670.0000.0000.0000.000
20B132ALA00.0180.01316.9730.0450.0450.0000.0000.0000.000
21B133VAL0-0.039-0.01217.3680.0240.0240.0000.0000.0000.000
22B134VAL0-0.006-0.00612.3850.0640.0640.0000.0000.0000.000
23B135LEU00.009-0.00813.1590.1160.1160.0000.0000.0000.000
24B136SER0-0.030-0.02814.034-0.001-0.0010.0000.0000.0000.000
25B137TYR0-0.048-0.02412.318-0.077-0.0770.0000.0000.0000.000
26B138LEU0-0.084-0.0287.9840.2090.2090.0000.0000.0000.000
27B139ASP-1-0.869-0.9408.8050.1200.1200.0000.0000.0000.000
28B140PRO00.0620.02710.8670.0020.0020.0000.0000.0000.000
29B141PRO00.0400.03110.888-0.023-0.0230.0000.0000.0000.000
30B142VAL0-0.002-0.0016.709-0.065-0.0650.0000.0000.0000.000
31B143ALA0-0.014-0.0109.564-0.073-0.0730.0000.0000.0000.000
32B144ALA00.0310.01012.558-0.047-0.0470.0000.0000.0000.000
33B145GLN0-0.023-0.0018.685-0.007-0.0070.0000.0000.0000.000
34B146ILE0-0.051-0.0189.290-0.030-0.0300.0000.0000.0000.000
35B147LEU0-0.001-0.00612.830-0.024-0.0240.0000.0000.0000.000
36B148GLY00.014-0.00215.981-0.013-0.0130.0000.0000.0000.000
37B149ALA0-0.062-0.02414.511-0.027-0.0270.0000.0000.0000.000
38B150LEU0-0.052-0.01516.5330.0160.0160.0000.0000.0000.000
39B151PRO00.0290.00818.563-0.024-0.0240.0000.0000.0000.000
40B152GLU-1-0.860-0.91822.2130.0480.0480.0000.0000.0000.000
41B153GLU-1-0.936-0.97624.3560.0930.0930.0000.0000.0000.000
42B154LEU0-0.023-0.01521.5620.0090.0090.0000.0000.0000.000
43B155GLN00.0280.03519.8880.0100.0100.0000.0000.0000.000
44B156THR00.0620.01222.7310.0110.0110.0000.0000.0000.000
45B157GLU-1-0.798-0.86925.5230.1640.1640.0000.0000.0000.000
46B158VAL0-0.003-0.01019.0210.0160.0160.0000.0000.0000.000
47B159LEU00.0150.01920.3230.0240.0240.0000.0000.0000.000
48B160LYS10.8630.91722.480-0.118-0.1180.0000.0000.0000.000
49B161ARG10.7960.86123.576-0.202-0.2020.0000.0000.0000.000
50B162ILE0-0.0090.00618.1630.0180.0180.0000.0000.0000.000
51B163ALA0-0.044-0.01721.8830.0070.0070.0000.0000.0000.000
52B164LEU0-0.039-0.02824.674-0.008-0.0080.0000.0000.0000.000
53B165LEU0-0.068-0.00620.3500.0030.0030.0000.0000.0000.000
54B166GLU-1-0.920-0.94824.3820.1890.1890.0000.0000.0000.000
55B167ARG10.9350.94221.276-0.398-0.3980.0000.0000.0000.000
56B168THR00.0180.01820.470-0.032-0.0320.0000.0000.0000.000
57B169SER0-0.0020.00123.3060.0160.0160.0000.0000.0000.000
58B170PRO00.0580.00622.0480.0320.0320.0000.0000.0000.000
59B171GLU-1-0.832-0.90421.7380.5090.5090.0000.0000.0000.000
60B172VAL0-0.019-0.00121.6420.0150.0150.0000.0000.0000.000
61B173VAL0-0.0040.00316.9440.0120.0120.0000.0000.0000.000
62B174LYS10.9070.93817.697-0.463-0.4630.0000.0000.0000.000
63B175GLU-1-0.868-0.90818.5580.5840.5840.0000.0000.0000.000
64B176ILE00.008-0.00515.5990.0150.0150.0000.0000.0000.000
65B177GLU-1-0.912-0.96913.6011.1141.1140.0000.0000.0000.000
66B178ARG10.9050.94614.321-0.508-0.5080.0000.0000.0000.000
67B179ASN0-0.066-0.04216.1680.0040.0040.0000.0000.0000.000
68B180LEU00.0120.00911.366-0.032-0.0320.0000.0000.0000.000
69B181GLU-1-0.927-0.95811.2931.3961.3960.0000.0000.0000.000
70B182LYS10.7990.89812.228-0.605-0.6050.0000.0000.0000.000
71B183LYS10.8340.92113.518-0.636-0.6360.0000.0000.0000.000
72B184ILE0-0.0110.0077.452-0.208-0.2080.0000.0000.0000.000
73B185SER0-0.017-0.0115.9210.3410.3410.0000.0000.0000.000
74B186GLY00.0080.0023.554-0.907-0.3610.039-0.328-0.2570.003
75B187PHE00.0210.0074.1010.9661.2860.002-0.058-0.2640.000
76B195VAL0-0.015-0.00617.371-0.001-0.0010.0000.0000.0000.000
77B196GLY00.0040.00018.8030.0080.0080.0000.0000.0000.000
78B197GLY00.0350.02820.835-0.012-0.0120.0000.0000.0000.000
79B198ILE0-0.012-0.02723.0850.0020.0020.0000.0000.0000.000
80B199ASP-1-0.836-0.91421.9820.0940.0940.0000.0000.0000.000
81B200THR00.0360.02517.422-0.030-0.0300.0000.0000.0000.000
82B201ALA0-0.0020.00019.421-0.008-0.0080.0000.0000.0000.000
83B202ALA00.0080.00721.510-0.020-0.0200.0000.0000.0000.000
84B203GLU-1-0.892-0.95215.7190.0350.0350.0000.0000.0000.000
85B204ILE0-0.012-0.00815.886-0.032-0.0320.0000.0000.0000.000
86B205MET0-0.037-0.02618.027-0.031-0.0310.0000.0000.0000.000
87B206ASN0-0.065-0.03820.641-0.021-0.0210.0000.0000.0000.000
88B207ASN0-0.075-0.04415.427-0.079-0.0790.0000.0000.0000.000
89B208LEU0-0.0510.00217.165-0.024-0.0240.0000.0000.0000.000
90B209ASP-1-0.808-0.87518.991-0.109-0.1090.0000.0000.0000.000
91B210ARG10.8200.86420.9920.0790.0790.0000.0000.0000.000
92B211THR0-0.046-0.02624.5030.0150.0150.0000.0000.0000.000
93B212THR0-0.044-0.04820.7260.0210.0210.0000.0000.0000.000
94B213GLU-1-0.823-0.89322.813-0.014-0.0140.0000.0000.0000.000
95B214LYS10.8780.91924.2050.0350.0350.0000.0000.0000.000
96B215LYS10.7920.89624.450-0.023-0.0230.0000.0000.0000.000
97B216ILE00.006-0.00722.2650.0120.0120.0000.0000.0000.000
98B217MET00.0210.01126.7550.0130.0130.0000.0000.0000.000
99B218ASP-1-0.819-0.90028.949-0.003-0.0030.0000.0000.0000.000
100B219LYS10.7630.88029.540-0.051-0.0510.0000.0000.0000.000
101B220LEU00.0320.00326.7770.0060.0060.0000.0000.0000.000
102B221VAL0-0.0070.00231.2350.0020.0020.0000.0000.0000.000
103B222GLN0-0.043-0.01434.3070.0050.0050.0000.0000.0000.000
104B223GLU-1-0.872-0.93131.5180.0890.0890.0000.0000.0000.000
105B224ASN0-0.055-0.03332.527-0.002-0.0020.0000.0000.0000.000
106B225PRO00.0920.03833.5560.0020.0020.0000.0000.0000.000
107B226GLU-1-0.917-0.94535.1170.0500.0500.0000.0000.0000.000
108B227LEU0-0.0170.00128.5030.0010.0010.0000.0000.0000.000
109B228ALA0-0.010-0.00630.3650.0000.0000.0000.0000.0000.000
110B229ASP-1-0.831-0.91130.9990.0150.0150.0000.0000.0000.000
111B230GLU-1-0.771-0.85230.4780.0570.0570.0000.0000.0000.000
112B231ILE0-0.019-0.02525.513-0.001-0.0010.0000.0000.0000.000
113B232ARG10.8890.92327.594-0.022-0.0220.0000.0000.0000.000
114B233ARG10.8150.88729.676-0.051-0.0510.0000.0000.0000.000
115B234ARG10.7370.85025.546-0.090-0.0900.0000.0000.0000.000
116B235MET0-0.0510.00424.4060.0000.0000.0000.0000.0000.000
117B236PHE0-0.0040.00225.752-0.023-0.0230.0000.0000.0000.000
118B237VAL00.0460.02027.1390.0090.0090.0000.0000.0000.000
119B238PHE00.0430.00929.761-0.012-0.0120.0000.0000.0000.000
120B239GLU-1-0.745-0.87528.817-0.098-0.0980.0000.0000.0000.000
121B240ASP-1-0.764-0.85525.585-0.104-0.1040.0000.0000.0000.000
122B241ILE0-0.0060.00128.308-0.012-0.0120.0000.0000.0000.000
123B242LEU0-0.034-0.01028.190-0.006-0.0060.0000.0000.0000.000
124B243LYS10.8110.90323.9130.0920.0920.0000.0000.0000.000
125B244LEU00.0010.01727.579-0.011-0.0110.0000.0000.0000.000
126B245ASP-1-0.819-0.89430.155-0.179-0.1790.0000.0000.0000.000
127B246ASP-1-0.772-0.87432.164-0.137-0.1370.0000.0000.0000.000
128B247ARG10.9520.97235.1470.1420.1420.0000.0000.0000.000
129B248SER00.0830.03533.3330.0070.0070.0000.0000.0000.000
130B249ILE00.0400.03033.5570.0080.0080.0000.0000.0000.000
131B250GLN0-0.079-0.05337.2440.0100.0100.0000.0000.0000.000
132B251LEU0-0.037-0.02138.4100.0050.0050.0000.0000.0000.000
133B252VAL00.0370.02537.0340.0060.0060.0000.0000.0000.000
134B253LEU0-0.031-0.02340.4110.0050.0050.0000.0000.0000.000
135B254ARG10.8530.93942.8070.0780.0780.0000.0000.0000.000
136B255GLU-1-0.793-0.86143.246-0.039-0.0390.0000.0000.0000.000
137B256VAL0-0.043-0.00741.7060.0040.0040.0000.0000.0000.000
138B257ASP-1-0.874-0.92445.186-0.036-0.0360.0000.0000.0000.000
139B258THR0-0.010-0.03346.750-0.001-0.0010.0000.0000.0000.000
140B259ARG10.9280.97147.2600.0220.0220.0000.0000.0000.000
141B260ASP-1-0.812-0.92044.877-0.025-0.0250.0000.0000.0000.000
142B261LEU00.0070.00840.817-0.001-0.0010.0000.0000.0000.000
143B262ALA00.017-0.00342.502-0.003-0.0030.0000.0000.0000.000
144B263LEU0-0.014-0.01743.6870.0000.0000.0000.0000.0000.000
145B264ALA00.0140.01439.3120.0010.0010.0000.0000.0000.000
146B265LEU00.009-0.00438.030-0.002-0.0020.0000.0000.0000.000
147B266LYS10.8530.92239.8370.0380.0380.0000.0000.0000.000
148B267GLY0-0.050-0.01438.0920.0010.0010.0000.0000.0000.000
149B268ALA0-0.0010.01635.0010.0000.0000.0000.0000.0000.000
150B269SER0-0.039-0.05531.687-0.002-0.0020.0000.0000.0000.000
151B270ASP-1-0.852-0.94134.010-0.087-0.0870.0000.0000.0000.000
152B271GLU-1-0.941-0.96328.785-0.176-0.1760.0000.0000.0000.000
153B272LEU00.0120.00832.553-0.003-0.0030.0000.0000.0000.000
154B273LYS10.8660.92433.9530.0760.0760.0000.0000.0000.000
155B274GLU-1-0.838-0.91536.195-0.097-0.0970.0000.0000.0000.000
156B275LYS10.8070.91831.2340.1460.1460.0000.0000.0000.000
157B276ILE00.0180.00935.5750.0010.0010.0000.0000.0000.000
158B277PHE00.044-0.01038.5440.0030.0030.0000.0000.0000.000
159B278LYS10.8110.90933.8030.1500.1500.0000.0000.0000.000
160B279ASN0-0.094-0.05336.091-0.003-0.0030.0000.0000.0000.000
161B280MET00.0070.02140.3810.0060.0060.0000.0000.0000.000
162B281SER0-0.0010.00043.991-0.002-0.0020.0000.0000.0000.000
163B282LYS11.0451.00247.1280.0720.0720.0000.0000.0000.000
164B283ARG10.9360.96348.6110.0520.0520.0000.0000.0000.000
165B284ALA00.0230.00947.7210.0020.0020.0000.0000.0000.000
166B285ALA00.0580.03245.2840.0020.0020.0000.0000.0000.000
167B286ALA0-0.037-0.01546.7470.0010.0010.0000.0000.0000.000
168B287LEU00.0210.00849.6740.0020.0020.0000.0000.0000.000
169B288LEU00.0050.01643.1680.0020.0020.0000.0000.0000.000
170B289LYS10.8040.89142.4210.0850.0850.0000.0000.0000.000
171B290ASP-1-0.879-0.93547.364-0.050-0.0500.0000.0000.0000.000
172B291GLU-1-0.939-0.97848.820-0.034-0.0340.0000.0000.0000.000
173B292LEU0-0.048-0.03843.4080.0020.0020.0000.0000.0000.000
174B293GLU-1-0.994-0.98747.258-0.050-0.0500.0000.0000.0000.000
175B294TYR0-0.030-0.01249.4580.0040.0040.0000.0000.0000.000
176B295MET0-0.0730.00546.9930.0020.0020.0000.0000.0000.000
177B296GLY0-0.001-0.00350.6510.0000.0000.0000.0000.0000.000
178B297PRO0-0.025-0.01648.436-0.002-0.0020.0000.0000.0000.000
179B298VAL00.0200.00844.7940.0020.0020.0000.0000.0000.000
180B299ARG10.9170.95745.4500.0020.0020.0000.0000.0000.000
181B300LEU00.0780.04337.626-0.001-0.0010.0000.0000.0000.000
182B301LYS10.9460.96440.978-0.002-0.0020.0000.0000.0000.000
183B302ASP-1-0.871-0.94442.583-0.006-0.0060.0000.0000.0000.000
184B303VAL0-0.0250.00239.294-0.002-0.0020.0000.0000.0000.000
185B304GLU-1-0.884-0.96036.822-0.005-0.0050.0000.0000.0000.000
186B305GLU-1-0.915-0.93539.092-0.007-0.0070.0000.0000.0000.000
187B306ALA0-0.007-0.00941.684-0.001-0.0010.0000.0000.0000.000
188B307GLN0-0.045-0.02935.6990.0000.0000.0000.0000.0000.000
189B308GLN0-0.019-0.00835.703-0.002-0.0020.0000.0000.0000.000
190B309LYS10.8210.90538.3620.0150.0150.0000.0000.0000.000
191B310ILE00.0070.00437.379-0.002-0.0020.0000.0000.0000.000
192B311ILE00.0160.00933.171-0.005-0.0050.0000.0000.0000.000
193B312ASN0-0.015-0.00536.0830.0000.0000.0000.0000.0000.000
194B313ILE0-0.0160.00538.4670.0000.0000.0000.0000.0000.000
195B314ILE00.0070.00733.235-0.003-0.0030.0000.0000.0000.000
196B315ARG10.8430.90733.7730.0010.0010.0000.0000.0000.000
197B316ARG10.8230.88335.1910.0370.0370.0000.0000.0000.000
198B317LEU0-0.011-0.02037.417-0.001-0.0010.0000.0000.0000.000
199B318GLU-1-0.871-0.92229.705-0.060-0.0600.0000.0000.0000.000
200B319GLU-1-0.876-0.91634.156-0.017-0.0170.0000.0000.0000.000
201B320ALA0-0.067-0.03135.6330.0000.0000.0000.0000.0000.000
202B321GLY0-0.0150.00034.773-0.002-0.0020.0000.0000.0000.000
203B322GLU-1-0.982-0.99235.854-0.070-0.0700.0000.0000.0000.000
204B323ILE0-0.079-0.03932.611-0.009-0.0090.0000.0000.0000.000
205B324VAL00.0110.00128.2940.0050.0050.0000.0000.0000.000
206B325ILE0-0.023-0.01426.569-0.013-0.0130.0000.0000.0000.000
207B326ALA0-0.024-0.00225.0790.0010.0010.0000.0000.0000.000
208B327ARG10.8580.91322.2170.2020.2020.0000.0000.0000.000