Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6Y38Z

Calculation Name: 3UKN-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UKN

Chain ID: C

ChEMBL ID:

UniProt ID: A8WHX9

Base Structure: X-ray

Registration Date: 2023-09-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167981.057341
FMO2-HF: Nuclear repulsion 2089903.008412
FMO2-HF: Total energy -78078.048929
FMO2-MP2: Total energy -78304.866839


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(C:549:ARG)


Summations of interaction energy for fragment #1(C:549: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.
-77.1-75.30221.454-11.08-12.172-0.117
Interaction energy analysis for fragmet #1(C:549:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.893 / q_NPA : 0.939
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].
3C551LEU00.0530.0323.8032.3344.181-0.029-0.870-0.9480.000
4C552TYR00.0410.0376.7032.7132.7130.0000.0000.0000.000
5C553HIS00.0240.0144.6982.4892.584-0.001-0.005-0.0900.000
6C554THR0-0.023-0.0314.6821.2441.319-0.001-0.004-0.0700.000
7C555ARG10.8920.9596.89121.93421.9340.0000.0000.0000.000
8C556THR0-0.029-0.0169.9661.8501.8500.0000.0000.0000.000
9C557LYS10.8280.9038.85418.07818.0780.0000.0000.0000.000
10C558ASP-1-0.817-0.89711.176-17.650-17.6500.0000.0000.0000.000
11C559LEU00.0090.01013.1061.0741.0740.0000.0000.0000.000
12C560LYS10.9280.95313.21516.40416.4040.0000.0000.0000.000
13C561ASP-1-0.795-0.88414.149-14.034-14.0340.0000.0000.0000.000
14C562PHE00.0120.01316.5400.6940.6940.0000.0000.0000.000
15C563ILE00.000-0.01618.4940.6270.6270.0000.0000.0000.000
16C564ARG10.8810.94217.18513.14513.1450.0000.0000.0000.000
17C565VAL0-0.029-0.02119.7510.5260.5260.0000.0000.0000.000
18C566HIS0-0.030-0.00622.3440.5830.5830.0000.0000.0000.000
19C567ARG10.8300.91824.59810.08410.0840.0000.0000.0000.000
20C568LEU00.0460.02323.4440.3110.3110.0000.0000.0000.000
21C569PRO00.0180.01825.237-0.153-0.1530.0000.0000.0000.000
22C570LYS10.9800.97522.63910.78010.7800.0000.0000.0000.000
23C571ALA00.010-0.00125.354-0.263-0.2630.0000.0000.0000.000
24C572LEU00.0160.00425.270-0.130-0.1300.0000.0000.0000.000
25C573ALA00.0530.02821.634-0.304-0.3040.0000.0000.0000.000
26C574GLN00.0050.00621.404-0.384-0.3840.0000.0000.0000.000
27C575ARG10.9920.99022.5849.1229.1220.0000.0000.0000.000
28C576MET0-0.031-0.00520.433-0.055-0.0550.0000.0000.0000.000
29C577LEU0-0.013-0.01616.103-0.471-0.4710.0000.0000.0000.000
30C578GLU-1-0.855-0.90818.299-13.087-13.0870.0000.0000.0000.000
31C579CYS00.0050.00320.717-0.124-0.1240.0000.0000.0000.000
32C580PHE0-0.031-0.02812.304-0.164-0.1640.0000.0000.0000.000
33C581GLN0-0.038-0.02016.233-1.369-1.3690.0000.0000.0000.000
34C582THR0-0.036-0.02517.283-0.358-0.3580.0000.0000.0000.000
35C583THR0-0.023-0.01819.2270.3280.3280.0000.0000.0000.000
36C584TRP0-0.059-0.02310.1960.3990.3990.0000.0000.0000.000
37C585SER00.0280.01914.9690.3330.3330.0000.0000.0000.000
38C586VAL00.0160.0219.9020.1120.1120.0000.0000.0000.000
39C587ASN00.0070.00312.640-0.251-0.2510.0000.0000.0000.000
40C588ASN0-0.064-0.05915.6600.2390.2390.0000.0000.0000.000
41C589GLY00.0070.01213.1840.7140.7140.0000.0000.0000.000
42C590ILE0-0.0170.00111.370-1.049-1.0490.0000.0000.0000.000
43C591ASP-1-0.790-0.8648.888-22.480-22.4800.0000.0000.0000.000
44C592VAL0-0.030-0.02110.925-0.324-0.3240.0000.0000.0000.000
45C593SER0-0.052-0.04011.2900.8630.8630.0000.0000.0000.000
46C594GLU-1-0.794-0.89413.760-16.477-16.4770.0000.0000.0000.000
47C595LEU0-0.006-0.01011.9530.8230.8230.0000.0000.0000.000
48C596LEU00.0300.01614.9420.5810.5810.0000.0000.0000.000
49C597LYS10.8140.90217.89214.61914.6190.0000.0000.0000.000
50C598ASP-1-0.906-0.95220.627-12.196-12.1960.0000.0000.0000.000
51C599PHE0-0.053-0.02018.1740.2290.2290.0000.0000.0000.000
52C600PRO00.0490.01922.9990.1490.1490.0000.0000.0000.000
53C601ASP-1-0.816-0.94124.766-12.964-12.9640.0000.0000.0000.000
54C602GLU-1-0.938-0.96124.356-11.761-11.7610.0000.0000.0000.000
55C603LEU0-0.0040.00321.280-0.349-0.3490.0000.0000.0000.000
56C604ARG10.8790.94520.15313.37413.3740.0000.0000.0000.000
57C605ALA0-0.021-0.00919.651-0.854-0.8540.0000.0000.0000.000
58C606ASP-1-0.884-0.95019.925-15.602-15.6020.0000.0000.0000.000
59C607ILE00.0020.01515.011-0.963-0.9630.0000.0000.0000.000
60C608ALA00.0350.01915.517-1.220-1.2200.0000.0000.0000.000
61C609MET0-0.085-0.03916.018-0.407-0.4070.0000.0000.0000.000
62C610HIS0-0.0170.00213.9010.0150.0150.0000.0000.0000.000
63C611LEU0-0.101-0.03310.301-2.213-2.2130.0000.0000.0000.000
64C612ASN0-0.017-0.02510.8111.6341.6340.0000.0000.0000.000
65C613LYS10.8980.9647.87130.81630.8160.0000.0000.0000.000
66C614GLU-1-0.744-0.8676.855-36.913-36.9130.0000.0000.0000.000
67C615LEU0-0.0190.00410.2411.8121.8120.0000.0000.0000.000
68C616LEU0-0.065-0.04712.0411.4731.4730.0000.0000.0000.000
69C617GLN0-0.067-0.03412.8611.1341.1340.0000.0000.0000.000
70C618LEU0-0.0570.00014.2870.6880.6880.0000.0000.0000.000
71C619PRO00.0900.03717.5390.2460.2460.0000.0000.0000.000
72C620LEU00.0150.02919.8550.4570.4570.0000.0000.0000.000
73C621PHE0-0.080-0.03116.6650.3960.3960.0000.0000.0000.000
74C622GLU-1-0.913-0.94220.887-12.357-12.3570.0000.0000.0000.000
75C623SER0-0.003-0.01523.3580.1540.1540.0000.0000.0000.000
76C624ALA0-0.034-0.00322.0140.2960.2960.0000.0000.0000.000
77C625SER00.0440.01923.991-0.057-0.0570.0000.0000.0000.000
78C626ARG10.9500.97623.04212.60212.6020.0000.0000.0000.000
79C627GLY0-0.005-0.01223.109-0.534-0.5340.0000.0000.0000.000
80C628CYS0-0.051-0.01122.793-0.281-0.2810.0000.0000.0000.000
81C629LEU00.0810.03118.142-0.643-0.6430.0000.0000.0000.000
82C630ARG10.8780.93015.91116.64316.6430.0000.0000.0000.000
83C631SER00.0230.01218.317-0.435-0.4350.0000.0000.0000.000
84C632LEU00.0200.01016.706-0.419-0.4190.0000.0000.0000.000
85C633SER0-0.040-0.02013.762-1.185-1.1850.0000.0000.0000.000
86C634LEU0-0.023-0.01413.139-1.797-1.7970.0000.0000.0000.000
87C635ILE0-0.055-0.01014.489-0.563-0.5630.0000.0000.0000.000
88C636ILE0-0.0280.0059.293-0.438-0.4380.0000.0000.0000.000
89C637LYS10.7460.8668.78821.95921.9590.0000.0000.0000.000
90C638THR00.0380.0073.9020.2420.5820.001-0.041-0.2990.000
91C639SER0-0.072-0.0484.4552.5922.776-0.001-0.023-0.1600.000
92C640PHE0-0.0030.0002.201-3.832-1.9643.281-1.616-3.533-0.011
93C641CYS0-0.047-0.0254.0255.5035.6000.003-0.053-0.0480.000
94C642ALA00.0220.0017.478-0.947-0.9470.0000.0000.0000.000
95C643PRO00.003-0.0189.4940.7820.7820.0000.0000.0000.000
96C644GLY00.0460.04712.8741.0951.0950.0000.0000.0000.000
97C645GLU-1-0.877-0.9249.066-25.857-25.8570.0000.0000.0000.000
98C646PHE00.007-0.00313.1830.0130.0130.0000.0000.0000.000
99C647LEU00.014-0.00111.583-0.894-0.8940.0000.0000.0000.000
100C648ILE0-0.015-0.02914.0060.2230.2230.0000.0000.0000.000
101C649ARG10.8800.94217.61214.95914.9590.0000.0000.0000.000
102C650GLN00.0240.01020.9530.1290.1290.0000.0000.0000.000
103C651GLY00.0030.01124.2130.3360.3360.0000.0000.0000.000
104C652ASP-1-0.859-0.91521.459-13.213-13.2130.0000.0000.0000.000
105C653ALA0-0.053-0.03723.3600.0050.0050.0000.0000.0000.000
106C654LEU00.0530.03418.923-0.548-0.5480.0000.0000.0000.000
107C655GLN0-0.054-0.02417.3640.4090.4090.0000.0000.0000.000
108C656ALA0-0.025-0.02315.124-0.037-0.0370.0000.0000.0000.000
109C657ILE00.0080.02715.8900.7530.7530.0000.0000.0000.000
110C658TYR0-0.025-0.04911.751-1.552-1.5520.0000.0000.0000.000
111C659PHE00.0790.0419.2060.9300.9300.0000.0000.0000.000
112C660VAL00.0010.0099.523-3.496-3.4960.0000.0000.0000.000
113C661CYS0-0.0110.0125.8530.5530.5530.0000.0000.0000.000
114C662SER0-0.055-0.0456.2391.7531.7530.0000.0000.0000.000
115C663GLY00.0560.0158.867-0.620-0.6200.0000.0000.0000.000
116C664SER00.001-0.00710.6431.2101.2100.0000.0000.0000.000
117C665MET0-0.022-0.02011.200-0.738-0.7380.0000.0000.0000.000
118C666GLU-1-0.779-0.87215.203-13.962-13.9620.0000.0000.0000.000
119C667VAL00.0240.00518.650-0.473-0.4730.0000.0000.0000.000
120C668LEU0-0.022-0.00421.0170.6660.6660.0000.0000.0000.000
121C669LYS10.8710.93323.84210.66610.6660.0000.0000.0000.000
122C670ASP-1-0.874-0.93627.008-10.069-10.0690.0000.0000.0000.000
123C671ASN0-0.027-0.01727.397-0.122-0.1220.0000.0000.0000.000
124C672THR0-0.027-0.03126.670-0.415-0.4150.0000.0000.0000.000
125C673VAL0-0.0090.00023.8290.2250.2250.0000.0000.0000.000
126C674LEU0-0.0010.00924.1680.4020.4020.0000.0000.0000.000
127C675ALA00.002-0.00321.7100.1350.1350.0000.0000.0000.000
128C676ILE0-0.035-0.02218.252-0.220-0.2200.0000.0000.0000.000
129C677LEU0-0.0200.00515.5760.1330.1330.0000.0000.0000.000
130C678GLY00.021-0.00913.779-0.689-0.6890.0000.0000.0000.000
131C679LYS10.8430.8939.22928.93928.9390.0000.0000.0000.000
132C680GLY00.0320.03011.843-1.255-1.2550.0000.0000.0000.000
133C681ASP-1-0.778-0.85114.314-17.197-17.1970.0000.0000.0000.000
134C682LEU00.006-0.00314.234-1.642-1.6420.0000.0000.0000.000
135C683ILE0-0.013-0.00314.2081.1681.1680.0000.0000.0000.000
136C684GLY00.031-0.00517.210-0.703-0.7030.0000.0000.0000.000
137C685SER0-0.031-0.02019.8710.6820.6820.0000.0000.0000.000
138C686ASP-1-0.833-0.91523.576-11.301-11.3010.0000.0000.0000.000
139C687SER00.014-0.00326.382-0.017-0.0170.0000.0000.0000.000
140C688LEU00.0080.01521.888-0.072-0.0720.0000.0000.0000.000
141C689THR00.007-0.00925.988-0.060-0.0600.0000.0000.0000.000
142C690LYS10.8290.89428.95410.76810.7680.0000.0000.0000.000
143C691GLU-1-0.720-0.84429.331-10.311-10.3110.0000.0000.0000.000
144C692GLN00.0380.01625.0430.0420.0420.0000.0000.0000.000
145C693VAL0-0.052-0.04028.5520.1140.1140.0000.0000.0000.000
146C694ILE0-0.0040.01824.110-0.440-0.4400.0000.0000.0000.000
147C695LYS10.9080.96624.93410.52610.5260.0000.0000.0000.000
148C696THR00.0520.03020.9810.2770.2770.0000.0000.0000.000
149C697ASN00.0070.02424.310-0.032-0.0320.0000.0000.0000.000
150C698ALA00.0570.02723.3840.3720.3720.0000.0000.0000.000
151C699ASN0-0.037-0.02620.852-0.505-0.5050.0000.0000.0000.000
152C700VAL00.0110.01015.5250.0390.0390.0000.0000.0000.000
153C701LYS10.8680.92815.67814.55814.5580.0000.0000.0000.000
154C702ALA00.0270.01211.4000.1580.1580.0000.0000.0000.000
155C703LEU00.0030.01613.4580.7180.7180.0000.0000.0000.000
156C704THR0-0.040-0.01711.1340.5740.5740.0000.0000.0000.000
157C705TYR00.010-0.0047.098-0.003-0.0030.0000.0000.0000.000
158C706CYS0-0.0520.0017.5690.8380.8380.0000.0000.0000.000
159C707ASP-1-0.843-0.8961.780-125.582-128.38318.202-8.449-6.951-0.106
160C708LEU00.0180.0004.6427.2747.367-0.001-0.019-0.0730.000
161C709GLN0-0.002-0.0215.686-1.291-1.2910.0000.0000.0000.000
162C710TYR00.0430.0138.2463.7823.7820.0000.0000.0000.000
163C711ILE00.0410.03311.625-0.656-0.6560.0000.0000.0000.000
164C712SER0-0.0040.00014.7831.2621.2620.0000.0000.0000.000
165C713LEU00.0730.01317.1680.3580.3580.0000.0000.0000.000
166C714LYS10.8670.95418.56315.79815.7980.0000.0000.0000.000
167C715GLY00.0500.02518.9300.4560.4560.0000.0000.0000.000
168C716LEU00.0330.01719.1590.3970.3970.0000.0000.0000.000
169C717ARG10.9010.95720.78811.81111.8110.0000.0000.0000.000
170C718GLU-1-0.843-0.89023.071-11.403-11.4030.0000.0000.0000.000
171C719VAL00.0320.00720.4200.4230.4230.0000.0000.0000.000
172C720LEU00.0030.00823.4050.5180.5180.0000.0000.0000.000
173C721ARG10.7580.83925.67111.73811.7380.0000.0000.0000.000
174C722LEU0-0.019-0.00125.3240.4200.4200.0000.0000.0000.000
175C723TYR00.0200.00724.7320.1890.1890.0000.0000.0000.000
176C724PRO00.0240.00928.142-0.128-0.1280.0000.0000.0000.000
177C725GLU-1-0.859-0.93129.143-10.625-10.6250.0000.0000.0000.000
178C726TYR00.041-0.00922.095-0.130-0.1300.0000.0000.0000.000
179C727ALA0-0.0300.00126.639-0.219-0.2190.0000.0000.0000.000
180C728GLN0-0.024-0.01527.688-0.051-0.0510.0000.0000.0000.000
181C729LYS10.9160.98628.08810.23110.2310.0000.0000.0000.000
182C730PHE00.001-0.02220.198-0.197-0.1970.0000.0000.0000.000
183C731VAL0-0.054-0.03824.907-0.194-0.1940.0000.0000.0000.000
184C732SER0-0.075-0.06126.9860.0490.0490.0000.0000.0000.000
185C733GLU-1-0.890-0.93826.644-10.641-10.6410.0000.0000.0000.000
186C734ILE0-0.0120.00622.206-0.413-0.4130.0000.0000.0000.000
187C735GLN0-0.061-0.06123.249-0.545-0.5450.0000.0000.0000.000
188C736HIS0-0.0120.00624.9500.0210.0210.0000.0000.0000.000
189C737ASP-1-0.848-0.94418.367-16.658-16.6580.0000.0000.0000.000
190C738LEU0-0.066-0.00919.479-0.811-0.8110.0000.0000.0000.000
191C739THR0-0.023-0.01418.6410.5230.5230.0000.0000.0000.000
192C740TYR0-0.026-0.03019.9200.5040.5040.0000.0000.0000.000
193C741ASN00.0350.01121.303-0.373-0.3730.0000.0000.0000.000
194C742LEU0-0.023-0.00619.5420.2520.2520.0000.0000.0000.000
195C743ARG10.8530.90824.09210.74410.7440.0000.0000.0000.000