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: 852VY

Calculation Name: 3NCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCY

Chain ID: A

ChEMBL ID:

UniProt ID: P60066

Base Structure: X-ray

Registration Date: 2023-06-21

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 432
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7132732.739426
FMO2-HF: Nuclear repulsion 6972478.934042
FMO2-HF: Total energy -160253.805384
FMO2-MP2: Total energy -160716.740588


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
1.646-27.17429.64118.087-18.907-0.035
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : 0.057
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].
3A12LEU00.0780.0102.30519.286-3.5600.11324.949-2.217-0.032
4A13ILE00.0490.0195.300-0.253-0.200-0.001-0.002-0.0500.000
5A14PRO00.0010.0014.0820.0550.3850.000-0.104-0.2260.000
6A15VAL00.0030.0062.427-0.733-0.0290.890-0.534-1.060-0.002
7A16THR00.022-0.0125.1620.8130.853-0.001-0.002-0.0360.000
8A17LEU0-0.0050.0228.3190.3100.3100.0000.0000.0000.000
9A18MET00.0060.0176.5620.3090.3090.0000.0000.0000.000
10A19VAL0-0.053-0.0398.4090.2820.2820.0000.0000.0000.000
11A20SER00.0530.03110.8680.0980.0980.0000.0000.0000.000
12A21GLY00.001-0.01012.4420.1110.1110.0000.0000.0000.000
13A22ASN0-0.026-0.01611.8770.0140.0140.0000.0000.0000.000
14A23ILE0-0.0690.02814.6490.0770.0770.0000.0000.0000.000
15A24MET0-0.060-0.01817.0910.0350.0350.0000.0000.0000.000
16A25GLY00.0240.02419.073-0.015-0.0150.0000.0000.0000.000
17A26SER00.016-0.01419.9240.0370.0370.0000.0000.0000.000
18A27GLY0-0.0110.00222.2110.0160.0160.0000.0000.0000.000
19A28VAL00.006-0.00223.3870.0080.0080.0000.0000.0000.000
20A29PHE00.0330.01225.8420.0150.0150.0000.0000.0000.000
21A30LEU0-0.019-0.00224.9230.0150.0150.0000.0000.0000.000
22A31LEU00.0500.01027.5790.0150.0150.0000.0000.0000.000
23A32PRO00.0160.01030.6310.0110.0110.0000.0000.0000.000
24A33ALA0-0.0070.00431.3680.0090.0090.0000.0000.0000.000
25A34ASN0-0.036-0.02531.4230.0070.0070.0000.0000.0000.000
26A35LEU0-0.031-0.00533.3650.0060.0060.0000.0000.0000.000
27A36ALA0-0.0080.01336.1650.0070.0070.0000.0000.0000.000
28A37ALA0-0.002-0.00336.9900.0070.0070.0000.0000.0000.000
29A38THR00.0350.01137.831-0.004-0.0040.0000.0000.0000.000
30A39GLY00.117-0.00336.039-0.006-0.0060.0000.0000.0000.000
31A40GLY0-0.106-0.06636.226-0.008-0.0080.0000.0000.0000.000
32A41ILE00.0390.02537.818-0.004-0.0040.0000.0000.0000.000
33A42ALA00.0400.02433.9470.0010.0010.0000.0000.0000.000
34A43ILE00.0530.01231.799-0.008-0.0080.0000.0000.0000.000
35A44TYR0-0.085-0.02033.149-0.005-0.0050.0000.0000.0000.000
36A45GLY00.0350.01133.3690.0080.0080.0000.0000.0000.000
37A46TRP00.0450.00525.294-0.006-0.0060.0000.0000.0000.000
38A47LEU00.0180.02328.333-0.012-0.0120.0000.0000.0000.000
39A48VAL00.0410.02229.025-0.006-0.0060.0000.0000.0000.000
40A49THR00.0050.02225.5600.0040.0040.0000.0000.0000.000
41A50ILE00.0220.00823.743-0.007-0.0070.0000.0000.0000.000
42A51ILE0-0.0080.00124.386-0.012-0.0120.0000.0000.0000.000
43A52GLY00.019-0.00325.5990.0000.0000.0000.0000.0000.000
44A53ALA00.021-0.00521.8320.0040.0040.0000.0000.0000.000
45A54LEU0-0.0060.00119.975-0.019-0.0190.0000.0000.0000.000
46A55ALA0-0.0110.02021.047-0.008-0.0080.0000.0000.0000.000
47A56LEU00.0640.01019.9310.0140.0140.0000.0000.0000.000
48A57SER0-0.078-0.04716.742-0.002-0.0020.0000.0000.0000.000
49A58MET0-0.009-0.01016.872-0.025-0.0250.0000.0000.0000.000
50A59VAL00.0150.00218.5640.0140.0140.0000.0000.0000.000
51A60TYR00.0460.00414.9050.0170.0170.0000.0000.0000.000
52A61ALA0-0.0010.01914.1150.0210.0210.0000.0000.0000.000
53A62LYS10.8910.95915.1560.0820.0820.0000.0000.0000.000
54A63MET00.0040.02117.4060.0300.0300.0000.0000.0000.000
55A64SER00.0030.00312.1480.0300.0300.0000.0000.0000.000
56A65SER0-0.106-0.07613.5490.0560.0560.0000.0000.0000.000
57A66LEU0-0.074-0.04615.1310.0310.0310.0000.0000.0000.000
58A67ASP-1-0.858-0.92916.1910.3480.3480.0000.0000.0000.000
59A68PRO0-0.033-0.01410.940-0.015-0.0150.0000.0000.0000.000
60A69SER0-0.0040.00512.6470.0840.0840.0000.0000.0000.000
61A70PRO0-0.050-0.00811.8090.0720.0720.0000.0000.0000.000
62A71GLY00.0960.02111.5810.1710.1710.0000.0000.0000.000
63A72GLY0-0.075-0.04613.740-0.033-0.0330.0000.0000.0000.000
64A73SER00.1170.04614.6000.0050.0050.0000.0000.0000.000
65A74TYR00.0060.04417.610-0.014-0.0140.0000.0000.0000.000
66A75ALA00.0420.01716.951-0.005-0.0050.0000.0000.0000.000
67A76TYR00.004-0.00114.065-0.041-0.0410.0000.0000.0000.000
68A77ALA00.0470.01620.144-0.013-0.0130.0000.0000.0000.000
69A78ARG10.9170.96621.865-0.277-0.2770.0000.0000.0000.000
70A79ARG10.8030.90818.912-0.260-0.2600.0000.0000.0000.000
71A80CYS0-0.041-0.00324.165-0.014-0.0140.0000.0000.0000.000
72A81PHE00.0310.00626.080-0.009-0.0090.0000.0000.0000.000
73A82GLY00.0200.02527.153-0.005-0.0050.0000.0000.0000.000
74A83PRO0-0.014-0.01426.6410.0100.0100.0000.0000.0000.000
75A84PHE00.0390.02827.3070.0060.0060.0000.0000.0000.000
76A85LEU00.0860.03227.3380.0040.0040.0000.0000.0000.000
77A86GLY00.0320.04323.762-0.004-0.0040.0000.0000.0000.000
78A87TYR00.024-0.01023.6300.0080.0080.0000.0000.0000.000
79A88GLN00.005-0.00925.214-0.005-0.0050.0000.0000.0000.000
80A89THR0-0.031-0.03420.933-0.014-0.0140.0000.0000.0000.000
81A90ASN00.0250.01120.2750.0120.0120.0000.0000.0000.000
82A91VAL0-0.0160.01121.660-0.006-0.0060.0000.0000.0000.000
83A92LEU00.001-0.00123.793-0.008-0.0080.0000.0000.0000.000
84A93TYR0-0.013-0.03615.0760.0110.0110.0000.0000.0000.000
85A94TRP00.000-0.00418.828-0.022-0.0220.0000.0000.0000.000
86A95LEU0-0.038-0.02820.481-0.009-0.0090.0000.0000.0000.000
87A96ALA00.009-0.00121.318-0.012-0.0120.0000.0000.0000.000
88A97CYS0-0.099-0.01617.177-0.024-0.0240.0000.0000.0000.000
89A98TRP00.0370.00419.133-0.031-0.0310.0000.0000.0000.000
90A99ILE0-0.023-0.02120.837-0.012-0.0120.0000.0000.0000.000
91A100GLY00.0350.02822.147-0.009-0.0090.0000.0000.0000.000
92A101ASN00.007-0.01417.330-0.044-0.0440.0000.0000.0000.000
93A102ILE0-0.017-0.00321.358-0.015-0.0150.0000.0000.0000.000
94A103ALA00.0200.01124.837-0.004-0.0040.0000.0000.0000.000
95A104MET0-0.001-0.00517.970-0.018-0.0180.0000.0000.0000.000
96A105VAL0-0.0150.00122.065-0.019-0.0190.0000.0000.0000.000
97A106VAL00.0060.01123.939-0.005-0.0050.0000.0000.0000.000
98A107ILE0-0.0010.00125.0960.0000.0000.0000.0000.0000.000
99A108GLY00.0410.01723.327-0.012-0.0120.0000.0000.0000.000
100A109VAL00.026-0.01024.150-0.008-0.0080.0000.0000.0000.000
101A110GLY0-0.0250.00126.6030.0040.0040.0000.0000.0000.000
102A111TYR00.000-0.01425.935-0.007-0.0070.0000.0000.0000.000
103A112LEU0-0.054-0.02124.298-0.005-0.0050.0000.0000.0000.000
104A113SER0-0.094-0.03528.4170.0080.0080.0000.0000.0000.000
105A114TYR0-0.023-0.00631.1310.0120.0120.0000.0000.0000.000
106A115PHE0-0.010-0.01031.4910.0050.0050.0000.0000.0000.000
107A116PHE0-0.0410.00732.703-0.005-0.0050.0000.0000.0000.000
108A117PRO00.000-0.00534.6170.0050.0050.0000.0000.0000.000
109A118ILE00.032-0.01430.3510.0070.0070.0000.0000.0000.000
110A119LEU0-0.012-0.00733.8740.0080.0080.0000.0000.0000.000
111A120LYS10.9970.98534.1140.0700.0700.0000.0000.0000.000
112A121ASP-1-0.866-0.91335.968-0.050-0.0500.0000.0000.0000.000
113A122PRO00.0850.02936.133-0.001-0.0010.0000.0000.0000.000
114A123LEU0-0.025-0.02935.138-0.002-0.0020.0000.0000.0000.000
115A124VAL00.0060.01234.3970.0040.0040.0000.0000.0000.000
116A125LEU00.0290.00929.603-0.002-0.0020.0000.0000.0000.000
117A126THR00.008-0.00130.162-0.004-0.0040.0000.0000.0000.000
118A127LEU00.0160.00730.0590.0050.0050.0000.0000.0000.000
119A128THR00.0190.00428.0900.0020.0020.0000.0000.0000.000
120A129CYS0-0.0100.02125.700-0.013-0.0130.0000.0000.0000.000
121A130VAL00.0430.01824.6460.0010.0010.0000.0000.0000.000
122A131ALA0-0.033-0.01424.8540.0110.0110.0000.0000.0000.000
123A132VAL00.027-0.00420.7020.0060.0060.0000.0000.0000.000
124A133LEU00.0270.01120.410-0.011-0.0110.0000.0000.0000.000
125A134TRP0-0.017-0.01719.5980.0180.0180.0000.0000.0000.000
126A135ILE0-0.0040.01818.5790.0230.0230.0000.0000.0000.000
127A136PHE00.000-0.01514.357-0.018-0.0180.0000.0000.0000.000
128A137VAL0-0.054-0.01915.1060.0320.0320.0000.0000.0000.000
129A138LEU0-0.016-0.01616.0600.0700.0700.0000.0000.0000.000
130A139LEU0-0.0040.00012.7930.0560.0560.0000.0000.0000.000
131A140ASN0-0.011-0.00210.301-0.021-0.0210.0000.0000.0000.000
132A141ILE0-0.071-0.01711.0690.1980.1980.0000.0000.0000.000
133A142VAL00.000-0.00812.0170.0950.0950.0000.0000.0000.000
134A143GLY00.0790.0258.582-0.046-0.0460.0000.0000.0000.000
135A144PRO00.0210.0184.631-0.246-0.180-0.001-0.004-0.0600.000
136A145LYS10.9670.9752.186-5.217-5.2962.871-0.522-2.2700.004
137A146MET00.0100.0074.448-0.940-0.901-0.001-0.014-0.0240.000
138A147ILE00.0560.0407.650-0.206-0.2060.0000.0000.0000.000
139A148THR0-0.016-0.0143.713-0.734-0.5410.000-0.033-0.1600.000
140A149ARG10.9040.9626.4690.4160.4160.0000.0000.0000.000
141A150VAL00.0480.0318.6240.0600.0600.0000.0000.0000.000
142A151GLN00.0290.0259.355-0.029-0.0290.0000.0000.0000.000
143A152ALA0-0.0140.0018.2840.0810.0810.0000.0000.0000.000
144A153VAL0-0.014-0.00510.2880.1240.1240.0000.0000.0000.000
145A154ALA00.015-0.00513.5010.0820.0820.0000.0000.0000.000
146A155THR0-0.026-0.04012.3470.0420.0420.0000.0000.0000.000
147A156VAL00.0130.01813.6910.0560.0560.0000.0000.0000.000
148A157LEU0-0.023-0.01416.1610.0810.0810.0000.0000.0000.000
149A158ALA0-0.014-0.00418.2410.0480.0480.0000.0000.0000.000
150A159LEU00.0100.00317.0740.0340.0340.0000.0000.0000.000
151A160VAL0-0.0020.01220.0520.0310.0310.0000.0000.0000.000
152A161PRO00.008-0.00422.5110.0260.0260.0000.0000.0000.000
153A162ILE00.014-0.00521.7270.0150.0150.0000.0000.0000.000
154A163VAL0-0.056-0.02121.5590.0080.0080.0000.0000.0000.000
155A164GLY00.0050.00923.6680.0120.0120.0000.0000.0000.000
156A165ILE0-0.063-0.02826.7870.0270.0270.0000.0000.0000.000
157A166ALA00.040-0.02827.9080.0010.0010.0000.0000.0000.000
158A167VAL0-0.077-0.01929.414-0.008-0.0080.0000.0000.0000.000
159A168PHE00.0430.03930.1990.0020.0020.0000.0000.0000.000
160A169GLY0-0.0620.00334.4220.0080.0080.0000.0000.0000.000
161A170TRP00.1130.01937.961-0.001-0.0010.0000.0000.0000.000
162A171PHE0-0.080-0.03837.2170.0050.0050.0000.0000.0000.000
163A172TRP00.0500.01639.5730.0040.0040.0000.0000.0000.000
164A173PHE0-0.012-0.00542.292-0.002-0.0020.0000.0000.0000.000
165A174LYS10.9360.99036.7680.1450.1450.0000.0000.0000.000
166A175GLY00.029-0.02442.4440.0040.0040.0000.0000.0000.000
167A176GLU-1-0.920-0.97640.865-0.107-0.1070.0000.0000.0000.000
168A177THR00.0550.01343.4660.0020.0020.0000.0000.0000.000
169A178TYR0-0.002-0.02146.1530.0000.0000.0000.0000.0000.000
170A179MET00.000-0.02248.021-0.001-0.0010.0000.0000.0000.000
171A180ALA00.0350.01846.3910.0020.0020.0000.0000.0000.000
172A181ALA00.057-0.03844.4340.0020.0020.0000.0000.0000.000
173A182TRP0-0.1300.05941.599-0.001-0.0010.0000.0000.0000.000
174A183ASN0-0.115-0.01340.9410.0040.0040.0000.0000.0000.000
175A184VAL0-0.047-0.00940.3270.0000.0000.0000.0000.0000.000
176A185SER00.0010.00042.7480.0040.0040.0000.0000.0000.000
177A186GLY00.0300.01144.994-0.001-0.0010.0000.0000.0000.000
178A187MET00.0250.02744.1570.0040.0040.0000.0000.0000.000
179A188ASN00.0140.00445.242-0.005-0.0050.0000.0000.0000.000
180A189THR00.0890.02542.281-0.001-0.0010.0000.0000.0000.000
181A190PHE00.0040.00139.077-0.005-0.0050.0000.0000.0000.000
182A191GLY00.040-0.00540.069-0.002-0.0020.0000.0000.0000.000
183A192ALA0-0.0270.00640.768-0.001-0.0010.0000.0000.0000.000
184A193ILE00.0120.00536.149-0.005-0.0050.0000.0000.0000.000
185A194GLN0-0.002-0.00435.527-0.005-0.0050.0000.0000.0000.000
186A195SER0-0.026-0.00735.7630.0000.0000.0000.0000.0000.000
187A196THR0-0.014-0.00932.625-0.004-0.0040.0000.0000.0000.000
188A197LEU00.014-0.00530.645-0.011-0.0110.0000.0000.0000.000
189A198ASN0-0.028-0.00830.432-0.007-0.0070.0000.0000.0000.000
190A199VAL0-0.0010.01229.250-0.001-0.0010.0000.0000.0000.000
191A200THR00.013-0.00727.333-0.008-0.0080.0000.0000.0000.000
192A201LEU0-0.0510.00425.883-0.019-0.0190.0000.0000.0000.000
193A202TRP00.0280.02624.986-0.012-0.0120.0000.0000.0000.000
194A203SER0-0.062-0.03223.489-0.013-0.0130.0000.0000.0000.000
195A204PHE00.040-0.01419.374-0.039-0.0390.0000.0000.0000.000
196A205ILE0-0.0020.01219.4590.0030.0030.0000.0000.0000.000
197A206GLY00.078-0.00716.1420.0010.0010.0000.0000.0000.000
198A207VAL00.0170.02414.125-0.074-0.0740.0000.0000.0000.000
199A208GLU-1-0.831-0.89113.545-0.124-0.1240.0000.0000.0000.000
200A209SER00.035-0.00710.2490.0610.0610.0000.0000.0000.000
201A210ALA0-0.017-0.0237.5780.0370.0370.0000.0000.0000.000
202A211SER0-0.043-0.0338.4070.2190.2190.0000.0000.0000.000
203A212VAL00.0250.01810.9010.1600.1600.0000.0000.0000.000
204A213ALA0-0.0170.0146.1280.1660.1660.0000.0000.0000.000
205A214ALA0-0.015-0.0116.7410.8550.8550.0000.0000.0000.000
206A215GLY00.0540.0578.138-0.004-0.0040.0000.0000.0000.000
207A216VAL0-0.071-0.0353.6300.7901.1380.012-0.097-0.2630.000
208A217VAL00.0290.0272.206-0.732-1.1634.866-2.544-1.8920.002
209A218LYS10.8640.8971.762-11.820-19.95220.657-2.781-9.743-0.007
210A219ASN00.0140.0022.500-1.457-0.5620.236-0.225-0.9060.000
211A220PRO00.0950.0606.389-0.474-0.4740.0000.0000.0000.000
212A221LYS10.9500.9968.003-0.315-0.3150.0000.0000.0000.000
213A222ARG10.9380.9519.7810.1200.1200.0000.0000.0000.000
214A223ASN00.023-0.0195.618-0.507-0.5070.0000.0000.0000.000
215A224VAL00.0640.0367.025-0.211-0.2110.0000.0000.0000.000
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