FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZV28N

Calculation Name: 4H05-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H05

Chain ID: A

ChEMBL ID:

UniProt ID: Q9F9M5

Base Structure: X-ray

Registration Date: 2023-09-20

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 270
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3517667.877539
FMO2-HF: Nuclear repulsion 3414046.984881
FMO2-HF: Total energy -103620.892658
FMO2-MP2: Total energy -103925.227812


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(A:-2:HIS)


Summations of interaction energy for fragment #1(A:-2: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.
-39.33-24.62612.866-10.532-17.04-0.029
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.020
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].
3A0HIS0-0.003-0.0042.384-10.264-6.2933.094-2.872-4.1930.020
4A1MET00.0080.0312.155-6.368-3.7492.838-1.698-3.7590.008
5A2ASP-1-0.777-0.8822.999-8.161-5.9710.164-1.157-1.198-0.009
6A3ASP-1-0.912-0.9675.5381.4211.4210.0000.0000.0000.000
7A4ALA0-0.0080.0027.325-0.303-0.3030.0000.0000.0000.000
8A5LEU00.0210.0136.2020.0140.0140.0000.0000.0000.000
9A6ARG10.9100.9549.4270.0260.0260.0000.0000.0000.000
10A7ALA0-0.038-0.02811.3830.0120.0120.0000.0000.0000.000
11A8LEU00.0110.00711.0550.0240.0240.0000.0000.0000.000
12A9ARG10.8840.95112.6500.5000.5000.0000.0000.0000.000
13A10GLY0-0.056-0.02115.4900.0330.0330.0000.0000.0000.000
14A11ARG10.8300.91013.2700.5160.5160.0000.0000.0000.000
15A12TYR0-0.062-0.04717.1280.0320.0320.0000.0000.0000.000
16A13PRO00.0190.01620.079-0.002-0.0020.0000.0000.0000.000
17A14GLY0-0.037-0.04221.7110.0010.0010.0000.0000.0000.000
18A15CYS0-0.077-0.01620.6360.0170.0170.0000.0000.0000.000
19A16GLU-1-0.819-0.89120.450-0.235-0.2350.0000.0000.0000.000
20A17TRP0-0.005-0.02112.047-0.021-0.0210.0000.0000.0000.000
21A18VAL0-0.0120.00217.6260.0020.0020.0000.0000.0000.000
22A19VAL00.0250.01114.019-0.029-0.0290.0000.0000.0000.000
23A20VAL0-0.085-0.05216.4680.0660.0660.0000.0000.0000.000
24A21GLU-1-0.875-0.92613.898-0.551-0.5510.0000.0000.0000.000
25A22ASP-1-0.892-0.94810.058-1.002-1.0020.0000.0000.0000.000
26A23GLY00.0480.0249.2120.1250.1250.0000.0000.0000.000
27A24ALA0-0.029-0.0293.745-0.722-0.5210.001-0.047-0.1550.000
28A25SER0-0.069-0.0592.237-4.125-1.9743.472-2.541-3.083-0.029
29A26GLY00.0140.0184.2450.3430.369-0.001-0.0370.0120.000
30A27ALA0-0.080-0.0325.345-0.021-0.0210.0000.0000.0000.000
31A28GLY00.0950.0607.4180.0010.0010.0000.0000.0000.000
32A29VAL0-0.013-0.01210.909-0.073-0.0730.0000.0000.0000.000
33A30TYR0-0.034-0.0429.7310.1690.1690.0000.0000.0000.000
34A31ARG10.9070.94316.3600.3190.3190.0000.0000.0000.000
35A32LEU0-0.029-0.01316.1300.0240.0240.0000.0000.0000.000
36A33ARG10.8380.90520.2650.2560.2560.0000.0000.0000.000
37A34GLY00.0480.01723.8490.0080.0080.0000.0000.0000.000
38A35GLY0-0.051-0.02026.408-0.002-0.0020.0000.0000.0000.000
39A36GLY0-0.007-0.00830.0750.0070.0070.0000.0000.0000.000
40A37ARG10.8980.96223.9710.2390.2390.0000.0000.0000.000
41A38GLU-1-0.813-0.91824.671-0.271-0.2710.0000.0000.0000.000
42A39LEU0-0.028-0.01120.8940.0120.0120.0000.0000.0000.000
43A40PHE00.0160.01918.8950.0130.0130.0000.0000.0000.000
44A41VAL0-0.018-0.01413.2550.0020.0020.0000.0000.0000.000
45A42LYS10.7940.88712.9630.8450.8450.0000.0000.0000.000
46A43VAL0-0.022-0.0357.0500.0210.0210.0000.0000.0000.000
47A44ALA00.0480.0427.6810.0180.0180.0000.0000.0000.000
48A45ALA00.018-0.0093.956-1.085-0.8980.000-0.034-0.1530.000
49A46LEU0-0.019-0.0184.1781.4431.552-0.001-0.007-0.1010.000
50A47GLY00.0620.0445.9690.1670.1670.0000.0000.0000.000
51A48ALA00.0260.0139.0610.2960.2960.0000.0000.0000.000
52A49GLY0-0.014-0.0127.9900.2270.2270.0000.0000.0000.000
53A50VAL00.008-0.0168.9190.3680.3680.0000.0000.0000.000
54A51GLY00.0220.01811.6660.2290.2290.0000.0000.0000.000
55A52LEU00.0030.00610.6650.1710.1710.0000.0000.0000.000
56A53LEU0-0.039-0.02111.5600.1610.1610.0000.0000.0000.000
57A54GLY00.0320.02114.7020.1250.1250.0000.0000.0000.000
58A55GLU-1-0.825-0.90616.391-0.704-0.7040.0000.0000.0000.000
59A56ALA0-0.005-0.00317.3750.0810.0810.0000.0000.0000.000
60A57GLU-1-0.912-0.95519.123-0.477-0.4770.0000.0000.0000.000
61A58ARG10.8250.91220.3670.5940.5940.0000.0000.0000.000
62A59LEU00.0060.01020.8300.0390.0390.0000.0000.0000.000
63A60VAL0-0.040-0.02823.0330.0380.0380.0000.0000.0000.000
64A61TRP00.0380.00725.2580.0230.0230.0000.0000.0000.000
65A62LEU00.0370.00025.8380.0230.0230.0000.0000.0000.000
66A63ALA0-0.0060.01027.8970.0210.0210.0000.0000.0000.000
67A64GLU-1-1.018-1.00129.723-0.207-0.2070.0000.0000.0000.000
68A65VAL0-0.038-0.01430.9550.0180.0180.0000.0000.0000.000
69A66GLY0-0.033-0.01333.1120.0100.0100.0000.0000.0000.000
70A67ILE0-0.021-0.00429.7350.0090.0090.0000.0000.0000.000
71A68PRO0-0.0130.00330.869-0.009-0.0090.0000.0000.0000.000
72A69VAL00.0260.00325.605-0.016-0.0160.0000.0000.0000.000
73A70PRO0-0.0230.01623.3020.0200.0200.0000.0000.0000.000
74A71ARG10.8770.92324.8010.2460.2460.0000.0000.0000.000
75A72VAL00.0400.01619.845-0.013-0.0130.0000.0000.0000.000
76A73VAL0-0.087-0.04120.8390.0400.0400.0000.0000.0000.000
77A74GLU-1-0.797-0.86816.331-0.506-0.5060.0000.0000.0000.000
78A75GLY00.0560.02015.109-0.035-0.0350.0000.0000.0000.000
79A76GLY0-0.035-0.00313.1230.1260.1260.0000.0000.0000.000
80A77GLY00.0020.0069.116-0.163-0.1630.0000.0000.0000.000
81A78ASP-1-0.848-0.9197.818-1.817-1.8170.0000.0000.0000.000
82A79GLU-1-0.713-0.8627.341-3.094-3.0940.0000.0000.0000.000
83A80ARG10.7330.8462.2902.1663.1280.875-0.400-1.437-0.001
84A81VAL0-0.030-0.0332.189-9.112-6.8592.425-1.728-2.950-0.018
85A82ALA0-0.0370.0244.6191.2821.317-0.001-0.011-0.0230.000
86A83TRP0-0.026-0.0398.354-0.101-0.1010.0000.0000.0000.000
87A84LEU00.0360.02111.3120.0910.0910.0000.0000.0000.000
88A85VAL0-0.029-0.01315.003-0.007-0.0070.0000.0000.0000.000
89A86THR00.0370.00817.6720.0150.0150.0000.0000.0000.000
90A87GLU-1-0.864-0.92321.175-0.266-0.2660.0000.0000.0000.000
91A88ALA0-0.033-0.00123.482-0.022-0.0220.0000.0000.0000.000
92A89VAL00.0200.02324.4300.0230.0230.0000.0000.0000.000
93A90PRO0-0.020-0.00526.5150.0030.0030.0000.0000.0000.000
94A91GLY0-0.0070.00129.511-0.001-0.0010.0000.0000.0000.000
95A92ARG10.7980.91029.6240.1580.1580.0000.0000.0000.000
96A93PRO00.1010.04526.0100.0050.0050.0000.0000.0000.000
97A94ALA00.0260.00428.1480.0200.0200.0000.0000.0000.000
98A95SER0-0.003-0.01225.3680.0190.0190.0000.0000.0000.000
99A96ALA0-0.0010.00428.5410.0120.0120.0000.0000.0000.000
100A97ARG10.9360.97930.0620.1350.1350.0000.0000.0000.000
101A98TRP0-0.005-0.02131.6550.0170.0170.0000.0000.0000.000
102A99PRO0-0.008-0.00635.5840.0070.0070.0000.0000.0000.000
103A100ARG10.9760.99239.3190.0880.0880.0000.0000.0000.000
104A101GLU-1-0.940-0.99941.505-0.104-0.1040.0000.0000.0000.000
105A102GLN00.0160.00338.583-0.003-0.0030.0000.0000.0000.000
106A103ARG10.8930.95937.0050.1200.1200.0000.0000.0000.000
107A104LEU00.0200.00638.287-0.005-0.0050.0000.0000.0000.000
108A105ASP-1-0.869-0.94240.166-0.126-0.1260.0000.0000.0000.000
109A106VAL00.0030.00533.695-0.006-0.0060.0000.0000.0000.000
110A107ALA00.0220.02035.599-0.010-0.0100.0000.0000.0000.000
111A108VAL0-0.023-0.02037.135-0.003-0.0030.0000.0000.0000.000
112A109ALA00.0060.00535.693-0.003-0.0030.0000.0000.0000.000
113A110LEU00.0100.00330.718-0.008-0.0080.0000.0000.0000.000
114A111ALA00.0160.01534.209-0.007-0.0070.0000.0000.0000.000
115A112GLY0-0.004-0.00736.9330.0000.0000.0000.0000.0000.000
116A113LEU0-0.0100.01430.0480.0000.0000.0000.0000.0000.000
117A114ALA00.0240.01533.152-0.007-0.0070.0000.0000.0000.000
118A115ARG10.7910.89134.1270.1460.1460.0000.0000.0000.000
119A116SER0-0.069-0.04835.1680.0040.0040.0000.0000.0000.000
120A117LEU0-0.011-0.00428.895-0.001-0.0010.0000.0000.0000.000
121A118HIS0-0.030-0.01631.6100.0160.0160.0000.0000.0000.000
122A119ALA0-0.022-0.00335.2400.0080.0080.0000.0000.0000.000
123A120LEU0-0.047-0.01132.2120.0070.0070.0000.0000.0000.000
124A121ASP-1-0.836-0.91435.865-0.176-0.1760.0000.0000.0000.000
125A122TRP00.0480.00833.240-0.015-0.0150.0000.0000.0000.000
126A123GLU-1-0.957-0.97633.187-0.175-0.1750.0000.0000.0000.000
127A124ARG10.7840.87634.3200.1710.1710.0000.0000.0000.000
128A125CYS0-0.0550.00428.858-0.017-0.0170.0000.0000.0000.000
129A126PRO0-0.053-0.01826.4060.0040.0040.0000.0000.0000.000
130A127PHE00.0090.00123.134-0.017-0.0170.0000.0000.0000.000
131A128ASP-1-0.805-0.87324.839-0.266-0.2660.0000.0000.0000.000
132A129ARG10.9010.97022.3410.3600.3600.0000.0000.0000.000
133A130SER00.027-0.00225.3420.0130.0130.0000.0000.0000.000
134A131LEU0-0.027-0.00927.123-0.020-0.0200.0000.0000.0000.000
135A132ALA0-0.062-0.03628.6740.0060.0060.0000.0000.0000.000
136A133VAL0-0.040-0.00922.557-0.005-0.0050.0000.0000.0000.000
137A134THR00.006-0.02223.335-0.011-0.0110.0000.0000.0000.000
138A135VAL00.0270.02524.030-0.002-0.0020.0000.0000.0000.000
139A136PRO0-0.025-0.02623.4100.0030.0030.0000.0000.0000.000
140A137GLN0-0.011-0.00519.2420.0070.0070.0000.0000.0000.000
141A138ALA00.0490.03520.303-0.015-0.0150.0000.0000.0000.000
142A139ALA00.007-0.01022.4400.0160.0160.0000.0000.0000.000
143A140ARG10.8730.94317.6990.4180.4180.0000.0000.0000.000
144A141ALA00.0590.04717.6520.0100.0100.0000.0000.0000.000
145A142VAL0-0.0180.00018.7310.0340.0340.0000.0000.0000.000
146A143ALA0-0.063-0.02720.2570.0390.0390.0000.0000.0000.000
147A144GLU-1-0.951-1.00114.603-0.389-0.3890.0000.0000.0000.000
148A145GLY0-0.061-0.02116.0920.0240.0240.0000.0000.0000.000
149A146SER0-0.035-0.02814.6030.0200.0200.0000.0000.0000.000
150A147VAL0-0.044-0.01116.358-0.045-0.0450.0000.0000.0000.000
151A148ASP-1-0.845-0.92018.469-0.103-0.1030.0000.0000.0000.000
152A149LEU0-0.033-0.03519.8700.0030.0030.0000.0000.0000.000
153A150GLU-1-1.036-1.01722.1480.0550.0550.0000.0000.0000.000
154A151ASP-1-0.925-0.96822.495-0.132-0.1320.0000.0000.0000.000
155A152LEU0-0.0210.01924.119-0.022-0.0220.0000.0000.0000.000
156A153ASP-1-0.811-0.90625.920-0.165-0.1650.0000.0000.0000.000
157A154GLU-1-0.873-0.95128.892-0.085-0.0850.0000.0000.0000.000
158A155GLU-1-0.951-0.96131.931-0.120-0.1200.0000.0000.0000.000
159A156ARG10.7470.84829.5690.1470.1470.0000.0000.0000.000
160A157LYS10.8220.91126.9250.1110.1110.0000.0000.0000.000
161A158GLY0-0.008-0.00228.1370.0100.0100.0000.0000.0000.000
162A159TRP0-0.081-0.03729.1310.0080.0080.0000.0000.0000.000
163A160SER0-0.004-0.02526.866-0.005-0.0050.0000.0000.0000.000
164A161GLY00.1230.05424.306-0.013-0.0130.0000.0000.0000.000
165A162GLU-1-0.854-0.91725.218-0.076-0.0760.0000.0000.0000.000
166A163ARG10.7490.86427.8530.0790.0790.0000.0000.0000.000
167A164LEU00.0830.04225.9700.0020.0020.0000.0000.0000.000
168A165LEU00.0120.00825.622-0.008-0.0080.0000.0000.0000.000
169A166ALA0-0.008-0.00528.104-0.001-0.0010.0000.0000.0000.000
170A167GLU-1-0.790-0.86131.449-0.092-0.0920.0000.0000.0000.000
171A168LEU00.0070.04227.3660.0000.0000.0000.0000.0000.000
172A169GLU-1-0.936-0.99229.893-0.149-0.1490.0000.0000.0000.000
173A170ARG10.7580.87432.3580.1020.1020.0000.0000.0000.000
174A171THR0-0.077-0.06933.7730.0030.0030.0000.0000.0000.000
175A172ARG10.9310.99030.9150.1760.1760.0000.0000.0000.000
176A173PRO0-0.0100.00033.3900.0110.0110.0000.0000.0000.000
177A174ALA0-0.053-0.02336.130-0.003-0.0030.0000.0000.0000.000
178A175ASP-1-0.912-0.94138.042-0.140-0.1400.0000.0000.0000.000
179A176GLU-1-0.770-0.90431.613-0.237-0.2370.0000.0000.0000.000
180A177ASP-1-0.850-0.89935.968-0.154-0.1540.0000.0000.0000.000
181A178LEU0-0.075-0.02832.723-0.008-0.0080.0000.0000.0000.000
182A179ALA00.0040.00633.6330.0120.0120.0000.0000.0000.000
183A180VAL00.0080.00229.480-0.015-0.0150.0000.0000.0000.000
184A181CYS0-0.0280.00328.7480.0170.0170.0000.0000.0000.000
185A182HIS0-0.015-0.03822.711-0.007-0.0070.0000.0000.0000.000
186A183GLY0-0.023-0.02524.287-0.037-0.0370.0000.0000.0000.000
187A184ASP-1-0.802-0.92020.281-0.479-0.4790.0000.0000.0000.000
188A185LEU0-0.0010.02323.688-0.005-0.0050.0000.0000.0000.000
189A186CYS00.0320.01323.0700.0300.0300.0000.0000.0000.000
190A187PRO0-0.007-0.02926.124-0.011-0.0110.0000.0000.0000.000
191A188ASP-1-0.806-0.88822.641-0.296-0.2960.0000.0000.0000.000
192A189ASN0-0.037-0.01620.949-0.030-0.0300.0000.0000.0000.000
193A190VAL00.002-0.00823.8640.0040.0040.0000.0000.0000.000
194A191LEU0-0.041-0.00824.5430.0110.0110.0000.0000.0000.000
195A192LEU0-0.0020.01028.7930.0060.0060.0000.0000.0000.000
196A193ASP-1-0.777-0.88832.524-0.157-0.1570.0000.0000.0000.000
197A194PRO0-0.078-0.04533.7690.0070.0070.0000.0000.0000.000
198A195ARG10.8820.95936.1380.1360.1360.0000.0000.0000.000
199A196THR0-0.028-0.04039.0610.0050.0050.0000.0000.0000.000
200A197CYS0-0.0370.00336.5230.0030.0030.0000.0000.0000.000
201A198GLU-1-0.916-0.95136.648-0.164-0.1640.0000.0000.0000.000
202A199VAL00.013-0.00531.140-0.004-0.0040.0000.0000.0000.000
203A200THR0-0.052-0.05030.3560.0010.0010.0000.0000.0000.000
204A201GLY0-0.029-0.02527.995-0.004-0.0040.0000.0000.0000.000
205A202LEU0-0.0070.00925.7100.0030.0030.0000.0000.0000.000
206A203ILE0-0.017-0.01720.439-0.009-0.0090.0000.0000.0000.000
207A204ASP-1-0.756-0.87317.112-0.694-0.6940.0000.0000.0000.000
208A205VAL0-0.0180.00519.7530.0040.0040.0000.0000.0000.000
209A206GLY00.009-0.00117.9350.0130.0130.0000.0000.0000.000
210A207ARG10.7170.85318.9170.4550.4550.0000.0000.0000.000
211A208VAL0-0.0110.01221.1650.0390.0390.0000.0000.0000.000
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