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: G5YQ1

Calculation Name: 4N0V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N0V

Chain ID: A

ChEMBL ID:

UniProt ID: A1TY67

Base Structure: X-ray

Registration Date: 2023-09-21

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 -2418474.203852
FMO2-HF: Nuclear repulsion 2336148.549988
FMO2-HF: Total energy -82325.653864
FMO2-MP2: Total energy -82563.74564


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-42.123-36.5530.928-14.638-21.862-0.089
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.010
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].
3A3ILE00.0000.0013.8730.1291.858-0.014-0.875-0.8400.002
4A4TYR0-0.040-0.0326.253-0.001-0.0010.0000.0000.0000.000
5A5ASP-1-0.816-0.9079.8220.1270.1270.0000.0000.0000.000
6A6THR00.018-0.00512.283-0.054-0.0540.0000.0000.0000.000
7A7GLU-1-0.801-0.88214.997-0.072-0.0720.0000.0000.0000.000
8A8GLY00.0250.02317.367-0.001-0.0010.0000.0000.0000.000
9A9PHE00.008-0.00517.5730.0160.0160.0000.0000.0000.000
10A10PRO00.0280.00917.5920.0200.0200.0000.0000.0000.000
11A11ASN00.0690.01815.8220.0510.0510.0000.0000.0000.000
12A12PRO00.001-0.00712.8530.0880.0880.0000.0000.0000.000
13A13LEU00.0210.02712.9760.0450.0450.0000.0000.0000.000
14A14ARG10.8020.87114.342-0.381-0.3810.0000.0000.0000.000
15A15VAL00.0200.0118.7560.0510.0510.0000.0000.0000.000
16A16ARG10.7500.8279.8010.1670.1670.0000.0000.0000.000
17A17ILE00.0260.02110.929-0.009-0.0090.0000.0000.0000.000
18A18ALA00.002-0.00510.390-0.004-0.0040.0000.0000.0000.000
19A19LEU0-0.007-0.0044.0750.0040.1470.000-0.018-0.1260.000
20A20ALA00.0090.0137.783-0.098-0.0980.0000.0000.0000.000
21A21GLU-1-0.820-0.85910.5340.3410.3410.0000.0000.0000.000
22A22LYS10.7280.8887.335-1.041-1.0410.0000.0000.0000.000
23A23GLY00.0020.0178.0640.0130.0130.0000.0000.0000.000
24A24ALA0-0.027-0.0353.911-0.182-0.0760.000-0.018-0.0880.000
25A25THR00.0440.0094.929-0.342-0.318-0.001-0.001-0.0210.000
26A26ASP-1-0.930-0.9646.573-0.262-0.2620.0000.0000.0000.000
27A27LYS10.8150.9162.815-0.5050.1430.282-0.165-0.7640.000
28A28VAL00.0160.0132.314-4.547-2.1513.868-2.153-4.111-0.022
29A29VAL0-0.017-0.0033.689-0.0440.5680.006-0.155-0.4640.000
30A30PHE00.017-0.0056.237-0.494-0.4940.0000.0000.0000.000
31A31VAL0-0.045-0.0178.036-0.002-0.0020.0000.0000.0000.000
32A32PRO0-0.003-0.01310.6590.1040.1040.0000.0000.0000.000
33A33VAL00.0180.02313.078-0.042-0.0420.0000.0000.0000.000
34A34ASP-1-0.831-0.91315.787-0.091-0.0910.0000.0000.0000.000
35A35VAL0-0.043-0.03617.8180.0120.0120.0000.0000.0000.000
36A36MET0-0.094-0.03920.3750.0230.0230.0000.0000.0000.000
37A37GLY00.0220.02023.2270.0100.0100.0000.0000.0000.000
38A38GLY0-0.043-0.01922.8520.0000.0000.0000.0000.0000.000
39A39GLU-1-0.859-0.92616.982-0.341-0.3410.0000.0000.0000.000
40A40HIS00.0320.02117.415-0.038-0.0380.0000.0000.0000.000
41A41ARG10.8570.92118.4040.0430.0430.0000.0000.0000.000
42A42THR0-0.006-0.00318.9160.0030.0030.0000.0000.0000.000
43A43THR0-0.006-0.01819.7290.0150.0150.0000.0000.0000.000
44A44ASP-1-0.879-0.93916.684-0.311-0.3110.0000.0000.0000.000
45A45PHE0-0.0110.01213.512-0.050-0.0500.0000.0000.0000.000
46A46ARG10.8660.92415.1470.0710.0710.0000.0000.0000.000
47A47ALA0-0.062-0.02415.7910.0400.0400.0000.0000.0000.000
48A48LYS10.8520.9269.6120.8920.8920.0000.0000.0000.000
49A49ASN0-0.007-0.02612.6970.1400.1400.0000.0000.0000.000
50A50PRO00.0330.02414.949-0.028-0.0280.0000.0000.0000.000
51A51ASP-1-0.889-0.94217.5450.2070.2070.0000.0000.0000.000
52A52ALA0-0.066-0.02118.186-0.006-0.0060.0000.0000.0000.000
53A53THR0-0.037-0.01416.5020.0030.0030.0000.0000.0000.000
54A54VAL00.0500.03513.546-0.026-0.0260.0000.0000.0000.000
55A55PRO0-0.033-0.0359.9120.0060.0060.0000.0000.0000.000
56A56VAL0-0.022-0.0239.1950.1110.1110.0000.0000.0000.000
57A57LEU00.0020.0252.762-1.479-0.6600.559-0.288-1.0900.001
58A58GLU-1-0.762-0.8404.498-1.937-1.734-0.001-0.032-0.1700.000
59A59LEU00.0150.0112.683-4.253-1.4581.631-1.701-2.725-0.015
60A60ASP-1-0.861-0.9361.934-23.732-26.79515.217-6.368-5.786-0.075
61A61ASP-1-0.869-0.9064.7330.2240.301-0.001-0.022-0.0540.000
62A62GLY0-0.026-0.0086.6870.2840.2840.0000.0000.0000.000
63A63THR0-0.068-0.0587.6110.2140.2140.0000.0000.0000.000
64A64CYS0-0.065-0.0187.1030.0730.0730.0000.0000.0000.000
65A65ILE0-0.014-0.0128.1340.0950.0950.0000.0000.0000.000
66A66ALA00.0510.0259.2680.0360.0360.0000.0000.0000.000
67A67GLN0-0.028-0.03312.0570.1540.1540.0000.0000.0000.000
68A68CYS0-0.0060.01012.7420.1160.1160.0000.0000.0000.000
69A69ASN0-0.001-0.00212.7710.1550.1550.0000.0000.0000.000
70A70ALA00.0380.02612.6000.1030.1030.0000.0000.0000.000
71A71ILE00.0030.0057.3540.3000.3000.0000.0000.0000.000
72A72THR0-0.010-0.0288.2910.5040.5040.0000.0000.0000.000
73A73GLU-1-0.864-0.9239.8961.0051.0050.0000.0000.0000.000
74A74TYR0-0.019-0.0122.461-6.458-8.3698.050-2.523-3.6160.019
75A75LEU00.014-0.0053.700-0.1200.2930.019-0.082-0.3500.000
76A76ASP-1-0.711-0.8206.2710.5210.5210.0000.0000.0000.000
77A77GLY0-0.018-0.0019.401-0.228-0.2280.0000.0000.0000.000
78A78VAL0-0.050-0.0224.696-0.416-0.2320.002-0.033-0.1520.000
79A79PHE0-0.030-0.0092.357-0.773-0.3751.311-0.204-1.5050.001
80A80ASP-1-0.878-0.9347.7700.6600.6600.0000.0000.0000.000
81A81GLY0-0.011-0.00411.0600.0080.0080.0000.0000.0000.000
82A82PRO0-0.011-0.02013.7320.0110.0110.0000.0000.0000.000
83A83SER0-0.0070.00613.3130.0490.0490.0000.0000.0000.000
84A84LEU00.016-0.00711.232-0.095-0.0950.0000.0000.0000.000
85A85THR0-0.021-0.03613.351-0.073-0.0730.0000.0000.0000.000
86A86GLY0-0.004-0.00416.014-0.065-0.0650.0000.0000.0000.000
87A87ALA00.0240.01117.5830.0600.0600.0000.0000.0000.000
88A88SER0-0.023-0.01019.133-0.036-0.0360.0000.0000.0000.000
89A89PRO00.037-0.00122.4770.0090.0090.0000.0000.0000.000
90A90LYS10.9680.98324.086-0.221-0.2210.0000.0000.0000.000
91A91GLU-1-0.760-0.86221.3250.4080.4080.0000.0000.0000.000
92A92ARG10.8550.90515.417-0.763-0.7630.0000.0000.0000.000
93A93ALA0-0.029-0.00321.2130.0060.0060.0000.0000.0000.000
94A94VAL0-0.020-0.01424.294-0.011-0.0110.0000.0000.0000.000
95A95ILE00.0560.03018.490-0.015-0.0150.0000.0000.0000.000
96A96ALA00.0060.00820.8130.0010.0010.0000.0000.0000.000
97A97MET0-0.045-0.01421.686-0.026-0.0260.0000.0000.0000.000
98A98MET0-0.025-0.00423.968-0.023-0.0230.0000.0000.0000.000
99A99ASN00.0440.02118.432-0.022-0.0220.0000.0000.0000.000
100A100ILE00.0150.00921.308-0.016-0.0160.0000.0000.0000.000
101A101ARG10.8980.95123.686-0.240-0.2400.0000.0000.0000.000
102A102ALA00.0450.02922.913-0.020-0.0200.0000.0000.0000.000
103A103GLU-1-0.795-0.88319.4160.3950.3950.0000.0000.0000.000
104A104SER0-0.073-0.05723.266-0.022-0.0220.0000.0000.0000.000
105A105GLY0-0.0050.00726.458-0.019-0.0190.0000.0000.0000.000
106A106LEU00.000-0.00325.976-0.016-0.0160.0000.0000.0000.000
107A107MET00.0000.01820.657-0.018-0.0180.0000.0000.0000.000
108A108ASN00.002-0.02222.196-0.022-0.0220.0000.0000.0000.000
109A109ALA0-0.0040.03225.324-0.017-0.0170.0000.0000.0000.000
110A110VAL00.0320.00326.970-0.017-0.0170.0000.0000.0000.000
111A111GLY0-0.0070.00025.611-0.014-0.0140.0000.0000.0000.000
112A112ALA0-0.039-0.02326.420-0.016-0.0160.0000.0000.0000.000
113A113TYR00.009-0.00529.436-0.012-0.0120.0000.0000.0000.000
114A114PHE0-0.0070.00226.387-0.009-0.0090.0000.0000.0000.000
115A115HIS10.8490.88923.817-0.071-0.0710.0000.0000.0000.000
116A116HIS0-0.0010.02029.306-0.012-0.0120.0000.0000.0000.000
117A117ALA0-0.023-0.00432.891-0.004-0.0040.0000.0000.0000.000
118A118THR0-0.033-0.01131.894-0.005-0.0050.0000.0000.0000.000
119A119ARG10.9510.97032.6640.0120.0120.0000.0000.0000.000
120A120GLY00.0240.02029.620-0.004-0.0040.0000.0000.0000.000
121A121LEU0-0.042-0.04223.618-0.004-0.0040.0000.0000.0000.000
122A122GLY00.0120.00728.009-0.010-0.0100.0000.0000.0000.000
123A123PRO0-0.0040.00330.4980.0030.0030.0000.0000.0000.000
124A124ASP-1-0.897-0.94929.760-0.038-0.0380.0000.0000.0000.000
125A125LEU0-0.040-0.02724.664-0.004-0.0040.0000.0000.0000.000
126A126GLU-1-0.789-0.84227.8180.0400.0400.0000.0000.0000.000
127A127THR0-0.028-0.02729.6840.0000.0000.0000.0000.0000.000
128A128TRP0-0.034-0.02631.6520.0010.0010.0000.0000.0000.000
129A129GLN0-0.070-0.02432.0340.0020.0020.0000.0000.0000.000
130A130CYS0-0.012-0.00834.331-0.002-0.0020.0000.0000.0000.000
131A131PRO00.0810.03035.9860.0070.0070.0000.0000.0000.000
132A132ASP-1-0.899-0.93437.6560.0490.0490.0000.0000.0000.000
133A133TRP00.005-0.00431.0020.0050.0050.0000.0000.0000.000
134A134GLY00.0410.01133.3540.0070.0070.0000.0000.0000.000
135A135ASN0-0.041-0.04534.3710.0050.0050.0000.0000.0000.000
136A136LYS10.8270.91336.844-0.079-0.0790.0000.0000.0000.000
137A137GLN00.022-0.00531.7340.0110.0110.0000.0000.0000.000
138A138LYS10.8210.92733.083-0.058-0.0580.0000.0000.0000.000
139A139GLU-1-0.804-0.89334.7240.0820.0820.0000.0000.0000.000
140A140VAL0-0.0400.01031.8310.0040.0040.0000.0000.0000.000
141A141ALA00.0350.02730.9930.0090.0090.0000.0000.0000.000
142A142GLN0-0.044-0.05031.9360.0040.0040.0000.0000.0000.000
143A143SER0-0.032-0.03234.645-0.002-0.0020.0000.0000.0000.000
144A144THR0-0.051-0.02728.7040.0060.0060.0000.0000.0000.000
145A145MET0-0.077-0.01630.4030.0050.0050.0000.0000.0000.000
146A146ALA00.0380.01431.9600.0020.0020.0000.0000.0000.000
147A147TYR00.004-0.00729.5740.0080.0080.0000.0000.0000.000
148A148LEU00.010-0.01026.9680.0050.0050.0000.0000.0000.000
149A149ASN0-0.0190.00130.8110.0060.0060.0000.0000.0000.000
150A150GLU-1-0.865-0.93433.2820.1130.1130.0000.0000.0000.000
151A151VAL0-0.042-0.01629.1090.0020.0020.0000.0000.0000.000
152A152LEU0-0.039-0.01727.1400.0040.0040.0000.0000.0000.000
153A153ALA0-0.0090.01431.222-0.003-0.0030.0000.0000.0000.000
154A154GLU-1-1.021-1.00133.5370.1330.1330.0000.0000.0000.000
155A155ASN0-0.107-0.05828.5540.0140.0140.0000.0000.0000.000
156A156GLU-1-0.846-0.89026.5270.1650.1650.0000.0000.0000.000
157A157PHE0-0.003-0.01823.2940.0010.0010.0000.0000.0000.000
158A158LEU0-0.016-0.02623.519-0.005-0.0050.0000.0000.0000.000
159A159ALA0-0.037-0.02622.770-0.004-0.0040.0000.0000.0000.000
160A160GLY0-0.0020.01224.8640.0060.0060.0000.0000.0000.000
161A161ASP-1-0.893-0.95025.8050.2440.2440.0000.0000.0000.000
162A162ARG10.7710.87117.980-0.426-0.4260.0000.0000.0000.000
163A163PHE00.0010.01216.282-0.002-0.0020.0000.0000.0000.000
164A164THR0-0.063-0.04517.4610.0390.0390.0000.0000.0000.000
165A165VAL00.048-0.00214.896-0.022-0.0220.0000.0000.0000.000
166A166ALA00.0000.00916.601-0.029-0.0290.0000.0000.0000.000
167A167ASP-1-0.743-0.85319.8490.2720.2720.0000.0000.0000.000
168A168ILE00.0220.02213.987-0.033-0.0330.0000.0000.0000.000
169A169THR0-0.037-0.02718.118-0.024-0.0240.0000.0000.0000.000
170A170ALA00.0150.00819.661-0.034-0.0340.0000.0000.0000.000
171A171TYR0-0.051-0.03619.909-0.026-0.0260.0000.0000.0000.000
172A172ALA00.0280.00919.001-0.027-0.0270.0000.0000.0000.000
173A173GLY00.005-0.00321.157-0.025-0.0250.0000.0000.0000.000
174A174LEU00.008-0.00124.194-0.022-0.0220.0000.0000.0000.000
175A175VAL00.0300.02322.853-0.017-0.0170.0000.0000.0000.000
176A176PHE0-0.002-0.01623.617-0.021-0.0210.0000.0000.0000.000
177A177ALA0-0.013-0.00225.516-0.014-0.0140.0000.0000.0000.000
178A178GLU-1-0.752-0.83728.7260.0760.0760.0000.0000.0000.000
179A179PHE0-0.045-0.01126.585-0.012-0.0120.0000.0000.0000.000
180A180ALA0-0.005-0.01228.795-0.011-0.0110.0000.0000.0000.000
181A181LYS10.8090.90430.400-0.050-0.0500.0000.0000.0000.000
182A182VAL0-0.036-0.00931.459-0.002-0.0020.0000.0000.0000.000
183A183ASP-1-0.794-0.89532.6500.0690.0690.0000.0000.0000.000
184A184ILE00.0560.02129.8100.0060.0060.0000.0000.0000.000
185A185PRO0-0.045-0.02534.158-0.006-0.0060.0000.0000.0000.000
186A186GLY00.0370.01436.7430.0040.0040.0000.0000.0000.000
187A187HIS0-0.011-0.00638.261-0.004-0.0040.0000.0000.0000.000
188A188LEU0-0.056-0.00634.3120.0010.0010.0000.0000.0000.000
189A189ASP-1-0.792-0.91534.5130.1060.1060.0000.0000.0000.000
190A190HIS00.0130.01432.9740.0070.0070.0000.0000.0000.000
191A191LEU0-0.001-0.00328.8950.0090.0090.0000.0000.0000.000
192A192LEU0-0.025-0.01729.6860.0060.0060.0000.0000.0000.000
193A193ALA00.0100.00430.5030.0010.0010.0000.0000.0000.000
194A194TRP0-0.079-0.03723.015-0.004-0.0040.0000.0000.0000.000
195A195ARG10.8320.87725.846-0.104-0.1040.0000.0000.0000.000
196A196ALA0-0.032-0.01225.7870.0020.0020.0000.0000.0000.000
197A197ARG10.8070.87526.297-0.152-0.1520.0000.0000.0000.000
198A198VAL0-0.032-0.00920.6860.0110.0110.0000.0000.0000.000
199A199ALA0-0.013-0.02021.5870.0080.0080.0000.0000.0000.000
200A200ALA0-0.0230.00022.901-0.010-0.0100.0000.0000.0000.000
201A201ARG10.8170.88916.974-0.301-0.3010.0000.0000.0000.000
202A202PRO00.004-0.00717.336-0.005-0.0050.0000.0000.0000.000
203A203SER0-0.083-0.06014.363-0.029-0.0290.0000.0000.0000.000
204A204ILE0-0.044-0.02715.2670.0160.0160.0000.0000.0000.000
205A205THR00.0000.00518.150-0.021-0.0210.0000.0000.0000.000
206A206GLY00.0050.01620.159-0.012-0.0120.0000.0000.0000.000
207A207ALA0-0.041-0.03523.172-0.005-0.0050.0000.0000.0000.000
208A208GLU-1-0.815-0.88119.2430.1030.1030.0000.0000.0000.000
209A209ASN0-0.047-0.03421.6220.0080.0080.0000.0000.0000.000
210A210LEU0-0.025-0.00120.827-0.005-0.0050.0000.0000.0000.000
211A211TYR0-0.027-0.02620.801-0.011-0.0110.0000.0000.0000.000
212A212PHE00.0360.01822.854-0.001-0.0010.0000.0000.0000.000
213A213GLN0-0.0070.00024.5770.0030.0030.0000.0000.0000.000