FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 4936N

Calculation Name: 3CGU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CGU

Chain ID: A

ChEMBL ID:

UniProt ID: Q00805

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2375081.244353
FMO2-HF: Nuclear repulsion 2288419.891774
FMO2-HF: Total energy -86661.352579
FMO2-MP2: Total energy -86902.120457


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:98:ARG)


Summations of interaction energy for fragment #1(A:98:ARG)
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.
16.80518.762-0.013-0.978-0.9660.004
Interaction energy analysis for fragmet #1(A:98:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.977
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].
3A100VAL0-0.044-0.0183.8382.1014.058-0.013-0.978-0.9660.004
4A101ARG10.9550.9875.98519.85619.8560.0000.0000.0000.000
5A102ILE00.002-0.0056.4942.0902.0900.0000.0000.0000.000
6A103LEU0-0.0020.0068.7760.0700.0700.0000.0000.0000.000
7A104TYR00.001-0.01310.382-0.665-0.6650.0000.0000.0000.000
8A105GLN00.0100.01815.0520.5930.5930.0000.0000.0000.000
9A106VAL0-0.027-0.02518.2340.6490.6490.0000.0000.0000.000
10A107GLY0-0.0170.00518.002-0.399-0.3990.0000.0000.0000.000
11A108ASP-1-0.999-1.01113.845-15.762-15.7620.0000.0000.0000.000
12A109SER00.033-0.00112.638-1.219-1.2190.0000.0000.0000.000
13A110GLU-1-0.862-0.95412.510-18.267-18.2670.0000.0000.0000.000
14A111GLU-1-0.961-0.98715.273-12.506-12.5060.0000.0000.0000.000
15A112ASP-1-0.811-0.87017.640-13.272-13.2720.0000.0000.0000.000
16A113LEU0-0.104-0.03616.1340.4840.4840.0000.0000.0000.000
17A114PRO00.0420.02119.7930.2680.2680.0000.0000.0000.000
18A115VAL0-0.040-0.03022.025-0.545-0.5450.0000.0000.0000.000
19A116CYS00.0150.03218.8390.6310.6310.0000.0000.0000.000
20A117ALA00.0470.04024.8310.2330.2330.0000.0000.0000.000
21A118PRO0-0.013-0.04027.235-0.321-0.3210.0000.0000.0000.000
22A119ASN0-0.046-0.02027.821-0.080-0.0800.0000.0000.0000.000
23A120ALA00.0840.05925.3540.1670.1670.0000.0000.0000.000
24A121VAL0-0.058-0.03520.799-0.372-0.3720.0000.0000.0000.000
25A122CYS00.018-0.00315.4520.4060.4060.0000.0000.0000.000
26A123SER00.0300.01714.969-0.433-0.4330.0000.0000.0000.000
27A124LYS10.9280.98116.82713.18713.1870.0000.0000.0000.000
28A125ILE00.0050.01114.060-0.578-0.5780.0000.0000.0000.000
29A126ASP-1-0.886-0.93515.702-13.847-13.8470.0000.0000.0000.000
30A127LEU0-0.021-0.04014.744-1.098-1.0980.0000.0000.0000.000
31A128TYR0-0.031-0.00417.0440.3520.3520.0000.0000.0000.000
32A129GLU-1-0.856-0.92817.026-14.158-14.1580.0000.0000.0000.000
33A130THR0-0.084-0.04410.978-0.936-0.9360.0000.0000.0000.000
34A131PRO0-0.011-0.01311.3980.3930.3930.0000.0000.0000.000
35A132TRP00.0120.00110.885-1.925-1.9250.0000.0000.0000.000
36A133ILE0-0.017-0.0139.6611.5441.5440.0000.0000.0000.000
37A134GLU-1-0.864-0.93911.974-15.088-15.0880.0000.0000.0000.000
38A135ARG10.7630.87912.37518.47818.4780.0000.0000.0000.000
39A136GLN0-0.064-0.04615.2711.0511.0510.0000.0000.0000.000
40A138ARG10.9760.99617.75412.41212.4120.0000.0000.0000.000
41A139CYS00.036-0.00219.5210.0880.0880.0000.0000.0000.000
42A140PRO00.0450.04321.555-0.100-0.1000.0000.0000.0000.000
43A141ASP-1-0.922-0.92022.153-13.192-13.1920.0000.0000.0000.000
44A142GLY00.004-0.04824.2520.5290.5290.0000.0000.0000.000
45A143ARG10.8460.91921.99711.98711.9870.0000.0000.0000.000
46A144THR00.0860.03816.048-0.085-0.0850.0000.0000.0000.000
47A261PRO0-0.0220.00514.673-1.226-1.2260.0000.0000.0000.000
48A262SER00.045-0.00110.5150.1280.1280.0000.0000.0000.000
49A263SER0-0.0180.00811.853-1.416-1.4160.0000.0000.0000.000
50A264LEU00.0850.03810.5361.2371.2370.0000.0000.0000.000
51A265GLY0-0.023-0.00314.3841.1221.1220.0000.0000.0000.000
52A266VAL0-0.030-0.04717.3570.0800.0800.0000.0000.0000.000
53A267GLU-1-0.903-0.95818.686-13.573-13.5730.0000.0000.0000.000
54A268ASP-1-0.814-0.90017.817-16.039-16.0390.0000.0000.0000.000
55A269GLY00.0440.03519.8730.4180.4180.0000.0000.0000.000
56A270HIS0-0.108-0.05620.1430.7820.7820.0000.0000.0000.000
57A271THR0-0.0270.00519.676-0.396-0.3960.0000.0000.0000.000
58A272ILE0-0.019-0.00621.8100.5500.5500.0000.0000.0000.000
59A273ALA0-0.009-0.00322.988-0.388-0.3880.0000.0000.0000.000
60A274ASP-1-0.826-0.93723.699-10.454-10.4540.0000.0000.0000.000
61A275LYS10.8600.94024.75710.26210.2620.0000.0000.0000.000
62A276THR00.040-0.00321.014-0.186-0.1860.0000.0000.0000.000
63A277ARG10.8960.99020.15412.24212.2420.0000.0000.0000.000
64A278HIS10.8080.91518.11015.94915.9490.0000.0000.0000.000
65A279TYR00.0480.02819.390-0.344-0.3440.0000.0000.0000.000
66A280LYS10.8260.92515.85918.10318.1030.0000.0000.0000.000
67A281MET00.0290.01219.7330.3410.3410.0000.0000.0000.000
68A283GLN0-0.025-0.02022.437-0.221-0.2210.0000.0000.0000.000
69A284PRO00.0260.01124.926-0.096-0.0960.0000.0000.0000.000
70A285VAL00.0430.01024.7000.5250.5250.0000.0000.0000.000
71A286HIS0-0.025-0.02927.2820.5470.5470.0000.0000.0000.000
72A287LYS10.9030.96629.52410.65410.6540.0000.0000.0000.000
73A288LEU00.0130.03228.5230.2880.2880.0000.0000.0000.000
74A289PRO00.0430.03532.448-0.031-0.0310.0000.0000.0000.000
75A290VAL0-0.0010.00034.495-0.198-0.1980.0000.0000.0000.000
76A291CYS0-0.086-0.04532.7240.4480.4480.0000.0000.0000.000
77A292LYS10.9170.94337.8137.5467.5460.0000.0000.0000.000
78A293HIS00.0240.03541.2770.2230.2230.0000.0000.0000.000
79A294PHE0-0.023-0.02641.897-0.176-0.1760.0000.0000.0000.000
80A295ARG10.8220.91939.5187.6627.6620.0000.0000.0000.000
81A296ASP-1-0.782-0.87038.933-7.462-7.4620.0000.0000.0000.000
82A297TYR0-0.055-0.05235.708-0.137-0.1370.0000.0000.0000.000
83A298THR0-0.028-0.02531.316-0.123-0.1230.0000.0000.0000.000
84A299TRP00.031-0.00227.434-0.272-0.2720.0000.0000.0000.000
85A300THR0-0.063-0.02131.2510.2440.2440.0000.0000.0000.000
86A301LEU0-0.015-0.00125.788-0.187-0.1870.0000.0000.0000.000
87A302THR00.006-0.00229.4710.4330.4330.0000.0000.0000.000
88A303THR0-0.0040.00229.140-0.231-0.2310.0000.0000.0000.000
89A304ALA00.0730.01330.2850.3100.3100.0000.0000.0000.000
90A305ALA0-0.020-0.00731.265-0.157-0.1570.0000.0000.0000.000
91A306GLU-1-0.935-0.96832.283-8.053-8.0530.0000.0000.0000.000
92A307LEU0-0.025-0.00328.460-0.132-0.1320.0000.0000.0000.000
93A308ASN0-0.022-0.00424.586-0.082-0.0820.0000.0000.0000.000
94A309VAL00.0700.03822.868-0.406-0.4060.0000.0000.0000.000
95A310THR0-0.090-0.03624.1570.4630.4630.0000.0000.0000.000
96A311GLU-1-0.870-0.93624.660-10.768-10.7680.0000.0000.0000.000
97A312GLN0-0.028-0.01824.9810.2250.2250.0000.0000.0000.000
98A313ILE00.0190.01426.564-0.310-0.3100.0000.0000.0000.000
99A314VAL0-0.027-0.04226.7960.2150.2150.0000.0000.0000.000
100A315HIS0-0.001-0.00229.7970.1090.1090.0000.0000.0000.000
101A317ARG10.9160.95729.3169.6449.6440.0000.0000.0000.000
102A318CYS00.0460.02531.9900.1170.1170.0000.0000.0000.000
103A319PRO00.0070.00232.917-0.220-0.2200.0000.0000.0000.000
104A320ARG10.9870.98431.8699.3649.3640.0000.0000.0000.000
105A321ASN0-0.016-0.02532.1200.1820.1820.0000.0000.0000.000
106A322SER0-0.0420.02633.0530.2220.2220.0000.0000.0000.000
107A323VAL00.0550.01330.310-0.295-0.2950.0000.0000.0000.000
108A324THR0-0.013-0.00929.2470.3810.3810.0000.0000.0000.000
109A325TYR0-0.045-0.04731.878-0.017-0.0170.0000.0000.0000.000
110A326LEU00.0420.02931.8240.0840.0840.0000.0000.0000.000
111A327THR0-0.091-0.05234.0780.2580.2580.0000.0000.0000.000
112A328LYS10.9700.98136.9737.2497.2490.0000.0000.0000.000
113A329ARG10.9491.00135.5757.5827.5820.0000.0000.0000.000
114A330GLU-1-0.956-0.97237.634-7.279-7.2790.0000.0000.0000.000
115A331PRO00.0400.01238.018-0.214-0.2140.0000.0000.0000.000
116A332ILE0-0.0400.00934.3330.0390.0390.0000.0000.0000.000
117A333GLY0-0.019-0.03138.0330.0300.0300.0000.0000.0000.000
118A334ASN0-0.0340.00341.443-0.094-0.0940.0000.0000.0000.000
119A335ASP-1-0.908-0.95939.920-7.182-7.1820.0000.0000.0000.000
120A336SER00.0120.00636.333-0.146-0.1460.0000.0000.0000.000
121A337PRO00.0390.03237.3670.0580.0580.0000.0000.0000.000
122A338GLY00.0490.00635.221-0.241-0.2410.0000.0000.0000.000
123A339TYR0-0.045-0.03534.4640.2080.2080.0000.0000.0000.000
124A340ARG10.9370.97833.7557.7447.7440.0000.0000.0000.000
125A341TYR00.003-0.00531.5090.2990.2990.0000.0000.0000.000
126A342LEU00.0160.00932.900-0.226-0.2260.0000.0000.0000.000
127A343PHE00.0290.01729.7840.0920.0920.0000.0000.0000.000
128A344ALA00.0310.01333.7640.0960.0960.0000.0000.0000.000
129A346SER00.0070.00835.6980.2130.2130.0000.0000.0000.000
130A347PRO0-0.052-0.02937.663-0.057-0.0570.0000.0000.0000.000
131A348LEU00.0620.03939.730-0.046-0.0460.0000.0000.0000.000
132A349THR0-0.0150.00240.8760.0630.0630.0000.0000.0000.000
133A350ARG10.9730.98544.5416.6236.6230.0000.0000.0000.000
134A351LEU00.0600.01846.2940.1540.1540.0000.0000.0000.000
135A352ARG10.9170.95449.2295.7925.7920.0000.0000.0000.000
136A353CYS0-0.0140.02142.860-0.007-0.0070.0000.0000.0000.000
137A354GLN00.0690.03250.8990.1350.1350.0000.0000.0000.000
138A355ARG11.0251.00251.6565.3555.3550.0000.0000.0000.000
139A356LYS10.9510.97049.3616.0726.0720.0000.0000.0000.000
140A357GLN0-0.005-0.00646.915-0.140-0.1400.0000.0000.0000.000
141A358PRO00.0270.01943.6170.0870.0870.0000.0000.0000.000
142A359CYS00.012-0.00645.537-0.042-0.0420.0000.0000.0000.000
143A360LYS10.9130.95741.5377.0607.0600.0000.0000.0000.000
144A361LEU00.0110.01538.0000.0990.0990.0000.0000.0000.000
145A362PHE0-0.021-0.00637.442-0.131-0.1310.0000.0000.0000.000
146A363THR0-0.027-0.02331.5060.0080.0080.0000.0000.0000.000
147A364VAL00.0090.01333.088-0.142-0.1420.0000.0000.0000.000
148A365ARG10.9570.97726.41410.59910.5990.0000.0000.0000.000
149A366LYS10.9900.99628.8969.1589.1580.0000.0000.0000.000
150A367ARG10.8240.92322.29011.78711.7870.0000.0000.0000.000
151A368GLN00.007-0.00523.513-0.222-0.2220.0000.0000.0000.000
152A369GLU-1-0.951-0.95925.965-9.451-9.4510.0000.0000.0000.000
153A370PHE0-0.017-0.01328.3220.3500.3500.0000.0000.0000.000
154A371LEU0-0.0160.00325.3350.0520.0520.0000.0000.0000.000
155A372ASP-1-0.872-0.93328.601-9.257-9.2570.0000.0000.0000.000
156A373GLU-1-0.856-0.92826.614-10.980-10.9800.0000.0000.0000.000
157A374VAL00.004-0.00730.3440.0610.0610.0000.0000.0000.000
158A375ASN0-0.089-0.03829.560-0.017-0.0170.0000.0000.0000.000
159A376ILE00.0230.00333.4460.2280.2280.0000.0000.0000.000
160A377ASN0-0.0040.00134.3240.0390.0390.0000.0000.0000.000
161A378SER00.007-0.01238.1440.2530.2530.0000.0000.0000.000
162A379LEU0-0.060-0.01939.639-0.062-0.0620.0000.0000.0000.000
163A381GLN0-0.065-0.02446.518-0.073-0.0730.0000.0000.0000.000
164A382CYS0-0.016-0.01748.7800.0740.0740.0000.0000.0000.000
165A383PRO0-0.009-0.00951.8470.0290.0290.0000.0000.0000.000
166A384LYS10.9790.97555.5345.5775.5770.0000.0000.0000.000
167A385GLY00.0620.03358.1620.0410.0410.0000.0000.0000.000
168A386HIS0-0.037-0.01654.5860.0290.0290.0000.0000.0000.000
169A387ARG10.9060.96651.7745.6815.6810.0000.0000.0000.000
170A389PRO00.0190.02246.202-0.020-0.0200.0000.0000.0000.000
171A390SER0-0.069-0.04144.670-0.141-0.1410.0000.0000.0000.000
172A391HIS00.0500.02541.944-0.291-0.2910.0000.0000.0000.000
173A392HIS00.0430.00737.8940.1190.1190.0000.0000.0000.000
174A393THR00.0120.01642.1110.0460.0460.0000.0000.0000.000
175A394GLN00.0070.01544.4410.0470.0470.0000.0000.0000.000
176A395SER00.0360.01547.389-0.059-0.0590.0000.0000.0000.000
177A396GLY00.036-0.00249.9780.0060.0060.0000.0000.0000.000
178A397VAL0-0.038-0.03043.403-0.076-0.0760.0000.0000.0000.000
179A398ILE0-0.0260.00544.0830.0680.0680.0000.0000.0000.000
180A399ALA00.010-0.01040.927-0.139-0.1390.0000.0000.0000.000
181A400GLY0-0.039-0.02040.0850.1290.1290.0000.0000.0000.000
182A401GLU-1-0.903-0.95535.969-7.596-7.5960.0000.0000.0000.000
183A402SER0-0.021-0.03734.751-0.066-0.0660.0000.0000.0000.000
184A403PHE0-0.010-0.01027.0630.0320.0320.0000.0000.0000.000
185A404LEU00.0790.00829.906-0.209-0.2090.0000.0000.0000.000
186A405GLU-1-0.960-0.95123.021-12.037-12.0370.0000.0000.0000.000
187A406ASP-1-0.814-0.89923.786-11.960-11.9600.0000.0000.0000.000
188A407ASN0-0.043-0.02725.7440.3300.3300.0000.0000.0000.000
189A408ILE0-0.060-0.03128.0670.1310.1310.0000.0000.0000.000
190A409GLN00.0380.04630.5910.1210.1210.0000.0000.0000.000
191A410THR0-0.058-0.03634.3950.0630.0630.0000.0000.0000.000
192A411TYR00.0370.02436.6860.1490.1490.0000.0000.0000.000
193A412SER00.0130.00340.249-0.146-0.1460.0000.0000.0000.000
194A413GLY00.0160.01842.7590.1300.1300.0000.0000.0000.000
195A414TYR0-0.033-0.03045.499-0.048-0.0480.0000.0000.0000.000
196A416MET00.0590.03651.5290.0540.0540.0000.0000.0000.000
197A417ALA00.0220.00253.798-0.004-0.0040.0000.0000.0000.000
198A418ASN0-0.036-0.03156.763-0.113-0.1130.0000.0000.0000.000
199A419ASP-1-0.931-0.93757.369-5.205-5.2050.0000.0000.0000.000