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: YYRZ2

Calculation Name: 3CUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q96H20

Base Structure: X-ray

Registration Date: 2023-03-14

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401185.876764
FMO2-HF: Nuclear repulsion 2315007.362035
FMO2-HF: Total energy -86178.514729
FMO2-MP2: Total energy -86430.490491


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:34:ALA)


Summations of interaction energy for fragment #1(A:34:ALA)
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.
-1.0681.2711.128-1.363-2.105-0.002
Interaction energy analysis for fragmet #1(A:34:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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].
3A36MET00.0460.0243.647-2.227-0.578-0.002-0.763-0.8840.001
4A37SER00.0190.0022.239-0.4650.0171.131-0.576-1.037-0.003
5A38LYS10.9630.9894.1101.2031.411-0.001-0.024-0.1840.000
6A39GLN00.043-0.0195.4680.3100.3100.0000.0000.0000.000
7A40LEU0-0.0080.0186.9850.1450.1450.0000.0000.0000.000
8A41ASP-1-0.833-0.9237.692-0.501-0.5010.0000.0000.0000.000
9A42MET0-0.078-0.0169.5460.0360.0360.0000.0000.0000.000
10A43PHE00.0280.01911.7100.0530.0530.0000.0000.0000.000
11A44LYS10.8610.93310.9880.3880.3880.0000.0000.0000.000
12A45THR00.0540.02314.2460.0320.0320.0000.0000.0000.000
13A46ASN0-0.045-0.01715.9960.0220.0220.0000.0000.0000.000
14A47LEU00.0080.00817.6800.0220.0220.0000.0000.0000.000
15A48GLU-1-0.880-0.94916.652-0.187-0.1870.0000.0000.0000.000
16A49GLU-1-0.942-0.94920.572-0.114-0.1140.0000.0000.0000.000
17A50PHE0-0.0080.00222.1980.0140.0140.0000.0000.0000.000
18A51ALA00.0350.00823.2330.0110.0110.0000.0000.0000.000
19A52SER0-0.108-0.06424.7360.0090.0090.0000.0000.0000.000
20A53LYS10.9370.96426.6670.0750.0750.0000.0000.0000.000
21A54HIS0-0.042-0.02827.0850.0090.0090.0000.0000.0000.000
22A55LYS10.9310.97628.7930.0620.0620.0000.0000.0000.000
23A56GLN0-0.039-0.03629.7350.0010.0010.0000.0000.0000.000
24A57GLU-1-0.824-0.90832.367-0.035-0.0350.0000.0000.0000.000
25A58ILE00.0280.02028.0400.0040.0040.0000.0000.0000.000
26A59ARG10.8890.93528.4730.0500.0500.0000.0000.0000.000
27A60LYS10.9370.99234.4300.0300.0300.0000.0000.0000.000
28A61ASN0-0.030-0.02936.2080.0040.0040.0000.0000.0000.000
29A62PRO00.0970.04236.575-0.001-0.0010.0000.0000.0000.000
30A63GLU-1-0.889-0.94936.679-0.006-0.0060.0000.0000.0000.000
31A64PHE0-0.039-0.01230.2040.0000.0000.0000.0000.0000.000
32A65ARG10.7840.88032.0010.0160.0160.0000.0000.0000.000
33A66VAL00.0350.02631.6050.0000.0000.0000.0000.0000.000
34A67GLN0-0.0190.00732.2230.0030.0030.0000.0000.0000.000
35A68PHE00.008-0.00524.0390.0020.0020.0000.0000.0000.000
36A69GLN00.0130.00827.5020.0050.0050.0000.0000.0000.000
37A70ASP-1-0.822-0.91928.1310.0130.0130.0000.0000.0000.000
38A71MET0-0.053-0.02226.9410.0030.0030.0000.0000.0000.000
39A72CYS0-0.062-0.02824.0850.0020.0020.0000.0000.0000.000
40A73ALA00.0250.00123.8990.0080.0080.0000.0000.0000.000
41A74THR0-0.051-0.01226.1890.0080.0080.0000.0000.0000.000
42A75ILE0-0.068-0.02920.0210.0070.0070.0000.0000.0000.000
43A76GLY00.0070.02121.1820.0130.0130.0000.0000.0000.000
44A77VAL0-0.081-0.04118.3280.0100.0100.0000.0000.0000.000
45A78ASP-1-0.739-0.86920.9940.0260.0260.0000.0000.0000.000
46A79PRO0-0.051-0.02922.005-0.002-0.0020.0000.0000.0000.000
47A80LEU00.0280.00523.432-0.006-0.0060.0000.0000.0000.000
48A81ALA0-0.0280.02921.5990.0010.0010.0000.0000.0000.000
49A82SER0-0.024-0.02620.1460.0000.0000.0000.0000.0000.000
50A83GLY00.0920.04822.286-0.007-0.0070.0000.0000.0000.000
51A84LYS10.9390.97314.1560.0240.0240.0000.0000.0000.000
52A85GLY00.0050.00717.249-0.005-0.0050.0000.0000.0000.000
53A86PHE00.0370.00611.795-0.011-0.0110.0000.0000.0000.000
54A87TRP00.0480.01418.031-0.011-0.0110.0000.0000.0000.000
55A88SER00.0490.02521.2630.0000.0000.0000.0000.0000.000
56A89GLU-1-0.946-0.95917.549-0.104-0.1040.0000.0000.0000.000
57A90MET0-0.020-0.01417.297-0.002-0.0020.0000.0000.0000.000
58A91LEU0-0.031-0.01722.3690.0030.0030.0000.0000.0000.000
59A92GLY0-0.021-0.00125.0400.0040.0040.0000.0000.0000.000
60A93VAL0-0.041-0.02825.4770.0040.0040.0000.0000.0000.000
61A94GLY00.0580.02626.4200.0060.0060.0000.0000.0000.000
62A95ASP-1-0.911-0.96327.193-0.029-0.0290.0000.0000.0000.000
63A96PHE0-0.055-0.00829.6930.0010.0010.0000.0000.0000.000
64A97TYR0-0.031-0.04830.0540.0030.0030.0000.0000.0000.000
65A98TYR0-0.085-0.06925.2380.0010.0010.0000.0000.0000.000
66A99GLU-1-0.864-0.91531.565-0.010-0.0100.0000.0000.0000.000
67A100LEU00.0370.02234.5410.0020.0020.0000.0000.0000.000
68A101GLY0-0.017-0.01634.9770.0020.0020.0000.0000.0000.000
69A102VAL00.0070.01335.2840.0020.0020.0000.0000.0000.000
70A103GLN00.1030.06637.8160.0010.0010.0000.0000.0000.000
71A104ILE0-0.033-0.01938.0940.0010.0010.0000.0000.0000.000
72A105ILE0-0.054-0.02437.1330.0020.0020.0000.0000.0000.000
73A106GLU-1-0.864-0.94841.286-0.003-0.0030.0000.0000.0000.000
74A107VAL0-0.024-0.01043.8940.0000.0000.0000.0000.0000.000
75A108CYS0-0.053-0.02843.7680.0010.0010.0000.0000.0000.000
76A109LEU0-0.035-0.01443.7020.0010.0010.0000.0000.0000.000
77A110ALA00.0360.02447.3850.0000.0000.0000.0000.0000.000
78A111LEU0-0.018-0.02749.2370.0000.0000.0000.0000.0000.000
79A112LYS10.9570.98747.899-0.009-0.0090.0000.0000.0000.000
80A113HIS0-0.043-0.01950.9360.0000.0000.0000.0000.0000.000
81A114ARG10.9010.96454.537-0.002-0.0020.0000.0000.0000.000
82A115ASN00.040-0.00750.7140.0010.0010.0000.0000.0000.000
83A116GLY00.0620.04852.9890.0010.0010.0000.0000.0000.000
84A117GLY0-0.022-0.00948.7910.0010.0010.0000.0000.0000.000
85A118LEU0-0.009-0.00747.7840.0010.0010.0000.0000.0000.000
86A119ILE0-0.0190.01046.514-0.001-0.0010.0000.0000.0000.000
87A120THR00.0670.03048.0530.0010.0010.0000.0000.0000.000
88A121LEU0-0.009-0.01842.720-0.001-0.0010.0000.0000.0000.000
89A122GLU-1-0.962-0.98546.4550.0010.0010.0000.0000.0000.000
90A123GLU-1-0.862-0.93348.9920.0020.0020.0000.0000.0000.000
91A124LEU00.0320.00542.419-0.001-0.0010.0000.0000.0000.000
92A125HIS0-0.051-0.04143.7840.0000.0000.0000.0000.0000.000
93A126GLN00.003-0.00745.975-0.002-0.0020.0000.0000.0000.000
94A127GLN0-0.015-0.02348.235-0.001-0.0010.0000.0000.0000.000
95A128VAL00.0280.01641.566-0.001-0.0010.0000.0000.0000.000
96A129LEU0-0.048-0.01943.569-0.002-0.0020.0000.0000.0000.000
97A130LYS10.8070.91245.9220.0020.0020.0000.0000.0000.000
98A131GLY00.0270.01746.4620.0000.0000.0000.0000.0000.000
99A132ARG10.7800.88736.3520.0130.0130.0000.0000.0000.000
100A133GLY0-0.0080.01343.691-0.002-0.0020.0000.0000.0000.000
101A134LYS10.8940.91545.4280.0220.0220.0000.0000.0000.000
102A135PHE0-0.076-0.02639.971-0.002-0.0020.0000.0000.0000.000
103A136ALA00.0790.05943.0120.0010.0010.0000.0000.0000.000
104A137GLN0-0.021-0.02943.7110.0000.0000.0000.0000.0000.000
105A138ASP-1-0.861-0.93038.659-0.016-0.0160.0000.0000.0000.000
106A139VAL00.0230.03138.560-0.001-0.0010.0000.0000.0000.000
107A140SER00.000-0.02338.7540.0010.0010.0000.0000.0000.000
108A141GLN00.0960.01840.4880.0000.0000.0000.0000.0000.000
109A142ASP-1-0.824-0.90136.2120.0050.0050.0000.0000.0000.000
110A143ASP-1-0.768-0.83435.641-0.007-0.0070.0000.0000.0000.000
111A144LEU00.0450.02536.4300.0010.0010.0000.0000.0000.000
112A145ILE00.0020.00337.0270.0020.0020.0000.0000.0000.000
113A146ARG10.7530.85031.459-0.002-0.0020.0000.0000.0000.000
114A147ALA00.0280.01733.3990.0030.0030.0000.0000.0000.000
115A148ILE00.0040.00834.3590.0030.0030.0000.0000.0000.000
116A149LYS10.9250.95232.934-0.021-0.0210.0000.0000.0000.000
117A150LYS10.8480.89926.527-0.024-0.0240.0000.0000.0000.000
118A151LEU00.0200.02731.5840.0030.0030.0000.0000.0000.000
119A152LYS10.8700.93433.959-0.030-0.0300.0000.0000.0000.000
120A153ALA0-0.0240.00129.5480.0040.0040.0000.0000.0000.000
121A154LEU0-0.075-0.03431.5620.0030.0030.0000.0000.0000.000
122A155GLY00.0040.01033.7040.0000.0000.0000.0000.0000.000
123A156THR0-0.053-0.04435.652-0.001-0.0010.0000.0000.0000.000
124A157GLY00.0690.02839.101-0.001-0.0010.0000.0000.0000.000
125A158PHE00.0410.02738.458-0.001-0.0010.0000.0000.0000.000
126A159GLY0-0.070-0.03239.6270.0040.0040.0000.0000.0000.000
127A160ILE0-0.0220.00337.920-0.002-0.0020.0000.0000.0000.000
128A161ILE00.0070.00642.1410.0020.0020.0000.0000.0000.000
129A162PRO00.0060.00743.714-0.002-0.0020.0000.0000.0000.000
130A163VAL00.0330.02146.3020.0010.0010.0000.0000.0000.000
131A164GLY00.0690.02949.4400.0000.0000.0000.0000.0000.000
132A165GLY0-0.040-0.00149.6100.0010.0010.0000.0000.0000.000
133A166THR0-0.033-0.02147.380-0.001-0.0010.0000.0000.0000.000
134A167TYR0-0.013-0.00942.5380.0020.0020.0000.0000.0000.000
135A168LEU00.0110.00446.177-0.002-0.0020.0000.0000.0000.000
136A169ILE0-0.042-0.02742.5110.0020.0020.0000.0000.0000.000
137A170GLN00.0260.02244.174-0.002-0.0020.0000.0000.0000.000
138A171SER0-0.017-0.02143.0750.0010.0010.0000.0000.0000.000
139A172VAL00.0120.00943.9880.0000.0000.0000.0000.0000.000
140A173PRO0-0.043-0.03143.0220.0010.0010.0000.0000.0000.000
141A174ALA00.0510.03545.135-0.001-0.0010.0000.0000.0000.000
142A175GLU-1-0.956-0.98245.6860.0280.0280.0000.0000.0000.000
143A176LEU0-0.018-0.01943.4020.0000.0000.0000.0000.0000.000
144A177ASN00.0460.02846.6830.0010.0010.0000.0000.0000.000
145A178MET00.0670.03548.451-0.001-0.0010.0000.0000.0000.000
146A179ASP-1-0.823-0.88649.7720.0220.0220.0000.0000.0000.000
147A180HIS00.007-0.00950.716-0.001-0.0010.0000.0000.0000.000
148A181THR0-0.0010.00647.720-0.001-0.0010.0000.0000.0000.000
149A182VAL00.006-0.00850.373-0.001-0.0010.0000.0000.0000.000
150A183VAL00.0070.01553.090-0.001-0.0010.0000.0000.0000.000
151A184LEU00.0150.02150.081-0.001-0.0010.0000.0000.0000.000
152A185GLN0-0.075-0.05548.848-0.001-0.0010.0000.0000.0000.000
153A186LEU0-0.036-0.01553.402-0.001-0.0010.0000.0000.0000.000
154A187ALA0-0.008-0.00756.159-0.001-0.0010.0000.0000.0000.000
155A188GLU-1-0.918-0.97152.8300.0090.0090.0000.0000.0000.000
156A189LYS10.8660.94355.959-0.008-0.0080.0000.0000.0000.000
157A190ASN0-0.042-0.02758.729-0.001-0.0010.0000.0000.0000.000
158A191GLY00.0170.02058.631-0.001-0.0010.0000.0000.0000.000
159A192TYR0-0.022-0.01659.6950.0000.0000.0000.0000.0000.000
160A193VAL00.0230.01859.7700.0000.0000.0000.0000.0000.000
161A194THR00.009-0.00362.225-0.001-0.0010.0000.0000.0000.000
162A195VAL00.0610.03264.8310.0000.0000.0000.0000.0000.000
163A196SER0-0.047-0.06265.8760.0010.0010.0000.0000.0000.000
164A197GLU-1-0.893-0.95663.0750.0110.0110.0000.0000.0000.000
165A198ILE0-0.0010.00060.0330.0010.0010.0000.0000.0000.000
166A199LYN00.0040.02862.4390.0010.0010.0000.0000.0000.000
167A200ALA0-0.0040.01064.6440.0000.0000.0000.0000.0000.000
168A201SER0-0.018-0.01761.1380.0000.0000.0000.0000.0000.000
169A202LEU0-0.024-0.01356.9700.0000.0000.0000.0000.0000.000
170A203LYS10.8100.90860.281-0.014-0.0140.0000.0000.0000.000
171A204TRP0-0.027-0.00855.7580.0010.0010.0000.0000.0000.000
172A205GLU-1-0.877-0.94562.5440.0160.0160.0000.0000.0000.000
173A206THR00.009-0.04163.9240.0000.0000.0000.0000.0000.000
174A207GLU-1-0.841-0.90463.8390.0160.0160.0000.0000.0000.000
175A208ARG10.8500.89455.568-0.022-0.0220.0000.0000.0000.000
176A209ALA00.0030.00260.2200.0000.0000.0000.0000.0000.000
177A210ARG10.8050.88861.449-0.015-0.0150.0000.0000.0000.000
178A211GLN0-0.005-0.00259.2360.0000.0000.0000.0000.0000.000
179A212VAL0-0.0040.00755.7690.0000.0000.0000.0000.0000.000
180A213LEU0-0.029-0.01457.9540.0000.0000.0000.0000.0000.000
181A214GLU-1-0.868-0.93660.0280.0150.0150.0000.0000.0000.000
182A215HIS0-0.0210.00352.1670.0000.0000.0000.0000.0000.000
183A216LEU00.0440.02654.7050.0000.0000.0000.0000.0000.000
184A217LEU0-0.050-0.02857.059-0.001-0.0010.0000.0000.0000.000
185A218LYS10.7770.88255.431-0.019-0.0190.0000.0000.0000.000
186A219GLU-1-0.864-0.93852.3970.0180.0180.0000.0000.0000.000
187A220GLY0-0.0110.01454.3180.0000.0000.0000.0000.0000.000
188A221LEU0-0.037-0.01751.533-0.001-0.0010.0000.0000.0000.000
189A222ALA0-0.024-0.02155.6360.0000.0000.0000.0000.0000.000
190A223TRP0-0.0030.00759.1350.0000.0000.0000.0000.0000.000
191A224LEU0-0.026-0.01562.5900.0000.0000.0000.0000.0000.000
192A225ASP-1-0.786-0.89065.8170.0060.0060.0000.0000.0000.000
193A226LEU0-0.044-0.04068.6080.0000.0000.0000.0000.0000.000
194A227GLN0-0.055-0.02471.8810.0000.0000.0000.0000.0000.000
195A228ALA00.0230.03970.2150.0000.0000.0000.0000.0000.000
196A229PRO00.001-0.02071.7380.0000.0000.0000.0000.0000.000
197A230GLY0-0.030-0.01372.5090.0000.0000.0000.0000.0000.000
198A231GLU-1-0.783-0.87269.3490.0110.0110.0000.0000.0000.000
199A232ALA0-0.0090.01568.9440.0000.0000.0000.0000.0000.000
200A233HIS10.8550.94166.083-0.008-0.0080.0000.0000.0000.000
201A234TYR00.005-0.00861.8750.0000.0000.0000.0000.0000.000
202A235TRP00.015-0.02161.6460.0000.0000.0000.0000.0000.000
203A236LEU0-0.007-0.00555.0120.0000.0000.0000.0000.0000.000
204A237PRO0-0.011-0.00456.9230.0000.0000.0000.0000.0000.000
205A238ALA0-0.0100.01552.345-0.001-0.0010.0000.0000.0000.000
206A239LEU0-0.051-0.01053.6920.0000.0000.0000.0000.0000.000
207A240PHE0-0.013-0.01655.9730.0000.0000.0000.0000.0000.000
208A241THR00.0040.00757.0320.0000.0000.0000.0000.0000.000
209A242ASP-1-0.899-0.95557.9630.0010.0010.0000.0000.0000.000
210A243LEU0-0.028-0.00955.5360.0000.0000.0000.0000.0000.000
211A244TYR0-0.023-0.02457.782-0.001-0.0010.0000.0000.0000.000
212A245SER0-0.040-0.03557.3430.0000.0000.0000.0000.0000.000
213A246GLN00.0570.05251.262-0.001-0.0010.0000.0000.0000.000
214A247GLU-1-0.872-0.93253.181-0.004-0.0040.0000.0000.0000.000
215A248ILE0-0.098-0.05155.2730.0010.0010.0000.0000.0000.000
216A249THR0-0.0080.00052.1840.0000.0000.0000.0000.0000.000
217A250ALA00.0080.00550.0610.0010.0010.0000.0000.0000.000
218A251GLU-1-0.999-0.99048.9440.0010.0010.0000.0000.0000.000
219A252GLU-1-0.984-0.98244.2320.0020.0020.0000.0000.0000.000