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: 16NZZ

Calculation Name: 3CDL-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3CDL

Chain ID: A

ChEMBL ID:
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UniProt ID: Q87Z81

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2170120.70123
FMO2-HF: Nuclear repulsion 2091549.073857
FMO2-HF: Total energy -78571.627372
FMO2-MP2: Total energy -78802.38784


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:3:LEU)


Summations of interaction energy for fragment #1(A:3: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.
1.6195.81-0.026-1.769-2.397-0.004
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.003
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].
3A5ASP-1-0.894-0.9233.8311.9145.591-0.029-1.708-1.941-0.004
4A6GLN00.005-0.0054.672-0.948-0.778-0.001-0.005-0.1640.000
5A7LYS10.9350.9703.5080.6410.9850.004-0.056-0.2920.000
6A8ARG10.9030.9737.485-0.330-0.3300.0000.0000.0000.000
7A9GLU-1-0.703-0.8239.9020.2290.2290.0000.0000.0000.000
8A10SER00.0030.00110.204-0.066-0.0660.0000.0000.0000.000
9A11ILE0-0.061-0.03110.867-0.046-0.0460.0000.0000.0000.000
10A12VAL00.0000.00813.465-0.017-0.0170.0000.0000.0000.000
11A13GLN00.013-0.00615.142-0.010-0.0100.0000.0000.0000.000
12A14ALA0-0.0160.00415.829-0.015-0.0150.0000.0000.0000.000
13A15ALA0-0.005-0.00717.534-0.007-0.0070.0000.0000.0000.000
14A16ILE00.0040.00419.470-0.006-0.0060.0000.0000.0000.000
15A17ALA0-0.0010.00320.661-0.006-0.0060.0000.0000.0000.000
16A18GLU-1-0.801-0.88321.031-0.012-0.0120.0000.0000.0000.000
17A19PHE0-0.043-0.03621.589-0.005-0.0050.0000.0000.0000.000
18A20GLY00.0210.01424.956-0.002-0.0020.0000.0000.0000.000
19A21ASP-1-0.885-0.91825.8470.0180.0180.0000.0000.0000.000
20A22ARG10.8540.92425.7990.0000.0000.0000.0000.0000.000
21A23GLY00.0600.03428.608-0.002-0.0020.0000.0000.0000.000
22A24PHE00.010-0.01323.866-0.004-0.0040.0000.0000.0000.000
23A25GLU-1-0.794-0.89926.5430.0140.0140.0000.0000.0000.000
24A26ILE0-0.0170.00328.283-0.005-0.0050.0000.0000.0000.000
25A27THR0-0.0200.00122.782-0.008-0.0080.0000.0000.0000.000
26A28SER00.0170.01123.5310.0030.0030.0000.0000.0000.000
27A29MET00.0700.01917.2930.0000.0000.0000.0000.0000.000
28A30ASP-1-0.827-0.92017.986-0.068-0.0680.0000.0000.0000.000
29A31ARG10.8220.92019.0610.0090.0090.0000.0000.0000.000
30A32ILE00.0230.00616.342-0.001-0.0010.0000.0000.0000.000
31A33ALA0-0.027-0.02414.582-0.001-0.0010.0000.0000.0000.000
32A34ALA0-0.0150.00514.538-0.019-0.0190.0000.0000.0000.000
33A35ARG10.8170.90116.529-0.011-0.0110.0000.0000.0000.000
34A36ALA0-0.002-0.00212.6480.0100.0100.0000.0000.0000.000
35A37GLU-1-0.968-0.96311.944-0.127-0.1270.0000.0000.0000.000
36A38VAL0-0.067-0.0368.476-0.083-0.0830.0000.0000.0000.000
37A39SER00.0390.00910.5230.0540.0540.0000.0000.0000.000
38A40LYS10.9090.93212.4700.0700.0700.0000.0000.0000.000
39A41ARG10.9540.96612.8270.1570.1570.0000.0000.0000.000
40A42THR0-0.0030.0007.4860.0060.0060.0000.0000.0000.000
41A43VAL00.0620.03710.1180.0160.0160.0000.0000.0000.000
42A44TYR0-0.048-0.03012.7980.0340.0340.0000.0000.0000.000
43A45ASN0-0.040-0.0198.5960.0280.0280.0000.0000.0000.000
44A46HIS00.0140.0227.1670.0660.0660.0000.0000.0000.000
45A47PHE00.0440.01112.1910.0490.0490.0000.0000.0000.000
46A48PRO0-0.008-0.00115.500-0.027-0.0270.0000.0000.0000.000
47A49SER0-0.020-0.01317.496-0.013-0.0130.0000.0000.0000.000
48A50LYS10.8960.93220.025-0.003-0.0030.0000.0000.0000.000
49A51GLU-1-0.783-0.86222.0750.0420.0420.0000.0000.0000.000
50A52GLU-1-0.883-0.93716.8800.1470.1470.0000.0000.0000.000
51A53LEU0-0.001-0.00917.6820.0140.0140.0000.0000.0000.000
52A54PHE0-0.0030.00320.5070.0100.0100.0000.0000.0000.000
53A55ALA00.0210.01122.0130.0040.0040.0000.0000.0000.000
54A56GLU-1-0.820-0.91017.3060.2240.2240.0000.0000.0000.000
55A57MET0-0.028-0.01619.3470.0050.0050.0000.0000.0000.000
56A58LEU0-0.031-0.00223.091-0.003-0.0030.0000.0000.0000.000
57A59GLN00.0160.02520.523-0.017-0.0170.0000.0000.0000.000
58A60ARG10.7560.83615.572-0.239-0.2390.0000.0000.0000.000
59A61LEU0-0.013-0.00423.096-0.003-0.0030.0000.0000.0000.000
60A62TRP0-0.025-0.03426.067-0.006-0.0060.0000.0000.0000.000
61A63ASN0-0.047-0.02222.1490.0090.0090.0000.0000.0000.000
62A64CYS0-0.0200.01425.6500.0000.0000.0000.0000.0000.000
63A65ALA0-0.064-0.03628.070-0.008-0.0080.0000.0000.0000.000
64A66PRO0-0.0200.00428.2520.0000.0000.0000.0000.0000.000
65A67PRO00.0060.00825.7930.0050.0050.0000.0000.0000.000
66A68GLN0-0.010-0.03228.050-0.006-0.0060.0000.0000.0000.000
67A69SER0-0.024-0.01831.0790.0030.0030.0000.0000.0000.000
68A70GLU-1-0.835-0.89433.9180.0650.0650.0000.0000.0000.000
69A71VAL0-0.058-0.04635.8830.0020.0020.0000.0000.0000.000
70A72VAL0-0.0060.01338.740-0.003-0.0030.0000.0000.0000.000
71A73TYR0-0.097-0.08140.791-0.001-0.0010.0000.0000.0000.000
72A74ARG10.8390.89142.498-0.057-0.0570.0000.0000.0000.000
73A75PRO00.0440.01746.844-0.001-0.0010.0000.0000.0000.000
74A76LEU0-0.035-0.02049.995-0.002-0.0020.0000.0000.0000.000
75A77VAL0-0.0010.02948.011-0.001-0.0010.0000.0000.0000.000
76A78SER0-0.024-0.04251.344-0.001-0.0010.0000.0000.0000.000
77A79LEU00.0240.00750.1700.0020.0020.0000.0000.0000.000
78A80ARG10.9250.95349.085-0.030-0.0300.0000.0000.0000.000
79A81GLU-1-0.765-0.83948.1130.0410.0410.0000.0000.0000.000
80A82GLN00.0130.01545.0310.0040.0040.0000.0000.0000.000
81A83LEU0-0.0010.00444.1130.0030.0030.0000.0000.0000.000
82A84LEU00.0260.00445.0930.0010.0010.0000.0000.0000.000
83A85GLU-1-0.871-0.91340.5470.0610.0610.0000.0000.0000.000
84A86LEU0-0.015-0.00740.2010.0030.0030.0000.0000.0000.000
85A87LEU0-0.019-0.01340.0060.0020.0020.0000.0000.0000.000
86A88TRP00.0850.04540.7700.0020.0020.0000.0000.0000.000
87A89GLY0-0.046-0.00236.9410.0020.0020.0000.0000.0000.000
88A90LYS10.8660.93733.612-0.068-0.0680.0000.0000.0000.000
89A91MET00.0300.01136.9300.0000.0000.0000.0000.0000.000
90A92ARG10.8930.93334.922-0.064-0.0640.0000.0000.0000.000
91A93ASN0-0.025-0.00231.248-0.001-0.0010.0000.0000.0000.000
92A94LEU0-0.016-0.01033.3050.0000.0000.0000.0000.0000.000
93A95THR0-0.033-0.00736.012-0.004-0.0040.0000.0000.0000.000
94A96ASP-1-0.833-0.90029.3290.0770.0770.0000.0000.0000.000
95A97SER00.0320.00130.0760.0000.0000.0000.0000.0000.000
96A98SER00.009-0.00425.897-0.002-0.0020.0000.0000.0000.000
97A99PHE0-0.016-0.00327.6510.0000.0000.0000.0000.0000.000
98A100LEU0-0.019-0.01629.436-0.001-0.0010.0000.0000.0000.000
99A101ASP-1-0.819-0.88427.9470.0430.0430.0000.0000.0000.000
100A102LEU0-0.021-0.00924.278-0.003-0.0030.0000.0000.0000.000
101A103ALA0-0.015-0.02627.497-0.002-0.0020.0000.0000.0000.000
102A104ARG10.8210.89430.545-0.040-0.0400.0000.0000.0000.000
103A105VAL0-0.025-0.00225.642-0.004-0.0040.0000.0000.0000.000
104A106VAL0-0.0020.00127.670-0.004-0.0040.0000.0000.0000.000
105A107VAL0-0.010-0.01029.870-0.003-0.0030.0000.0000.0000.000
106A108GLY00.0260.00932.570-0.003-0.0030.0000.0000.0000.000
107A109ALA0-0.022-0.01829.152-0.004-0.0040.0000.0000.0000.000
108A110THR0-0.045-0.01431.177-0.002-0.0020.0000.0000.0000.000
109A111ILE0-0.0160.00033.864-0.002-0.0020.0000.0000.0000.000
110A112HIS0-0.077-0.03832.800-0.002-0.0020.0000.0000.0000.000
111A113SER00.0220.02232.042-0.002-0.0020.0000.0000.0000.000
112A114PRO00.0440.00934.4500.0030.0030.0000.0000.0000.000
113A115GLU-1-0.934-0.96131.4220.0210.0210.0000.0000.0000.000
114A116ARG10.7510.81828.146-0.028-0.0280.0000.0000.0000.000
115A117ALA0-0.002-0.01432.3830.0050.0050.0000.0000.0000.000
116A118GLN0-0.066-0.02735.0050.0020.0020.0000.0000.0000.000
117A119VAL0-0.0260.00530.4910.0010.0010.0000.0000.0000.000
118A120TRP0-0.041-0.02026.0160.0070.0070.0000.0000.0000.000
119A121LEU00.019-0.03232.5360.0020.0020.0000.0000.0000.000
120A122ALA00.0620.05334.7310.0040.0040.0000.0000.0000.000
121A123ARG10.8150.93930.877-0.065-0.0650.0000.0000.0000.000
122A124ILE00.000-0.01136.5080.0000.0000.0000.0000.0000.000
123A125ASN0-0.004-0.03736.1250.0010.0010.0000.0000.0000.000
124A126GLU-1-0.689-0.83231.2150.0670.0670.0000.0000.0000.000
125A127ARG10.7350.85332.254-0.051-0.0510.0000.0000.0000.000
126A128GLU-1-0.842-0.88834.2930.0450.0450.0000.0000.0000.000
127A129GLU-1-0.754-0.86036.6230.0540.0540.0000.0000.0000.000
128A130THR00.0080.01435.776-0.002-0.0020.0000.0000.0000.000
129A131PHE00.029-0.00338.307-0.001-0.0010.0000.0000.0000.000
130A132SER0-0.023-0.01241.378-0.004-0.0040.0000.0000.0000.000
131A133ALA00.008-0.01040.685-0.003-0.0030.0000.0000.0000.000
132A134TRP00.0230.00342.450-0.002-0.0020.0000.0000.0000.000
133A135ILE00.0070.01144.042-0.002-0.0020.0000.0000.0000.000
134A136ARG10.8730.92642.108-0.051-0.0510.0000.0000.0000.000
135A137ALA00.0180.01245.485-0.002-0.0020.0000.0000.0000.000
136A138ALA00.0760.03547.539-0.002-0.0020.0000.0000.0000.000
137A139GLN0-0.089-0.05150.025-0.001-0.0010.0000.0000.0000.000
138A140LYS10.8030.90449.447-0.040-0.0400.0000.0000.0000.000
139A141ASP-1-0.799-0.87951.1780.0370.0370.0000.0000.0000.000
140A142GLY00.0120.01953.144-0.001-0.0010.0000.0000.0000.000
141A143ARG10.8460.91752.082-0.038-0.0380.0000.0000.0000.000
142A144LEU0-0.0220.00849.9630.0000.0000.0000.0000.0000.000
143A145LYS10.8750.92454.365-0.026-0.0260.0000.0000.0000.000
144A146PRO0-0.028-0.00954.4830.0010.0010.0000.0000.0000.000
145A147VAL00.0150.00351.154-0.001-0.0010.0000.0000.0000.000
146A148ASP-1-0.812-0.90247.6790.0390.0390.0000.0000.0000.000
147A149PRO0-0.012-0.00945.7520.0000.0000.0000.0000.0000.000
148A150GLY00.0510.02544.2460.0010.0010.0000.0000.0000.000
149A151PHE0-0.026-0.00145.2290.0000.0000.0000.0000.0000.000
150A152ALA00.0190.00348.001-0.001-0.0010.0000.0000.0000.000
151A153ALA00.003-0.00142.9970.0000.0000.0000.0000.0000.000
152A154THR0-0.005-0.01043.8030.0010.0010.0000.0000.0000.000
153A155GLN00.0050.01844.8410.0000.0000.0000.0000.0000.000
154A156MET00.0030.02345.017-0.001-0.0010.0000.0000.0000.000
155A157HIS10.8240.89239.595-0.050-0.0500.0000.0000.0000.000
156A158ALA0-0.0060.02043.2590.0000.0000.0000.0000.0000.000
157A159LEU00.0200.02245.334-0.001-0.0010.0000.0000.0000.000
158A160LEU00.0350.02642.0280.0000.0000.0000.0000.0000.000
159A161LYS10.9030.93438.202-0.045-0.0450.0000.0000.0000.000
160A162SER0-0.075-0.04742.008-0.001-0.0010.0000.0000.0000.000
161A163PHE0-0.0010.00844.395-0.002-0.0020.0000.0000.0000.000
162A164ALA00.0240.01040.466-0.001-0.0010.0000.0000.0000.000
163A165PHE0-0.0080.00734.4630.0030.0030.0000.0000.0000.000
164A166TRP00.0720.00338.2800.0010.0010.0000.0000.0000.000
165A167PRO00.0450.04940.550-0.001-0.0010.0000.0000.0000.000
166A168GLN0-0.040-0.01437.327-0.001-0.0010.0000.0000.0000.000
167A169VAL00.0000.00234.654-0.001-0.0010.0000.0000.0000.000
168A170THR0-0.101-0.08236.620-0.002-0.0020.0000.0000.0000.000
169A171PHE0-0.010-0.00739.269-0.002-0.0020.0000.0000.0000.000
170A172ASN0-0.034-0.00335.5870.0000.0000.0000.0000.0000.000
171A173ALA0-0.0010.01638.576-0.001-0.0010.0000.0000.0000.000
172A174ALA00.0170.00239.8420.0020.0020.0000.0000.0000.000
173A175LEU00.0170.00035.5280.0000.0000.0000.0000.0000.000
174A176LEU0-0.0100.01439.913-0.002-0.0020.0000.0000.0000.000
175A177THR00.008-0.01941.8700.0020.0020.0000.0000.0000.000
176A178PRO00.0430.00042.3600.0010.0010.0000.0000.0000.000
177A179GLN00.0520.02144.3920.0020.0020.0000.0000.0000.000
178A180GLU-1-0.815-0.87646.1780.0270.0270.0000.0000.0000.000
179A181GLN0-0.082-0.05340.6080.0020.0020.0000.0000.0000.000
180A182SER00.0470.00044.6880.0010.0010.0000.0000.0000.000
181A183ASN0-0.040-0.01146.9560.0000.0000.0000.0000.0000.000
182A184VAL0-0.010-0.00245.0640.0000.0000.0000.0000.0000.000
183A185VAL0-0.014-0.00543.8250.0000.0000.0000.0000.0000.000
184A186GLU-1-0.846-0.93446.8760.0350.0350.0000.0000.0000.000
185A187SER0-0.0030.00350.488-0.001-0.0010.0000.0000.0000.000
186A188ALA00.006-0.00147.835-0.001-0.0010.0000.0000.0000.000
187A189LEU00.0060.00547.8070.0000.0000.0000.0000.0000.000
188A190ASN0-0.064-0.04250.606-0.001-0.0010.0000.0000.0000.000
189A191MET0-0.0160.00452.7560.0000.0000.0000.0000.0000.000
190A192PHE00.004-0.00949.2290.0000.0000.0000.0000.0000.000
191A193LEU0-0.051-0.02151.3380.0000.0000.0000.0000.0000.000
192A194GLY00.0100.01154.262-0.001-0.0010.0000.0000.0000.000
193A195TRP0-0.042-0.00655.242-0.001-0.0010.0000.0000.0000.000
194A196TYR00.014-0.02752.041-0.001-0.0010.0000.0000.0000.000
195A197GLU-1-0.862-0.92855.1040.0330.0330.0000.0000.0000.000
196A198ILE0-0.082-0.05056.206-0.002-0.0020.0000.0000.0000.000
197A199PRO0-0.0070.00358.2680.0010.0010.0000.0000.0000.000