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: G6QV1

Calculation Name: 5X5V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5V

Chain ID: A

ChEMBL ID:

UniProt ID: G3G933

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 -3132253.188574
FMO2-HF: Nuclear repulsion 3036089.942107
FMO2-HF: Total energy -96163.246467
FMO2-MP2: Total energy -96441.689009


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:26:PRO)


Summations of interaction energy for fragment #1(A:26:PRO)
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.
-1.0970.689-0.018-0.863-0.9040
Interaction energy analysis for fragmet #1(A:26:PRO)
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 : -0.036
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].
3A28PHE0-0.019-0.0053.803-0.4361.350-0.018-0.863-0.9040.000
4A29PRO00.015-0.0046.0850.1800.1800.0000.0000.0000.000
5A30PRO00.0300.0298.942-0.045-0.0450.0000.0000.0000.000
6A31PRO0-0.010-0.00611.8700.0370.0370.0000.0000.0000.000
7A32ALA00.0170.00915.1310.0410.0410.0000.0000.0000.000
8A33TYR0-0.039-0.03017.6080.0010.0010.0000.0000.0000.000
9A34PRO0-0.0030.00521.0750.0070.0070.0000.0000.0000.000
10A35TYR0-0.001-0.01021.0930.0120.0120.0000.0000.0000.000
11A36THR0-0.040-0.02025.829-0.001-0.0010.0000.0000.0000.000
12A37GLU-1-0.846-0.91425.431-0.043-0.0430.0000.0000.0000.000
13A38SER0-0.042-0.02828.209-0.001-0.0010.0000.0000.0000.000
14A39TRP00.0450.01230.2650.0030.0030.0000.0000.0000.000
15A40GLN00.033-0.00932.3530.0080.0080.0000.0000.0000.000
16A41LEU0-0.034-0.00930.271-0.006-0.0060.0000.0000.0000.000
17A42THR0-0.117-0.07634.4360.0010.0010.0000.0000.0000.000
18A43LEU0-0.051-0.01533.7130.0020.0020.0000.0000.0000.000
19A44THR00.0270.01736.076-0.001-0.0010.0000.0000.0000.000
20A45THR0-0.050-0.02138.4290.0020.0020.0000.0000.0000.000
21A46VAL0-0.009-0.01134.0320.0000.0000.0000.0000.0000.000
22A47PRO00.0210.01833.4140.0000.0000.0000.0000.0000.000
23A48SER00.0280.01235.7720.0040.0040.0000.0000.0000.000
24A49PRO0-0.0080.01534.1830.0010.0010.0000.0000.0000.000
25A50PHE0-0.051-0.03035.4900.0050.0050.0000.0000.0000.000
26A51VAL00.0080.01335.929-0.002-0.0020.0000.0000.0000.000
27A52GLY00.000-0.00937.380-0.002-0.0020.0000.0000.0000.000
28A53PRO0-0.029-0.00536.4290.0010.0010.0000.0000.0000.000
29A54ALA00.006-0.00631.9890.0000.0000.0000.0000.0000.000
30A55ASP-1-0.892-0.92329.8570.1000.1000.0000.0000.0000.000
31A56VAL0-0.020-0.01830.2700.0030.0030.0000.0000.0000.000
32A57TYR0-0.037-0.02225.2830.0120.0120.0000.0000.0000.000
33A58HIS00.0090.00226.676-0.008-0.0080.0000.0000.0000.000
34A59THR00.0060.00223.1080.0130.0130.0000.0000.0000.000
35A60ARG10.8920.94619.546-0.317-0.3170.0000.0000.0000.000
36A61PRO00.0390.02322.9290.0020.0020.0000.0000.0000.000
37A62LEU0-0.055-0.02021.2430.0210.0210.0000.0000.0000.000
38A63GLU-1-0.939-0.96218.3070.3290.3290.0000.0000.0000.000
39A64ASP-1-0.788-0.88020.8060.2100.2100.0000.0000.0000.000
40A65PRO00.0410.01722.9380.0090.0090.0000.0000.0000.000
41A66CYS0-0.125-0.01422.037-0.012-0.0120.0000.0000.0000.000
42A67GLY00.0740.06419.0950.0100.0100.0000.0000.0000.000
43A68VAL0-0.032-0.03016.106-0.021-0.0210.0000.0000.0000.000
44A69VAL00.0420.02418.8920.0250.0250.0000.0000.0000.000
45A70ALA00.006-0.00917.258-0.005-0.0050.0000.0000.0000.000
46A71LEU0-0.025-0.00119.120-0.002-0.0020.0000.0000.0000.000
47A72ILE00.0380.01115.267-0.012-0.0120.0000.0000.0000.000
48A73SER00.0280.00119.5210.0100.0100.0000.0000.0000.000
49A74ASP-1-0.814-0.89119.6590.1480.1480.0000.0000.0000.000
50A75PRO0-0.036-0.01320.930-0.008-0.0080.0000.0000.0000.000
51A76GLN00.0160.00022.804-0.023-0.0230.0000.0000.0000.000
52A77VAL00.0210.00822.214-0.013-0.0130.0000.0000.0000.000
53A78ASP-1-0.827-0.91821.8350.0830.0830.0000.0000.0000.000
54A79ARG10.9210.95123.840-0.083-0.0830.0000.0000.0000.000
55A80LEU00.0340.01727.267-0.007-0.0070.0000.0000.0000.000
56A81LEU0-0.0150.00422.863-0.008-0.0080.0000.0000.0000.000
57A82ASN00.007-0.00924.935-0.018-0.0180.0000.0000.0000.000
58A83GLU-1-0.948-0.96128.0960.0240.0240.0000.0000.0000.000
59A84ALA0-0.007-0.00129.569-0.005-0.0050.0000.0000.0000.000
60A85VAL0-0.026-0.01027.292-0.007-0.0070.0000.0000.0000.000
61A86ALA0-0.034-0.01330.624-0.004-0.0040.0000.0000.0000.000
62A87HIS0-0.053-0.02533.310-0.004-0.0040.0000.0000.0000.000
63A88ARG10.8670.93533.8100.0120.0120.0000.0000.0000.000
64A89ARG10.9600.98533.241-0.007-0.0070.0000.0000.0000.000
65A90PRO0-0.033-0.01831.746-0.001-0.0010.0000.0000.0000.000
66A91THR0-0.070-0.03929.701-0.005-0.0050.0000.0000.0000.000
67A92TYR00.0500.03623.3730.0070.0070.0000.0000.0000.000
68A93ARG10.9240.96729.562-0.011-0.0110.0000.0000.0000.000
69A94ALA00.025-0.00726.9180.0050.0050.0000.0000.0000.000
70A95HIS0-0.0050.00628.136-0.003-0.0030.0000.0000.0000.000
71A96VAL00.0240.02523.7980.0060.0060.0000.0000.0000.000
72A97ALA0-0.006-0.00227.045-0.006-0.0060.0000.0000.0000.000
73A98TRP00.0050.00822.4770.0100.0100.0000.0000.0000.000
74A99TYR0-0.037-0.04528.595-0.007-0.0070.0000.0000.0000.000
75A100ARG10.8610.94228.698-0.073-0.0730.0000.0000.0000.000
76A101ILE0-0.029-0.02032.903-0.007-0.0070.0000.0000.0000.000
77A102ALA00.0170.00335.5120.0030.0030.0000.0000.0000.000
78A103ASP-1-0.927-0.97038.7330.0510.0510.0000.0000.0000.000
79A104GLY00.0340.02242.051-0.003-0.0030.0000.0000.0000.000
80A105CYS0-0.114-0.05838.7600.0000.0000.0000.0000.0000.000
81A106ALA00.0290.01535.7460.0040.0040.0000.0000.0000.000
82A107HIS0-0.026-0.00434.616-0.002-0.0020.0000.0000.0000.000
83A108LEU0-0.003-0.00733.6680.0040.0040.0000.0000.0000.000
84A109LEU0-0.031-0.01226.8860.0020.0020.0000.0000.0000.000
85A110TYR00.029-0.00723.106-0.002-0.0020.0000.0000.0000.000
86A111PHE00.0350.01728.2760.0020.0020.0000.0000.0000.000
87A112ILE0-0.0120.01823.861-0.004-0.0040.0000.0000.0000.000
88A113GLU-1-0.738-0.85227.6980.0040.0040.0000.0000.0000.000
89A114TYR0-0.036-0.06122.013-0.005-0.0050.0000.0000.0000.000
90A115ALA00.011-0.01427.9320.0050.0050.0000.0000.0000.000
91A116ASP-1-0.874-0.94128.703-0.044-0.0440.0000.0000.0000.000
92A117CYS0-0.091-0.01721.402-0.004-0.0040.0000.0000.0000.000
93A118ASP-1-0.815-0.92623.787-0.068-0.0680.0000.0000.0000.000
94A119PRO0-0.020-0.00724.0230.0010.0010.0000.0000.0000.000
95A120ARG10.9190.95923.9140.0490.0490.0000.0000.0000.000
96A121GLN0-0.061-0.01819.557-0.030-0.0300.0000.0000.0000.000
97A122VAL00.0330.01815.1690.0160.0160.0000.0000.0000.000
98A123PHE00.0330.00018.591-0.013-0.0130.0000.0000.0000.000
99A124GLY00.0810.04819.321-0.002-0.0020.0000.0000.0000.000
100A125ARG10.9000.97218.1870.1570.1570.0000.0000.0000.000
101A127ARG10.9940.98324.8360.0520.0520.0000.0000.0000.000
102A128ARG10.8590.93527.2800.0300.0300.0000.0000.0000.000
103A129ARG10.8070.89320.6380.0390.0390.0000.0000.0000.000
104A130THR00.0140.02627.324-0.004-0.0040.0000.0000.0000.000
105A131THR00.0370.01626.201-0.002-0.0020.0000.0000.0000.000
106A132PRO0-0.048-0.01422.9860.0050.0050.0000.0000.0000.000
107A133MET0-0.060-0.00626.107-0.004-0.0040.0000.0000.0000.000
108A134TRP00.0580.00922.3930.0100.0100.0000.0000.0000.000
109A135TRP0-0.0180.00328.645-0.007-0.0070.0000.0000.0000.000
110A136THR00.030-0.00528.8410.0070.0070.0000.0000.0000.000
111A137PRO00.0220.01228.5260.0030.0030.0000.0000.0000.000
112A138SER00.004-0.00727.0760.0060.0060.0000.0000.0000.000
113A139ALA00.0110.02224.4560.0090.0090.0000.0000.0000.000
114A140ASP-1-0.893-0.93923.5450.0470.0470.0000.0000.0000.000
115A141TYR0-0.124-0.10222.0720.0000.0000.0000.0000.0000.000
116A142MET0-0.035-0.00221.3710.0170.0170.0000.0000.0000.000
117A143PHE00.0060.00414.535-0.011-0.0110.0000.0000.0000.000
118A144PRO00.0300.01518.5920.0220.0220.0000.0000.0000.000
119A145THR0-0.015-0.02614.6910.0010.0010.0000.0000.0000.000
120A146GLU-1-0.949-0.9799.5900.0150.0150.0000.0000.0000.000
121A147ASP-1-0.857-0.91513.5200.1390.1390.0000.0000.0000.000
122A148GLU-1-0.793-0.86815.512-0.025-0.0250.0000.0000.0000.000
123A149LEU0-0.020-0.00518.187-0.008-0.0080.0000.0000.0000.000
124A150GLY00.0140.01518.6480.0070.0070.0000.0000.0000.000
125A151LEU0-0.043-0.01619.573-0.019-0.0190.0000.0000.0000.000
126A152LEU0-0.024-0.00414.1720.0300.0300.0000.0000.0000.000
127A153MET00.0060.00318.793-0.025-0.0250.0000.0000.0000.000
128A154VAL0-0.034-0.01917.9100.0180.0180.0000.0000.0000.000
129A155ALA0-0.011-0.00120.530-0.019-0.0190.0000.0000.0000.000
130A156PRO0-0.015-0.00122.954-0.016-0.0160.0000.0000.0000.000
131A157GLY00.0590.02025.8490.0000.0000.0000.0000.0000.000
132A158ARG10.9080.93629.488-0.095-0.0950.0000.0000.0000.000
133A159PHE0-0.077-0.03530.0380.0000.0000.0000.0000.0000.000
134A160ASN0-0.0240.02628.130-0.006-0.0060.0000.0000.0000.000
135A161GLU-1-0.792-0.86929.9080.1090.1090.0000.0000.0000.000
136A162GLY00.0100.00831.293-0.008-0.0080.0000.0000.0000.000
137A163GLN0-0.0250.00330.9350.0080.0080.0000.0000.0000.000
138A164TYR0-0.051-0.05327.649-0.010-0.0100.0000.0000.0000.000
139A165ARG10.8300.87728.843-0.065-0.0650.0000.0000.0000.000
140A166ARG10.8150.89321.848-0.135-0.1350.0000.0000.0000.000
141A167LEU0-0.024-0.01327.7830.0000.0000.0000.0000.0000.000
142A168VAL00.0070.00224.523-0.002-0.0020.0000.0000.0000.000
143A169SER0-0.0130.00027.581-0.001-0.0010.0000.0000.0000.000
144A170VAL00.0580.01626.779-0.005-0.0050.0000.0000.0000.000
145A171ASP-1-0.883-0.96229.9160.0050.0050.0000.0000.0000.000
146A172GLY0-0.073-0.03833.1760.0000.0000.0000.0000.0000.000
147A173VAL00.0070.02232.4560.0020.0020.0000.0000.0000.000
148A174ASN0-0.002-0.01631.8140.0000.0000.0000.0000.0000.000
149A175ILE00.0020.01027.2720.0000.0000.0000.0000.0000.000
150A176LEU0-0.0010.00229.5990.0000.0000.0000.0000.0000.000
151A177THR0-0.047-0.01925.7990.0050.0050.0000.0000.0000.000
152A178ASP-1-0.722-0.82628.7930.0820.0820.0000.0000.0000.000
153A179PHE0-0.032-0.02622.8090.0110.0110.0000.0000.0000.000
154A180MET0-0.014-0.00827.644-0.010-0.0100.0000.0000.0000.000
155A181VAL0-0.006-0.00625.9330.0130.0130.0000.0000.0000.000
156A182ALA00.0110.00828.260-0.011-0.0110.0000.0000.0000.000
157A183LEU0-0.046-0.04426.3190.0120.0120.0000.0000.0000.000
158A184PRO00.0680.03029.233-0.010-0.0100.0000.0000.0000.000
159A185GLU-1-0.917-0.97532.3130.0800.0800.0000.0000.0000.000
160A186GLY0-0.040-0.01934.8030.0020.0020.0000.0000.0000.000
161A187GLN0-0.0110.00429.3850.0030.0030.0000.0000.0000.000
162A188GLU-1-0.866-0.94229.3940.0870.0870.0000.0000.0000.000
163A190PRO00.0380.00526.734-0.007-0.0070.0000.0000.0000.000
164A191PHE00.005-0.00521.371-0.006-0.0060.0000.0000.0000.000
165A192ALA00.0340.02126.336-0.001-0.0010.0000.0000.0000.000
166A193ARG10.8500.92625.777-0.067-0.0670.0000.0000.0000.000
167A194VAL00.0630.01928.4580.0000.0000.0000.0000.0000.000
168A195ASP-1-0.842-0.90731.2920.0460.0460.0000.0000.0000.000
169A196GLN00.014-0.01431.090-0.006-0.0060.0000.0000.0000.000
170A197HIS00.0500.04132.544-0.004-0.0040.0000.0000.0000.000
171A198ARG10.8970.93934.266-0.051-0.0510.0000.0000.0000.000
172A199THR0-0.0280.00636.925-0.003-0.0030.0000.0000.0000.000
173A200TYR00.003-0.00435.178-0.003-0.0030.0000.0000.0000.000
174A201LYS10.8840.95436.011-0.050-0.0500.0000.0000.0000.000
175A202PHE00.015-0.00831.9570.0010.0010.0000.0000.0000.000
176A203GLY00.0520.04335.317-0.001-0.0010.0000.0000.0000.000
177A204ALA0-0.035-0.01937.8160.0020.0020.0000.0000.0000.000
178A206TRP00.008-0.00438.381-0.005-0.0050.0000.0000.0000.000
179A207SER00.0910.03940.7660.0020.0020.0000.0000.0000.000
180A208ASP-1-0.790-0.91141.9480.0340.0340.0000.0000.0000.000
181A209ASP-1-0.878-0.93442.9540.0260.0260.0000.0000.0000.000
182A210SER0-0.068-0.05043.529-0.003-0.0030.0000.0000.0000.000
183A211PHE0-0.008-0.01337.117-0.001-0.0010.0000.0000.0000.000
184A212LYS10.8920.95641.754-0.031-0.0310.0000.0000.0000.000
185A213ARG10.8780.96944.301-0.022-0.0220.0000.0000.0000.000
186A214GLY00.0310.02742.503-0.002-0.0020.0000.0000.0000.000
187A215VAL0-0.050-0.02338.837-0.001-0.0010.0000.0000.0000.000
188A216ASP-1-0.850-0.92839.0830.0110.0110.0000.0000.0000.000
189A217VAL00.0460.00733.3050.0020.0020.0000.0000.0000.000
190A218MET0-0.009-0.02634.0350.0010.0010.0000.0000.0000.000
191A219ARG10.8380.95136.529-0.014-0.0140.0000.0000.0000.000
192A220PHE0-0.029-0.03037.1710.0000.0000.0000.0000.0000.000
193A221LEU0-0.0290.00231.2710.0040.0040.0000.0000.0000.000
194A222THR0-0.018-0.02030.964-0.004-0.0040.0000.0000.0000.000
195A223PRO00.0070.00229.4780.0040.0040.0000.0000.0000.000
196A224PHE00.002-0.00323.0660.0000.0000.0000.0000.0000.000
197A225TYR0-0.0070.00321.110-0.011-0.0110.0000.0000.0000.000
198A226GLN00.016-0.01720.0360.0160.0160.0000.0000.0000.000
199A227GLN00.0270.00113.394-0.034-0.0340.0000.0000.0000.000
200A228PRO00.0240.02213.8490.0140.0140.0000.0000.0000.000
201A229PRO00.0210.00415.2850.0120.0120.0000.0000.0000.000
202A230HIS0-0.020-0.00917.6740.0090.0090.0000.0000.0000.000
203A231ARG10.9550.9839.333-0.195-0.1950.0000.0000.0000.000
204A232GLU-1-0.885-0.96111.6210.0380.0380.0000.0000.0000.000
205A233VAL0-0.0210.00615.5650.0040.0040.0000.0000.0000.000
206A234VAL00.0100.00718.0690.0060.0060.0000.0000.0000.000
207A235ASN0-0.024-0.02712.0840.0460.0460.0000.0000.0000.000
208A236TYR0-0.0020.00616.0480.0070.0070.0000.0000.0000.000
209A237TRP0-0.025-0.01018.1670.0010.0010.0000.0000.0000.000
210A238TYR0-0.029-0.04615.6750.0120.0120.0000.0000.0000.000
211A239ARG10.9610.97611.572-0.145-0.1450.0000.0000.0000.000
212A240LYS10.8780.96117.458-0.043-0.0430.0000.0000.0000.000
213A241ASN0-0.082-0.04220.898-0.011-0.0110.0000.0000.0000.000
214A242GLY00.0060.00919.1060.0070.0070.0000.0000.0000.000
215A243ARG10.7950.88617.054-0.212-0.2120.0000.0000.0000.000
216A244THR0-0.019-0.02510.578-0.032-0.0320.0000.0000.0000.000
217A245LEU0-0.026-0.00711.4600.0260.0260.0000.0000.0000.000
218A246PRO00.0420.02210.7360.0740.0740.0000.0000.0000.000
219A247ARG10.9250.9585.396-1.264-1.2640.0000.0000.0000.000
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