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: 3JQGL

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1718451.703291
FMO2-HF: Nuclear repulsion 1646730.306309
FMO2-HF: Total energy -71721.396981
FMO2-MP2: Total energy -71931.137703


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.
-29.227-23.43210.412-8.195-8.013-0.076
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 : 0.005 / q_NPA : -0.002
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].
3A1MET00.0530.0353.8570.8542.970-0.026-1.184-0.9060.001
4A2SER00.0690.0317.396-0.209-0.2090.0000.0000.0000.000
5A3GLU-1-0.841-0.9245.547-1.593-1.5930.0000.0000.0000.000
6A4GLN00.0340.0047.5630.7020.7020.0000.0000.0000.000
7A5LEU00.0300.02910.684-0.029-0.0290.0000.0000.0000.000
8A6THR00.000-0.00712.853-0.043-0.0430.0000.0000.0000.000
9A7ASP-1-0.778-0.86410.3100.6400.6400.0000.0000.0000.000
10A8GLN0-0.003-0.00213.6740.0430.0430.0000.0000.0000.000
11A9VAL00.0070.00616.387-0.034-0.0340.0000.0000.0000.000
12A10LEU0-0.049-0.02215.087-0.028-0.0280.0000.0000.0000.000
13A11VAL00.0150.00316.432-0.011-0.0110.0000.0000.0000.000
14A12GLU-1-0.787-0.87919.0040.1830.1830.0000.0000.0000.000
15A13ARG10.8500.91721.403-0.069-0.0690.0000.0000.0000.000
16A14VAL0-0.032-0.01120.537-0.012-0.0120.0000.0000.0000.000
17A15GLN0-0.071-0.04722.417-0.018-0.0180.0000.0000.0000.000
18A16LYS10.8400.92124.889-0.162-0.1620.0000.0000.0000.000
19A17GLY00.0290.02326.730-0.016-0.0160.0000.0000.0000.000
20A18ASP-1-0.834-0.91424.3830.0620.0620.0000.0000.0000.000
21A19GLN00.037-0.00823.8960.0030.0030.0000.0000.0000.000
22A20LYS10.9270.96723.705-0.017-0.0170.0000.0000.0000.000
23A21ALA00.0060.00320.446-0.010-0.0100.0000.0000.0000.000
24A22PHE00.0430.01519.0930.0200.0200.0000.0000.0000.000
25A23ASN00.0070.00919.0910.0280.0280.0000.0000.0000.000
26A24LEU0-0.010-0.00417.109-0.005-0.0050.0000.0000.0000.000
27A25LEU0-0.029-0.00414.251-0.003-0.0030.0000.0000.0000.000
28A26VAL0-0.005-0.00314.4260.0510.0510.0000.0000.0000.000
29A27VAL00.0100.00215.0960.0250.0250.0000.0000.0000.000
30A28ARG10.7960.8939.097-0.035-0.0350.0000.0000.0000.000
31A29TYR0-0.059-0.0717.8180.2090.2090.0000.0000.0000.000
32A30GLN00.0250.02112.0300.0540.0540.0000.0000.0000.000
33A31HIS00.0770.03712.2760.0780.0780.0000.0000.0000.000
34A32LYS10.8440.9356.599-0.429-0.4290.0000.0000.0000.000
35A33VAL00.012-0.00310.8220.0960.0960.0000.0000.0000.000
36A34ALA00.0410.01613.730-0.004-0.0040.0000.0000.0000.000
37A35SER0-0.0170.00712.0680.0300.0300.0000.0000.0000.000
38A36LEU0-0.027-0.00912.013-0.007-0.0070.0000.0000.0000.000
39A37VAL00.010-0.00514.021-0.024-0.0240.0000.0000.0000.000
40A38SER0-0.024-0.02616.511-0.043-0.0430.0000.0000.0000.000
41A39ARG10.8950.95512.395-0.800-0.8000.0000.0000.0000.000
42A40TYR0-0.061-0.03616.847-0.010-0.0100.0000.0000.0000.000
43A41VAL00.0020.00321.158-0.024-0.0240.0000.0000.0000.000
44A42PRO00.0770.04122.7880.0110.0110.0000.0000.0000.000
45A43SER00.005-0.00923.1650.0080.0080.0000.0000.0000.000
46A44GLY00.0330.02024.207-0.003-0.0030.0000.0000.0000.000
47A45ASP-1-0.777-0.86925.6090.1840.1840.0000.0000.0000.000
48A46VAL0-0.071-0.02919.4340.0170.0170.0000.0000.0000.000
49A47PRO00.0070.00021.6900.0250.0250.0000.0000.0000.000
50A48ASP-1-0.831-0.90923.1660.1740.1740.0000.0000.0000.000
51A49VAL0-0.001-0.00121.3500.0170.0170.0000.0000.0000.000
52A50VAL0-0.039-0.02117.9220.0400.0400.0000.0000.0000.000
53A51GLN0-0.0020.00320.3550.0180.0180.0000.0000.0000.000
54A52GLU-1-0.815-0.90123.0970.2700.2700.0000.0000.0000.000
55A53ALA0-0.013-0.00418.8960.0100.0100.0000.0000.0000.000
56A54PHE00.020-0.00514.9350.0310.0310.0000.0000.0000.000
57A55ILE00.0070.01020.328-0.008-0.0080.0000.0000.0000.000
58A56LYS10.7750.86522.491-0.325-0.3250.0000.0000.0000.000
59A57ALA0-0.016-0.01218.6140.0010.0010.0000.0000.0000.000
60A58TYR0-0.017-0.00220.648-0.008-0.0080.0000.0000.0000.000
61A59ARG10.9570.96922.897-0.203-0.2030.0000.0000.0000.000
62A60ALA00.0200.02322.545-0.009-0.0090.0000.0000.0000.000
63A61LEU0-0.009-0.00418.9720.0200.0200.0000.0000.0000.000
64A62ASP-1-0.849-0.91222.5990.2280.2280.0000.0000.0000.000
65A63SER0-0.050-0.02224.498-0.016-0.0160.0000.0000.0000.000
66A64PHE0-0.074-0.01316.0250.0210.0210.0000.0000.0000.000
67A65ARG10.8640.90421.249-0.337-0.3370.0000.0000.0000.000
68A66GLY00.0360.02917.885-0.025-0.0250.0000.0000.0000.000
69A67ASP-1-0.907-0.95218.0590.5100.5100.0000.0000.0000.000
70A68SER0-0.062-0.03214.4840.0750.0750.0000.0000.0000.000
71A69ALA00.0350.01710.304-0.080-0.0800.0000.0000.0000.000
72A70PHE00.0690.02812.3590.0480.0480.0000.0000.0000.000
73A71TYR00.0460.0187.1600.0340.0340.0000.0000.0000.000
74A72THR00.0060.00410.006-0.042-0.0420.0000.0000.0000.000
75A73TRP00.0000.00411.835-0.099-0.0990.0000.0000.0000.000
76A74LEU00.0260.01712.625-0.063-0.0630.0000.0000.0000.000
77A75TYR00.026-0.0087.108-0.152-0.1520.0000.0000.0000.000
78A76ARG10.9590.98813.583-0.830-0.8300.0000.0000.0000.000
79A77ILE00.0370.03916.575-0.074-0.0740.0000.0000.0000.000
80A78ALA00.0040.01515.738-0.063-0.0630.0000.0000.0000.000
81A79VAL00.0100.00515.568-0.054-0.0540.0000.0000.0000.000
82A80ASN0-0.060-0.04518.258-0.080-0.0800.0000.0000.0000.000
83A81THR0-0.031-0.00321.016-0.058-0.0580.0000.0000.0000.000
84A82ALA00.0510.02420.313-0.035-0.0350.0000.0000.0000.000
85A83LYS10.9510.97420.884-0.490-0.4900.0000.0000.0000.000
86A84ASN0-0.061-0.03923.875-0.044-0.0440.0000.0000.0000.000
87A85TYR0-0.013-0.02925.383-0.017-0.0170.0000.0000.0000.000
88A86LEU00.0140.00423.854-0.017-0.0170.0000.0000.0000.000
89A87VAL0-0.055-0.02327.369-0.019-0.0190.0000.0000.0000.000
90A88ALA0-0.023-0.01029.984-0.016-0.0160.0000.0000.0000.000
91A89GLN00.0310.02329.182-0.028-0.0280.0000.0000.0000.000
92A90GLY0-0.010-0.00331.397-0.011-0.0110.0000.0000.0000.000
93A91ARG10.8670.92632.959-0.198-0.1980.0000.0000.0000.000
94A92ARG10.9310.97733.197-0.152-0.1520.0000.0000.0000.000
95A93PRO00.010-0.00237.519-0.001-0.0010.0000.0000.0000.000
96A94PRO00.009-0.00440.8440.0010.0010.0000.0000.0000.000
97A95SER0-0.043-0.02642.943-0.001-0.0010.0000.0000.0000.000
98A96SER0-0.070-0.03037.9560.0000.0000.0000.0000.0000.000
99A97ASP-1-0.850-0.91737.1490.1250.1250.0000.0000.0000.000
100A98VAL0-0.018-0.00739.617-0.003-0.0030.0000.0000.0000.000
101A99ASP-1-0.821-0.91641.2510.0860.0860.0000.0000.0000.000
102A100ALA0-0.041-0.01837.440-0.003-0.0030.0000.0000.0000.000
103A101ILE0-0.041-0.02739.459-0.004-0.0040.0000.0000.0000.000
104A102GLU-1-0.986-0.99741.2710.0600.0600.0000.0000.0000.000
105A103ALA0-0.030-0.01240.495-0.004-0.0040.0000.0000.0000.000
106A104GLU-1-0.995-0.97936.2800.0820.0820.0000.0000.0000.000
107A105ASN0-0.080-0.03739.697-0.007-0.0070.0000.0000.0000.000
108A106PHE0-0.008-0.01542.171-0.002-0.0020.0000.0000.0000.000
109A107GLU-1-0.886-0.93943.6160.0450.0450.0000.0000.0000.000
110A108SER0-0.058-0.03647.156-0.002-0.0020.0000.0000.0000.000
111A109GLY0-0.013-0.02648.370-0.001-0.0010.0000.0000.0000.000
112A110GLY0-0.052-0.01846.055-0.001-0.0010.0000.0000.0000.000
113A111ALA0-0.0040.02941.4520.0030.0030.0000.0000.0000.000
114A120ASN00.001-0.01424.654-0.004-0.0040.0000.0000.0000.000
115A121LEU0-0.035-0.01722.7750.0170.0170.0000.0000.0000.000
116A122MET00.0380.02618.290-0.026-0.0260.0000.0000.0000.000
117A123LEU00.0070.01420.4570.0300.0300.0000.0000.0000.000
118A124SER00.005-0.00714.946-0.041-0.0410.0000.0000.0000.000
119A125GLU-1-0.802-0.91115.033-0.173-0.1730.0000.0000.0000.000
120A126GLU-1-0.880-0.93117.157-0.124-0.1240.0000.0000.0000.000
121A127LEU00.0550.02414.308-0.038-0.0380.0000.0000.0000.000
122A128ARG10.8710.9379.6430.1330.1330.0000.0000.0000.000
123A129GLN0-0.035-0.02914.700-0.113-0.1130.0000.0000.0000.000
124A130ILE00.0030.01417.581-0.036-0.0360.0000.0000.0000.000
125A131VAL00.0040.01211.540-0.046-0.0460.0000.0000.0000.000
126A132PHE00.008-0.0148.441-0.069-0.0690.0000.0000.0000.000
127A133ARG10.9360.98014.3150.2610.2610.0000.0000.0000.000
128A134THR0-0.033-0.01916.8100.0270.0270.0000.0000.0000.000
129A135ILE0-0.003-0.00510.854-0.004-0.0040.0000.0000.0000.000
130A136GLU-1-0.840-0.88815.128-0.679-0.6790.0000.0000.0000.000
131A137SER0-0.096-0.04817.3260.0560.0560.0000.0000.0000.000
132A138LEU0-0.043-0.01214.9170.0340.0340.0000.0000.0000.000
133A139PRO00.0330.00418.887-0.005-0.0050.0000.0000.0000.000
134A140GLU-1-0.786-0.89016.633-0.862-0.8620.0000.0000.0000.000
135A141ASP-1-0.839-0.89716.263-0.721-0.7210.0000.0000.0000.000
136A142LEU0-0.064-0.03115.329-0.057-0.0570.0000.0000.0000.000
137A143ARG10.8070.87113.3480.5700.5700.0000.0000.0000.000
138A144MET00.0560.03511.327-0.221-0.2210.0000.0000.0000.000
139A145ALA00.0370.01010.775-0.298-0.2980.0000.0000.0000.000
140A146ILE0-0.025-0.0268.959-0.315-0.3150.0000.0000.0000.000
141A147THR0-0.034-0.0147.347-0.590-0.5900.0000.0000.0000.000
142A148LEU00.0240.0115.991-1.298-1.2980.0000.0000.0000.000
143A149ARG10.7150.8454.2423.4783.723-0.001-0.072-0.1720.000
144A150GLU-1-0.825-0.8973.888-4.749-4.3700.004-0.168-0.216-0.001
145A151LEU0-0.067-0.0252.661-3.272-0.5821.164-1.707-2.146-0.013
146A152ASP-1-0.843-0.9211.836-22.098-21.8608.324-4.956-3.607-0.061
147A153GLY0-0.022-0.0172.609-0.0530.5110.882-0.605-0.841-0.001
148A154LEU0-0.0250.0123.2822.8682.4310.0650.497-0.125-0.001
149A155SER0-0.071-0.0757.015-0.182-0.1820.0000.0000.0000.000
150A156TYR0-0.003-0.0469.862-0.038-0.0380.0000.0000.0000.000
151A157GLU-1-0.853-0.92912.632-0.417-0.4170.0000.0000.0000.000
152A158GLU-1-0.816-0.8679.702-0.893-0.8930.0000.0000.0000.000
153A159ILE00.001-0.0038.4720.0540.0540.0000.0000.0000.000
154A160ALA0-0.013-0.01512.6780.0650.0650.0000.0000.0000.000
155A161ALA00.0080.01116.1050.0590.0590.0000.0000.0000.000
156A162ILE0-0.038-0.02111.9020.0320.0320.0000.0000.0000.000
157A163MET0-0.093-0.04214.343-0.049-0.0490.0000.0000.0000.000
158A164ASP-1-0.911-0.94417.150-0.367-0.3670.0000.0000.0000.000
159A165CYS0-0.082-0.01117.9440.0000.0000.0000.0000.0000.000
160A166PRO00.0590.01619.426-0.016-0.0160.0000.0000.0000.000
161A167VAL00.0790.03316.539-0.052-0.0520.0000.0000.0000.000
162A168GLY0-0.036-0.01117.214-0.045-0.0450.0000.0000.0000.000
163A169THR00.0470.02219.212-0.001-0.0010.0000.0000.0000.000
164A170VAL00.0230.02713.056-0.040-0.0400.0000.0000.0000.000
165A171ARG10.9330.96814.5550.3860.3860.0000.0000.0000.000
166A172SER0-0.036-0.03315.642-0.005-0.0050.0000.0000.0000.000
167A173ARG10.8180.89515.2870.7150.7150.0000.0000.0000.000
168A174ILE00.0290.01010.115-0.013-0.0130.0000.0000.0000.000
169A175PHE0-0.057-0.02313.0530.0020.0020.0000.0000.0000.000
170A176ARG10.8930.91615.6600.4480.4480.0000.0000.0000.000
171A177ALA00.0320.02613.3440.0460.0460.0000.0000.0000.000
172A178ARG10.8290.8858.4561.4521.4520.0000.0000.0000.000
173A179GLU-1-0.817-0.88714.327-0.345-0.3450.0000.0000.0000.000
174A180ALA0-0.0100.00817.6350.0630.0630.0000.0000.0000.000
175A181ILE00.002-0.00312.5350.0410.0410.0000.0000.0000.000
176A182ASP-1-0.842-0.90416.643-0.274-0.2740.0000.0000.0000.000
177A183ASN0-0.047-0.04718.0240.0780.0780.0000.0000.0000.000
178A184LYS10.8590.93519.3710.3440.3440.0000.0000.0000.000
179A185VAL0-0.011-0.00115.5880.0250.0250.0000.0000.0000.000
180A186GLN0-0.081-0.03718.8810.0680.0680.0000.0000.0000.000
181A187PRO0-0.075-0.03320.6150.0480.0480.0000.0000.0000.000