FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VQ271

Calculation Name: 4NN1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NN1

Chain ID: A

ChEMBL ID:

UniProt ID: O86312

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093271.381088
FMO2-HF: Nuclear repulsion 2013688.192085
FMO2-HF: Total energy -79583.189004
FMO2-MP2: Total energy -79812.622693


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-14.387-8.070.916-2.837-4.3950.022
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.023
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].
3A8ALA00.0340.0172.760-3.610-0.4280.348-1.495-2.0350.008
4A9HIS00.0650.0392.887-5.172-3.1930.443-0.826-1.5950.009
5A10ALA0-0.033-0.0104.491-1.788-1.5380.000-0.073-0.1770.000
6A11ARG10.9950.9906.433-1.010-1.0100.0000.0000.0000.000
7A12ILE00.0030.0057.021-0.369-0.3690.0000.0000.0000.000
8A13ARG10.8240.9316.764-0.996-0.9960.0000.0000.0000.000
9A14GLU-1-0.937-0.96010.3740.3810.3810.0000.0000.0000.000
10A15ALA00.0420.01712.341-0.115-0.1150.0000.0000.0000.000
11A16ALA0-0.028-0.02113.431-0.097-0.0970.0000.0000.0000.000
12A17ILE00.005-0.00213.606-0.085-0.0850.0000.0000.0000.000
13A18GLU-1-0.780-0.85516.4040.2930.2930.0000.0000.0000.000
14A19GLN0-0.002-0.02118.056-0.068-0.0680.0000.0000.0000.000
15A20PHE0-0.045-0.03416.730-0.036-0.0360.0000.0000.0000.000
16A21GLY00.0530.03320.414-0.034-0.0340.0000.0000.0000.000
17A22ARG10.8160.89121.221-0.302-0.3020.0000.0000.0000.000
18A23HIS0-0.037-0.01722.581-0.039-0.0390.0000.0000.0000.000
19A24GLY00.0590.04824.204-0.013-0.0130.0000.0000.0000.000
20A25PHE00.021-0.01419.8650.0220.0220.0000.0000.0000.000
21A26GLY00.0200.02123.4250.0120.0120.0000.0000.0000.000
22A27VAL0-0.0010.01720.4000.0020.0020.0000.0000.0000.000
23A28GLY00.0330.01921.8230.0160.0160.0000.0000.0000.000
24A29LEU00.051-0.00116.3850.0120.0120.0000.0000.0000.000
25A30ARG10.9130.95616.964-0.277-0.2770.0000.0000.0000.000
26A31ALA00.1100.06518.3180.0270.0270.0000.0000.0000.000
27A32ILE0-0.0070.00813.8670.0140.0140.0000.0000.0000.000
28A33ALA0-0.038-0.02513.5630.0830.0830.0000.0000.0000.000
29A34GLU-1-0.947-0.96914.2910.3970.3970.0000.0000.0000.000
30A35ALA00.0010.00316.4590.0000.0000.0000.0000.0000.000
31A36ALA0-0.014-0.00710.8630.0080.0080.0000.0000.0000.000
32A37GLY0-0.0240.01211.5180.1070.1070.0000.0000.0000.000
33A38VAL0-0.068-0.0398.8850.0600.0600.0000.0000.0000.000
34A39SER00.0350.01212.265-0.077-0.0770.0000.0000.0000.000
35A40ALA00.047-0.00812.9720.1100.1100.0000.0000.0000.000
36A41ALA0-0.006-0.00114.4760.0290.0290.0000.0000.0000.000
37A42LEU00.0200.0246.988-0.045-0.0450.0000.0000.0000.000
38A43VAL00.0310.0099.6230.2530.2530.0000.0000.0000.000
39A44ILE0-0.027-0.01611.4410.0020.0020.0000.0000.0000.000
40A45HIS0-0.003-0.0109.707-0.053-0.0530.0000.0000.0000.000
41A46HIS0-0.062-0.0303.152-1.499-0.5930.125-0.443-0.5880.005
42A47PHE0-0.012-0.0148.170-0.090-0.0900.0000.0000.0000.000
43A48GLY00.0170.03211.650-0.144-0.1440.0000.0000.0000.000
44A49SER0-0.030-0.03214.576-0.051-0.0510.0000.0000.0000.000
45A50LYS10.8400.90016.252-0.275-0.2750.0000.0000.0000.000
46A51GLU-1-0.922-0.94518.3150.2450.2450.0000.0000.0000.000
47A52GLY00.0260.02015.605-0.014-0.0140.0000.0000.0000.000
48A53LEU0-0.015-0.00812.4230.0250.0250.0000.0000.0000.000
49A54ARG10.8310.92114.606-0.225-0.2250.0000.0000.0000.000
50A55LYS10.9010.93616.045-0.229-0.2290.0000.0000.0000.000
51A56ALA00.0130.00311.140-0.029-0.0290.0000.0000.0000.000
52A57CYS0-0.062-0.02712.8620.0220.0220.0000.0000.0000.000
53A58ASP-1-0.725-0.84714.7510.2090.2090.0000.0000.0000.000
54A59ASP-1-0.837-0.90014.3780.1610.1610.0000.0000.0000.000
55A60PHE00.0680.03811.2550.0010.0010.0000.0000.0000.000
56A61VAL00.0470.02313.947-0.042-0.0420.0000.0000.0000.000
57A62ALA00.020-0.00217.136-0.028-0.0280.0000.0000.0000.000
58A63GLU-1-0.852-0.89014.288-0.021-0.0210.0000.0000.0000.000
59A64GLU-1-0.889-0.94413.7010.0620.0620.0000.0000.0000.000
60A65ILE0-0.017-0.01516.779-0.021-0.0210.0000.0000.0000.000
61A66ARG10.7300.82717.6530.0090.0090.0000.0000.0000.000
62A67SER0-0.004-0.01117.081-0.014-0.0140.0000.0000.0000.000
63A68SER0-0.0040.00519.376-0.008-0.0080.0000.0000.0000.000
64A69LYS10.9630.97721.398-0.045-0.0450.0000.0000.0000.000
65A70ALA00.0380.00722.265-0.005-0.0050.0000.0000.0000.000
66A71ALA0-0.035-0.00921.562-0.008-0.0080.0000.0000.0000.000
67A72ALA00.0090.00823.647-0.003-0.0030.0000.0000.0000.000
68A73LEU0-0.007-0.00726.845-0.001-0.0010.0000.0000.0000.000
69A74LYS10.8580.92624.2930.0580.0580.0000.0000.0000.000
70A75SER0-0.0250.01927.087-0.005-0.0050.0000.0000.0000.000
71A76ASN00.0120.00528.9050.0080.0080.0000.0000.0000.000
72A77ASP-1-0.816-0.90329.972-0.032-0.0320.0000.0000.0000.000
73A78PRO00.0210.00530.7070.0010.0010.0000.0000.0000.000
74A79THR0-0.037-0.03529.8740.0060.0060.0000.0000.0000.000
75A80THR0-0.014-0.02425.8430.0060.0060.0000.0000.0000.000
76A81TRP0-0.0110.00926.7150.0090.0090.0000.0000.0000.000
77A82LEU00.000-0.00629.0430.0070.0070.0000.0000.0000.000
78A83ALA0-0.0040.00225.7030.0050.0050.0000.0000.0000.000
79A84GLN0-0.007-0.01223.3080.0100.0100.0000.0000.0000.000
80A85MET0-0.0010.00325.6620.0120.0120.0000.0000.0000.000
81A86ALA0-0.0170.01227.5410.0060.0060.0000.0000.0000.000
82A87GLU-1-0.862-0.93422.2120.0480.0480.0000.0000.0000.000
83A88ILE00.0010.01623.8940.0140.0140.0000.0000.0000.000
84A89GLU-1-0.788-0.87725.1440.0830.0830.0000.0000.0000.000
85A90SER0-0.075-0.04820.1900.0180.0180.0000.0000.0000.000
86A91TYR00.004-0.00620.2360.0240.0240.0000.0000.0000.000
87A92ALA00.0260.02021.6090.0160.0160.0000.0000.0000.000
88A93PRO0-0.003-0.00718.4370.0080.0080.0000.0000.0000.000
89A94LEU00.0220.01016.4970.0210.0210.0000.0000.0000.000
90A95MET00.0060.00319.553-0.002-0.0020.0000.0000.0000.000
91A96ALA00.0250.02122.608-0.004-0.0040.0000.0000.0000.000
92A97TYR0-0.053-0.06818.5330.0190.0190.0000.0000.0000.000
93A98LEU00.001-0.00221.513-0.003-0.0030.0000.0000.0000.000
94A99VAL00.0200.00123.200-0.009-0.0090.0000.0000.0000.000
95A100ARG10.8140.90123.716-0.191-0.1910.0000.0000.0000.000
96A101SER0-0.038-0.02021.951-0.006-0.0060.0000.0000.0000.000
97A102MET0-0.008-0.00324.472-0.005-0.0050.0000.0000.0000.000
98A103GLN00.0700.04128.1490.0000.0000.0000.0000.0000.000
99A104SER0-0.068-0.02725.9730.0000.0000.0000.0000.0000.000
100A105GLY00.0450.02827.0370.0110.0110.0000.0000.0000.000
101A106GLY0-0.009-0.00528.443-0.011-0.0110.0000.0000.0000.000
102A107GLU-1-0.815-0.90927.2600.1150.1150.0000.0000.0000.000
103A108LEU00.0250.00820.342-0.007-0.0070.0000.0000.0000.000
104A109ALA00.0150.02423.4480.0020.0020.0000.0000.0000.000
105A110LYS10.8060.88925.262-0.109-0.1090.0000.0000.0000.000
106A111MET0-0.017-0.00622.544-0.007-0.0070.0000.0000.0000.000
107A112LEU0-0.0060.01820.162-0.008-0.0080.0000.0000.0000.000
108A113TRP00.039-0.00623.079-0.013-0.0130.0000.0000.0000.000
109A114GLN0-0.017-0.00326.358-0.012-0.0120.0000.0000.0000.000
110A115LYS10.8590.93116.670-0.132-0.1320.0000.0000.0000.000
111A116MET0-0.032-0.01722.224-0.007-0.0070.0000.0000.0000.000
112A117ILE0-0.023-0.00524.238-0.010-0.0100.0000.0000.0000.000
113A118ASP-1-0.801-0.89025.2250.0380.0380.0000.0000.0000.000
114A119ASN0-0.015-0.02219.574-0.013-0.0130.0000.0000.0000.000
115A120ALA00.0140.01024.013-0.008-0.0080.0000.0000.0000.000
116A121GLU-1-0.847-0.93027.0500.0090.0090.0000.0000.0000.000
117A122GLU-1-0.879-0.90322.467-0.022-0.0220.0000.0000.0000.000
118A123TYR00.0650.01523.863-0.007-0.0070.0000.0000.0000.000
119A124LEU0-0.030-0.01326.501-0.003-0.0030.0000.0000.0000.000
120A125ASP-1-0.835-0.89329.756-0.024-0.0240.0000.0000.0000.000
121A126GLU-1-0.824-0.89324.759-0.057-0.0570.0000.0000.0000.000
122A127GLY00.0240.01728.763-0.004-0.0040.0000.0000.0000.000
123A128VAL0-0.073-0.03731.040-0.001-0.0010.0000.0000.0000.000
124A129ARG10.7400.83427.8090.0320.0320.0000.0000.0000.000
125A130ALA0-0.043-0.00230.388-0.004-0.0040.0000.0000.0000.000
126A131GLY0-0.030-0.00832.527-0.001-0.0010.0000.0000.0000.000
127A132THR0-0.057-0.04131.5930.0040.0040.0000.0000.0000.000
128A133VAL0-0.015-0.00233.0120.0050.0050.0000.0000.0000.000
129A134LYS10.8960.94835.918-0.006-0.0060.0000.0000.0000.000
130A135PRO00.0750.04037.7990.0020.0020.0000.0000.0000.000
131A136SER0-0.030-0.03438.4860.0030.0030.0000.0000.0000.000
132A137ARG10.8830.93940.213-0.012-0.0120.0000.0000.0000.000
133A138ASP-1-0.794-0.90039.2150.0140.0140.0000.0000.0000.000
134A139PRO00.0110.00834.7690.0030.0030.0000.0000.0000.000
135A140ARG10.8330.90929.591-0.025-0.0250.0000.0000.0000.000
136A141ALA0-0.005-0.00434.8270.0050.0050.0000.0000.0000.000
137A142ARG10.8580.92335.129-0.004-0.0040.0000.0000.0000.000
138A143ALA00.0370.02131.0540.0020.0020.0000.0000.0000.000
139A144ARG10.9150.95132.088-0.045-0.0450.0000.0000.0000.000
140A145PHE00.0220.00833.5480.0050.0050.0000.0000.0000.000
141A146LEU00.0160.02033.0150.0030.0030.0000.0000.0000.000
142A147ALA0-0.0050.00929.5000.0040.0040.0000.0000.0000.000
143A148ILE0-0.049-0.03031.0010.0060.0060.0000.0000.0000.000
144A149THR0-0.024-0.03233.3750.0030.0030.0000.0000.0000.000
145A150GLY00.0280.02432.1910.0010.0010.0000.0000.0000.000
146A151GLY0-0.017-0.01129.7860.0040.0040.0000.0000.0000.000
147A152GLY0-0.002-0.01030.4690.0060.0060.0000.0000.0000.000
148A153GLY00.0250.01533.4650.0010.0010.0000.0000.0000.000
149A154PHE0-0.0010.00727.1090.0020.0020.0000.0000.0000.000
150A155LEU0-0.037-0.03028.2560.0050.0050.0000.0000.0000.000
151A156LEU0-0.011-0.00232.0620.0020.0020.0000.0000.0000.000
152A157TYR0-0.049-0.05233.8980.0020.0020.0000.0000.0000.000
153A158LEU0-0.002-0.01129.2690.0010.0010.0000.0000.0000.000
154A159GLN0-0.062-0.03233.8550.0030.0030.0000.0000.0000.000
155A160MET0-0.079-0.03535.945-0.001-0.0010.0000.0000.0000.000
156A161HIS0-0.017-0.00434.8770.0000.0000.0000.0000.0000.000
157A162GLU-1-0.903-0.95637.5860.0640.0640.0000.0000.0000.000
158A163ASN0-0.024-0.01133.1920.0080.0080.0000.0000.0000.000
159A164PRO00.0220.01833.0270.0050.0050.0000.0000.0000.000
160A165THR0-0.125-0.06829.7480.0110.0110.0000.0000.0000.000
161A166ASP-1-0.864-0.92928.5380.1220.1220.0000.0000.0000.000
162A167LEU00.001-0.02025.662-0.007-0.0070.0000.0000.0000.000
163A168ARG10.8310.91324.753-0.108-0.1080.0000.0000.0000.000
164A169ALA00.0210.01927.800-0.009-0.0090.0000.0000.0000.000
165A170ALA00.0590.03630.391-0.006-0.0060.0000.0000.0000.000
166A171LEU0-0.054-0.03025.354-0.005-0.0050.0000.0000.0000.000
167A172ARG10.7680.86729.316-0.059-0.0590.0000.0000.0000.000
168A173ASP-1-0.810-0.89231.7140.0580.0580.0000.0000.0000.000
169A174TYR0-0.001-0.00131.104-0.005-0.0050.0000.0000.0000.000
170A175ALA0-0.047-0.04531.076-0.005-0.0050.0000.0000.0000.000
171A176HIS0-0.074-0.01533.147-0.006-0.0060.0000.0000.0000.000
172A177ASP-1-0.838-0.90836.7520.0440.0440.0000.0000.0000.000
173A178MET0-0.041-0.02635.466-0.004-0.0040.0000.0000.0000.000
174A179VAL00.0010.00932.934-0.003-0.0030.0000.0000.0000.000
175A180LEU00.0290.02235.734-0.003-0.0030.0000.0000.0000.000
176A181PRO00.0770.03639.156-0.003-0.0030.0000.0000.0000.000
177A182SER0-0.060-0.02736.032-0.001-0.0010.0000.0000.0000.000
178A183LEU0-0.006-0.01434.607-0.003-0.0030.0000.0000.0000.000
179A184GLU-1-0.929-0.93938.2890.0140.0140.0000.0000.0000.000
180A185VAL00.0110.00641.094-0.002-0.0020.0000.0000.0000.000
181A186TYR0-0.070-0.04235.2190.0000.0000.0000.0000.0000.000
182A187THR0-0.067-0.03739.777-0.004-0.0040.0000.0000.0000.000
183A188GLU-1-0.914-0.95741.5830.0030.0030.0000.0000.0000.000
184A189GLY0-0.044-0.01244.304-0.001-0.0010.0000.0000.0000.000
185A190LEU0-0.011-0.02444.7860.0020.0020.0000.0000.0000.000
186A191LEU0-0.035-0.01447.4950.0000.0000.0000.0000.0000.000
187A192ALA00.0330.01750.392-0.001-0.0010.0000.0000.0000.000
188A193ASP-1-0.877-0.93753.0910.0080.0080.0000.0000.0000.000
189A194ARG10.8720.90649.081-0.003-0.0030.0000.0000.0000.000
190A195ALA00.0180.03152.5770.0000.0000.0000.0000.0000.000
191A196MET00.0250.00051.7470.0000.0000.0000.0000.0000.000
192A197TYR0-0.012-0.00545.0230.0010.0010.0000.0000.0000.000
193A198GLU-1-0.842-0.92050.4570.0050.0050.0000.0000.0000.000
194A199ALA00.0110.01553.1700.0000.0000.0000.0000.0000.000
195A200PHE00.007-0.00649.8440.0000.0000.0000.0000.0000.000
196A201LEU0-0.051-0.02047.2990.0000.0000.0000.0000.0000.000
197A202ALA0-0.007-0.00150.8570.0000.0000.0000.0000.0000.000
198A203GLU-1-0.884-0.93253.2380.0130.0130.0000.0000.0000.000
199A204ALA0-0.031-0.01848.8530.0000.0000.0000.0000.0000.000
200A205GLN0-0.051-0.02649.484-0.001-0.0010.0000.0000.0000.000
201A206GLN0-0.089-0.05652.238-0.001-0.0010.0000.0000.0000.000
202A207GLY00.0240.01652.7690.0000.0000.0000.0000.0000.000
203A208GLU-1-0.969-0.98647.0420.0100.0100.0000.0000.0000.000
204A209ALA0-0.066-0.02651.373-0.001-0.0010.0000.0000.0000.000
205A210HIS0-0.080-0.02754.2010.0000.0000.0000.0000.0000.000