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: 6YM2Z

Calculation Name: 3CEY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CEY

Chain ID: A

ChEMBL ID:

UniProt ID: Q969R5

Base Structure: X-ray

Registration Date: 2023-09-24

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 407
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7140079.785422
FMO2-HF: Nuclear repulsion 6972238.013928
FMO2-HF: Total energy -167841.771494
FMO2-MP2: Total energy -168319.23642


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:172:GLN)


Summations of interaction energy for fragment #1(A:172:GLN)
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.
-3.271.3391.505-2.039-4.0750.006
Interaction energy analysis for fragmet #1(A:172:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.034
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].
3A174ALA00.0430.0192.988-0.2431.8770.047-0.882-1.2840.002
4A175LEU0-0.072-0.0222.544-0.3122.0431.459-1.142-2.6720.004
5A176VAL00.0120.0014.423-1.672-1.538-0.001-0.015-0.1190.000
6A177LEU0-0.027-0.0295.4060.9870.9870.0000.0000.0000.000
7A178GLY00.0130.0278.2140.5180.5180.0000.0000.0000.000
8A179PHE0-0.006-0.0089.599-0.303-0.3030.0000.0000.0000.000
9A180ASP-1-0.744-0.8629.312-0.216-0.2160.0000.0000.0000.000
10A181TRP0-0.020-0.03711.3630.0310.0310.0000.0000.0000.000
11A182GLY0-0.022-0.03212.5220.0580.0580.0000.0000.0000.000
12A183LYS10.7830.86110.1400.5830.5830.0000.0000.0000.000
13A184PHE00.0570.03412.3870.0510.0510.0000.0000.0000.000
14A185LEU00.000-0.00615.3170.0410.0410.0000.0000.0000.000
15A186LYS10.8720.94515.186-0.232-0.2320.0000.0000.0000.000
16A187ASP-1-0.790-0.86814.269-0.351-0.3510.0000.0000.0000.000
17A188HIS0-0.047-0.03117.179-0.005-0.0050.0000.0000.0000.000
18A189SER0-0.052-0.01920.5560.0270.0270.0000.0000.0000.000
19A190TYR0-0.0050.00919.6900.0290.0290.0000.0000.0000.000
20A191LYS10.8580.93722.3900.1220.1220.0000.0000.0000.000
21A192ALA00.0290.00222.470-0.026-0.0260.0000.0000.0000.000
22A193ALA00.0280.01524.6240.0210.0210.0000.0000.0000.000
23A194PRO0-0.013-0.00525.859-0.002-0.0020.0000.0000.0000.000
24A195VAL00.0500.01225.561-0.011-0.0110.0000.0000.0000.000
25A196SER00.0170.00828.075-0.004-0.0040.0000.0000.0000.000
26A197CYS0-0.100-0.04130.5300.0030.0030.0000.0000.0000.000
27A198PHE00.0020.00427.574-0.009-0.0090.0000.0000.0000.000
28A199LYS10.8740.93031.4760.0430.0430.0000.0000.0000.000
29A200HIS0-0.048-0.02330.0830.0180.0180.0000.0000.0000.000
30A201VAL0-0.0240.00127.402-0.010-0.0100.0000.0000.0000.000
31A202PRO00.0680.02626.3520.0130.0130.0000.0000.0000.000
32A203LEU0-0.007-0.00824.666-0.003-0.0030.0000.0000.0000.000
33A204TYR00.0090.03228.9540.0090.0090.0000.0000.0000.000
34A205ASP-1-0.914-0.96531.3920.0110.0110.0000.0000.0000.000
35A206GLN0-0.105-0.06329.8120.0130.0130.0000.0000.0000.000
36A207TRP00.0540.01423.8590.0130.0130.0000.0000.0000.000
37A208GLU-1-0.928-0.97030.1720.0480.0480.0000.0000.0000.000
38A209ASP-1-0.934-0.96231.8820.1090.1090.0000.0000.0000.000
39A210VAL0-0.057-0.05125.8060.0180.0180.0000.0000.0000.000
40A211MET0-0.0010.02428.451-0.011-0.0110.0000.0000.0000.000
41A212LYS10.9280.93925.803-0.138-0.1380.0000.0000.0000.000
42A213GLY0-0.021-0.00926.751-0.008-0.0080.0000.0000.0000.000
43A214MET0-0.0470.01826.6940.0120.0120.0000.0000.0000.000
44A215LYS10.8480.92126.128-0.222-0.2220.0000.0000.0000.000
45A216VAL00.0380.02922.004-0.024-0.0240.0000.0000.0000.000
46A217GLU-1-0.778-0.86623.9140.3410.3410.0000.0000.0000.000
47A218VAL00.027-0.00218.419-0.023-0.0230.0000.0000.0000.000
48A219LEU00.0050.00014.635-0.003-0.0030.0000.0000.0000.000
49A220ASN0-0.036-0.01716.6690.1430.1430.0000.0000.0000.000
50A221SER00.0590.02111.5510.0190.0190.0000.0000.0000.000
51A222ASP-1-0.833-0.87212.8461.6491.6490.0000.0000.0000.000
52A223ALA00.0190.00314.605-0.195-0.1950.0000.0000.0000.000
53A224VAL0-0.009-0.02116.7300.0380.0380.0000.0000.0000.000
54A225LEU0-0.013-0.00318.952-0.060-0.0600.0000.0000.0000.000
55A226PRO00.0230.02117.2940.0700.0700.0000.0000.0000.000
56A227SER00.002-0.01318.337-0.072-0.0720.0000.0000.0000.000
57A228ARG10.8720.92716.323-0.545-0.5450.0000.0000.0000.000
58A229VAL00.0000.00719.556-0.077-0.0770.0000.0000.0000.000
59A230TYR00.0210.00919.6410.0670.0670.0000.0000.0000.000
60A231TRP0-0.055-0.03520.557-0.015-0.0150.0000.0000.0000.000
61A232ILE00.0370.02222.304-0.014-0.0140.0000.0000.0000.000
62A233ALA00.0070.00520.3340.0440.0440.0000.0000.0000.000
63A234SER00.0020.00422.322-0.055-0.0550.0000.0000.0000.000
64A235VAL00.0160.02222.3760.0320.0320.0000.0000.0000.000
65A236ILE0-0.037-0.01321.158-0.033-0.0330.0000.0000.0000.000
66A237GLN0-0.003-0.01120.082-0.001-0.0010.0000.0000.0000.000
67A238THR00.0330.01121.5940.0360.0360.0000.0000.0000.000
68A239ALA0-0.026-0.00819.917-0.018-0.0180.0000.0000.0000.000
69A240GLY00.0430.03320.936-0.014-0.0140.0000.0000.0000.000
70A241TYR0-0.005-0.03720.7140.0220.0220.0000.0000.0000.000
71A242ARG10.7600.88112.2210.1590.1590.0000.0000.0000.000
72A243VAL00.001-0.01018.605-0.009-0.0090.0000.0000.0000.000
73A244LEU0-0.028-0.00415.9950.0410.0410.0000.0000.0000.000
74A245LEU0-0.010-0.01017.408-0.041-0.0410.0000.0000.0000.000
75A246ARG10.8190.88017.588-0.318-0.3180.0000.0000.0000.000
76A247TYR00.0330.01014.557-0.119-0.1190.0000.0000.0000.000
77A248GLU-1-0.788-0.88920.4500.2940.2940.0000.0000.0000.000
78A249GLY00.0380.01823.4830.0350.0350.0000.0000.0000.000
79A250PHE00.0240.00517.3140.0070.0070.0000.0000.0000.000
80A251GLU-1-0.838-0.88422.7890.3080.3080.0000.0000.0000.000
81A252ASN00.0340.01724.606-0.003-0.0030.0000.0000.0000.000
82A253ASP-1-0.810-0.87119.4340.5610.5610.0000.0000.0000.000
83A254ALA00.0210.00118.8980.0080.0080.0000.0000.0000.000
84A255SER0-0.089-0.06915.8430.0960.0960.0000.0000.0000.000
85A256HIS10.8460.91213.299-1.130-1.1300.0000.0000.0000.000
86A257ASP-1-0.790-0.85714.7230.4570.4570.0000.0000.0000.000
87A258PHE0-0.025-0.01112.6020.0940.0940.0000.0000.0000.000
88A259TRP0-0.0090.00312.504-0.154-0.1540.0000.0000.0000.000
89A260CYS0-0.0330.00013.4740.0730.0730.0000.0000.0000.000
90A261ASN00.0300.00115.926-0.033-0.0330.0000.0000.0000.000
91A262LEU0-0.007-0.01417.9190.0300.0300.0000.0000.0000.000
92A263GLY00.0880.03820.370-0.001-0.0010.0000.0000.0000.000
93A264THR0-0.039-0.01215.737-0.015-0.0150.0000.0000.0000.000
94A265VAL00.0310.00819.1300.0110.0110.0000.0000.0000.000
95A266ASP-1-0.898-0.93917.0100.4840.4840.0000.0000.0000.000
96A267VAL00.0490.04319.1510.0540.0540.0000.0000.0000.000
97A268HIS10.7960.90021.340-0.341-0.3410.0000.0000.0000.000
98A269PRO00.0560.04224.9060.0120.0120.0000.0000.0000.000
99A270ILE0-0.004-0.02327.4050.0190.0190.0000.0000.0000.000
100A271GLY00.0100.00229.524-0.021-0.0210.0000.0000.0000.000
101A272TRP00.0250.01024.7430.0090.0090.0000.0000.0000.000
102A273CYS0-0.045-0.04725.9700.0070.0070.0000.0000.0000.000
103A274ALA0-0.032-0.00728.510-0.001-0.0010.0000.0000.0000.000
104A275ILE00.0090.00832.127-0.006-0.0060.0000.0000.0000.000
105A276ASN0-0.032-0.01128.569-0.012-0.0120.0000.0000.0000.000
106A277SER0-0.0060.01629.7370.0110.0110.0000.0000.0000.000
107A278LYS10.8240.90224.854-0.305-0.3050.0000.0000.0000.000
108A279ILE00.0220.00525.911-0.018-0.0180.0000.0000.0000.000
109A280LEU0-0.0030.00724.5530.0400.0400.0000.0000.0000.000
110A281VAL0-0.008-0.01922.221-0.026-0.0260.0000.0000.0000.000
111A282PRO00.0430.02821.7490.0460.0460.0000.0000.0000.000
112A283PRO0-0.004-0.00317.3640.0230.0230.0000.0000.0000.000
113A284ARG10.9760.98617.125-0.954-0.9540.0000.0000.0000.000
114A285THR0-0.064-0.04415.646-0.035-0.0350.0000.0000.0000.000
115A286ILE0-0.0030.00718.235-0.066-0.0660.0000.0000.0000.000
116A287HIS0-0.077-0.04721.562-0.095-0.0950.0000.0000.0000.000
117A288ALA00.0230.01123.709-0.039-0.0390.0000.0000.0000.000
118A289LYS10.7840.90525.207-0.400-0.4000.0000.0000.0000.000
119A290PHE0-0.011-0.01227.288-0.033-0.0330.0000.0000.0000.000
120A291THR00.0430.02029.5540.0090.0090.0000.0000.0000.000
121A292ASP-1-0.820-0.91532.0250.2350.2350.0000.0000.0000.000
122A293TRP00.0120.00024.979-0.006-0.0060.0000.0000.0000.000
123A294LYS10.9720.99230.313-0.220-0.2200.0000.0000.0000.000
124A295GLY00.0400.01032.538-0.008-0.0080.0000.0000.0000.000
125A296TYR0-0.084-0.06827.262-0.011-0.0110.0000.0000.0000.000
126A297LEU00.0240.00526.717-0.008-0.0080.0000.0000.0000.000
127A298MET0-0.028-0.02030.785-0.010-0.0100.0000.0000.0000.000
128A299LYS10.8670.93234.207-0.219-0.2190.0000.0000.0000.000
129A300ARG10.8430.90627.077-0.283-0.2830.0000.0000.0000.000
130A301LEU0-0.0010.00829.3540.0010.0010.0000.0000.0000.000
131A302VAL0-0.0050.01032.765-0.012-0.0120.0000.0000.0000.000
132A303GLY0-0.0020.00136.113-0.001-0.0010.0000.0000.0000.000
133A304SER0-0.080-0.03231.655-0.003-0.0030.0000.0000.0000.000
134A305ARG10.9890.98131.812-0.127-0.1270.0000.0000.0000.000
135A306THR0-0.011-0.02528.1330.0200.0200.0000.0000.0000.000
136A307LEU00.0230.01224.184-0.013-0.0130.0000.0000.0000.000
137A308PRO00.0350.02328.7590.0040.0040.0000.0000.0000.000
138A309VAL00.0330.01031.0610.0090.0090.0000.0000.0000.000
139A310ASP-1-0.831-0.91031.8560.0900.0900.0000.0000.0000.000
140A311PHE0-0.0190.01725.189-0.006-0.0060.0000.0000.0000.000
141A312HIS00.031-0.00322.476-0.010-0.0100.0000.0000.0000.000
142A313ILE00.0090.00627.300-0.011-0.0110.0000.0000.0000.000
143A314LYS10.8470.89130.306-0.095-0.0950.0000.0000.0000.000
144A315MET00.0010.03423.293-0.013-0.0130.0000.0000.0000.000
145A316VAL00.0230.02126.367-0.016-0.0160.0000.0000.0000.000
146A317GLU-1-0.837-0.90128.8900.0370.0370.0000.0000.0000.000
147A318SER0-0.079-0.05230.060-0.011-0.0110.0000.0000.0000.000
148A319MET0-0.011-0.00924.269-0.008-0.0080.0000.0000.0000.000
149A320LYS10.7740.88830.106-0.050-0.0500.0000.0000.0000.000
150A321TYR00.0520.01728.623-0.003-0.0030.0000.0000.0000.000
151A322PRO00.0060.01233.9960.0020.0020.0000.0000.0000.000
152A323PHE00.0430.00635.7280.0010.0010.0000.0000.0000.000
153A324ARG10.8460.89134.6770.0230.0230.0000.0000.0000.000
154A325GLN00.006-0.00832.8980.0050.0050.0000.0000.0000.000
155A326GLY00.0080.00636.0180.0080.0080.0000.0000.0000.000
156A327MET0-0.066-0.00439.2460.0020.0020.0000.0000.0000.000
157A328ARG10.8090.87240.4000.0490.0490.0000.0000.0000.000
158A329LEU0-0.052-0.03139.0820.0050.0050.0000.0000.0000.000
159A330GLU-1-0.732-0.83243.449-0.062-0.0620.0000.0000.0000.000
160A331VAL0-0.0020.00438.9750.0010.0010.0000.0000.0000.000
161A332VAL00.0200.00141.1990.0020.0020.0000.0000.0000.000
162A333ASP-1-0.758-0.85541.480-0.117-0.1170.0000.0000.0000.000
163A334LYS10.8810.93735.5360.1600.1600.0000.0000.0000.000
164A335SER0-0.042-0.02840.533-0.002-0.0020.0000.0000.0000.000
165A336GLN0-0.044-0.03842.7830.0020.0020.0000.0000.0000.000
166A337VAL00.0360.02242.1020.0060.0060.0000.0000.0000.000
167A338SER00.0040.02745.0560.0030.0030.0000.0000.0000.000
168A339ARG10.7480.87145.9250.1020.1020.0000.0000.0000.000
169A340THR0-0.002-0.02745.682-0.005-0.0050.0000.0000.0000.000
170A341ARG10.8090.90340.6240.1180.1180.0000.0000.0000.000
171A342MET00.0050.01444.1620.0000.0000.0000.0000.0000.000
172A343ALA00.0080.01339.656-0.005-0.0050.0000.0000.0000.000
173A344VAL00.0100.00339.3160.0090.0090.0000.0000.0000.000
174A345VAL0-0.019-0.00434.778-0.009-0.0090.0000.0000.0000.000
175A346ASP-1-0.810-0.88031.611-0.124-0.1240.0000.0000.0000.000
176A347THR00.010-0.01327.4440.0060.0060.0000.0000.0000.000
177A348VAL0-0.055-0.03229.873-0.001-0.0010.0000.0000.0000.000
178A349ILE0-0.0020.00322.5260.0090.0090.0000.0000.0000.000
179A350GLY00.0420.01626.093-0.010-0.0100.0000.0000.0000.000
180A351GLY0-0.0120.00226.9750.0000.0000.0000.0000.0000.000
181A352ARG10.7790.87626.3970.1840.1840.0000.0000.0000.000
182A353LEU0-0.038-0.02329.9940.0110.0110.0000.0000.0000.000
183A354ARG10.8500.92229.2750.1560.1560.0000.0000.0000.000
184A355LEU0-0.042-0.03731.9920.0160.0160.0000.0000.0000.000
185A356LEU00.0470.03434.180-0.010-0.0100.0000.0000.0000.000
186A357TYR00.009-0.01437.4370.0080.0080.0000.0000.0000.000
187A358GLU-1-0.839-0.92540.933-0.065-0.0650.0000.0000.0000.000
188A359ASP-1-0.855-0.91043.902-0.085-0.0850.0000.0000.0000.000
189A360GLY0-0.055-0.04541.145-0.003-0.0030.0000.0000.0000.000
190A361ASP-1-0.862-0.93238.022-0.108-0.1080.0000.0000.0000.000
191A362SER0-0.027-0.01836.634-0.004-0.0040.0000.0000.0000.000
192A363ASP-1-0.975-0.98233.470-0.191-0.1910.0000.0000.0000.000
193A364ASP-1-0.831-0.89333.838-0.158-0.1580.0000.0000.0000.000
194A365ASP-1-0.812-0.89031.031-0.188-0.1880.0000.0000.0000.000
195A366PHE0-0.004-0.02233.904-0.003-0.0030.0000.0000.0000.000
196A367TRP00.0320.01026.2560.0040.0040.0000.0000.0000.000
197A368CYS0-0.046-0.01932.1370.0010.0010.0000.0000.0000.000
198A369HIS00.0730.04430.4370.0040.0040.0000.0000.0000.000
199A370MET0-0.0050.00432.8220.0080.0080.0000.0000.0000.000
200A371TRP0-0.031-0.04235.4160.0090.0090.0000.0000.0000.000
201A372SER00.0280.02935.5310.0030.0030.0000.0000.0000.000
202A373PRO0-0.009-0.01037.4450.0040.0040.0000.0000.0000.000
203A374LEU00.0410.02136.8800.0050.0050.0000.0000.0000.000
204A375ILE0-0.0170.00137.5680.0010.0010.0000.0000.0000.000
205A376HIS10.8470.92041.2890.0800.0800.0000.0000.0000.000
206A377PRO00.0000.02244.499-0.001-0.0010.0000.0000.0000.000
207A378VAL00.0400.01046.337-0.001-0.0010.0000.0000.0000.000
208A379GLY0-0.033-0.02048.6780.0040.0040.0000.0000.0000.000
209A380TRP0-0.048-0.01847.9180.0020.0020.0000.0000.0000.000
210A381SER00.000-0.02449.2260.0000.0000.0000.0000.0000.000
211A382ARG10.9250.94451.4590.0520.0520.0000.0000.0000.000
212A383ARG10.8380.92750.9630.0430.0430.0000.0000.0000.000
213A384VAL0-0.035-0.02051.5320.0010.0010.0000.0000.0000.000
214A385GLY00.0540.02954.8130.0000.0000.0000.0000.0000.000
215A386HIS0-0.015-0.02147.991-0.002-0.0020.0000.0000.0000.000
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