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: N91GQ

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 OptHSide
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 -7130080.45217
FMO2-HF: Nuclear repulsion 6969824.555479
FMO2-HF: Total energy -160255.896691
FMO2-MP2: Total energy -160718.525579


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.
6.252-13.82819.73117.597-17.243-0.054
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 : -0.027 / q_NPA : 0.049
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].
3A12LEU00.0790.0162.31718.276-3.2410.15123.579-2.212-0.031
4A13ILE00.0410.0135.285-0.201-0.145-0.001-0.003-0.0520.000
5A14PRO00.0100.0044.2740.0370.337-0.001-0.085-0.2140.000
6A15VAL00.0030.0042.284-0.675-0.1241.336-0.692-1.194-0.003
7A16THR00.021-0.0025.0800.6810.734-0.001-0.004-0.0470.000
8A17LEU0-0.0070.0148.1990.2740.2740.0000.0000.0000.000
9A18MET00.0020.0267.0240.2540.2540.0000.0000.0000.000
10A19VAL0-0.049-0.0358.4460.2220.2220.0000.0000.0000.000
11A20SER00.0100.00510.8230.1020.1020.0000.0000.0000.000
12A21GLY00.0320.00212.3840.0860.0860.0000.0000.0000.000
13A22ASN0-0.043-0.03411.5680.0170.0170.0000.0000.0000.000
14A23ILE0-0.0590.01414.5820.0580.0580.0000.0000.0000.000
15A24MET0-0.056-0.01517.0070.0250.0250.0000.0000.0000.000
16A25GLY00.0400.03318.986-0.013-0.0130.0000.0000.0000.000
17A26SER00.021-0.01619.9570.0270.0270.0000.0000.0000.000
18A27GLY0-0.0110.00022.1190.0120.0120.0000.0000.0000.000
19A28VAL00.0090.00223.2940.0050.0050.0000.0000.0000.000
20A29PHE00.0110.00425.7910.0110.0110.0000.0000.0000.000
21A30LEU0-0.0190.00424.9420.0110.0110.0000.0000.0000.000
22A31LEU00.0550.01427.4900.0120.0120.0000.0000.0000.000
23A32PRO00.0140.01030.5440.0080.0080.0000.0000.0000.000
24A33ALA0-0.0040.00631.2690.0070.0070.0000.0000.0000.000
25A34ASN0-0.029-0.02531.2970.0000.0000.0000.0000.0000.000
26A35LEU0-0.054-0.02133.2950.0040.0040.0000.0000.0000.000
27A36ALA00.0080.02136.0880.0050.0050.0000.0000.0000.000
28A37ALA0-0.007-0.00336.9170.0050.0050.0000.0000.0000.000
29A38THR00.0360.00537.772-0.003-0.0030.0000.0000.0000.000
30A39GLY00.1040.01135.941-0.004-0.0040.0000.0000.0000.000
31A40GLY0-0.131-0.07236.156-0.006-0.0060.0000.0000.0000.000
32A41ILE00.0640.02737.760-0.003-0.0030.0000.0000.0000.000
33A42ALA00.0160.01833.8860.0010.0010.0000.0000.0000.000
34A43ILE00.0530.01231.715-0.005-0.0050.0000.0000.0000.000
35A44TYR0-0.069-0.01633.106-0.004-0.0040.0000.0000.0000.000
36A45GLY00.0430.01633.3350.0060.0060.0000.0000.0000.000
37A46TRP00.0380.00025.408-0.001-0.0010.0000.0000.0000.000
38A47LEU00.0160.02528.303-0.008-0.0080.0000.0000.0000.000
39A48VAL00.0420.01829.011-0.003-0.0030.0000.0000.0000.000
40A49THR0-0.0080.02725.6050.0040.0040.0000.0000.0000.000
41A50ILE00.0280.00923.671-0.003-0.0030.0000.0000.0000.000
42A51ILE0-0.018-0.00424.380-0.007-0.0070.0000.0000.0000.000
43A52GLY00.0260.00425.6120.0020.0020.0000.0000.0000.000
44A53ALA00.0250.00121.8490.0060.0060.0000.0000.0000.000
45A54LEU0-0.022-0.00419.873-0.011-0.0110.0000.0000.0000.000
46A55ALA0-0.0090.00721.072-0.003-0.0030.0000.0000.0000.000
47A56LEU00.0520.00920.0230.0130.0130.0000.0000.0000.000
48A57SER0-0.078-0.04016.7000.0020.0020.0000.0000.0000.000
49A58MET00.003-0.00416.917-0.013-0.0130.0000.0000.0000.000
50A59VAL00.0020.00118.6310.0150.0150.0000.0000.0000.000
51A60TYR00.0750.03814.9880.0380.0380.0000.0000.0000.000
52A61ALA00.0010.03314.1930.0310.0310.0000.0000.0000.000
53A62LYS10.8740.94015.2470.0360.0360.0000.0000.0000.000
54A63MET00.0200.02217.5770.0200.0200.0000.0000.0000.000
55A64SER0-0.010-0.01712.2430.0250.0250.0000.0000.0000.000
56A65SER0-0.119-0.07113.6750.0490.0490.0000.0000.0000.000
57A66LEU0-0.063-0.04115.2510.0190.0190.0000.0000.0000.000
58A67ASP-1-0.819-0.88316.3050.3160.3160.0000.0000.0000.000
59A68PRO00.0010.00311.111-0.009-0.0090.0000.0000.0000.000
60A69SER00.001-0.00412.7860.0680.0680.0000.0000.0000.000
61A70PRO0-0.041-0.00811.9320.0910.0910.0000.0000.0000.000
62A71GLY00.0880.02411.5800.1530.1530.0000.0000.0000.000
63A72GLY0-0.069-0.04213.826-0.017-0.0170.0000.0000.0000.000
64A73SER00.0620.01214.6970.0280.0280.0000.0000.0000.000
65A74TYR00.0040.02017.691-0.016-0.0160.0000.0000.0000.000
66A75ALA00.0470.01517.045-0.010-0.0100.0000.0000.0000.000
67A76TYR0-0.025-0.02214.424-0.028-0.0280.0000.0000.0000.000
68A77ALA00.0540.01520.253-0.016-0.0160.0000.0000.0000.000
69A78ARG10.8260.90621.448-0.255-0.2550.0000.0000.0000.000
70A79ARG10.7640.86918.445-0.251-0.2510.0000.0000.0000.000
71A80CYS0-0.049-0.00924.280-0.014-0.0140.0000.0000.0000.000
72A81PHE00.0260.00626.192-0.010-0.0100.0000.0000.0000.000
73A82GLY00.0250.02827.261-0.006-0.0060.0000.0000.0000.000
74A83PRO0-0.018-0.01326.7460.0100.0100.0000.0000.0000.000
75A84PHE00.0520.02827.4000.0060.0060.0000.0000.0000.000
76A85LEU00.0950.03627.3180.0030.0030.0000.0000.0000.000
77A86GLY00.0310.04923.8510.0000.0000.0000.0000.0000.000
78A87TYR00.028-0.00823.7090.0100.0100.0000.0000.0000.000
79A88GLN00.004-0.00125.280-0.002-0.0020.0000.0000.0000.000
80A89THR0-0.028-0.04221.045-0.010-0.0100.0000.0000.0000.000
81A90ASN00.0200.01720.1820.0090.0090.0000.0000.0000.000
82A91VAL0-0.0060.01421.703-0.004-0.0040.0000.0000.0000.000
83A92LEU00.0030.00223.822-0.006-0.0060.0000.0000.0000.000
84A93TYR00.017-0.03115.0000.0100.0100.0000.0000.0000.000
85A94TRP00.0050.00318.872-0.019-0.0190.0000.0000.0000.000
86A95LEU0-0.044-0.03020.462-0.008-0.0080.0000.0000.0000.000
87A96ALA00.0150.00021.260-0.010-0.0100.0000.0000.0000.000
88A97CYS0-0.090-0.01317.283-0.014-0.0140.0000.0000.0000.000
89A98TRP00.023-0.00919.138-0.027-0.0270.0000.0000.0000.000
90A99ILE0-0.037-0.02220.829-0.012-0.0120.0000.0000.0000.000
91A100GLY00.0380.03222.180-0.009-0.0090.0000.0000.0000.000
92A101ASN00.008-0.01917.254-0.035-0.0350.0000.0000.0000.000
93A102ILE0-0.011-0.00121.379-0.013-0.0130.0000.0000.0000.000
94A103ALA00.0150.01024.861-0.005-0.0050.0000.0000.0000.000
95A104MET0-0.008-0.01217.641-0.019-0.0190.0000.0000.0000.000
96A105VAL00.0060.01022.051-0.015-0.0150.0000.0000.0000.000
97A106VAL0-0.0060.00723.975-0.005-0.0050.0000.0000.0000.000
98A107ILE00.0000.00025.074-0.002-0.0020.0000.0000.0000.000
99A108GLY00.0320.01923.385-0.010-0.0100.0000.0000.0000.000
100A109VAL00.025-0.01324.213-0.007-0.0070.0000.0000.0000.000
101A110GLY0-0.0230.00726.6540.0020.0020.0000.0000.0000.000
102A111TYR00.002-0.01626.060-0.005-0.0050.0000.0000.0000.000
103A112LEU0-0.062-0.02124.327-0.004-0.0040.0000.0000.0000.000
104A113SER0-0.098-0.04528.4850.0020.0020.0000.0000.0000.000
105A114TYR0-0.017-0.00131.1980.0090.0090.0000.0000.0000.000
106A115PHE0-0.011-0.00931.6070.0030.0030.0000.0000.0000.000
107A116PHE0-0.0300.00932.782-0.004-0.0040.0000.0000.0000.000
108A117PRO0-0.020-0.00734.6780.0040.0040.0000.0000.0000.000
109A118ILE00.043-0.01430.3450.0060.0060.0000.0000.0000.000
110A119LEU00.0080.00433.9060.0060.0060.0000.0000.0000.000
111A120LYS10.9930.98734.1580.0510.0510.0000.0000.0000.000
112A121ASP-1-0.859-0.92036.006-0.036-0.0360.0000.0000.0000.000
113A122PRO00.1020.03736.158-0.001-0.0010.0000.0000.0000.000
114A123LEU0-0.037-0.02435.153-0.001-0.0010.0000.0000.0000.000
115A124VAL00.0020.00534.5160.0020.0020.0000.0000.0000.000
116A125LEU00.0280.01329.720-0.001-0.0010.0000.0000.0000.000
117A126THR00.0270.00730.178-0.003-0.0030.0000.0000.0000.000
118A127LEU00.0160.01030.0550.0040.0040.0000.0000.0000.000
119A128THR00.0180.00228.1320.0010.0010.0000.0000.0000.000
120A129CYS0-0.0210.01725.700-0.010-0.0100.0000.0000.0000.000
121A130VAL00.0320.01024.6440.0010.0010.0000.0000.0000.000
122A131ALA0-0.033-0.01624.8290.0080.0080.0000.0000.0000.000
123A132VAL00.013-0.00820.6900.0040.0040.0000.0000.0000.000
124A133LEU00.0200.01120.404-0.007-0.0070.0000.0000.0000.000
125A134TRP00.011-0.00619.5720.0160.0160.0000.0000.0000.000
126A135ILE0-0.0020.01518.7280.0160.0160.0000.0000.0000.000
127A136PHE00.009-0.00814.170-0.016-0.0160.0000.0000.0000.000
128A137VAL0-0.058-0.02715.0450.0270.0270.0000.0000.0000.000
129A138LEU00.001-0.01116.0380.0530.0530.0000.0000.0000.000
130A139LEU00.0110.00512.6110.0370.0370.0000.0000.0000.000
131A140ASN0-0.021-0.00110.883-0.015-0.0150.0000.0000.0000.000
132A141ILE0-0.084-0.02011.0780.1460.1460.0000.0000.0000.000
133A142VAL0-0.006-0.00811.9090.0600.0600.0000.0000.0000.000
134A143GLY00.0760.0258.442-0.043-0.0430.0000.0000.0000.000
135A144PRO00.0240.0224.668-0.211-0.151-0.001-0.003-0.0560.000
136A145LYS10.9490.9722.206-3.979-4.0033.263-0.799-2.4400.010
137A146MET0-0.0010.0024.632-0.623-0.609-0.001-0.0130.0000.000
138A147ILE00.0450.0327.660-0.163-0.1630.0000.0000.0000.000
139A148THR00.008-0.0013.4400.2410.5210.003-0.060-0.2230.000
140A149ARG10.9250.9706.5130.3470.3470.0000.0000.0000.000
141A150VAL00.0350.0248.6770.0460.0460.0000.0000.0000.000
142A151GLN00.0360.0219.434-0.002-0.0020.0000.0000.0000.000
143A152ALA0-0.0150.0078.3810.0630.0630.0000.0000.0000.000
144A153VAL0-0.013-0.00710.4090.0960.0960.0000.0000.0000.000
145A154ALA00.008-0.00413.6040.0640.0640.0000.0000.0000.000
146A155THR0-0.017-0.03612.4890.0320.0320.0000.0000.0000.000
147A156VAL00.0060.01113.8100.0440.0440.0000.0000.0000.000
148A157LEU0-0.014-0.00716.3010.0630.0630.0000.0000.0000.000
149A158ALA0-0.014-0.00318.3590.0380.0380.0000.0000.0000.000
150A159LEU00.0140.00117.1330.0280.0280.0000.0000.0000.000
151A160VAL0-0.0110.00720.0230.0240.0240.0000.0000.0000.000
152A161PRO00.005-0.00222.5890.0190.0190.0000.0000.0000.000
153A162ILE00.009-0.00921.5980.0110.0110.0000.0000.0000.000
154A163VAL0-0.044-0.02221.2640.0060.0060.0000.0000.0000.000
155A164GLY00.0020.01223.5540.0090.0090.0000.0000.0000.000
156A165ILE0-0.072-0.03526.6650.0210.0210.0000.0000.0000.000
157A166ALA00.040-0.01427.8070.0010.0010.0000.0000.0000.000
158A167VAL0-0.068-0.02429.310-0.006-0.0060.0000.0000.0000.000
159A168PHE00.0550.03830.1230.0010.0010.0000.0000.0000.000
160A169GLY0-0.0630.00434.3210.0070.0070.0000.0000.0000.000
161A170TRP00.1160.01537.850-0.001-0.0010.0000.0000.0000.000
162A171PHE0-0.082-0.02936.9310.0040.0040.0000.0000.0000.000
163A172TRP00.0380.01239.4790.0030.0030.0000.0000.0000.000
164A173PHE0-0.013-0.00542.203-0.002-0.0020.0000.0000.0000.000
165A174LYS10.9350.97636.6250.1050.1050.0000.0000.0000.000
166A175GLY00.022-0.01342.3710.0030.0030.0000.0000.0000.000
167A176GLU-1-0.897-0.98040.902-0.076-0.0760.0000.0000.0000.000
168A177THR00.0210.00143.4010.0020.0020.0000.0000.0000.000
169A178TYR00.004-0.02246.1350.0000.0000.0000.0000.0000.000
170A179MET0-0.016-0.02448.0850.0000.0000.0000.0000.0000.000
171A180ALA00.0470.02446.2800.0020.0020.0000.0000.0000.000
172A181ALA00.035-0.06244.4400.0010.0010.0000.0000.0000.000
173A182TRP0-0.1690.06441.602-0.001-0.0010.0000.0000.0000.000
174A183ASN0-0.066-0.00140.8060.0030.0030.0000.0000.0000.000
175A184VAL0-0.0340.00340.3150.0000.0000.0000.0000.0000.000
176A185SER00.0280.00942.6900.0030.0030.0000.0000.0000.000
177A186GLY00.0080.00144.947-0.001-0.0010.0000.0000.0000.000
178A187MET00.0260.02944.0920.0030.0030.0000.0000.0000.000
179A188ASN00.0160.00545.215-0.004-0.0040.0000.0000.0000.000
180A189THR00.0920.02442.2300.0000.0000.0000.0000.0000.000
181A190PHE00.0070.00439.189-0.004-0.0040.0000.0000.0000.000
182A191GLY00.031-0.00840.049-0.001-0.0010.0000.0000.0000.000
183A192ALA0-0.0310.00840.7330.0000.0000.0000.0000.0000.000
184A193ILE00.016-0.00136.024-0.004-0.0040.0000.0000.0000.000
185A194GLN0-0.003-0.00435.498-0.003-0.0030.0000.0000.0000.000
186A195SER00.0040.00835.7380.0010.0010.0000.0000.0000.000
187A196THR0-0.039-0.02032.654-0.003-0.0030.0000.0000.0000.000
188A197LEU00.0140.00130.617-0.007-0.0070.0000.0000.0000.000
189A198ASN0-0.032-0.00930.403-0.004-0.0040.0000.0000.0000.000
190A199VAL0-0.0020.00629.2000.0000.0000.0000.0000.0000.000
191A200THR00.008-0.01527.278-0.005-0.0050.0000.0000.0000.000
192A201LEU0-0.0300.00125.849-0.013-0.0130.0000.0000.0000.000
193A202TRP00.0320.01724.970-0.005-0.0050.0000.0000.0000.000
194A203SER0-0.050-0.01723.448-0.010-0.0100.0000.0000.0000.000
195A204PHE00.039-0.00219.555-0.029-0.0290.0000.0000.0000.000
196A205ILE0-0.0040.01319.5470.0050.0050.0000.0000.0000.000
197A206GLY00.0650.00016.1100.0030.0030.0000.0000.0000.000
198A207VAL00.0110.00914.103-0.046-0.0460.0000.0000.0000.000
199A208GLU-1-0.834-0.87113.535-0.009-0.0090.0000.0000.0000.000
200A209SER00.0500.02310.1760.0630.0630.0000.0000.0000.000
201A210ALA0-0.023-0.0197.6200.0700.0700.0000.0000.0000.000
202A211SER0-0.042-0.0338.4850.2300.2300.0000.0000.0000.000
203A212VAL00.0350.02611.0700.1310.1310.0000.0000.0000.000
204A213ALA00.0020.0206.2450.1370.1370.0000.0000.0000.000
205A214ALA0-0.019-0.0126.8290.8490.8490.0000.0000.0000.000
206A215GLY00.0630.0648.256-0.055-0.0550.0000.0000.0000.000
207A216VAL0-0.097-0.0583.6900.4150.6790.004-0.057-0.2110.000
208A217VAL00.0450.0352.308-1.113-1.9045.715-2.913-2.0100.002
209A218LYS10.8370.8842.126-7.306-8.3359.076-0.697-7.351-0.028
210A219ASN00.0170.0052.724-1.959-0.3150.189-0.655-1.177-0.004
211A220PRO00.0850.0455.913-0.357-0.3570.0000.0000.0000.000
212A221LYS10.9380.9947.991-0.331-0.3310.0000.0000.0000.000
213A222ARG10.9380.9529.7540.0300.0300.0000.0000.0000.000
214A223ASN00.0370.0025.153-0.588-0.529-0.001-0.001-0.0560.000
215A224VAL00.0630.0316.944-0.175-0.1750.0000.0000.0000.000
216A225PRO0-0.0050.0218.503-0.090-0.0900.0000.0000.0000.000
217A226ILE00.0100.00810.116-0.010-0.0100.0000.0000.0000.000
218A227ALA00.0060.0017.452-0.016-0.0160.0000.0000.0000.000
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