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: NN16Q

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1718213.325496
FMO2-HF: Nuclear repulsion 1646494.667485
FMO2-HF: Total energy -71718.658011
FMO2-MP2: Total energy -71928.682156


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.
-27.474-18.9684.604-6.18-6.934-0.051
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 : 0.012 / q_NPA : 0.010
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].
3A1MET00.062-0.0033.820-0.7791.897-0.041-1.573-1.0630.003
4A2SER00.0980.0627.4270.0440.0440.0000.0000.0000.000
5A3GLU-1-0.736-0.8464.6181.3441.458-0.001-0.020-0.0940.000
6A4GLN0-0.006-0.0508.2940.3240.3240.0000.0000.0000.000
7A5LEU00.0140.02010.273-0.121-0.1210.0000.0000.0000.000
8A6THR0-0.021-0.01012.036-0.091-0.0910.0000.0000.0000.000
9A7ASP-1-0.751-0.81110.7971.5621.5620.0000.0000.0000.000
10A8GLN00.017-0.00613.7280.0130.0130.0000.0000.0000.000
11A9VAL00.0020.00716.186-0.067-0.0670.0000.0000.0000.000
12A10LEU0-0.039-0.03314.973-0.051-0.0510.0000.0000.0000.000
13A11VAL00.009-0.00216.509-0.034-0.0340.0000.0000.0000.000
14A12GLU-1-0.869-0.90919.0560.3030.3030.0000.0000.0000.000
15A13ARG10.8890.94021.576-0.210-0.2100.0000.0000.0000.000
16A14VAL0-0.018-0.00120.687-0.023-0.0230.0000.0000.0000.000
17A15GLN0-0.043-0.02322.293-0.032-0.0320.0000.0000.0000.000
18A16LYS10.9150.96624.982-0.225-0.2250.0000.0000.0000.000
19A17GLY00.0240.02126.877-0.023-0.0230.0000.0000.0000.000
20A18ASP-1-0.895-0.95024.7290.1810.1810.0000.0000.0000.000
21A19GLN00.0580.00524.2850.0200.0200.0000.0000.0000.000
22A20LYS10.9310.96923.700-0.093-0.0930.0000.0000.0000.000
23A21ALA0-0.003-0.00620.6680.0070.0070.0000.0000.0000.000
24A22PHE00.0400.01119.2960.0530.0530.0000.0000.0000.000
25A23ASN00.0260.01319.2050.0590.0590.0000.0000.0000.000
26A24LEU0-0.0180.00016.7610.0120.0120.0000.0000.0000.000
27A25LEU0-0.027-0.00814.4010.0520.0520.0000.0000.0000.000
28A26VAL00.0070.00414.6880.1330.1330.0000.0000.0000.000
29A27VAL00.0090.00614.8290.0570.0570.0000.0000.0000.000
30A28ARG10.8170.9289.752-0.878-0.8780.0000.0000.0000.000
31A29TYR0-0.140-0.1579.0620.4670.4670.0000.0000.0000.000
32A30GLN00.0130.00812.4670.0240.0240.0000.0000.0000.000
33A31HIS00.0770.03312.0480.0530.0530.0000.0000.0000.000
34A32LYS10.9250.9735.440-4.171-4.1710.0000.0000.0000.000
35A33VAL00.0190.00510.8950.0460.0460.0000.0000.0000.000
36A34ALA00.0360.01613.945-0.050-0.0500.0000.0000.0000.000
37A35SER0-0.026-0.00611.538-0.060-0.0600.0000.0000.0000.000
38A36LEU0-0.0020.00311.873-0.045-0.0450.0000.0000.0000.000
39A37VAL00.017-0.00414.127-0.074-0.0740.0000.0000.0000.000
40A38SER0-0.056-0.02616.301-0.074-0.0740.0000.0000.0000.000
41A39ARG10.9050.95912.989-0.835-0.8350.0000.0000.0000.000
42A40TYR0-0.077-0.04216.744-0.036-0.0360.0000.0000.0000.000
43A41VAL00.0100.00821.159-0.028-0.0280.0000.0000.0000.000
44A42PRO00.0670.03522.9730.0090.0090.0000.0000.0000.000
45A43SER00.0330.00223.3180.0140.0140.0000.0000.0000.000
46A44GLY00.0290.01624.3730.0070.0070.0000.0000.0000.000
47A45ASP-1-0.813-0.91625.9980.2270.2270.0000.0000.0000.000
48A46VAL0-0.080-0.03319.7790.0290.0290.0000.0000.0000.000
49A47PRO0-0.003-0.01221.9100.0430.0430.0000.0000.0000.000
50A48ASP-1-0.822-0.90623.3700.2530.2530.0000.0000.0000.000
51A49VAL00.0000.00521.2720.0230.0230.0000.0000.0000.000
52A50VAL0-0.036-0.01818.1240.0500.0500.0000.0000.0000.000
53A51GLN0-0.015-0.00720.4720.0340.0340.0000.0000.0000.000
54A52GLU-1-0.871-0.94023.1740.3420.3420.0000.0000.0000.000
55A53ALA0-0.023-0.02019.2450.0130.0130.0000.0000.0000.000
56A54PHE00.008-0.00915.6090.0440.0440.0000.0000.0000.000
57A55ILE0-0.0040.00820.701-0.006-0.0060.0000.0000.0000.000
58A56LYS10.8730.93822.991-0.412-0.4120.0000.0000.0000.000
59A57ALA0-0.010-0.00219.239-0.001-0.0010.0000.0000.0000.000
60A58TYR0-0.027-0.01721.227-0.018-0.0180.0000.0000.0000.000
61A59ARG10.9590.97223.213-0.301-0.3010.0000.0000.0000.000
62A60ALA00.0060.01823.090-0.019-0.0190.0000.0000.0000.000
63A61LEU00.0120.00119.3740.0230.0230.0000.0000.0000.000
64A62ASP-1-0.886-0.92722.9640.3110.3110.0000.0000.0000.000
65A63SER0-0.093-0.06224.449-0.023-0.0230.0000.0000.0000.000
66A64PHE0-0.073-0.01015.7390.0310.0310.0000.0000.0000.000
67A65ARG10.9750.97421.216-0.363-0.3630.0000.0000.0000.000
68A66GLY00.0130.01217.580-0.023-0.0230.0000.0000.0000.000
69A67ASP-1-0.904-0.93818.0910.4770.4770.0000.0000.0000.000
70A68SER0-0.067-0.04314.3120.0020.0020.0000.0000.0000.000
71A69ALA0-0.002-0.00510.275-0.024-0.0240.0000.0000.0000.000
72A70PHE00.0660.03012.2850.0100.0100.0000.0000.0000.000
73A71TYR00.0310.0166.6810.1500.1500.0000.0000.0000.000
74A72THR0-0.0070.0009.714-0.161-0.1610.0000.0000.0000.000
75A73TRP00.0010.00911.824-0.127-0.1270.0000.0000.0000.000
76A74LEU00.0210.00913.164-0.100-0.1000.0000.0000.0000.000
77A75TYR00.044-0.0057.850-0.199-0.1990.0000.0000.0000.000
78A76ARG10.9500.98714.049-0.884-0.8840.0000.0000.0000.000
79A77ILE00.0390.03216.728-0.094-0.0940.0000.0000.0000.000
80A78ALA00.0160.02216.078-0.083-0.0830.0000.0000.0000.000
81A79VAL00.0050.00115.923-0.071-0.0710.0000.0000.0000.000
82A80ASN0-0.021-0.01918.549-0.100-0.1000.0000.0000.0000.000
83A81THR0-0.072-0.03921.278-0.069-0.0690.0000.0000.0000.000
84A82ALA00.0610.03120.343-0.044-0.0440.0000.0000.0000.000
85A83LYS10.9420.96621.108-0.527-0.5270.0000.0000.0000.000
86A84ASN0-0.056-0.04523.981-0.052-0.0520.0000.0000.0000.000
87A85TYR00.0340.02725.572-0.022-0.0220.0000.0000.0000.000
88A86LEU0-0.006-0.00723.975-0.023-0.0230.0000.0000.0000.000
89A87VAL0-0.060-0.01827.519-0.023-0.0230.0000.0000.0000.000
90A88ALA0-0.020-0.01330.167-0.019-0.0190.0000.0000.0000.000
91A89GLN00.0280.02929.205-0.033-0.0330.0000.0000.0000.000
92A90GLY00.0080.01431.575-0.014-0.0140.0000.0000.0000.000
93A91ARG10.8650.92833.016-0.223-0.2230.0000.0000.0000.000
94A92ARG10.8940.95133.006-0.184-0.1840.0000.0000.0000.000
95A93PRO00.0120.00237.547-0.001-0.0010.0000.0000.0000.000
96A94PRO00.0090.00240.6990.0020.0020.0000.0000.0000.000
97A95SER00.032-0.01842.7170.0000.0000.0000.0000.0000.000
98A96SER0-0.0030.03438.5490.0020.0020.0000.0000.0000.000
99A97ASP-1-0.892-0.94837.4370.1380.1380.0000.0000.0000.000
100A98VAL0-0.033-0.02039.685-0.004-0.0040.0000.0000.0000.000
101A99ASP-1-0.865-0.93241.2350.0970.0970.0000.0000.0000.000
102A100ALA0-0.037-0.01837.276-0.003-0.0030.0000.0000.0000.000
103A101ILE0-0.057-0.03839.250-0.004-0.0040.0000.0000.0000.000
104A102GLU-1-0.999-1.00441.2430.0720.0720.0000.0000.0000.000
105A103ALA0-0.045-0.01440.419-0.004-0.0040.0000.0000.0000.000
106A104GLU-1-1.013-0.97736.6220.0950.0950.0000.0000.0000.000
107A105ASN0-0.032-0.02739.875-0.002-0.0020.0000.0000.0000.000
108A106PHE0-0.027-0.01441.947-0.001-0.0010.0000.0000.0000.000
109A107GLU-1-0.913-0.97843.2720.0590.0590.0000.0000.0000.000
110A108SER0-0.075-0.02746.791-0.002-0.0020.0000.0000.0000.000
111A109GLY0-0.044-0.03549.270-0.001-0.0010.0000.0000.0000.000
112A110GLY0-0.019-0.03845.5150.0020.0020.0000.0000.0000.000
113A111ALA00.0530.08741.1360.0030.0030.0000.0000.0000.000
114A120ASN00.015-0.00824.389-0.004-0.0040.0000.0000.0000.000
115A121LEU0-0.030-0.01423.0220.0210.0210.0000.0000.0000.000
116A122MET00.0410.01817.820-0.033-0.0330.0000.0000.0000.000
117A123LEU00.0230.02720.1340.0340.0340.0000.0000.0000.000
118A124SER00.022-0.00514.662-0.055-0.0550.0000.0000.0000.000
119A125GLU-1-0.818-0.91315.531-0.334-0.3340.0000.0000.0000.000
120A126GLU-1-0.932-0.94716.877-0.174-0.1740.0000.0000.0000.000
121A127LEU00.0270.00814.136-0.045-0.0450.0000.0000.0000.000
122A128ARG10.9180.9548.2010.5370.5370.0000.0000.0000.000
123A129GLN0-0.012-0.02413.999-0.156-0.1560.0000.0000.0000.000
124A130ILE0-0.041-0.01016.793-0.052-0.0520.0000.0000.0000.000
125A131VAL00.0240.00811.192-0.043-0.0430.0000.0000.0000.000
126A132PHE00.002-0.0128.200-0.093-0.0930.0000.0000.0000.000
127A133ARG10.9540.99613.9470.3460.3460.0000.0000.0000.000
128A134THR0-0.021-0.01616.1470.0390.0390.0000.0000.0000.000
129A135ILE00.0000.01310.395-0.005-0.0050.0000.0000.0000.000
130A136GLU-1-0.944-0.97814.703-0.733-0.7330.0000.0000.0000.000
131A137SER0-0.088-0.04216.9960.0670.0670.0000.0000.0000.000
132A138LEU0-0.061-0.02214.6810.0390.0390.0000.0000.0000.000
133A139PRO00.029-0.00718.5820.0040.0040.0000.0000.0000.000
134A140GLU-1-0.876-0.94317.344-0.856-0.8560.0000.0000.0000.000
135A141ASP-1-0.881-0.94616.423-0.752-0.7520.0000.0000.0000.000
136A142LEU0-0.044-0.04015.298-0.089-0.0890.0000.0000.0000.000
137A143ARG10.9891.02113.1620.6310.6310.0000.0000.0000.000
138A144MET00.0610.10011.102-0.308-0.3080.0000.0000.0000.000
139A145ALA00.0340.01210.800-0.306-0.3060.0000.0000.0000.000
140A146ILE0-0.041-0.0358.793-0.317-0.3170.0000.0000.0000.000
141A147THR0-0.046-0.0747.362-0.781-0.7810.0000.0000.0000.000
142A148LEU00.0180.0046.308-1.180-1.1800.0000.0000.0000.000
143A149ARG10.7280.8604.4692.9363.103-0.001-0.023-0.1430.000
144A150GLU-1-0.861-0.9373.493-5.967-5.2180.016-0.339-0.427-0.002
145A151LEU0-0.098-0.0512.192-16.070-13.2134.116-3.431-3.541-0.043
146A152ASP-1-0.873-0.9263.033-1.848-0.5740.173-0.634-0.813-0.005
147A153GLY0-0.021-0.0432.913-0.4870.2490.299-0.317-0.719-0.003
148A154LEU0-0.033-0.0033.3902.2642.1970.0430.157-0.134-0.001
149A155SER0-0.049-0.0287.073-0.078-0.0780.0000.0000.0000.000
150A156TYR00.009-0.0329.607-0.023-0.0230.0000.0000.0000.000
151A157GLU-1-0.913-0.94612.278-0.409-0.4090.0000.0000.0000.000
152A158GLU-1-0.824-0.9089.639-1.044-1.0440.0000.0000.0000.000
153A159ILE0-0.022-0.0158.2990.0670.0670.0000.0000.0000.000
154A160ALA0-0.019-0.02312.4180.0700.0700.0000.0000.0000.000
155A161ALA00.0170.01915.8230.0590.0590.0000.0000.0000.000
156A162ILE0-0.026-0.00811.8770.0330.0330.0000.0000.0000.000
157A163MET0-0.115-0.06514.517-0.030-0.0300.0000.0000.0000.000
158A164ASP-1-0.908-0.92417.205-0.367-0.3670.0000.0000.0000.000
159A165CYS0-0.062-0.02818.0000.0020.0020.0000.0000.0000.000
160A166PRO00.0340.01419.209-0.018-0.0180.0000.0000.0000.000
161A167VAL00.1160.04316.795-0.060-0.0600.0000.0000.0000.000
162A168GLY0-0.054-0.02317.035-0.048-0.0480.0000.0000.0000.000
163A169THR00.016-0.00619.0520.0040.0040.0000.0000.0000.000
164A170VAL00.0530.03712.654-0.040-0.0400.0000.0000.0000.000
165A171ARG10.9210.96514.3920.3220.3220.0000.0000.0000.000
166A172SER0-0.023-0.02515.486-0.012-0.0120.0000.0000.0000.000
167A173ARG10.9020.96915.3610.7360.7360.0000.0000.0000.000
168A174ILE00.0460.0209.823-0.029-0.0290.0000.0000.0000.000
169A175PHE0-0.045-0.01912.992-0.005-0.0050.0000.0000.0000.000
170A176ARG10.9670.97515.5110.4720.4720.0000.0000.0000.000
171A177ALA00.0530.04413.2050.0470.0470.0000.0000.0000.000
172A178ARG10.8460.9008.1031.4781.4780.0000.0000.0000.000
173A179GLU-1-0.917-0.95714.389-0.328-0.3280.0000.0000.0000.000
174A180ALA0-0.048-0.01217.5700.0600.0600.0000.0000.0000.000
175A181ILE0-0.025-0.03412.2830.0390.0390.0000.0000.0000.000
176A182ASP-1-0.828-0.91416.449-0.266-0.2660.0000.0000.0000.000
177A183ASN00.0150.01117.7830.0850.0850.0000.0000.0000.000
178A184LYS10.8500.93019.2430.3800.3800.0000.0000.0000.000
179A185VAL0-0.038-0.01015.5220.0220.0220.0000.0000.0000.000
180A186GLN0-0.057-0.04618.9460.0990.0990.0000.0000.0000.000
181A187PRO0-0.077-0.00720.5690.0260.0260.0000.0000.0000.000