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: JQ3K9

Calculation Name: 1OR7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OR7

Chain ID: A

ChEMBL ID:

UniProt ID: P0AGB6

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1717326.418729
FMO2-HF: Nuclear repulsion 1645605.770158
FMO2-HF: Total energy -71720.648572
FMO2-MP2: Total energy -71930.464964


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:SER)


Summations of interaction energy for fragment #1(A:-1: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.
-24.569-16.7273.982-5.485-6.337-0.044
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.017
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].
3A1MET00.0710.0163.820-0.4272.076-0.037-1.483-0.9830.003
4A2SER00.0930.0507.427-0.016-0.0160.0000.0000.0000.000
5A3GLU-1-0.861-0.9164.5600.4720.548-0.001-0.011-0.0640.000
6A4GLN00.019-0.0118.1420.4400.4400.0000.0000.0000.000
7A5LEU00.0000.01210.273-0.137-0.1370.0000.0000.0000.000
8A6THR00.000-0.00212.152-0.066-0.0660.0000.0000.0000.000
9A7ASP-1-0.771-0.85410.5531.6191.6190.0000.0000.0000.000
10A8GLN00.0140.02113.728-0.005-0.0050.0000.0000.0000.000
11A9VAL00.0150.01016.186-0.067-0.0670.0000.0000.0000.000
12A10LEU0-0.034-0.02714.904-0.052-0.0520.0000.0000.0000.000
13A11VAL00.011-0.00416.446-0.038-0.0380.0000.0000.0000.000
14A12GLU-1-0.823-0.90419.0560.2670.2670.0000.0000.0000.000
15A13ARG10.8480.92021.072-0.239-0.2390.0000.0000.0000.000
16A14VAL0-0.030-0.01120.681-0.024-0.0240.0000.0000.0000.000
17A15GLN0-0.057-0.03322.370-0.032-0.0320.0000.0000.0000.000
18A16LYS10.8300.92224.982-0.280-0.2800.0000.0000.0000.000
19A17GLY00.0310.02626.872-0.024-0.0240.0000.0000.0000.000
20A18ASP-1-0.856-0.92624.5950.2050.2050.0000.0000.0000.000
21A19GLN00.048-0.00324.3030.0190.0190.0000.0000.0000.000
22A20LYS10.9380.97123.737-0.108-0.1080.0000.0000.0000.000
23A21ALA0-0.002-0.00320.6880.0090.0090.0000.0000.0000.000
24A22PHE00.0440.00919.3110.0580.0580.0000.0000.0000.000
25A23ASN00.0160.01119.2730.0530.0530.0000.0000.0000.000
26A24LEU0-0.018-0.00316.8140.0150.0150.0000.0000.0000.000
27A25LEU0-0.024-0.00714.3560.0580.0580.0000.0000.0000.000
28A26VAL0-0.0010.00414.7860.1370.1370.0000.0000.0000.000
29A27VAL00.0170.00714.9190.0580.0580.0000.0000.0000.000
30A28ARG10.8030.8929.146-0.950-0.9500.0000.0000.0000.000
31A29TYR0-0.083-0.0978.6680.5700.5700.0000.0000.0000.000
32A30GLN00.0130.01412.6080.0180.0180.0000.0000.0000.000
33A31HIS00.0690.03312.1810.0360.0360.0000.0000.0000.000
34A32LYS10.8750.9526.648-2.363-2.3630.0000.0000.0000.000
35A33VAL00.0140.00510.8700.0380.0380.0000.0000.0000.000
36A34ALA00.0350.01413.922-0.055-0.0550.0000.0000.0000.000
37A35SER0-0.029-0.00511.775-0.004-0.0040.0000.0000.0000.000
38A36LEU0-0.012-0.00512.363-0.051-0.0510.0000.0000.0000.000
39A37VAL00.014-0.00414.115-0.079-0.0790.0000.0000.0000.000
40A38SER0-0.044-0.02016.338-0.077-0.0770.0000.0000.0000.000
41A39ARG10.9030.95512.475-0.844-0.8440.0000.0000.0000.000
42A40TYR0-0.062-0.03816.888-0.040-0.0400.0000.0000.0000.000
43A41VAL00.0060.00621.153-0.029-0.0290.0000.0000.0000.000
44A42PRO00.0740.04422.9610.0090.0090.0000.0000.0000.000
45A43SER00.0360.00523.3150.0150.0150.0000.0000.0000.000
46A44GLY00.0240.01424.3570.0070.0070.0000.0000.0000.000
47A45ASP-1-0.796-0.88425.8480.2330.2330.0000.0000.0000.000
48A46VAL0-0.067-0.02919.6340.0300.0300.0000.0000.0000.000
49A47PRO00.001-0.00821.8890.0450.0450.0000.0000.0000.000
50A48ASP-1-0.822-0.90723.3450.2650.2650.0000.0000.0000.000
51A49VAL00.0080.00721.3360.0240.0240.0000.0000.0000.000
52A50VAL0-0.034-0.01618.0660.0520.0520.0000.0000.0000.000
53A51GLN0-0.017-0.00520.4490.0440.0440.0000.0000.0000.000
54A52GLU-1-0.800-0.89823.1480.3630.3630.0000.0000.0000.000
55A53ALA0-0.026-0.01819.2050.0130.0130.0000.0000.0000.000
56A54PHE00.015-0.00815.4200.0470.0470.0000.0000.0000.000
57A55ILE0-0.0080.00520.676-0.007-0.0070.0000.0000.0000.000
58A56LYS10.8030.88823.009-0.425-0.4250.0000.0000.0000.000
59A57ALA0-0.014-0.00519.191-0.001-0.0010.0000.0000.0000.000
60A58TYR0-0.022-0.01021.227-0.021-0.0210.0000.0000.0000.000
61A59ARG10.9640.97523.213-0.309-0.3090.0000.0000.0000.000
62A60ALA00.0060.01823.097-0.021-0.0210.0000.0000.0000.000
63A61LEU00.0070.00019.3910.0250.0250.0000.0000.0000.000
64A62ASP-1-0.885-0.92622.9640.3270.3270.0000.0000.0000.000
65A63SER0-0.081-0.05824.548-0.025-0.0250.0000.0000.0000.000
66A64PHE0-0.065-0.00915.7140.0360.0360.0000.0000.0000.000
67A65ARG10.9670.97521.208-0.384-0.3840.0000.0000.0000.000
68A66GLY00.0070.01117.578-0.023-0.0230.0000.0000.0000.000
69A67ASP-1-0.909-0.94418.0900.5050.5050.0000.0000.0000.000
70A68SER0-0.055-0.03414.212-0.003-0.0030.0000.0000.0000.000
71A69ALA00.0010.00310.222-0.029-0.0290.0000.0000.0000.000
72A70PHE00.0610.01912.2800.0120.0120.0000.0000.0000.000
73A71TYR00.0220.0116.5830.2010.2010.0000.0000.0000.000
74A72THR00.0170.0129.983-0.134-0.1340.0000.0000.0000.000
75A73TRP0-0.0030.00511.809-0.133-0.1330.0000.0000.0000.000
76A74LEU00.0270.01213.222-0.103-0.1030.0000.0000.0000.000
77A75TYR00.045-0.0047.391-0.197-0.1970.0000.0000.0000.000
78A76ARG10.9550.99214.036-0.912-0.9120.0000.0000.0000.000
79A77ILE00.0520.04516.709-0.098-0.0980.0000.0000.0000.000
80A78ALA00.0090.00816.008-0.086-0.0860.0000.0000.0000.000
81A79VAL00.0030.00015.874-0.072-0.0720.0000.0000.0000.000
82A80ASN0-0.065-0.04418.540-0.113-0.1130.0000.0000.0000.000
83A81THR0-0.040-0.01121.263-0.072-0.0720.0000.0000.0000.000
84A82ALA00.0530.02820.350-0.045-0.0450.0000.0000.0000.000
85A83LYS10.9450.96820.963-0.524-0.5240.0000.0000.0000.000
86A84ASN0-0.060-0.04523.974-0.057-0.0570.0000.0000.0000.000
87A85TYR0-0.010-0.01925.625-0.022-0.0220.0000.0000.0000.000
88A86LEU00.005-0.00424.030-0.022-0.0220.0000.0000.0000.000
89A87VAL0-0.064-0.02327.511-0.024-0.0240.0000.0000.0000.000
90A88ALA0-0.019-0.01030.161-0.019-0.0190.0000.0000.0000.000
91A89GLN00.0420.02929.287-0.034-0.0340.0000.0000.0000.000
92A90GLY0-0.0020.01031.582-0.014-0.0140.0000.0000.0000.000
93A91ARG10.8660.92833.010-0.222-0.2220.0000.0000.0000.000
94A92ARG10.9010.95733.508-0.181-0.1810.0000.0000.0000.000
95A93PRO00.004-0.00237.538-0.002-0.0020.0000.0000.0000.000
96A94PRO00.0180.00040.6920.0010.0010.0000.0000.0000.000
97A95SER00.021-0.01242.7090.0000.0000.0000.0000.0000.000
98A96SER0-0.0270.01438.1350.0010.0010.0000.0000.0000.000
99A97ASP-1-0.865-0.93537.2560.1390.1390.0000.0000.0000.000
100A98VAL0-0.025-0.01639.676-0.004-0.0040.0000.0000.0000.000
101A99ASP-1-0.878-0.93241.1660.0990.0990.0000.0000.0000.000
102A100ALA0-0.037-0.02037.216-0.003-0.0030.0000.0000.0000.000
103A101ILE0-0.053-0.03839.238-0.004-0.0040.0000.0000.0000.000
104A102GLU-1-0.993-0.99941.2330.0710.0710.0000.0000.0000.000
105A103ALA0-0.052-0.01840.426-0.004-0.0040.0000.0000.0000.000
106A104GLU-1-1.008-0.97636.5830.0960.0960.0000.0000.0000.000
107A105ASN0-0.054-0.03439.862-0.005-0.0050.0000.0000.0000.000
108A106PHE0-0.010-0.00741.575-0.001-0.0010.0000.0000.0000.000
109A107GLU-1-0.894-0.96443.0500.0580.0580.0000.0000.0000.000
110A108SER0-0.086-0.03046.629-0.001-0.0010.0000.0000.0000.000
111A109GLY0-0.052-0.04048.909-0.001-0.0010.0000.0000.0000.000
112A110GLY0-0.016-0.03545.2140.0020.0020.0000.0000.0000.000
113A111ALA00.0510.07841.0730.0040.0040.0000.0000.0000.000
114A120ASN00.005-0.01324.681-0.001-0.0010.0000.0000.0000.000
115A121LEU0-0.026-0.01222.8510.0220.0220.0000.0000.0000.000
116A122MET00.0400.02017.721-0.034-0.0340.0000.0000.0000.000
117A123LEU00.0250.02919.7580.0350.0350.0000.0000.0000.000
118A124SER00.0340.00214.243-0.051-0.0510.0000.0000.0000.000
119A125GLU-1-0.837-0.92614.792-0.355-0.3550.0000.0000.0000.000
120A126GLU-1-0.926-0.95416.611-0.171-0.1710.0000.0000.0000.000
121A127LEU00.0240.00914.039-0.046-0.0460.0000.0000.0000.000
122A128ARG10.9140.9598.5380.5280.5280.0000.0000.0000.000
123A129GLN0-0.033-0.02913.778-0.140-0.1400.0000.0000.0000.000
124A130ILE0-0.022-0.00416.640-0.049-0.0490.0000.0000.0000.000
125A131VAL00.0180.01110.970-0.039-0.0390.0000.0000.0000.000
126A132PHE0-0.002-0.0168.066-0.107-0.1070.0000.0000.0000.000
127A133ARG10.9700.99913.9020.3480.3480.0000.0000.0000.000
128A134THR0-0.032-0.02016.0950.0410.0410.0000.0000.0000.000
129A135ILE00.0020.00310.403-0.001-0.0010.0000.0000.0000.000
130A136GLU-1-0.869-0.90914.752-0.750-0.7500.0000.0000.0000.000
131A137SER0-0.093-0.04817.0940.0720.0720.0000.0000.0000.000
132A138LEU0-0.059-0.01914.7110.0440.0440.0000.0000.0000.000
133A139PRO00.0330.00018.6960.0030.0030.0000.0000.0000.000
134A140GLU-1-0.805-0.90716.994-0.891-0.8910.0000.0000.0000.000
135A141ASP-1-0.828-0.89816.382-0.741-0.7410.0000.0000.0000.000
136A142LEU0-0.041-0.03715.357-0.088-0.0880.0000.0000.0000.000
137A143ARG10.8440.92213.2520.6240.6240.0000.0000.0000.000
138A144MET00.0630.04011.316-0.278-0.2780.0000.0000.0000.000
139A145ALA00.0250.01110.761-0.292-0.2920.0000.0000.0000.000
140A146ILE0-0.038-0.0298.917-0.303-0.3030.0000.0000.0000.000
141A147THR0-0.007-0.0117.400-0.828-0.8280.0000.0000.0000.000
142A148LEU00.0130.0106.215-1.123-1.1230.0000.0000.0000.000
143A149ARG10.7340.8714.0612.9403.241-0.001-0.087-0.2130.000
144A150GLU-1-0.837-0.9173.721-5.036-4.4610.012-0.239-0.349-0.001
145A151LEU0-0.078-0.0452.282-14.873-12.2173.602-2.999-3.258-0.037
146A152ASP-1-0.867-0.9273.460-2.204-1.2400.058-0.444-0.577-0.003
147A153GLY0-0.023-0.0462.946-0.7820.0500.304-0.370-0.766-0.005
148A154LEU0-0.050-0.0123.3992.2882.2230.0450.148-0.127-0.001
149A155SER0-0.063-0.0767.092-0.044-0.0440.0000.0000.0000.000
150A156TYR00.003-0.0389.722-0.023-0.0230.0000.0000.0000.000
151A157GLU-1-0.884-0.93812.404-0.410-0.4100.0000.0000.0000.000
152A158GLU-1-0.790-0.85310.007-1.031-1.0310.0000.0000.0000.000
153A159ILE0-0.021-0.0158.3480.0690.0690.0000.0000.0000.000
154A160ALA0-0.018-0.02612.4340.0670.0670.0000.0000.0000.000
155A161ALA00.0150.02015.8320.0580.0580.0000.0000.0000.000
156A162ILE0-0.030-0.01211.8460.0330.0330.0000.0000.0000.000
157A163MET0-0.112-0.06314.446-0.017-0.0170.0000.0000.0000.000
158A164ASP-1-0.915-0.93217.172-0.364-0.3640.0000.0000.0000.000
159A165CYS0-0.107-0.02817.7210.0040.0040.0000.0000.0000.000
160A166PRO00.0760.01919.264-0.015-0.0150.0000.0000.0000.000
161A167VAL00.0980.04216.969-0.057-0.0570.0000.0000.0000.000
162A168GLY0-0.040-0.01817.181-0.044-0.0440.0000.0000.0000.000
163A169THR00.0270.00519.0460.0050.0050.0000.0000.0000.000
164A170VAL00.0440.03212.801-0.044-0.0440.0000.0000.0000.000
165A171ARG10.9120.96214.5290.3010.3010.0000.0000.0000.000
166A172SER0-0.029-0.02915.666-0.006-0.0060.0000.0000.0000.000
167A173ARG10.8450.91715.4030.7190.7190.0000.0000.0000.000
168A174ILE00.0310.01510.004-0.032-0.0320.0000.0000.0000.000
169A175PHE0-0.051-0.01913.137-0.010-0.0100.0000.0000.0000.000
170A176ARG10.9120.93715.5740.4390.4390.0000.0000.0000.000
171A177ALA00.0460.04113.3220.0440.0440.0000.0000.0000.000
172A178ARG10.8290.8867.8071.4341.4340.0000.0000.0000.000
173A179GLU-1-0.843-0.91214.256-0.305-0.3050.0000.0000.0000.000
174A180ALA0-0.0230.00617.6190.0640.0640.0000.0000.0000.000
175A181ILE0-0.015-0.02612.1800.0420.0420.0000.0000.0000.000
176A182ASP-1-0.855-0.92116.341-0.249-0.2490.0000.0000.0000.000
177A183ASN0-0.051-0.03417.7110.0910.0910.0000.0000.0000.000
178A184LYS10.8870.94918.9970.3830.3830.0000.0000.0000.000
179A185VAL0-0.042-0.01915.3310.0210.0210.0000.0000.0000.000
180A186GLN0-0.061-0.05018.7140.0890.0890.0000.0000.0000.000
181A187PRO0-0.0600.00420.5670.0250.0250.0000.0000.0000.000