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: JL399

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 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 432
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7142047.187366
FMO2-HF: Nuclear repulsion 6981788.056256
FMO2-HF: Total energy -160259.13111
FMO2-MP2: Total energy -160721.246049


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.
-11.017-10.21212.0631.309-14.177-0.032
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 : 0.019 / q_NPA : 0.030
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].
3A12LEU00.0640.0132.6114.239-1.5620.6046.807-1.611-0.016
4A13ILE00.0420.0285.264-0.242-0.175-0.001-0.004-0.0620.000
5A14PRO00.0180.0003.6730.2730.6740.003-0.122-0.2810.000
6A15VAL0-0.0020.0032.239-0.1510.4381.389-0.714-1.264-0.004
7A16THR00.0190.0024.9260.6690.721-0.001-0.009-0.0420.000
8A17LEU0-0.0190.0157.8560.2670.2670.0000.0000.0000.000
9A18MET0-0.0220.0066.5000.3860.3860.0000.0000.0000.000
10A19VAL0-0.044-0.0208.5500.2220.2220.0000.0000.0000.000
11A20SER0-0.002-0.00910.7110.0720.0720.0000.0000.0000.000
12A21GLY00.008-0.00611.9190.0740.0740.0000.0000.0000.000
13A22ASN0-0.016-0.02511.0560.0000.0000.0000.0000.0000.000
14A23ILE0-0.0430.01413.9560.0480.0480.0000.0000.0000.000
15A24MET0-0.027-0.00516.3310.0100.0100.0000.0000.0000.000
16A25GLY00.0320.02917.849-0.003-0.0030.0000.0000.0000.000
17A26SER00.0330.00318.8840.0220.0220.0000.0000.0000.000
18A27GLY0-0.024-0.01321.2760.0120.0120.0000.0000.0000.000
19A28VAL00.003-0.00922.6530.0070.0070.0000.0000.0000.000
20A29PHE0-0.014-0.00325.3340.0110.0110.0000.0000.0000.000
21A30LEU0-0.0070.00524.2590.0120.0120.0000.0000.0000.000
22A31LEU00.0510.02126.6020.0110.0110.0000.0000.0000.000
23A32PRO0-0.002-0.00529.9410.0080.0080.0000.0000.0000.000
24A33ALA0-0.0080.01230.3870.0070.0070.0000.0000.0000.000
25A34ASN0-0.020-0.01330.7750.0000.0000.0000.0000.0000.000
26A35LEU0-0.018-0.02332.6270.0060.0060.0000.0000.0000.000
27A36ALA00.0160.01735.4960.0030.0030.0000.0000.0000.000
28A37ALA0-0.059-0.02936.0470.0050.0050.0000.0000.0000.000
29A38THR00.0090.00637.395-0.003-0.0030.0000.0000.0000.000
30A39GLY00.0670.00235.075-0.004-0.0040.0000.0000.0000.000
31A40GLY0-0.066-0.03635.831-0.006-0.0060.0000.0000.0000.000
32A41ILE00.020-0.00536.448-0.003-0.0030.0000.0000.0000.000
33A42ALA00.0210.02833.4450.0010.0010.0000.0000.0000.000
34A43ILE0-0.008-0.01131.360-0.004-0.0040.0000.0000.0000.000
35A44TYR0-0.025-0.01532.549-0.003-0.0030.0000.0000.0000.000
36A45GLY00.0240.02233.3260.0050.0050.0000.0000.0000.000
37A46TRP00.025-0.01825.2710.0020.0020.0000.0000.0000.000
38A47LEU0-0.0030.01128.310-0.005-0.0050.0000.0000.0000.000
39A48VAL00.0190.01029.1640.0000.0000.0000.0000.0000.000
40A49THR00.0150.00425.4580.0070.0070.0000.0000.0000.000
41A50ILE0-0.0020.00323.5760.0000.0000.0000.0000.0000.000
42A51ILE0-0.021-0.00124.407-0.003-0.0030.0000.0000.0000.000
43A52GLY00.0230.01225.7360.0060.0060.0000.0000.0000.000
44A53ALA00.0400.01221.3070.0110.0110.0000.0000.0000.000
45A54LEU0-0.0090.00519.8760.0000.0000.0000.0000.0000.000
46A55ALA00.0060.02221.0650.0050.0050.0000.0000.0000.000
47A56LEU00.0520.00420.2940.0170.0170.0000.0000.0000.000
48A57SER0-0.068-0.04216.6910.0140.0140.0000.0000.0000.000
49A58MET00.007-0.00817.3280.0090.0090.0000.0000.0000.000
50A59VAL0-0.015-0.00619.6540.0210.0210.0000.0000.0000.000
51A60TYR00.030-0.00215.3300.0390.0390.0000.0000.0000.000
52A61ALA0-0.0150.01714.7300.0510.0510.0000.0000.0000.000
53A62LYS10.8640.93815.782-0.020-0.0200.0000.0000.0000.000
54A63MET00.0350.03417.9940.0130.0130.0000.0000.0000.000
55A64SER0-0.002-0.01412.7660.0250.0250.0000.0000.0000.000
56A65SER0-0.095-0.06714.0000.0400.0400.0000.0000.0000.000
57A66LEU0-0.061-0.02615.668-0.001-0.0010.0000.0000.0000.000
58A67ASP-1-0.776-0.84716.5190.4290.4290.0000.0000.0000.000
59A68PRO0-0.035-0.01511.0500.0140.0140.0000.0000.0000.000
60A69SER0-0.007-0.02812.3590.0850.0850.0000.0000.0000.000
61A70PRO0-0.008-0.02012.0310.1290.1290.0000.0000.0000.000
62A71GLY00.0260.02911.8980.1330.1330.0000.0000.0000.000
63A72GLY0-0.019-0.02313.899-0.046-0.0460.0000.0000.0000.000
64A73SER00.0540.03815.0920.0200.0200.0000.0000.0000.000
65A74TYR0-0.016-0.02917.887-0.033-0.0330.0000.0000.0000.000
66A75ALA00.0350.01217.563-0.030-0.0300.0000.0000.0000.000
67A76TYR0-0.033-0.03015.039-0.032-0.0320.0000.0000.0000.000
68A77ALA00.0720.03520.768-0.026-0.0260.0000.0000.0000.000
69A78ARG10.8260.90421.369-0.328-0.3280.0000.0000.0000.000
70A79ARG10.7730.85318.201-0.347-0.3470.0000.0000.0000.000
71A80CYS0-0.046-0.00424.469-0.019-0.0190.0000.0000.0000.000
72A81PHE00.0080.00626.769-0.016-0.0160.0000.0000.0000.000
73A82GLY00.0380.03727.725-0.009-0.0090.0000.0000.0000.000
74A83PRO0-0.023-0.02427.2060.0110.0110.0000.0000.0000.000
75A84PHE00.0430.02727.5920.0110.0110.0000.0000.0000.000
76A85LEU00.0750.03427.4730.0050.0050.0000.0000.0000.000
77A86GLY00.0260.03623.9820.0070.0070.0000.0000.0000.000
78A87TYR00.003-0.01023.8280.0100.0100.0000.0000.0000.000
79A88GLN00.0270.01925.2450.0020.0020.0000.0000.0000.000
80A89THR0-0.011-0.02821.149-0.010-0.0100.0000.0000.0000.000
81A90ASN00.0200.02020.2170.0270.0270.0000.0000.0000.000
82A91VAL0-0.0190.00221.6210.0020.0020.0000.0000.0000.000
83A92LEU00.0090.00423.978-0.008-0.0080.0000.0000.0000.000
84A93TYR00.001-0.04314.7850.0130.0130.0000.0000.0000.000
85A94TRP00.0050.00418.851-0.020-0.0200.0000.0000.0000.000
86A95LEU0-0.027-0.01320.331-0.010-0.0100.0000.0000.0000.000
87A96ALA00.0310.01820.838-0.015-0.0150.0000.0000.0000.000
88A97CYS0-0.098-0.03616.921-0.007-0.0070.0000.0000.0000.000
89A98TRP0-0.008-0.01418.635-0.028-0.0280.0000.0000.0000.000
90A99ILE0-0.025-0.01820.767-0.020-0.0200.0000.0000.0000.000
91A100GLY00.0590.04021.565-0.016-0.0160.0000.0000.0000.000
92A101ASN00.001-0.02616.604-0.040-0.0400.0000.0000.0000.000
93A102ILE0-0.016-0.01020.892-0.017-0.0170.0000.0000.0000.000
94A103ALA00.0120.01924.406-0.009-0.0090.0000.0000.0000.000
95A104MET00.0050.00617.269-0.023-0.0230.0000.0000.0000.000
96A105VAL00.0020.01121.530-0.019-0.0190.0000.0000.0000.000
97A106VAL00.0190.00823.449-0.010-0.0100.0000.0000.0000.000
98A107ILE0-0.004-0.00424.698-0.006-0.0060.0000.0000.0000.000
99A108GLY00.0260.00722.853-0.011-0.0110.0000.0000.0000.000
100A109VAL0-0.005-0.01723.804-0.012-0.0120.0000.0000.0000.000
101A110GLY00.0130.01826.259-0.002-0.0020.0000.0000.0000.000
102A111TYR0-0.006-0.00325.451-0.005-0.0050.0000.0000.0000.000
103A112LEU0-0.056-0.02223.830-0.010-0.0100.0000.0000.0000.000
104A113SER0-0.020-0.01628.1710.0010.0010.0000.0000.0000.000
105A114TYR0-0.033-0.00330.9370.0070.0070.0000.0000.0000.000
106A115PHE0-0.010-0.00830.8700.0030.0030.0000.0000.0000.000
107A116PHE00.0070.00532.193-0.006-0.0060.0000.0000.0000.000
108A117PRO0-0.052-0.01134.1930.0030.0030.0000.0000.0000.000
109A118ILE00.025-0.01229.8640.0070.0070.0000.0000.0000.000
110A119LEU00.0260.01033.6960.0060.0060.0000.0000.0000.000
111A120LYS10.9490.97533.6770.0490.0490.0000.0000.0000.000
112A121ASP-1-0.851-0.91435.544-0.030-0.0300.0000.0000.0000.000
113A122PRO00.0450.01835.5340.0000.0000.0000.0000.0000.000
114A123LEU00.0300.00234.4170.0010.0010.0000.0000.0000.000
115A124VAL00.0080.01033.4820.0030.0030.0000.0000.0000.000
116A125LEU00.0240.01729.414-0.002-0.0020.0000.0000.0000.000
117A126THR00.0350.02529.673-0.001-0.0010.0000.0000.0000.000
118A127LEU00.0250.01529.2110.0040.0040.0000.0000.0000.000
119A128THR0-0.017-0.01927.6960.0000.0000.0000.0000.0000.000
120A129CYS0-0.042-0.00325.298-0.009-0.0090.0000.0000.0000.000
121A130VAL00.007-0.00424.3670.0060.0060.0000.0000.0000.000
122A131ALA0-0.013-0.00524.5060.0100.0100.0000.0000.0000.000
123A132VAL00.004-0.00619.9750.0040.0040.0000.0000.0000.000
124A133LEU00.0140.00119.810-0.001-0.0010.0000.0000.0000.000
125A134TRP00.001-0.00919.3050.0290.0290.0000.0000.0000.000
126A135ILE00.0090.01517.7120.0190.0190.0000.0000.0000.000
127A136PHE00.0290.01113.474-0.005-0.0050.0000.0000.0000.000
128A137VAL0-0.012-0.00614.5760.0460.0460.0000.0000.0000.000
129A138LEU0-0.013-0.01215.5440.0620.0620.0000.0000.0000.000
130A139LEU00.002-0.00512.2420.0320.0320.0000.0000.0000.000
131A140ASN0-0.020-0.01110.8460.0100.0100.0000.0000.0000.000
132A141ILE0-0.069-0.02510.9000.1680.1680.0000.0000.0000.000
133A142VAL0-0.003-0.00412.0550.0790.0790.0000.0000.0000.000
134A143GLY00.0740.0398.850-0.035-0.0350.0000.0000.0000.000
135A144PRO00.0530.0394.956-0.178-0.1780.0000.0000.0000.000
136A145LYS10.9190.9622.211-3.892-3.6172.668-0.693-2.2490.008
137A146MET0-0.029-0.0134.531-0.680-0.654-0.001-0.012-0.0130.000
138A147ILE00.0570.0377.458-0.196-0.1960.0000.0000.0000.000
139A148THR00.000-0.0123.116-0.831-0.4790.025-0.083-0.2940.000
140A149ARG10.9180.9686.1330.7350.7350.0000.0000.0000.000
141A150VAL00.0200.0188.3470.0820.0820.0000.0000.0000.000
142A151GLN00.0440.0189.0130.0480.0480.0000.0000.0000.000
143A152ALA0-0.0180.0028.0970.0630.0630.0000.0000.0000.000
144A153VAL0-0.001-0.00710.1330.1160.1160.0000.0000.0000.000
145A154ALA00.0060.00513.3570.0750.0750.0000.0000.0000.000
146A155THR0-0.006-0.02512.0110.0400.0400.0000.0000.0000.000
147A156VAL00.0070.00513.1180.0610.0610.0000.0000.0000.000
148A157LEU0-0.017-0.01515.6250.0700.0700.0000.0000.0000.000
149A158ALA0-0.0110.00117.9350.0440.0440.0000.0000.0000.000
150A159LEU00.001-0.00416.4170.0350.0350.0000.0000.0000.000
151A160VAL0-0.0100.00819.3820.0260.0260.0000.0000.0000.000
152A161PRO00.007-0.01121.9750.0210.0210.0000.0000.0000.000
153A162ILE0-0.025-0.01220.6330.0160.0160.0000.0000.0000.000
154A163VAL0-0.026-0.01720.9760.0100.0100.0000.0000.0000.000
155A164GLY00.0030.01723.2480.0080.0080.0000.0000.0000.000
156A165ILE0-0.045-0.02626.2790.0190.0190.0000.0000.0000.000
157A166ALA00.0140.00127.0700.0050.0050.0000.0000.0000.000
158A167VAL0-0.051-0.02729.114-0.003-0.0030.0000.0000.0000.000
159A168PHE00.0600.03029.4080.0020.0020.0000.0000.0000.000
160A169GLY0-0.053-0.00933.9630.0090.0090.0000.0000.0000.000
161A170TRP00.0360.00037.2810.0000.0000.0000.0000.0000.000
162A171PHE0-0.0160.00636.5440.0040.0040.0000.0000.0000.000
163A172TRP00.0200.01238.8510.0040.0040.0000.0000.0000.000
164A173PHE0-0.0030.00141.046-0.002-0.0020.0000.0000.0000.000
165A174LYS10.8940.93336.5670.0970.0970.0000.0000.0000.000
166A175GLY00.0210.00742.1920.0030.0030.0000.0000.0000.000
167A176GLU-1-0.798-0.91140.223-0.065-0.0650.0000.0000.0000.000
168A177THR00.006-0.01443.3840.0020.0020.0000.0000.0000.000
169A178TYR0-0.019-0.02146.101-0.001-0.0010.0000.0000.0000.000
170A179MET0-0.014-0.01947.732-0.001-0.0010.0000.0000.0000.000
171A180ALA00.0590.04145.9620.0010.0010.0000.0000.0000.000
172A181ALA0-0.098-0.03045.1870.0020.0020.0000.0000.0000.000
173A182TRP00.0030.01241.8590.0020.0020.0000.0000.0000.000
174A183ASN0-0.079-0.03640.4010.0010.0010.0000.0000.0000.000
175A184VAL0-0.0040.01739.9090.0000.0000.0000.0000.0000.000
176A185SER00.0130.00241.9950.0020.0020.0000.0000.0000.000
177A186GLY00.011-0.00244.6650.0000.0000.0000.0000.0000.000
178A187MET00.0290.04743.7580.0030.0030.0000.0000.0000.000
179A188ASN00.027-0.00244.891-0.004-0.0040.0000.0000.0000.000
180A189THR00.0620.01942.0100.0010.0010.0000.0000.0000.000
181A190PHE00.0270.01939.343-0.003-0.0030.0000.0000.0000.000
182A191GLY00.0510.01339.5570.0000.0000.0000.0000.0000.000
183A192ALA0-0.0070.01139.9040.0000.0000.0000.0000.0000.000
184A193ILE00.0180.01335.564-0.002-0.0020.0000.0000.0000.000
185A194GLN0-0.008-0.00835.158-0.002-0.0020.0000.0000.0000.000
186A195SER0-0.028-0.02335.3340.0000.0000.0000.0000.0000.000
187A196THR00.0260.01631.982-0.003-0.0030.0000.0000.0000.000
188A197LEU0-0.047-0.01130.704-0.005-0.0050.0000.0000.0000.000
189A198ASN00.0170.00830.338-0.001-0.0010.0000.0000.0000.000
190A199VAL0-0.0090.01329.1020.0020.0020.0000.0000.0000.000
191A200THR0-0.017-0.01727.235-0.005-0.0050.0000.0000.0000.000
192A201LEU0-0.033-0.00125.890-0.008-0.0080.0000.0000.0000.000
193A202TRP00.0420.01424.7070.0030.0030.0000.0000.0000.000
194A203SER0-0.064-0.03123.427-0.006-0.0060.0000.0000.0000.000
195A204PHE00.0380.00519.264-0.027-0.0270.0000.0000.0000.000
196A205ILE0-0.0020.01018.5890.0050.0050.0000.0000.0000.000
197A206GLY00.0720.02615.116-0.017-0.0170.0000.0000.0000.000
198A207VAL00.0560.02913.410-0.033-0.0330.0000.0000.0000.000
199A208GLU-1-0.820-0.84213.3390.1960.1960.0000.0000.0000.000
200A209SER00.0270.0029.9430.1190.1190.0000.0000.0000.000
201A210ALA0-0.001-0.0107.5010.2060.2060.0000.0000.0000.000
202A211SER0-0.051-0.0358.4640.2800.2800.0000.0000.0000.000
203A212VAL00.0040.01311.4010.1030.1030.0000.0000.0000.000
204A213ALA00.0340.0276.3950.1360.1360.0000.0000.0000.000
205A214ALA00.0100.0147.0720.9800.9800.0000.0000.0000.000
206A215GLY00.0580.0498.044-0.123-0.1230.0000.0000.0000.000
207A216VAL0-0.044-0.0253.4880.2690.6900.015-0.130-0.3060.001
208A217VAL00.0340.0252.644-2.848-1.5071.665-1.340-1.6660.007
209A218LYS10.7700.8442.389-10.011-7.8245.661-2.099-5.749-0.026
210A219ASN00.0220.0003.175-1.033-0.1380.036-0.292-0.640-0.002
211A220PRO00.0820.0436.089-0.269-0.2690.0000.0000.0000.000
212A221LYS10.8860.9618.577-0.455-0.4550.0000.0000.0000.000
213A222ARG10.9350.96710.254-0.042-0.0420.0000.0000.0000.000
214A223ASN00.008-0.0065.570-0.543-0.5430.0000.0000.0000.000
215A224VAL00.0600.0407.645-0.140-0.1400.0000.0000.0000.000
216A225PRO0-0.0040.0109.069-0.107-0.1070.0000.0000.0000.000
217A226ILE00.0150.01010.148-0.028-0.0280.0000.0000.0000.000
218A227ALA00.001-0.0077.384-0.056-0.0560.0000.0000.0000.000
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