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

tag_button

FMODB ID: 89Q2Y

Calculation Name: 2G5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G5X

Chain ID: A

ChEMBL ID:

UniProt ID: P85101

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2989964.868182
FMO2-HF: Nuclear repulsion 2898784.212826
FMO2-HF: Total energy -91180.655356
FMO2-MP2: Total energy -91448.642142


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:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
-38.712-30.28925.522-14.738-19.21-0.156
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.912
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].
3A3SER0-0.020-0.0233.072-7.139-4.6970.098-1.135-1.405-0.001
4A4TRP00.0720.0305.4853.3923.3920.0000.0000.0000.000
5A5THR0-0.032-0.0109.033-0.562-0.5620.0000.0000.0000.000
6A6VAL0-0.017-0.01411.7551.1921.1920.0000.0000.0000.000
7A7ASP-1-0.832-0.91414.010-15.086-15.0860.0000.0000.0000.000
8A8SER0-0.041-0.02617.071-0.051-0.0510.0000.0000.0000.000
9A9ASP-1-0.785-0.87416.929-15.388-15.3880.0000.0000.0000.000
10A10SER00.1030.01216.860-0.765-0.7650.0000.0000.0000.000
11A11ALA00.0060.02517.289-0.364-0.3640.0000.0000.0000.000
12A12LYS10.8580.91212.75816.60916.6090.0000.0000.0000.000
13A13TYR0-0.048-0.03012.397-1.231-1.2310.0000.0000.0000.000
14A14SER00.048-0.00713.009-0.805-0.8050.0000.0000.0000.000
15A15SER0-0.041-0.02311.327-0.081-0.0810.0000.0000.0000.000
16A16PHE0-0.057-0.0196.053-1.423-1.4230.0000.0000.0000.000
17A17LEU00.0060.0008.964-1.737-1.7370.0000.0000.0000.000
18A18ASP-1-0.840-0.90211.078-17.248-17.2480.0000.0000.0000.000
19A19SER0-0.054-0.0235.600-1.668-1.6680.0000.0000.0000.000
20A20LEU0-0.026-0.0246.615-1.209-1.2090.0000.0000.0000.000
21A21ARG10.7130.8097.85717.29317.2930.0000.0000.0000.000
22A22GLU-1-0.786-0.8829.027-16.699-16.6990.0000.0000.0000.000
23A23GLU-1-0.889-0.9354.390-31.718-31.491-0.001-0.029-0.1970.000
24A24PHE0-0.055-0.0337.8390.3460.3460.0000.0000.0000.000
25A25GLY00.0070.01110.8421.1151.1150.0000.0000.0000.000
26A26ARG10.8450.9395.61329.77629.7760.0000.0000.0000.000
27A27GLY00.006-0.00412.192-0.031-0.0310.0000.0000.0000.000
28A28THR0-0.022-0.00615.2110.5850.5850.0000.0000.0000.000
29A29PRO00.0110.00417.297-0.467-0.4670.0000.0000.0000.000
30A30LYS10.8300.91614.52615.49815.4980.0000.0000.0000.000
31A31VAL00.0340.01219.5930.5360.5360.0000.0000.0000.000
32A32CYS0-0.028-0.01122.182-0.342-0.3420.0000.0000.0000.000
33A33ASN0-0.031-0.01919.527-0.351-0.3510.0000.0000.0000.000
34A34ILE00.0360.03618.278-0.414-0.4140.0000.0000.0000.000
35A35PRO00.0040.01413.8860.3900.3900.0000.0000.0000.000
36A36VAL00.0460.02316.1890.2330.2330.0000.0000.0000.000
37A37THR00.0040.01014.714-0.263-0.2630.0000.0000.0000.000
38A38LYS10.8160.87714.73816.95916.9590.0000.0000.0000.000
39A39LYS10.9690.98117.54211.17711.1770.0000.0000.0000.000
40A40ALA0-0.001-0.00219.641-0.055-0.0550.0000.0000.0000.000
41A41ASN0-0.0130.00213.4790.1650.1650.0000.0000.0000.000
42A42ASN00.0530.02114.697-0.872-0.8720.0000.0000.0000.000
43A43ASP-1-0.851-0.91415.846-18.118-18.1180.0000.0000.0000.000
44A44LYS10.8240.90011.48217.31117.3110.0000.0000.0000.000
45A45PHE00.013-0.0058.9251.1241.1240.0000.0000.0000.000
46A46VAL00.0120.0205.620-1.860-1.8600.0000.0000.0000.000
47A47LEU0-0.039-0.0152.426-2.312-0.4301.850-0.834-2.8990.001
48A48VAL00.0140.0052.961-4.266-2.4670.523-0.864-1.460-0.009
49A49ASN00.0050.0132.512-16.009-12.5432.577-2.103-3.941-0.026
50A50LEU00.0390.0344.7814.0464.079-0.001-0.012-0.0200.000
51A51VAL0-0.039-0.0327.700-0.648-0.6480.0000.0000.0000.000
52A52LEU00.0280.02310.1391.8041.8040.0000.0000.0000.000
53A53PRO00.007-0.00613.921-0.528-0.5280.0000.0000.0000.000
54A54PHE0-0.019-0.01015.9040.2220.2220.0000.0000.0000.000
55A55ASN00.0530.01115.597-0.508-0.5080.0000.0000.0000.000
56A56ARG10.9240.98011.12622.17422.1740.0000.0000.0000.000
57A57ASN00.0290.02911.335-2.468-2.4680.0000.0000.0000.000
58A58THR0-0.032-0.0295.634-0.681-0.6810.0000.0000.0000.000
59A59ILE0-0.0210.0067.8210.1830.1830.0000.0000.0000.000
60A60THR0-0.060-0.0382.573-2.799-1.2910.584-0.694-1.398-0.001
61A61LEU00.006-0.0035.1443.8243.876-0.001-0.003-0.0480.000
62A62ALA00.0400.0195.598-4.849-4.8490.0000.0000.0000.000
63A63PHE00.004-0.0087.8323.5343.5340.0000.0000.0000.000
64A64ARG10.8120.8799.87316.50116.5010.0000.0000.0000.000
65A65ALA00.004-0.02610.5710.4970.4970.0000.0000.0000.000
66A66SER0-0.021-0.01412.1430.3710.3710.0000.0000.0000.000
67A67ASP-1-0.841-0.92915.424-16.124-16.1240.0000.0000.0000.000
68A68ALA00.0230.02812.6830.4580.4580.0000.0000.0000.000
69A69TYR0-0.042-0.01713.7230.1800.1800.0000.0000.0000.000
70A70LEU0-0.0260.00010.633-1.160-1.1600.0000.0000.0000.000
71A71VAL00.0210.00311.6391.2881.2880.0000.0000.0000.000
72A72GLY00.010-0.00211.7991.1891.1890.0000.0000.0000.000
73A73PHE0-0.045-0.0288.793-1.635-1.6350.0000.0000.0000.000
74A74GLN00.0320.0223.1385.5135.7660.004-0.066-0.1910.000
75A75ASP-1-0.724-0.8457.670-24.557-24.5570.0000.0000.0000.000
76A76ARG10.8910.9438.49926.83826.8380.0000.0000.0000.000
77A77ASP-1-0.824-0.90411.680-15.701-15.7010.0000.0000.0000.000
78A78SER00.0110.00615.0020.0170.0170.0000.0000.0000.000
79A79LYS10.9400.98517.90413.20413.2040.0000.0000.0000.000
80A80THR0-0.049-0.04916.5110.0560.0560.0000.0000.0000.000
81A81ASN00.0110.00414.327-0.869-0.8690.0000.0000.0000.000
82A82LYS10.9090.96612.23518.94218.9420.0000.0000.0000.000
83A83LEU0-0.040-0.0195.3770.4260.4260.0000.0000.0000.000
84A84ARG10.8040.8809.25620.87320.8730.0000.0000.0000.000
85A85ALA00.0020.0009.493-1.712-1.7120.0000.0000.0000.000
86A86ASN0-0.004-0.01910.5063.4253.4250.0000.0000.0000.000
87A87PHE00.0230.00911.809-1.136-1.1360.0000.0000.0000.000
88A88PHE00.0290.01214.8590.9570.9570.0000.0000.0000.000
89A89SER0-0.004-0.02917.7140.2390.2390.0000.0000.0000.000
90A90ASP-1-0.802-0.87320.207-14.668-14.6680.0000.0000.0000.000
91A91GLU-1-0.744-0.85016.635-17.484-17.4840.0000.0000.0000.000
92A92TYR0-0.032-0.00817.249-0.120-0.1200.0000.0000.0000.000
93A93ARG10.9510.97218.84412.13912.1390.0000.0000.0000.000
94A94ALA00.0260.02119.5660.1490.1490.0000.0000.0000.000
95A95LEU0-0.013-0.00713.874-0.429-0.4290.0000.0000.0000.000
96A96SER0-0.037-0.01615.204-0.879-0.8790.0000.0000.0000.000
97A97GLY00.0290.00915.750-0.682-0.6820.0000.0000.0000.000
98A98LYS10.9130.97413.60220.60820.6080.0000.0000.0000.000
99A99TYR00.0810.03010.516-2.296-2.2960.0000.0000.0000.000
100A100LYS10.8270.9107.03230.90330.9030.0000.0000.0000.000
101A101SER0-0.072-0.0448.464-1.883-1.8830.0000.0000.0000.000
102A102ILE0-0.034-0.0038.872-0.856-0.8560.0000.0000.0000.000
103A103PHE00.001-0.0075.479-4.623-4.6230.0000.0000.0000.000
104A104THR00.0400.0152.911-0.858-0.2290.110-0.187-0.5520.001
105A105ASP-1-0.795-0.8821.798-122.286-126.21019.780-8.797-7.059-0.121
106A106ALA0-0.0180.0104.7045.1285.184-0.001-0.014-0.0400.000
107A107GLU-1-0.828-0.9007.685-23.299-23.2990.0000.0000.0000.000
108A108VAL0-0.009-0.00110.9402.2072.2070.0000.0000.0000.000
109A109LEU0-0.0150.01012.068-1.767-1.7670.0000.0000.0000.000
110A110ALA00.0010.01014.0421.2431.2430.0000.0000.0000.000
111A111PRO0-0.005-0.02315.8300.0750.0750.0000.0000.0000.000
112A112ALA0-0.008-0.00117.601-0.750-0.7500.0000.0000.0000.000
113A113LEU0-0.0010.01014.5310.5640.5640.0000.0000.0000.000
114A114PRO0-0.031-0.01418.8900.5540.5540.0000.0000.0000.000
115A115CYS0-0.031-0.02719.9020.4710.4710.0000.0000.0000.000
116A116ALA0-0.045-0.00220.569-0.681-0.6810.0000.0000.0000.000
117A117SER00.003-0.02917.656-0.107-0.1070.0000.0000.0000.000
118A118THR00.0290.03319.1320.1110.1110.0000.0000.0000.000
119A119TYR00.057-0.02320.0220.0510.0510.0000.0000.0000.000
120A120THR0-0.0040.00923.1710.1990.1990.0000.0000.0000.000
121A121ASP-1-0.784-0.88323.778-12.047-12.0470.0000.0000.0000.000
122A122LEU00.0070.01418.5050.1020.1020.0000.0000.0000.000
123A123GLN00.0360.00122.7670.2130.2130.0000.0000.0000.000
124A124ASN0-0.0200.00025.6670.4290.4290.0000.0000.0000.000
125A125LYS10.7830.88424.16512.22912.2290.0000.0000.0000.000
126A126ALA0-0.051-0.02423.2910.0750.0750.0000.0000.0000.000
127A127GLY0-0.024-0.01025.2160.1880.1880.0000.0000.0000.000
128A128VAL0-0.071-0.03725.5570.3210.3210.0000.0000.0000.000
129A129SER0-0.005-0.02726.668-0.316-0.3160.0000.0000.0000.000
130A130ARG10.8580.89423.18512.07612.0760.0000.0000.0000.000
131A131GLU-1-0.872-0.90925.306-10.666-10.6660.0000.0000.0000.000
132A132LYS10.8960.93428.01010.20110.2010.0000.0000.0000.000
133A133LEU0-0.0230.01921.1890.0530.0530.0000.0000.0000.000
134A134SER0-0.016-0.01324.855-0.036-0.0360.0000.0000.0000.000
135A135LEU0-0.030-0.01020.103-0.722-0.7220.0000.0000.0000.000
136A136GLY00.0660.01619.8110.6240.6240.0000.0000.0000.000
137A137VAL00.0050.00417.307-0.613-0.6130.0000.0000.0000.000
138A138SER00.0600.02818.840-0.438-0.4380.0000.0000.0000.000
139A139SER0-0.016-0.00120.9450.0040.0040.0000.0000.0000.000
140A140LEU00.0090.00713.296-0.107-0.1070.0000.0000.0000.000
141A141GLN00.000-0.01216.971-0.069-0.0690.0000.0000.0000.000
142A142THR0-0.020-0.01118.023-0.056-0.0560.0000.0000.0000.000
143A143ALA0-0.037-0.02218.0560.0990.0990.0000.0000.0000.000
144A144PHE00.0220.01110.5520.0980.0980.0000.0000.0000.000
145A145THR0-0.012-0.01315.738-0.415-0.4150.0000.0000.0000.000
146A146ALA0-0.053-0.00818.0020.3650.3650.0000.0000.0000.000
147A147VAL0-0.024-0.01314.4210.4700.4700.0000.0000.0000.000
148A148TYR0-0.014-0.01910.406-0.540-0.5400.0000.0000.0000.000
149A149GLY00.0200.01914.2491.0051.0050.0000.0000.0000.000
150A150LYS10.8270.91315.80216.10416.1040.0000.0000.0000.000
151A151VAL00.0110.00518.510-0.501-0.5010.0000.0000.0000.000
152A152PHE0-0.022-0.00714.3510.4000.4000.0000.0000.0000.000
153A153THR00.0450.01820.3120.4890.4890.0000.0000.0000.000
154A154GLY00.0590.01121.726-0.489-0.4890.0000.0000.0000.000
155A155LYS10.9780.99622.52110.63210.6320.0000.0000.0000.000
156A156ASN0-0.025-0.01520.3360.1700.1700.0000.0000.0000.000
157A157VAL00.0210.01016.601-0.602-0.6020.0000.0000.0000.000
158A158ALA00.0480.02417.965-0.719-0.7190.0000.0000.0000.000
159A159LYS10.9540.97619.82612.58712.5870.0000.0000.0000.000
160A160PHE00.0130.01211.524-0.036-0.0360.0000.0000.0000.000
161A161ALA00.0150.01415.009-0.835-0.8350.0000.0000.0000.000
162A162LEU00.0090.00316.086-0.331-0.3310.0000.0000.0000.000
163A163ILE00.0080.00317.1170.0830.0830.0000.0000.0000.000
164A164SER0-0.014-0.01612.423-0.618-0.6180.0000.0000.0000.000
165A165ILE0-0.026-0.01513.711-0.725-0.7250.0000.0000.0000.000
166A166GLN0-0.036-0.02415.4780.3390.3390.0000.0000.0000.000
167A167MET0-0.0020.01015.0600.1960.1960.0000.0000.0000.000
168A168VAL0-0.0050.0179.200-0.589-0.5890.0000.0000.0000.000
169A169ALA00.0090.00512.455-0.012-0.0120.0000.0000.0000.000
170A170GLU-1-0.763-0.85813.756-14.451-14.4510.0000.0000.0000.000
171A171ALA00.0140.01315.1170.6260.6260.0000.0000.0000.000
172A172ALA00.0150.01912.4740.3380.3380.0000.0000.0000.000
173A173ARG10.8120.90314.57916.57516.5750.0000.0000.0000.000
174A174PHE00.0220.01517.5650.6740.6740.0000.0000.0000.000
175A175LYS10.9510.95918.21814.10914.1090.0000.0000.0000.000
176A176TYR00.0440.03320.759-0.022-0.0220.0000.0000.0000.000
177A177ILE0-0.011-0.01319.5770.2430.2430.0000.0000.0000.000
178A178GLU-1-0.724-0.81317.351-15.809-15.8090.0000.0000.0000.000
179A179ASP-1-0.881-0.94719.090-12.436-12.4360.0000.0000.0000.000
180A180GLN0-0.0200.00922.4090.4030.4030.0000.0000.0000.000
181A181VAL0-0.018-0.01017.5830.2240.2240.0000.0000.0000.000
182A182ILE0-0.030-0.01218.8450.0020.0020.0000.0000.0000.000
183A183ASN0-0.063-0.04721.2200.4800.4800.0000.0000.0000.000
184A184ARG10.8840.94424.11511.15911.1590.0000.0000.0000.000
185A185GLY0-0.032-0.00621.6260.1410.1410.0000.0000.0000.000
186A186MET0-0.0350.00417.212-0.814-0.8140.0000.0000.0000.000
187A187TYR00.018-0.01321.475-0.078-0.0780.0000.0000.0000.000
188A188SER0-0.0030.01124.3950.3610.3610.0000.0000.0000.000
189A189SER0-0.026-0.01123.876-0.560-0.5600.0000.0000.0000.000
190A190PHE0-0.049-0.02721.8010.5050.5050.0000.0000.0000.000
191A191GLU-1-0.858-0.92925.080-10.537-10.5370.0000.0000.0000.000
192A192ALA00.0270.01524.0040.2410.2410.0000.0000.0000.000
193A193GLY00.0520.02525.9700.2910.2910.0000.0000.0000.000
194A194ALA00.0320.00428.483-0.263-0.2630.0000.0000.0000.000
195A195ARG10.7850.86230.3318.9898.9890.0000.0000.0000.000
196A196ILE00.0390.01624.278-0.042-0.0420.0000.0000.0000.000
197A197THR00.0160.01025.658-0.432-0.4320.0000.0000.0000.000
198A198LEU0-0.015-0.01126.570-0.195-0.1950.0000.0000.0000.000
199A199LEU0-0.0070.00325.2300.0210.0210.0000.0000.0000.000
200A200GLU-1-0.780-0.87421.637-13.248-13.2480.0000.0000.0000.000
201A201ASN0-0.023-0.00923.620-0.631-0.6310.0000.0000.0000.000
202A202ASN0-0.081-0.04525.9600.2790.2790.0000.0000.0000.000
203A203TRP00.0420.02117.3630.0320.0320.0000.0000.0000.000
204A204SER00.016-0.00323.837-0.059-0.0590.0000.0000.0000.000
205A205LYS10.8260.90425.1829.9479.9470.0000.0000.0000.000
206A206ILE00.0400.02025.6570.2950.2950.0000.0000.0000.000
207A207SER00.0610.02922.8340.0090.0090.0000.0000.0000.000
208A208GLU-1-0.855-0.92424.708-9.962-9.9620.0000.0000.0000.000
209A209GLN00.0010.00127.6750.4660.4660.0000.0000.0000.000
210A210TYR00.0470.01924.8660.2280.2280.0000.0000.0000.000
211A211HIS0-0.078-0.03122.6650.2860.2860.0000.0000.0000.000
212A212LYS10.8180.91127.1999.0789.0780.0000.0000.0000.000
213A213SER00.0080.00529.7130.2790.2790.0000.0000.0000.000
214A215LYS10.9250.96028.8568.3868.3860.0000.0000.0000.000
215A216LEU0-0.011-0.00228.3100.2390.2390.0000.0000.0000.000
216A217GLY00.0510.04332.2880.2310.2310.0000.0000.0000.000
217A218GLY0-0.035-0.02234.194-0.137-0.1370.0000.0000.0000.000
218A219GLY00.0480.01434.7320.1950.1950.0000.0000.0000.000
219A220GLN0-0.065-0.01332.6400.1760.1760.0000.0000.0000.000
220A221PHE0-0.014-0.02030.331-0.032-0.0320.0000.0000.0000.000
221A222THR00.028-0.01631.7270.0820.0820.0000.0000.0000.000
222A223GLU-1-0.855-0.93229.889-9.413-9.4130.0000.0000.0000.000
223A224GLU-1-0.848-0.91628.191-9.475-9.4750.0000.0000.0000.000
224A225GLU-1-0.758-0.84426.665-9.934-9.9340.0000.0000.0000.000
225A226MET0-0.042-0.02225.983-0.446-0.4460.0000.0000.0000.000
226A227LYS10.8680.94524.0769.9659.9650.0000.0000.0000.000
227A228LEU0-0.028-0.00620.672-0.381-0.3810.0000.0000.0000.000
228A229GLY0-0.0040.00117.4590.1700.1700.0000.0000.0000.000
229A230LEU0-0.040-0.03013.489-0.817-0.8170.0000.0000.0000.000
230A231LEU0-0.0080.01016.8910.4760.4760.0000.0000.0000.000
231A232LEU00.0010.00218.248-0.734-0.7340.0000.0000.0000.000
232A233TYR00.004-0.00819.4810.7520.7520.0000.0000.0000.000
233A234ASN00.0180.00521.566-0.114-0.1140.0000.0000.0000.000