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: N93LQ

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3137468.985087
FMO2-HF: Nuclear repulsion 3041305.050508
FMO2-HF: Total energy -96163.934579
FMO2-MP2: Total energy -96442.486256


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.
-1.6640.314-0.007-1.018-0.9530.001
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 : -0.004 / q_NPA : -0.020
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].
3A28PHE0-0.0100.0033.757-0.5541.424-0.007-1.018-0.9530.001
4A29PRO00.0320.0086.1360.0770.0770.0000.0000.0000.000
5A30PRO00.0340.0328.838-0.081-0.0810.0000.0000.0000.000
6A31PRO0-0.008-0.00211.8130.0550.0550.0000.0000.0000.000
7A32ALA00.0360.00815.0350.0520.0520.0000.0000.0000.000
8A33TYR0-0.027-0.01917.359-0.008-0.0080.0000.0000.0000.000
9A34PRO0-0.0070.00921.0020.0110.0110.0000.0000.0000.000
10A35TYR0-0.075-0.06321.3280.0010.0010.0000.0000.0000.000
11A36THR0-0.047-0.02025.9170.0000.0000.0000.0000.0000.000
12A37GLU-1-0.783-0.86924.601-0.018-0.0180.0000.0000.0000.000
13A38SER0-0.039-0.03628.386-0.002-0.0020.0000.0000.0000.000
14A39TRP00.0420.00830.4330.0040.0040.0000.0000.0000.000
15A40GLN00.023-0.00132.5410.0090.0090.0000.0000.0000.000
16A41LEU0-0.052-0.00129.872-0.007-0.0070.0000.0000.0000.000
17A42THR0-0.120-0.09234.167-0.002-0.0020.0000.0000.0000.000
18A43LEU0-0.0200.00533.5030.0020.0020.0000.0000.0000.000
19A44THR00.0270.00435.882-0.001-0.0010.0000.0000.0000.000
20A45THR0-0.067-0.02237.9880.0020.0020.0000.0000.0000.000
21A46VAL00.0090.00533.5910.0000.0000.0000.0000.0000.000
22A47PRO00.0320.01833.333-0.001-0.0010.0000.0000.0000.000
23A48SER00.016-0.00936.0120.0060.0060.0000.0000.0000.000
24A49PRO0-0.0060.01434.1150.0010.0010.0000.0000.0000.000
25A50PHE0-0.018-0.02335.4230.0050.0050.0000.0000.0000.000
26A51VAL0-0.032-0.00235.819-0.002-0.0020.0000.0000.0000.000
27A52GLY00.0280.01237.311-0.003-0.0030.0000.0000.0000.000
28A53PRO0-0.019-0.00736.6890.0030.0030.0000.0000.0000.000
29A54ALA00.004-0.01031.667-0.001-0.0010.0000.0000.0000.000
30A55ASP-1-0.836-0.88929.4450.1210.1210.0000.0000.0000.000
31A56VAL0-0.025-0.02030.3230.0030.0030.0000.0000.0000.000
32A57TYR0-0.063-0.04725.3830.0110.0110.0000.0000.0000.000
33A58HIS0-0.009-0.00326.721-0.006-0.0060.0000.0000.0000.000
34A59THR0-0.023-0.02023.1480.0170.0170.0000.0000.0000.000
35A60ARG10.8490.91919.483-0.391-0.3910.0000.0000.0000.000
36A61PRO00.0330.01923.1290.0050.0050.0000.0000.0000.000
37A62LEU0-0.060-0.01620.9390.0320.0320.0000.0000.0000.000
38A63GLU-1-0.946-0.97017.9130.4850.4850.0000.0000.0000.000
39A64ASP-1-0.775-0.86921.4020.2870.2870.0000.0000.0000.000
40A65PRO00.0380.01023.4240.0140.0140.0000.0000.0000.000
41A66CYS0-0.111-0.01022.386-0.014-0.0140.0000.0000.0000.000
42A67GLY00.0800.05719.3480.0240.0240.0000.0000.0000.000
43A68VAL0-0.051-0.04316.167-0.020-0.0200.0000.0000.0000.000
44A69VAL00.0460.03318.6480.0330.0330.0000.0000.0000.000
45A70ALA00.012-0.01117.4620.0050.0050.0000.0000.0000.000
46A71LEU0-0.0270.00119.255-0.010-0.0100.0000.0000.0000.000
47A72ILE00.0290.00715.385-0.013-0.0130.0000.0000.0000.000
48A73SER00.0330.00819.5820.0170.0170.0000.0000.0000.000
49A74ASP-1-0.808-0.89720.0880.1490.1490.0000.0000.0000.000
50A75PRO0-0.048-0.01421.218-0.011-0.0110.0000.0000.0000.000
51A76GLN00.0440.01923.046-0.030-0.0300.0000.0000.0000.000
52A77VAL00.0270.00522.066-0.016-0.0160.0000.0000.0000.000
53A78ASP-1-0.848-0.93421.8530.0540.0540.0000.0000.0000.000
54A79ARG10.9180.97423.857-0.086-0.0860.0000.0000.0000.000
55A80LEU00.0510.02927.429-0.009-0.0090.0000.0000.0000.000
56A81LEU0-0.0320.00222.825-0.009-0.0090.0000.0000.0000.000
57A82ASN0-0.019-0.03224.762-0.019-0.0190.0000.0000.0000.000
58A83GLU-1-0.934-0.96628.2570.0220.0220.0000.0000.0000.000
59A84ALA0-0.026-0.01629.489-0.004-0.0040.0000.0000.0000.000
60A85VAL0-0.025-0.01227.372-0.006-0.0060.0000.0000.0000.000
61A86ALA0-0.024-0.01230.690-0.004-0.0040.0000.0000.0000.000
62A87HIS0-0.060-0.03533.543-0.003-0.0030.0000.0000.0000.000
63A88ARG10.8850.94733.8810.0310.0310.0000.0000.0000.000
64A89ARG10.9180.96832.510-0.001-0.0010.0000.0000.0000.000
65A90PRO0-0.013-0.00231.941-0.004-0.0040.0000.0000.0000.000
66A91THR0-0.028-0.02829.200-0.008-0.0080.0000.0000.0000.000
67A92TYR00.0430.02423.3830.0090.0090.0000.0000.0000.000
68A93ARG10.8410.93429.597-0.012-0.0120.0000.0000.0000.000
69A94ALA00.024-0.00526.9030.0040.0040.0000.0000.0000.000
70A95HIS00.0070.00727.975-0.001-0.0010.0000.0000.0000.000
71A96VAL00.0090.01323.4570.0040.0040.0000.0000.0000.000
72A97ALA0-0.019-0.01126.674-0.005-0.0050.0000.0000.0000.000
73A98TRP00.0090.00122.5050.0110.0110.0000.0000.0000.000
74A99TYR0-0.026-0.03728.571-0.008-0.0080.0000.0000.0000.000
75A100ARG10.8350.92328.656-0.116-0.1160.0000.0000.0000.000
76A101ILE0-0.031-0.02032.756-0.008-0.0080.0000.0000.0000.000
77A102ALA00.009-0.00435.5440.0050.0050.0000.0000.0000.000
78A103ASP-1-0.895-0.95338.7580.0650.0650.0000.0000.0000.000
79A104GLY00.0170.01642.243-0.003-0.0030.0000.0000.0000.000
80A105CYS0-0.111-0.05238.5400.0010.0010.0000.0000.0000.000
81A106ALA00.0380.01335.7030.0050.0050.0000.0000.0000.000
82A107HIS0-0.0310.00134.831-0.004-0.0040.0000.0000.0000.000
83A108LEU0-0.011-0.00833.4750.0040.0040.0000.0000.0000.000
84A109LEU0-0.037-0.01826.7480.0040.0040.0000.0000.0000.000
85A110TYR00.0210.00022.9140.0030.0030.0000.0000.0000.000
86A111PHE00.0340.01328.177-0.001-0.0010.0000.0000.0000.000
87A112ILE0-0.0150.01323.653-0.001-0.0010.0000.0000.0000.000
88A113GLU-1-0.723-0.83627.4820.0140.0140.0000.0000.0000.000
89A114TYR0-0.022-0.05722.038-0.006-0.0060.0000.0000.0000.000
90A115ALA00.004-0.00727.8150.0040.0040.0000.0000.0000.000
91A116ASP-1-0.821-0.88328.567-0.047-0.0470.0000.0000.0000.000
92A117CYS0-0.0510.00321.032-0.009-0.0090.0000.0000.0000.000
93A118ASP-1-0.737-0.87924.012-0.085-0.0850.0000.0000.0000.000
94A119PRO0-0.050-0.02224.0550.0000.0000.0000.0000.0000.000
95A120ARG10.8090.90624.0410.0710.0710.0000.0000.0000.000
96A121GLN0-0.069-0.03020.022-0.046-0.0460.0000.0000.0000.000
97A122VAL00.0370.01815.1130.0180.0180.0000.0000.0000.000
98A123PHE00.0590.01518.568-0.011-0.0110.0000.0000.0000.000
99A124GLY00.0650.04019.165-0.005-0.0050.0000.0000.0000.000
100A125ARG10.8400.94117.7250.1950.1950.0000.0000.0000.000
101A127ARG10.9270.94424.6670.0610.0610.0000.0000.0000.000
102A128ARG10.8290.89027.0330.0290.0290.0000.0000.0000.000
103A129ARG10.8230.88420.1810.0110.0110.0000.0000.0000.000
104A130THR00.0040.01427.124-0.004-0.0040.0000.0000.0000.000
105A131THR00.0630.02426.155-0.002-0.0020.0000.0000.0000.000
106A132PRO0-0.042-0.01122.9050.0020.0020.0000.0000.0000.000
107A133MET0-0.0390.00525.999-0.006-0.0060.0000.0000.0000.000
108A134TRP00.0660.01422.3450.0080.0080.0000.0000.0000.000
109A135TRP0-0.0110.00228.668-0.010-0.0100.0000.0000.0000.000
110A136THR00.0290.00229.2540.0100.0100.0000.0000.0000.000
111A137PRO0-0.012-0.01028.8840.0070.0070.0000.0000.0000.000
112A138SER00.0290.00227.2240.0050.0050.0000.0000.0000.000
113A139ALA00.0210.02724.8050.0140.0140.0000.0000.0000.000
114A140ASP-1-0.847-0.90823.7920.1030.1030.0000.0000.0000.000
115A141TYR0-0.097-0.06522.619-0.001-0.0010.0000.0000.0000.000
116A142MET0-0.0350.00121.5790.0220.0220.0000.0000.0000.000
117A143PHE00.0140.00814.619-0.014-0.0140.0000.0000.0000.000
118A144PRO00.0350.01518.4360.0270.0270.0000.0000.0000.000
119A145THR0-0.034-0.04514.6410.0170.0170.0000.0000.0000.000
120A146GLU-1-0.962-0.9889.3140.1680.1680.0000.0000.0000.000
121A147ASP-1-0.836-0.89513.3680.1890.1890.0000.0000.0000.000
122A148GLU-1-0.809-0.87315.5480.0000.0000.0000.0000.0000.000
123A149LEU0-0.0120.01118.474-0.008-0.0080.0000.0000.0000.000
124A150GLY00.0310.02018.7330.0010.0010.0000.0000.0000.000
125A151LEU0-0.046-0.01019.445-0.016-0.0160.0000.0000.0000.000
126A152LEU0-0.0120.00213.9800.0350.0350.0000.0000.0000.000
127A153MET0-0.015-0.00918.694-0.036-0.0360.0000.0000.0000.000
128A154VAL0-0.021-0.00717.7350.0230.0230.0000.0000.0000.000
129A155ALA00.0050.00320.493-0.028-0.0280.0000.0000.0000.000
130A156PRO00.0000.00622.981-0.023-0.0230.0000.0000.0000.000
131A157GLY00.0460.01526.0060.0000.0000.0000.0000.0000.000
132A158ARG10.8280.87329.662-0.136-0.1360.0000.0000.0000.000
133A159PHE0-0.055-0.02229.857-0.001-0.0010.0000.0000.0000.000
134A160ASN0-0.0090.01728.051-0.007-0.0070.0000.0000.0000.000
135A161GLU-1-0.757-0.84629.6100.1500.1500.0000.0000.0000.000
136A162GLY00.0030.00231.531-0.010-0.0100.0000.0000.0000.000
137A163GLN0-0.037-0.01931.1520.0090.0090.0000.0000.0000.000
138A164TYR0-0.043-0.04727.435-0.011-0.0110.0000.0000.0000.000
139A165ARG10.8000.87528.427-0.083-0.0830.0000.0000.0000.000
140A166ARG10.8200.89321.937-0.169-0.1690.0000.0000.0000.000
141A167LEU0-0.039-0.02527.723-0.005-0.0050.0000.0000.0000.000
142A168VAL00.0150.00924.7180.0020.0020.0000.0000.0000.000
143A169SER0-0.013-0.01427.566-0.004-0.0040.0000.0000.0000.000
144A170VAL00.0400.01426.660-0.004-0.0040.0000.0000.0000.000
145A171ASP-1-0.805-0.92229.783-0.002-0.0020.0000.0000.0000.000
146A172GLY0-0.029-0.01233.060-0.003-0.0030.0000.0000.0000.000
147A173VAL0-0.0020.01732.4090.0030.0030.0000.0000.0000.000
148A174ASN00.0130.00731.7280.0010.0010.0000.0000.0000.000
149A175ILE00.0080.00927.4710.0000.0000.0000.0000.0000.000
150A176LEU00.0100.01229.6040.0020.0020.0000.0000.0000.000
151A177THR0-0.063-0.03225.7900.0070.0070.0000.0000.0000.000
152A178ASP-1-0.732-0.81128.4440.1090.1090.0000.0000.0000.000
153A179PHE0-0.002-0.01522.8910.0110.0110.0000.0000.0000.000
154A180MET00.0060.00427.359-0.010-0.0100.0000.0000.0000.000
155A181VAL0-0.017-0.00225.9340.0180.0180.0000.0000.0000.000
156A182ALA00.0190.00428.059-0.015-0.0150.0000.0000.0000.000
157A183LEU0-0.008-0.01226.2120.0180.0180.0000.0000.0000.000
158A184PRO00.0680.03229.216-0.014-0.0140.0000.0000.0000.000
159A185GLU-1-0.825-0.90132.2370.1100.1100.0000.0000.0000.000
160A186GLY0-0.024-0.01235.0520.0020.0020.0000.0000.0000.000
161A187GLN0-0.045-0.01129.5250.0090.0090.0000.0000.0000.000
162A188GLU-1-0.846-0.92629.5460.1340.1340.0000.0000.0000.000
163A190PRO00.003-0.01827.310-0.009-0.0090.0000.0000.0000.000
164A191PHE00.0170.00321.590-0.007-0.0070.0000.0000.0000.000
165A192ALA00.0400.02526.6890.0010.0010.0000.0000.0000.000
166A193ARG10.7450.84925.974-0.125-0.1250.0000.0000.0000.000
167A194VAL00.011-0.01328.768-0.005-0.0050.0000.0000.0000.000
168A195ASP-1-0.840-0.88030.9040.0910.0910.0000.0000.0000.000
169A196GLN00.0370.00130.971-0.011-0.0110.0000.0000.0000.000
170A197HIS00.0710.05332.675-0.006-0.0060.0000.0000.0000.000
171A198ARG10.9320.95734.476-0.088-0.0880.0000.0000.0000.000
172A199THR0-0.0100.00437.088-0.003-0.0030.0000.0000.0000.000
173A200TYR00.0110.00235.152-0.005-0.0050.0000.0000.0000.000
174A201LYS10.8100.90836.426-0.077-0.0770.0000.0000.0000.000
175A202PHE00.0270.00031.8710.0030.0030.0000.0000.0000.000
176A203GLY00.0490.03835.343-0.002-0.0020.0000.0000.0000.000
177A204ALA0-0.028-0.01638.1020.0010.0010.0000.0000.0000.000
178A206TRP00.011-0.00138.396-0.006-0.0060.0000.0000.0000.000
179A207SER00.1000.04440.6350.0030.0030.0000.0000.0000.000
180A208ASP-1-0.763-0.87141.5220.0460.0460.0000.0000.0000.000
181A209ASP-1-0.826-0.90742.5460.0380.0380.0000.0000.0000.000
182A210SER0-0.025-0.01743.246-0.003-0.0030.0000.0000.0000.000
183A211PHE00.001-0.00436.972-0.001-0.0010.0000.0000.0000.000
184A212LYS10.7730.88741.512-0.043-0.0430.0000.0000.0000.000
185A213ARG10.8290.92944.087-0.038-0.0380.0000.0000.0000.000
186A214GLY00.0240.02442.061-0.002-0.0020.0000.0000.0000.000
187A215VAL0-0.023-0.01838.4720.0000.0000.0000.0000.0000.000
188A216ASP-1-0.818-0.90338.6000.0270.0270.0000.0000.0000.000
189A217VAL00.0300.01133.0180.0020.0020.0000.0000.0000.000
190A218MET0-0.011-0.01534.8050.0020.0020.0000.0000.0000.000
191A219ARG10.7950.90736.794-0.030-0.0300.0000.0000.0000.000
192A220PHE0-0.038-0.03237.2990.0000.0000.0000.0000.0000.000
193A221LEU0-0.0200.00131.0690.0060.0060.0000.0000.0000.000
194A222THR0-0.007-0.00431.116-0.007-0.0070.0000.0000.0000.000
195A223PRO00.013-0.00629.8450.0060.0060.0000.0000.0000.000
196A224PHE0-0.019-0.01423.8010.0010.0010.0000.0000.0000.000
197A225TYR0-0.0070.00121.506-0.011-0.0110.0000.0000.0000.000
198A226GLN00.0360.00020.1250.0200.0200.0000.0000.0000.000
199A227GLN00.001-0.00313.546-0.033-0.0330.0000.0000.0000.000
200A228PRO00.0380.02413.7400.0240.0240.0000.0000.0000.000
201A229PRO0-0.002-0.01115.4110.0240.0240.0000.0000.0000.000
202A230HIS0-0.024-0.01517.8130.0110.0110.0000.0000.0000.000
203A231ARG10.8870.9279.939-0.341-0.3410.0000.0000.0000.000
204A232GLU-1-0.783-0.87711.6400.2480.2480.0000.0000.0000.000
205A233VAL0-0.032-0.00115.7610.0020.0020.0000.0000.0000.000
206A234VAL00.0100.01018.2640.0030.0030.0000.0000.0000.000
207A235ASN0-0.034-0.03812.1540.0530.0530.0000.0000.0000.000
208A236TYR00.0000.00816.1960.0030.0030.0000.0000.0000.000
209A237TRP0-0.029-0.01018.538-0.002-0.0020.0000.0000.0000.000
210A238TYR0-0.012-0.03115.6350.0120.0120.0000.0000.0000.000
211A239ARG10.9020.94512.932-0.306-0.3060.0000.0000.0000.000
212A240LYS10.8740.94217.657-0.105-0.1050.0000.0000.0000.000
213A241ASN0-0.062-0.02920.997-0.022-0.0220.0000.0000.0000.000
214A242GLY00.0090.01319.6920.0080.0080.0000.0000.0000.000
215A243ARG10.8080.89117.212-0.329-0.3290.0000.0000.0000.000
216A244THR0-0.010-0.02810.708-0.037-0.0370.0000.0000.0000.000
217A245LEU00.0140.02011.4590.0220.0220.0000.0000.0000.000
218A246PRO00.0320.02210.6680.1400.1400.0000.0000.0000.000
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