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

tag_button

FMODB ID: 1NL9Z

Calculation Name: 2GZ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D028

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2257082.48844
FMO2-HF: Nuclear repulsion 2178706.096938
FMO2-HF: Total energy -78376.391502
FMO2-MP2: Total energy -78603.165246


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:6:SER)


Summations of interaction energy for fragment #1(A:6:SER)
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.
1.5622.6-0.008-0.417-0.6130.002
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.005
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].
3A8ARG10.9270.9453.8870.5991.637-0.008-0.417-0.6130.002
4A9ALA00.0520.0316.0750.6780.6780.0000.0000.0000.000
5A10TRP00.0060.0027.0770.2300.2300.0000.0000.0000.000
6A11GLN0-0.007-0.01010.508-0.260-0.2600.0000.0000.0000.000
7A12ARG10.8670.92511.9000.6830.6830.0000.0000.0000.000
8A13MET0-0.0020.02014.075-0.011-0.0110.0000.0000.0000.000
9A14LEU00.007-0.01217.841-0.008-0.0080.0000.0000.0000.000
10A15SER0-0.044-0.04419.9170.0050.0050.0000.0000.0000.000
11A16GLY00.0110.01618.3370.0270.0270.0000.0000.0000.000
12A17ARG10.9040.95717.1980.2080.2080.0000.0000.0000.000
13A18ARG10.8510.89811.5210.3720.3720.0000.0000.0000.000
14A19LEU00.0560.06115.3680.0490.0490.0000.0000.0000.000
15A20ASP-1-0.816-0.92411.860-0.533-0.5330.0000.0000.0000.000
16A21LEU0-0.023-0.01410.7880.0460.0460.0000.0000.0000.000
17A22LEU0-0.032-0.00711.5470.0720.0720.0000.0000.0000.000
18A23ASP-1-0.861-0.90914.619-0.008-0.0080.0000.0000.0000.000
19A24PRO0-0.030-0.00316.577-0.011-0.0110.0000.0000.0000.000
20A25SER00.034-0.00618.0050.0410.0410.0000.0000.0000.000
21A26PRO00.027-0.01220.009-0.020-0.0200.0000.0000.0000.000
22A27LEU0-0.025-0.00622.4110.0010.0010.0000.0000.0000.000
23A28ASP-1-0.900-0.92218.499-0.231-0.2310.0000.0000.0000.000
24A29VAL0-0.038-0.01720.252-0.036-0.0360.0000.0000.0000.000
25A30GLU-1-0.826-0.90822.684-0.146-0.1460.0000.0000.0000.000
26A31ILE00.0220.02425.326-0.017-0.0170.0000.0000.0000.000
27A32ALA00.0270.01826.612-0.004-0.0040.0000.0000.0000.000
28A33ASP-1-0.779-0.85821.671-0.296-0.2960.0000.0000.0000.000
29A34ILE00.005-0.00423.462-0.017-0.0170.0000.0000.0000.000
30A35ALA00.0110.01325.111-0.004-0.0040.0000.0000.0000.000
31A36HIS0-0.011-0.00723.0020.0160.0160.0000.0000.0000.000
32A37GLY00.0290.02622.920-0.011-0.0110.0000.0000.0000.000
33A38LEU00.0280.00423.5630.0020.0020.0000.0000.0000.000
34A39ALA00.0000.01626.5380.0120.0120.0000.0000.0000.000
35A40ARG10.7950.88024.6030.2470.2470.0000.0000.0000.000
36A41VAL0-0.038-0.00222.475-0.006-0.0060.0000.0000.0000.000
37A42ALA00.0260.01725.1480.0180.0180.0000.0000.0000.000
38A43ARG10.8560.92127.3780.1100.1100.0000.0000.0000.000
39A44TRP0-0.060-0.04529.9760.0040.0040.0000.0000.0000.000
40A45ASN0-0.032-0.02427.264-0.001-0.0010.0000.0000.0000.000
41A46GLY00.0350.02228.270-0.005-0.0050.0000.0000.0000.000
42A47GLN0-0.057-0.00230.1150.0020.0020.0000.0000.0000.000
43A48THR0-0.037-0.03833.1060.0060.0060.0000.0000.0000.000
44A49ARG10.8360.89635.5760.0690.0690.0000.0000.0000.000
45A50GLY00.0390.00837.9850.0010.0010.0000.0000.0000.000
46A51ASP-1-0.938-0.95136.732-0.108-0.1080.0000.0000.0000.000
47A52HIS0-0.028-0.01533.696-0.016-0.0160.0000.0000.0000.000
48A53ALA00.0160.00730.1780.0060.0060.0000.0000.0000.000
49A54PHE00.0240.01132.147-0.003-0.0030.0000.0000.0000.000
50A55THR00.0290.02129.918-0.006-0.0060.0000.0000.0000.000
51A56VAL00.0180.00226.8990.0130.0130.0000.0000.0000.000
52A57ALA00.0090.01229.8050.0100.0100.0000.0000.0000.000
53A58GLN00.022-0.01231.2450.0030.0030.0000.0000.0000.000
54A59HIS10.7700.87731.9940.1200.1200.0000.0000.0000.000
55A60CYS0-0.059-0.02431.2400.0070.0070.0000.0000.0000.000
56A61LEU00.0190.01434.1220.0080.0080.0000.0000.0000.000
57A62ILE0-0.0130.01737.1550.0080.0080.0000.0000.0000.000
58A63VAL00.000-0.00535.6760.0070.0070.0000.0000.0000.000
59A64GLU-1-0.755-0.84837.273-0.072-0.0720.0000.0000.0000.000
60A65THR00.0160.00339.0930.0060.0060.0000.0000.0000.000
61A66ILE0-0.038-0.02241.1890.0060.0060.0000.0000.0000.000
62A67PHE0-0.013-0.02040.1340.0050.0050.0000.0000.0000.000
63A68CYS00.000-0.01042.2430.0050.0050.0000.0000.0000.000
64A69ARG10.9150.96144.6770.0560.0560.0000.0000.0000.000
65A70MET0-0.057-0.03444.5630.0030.0030.0000.0000.0000.000
66A71CYS0-0.076-0.01344.1440.0040.0040.0000.0000.0000.000
67A72PRO00.0350.01046.644-0.001-0.0010.0000.0000.0000.000
68A73GLY0-0.0110.00048.7960.0010.0010.0000.0000.0000.000
69A74ALA0-0.043-0.00943.4100.0010.0010.0000.0000.0000.000
70A75THR0-0.050-0.06842.435-0.001-0.0010.0000.0000.0000.000
71A76PRO00.026-0.01041.765-0.002-0.0020.0000.0000.0000.000
72A77ASP-1-0.778-0.88238.115-0.068-0.0680.0000.0000.0000.000
73A78GLU-1-0.783-0.85737.325-0.053-0.0530.0000.0000.0000.000
74A79MET0-0.0180.01038.213-0.004-0.0040.0000.0000.0000.000
75A80GLN0-0.012-0.02133.884-0.008-0.0080.0000.0000.0000.000
76A81MET0-0.017-0.01833.508-0.005-0.0050.0000.0000.0000.000
77A82ALA0-0.042-0.02633.727-0.005-0.0050.0000.0000.0000.000
78A83LEU0-0.044-0.00833.543-0.004-0.0040.0000.0000.0000.000
79A84LEU0-0.016-0.01729.292-0.012-0.0120.0000.0000.0000.000
80A85HIS00.0030.01329.2740.0000.0000.0000.0000.0000.000
81A86ASP-1-0.826-0.90928.347-0.120-0.1200.0000.0000.0000.000
82A87ALA00.0310.01126.578-0.017-0.0170.0000.0000.0000.000
83A88PRO00.0220.00023.009-0.026-0.0260.0000.0000.0000.000
84A89GLH0-0.047-0.06021.855-0.024-0.0240.0000.0000.0000.000
85A90TYR0-0.036-0.01620.787-0.021-0.0210.0000.0000.0000.000
86A91VAL0-0.036-0.01216.276-0.041-0.0410.0000.0000.0000.000
87A92ILE0-0.060-0.02417.416-0.044-0.0440.0000.0000.0000.000
88A93GLY00.0050.01219.5100.0090.0090.0000.0000.0000.000
89A94ASP-1-0.821-0.89321.484-0.130-0.1300.0000.0000.0000.000
90A95MET0-0.038-0.02323.545-0.006-0.0060.0000.0000.0000.000
91A96ILE00.0330.02625.6420.0120.0120.0000.0000.0000.000
92A97SER00.033-0.00528.7440.0020.0020.0000.0000.0000.000
93A98PRO00.0120.00730.4770.0050.0050.0000.0000.0000.000
94A99PHE00.0810.03425.6070.0090.0090.0000.0000.0000.000
95A100LYS10.8810.94624.8520.1320.1320.0000.0000.0000.000
96A101SER0-0.041-0.01727.4300.0050.0050.0000.0000.0000.000
97A102VAL0-0.031-0.01025.2820.0100.0100.0000.0000.0000.000
98A103VAL0-0.0240.00021.0180.0120.0120.0000.0000.0000.000
99A104GLY00.0380.03021.7040.0020.0020.0000.0000.0000.000
100A105GLY00.011-0.01123.486-0.014-0.0140.0000.0000.0000.000
101A106GLY00.0240.01719.082-0.006-0.0060.0000.0000.0000.000
102A107TYR00.0630.02819.282-0.006-0.0060.0000.0000.0000.000
103A108LYS10.9260.95620.4580.0400.0400.0000.0000.0000.000
104A109THR0-0.052-0.02620.8320.0020.0020.0000.0000.0000.000
105A110VAL00.0300.01816.9950.0000.0000.0000.0000.0000.000
106A111GLU-1-0.826-0.91520.046-0.124-0.1240.0000.0000.0000.000
107A112LYS10.9220.96523.2000.0440.0440.0000.0000.0000.000
108A113ARG10.8020.87418.0900.0800.0800.0000.0000.0000.000
109A114LEU00.0370.01618.453-0.003-0.0030.0000.0000.0000.000
110A115GLU-1-0.810-0.88622.202-0.080-0.0800.0000.0000.0000.000
111A116ALA0-0.0150.00124.8430.0030.0030.0000.0000.0000.000
112A117ALA00.0010.00121.9470.0040.0040.0000.0000.0000.000
113A118VAL00.005-0.00923.963-0.001-0.0010.0000.0000.0000.000
114A119HIS0-0.062-0.04126.0490.0030.0030.0000.0000.0000.000
115A120LEU00.0030.00026.5070.0060.0060.0000.0000.0000.000
116A121ARG10.8050.90425.5480.1460.1460.0000.0000.0000.000
117A122PHE0-0.008-0.00727.7770.0000.0000.0000.0000.0000.000
118A123GLY00.0360.02031.1860.0070.0070.0000.0000.0000.000
119A124LEU0-0.041-0.00132.0640.0060.0060.0000.0000.0000.000
120A125PRO00.011-0.01432.3270.0000.0000.0000.0000.0000.000
121A126PRO00.0240.01729.136-0.005-0.0050.0000.0000.0000.000
122A127HIS0-0.089-0.05827.1000.0000.0000.0000.0000.0000.000
123A128ALA00.0830.05031.6570.0050.0050.0000.0000.0000.000
124A129SER00.0220.01334.8080.0030.0030.0000.0000.0000.000
125A130ARG10.9690.96637.0070.0210.0210.0000.0000.0000.000
126A131GLU-1-0.829-0.88738.502-0.041-0.0410.0000.0000.0000.000
127A132LEU00.0660.04737.237-0.001-0.0010.0000.0000.0000.000
128A133LYS10.8480.89430.3010.0750.0750.0000.0000.0000.000
129A134ASP-1-0.856-0.89836.778-0.043-0.0430.0000.0000.0000.000
130A135ARG10.7740.84639.5240.0430.0430.0000.0000.0000.000
131A136ILE00.0260.01834.978-0.002-0.0020.0000.0000.0000.000
132A137LYS10.8700.93734.0200.0690.0690.0000.0000.0000.000
133A138LYS10.8120.89037.2570.0390.0390.0000.0000.0000.000
134A139ALA00.0520.03339.3140.0000.0000.0000.0000.0000.000
135A140ASP-1-0.806-0.91134.447-0.092-0.0920.0000.0000.0000.000
136A141THR0-0.077-0.04837.261-0.002-0.0020.0000.0000.0000.000
137A142VAL00.012-0.00639.1280.0010.0010.0000.0000.0000.000
138A143ALA00.0240.01238.0730.0000.0000.0000.0000.0000.000
139A144ALA0-0.021-0.00736.691-0.002-0.0020.0000.0000.0000.000
140A145PHE00.0230.00538.3090.0010.0010.0000.0000.0000.000
141A146PHE00.0420.01441.8760.0020.0020.0000.0000.0000.000
142A147GLU-1-0.727-0.82935.410-0.103-0.1030.0000.0000.0000.000
143A148ALA0-0.011-0.00238.736-0.002-0.0020.0000.0000.0000.000
144A149THR0-0.029-0.02339.6420.0010.0010.0000.0000.0000.000
145A150GLU-1-0.842-0.90742.067-0.068-0.0680.0000.0000.0000.000
146A151LEU0-0.049-0.01337.399-0.001-0.0010.0000.0000.0000.000
147A152ALA0-0.014-0.01035.879-0.001-0.0010.0000.0000.0000.000
148A153GLY0-0.0080.00537.4690.0000.0000.0000.0000.0000.000
149A154PHE0-0.059-0.01536.2630.0040.0040.0000.0000.0000.000
150A155SER0-0.003-0.03841.9070.0010.0010.0000.0000.0000.000
151A156THR00.035-0.00944.900-0.001-0.0010.0000.0000.0000.000
152A157ALA00.0160.01847.0880.0010.0010.0000.0000.0000.000
153A158GLU-1-0.804-0.86642.090-0.049-0.0490.0000.0000.0000.000
154A159ALA00.0220.01642.1960.0000.0000.0000.0000.0000.000
155A160GLN0-0.009-0.01243.2630.0000.0000.0000.0000.0000.000
156A161LYS10.8840.94643.9060.0300.0300.0000.0000.0000.000
157A162PHE0-0.044-0.02439.1960.0030.0030.0000.0000.0000.000
158A163PHE0-0.031-0.01536.921-0.002-0.0020.0000.0000.0000.000
159A164GLY00.0160.02841.7400.0000.0000.0000.0000.0000.000
160A165LEU0-0.009-0.01745.505-0.002-0.0020.0000.0000.0000.000
161A166PRO0-0.0030.01045.5110.0020.0020.0000.0000.0000.000
162A167ARG10.9410.96947.9410.0360.0360.0000.0000.0000.000
163A168GLY0-0.004-0.01350.9960.0010.0010.0000.0000.0000.000
164A169ILE0-0.017-0.00245.365-0.001-0.0010.0000.0000.0000.000
165A170THR0-0.024-0.06548.8360.0010.0010.0000.0000.0000.000
166A171ARG10.8880.92945.3690.0680.0680.0000.0000.0000.000
167A172ASP-1-0.855-0.89447.299-0.056-0.0560.0000.0000.0000.000
168A173MET0-0.100-0.02246.980-0.001-0.0010.0000.0000.0000.000
169A174PHE00.0250.00242.253-0.002-0.0020.0000.0000.0000.000
170A175ASP-1-0.884-0.92741.504-0.081-0.0810.0000.0000.0000.000
171A176ILE0-0.045-0.02639.130-0.006-0.0060.0000.0000.0000.000
172A177ILE00.0260.00939.425-0.003-0.0030.0000.0000.0000.000
173A178PRO0-0.0150.00535.537-0.002-0.0020.0000.0000.0000.000
174A179LEU00.0090.01736.3040.0010.0010.0000.0000.0000.000
175A180PRO00.0230.00834.037-0.009-0.0090.0000.0000.0000.000
176A181SER00.008-0.01229.1000.0010.0010.0000.0000.0000.000
177A182THR0-0.015-0.01731.190-0.003-0.0030.0000.0000.0000.000
178A183GLU-1-0.739-0.82432.699-0.111-0.1110.0000.0000.0000.000
179A184ALA0-0.008-0.00232.3080.0040.0040.0000.0000.0000.000
180A185GLN00.0400.01627.514-0.001-0.0010.0000.0000.0000.000
181A186ARG10.8040.86731.6970.1130.1130.0000.0000.0000.000
182A187LEU00.0090.00234.9200.0050.0050.0000.0000.0000.000
183A188PHE00.0080.00429.6200.0040.0040.0000.0000.0000.000
184A189ILE0-0.025-0.01230.4080.0010.0010.0000.0000.0000.000
185A190ALA00.0540.03433.9330.0060.0060.0000.0000.0000.000
186A191ARG10.8000.87437.2450.0870.0870.0000.0000.0000.000
187A192PHE00.0660.02032.1430.0040.0040.0000.0000.0000.000
188A193GLU-1-0.872-0.94735.560-0.108-0.1080.0000.0000.0000.000
189A194ALA0-0.0180.00237.5840.0070.0070.0000.0000.0000.000
190A195ILE0-0.037-0.01737.5180.0060.0060.0000.0000.0000.000
191A196GLU-1-0.798-0.87435.388-0.086-0.0860.0000.0000.0000.000
192A197THR0-0.021-0.01338.5750.0060.0060.0000.0000.0000.000
193A198LEU0-0.031-0.00942.0490.0050.0050.0000.0000.0000.000
194A199ARG10.7830.85634.8220.0820.0820.0000.0000.0000.000
195A200VAL00.0030.01740.5380.0040.0040.0000.0000.0000.000
196A201THR0-0.054-0.03742.9370.0040.0040.0000.0000.0000.000
197A202ARG10.8660.93444.3560.0480.0480.0000.0000.0000.000
198A203THR0-0.041-0.02042.4740.0030.0030.0000.0000.0000.000
199A204GLY0-0.0140.00845.0910.0030.0030.0000.0000.0000.000
200A205GLY0-0.029-0.01745.923-0.002-0.0020.0000.0000.0000.000