Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1N37Z

Calculation Name: 1N7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N7K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y948

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2665312.097
FMO2-HF: Nuclear repulsion 2581037.249299
FMO2-HF: Total energy -84274.847701
FMO2-MP2: Total energy -84525.239394


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:2:PRO)


Summations of interaction energy for fragment #1(A:2: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.
-4.760.7695.408-3.394-7.543-0.016
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.006
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].
3A4ALA00.037-0.0063.856-0.8400.6590.000-0.767-0.7320.003
4A5ARG10.9810.9806.2870.3200.3200.0000.0000.0000.000
5A6ASP-1-0.786-0.8452.294-0.7720.6911.268-1.202-1.528-0.008
6A7ILE0-0.0090.0062.592-0.5430.1430.418-0.232-0.8720.000
7A8LEU0-0.015-0.0114.8830.0680.122-0.001-0.007-0.0470.000
8A9GLN0-0.109-0.0567.1180.0470.0470.0000.0000.0000.000
9A10GLN00.0410.0162.955-0.5040.0170.061-0.128-0.4540.000
10A11GLY00.0180.0087.744-0.013-0.0130.0000.0000.0000.000
11A12LEU0-0.043-0.02710.2680.0330.0330.0000.0000.0000.000
12A13ASP-1-0.865-0.9229.5840.1470.1470.0000.0000.0000.000
13A14ARG10.7660.8716.6300.1210.1210.0000.0000.0000.000
14A15LEU0-0.049-0.03013.582-0.009-0.0090.0000.0000.0000.000
15A16GLY00.0500.03916.173-0.007-0.0070.0000.0000.0000.000
16A17SER0-0.053-0.03818.4770.0020.0020.0000.0000.0000.000
17A18PRO0-0.005-0.01720.528-0.014-0.0140.0000.0000.0000.000
18A19GLU-1-0.813-0.91622.710-0.080-0.0800.0000.0000.0000.000
19A20ASP-1-0.838-0.87818.523-0.060-0.0600.0000.0000.0000.000
20A21LEU0-0.058-0.02817.989-0.015-0.0150.0000.0000.0000.000
21A22ALA00.0300.00319.830-0.012-0.0120.0000.0000.0000.000
22A23SER00.014-0.01021.3170.0000.0000.0000.0000.0000.000
23A24ARG10.8480.92314.7100.1240.1240.0000.0000.0000.000
24A25ILE0-0.054-0.01419.231-0.021-0.0210.0000.0000.0000.000
25A26ASP-1-0.698-0.81221.004-0.121-0.1210.0000.0000.0000.000
26A27SER00.0590.02522.831-0.017-0.0170.0000.0000.0000.000
27A28THR0-0.057-0.03524.2450.0060.0060.0000.0000.0000.000
28A29LEU00.0090.00626.652-0.003-0.0030.0000.0000.0000.000
29A30LEU0-0.002-0.00326.2860.0050.0050.0000.0000.0000.000
30A31SER0-0.0060.00730.169-0.002-0.0020.0000.0000.0000.000
31A32PRO00.019-0.00932.3800.0060.0060.0000.0000.0000.000
32A33ARG10.9260.95935.3900.1010.1010.0000.0000.0000.000
33A34ALA00.0000.02434.2890.0030.0030.0000.0000.0000.000
34A35THR0-0.011-0.02136.4080.0050.0050.0000.0000.0000.000
35A36GLU-1-0.792-0.92438.337-0.062-0.0620.0000.0000.0000.000
36A37GLU-1-0.762-0.84039.633-0.059-0.0590.0000.0000.0000.000
37A38ASP-1-0.841-0.88035.476-0.085-0.0850.0000.0000.0000.000
38A39VAL00.0170.00134.681-0.004-0.0040.0000.0000.0000.000
39A40ARG10.8120.87735.4460.0570.0570.0000.0000.0000.000
40A41ASN0-0.027-0.00835.9520.0030.0030.0000.0000.0000.000
41A42LEU0-0.0080.00728.863-0.001-0.0010.0000.0000.0000.000
42A43VAL0-0.005-0.00731.894-0.002-0.0020.0000.0000.0000.000
43A44ARG10.8090.89333.9050.0630.0630.0000.0000.0000.000
44A45GLU-1-0.868-0.94431.213-0.097-0.0970.0000.0000.0000.000
45A46ALA0-0.066-0.04329.409-0.003-0.0030.0000.0000.0000.000
46A47SER00.0090.00830.1400.0020.0020.0000.0000.0000.000
47A48ASP-1-0.959-0.98132.400-0.061-0.0610.0000.0000.0000.000
48A49TYR0-0.097-0.07827.8260.0010.0010.0000.0000.0000.000
49A50GLY00.0020.01527.828-0.003-0.0030.0000.0000.0000.000
50A51PHE0-0.072-0.03724.686-0.006-0.0060.0000.0000.0000.000
51A52ARG10.7530.85620.7150.1150.1150.0000.0000.0000.000
52A53CYS0-0.099-0.05924.1950.0050.0050.0000.0000.0000.000
53A54ALA00.0580.03926.705-0.008-0.0080.0000.0000.0000.000
54A55VAL0-0.052-0.03424.2840.0040.0040.0000.0000.0000.000
55A56LEU00.0230.01127.761-0.005-0.0050.0000.0000.0000.000
56A57THR00.0380.00430.495-0.001-0.0010.0000.0000.0000.000
57A58PRO00.0690.04832.4000.0040.0040.0000.0000.0000.000
58A59VAL00.0140.00434.8900.0030.0030.0000.0000.0000.000
59A60TYR0-0.033-0.04435.3100.0050.0050.0000.0000.0000.000
60A61THR0-0.0030.00032.9610.0000.0000.0000.0000.0000.000
61A62VAL00.0410.01935.2320.0030.0030.0000.0000.0000.000
62A63LYS10.8470.94338.7000.0600.0600.0000.0000.0000.000
63A64ILE00.0110.00835.1320.0030.0030.0000.0000.0000.000
64A65SER00.0300.01037.4910.0020.0020.0000.0000.0000.000
65A66GLY00.0670.04138.5130.0010.0010.0000.0000.0000.000
66A67LEU0-0.076-0.04238.5710.0020.0020.0000.0000.0000.000
67A68ALA00.017-0.00934.6540.0000.0000.0000.0000.0000.000
68A69GLU-1-0.919-0.95036.361-0.035-0.0350.0000.0000.0000.000
69A70LYS10.8990.94938.2350.0390.0390.0000.0000.0000.000
70A71LEU0-0.043-0.02736.5230.0020.0020.0000.0000.0000.000
71A72GLY00.0180.02435.192-0.001-0.0010.0000.0000.0000.000
72A73VAL0-0.051-0.01331.004-0.002-0.0020.0000.0000.0000.000
73A74LYS10.8760.93424.8610.0750.0750.0000.0000.0000.000
74A75LEU00.0340.02129.731-0.008-0.0080.0000.0000.0000.000
75A76CYS0-0.041-0.00926.1550.0000.0000.0000.0000.0000.000
76A77SER00.009-0.00928.688-0.002-0.0020.0000.0000.0000.000
77A78VAL0-0.061-0.02326.163-0.005-0.0050.0000.0000.0000.000
78A79ILE00.0210.00928.1190.0060.0060.0000.0000.0000.000
79A80GLY00.002-0.00728.692-0.008-0.0080.0000.0000.0000.000
80A81PHE0-0.0230.01425.114-0.007-0.0070.0000.0000.0000.000
81A82PRO0-0.023-0.02327.7830.0060.0060.0000.0000.0000.000
82A83LEU00.004-0.02027.453-0.008-0.0080.0000.0000.0000.000
83A84GLY00.0840.04528.380-0.002-0.0020.0000.0000.0000.000
84A85GLN0-0.043-0.02229.3440.0060.0060.0000.0000.0000.000
85A86ALA00.0090.02532.2450.0060.0060.0000.0000.0000.000
86A87PRO00.0330.00433.724-0.002-0.0020.0000.0000.0000.000
87A88LEU00.0320.00432.691-0.001-0.0010.0000.0000.0000.000
88A89GLU-1-0.931-0.96034.979-0.042-0.0420.0000.0000.0000.000
89A90VAL00.0230.00636.7350.0010.0010.0000.0000.0000.000
90A91LYS10.7790.88730.1370.0850.0850.0000.0000.0000.000
91A92LEU0-0.0080.00034.299-0.001-0.0010.0000.0000.0000.000
92A93VAL00.0180.01936.1250.0020.0020.0000.0000.0000.000
93A94GLU-1-0.847-0.92133.268-0.081-0.0810.0000.0000.0000.000
94A95ALA00.003-0.01632.684-0.001-0.0010.0000.0000.0000.000
95A96GLN0-0.0010.00834.3530.0000.0000.0000.0000.0000.000
96A97THR0-0.023-0.01037.6450.0000.0000.0000.0000.0000.000
97A98VAL0-0.036-0.01932.5100.0000.0000.0000.0000.0000.000
98A99LEU0-0.054-0.02332.088-0.001-0.0010.0000.0000.0000.000
99A100GLU-1-0.875-0.92535.901-0.036-0.0360.0000.0000.0000.000
100A101ALA0-0.063-0.02237.7570.0020.0020.0000.0000.0000.000
101A102GLY00.0260.01736.702-0.001-0.0010.0000.0000.0000.000
102A103ALA0-0.058-0.02031.677-0.002-0.0020.0000.0000.0000.000
103A104THR00.0370.00630.1070.0020.0020.0000.0000.0000.000
104A105GLU-1-0.780-0.86524.599-0.094-0.0940.0000.0000.0000.000
105A106LEU00.0410.01726.424-0.002-0.0020.0000.0000.0000.000
106A107ASP-1-0.758-0.86722.632-0.163-0.1630.0000.0000.0000.000
107A108VAL00.0160.00224.563-0.001-0.0010.0000.0000.0000.000
108A109VAL0-0.027-0.01024.205-0.014-0.0140.0000.0000.0000.000
109A110PRO00.0200.01124.2200.0110.0110.0000.0000.0000.000
110A111HIS00.022-0.00326.886-0.013-0.0130.0000.0000.0000.000
111A112LEU0-0.033-0.02221.9330.0060.0060.0000.0000.0000.000
112A113SER0-0.003-0.00125.4080.0010.0010.0000.0000.0000.000
113A114LEU0-0.035-0.00527.4210.0070.0070.0000.0000.0000.000
114A115GLY00.0190.01925.5150.0080.0080.0000.0000.0000.000
115A116PRO00.020-0.01022.6040.0030.0030.0000.0000.0000.000
116A117GLU-1-0.772-0.84924.758-0.027-0.0270.0000.0000.0000.000
117A118ALA0-0.0020.00528.1310.0040.0040.0000.0000.0000.000
118A119VAL00.0220.01123.2280.0010.0010.0000.0000.0000.000
119A120TYR0-0.0040.00925.8840.0020.0020.0000.0000.0000.000
120A121ARG10.8430.90826.9950.0330.0330.0000.0000.0000.000
121A122GLU-1-0.784-0.88729.250-0.078-0.0780.0000.0000.0000.000
122A123VAL00.0140.00024.4220.0010.0010.0000.0000.0000.000
123A124SER00.018-0.01127.7390.0050.0050.0000.0000.0000.000
124A125GLY0-0.067-0.01929.7210.0050.0050.0000.0000.0000.000
125A126ILE00.021-0.00827.2220.0020.0020.0000.0000.0000.000
126A127VAL0-0.0140.00926.3520.0000.0000.0000.0000.0000.000
127A128LYS10.9200.96429.3970.0270.0270.0000.0000.0000.000
128A129LEU00.0060.01832.8470.0030.0030.0000.0000.0000.000
129A130ALA00.0450.02929.7400.0020.0020.0000.0000.0000.000
130A131LYS10.8710.92025.6190.0400.0400.0000.0000.0000.000
131A132SER0-0.096-0.04631.6920.0040.0040.0000.0000.0000.000
132A133TYR00.000-0.02433.9310.0030.0030.0000.0000.0000.000
133A134GLY0-0.040-0.01531.7130.0000.0000.0000.0000.0000.000
134A135ALA0-0.031-0.00729.714-0.002-0.0020.0000.0000.0000.000
135A136VAL0-0.044-0.02223.1250.0010.0010.0000.0000.0000.000
136A137VAL0-0.016-0.01824.022-0.006-0.0060.0000.0000.0000.000
137A138LYS10.7800.87620.3000.1200.1200.0000.0000.0000.000
138A139VAL00.0160.01420.512-0.002-0.0020.0000.0000.0000.000
139A140ILE0-0.038-0.02419.495-0.025-0.0250.0000.0000.0000.000
140A141LEU00.0420.01016.5570.0160.0160.0000.0000.0000.000
141A142GLU-1-0.749-0.82519.279-0.235-0.2350.0000.0000.0000.000
142A143ALA00.0530.02713.7500.0020.0020.0000.0000.0000.000
143A144PRO0-0.039-0.02815.327-0.012-0.0120.0000.0000.0000.000
144A145LEU0-0.032-0.00216.3010.0080.0080.0000.0000.0000.000
145A146TRP0-0.036-0.01317.0290.0410.0410.0000.0000.0000.000
146A147ASP-1-0.763-0.85815.405-0.213-0.2130.0000.0000.0000.000
147A148ASP-1-0.772-0.87210.975-0.499-0.4990.0000.0000.0000.000
148A149LYS10.9350.97913.4040.0960.0960.0000.0000.0000.000
149A150THR0-0.047-0.05416.4410.0260.0260.0000.0000.0000.000
150A151LEU00.0070.00712.0650.0150.0150.0000.0000.0000.000
151A152SER00.0280.01414.0010.0200.0200.0000.0000.0000.000
152A153LEU0-0.036-0.02215.5170.0250.0250.0000.0000.0000.000
153A154LEU00.0110.01118.7410.0130.0130.0000.0000.0000.000
154A155VAL00.0120.02014.3350.0080.0080.0000.0000.0000.000
155A156ASP-1-0.799-0.87617.6780.0090.0090.0000.0000.0000.000
156A157SER0-0.051-0.05119.3840.0140.0140.0000.0000.0000.000
157A158SER0-0.010-0.02519.7560.0040.0040.0000.0000.0000.000
158A159ARG10.8820.93018.5710.0080.0080.0000.0000.0000.000
159A160ARG10.7870.86721.0870.0080.0080.0000.0000.0000.000
160A161ALA0-0.016-0.00124.4550.0050.0050.0000.0000.0000.000
161A162GLY0-0.0200.00024.5280.0010.0010.0000.0000.0000.000
162A163ALA0-0.008-0.01021.9800.0000.0000.0000.0000.0000.000
163A164ASP-1-0.817-0.88821.364-0.042-0.0420.0000.0000.0000.000
164A165ILE0-0.039-0.02317.111-0.002-0.0020.0000.0000.0000.000
165A166VAL00.0000.01015.3310.0060.0060.0000.0000.0000.000
166A167LYS10.8410.90915.8300.1650.1650.0000.0000.0000.000
167A168THR0-0.027-0.01613.7940.0190.0190.0000.0000.0000.000
168A169SER0-0.019-0.02615.6400.0110.0110.0000.0000.0000.000
169A170THR0-0.014-0.04019.0360.0100.0100.0000.0000.0000.000
170A171GLY0-0.029-0.01421.4180.0100.0100.0000.0000.0000.000
171A172VAL0-0.064-0.02522.4050.0060.0060.0000.0000.0000.000
172A173TYR00.0330.00524.563-0.002-0.0020.0000.0000.0000.000
173A174THR00.0200.01719.192-0.018-0.0180.0000.0000.0000.000
174A175LYS10.7740.86518.7610.2680.2680.0000.0000.0000.000
175A176GLY00.0810.04615.028-0.016-0.0160.0000.0000.0000.000
176A177GLY0-0.0200.00513.790-0.034-0.0340.0000.0000.0000.000
177A178ASP-1-0.768-0.85111.221-0.854-0.8540.0000.0000.0000.000
178A179PRO00.045-0.0066.537-0.010-0.0100.0000.0000.0000.000
179A180VAL00.0190.0236.943-0.325-0.3250.0000.0000.0000.000
180A181THR0-0.049-0.0628.002-0.004-0.0040.0000.0000.0000.000
181A182VAL0-0.036-0.0138.2390.0890.0890.0000.0000.0000.000
182A183PHE00.0460.0302.646-2.569-1.3383.663-1.057-3.837-0.011
183A184ARG10.7640.8606.1250.7940.7940.0000.0000.0000.000
184A185LEU0-0.0030.0078.2140.1720.1720.0000.0000.0000.000
185A186ALA00.001-0.0096.8560.1220.1220.0000.0000.0000.000
186A187SER0-0.065-0.0475.4190.2350.2350.0000.0000.0000.000
187A188LEU00.0000.0037.4430.1990.1990.0000.0000.0000.000
188A189ALA0-0.004-0.01510.9650.0680.0680.0000.0000.0000.000
189A190LYS10.8400.8959.1140.2280.2280.0000.0000.0000.000
190A191PRO0-0.027-0.00610.0080.0470.0470.0000.0000.0000.000
191A192LEU0-0.0040.00612.7500.0180.0180.0000.0000.0000.000
192A193GLY0-0.021-0.00614.957-0.005-0.0050.0000.0000.0000.000
193A194MET0-0.066-0.00415.457-0.009-0.0090.0000.0000.0000.000
194A195GLY00.0370.02514.303-0.008-0.0080.0000.0000.0000.000
195A196VAL0-0.013-0.01310.681-0.015-0.0150.0000.0000.0000.000
196A197LYS10.7640.86713.7490.1740.1740.0000.0000.0000.000
197A198ALA00.0660.03712.924-0.026-0.0260.0000.0000.0000.000
198A199SER0-0.007-0.02914.7040.0670.0670.0000.0000.0000.000
199A200GLY00.0370.01817.490-0.025-0.0250.0000.0000.0000.000
200A201GLY00.000-0.01418.091-0.038-0.0380.0000.0000.0000.000
201A202ILE0-0.0260.00414.7270.0090.0090.0000.0000.0000.000
202A203ARG10.8850.94318.5600.2360.2360.0000.0000.0000.000
203A204SER0-0.018-0.04318.9960.0320.0320.0000.0000.0000.000
204A205GLY00.0770.03318.333-0.019-0.0190.0000.0000.0000.000
205A206ILE00.0130.00815.318-0.013-0.0130.0000.0000.0000.000
206A207ASP-1-0.731-0.84013.683-0.379-0.3790.0000.0000.0000.000
207A208ALA00.0080.00413.356-0.051-0.0510.0000.0000.0000.000
208A209VAL00.0220.01911.935-0.018-0.0180.0000.0000.0000.000
209A210LEU0-0.023-0.0119.239-0.035-0.0350.0000.0000.0000.000
210A211ALA0-0.0070.0068.610-0.148-0.1480.0000.0000.0000.000
211A212VAL00.0170.0019.325-0.056-0.0560.0000.0000.0000.000
212A213GLY00.0260.0247.8810.0650.0650.0000.0000.0000.000
213A214ALA0-0.093-0.0464.8350.0080.0080.0000.0000.0000.000
214A215GLY00.0410.0165.125-0.302-0.227-0.001-0.001-0.0730.000
215A216ALA0-0.053-0.0177.2720.1240.1240.0000.0000.0000.000
216A217ASP-1-0.814-0.89110.965-0.117-0.1170.0000.0000.0000.000
217A218ILE0-0.015-0.00513.8440.0220.0220.0000.0000.0000.000
218A219ILE00.023-0.00315.493-0.049-0.0490.0000.0000.0000.000
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