Manual

About

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: GNM41

Calculation Name: 2C24-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C24

Chain ID: A

ChEMBL ID:

UniProt ID: P71140

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1887546.605898
FMO2-HF: Nuclear repulsion 1818767.153172
FMO2-HF: Total energy -68779.452726
FMO2-MP2: Total energy -68983.049071


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:13:LEU)


Summations of interaction energy for fragment #1(A:13: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.
-28.536-14.8216.93-7.806-12.839-0.05
Interaction energy analysis for fragmet #1(A:13:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.025
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].
3A15ASP-1-0.806-0.8993.761-4.235-2.744-0.007-0.687-0.7960.003
4A16VAL0-0.102-0.0515.7810.6930.6930.0000.0000.0000.000
5A17GLN0-0.089-0.0598.107-0.060-0.0600.0000.0000.0000.000
6A18ILE0-0.026-0.01811.6420.0850.0850.0000.0000.0000.000
7A19PHE0-0.012-0.01414.3710.0700.0700.0000.0000.0000.000
8A20LYS10.9500.98015.9730.1100.1100.0000.0000.0000.000
9A21ASP-1-0.868-0.94617.906-0.120-0.1200.0000.0000.0000.000
10A22SER0-0.038-0.01420.9560.0240.0240.0000.0000.0000.000
11A23PRO0-0.010-0.02221.763-0.019-0.0190.0000.0000.0000.000
12A24VAL00.0450.04718.7510.0080.0080.0000.0000.0000.000
13A25VAL00.0030.01620.8970.0100.0100.0000.0000.0000.000
14A26GLY00.0290.01920.912-0.025-0.0250.0000.0000.0000.000
15A27TRP00.0100.01723.1150.0120.0120.0000.0000.0000.000
16A28SER0-0.0070.01125.690-0.024-0.0240.0000.0000.0000.000
17A29GLY00.0560.02927.7820.0110.0110.0000.0000.0000.000
18A30SER0-0.033-0.03031.055-0.010-0.0100.0000.0000.0000.000
19A31GLY0-0.059-0.00633.7900.0060.0060.0000.0000.0000.000
20A32MET0-0.051-0.04337.0370.0070.0070.0000.0000.0000.000
21A33GLY00.0180.02436.4850.0040.0040.0000.0000.0000.000
22A34GLU-1-0.825-0.92835.752-0.104-0.1040.0000.0000.0000.000
23A35LEU0-0.044-0.00628.672-0.004-0.0040.0000.0000.0000.000
24A36GLU-1-0.846-0.92132.224-0.109-0.1090.0000.0000.0000.000
25A37THR0-0.051-0.02729.689-0.008-0.0080.0000.0000.0000.000
26A38ILE0-0.010-0.01230.1140.0090.0090.0000.0000.0000.000
27A39GLY0-0.030-0.01629.983-0.003-0.0030.0000.0000.0000.000
28A40ASP-1-0.915-0.94929.564-0.080-0.0800.0000.0000.0000.000
29A41THR0-0.014-0.02424.282-0.015-0.0150.0000.0000.0000.000
30A42LEU00.018-0.00323.7440.0070.0070.0000.0000.0000.000
31A43PRO0-0.0180.00626.4490.0050.0050.0000.0000.0000.000
32A44VAL00.0040.00324.460-0.015-0.0150.0000.0000.0000.000
33A45ASP-1-0.823-0.91426.968-0.114-0.1140.0000.0000.0000.000
34A46THR00.016-0.00527.846-0.008-0.0080.0000.0000.0000.000
35A47THR0-0.082-0.03129.9690.0050.0050.0000.0000.0000.000
36A48VAL0-0.023-0.00428.0720.0000.0000.0000.0000.0000.000
37A49THR0-0.052-0.00426.742-0.009-0.0090.0000.0000.0000.000
38A50TYR0-0.012-0.01220.5630.0140.0140.0000.0000.0000.000
39A51ASN00.0060.00319.5100.0170.0170.0000.0000.0000.000
40A52GLY0-0.027-0.00422.2660.0060.0060.0000.0000.0000.000
41A53LEU0-0.018-0.00719.6580.0190.0190.0000.0000.0000.000
42A54PRO00.008-0.00323.670-0.006-0.0060.0000.0000.0000.000
43A55THR00.003-0.00623.290-0.019-0.0190.0000.0000.0000.000
44A56LEU0-0.0130.01220.8450.0210.0210.0000.0000.0000.000
45A57ARG10.8510.92424.1820.1110.1110.0000.0000.0000.000
46A58LEU00.0060.02425.0190.0080.0080.0000.0000.0000.000
47A59ASN00.011-0.00627.521-0.004-0.0040.0000.0000.0000.000
48A60VAL0-0.0130.03531.3140.0080.0080.0000.0000.0000.000
49A61GLN0-0.025-0.03033.5430.0040.0040.0000.0000.0000.000
50A62THR0-0.057-0.04037.0480.0050.0050.0000.0000.0000.000
51A63THR00.0220.01137.866-0.002-0.0020.0000.0000.0000.000
52A64VAL00.0520.04138.370-0.002-0.0020.0000.0000.0000.000
53A65GLN0-0.054-0.01939.288-0.006-0.0060.0000.0000.0000.000
54A66SER0-0.019-0.05340.3060.0030.0030.0000.0000.0000.000
55A67GLY00.0040.03037.474-0.004-0.0040.0000.0000.0000.000
56A68TRP0-0.018-0.00931.111-0.007-0.0070.0000.0000.0000.000
57A69TRP00.0670.02226.5800.0060.0060.0000.0000.0000.000
58A70ILE0-0.021-0.01724.878-0.008-0.0080.0000.0000.0000.000
59A71SER0-0.008-0.01524.3470.0060.0060.0000.0000.0000.000
60A72LEU0-0.011-0.00521.718-0.020-0.0200.0000.0000.0000.000
61A73LEU00.0180.00818.6530.0200.0200.0000.0000.0000.000
62A74THR0-0.046-0.05017.711-0.025-0.0250.0000.0000.0000.000
63A75LEU00.0290.02210.820-0.012-0.0120.0000.0000.0000.000
64A76ARG10.9090.9429.4350.1870.1870.0000.0000.0000.000
65A77GLY00.0260.01415.4630.0360.0360.0000.0000.0000.000
66A78TRP0-0.008-0.01218.5520.0120.0120.0000.0000.0000.000
67A79ASN0-0.064-0.01616.3330.0060.0060.0000.0000.0000.000
68A80THR0-0.035-0.00314.762-0.025-0.0250.0000.0000.0000.000
69A81HIS0-0.006-0.0157.1410.1300.1300.0000.0000.0000.000
70A82ASP-1-0.818-0.8827.918-0.204-0.2040.0000.0000.0000.000
71A83LEU0-0.019-0.0176.003-0.063-0.0630.0000.0000.0000.000
72A84SER0-0.041-0.0516.468-0.170-0.1700.0000.0000.0000.000
73A85GLN0-0.027-0.0232.339-1.3100.1071.286-0.791-1.912-0.003
74A86TYR0-0.030-0.0263.106-3.784-0.0910.942-1.359-3.276-0.012
75A87VAL0-0.021-0.0074.165-0.112-0.0570.001-0.008-0.0480.000
76A88GLU-1-0.996-0.9986.313-0.815-0.8150.0000.0000.0000.000
77A89ASN0-0.055-0.0636.0940.4420.4420.0000.0000.0000.000
78A90GLY00.0450.0415.989-0.154-0.1540.0000.0000.0000.000
79A91TYR0-0.055-0.0426.4720.5600.5600.0000.0000.0000.000
80A92LEU0-0.001-0.0019.345-0.122-0.1220.0000.0000.0000.000
81A93GLU-1-0.856-0.8989.959-1.313-1.3130.0000.0000.0000.000
82A94PHE0-0.001-0.00813.2620.0340.0340.0000.0000.0000.000
83A95ASP-1-0.861-0.91816.512-0.442-0.4420.0000.0000.0000.000
84A96ILE0-0.030-0.03819.8170.0190.0190.0000.0000.0000.000
85A97LYS10.9330.98223.0290.1820.1820.0000.0000.0000.000
86A98GLY00.0660.03026.7890.0010.0010.0000.0000.0000.000
87A99LYS10.8670.93129.7880.1280.1280.0000.0000.0000.000
88A100GLU-1-1.020-1.01733.229-0.119-0.1190.0000.0000.0000.000
89A101GLY0-0.027-0.01031.3320.0010.0010.0000.0000.0000.000
90A102GLY0-0.056-0.03330.7920.0080.0080.0000.0000.0000.000
91A103GLU-1-0.789-0.91028.994-0.182-0.1820.0000.0000.0000.000
92A104ASP-1-0.790-0.90027.307-0.246-0.2460.0000.0000.0000.000
93A105PHE0-0.077-0.04723.0050.0160.0160.0000.0000.0000.000
94A106VAL0-0.022-0.00523.482-0.018-0.0180.0000.0000.0000.000
95A107ILE00.0180.00018.7370.0060.0060.0000.0000.0000.000
96A108GLY00.016-0.00317.594-0.008-0.0080.0000.0000.0000.000
97A109PHE0-0.0040.01012.730-0.018-0.0180.0000.0000.0000.000
98A110ARG10.8670.92316.6780.1990.1990.0000.0000.0000.000
99A111ASP-1-0.744-0.80416.022-0.209-0.2090.0000.0000.0000.000
100A112LYS10.9080.92017.3130.0920.0920.0000.0000.0000.000
101A113VAL00.0310.02218.0840.0090.0090.0000.0000.0000.000
102A114TYR00.0290.01220.656-0.004-0.0040.0000.0000.0000.000
103A115GLU-1-0.922-0.96022.011-0.024-0.0240.0000.0000.0000.000
104A116ARG10.7340.82518.9070.1510.1510.0000.0000.0000.000
105A117VAL0-0.002-0.02224.710-0.006-0.0060.0000.0000.0000.000
106A118TYR0-0.053-0.02323.552-0.001-0.0010.0000.0000.0000.000
107A119GLY00.0480.01425.385-0.007-0.0070.0000.0000.0000.000
108A120LEU0-0.0060.02123.804-0.005-0.0050.0000.0000.0000.000
109A121GLU-1-0.969-0.98221.502-0.123-0.1230.0000.0000.0000.000
110A122ILE0-0.042-0.01020.1390.0050.0050.0000.0000.0000.000
111A123ASP-1-0.761-0.86419.561-0.223-0.2230.0000.0000.0000.000
112A124VAL0-0.071-0.02915.8370.0120.0120.0000.0000.0000.000
113A125THR0-0.024-0.02418.464-0.026-0.0260.0000.0000.0000.000
114A126THR00.0320.01819.3950.0190.0190.0000.0000.0000.000
115A127VAL0-0.0060.00222.0010.0120.0120.0000.0000.0000.000
116A128ILE00.0230.00721.545-0.023-0.0230.0000.0000.0000.000
117A129SER0-0.001-0.02523.356-0.020-0.0200.0000.0000.0000.000
118A130ASN0-0.072-0.03022.8790.0220.0220.0000.0000.0000.000
119A131TYR0-0.121-0.09517.575-0.003-0.0030.0000.0000.0000.000
120A132VAL0-0.0100.00321.402-0.019-0.0190.0000.0000.0000.000
121A133THR0-0.0160.00123.7130.0190.0190.0000.0000.0000.000
122A134VAL00.0140.02225.488-0.003-0.0030.0000.0000.0000.000
123A135THR00.0540.04027.6560.0180.0180.0000.0000.0000.000
124A136THR0-0.005-0.00729.110-0.006-0.0060.0000.0000.0000.000
125A137ASP-1-0.970-0.97528.613-0.171-0.1710.0000.0000.0000.000
126A138TRP0-0.035-0.03222.891-0.009-0.0090.0000.0000.0000.000
127A139GLN0-0.017-0.00323.041-0.013-0.0130.0000.0000.0000.000
128A140HIS0-0.0070.00614.0460.0610.0610.0000.0000.0000.000
129A141VAL0-0.020-0.00417.9150.0030.0030.0000.0000.0000.000
130A142LYS10.9110.95811.2671.0691.0690.0000.0000.0000.000
131A143ILE0-0.015-0.00214.2810.0580.0580.0000.0000.0000.000
132A144PRO00.0250.02411.473-0.113-0.1130.0000.0000.0000.000
133A145LEU00.0470.0167.2800.1380.1380.0000.0000.0000.000
134A146ARG10.8520.93410.9080.8470.8470.0000.0000.0000.000
135A147ASP-1-0.834-0.89112.540-0.466-0.4660.0000.0000.0000.000
136A148LEU0-0.032-0.01414.6020.0580.0580.0000.0000.0000.000
137A149MET0-0.039-0.01910.3810.0480.0480.0000.0000.0000.000
138A150LYS10.9400.96812.4850.5040.5040.0000.0000.0000.000
139A151ILE00.0130.02415.5960.0390.0390.0000.0000.0000.000
140A152ASN0-0.044-0.00718.8850.0020.0020.0000.0000.0000.000
141A153ASN00.012-0.01920.2370.0370.0370.0000.0000.0000.000
142A154GLY00.0040.01120.4570.0170.0170.0000.0000.0000.000
143A155PHE0-0.057-0.03113.1410.0100.0100.0000.0000.0000.000
144A156ASP-1-0.787-0.87914.093-0.183-0.1830.0000.0000.0000.000
145A157PRO0-0.028-0.02810.211-0.007-0.0070.0000.0000.0000.000
146A158SER0-0.064-0.04210.006-0.047-0.0470.0000.0000.0000.000
147A159SER0-0.008-0.01011.2530.0720.0720.0000.0000.0000.000
148A160VAL00.0260.01111.6280.0120.0120.0000.0000.0000.000
149A161THR0-0.013-0.00413.6690.0060.0060.0000.0000.0000.000
150A162CYS0-0.064-0.03016.2430.0100.0100.0000.0000.0000.000
151A163LEU00.0510.04315.684-0.031-0.0310.0000.0000.0000.000
152A164VAL0-0.026-0.02217.1260.0430.0430.0000.0000.0000.000
153A165PHE00.0340.01619.848-0.021-0.0210.0000.0000.0000.000
154A166SER0-0.005-0.02023.3270.0180.0180.0000.0000.0000.000
155A167LYS10.9510.99626.5640.1220.1220.0000.0000.0000.000
156A168ARG10.9561.00528.4880.1730.1730.0000.0000.0000.000
157A169TYR0-0.020-0.02930.3400.0140.0140.0000.0000.0000.000
158A170ALA0-0.063-0.04333.687-0.002-0.0020.0000.0000.0000.000
159A171ASP-1-0.896-0.93635.801-0.119-0.1190.0000.0000.0000.000
160A172PRO0-0.020-0.01334.880-0.007-0.0070.0000.0000.0000.000
161A173PHE00.0200.00928.344-0.003-0.0030.0000.0000.0000.000
162A174THR0-0.047-0.04931.0040.0080.0080.0000.0000.0000.000
163A175VAL0-0.0030.00925.832-0.002-0.0020.0000.0000.0000.000
164A176TRP0-0.079-0.04725.9590.0110.0110.0000.0000.0000.000
165A177PHE00.0250.00719.975-0.014-0.0140.0000.0000.0000.000
166A178SER00.004-0.02820.2720.0290.0290.0000.0000.0000.000
167A179ASP-1-0.797-0.89114.784-0.619-0.6190.0000.0000.0000.000
168A180ILE0-0.0110.00614.596-0.075-0.0750.0000.0000.0000.000
169A181LYS10.9210.97410.0180.9510.9510.0000.0000.0000.000
170A182ILE0-0.028-0.0046.5380.0300.0300.0000.0000.0000.000
171A183THR00.001-0.0415.616-0.216-0.2160.0000.0000.0000.000
172A184SER00.046-0.0142.239-0.3080.7891.882-1.038-1.9410.002
173A185GLU-1-0.966-0.9563.063-6.564-5.1440.150-0.845-0.726-0.008
174A186ASP-1-0.866-0.8962.797-1.973-1.1930.162-0.209-0.734-0.001
175A187ASN0-0.036-0.0272.262-10.719-6.9572.514-2.869-3.406-0.031