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: 2NK8R

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166272.377209
FMO2-HF: Nuclear repulsion 2088195.019995
FMO2-HF: Total energy -78077.357214
FMO2-MP2: Total energy -78304.20605


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.
-75.399-73.47821.61-11.128-12.405-0.119
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 : 0.900 / q_NPA : 0.942
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].
3C551LEU00.0610.0293.8033.2935.172-0.029-0.876-0.9750.000
4C552TYR00.0500.0426.7172.8182.8180.0000.0000.0000.000
5C553HIS00.0220.0225.3492.2462.332-0.001-0.003-0.0820.000
6C554THR0-0.023-0.0195.3491.5341.609-0.001-0.001-0.0730.000
7C555ARG10.8840.9457.76620.82620.8260.0000.0000.0000.000
8C556THR0-0.034-0.02810.6701.5301.5300.0000.0000.0000.000
9C557LYS10.8080.9139.43817.45017.4500.0000.0000.0000.000
10C558ASP-1-0.795-0.88812.063-16.792-16.7920.0000.0000.0000.000
11C559LEU0-0.0070.00414.0530.9930.9930.0000.0000.0000.000
12C560LYS10.9420.95113.71816.09916.0990.0000.0000.0000.000
13C561ASP-1-0.875-0.94314.402-14.160-14.1600.0000.0000.0000.000
14C562PHE00.0130.00817.4880.6680.6680.0000.0000.0000.000
15C563ILE00.014-0.00819.3850.6050.6050.0000.0000.0000.000
16C564ARG10.9610.99018.97312.42312.4230.0000.0000.0000.000
17C565VAL0-0.053-0.02820.7930.5020.5020.0000.0000.0000.000
18C566HIS0-0.022-0.00323.3070.5560.5560.0000.0000.0000.000
19C567ARG10.8290.91525.5179.8979.8970.0000.0000.0000.000
20C568LEU00.0470.02324.2060.2950.2950.0000.0000.0000.000
21C569PRO00.0150.02326.057-0.142-0.1420.0000.0000.0000.000
22C570LYS10.9950.97923.14910.69210.6920.0000.0000.0000.000
23C571ALA00.010-0.00426.019-0.260-0.2600.0000.0000.0000.000
24C572LEU00.0100.00325.909-0.127-0.1270.0000.0000.0000.000
25C573ALA00.0510.02722.304-0.290-0.2900.0000.0000.0000.000
26C574GLN0-0.0050.00021.598-0.325-0.3250.0000.0000.0000.000
27C575ARG11.0080.99623.1209.0989.0980.0000.0000.0000.000
28C576MET0-0.042-0.01021.153-0.067-0.0670.0000.0000.0000.000
29C577LEU0-0.016-0.01416.734-0.432-0.4320.0000.0000.0000.000
30C578GLU-1-0.883-0.92618.777-12.905-12.9050.0000.0000.0000.000
31C579CYS0-0.009-0.00921.094-0.278-0.2780.0000.0000.0000.000
32C580PHE0-0.002-0.02113.142-0.179-0.1790.0000.0000.0000.000
33C581GLN0-0.031-0.00916.096-1.280-1.2800.0000.0000.0000.000
34C582THR0-0.027-0.01017.602-0.388-0.3880.0000.0000.0000.000
35C583THR0-0.032-0.02419.5310.2850.2850.0000.0000.0000.000
36C584TRP0-0.046-0.02210.3090.5560.5560.0000.0000.0000.000
37C585SER00.0260.01214.9190.2410.2410.0000.0000.0000.000
38C586VAL00.0180.0219.9680.1770.1770.0000.0000.0000.000
39C587ASN00.0270.01612.640-0.247-0.2470.0000.0000.0000.000
40C588ASN0-0.036-0.03615.6490.3780.3780.0000.0000.0000.000
41C589GLY00.0020.01113.1940.7170.7170.0000.0000.0000.000
42C590ILE0-0.0230.00611.368-0.928-0.9280.0000.0000.0000.000
43C591ASP-1-0.814-0.8868.868-21.770-21.7700.0000.0000.0000.000
44C592VAL0-0.017-0.01310.922-0.406-0.4060.0000.0000.0000.000
45C593SER0-0.061-0.04111.3330.8000.8000.0000.0000.0000.000
46C594GLU-1-0.791-0.90513.751-16.197-16.1970.0000.0000.0000.000
47C595LEU0-0.009-0.00812.2270.7810.7810.0000.0000.0000.000
48C596LEU00.0290.01615.2730.5860.5860.0000.0000.0000.000
49C597LYS10.8150.90217.87914.44114.4410.0000.0000.0000.000
50C598ASP-1-0.901-0.94720.615-11.807-11.8070.0000.0000.0000.000
51C599PHE0-0.066-0.02718.6430.2120.2120.0000.0000.0000.000
52C600PRO00.0600.01922.9870.1110.1110.0000.0000.0000.000
53C601ASP-1-0.861-0.95224.761-12.352-12.3520.0000.0000.0000.000
54C602GLU-1-0.933-0.95824.552-11.670-11.6700.0000.0000.0000.000
55C603LEU00.0020.00421.417-0.371-0.3710.0000.0000.0000.000
56C604ARG10.9070.94919.78113.49013.4900.0000.0000.0000.000
57C605ALA0-0.020-0.00519.848-0.844-0.8440.0000.0000.0000.000
58C606ASP-1-0.910-0.96320.110-15.435-15.4350.0000.0000.0000.000
59C607ILE00.0030.00815.218-0.930-0.9300.0000.0000.0000.000
60C608ALA00.0390.02015.699-1.198-1.1980.0000.0000.0000.000
61C609MET0-0.118-0.05616.200-0.485-0.4850.0000.0000.0000.000
62C610HIS00.0140.02313.951-0.089-0.0890.0000.0000.0000.000
63C611LEU0-0.107-0.04010.577-2.241-2.2410.0000.0000.0000.000
64C612ASN0-0.028-0.03110.9761.7661.7660.0000.0000.0000.000
65C613LYS10.9250.9727.38332.93632.9360.0000.0000.0000.000
66C614GLU-1-0.771-0.8887.348-35.029-35.0290.0000.0000.0000.000
67C615LEU0-0.034-0.00210.3401.8871.8870.0000.0000.0000.000
68C616LEU0-0.071-0.05712.1641.5171.5170.0000.0000.0000.000
69C617GLN0-0.039-0.01913.3220.2760.2760.0000.0000.0000.000
70C618LEU0-0.053-0.00114.8600.7170.7170.0000.0000.0000.000
71C619PRO00.0960.04617.6290.2440.2440.0000.0000.0000.000
72C620LEU00.0200.03520.0490.4470.4470.0000.0000.0000.000
73C621PHE0-0.072-0.00216.6500.4120.4120.0000.0000.0000.000
74C622GLU-1-0.916-0.94821.017-12.463-12.4630.0000.0000.0000.000
75C623SER00.002-0.00923.4720.0970.0970.0000.0000.0000.000
76C624ALA0-0.021-0.00822.1620.3040.3040.0000.0000.0000.000
77C625SER00.0380.01324.1390.0100.0100.0000.0000.0000.000
78C626ARG10.9790.99523.35412.47412.4740.0000.0000.0000.000
79C627GLY0-0.006-0.01423.261-0.533-0.5330.0000.0000.0000.000
80C628CYS0-0.042-0.00722.968-0.261-0.2610.0000.0000.0000.000
81C629LEU00.0770.02818.240-0.609-0.6090.0000.0000.0000.000
82C630ARG10.8800.93216.10616.48916.4890.0000.0000.0000.000
83C631SER00.0240.01118.500-0.440-0.4400.0000.0000.0000.000
84C632LEU00.0090.00816.903-0.381-0.3810.0000.0000.0000.000
85C633SER0-0.042-0.02213.940-1.178-1.1780.0000.0000.0000.000
86C634LEU0-0.047-0.02313.333-1.627-1.6270.0000.0000.0000.000
87C635ILE0-0.052-0.00514.571-0.489-0.4890.0000.0000.0000.000
88C636ILE0-0.0370.0009.493-0.260-0.2600.0000.0000.0000.000
89C637LYS10.7740.8988.67421.93121.9310.0000.0000.0000.000
90C638THR00.027-0.0054.020-0.937-0.646-0.001-0.025-0.2650.000
91C639SER0-0.067-0.0414.4392.9133.101-0.001-0.023-0.1640.000
92C640PHE0-0.013-0.0052.124-4.164-2.6704.249-1.868-3.875-0.013
93C641CYS0-0.040-0.0174.0046.0746.2080.004-0.067-0.0720.000
94C642ALA00.0220.0047.377-1.214-1.2140.0000.0000.0000.000
95C643PRO00.003-0.0179.3830.8900.8900.0000.0000.0000.000
96C644GLY00.0560.05312.7891.1681.1680.0000.0000.0000.000
97C645GLU-1-0.904-0.9489.155-25.365-25.3650.0000.0000.0000.000
98C646PHE00.006-0.00413.0810.0870.0870.0000.0000.0000.000
99C647LEU00.0320.00511.505-0.860-0.8600.0000.0000.0000.000
100C648ILE0-0.020-0.03314.0120.3120.3120.0000.0000.0000.000
101C649ARG10.8750.95117.62514.78714.7870.0000.0000.0000.000
102C650GLN00.0140.00920.906-0.063-0.0630.0000.0000.0000.000
103C651GLY0-0.0080.00424.2250.3450.3450.0000.0000.0000.000
104C652ASP-1-0.889-0.93621.161-13.231-13.2310.0000.0000.0000.000
105C653ALA0-0.033-0.02723.2620.0100.0100.0000.0000.0000.000
106C654LEU00.0510.03519.016-0.532-0.5320.0000.0000.0000.000
107C655GLN0-0.094-0.05217.3760.4490.4490.0000.0000.0000.000
108C656ALA0-0.027-0.01915.246-0.005-0.0050.0000.0000.0000.000
109C657ILE00.0040.02515.7180.7310.7310.0000.0000.0000.000
110C658TYR0-0.023-0.05011.692-1.503-1.5030.0000.0000.0000.000
111C659PHE00.0820.0469.2420.9490.9490.0000.0000.0000.000
112C660VAL00.0190.0149.560-3.513-3.5130.0000.0000.0000.000
113C661CYS0-0.0030.0205.6821.5541.5540.0000.0000.0000.000
114C662SER0-0.049-0.0456.4961.4671.4670.0000.0000.0000.000
115C663GLY00.0590.0168.790-0.586-0.5860.0000.0000.0000.000
116C664SER00.010-0.00410.5611.1251.1250.0000.0000.0000.000
117C665MET0-0.013-0.02011.807-1.025-1.0250.0000.0000.0000.000
118C666GLU-1-0.856-0.91615.165-14.153-14.1530.0000.0000.0000.000
119C667VAL00.0160.00018.635-0.460-0.4600.0000.0000.0000.000
120C668LEU0-0.018-0.00521.0080.6840.6840.0000.0000.0000.000
121C669LYS10.8940.95023.83210.65210.6520.0000.0000.0000.000
122C670ASP-1-0.878-0.93926.996-10.085-10.0850.0000.0000.0000.000
123C671ASN0-0.037-0.02127.647-0.109-0.1090.0000.0000.0000.000
124C672THR0-0.028-0.03126.775-0.415-0.4150.0000.0000.0000.000
125C673VAL00.0100.00323.9630.2220.2220.0000.0000.0000.000
126C674LEU0-0.0070.00724.1510.4080.4080.0000.0000.0000.000
127C675ALA0-0.004-0.00821.7160.1310.1310.0000.0000.0000.000
128C676ILE0-0.022-0.01117.841-0.221-0.2210.0000.0000.0000.000
129C677LEU0-0.0240.00215.4360.1430.1430.0000.0000.0000.000
130C678GLY00.014-0.00813.730-0.746-0.7460.0000.0000.0000.000
131C679LYS10.8490.8999.35129.27429.2740.0000.0000.0000.000
132C680GLY00.0250.02711.839-1.264-1.2640.0000.0000.0000.000
133C681ASP-1-0.819-0.89014.326-17.537-17.5370.0000.0000.0000.000
134C682LEU00.003-0.00214.297-1.605-1.6050.0000.0000.0000.000
135C683ILE0-0.011-0.00514.2061.1611.1610.0000.0000.0000.000
136C684GLY00.028-0.00817.269-0.669-0.6690.0000.0000.0000.000
137C685SER0-0.022-0.01619.9320.6580.6580.0000.0000.0000.000
138C686ASP-1-0.842-0.91823.641-11.185-11.1850.0000.0000.0000.000
139C687SER00.013-0.00526.460-0.027-0.0270.0000.0000.0000.000
140C688LEU0-0.0150.00622.124-0.059-0.0590.0000.0000.0000.000
141C689THR00.015-0.00726.081-0.048-0.0480.0000.0000.0000.000
142C690LYS10.8410.89328.96010.65710.6570.0000.0000.0000.000
143C691GLU-1-0.739-0.85129.323-10.275-10.2750.0000.0000.0000.000
144C692GLN00.0140.00724.9200.0510.0510.0000.0000.0000.000
145C693VAL0-0.035-0.02728.5580.1190.1190.0000.0000.0000.000
146C694ILE00.0120.01924.052-0.426-0.4260.0000.0000.0000.000
147C695LYS10.9230.96924.98610.35210.3520.0000.0000.0000.000
148C696THR00.0510.03021.0880.2760.2760.0000.0000.0000.000
149C697ASN0-0.0050.01024.3410.0090.0090.0000.0000.0000.000
150C698ALA00.0360.01423.6540.3610.3610.0000.0000.0000.000
151C699ASN0-0.031-0.01920.748-0.503-0.5030.0000.0000.0000.000
152C700VAL00.0150.01515.3940.0360.0360.0000.0000.0000.000
153C701LYS10.9260.96815.64014.76014.7600.0000.0000.0000.000
154C702ALA00.0320.01411.3580.1470.1470.0000.0000.0000.000
155C703LEU00.0010.01513.4030.6750.6750.0000.0000.0000.000
156C704THR0-0.040-0.01310.7250.5770.5770.0000.0000.0000.000
157C705TYR0-0.012-0.0137.004-0.014-0.0140.0000.0000.0000.000
158C706CYS0-0.0340.0087.5060.8480.8480.0000.0000.0000.000
159C707ASP-1-0.831-0.8881.785-127.267-129.58517.391-8.247-6.826-0.106
160C708LEU0-0.004-0.0124.6097.4517.543-0.001-0.018-0.0730.000
161C709GLN00.011-0.0135.901-1.325-1.3250.0000.0000.0000.000
162C710TYR00.0430.0218.3733.4693.4690.0000.0000.0000.000
163C711ILE00.0420.03211.725-0.582-0.5820.0000.0000.0000.000
164C712SER00.0060.00414.8961.1921.1920.0000.0000.0000.000
165C713LEU00.0690.01017.2100.3660.3660.0000.0000.0000.000
166C714LYS10.8960.97018.84615.30415.3040.0000.0000.0000.000
167C715GLY00.0610.02418.9020.4630.4630.0000.0000.0000.000
168C716LEU00.0390.02019.3020.3840.3840.0000.0000.0000.000
169C717ARG10.8820.94720.97811.70911.7090.0000.0000.0000.000
170C718GLU-1-0.838-0.88523.026-11.246-11.2460.0000.0000.0000.000
171C719VAL00.0320.00620.5010.4100.4100.0000.0000.0000.000
172C720LEU00.0000.00423.6650.5050.5050.0000.0000.0000.000
173C721ARG10.7560.83825.85811.60611.6060.0000.0000.0000.000
174C722LEU0-0.0130.00225.3790.4060.4060.0000.0000.0000.000
175C723TYR00.0080.00125.1350.1560.1560.0000.0000.0000.000
176C724PRO00.0220.00628.325-0.138-0.1380.0000.0000.0000.000
177C725GLU-1-0.902-0.95029.619-10.369-10.3690.0000.0000.0000.000
178C726TYR00.031-0.02822.359-0.126-0.1260.0000.0000.0000.000
179C727ALA0-0.031-0.00326.813-0.221-0.2210.0000.0000.0000.000
180C728GLN0-0.019-0.01527.859-0.070-0.0700.0000.0000.0000.000
181C729LYS10.9481.00428.36710.06510.0650.0000.0000.0000.000
182C730PHE0-0.024-0.02020.432-0.244-0.2440.0000.0000.0000.000
183C731VAL0-0.056-0.04925.217-0.192-0.1920.0000.0000.0000.000
184C732SER0-0.075-0.05727.3150.0730.0730.0000.0000.0000.000
185C733GLU-1-0.890-0.93726.764-10.611-10.6110.0000.0000.0000.000
186C734ILE0-0.0140.00422.469-0.436-0.4360.0000.0000.0000.000
187C735GLN0-0.040-0.05323.357-0.579-0.5790.0000.0000.0000.000
188C736HIS0-0.0090.00525.0360.0340.0340.0000.0000.0000.000
189C737ASP-1-0.835-0.93518.249-16.552-16.5520.0000.0000.0000.000
190C738LEU0-0.076-0.01819.558-0.807-0.8070.0000.0000.0000.000
191C739THR00.0220.03018.7770.4190.4190.0000.0000.0000.000
192C740TYR00.000-0.01019.9460.5350.5350.0000.0000.0000.000
193C741ASN00.0410.01621.340-0.376-0.3760.0000.0000.0000.000
194C742LEU0-0.033-0.00719.5750.2480.2480.0000.0000.0000.000
195C743ARG10.8560.90624.13710.74210.7420.0000.0000.0000.000