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: GYNZ1

Calculation Name: 3KB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q6ZMU5

Base Structure: X-ray

Registration Date: 2023-09-26

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2186834.525659
FMO2-HF: Nuclear repulsion 2112070.22849
FMO2-HF: Total energy -74764.29717
FMO2-MP2: Total energy -74985.730475


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:278:ARG)


Summations of interaction energy for fragment #1(A:278: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.
-150.902-148.42631.982-15.798-18.656-0.156
Interaction energy analysis for fragmet #1(A:278:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.887 / q_NPA : 0.910
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].
3A280MET00.0150.0103.227-0.3261.7020.002-0.907-1.1230.001
4A281PHE00.0070.0002.3280.3631.6810.979-0.937-1.360-0.005
5A282ARG10.8150.8994.69131.50731.660-0.001-0.023-0.1280.000
6A283ALA0-0.016-0.0096.7422.1902.1900.0000.0000.0000.000
7A284LEU0-0.029-0.0087.4141.5951.5950.0000.0000.0000.000
8A285MET0-0.0510.0028.1940.8290.8290.0000.0000.0000.000
9A286PRO00.0190.01611.2940.5450.5450.0000.0000.0000.000
10A287ALA0-0.008-0.01914.606-0.627-0.6270.0000.0000.0000.000
11A288LEU0-0.055-0.02214.3980.0610.0610.0000.0000.0000.000
12A289GLU-1-0.827-0.90517.061-12.774-12.7740.0000.0000.0000.000
13A290GLU-1-0.974-0.97419.888-11.131-11.1310.0000.0000.0000.000
14A291LEU0-0.044-0.03220.3750.2690.2690.0000.0000.0000.000
15A292THR0-0.031-0.02923.902-0.105-0.1050.0000.0000.0000.000
16A293PHE0-0.030-0.01022.8790.1940.1940.0000.0000.0000.000
17A294ASP-1-0.741-0.85427.869-8.892-8.8920.0000.0000.0000.000
18A295PRO0-0.028-0.03631.4180.0120.0120.0000.0000.0000.000
19A296SER0-0.075-0.04433.9830.1790.1790.0000.0000.0000.000
20A297SER00.0270.00632.2100.0770.0770.0000.0000.0000.000
21A298ALA0-0.020-0.00832.012-0.141-0.1410.0000.0000.0000.000
22A299HIS00.0390.05432.5700.2540.2540.0000.0000.0000.000
23A300PRO00.0060.00534.489-0.096-0.0960.0000.0000.0000.000
24A301SER0-0.081-0.04733.9310.0280.0280.0000.0000.0000.000
25A302LEU0-0.045-0.02429.919-0.173-0.1730.0000.0000.0000.000
26A303VAL0-0.012-0.00232.4660.3550.3550.0000.0000.0000.000
27A304VAL00.0060.00829.421-0.390-0.3900.0000.0000.0000.000
28A305SER00.020-0.00329.6780.2680.2680.0000.0000.0000.000
29A306SER0-0.004-0.01527.068-0.273-0.2730.0000.0000.0000.000
30A307SER0-0.023-0.01827.671-0.403-0.4030.0000.0000.0000.000
31A308GLY00.0750.04328.7610.0190.0190.0000.0000.0000.000
32A309ARG10.9520.98423.58711.63711.6370.0000.0000.0000.000
33A310ARG10.8060.89923.82410.96910.9690.0000.0000.0000.000
34A311VAL00.0200.01725.5010.5320.5320.0000.0000.0000.000
35A312GLU-1-0.780-0.87026.770-11.670-11.6700.0000.0000.0000.000
36A313CYS00.0230.01829.0380.2340.2340.0000.0000.0000.000
37A314SER0-0.0010.01331.6020.1430.1430.0000.0000.0000.000
38A315GLU-1-0.848-0.94133.928-9.042-9.0420.0000.0000.0000.000
39A316GLN0-0.063-0.02935.9200.3550.3550.0000.0000.0000.000
40A317LYS10.9160.93039.6777.4387.4380.0000.0000.0000.000
41A318ALA00.0200.02338.4270.0380.0380.0000.0000.0000.000
42A319PRO00.0030.02439.6970.1750.1750.0000.0000.0000.000
43A320PRO0-0.016-0.01441.335-0.157-0.1570.0000.0000.0000.000
44A321ALA00.0100.00239.945-0.080-0.0800.0000.0000.0000.000
45A322GLY00.0190.01541.2330.2240.2240.0000.0000.0000.000
46A323GLU-1-0.914-0.97042.211-7.322-7.3220.0000.0000.0000.000
47A324ASP-1-0.811-0.88039.506-8.026-8.0260.0000.0000.0000.000
48A325PRO0-0.013-0.00939.628-0.189-0.1890.0000.0000.0000.000
49A326ARG10.8180.87134.9238.3848.3840.0000.0000.0000.000
50A327GLN0-0.0140.00634.888-0.102-0.1020.0000.0000.0000.000
51A328PHE00.0210.02430.1200.1550.1550.0000.0000.0000.000
52A329ASP-1-0.731-0.86435.131-8.314-8.3140.0000.0000.0000.000
53A330LYS10.7060.83335.9268.4538.4530.0000.0000.0000.000
54A331ALA00.0650.04930.549-0.124-0.1240.0000.0000.0000.000
55A332VAL0-0.018-0.00429.6380.2470.2470.0000.0000.0000.000
56A333ALA00.0090.00528.288-0.436-0.4360.0000.0000.0000.000
57A334VAL0-0.007-0.00226.8880.4940.4940.0000.0000.0000.000
58A335VAL00.0080.00626.659-0.433-0.4330.0000.0000.0000.000
59A336ALA00.0210.00924.6600.1940.1940.0000.0000.0000.000
60A337HIS00.0030.00726.8030.0580.0580.0000.0000.0000.000
61A338GLN00.0390.02125.4550.1540.1540.0000.0000.0000.000
62A339GLN00.0240.02926.009-0.286-0.2860.0000.0000.0000.000
63A340LEU0-0.026-0.01021.522-0.073-0.0730.0000.0000.0000.000
64A341SER0-0.003-0.05325.6510.1410.1410.0000.0000.0000.000
65A342GLU-1-0.799-0.84825.021-9.850-9.8500.0000.0000.0000.000
66A343GLY00.0410.04022.393-0.097-0.0970.0000.0000.0000.000
67A344GLU-1-0.921-0.97016.846-13.082-13.0820.0000.0000.0000.000
68A345HIS10.7900.86217.32813.25813.2580.0000.0000.0000.000
69A346TYR00.018-0.03910.353-1.499-1.4990.0000.0000.0000.000
70A347TRP00.0170.02315.1020.6930.6930.0000.0000.0000.000
71A348GLU-1-0.749-0.84411.120-24.203-24.2030.0000.0000.0000.000
72A349VAL0-0.017-0.01014.8351.3541.3540.0000.0000.0000.000
73A350ASP-1-0.792-0.85415.572-20.480-20.4800.0000.0000.0000.000
74A351VAL0-0.026-0.02915.2271.0691.0690.0000.0000.0000.000
75A352GLY00.0040.00616.2630.7730.7730.0000.0000.0000.000
76A353ASP-1-0.864-0.94216.060-16.066-16.0660.0000.0000.0000.000
77A354LYS10.7940.93218.04713.58413.5840.0000.0000.0000.000
78A355PRO0-0.040-0.01819.029-0.851-0.8510.0000.0000.0000.000
79A356ARG10.8040.85720.29512.04612.0460.0000.0000.0000.000
80A357TRP00.0840.04215.0390.2920.2920.0000.0000.0000.000
81A358ALA0-0.001-0.00820.880-0.475-0.4750.0000.0000.0000.000
82A359LEU00.0030.00716.9410.5180.5180.0000.0000.0000.000
83A360GLY00.0440.01119.052-0.665-0.6650.0000.0000.0000.000
84A361VAL0-0.0200.00520.0720.1960.1960.0000.0000.0000.000
85A362ILE0-0.0170.00122.862-0.029-0.0290.0000.0000.0000.000
86A363ALA00.0260.00126.5950.0140.0140.0000.0000.0000.000
87A364ALA0-0.038-0.02628.7740.0910.0910.0000.0000.0000.000
88A365GLU-1-0.922-0.96231.596-8.530-8.5300.0000.0000.0000.000
89A366ALA0-0.0370.00330.6900.1300.1300.0000.0000.0000.000
90A367PRO0-0.0110.00032.8270.1680.1680.0000.0000.0000.000
91A368ARG10.9430.95731.3729.3839.3830.0000.0000.0000.000
92A369ARG10.8090.90134.7977.9997.9990.0000.0000.0000.000
93A370GLY00.0040.00037.8890.0410.0410.0000.0000.0000.000
94A371ARG10.8910.92534.4968.6508.6500.0000.0000.0000.000
95A372LEU00.0130.02631.4670.0680.0680.0000.0000.0000.000
96A373HIS0-0.001-0.00531.158-0.256-0.2560.0000.0000.0000.000
97A374ALA0-0.0070.00225.554-0.014-0.0140.0000.0000.0000.000
98A375VAL00.002-0.00426.232-0.348-0.3480.0000.0000.0000.000
99A376PRO00.0360.01423.9700.2920.2920.0000.0000.0000.000
100A377SER0-0.080-0.06126.5580.3320.3320.0000.0000.0000.000
101A378GLN0-0.064-0.03429.9190.5420.5420.0000.0000.0000.000
102A379GLY00.0030.01328.5490.1710.1710.0000.0000.0000.000
103A380LEU0-0.010-0.01425.989-0.120-0.1200.0000.0000.0000.000
104A381TRP0-0.032-0.01821.143-0.031-0.0310.0000.0000.0000.000
105A382LEU0-0.014-0.01320.338-0.438-0.4380.0000.0000.0000.000
106A383LEU0-0.0110.00913.592-0.303-0.3030.0000.0000.0000.000
107A384GLY00.022-0.00317.8450.7390.7390.0000.0000.0000.000
108A385LEU0-0.068-0.01115.067-1.272-1.2720.0000.0000.0000.000
109A386ARG10.8570.89618.19215.27115.2710.0000.0000.0000.000
110A387GLU-1-0.807-0.91619.001-14.294-14.2940.0000.0000.0000.000
111A388GLY0-0.016-0.00118.196-0.140-0.1400.0000.0000.0000.000
112A389LYS10.8100.89214.98415.79615.7960.0000.0000.0000.000
113A390ILE0-0.0170.00414.637-1.239-1.2390.0000.0000.0000.000
114A391LEU00.0410.02911.1260.7170.7170.0000.0000.0000.000
115A392GLU-1-0.828-0.90615.069-14.861-14.8610.0000.0000.0000.000
116A393ALA00.0310.01616.671-0.056-0.0560.0000.0000.0000.000
117A394HIS0-0.026-0.01018.4450.9940.9940.0000.0000.0000.000
118A395VAL0-0.015-0.01620.2090.1580.1580.0000.0000.0000.000
119A396GLU-1-0.753-0.84522.968-10.672-10.6720.0000.0000.0000.000
120A397ALA0-0.043-0.02625.1510.1590.1590.0000.0000.0000.000
121A398LYS10.8580.91927.11910.63710.6370.0000.0000.0000.000
122A399GLU-1-0.871-0.93124.989-10.934-10.9340.0000.0000.0000.000
123A400PRO00.0040.01621.602-0.164-0.1640.0000.0000.0000.000
124A401ARG10.9480.98317.18716.44116.4410.0000.0000.0000.000
125A402ALA00.0240.01417.327-0.882-0.8820.0000.0000.0000.000
126A403LEU0-0.025-0.00812.291-0.317-0.3170.0000.0000.0000.000
127A404ARG10.9040.9429.33024.28524.2850.0000.0000.0000.000
128A405SER00.0100.0229.231-0.998-0.9980.0000.0000.0000.000
129A406PRO0-0.0010.0014.192-0.702-0.600-0.001-0.004-0.0960.000
130A407GLU-1-0.781-0.8751.741-124.367-131.35323.378-9.419-6.973-0.117
131A408ARG10.7670.8343.03559.82260.1610.010-0.068-0.2800.000
132A409ARG10.8180.9118.03518.58318.5830.0000.0000.0000.000
133A410PRO00.0250.0278.7290.4700.4700.0000.0000.0000.000
134A411THR0-0.055-0.03210.1852.9202.9200.0000.0000.0000.000
135A412ARG10.8300.87211.59422.66422.6640.0000.0000.0000.000
136A413ILE0-0.0320.00111.159-2.664-2.6640.0000.0000.0000.000
137A414GLY00.0490.01910.7531.5841.5840.0000.0000.0000.000
138A415LEU0-0.055-0.02911.667-0.910-0.9100.0000.0000.0000.000
139A416TYR00.0070.00211.8280.4680.4680.0000.0000.0000.000
140A417LEU0-0.017-0.00413.7320.0510.0510.0000.0000.0000.000
141A418SER0-0.006-0.02617.0160.5550.5550.0000.0000.0000.000
142A419PHE0-0.017-0.00218.5800.0800.0800.0000.0000.0000.000
143A420GLY0-0.040-0.00721.2210.4370.4370.0000.0000.0000.000
144A421ASP-1-0.850-0.91116.790-14.824-14.8240.0000.0000.0000.000
145A422GLY0-0.072-0.02019.4770.0730.0730.0000.0000.0000.000
146A423VAL0-0.014-0.01015.015-0.231-0.2310.0000.0000.0000.000
147A424LEU00.0190.01016.1140.3040.3040.0000.0000.0000.000
148A425SER0-0.030-0.02010.9110.2320.2320.0000.0000.0000.000
149A426PHE00.0180.00411.8790.4840.4840.0000.0000.0000.000
150A427TYR00.015-0.0015.866-1.554-1.5540.0000.0000.0000.000
151A428ASP-1-0.782-0.8656.469-35.328-35.3280.0000.0000.0000.000
152A429ALA00.021-0.0106.509-3.629-3.6290.0000.0000.0000.000
153A430SER0-0.037-0.0457.9533.4613.4610.0000.0000.0000.000
154A431ASP-1-0.808-0.8573.928-52.309-51.977-0.001-0.081-0.2500.000
155A432ALA00.0290.0046.837-0.581-0.5810.0000.0000.0000.000
156A433ASP-1-0.834-0.9027.241-29.280-29.2800.0000.0000.0000.000
157A434ALA0-0.054-0.0382.157-1.945-2.1811.911-0.588-1.0870.001
158A435LEU00.0340.0362.5002.8473.9440.285-0.413-0.968-0.004
159A436VAL0-0.019-0.0192.196-15.544-11.5095.418-3.323-6.130-0.032
160A437PRO0-0.0030.0103.9654.4514.7450.002-0.035-0.2610.000
161A438LEU0-0.049-0.0186.897-1.933-1.9330.0000.0000.0000.000
162A439PHE0-0.021-0.0279.9261.5791.5790.0000.0000.0000.000
163A440ALA00.003-0.00812.531-0.732-0.7320.0000.0000.0000.000
164A441PHE0-0.0230.00814.6520.4580.4580.0000.0000.0000.000
165A442HIS00.0360.00014.1500.2760.2760.0000.0000.0000.000
166A443GLU-1-0.857-0.90419.184-11.999-11.9990.0000.0000.0000.000
167A444ARG10.9660.96922.37010.28710.2870.0000.0000.0000.000
168A445LEU00.0220.01620.0350.4350.4350.0000.0000.0000.000
169A446PRO0-0.0200.00524.5030.2430.2430.0000.0000.0000.000
170A447ARG10.8140.88626.4799.4259.4250.0000.0000.0000.000
171A448PRO00.0220.00328.3900.2640.2640.0000.0000.0000.000
172A449VAL0-0.019-0.00823.4760.0370.0370.0000.0000.0000.000
173A450TYR0-0.011-0.01926.0740.1970.1970.0000.0000.0000.000
174A451PRO00.0340.02221.536-0.232-0.2320.0000.0000.0000.000
175A452PHE00.003-0.00122.5920.5750.5750.0000.0000.0000.000
176A453PHE00.006-0.01320.209-0.833-0.8330.0000.0000.0000.000
177A454ASP-1-0.794-0.89623.995-11.238-11.2380.0000.0000.0000.000
178A455VAL00.012-0.00824.149-0.710-0.7100.0000.0000.0000.000
179A456CYS0-0.052-0.03825.305-0.260-0.2600.0000.0000.0000.000
180A457TRP00.0260.02227.2060.2080.2080.0000.0000.0000.000
181A458HIS00.0360.02428.075-0.617-0.6170.0000.0000.0000.000
182A459ASP-1-0.793-0.86726.729-11.804-11.8040.0000.0000.0000.000
183A460LYS10.9110.94129.8669.0319.0310.0000.0000.0000.000
184A461GLY00.0360.01330.7120.0360.0360.0000.0000.0000.000
185A462LYS10.8550.93226.03610.39510.3950.0000.0000.0000.000
186A463ASN00.014-0.00523.560-1.049-1.0490.0000.0000.0000.000
187A464ALA0-0.009-0.01325.747-0.002-0.0020.0000.0000.0000.000
188A465GLN0-0.003-0.00122.3020.5540.5540.0000.0000.0000.000
189A466PRO00.0000.00123.4910.0450.0450.0000.0000.0000.000
190A467LEU0-0.0260.00220.815-0.717-0.7170.0000.0000.0000.000
191A468LEU00.000-0.02320.2610.8360.8360.0000.0000.0000.000
192A469LEU0-0.0110.00919.373-0.955-0.9550.0000.0000.0000.000
193A470VAL0-0.040-0.01315.3840.8000.8000.0000.0000.0000.000