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: YZMZ2

Calculation Name: 4N8C-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N8C

Chain ID: L

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280717.641021
FMO2-HF: Nuclear repulsion 2194984.437557
FMO2-HF: Total energy -85733.203465
FMO2-MP2: Total energy -85982.30622


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(L:1:ASP)


Summations of interaction energy for fragment #1(L:1:ASP)
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.
-36.982-30.2762.879-3.803-5.7840.035
Interaction energy analysis for fragmet #1(L:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.903 / q_NPA : -0.956
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].
3L3VAL00.0090.0133.4980.1922.5540.021-1.084-1.2990.005
4L4MET0-0.0170.0025.619-3.159-3.1590.0000.0000.0000.000
5L5SER00.010-0.0118.470-0.283-0.2830.0000.0000.0000.000
6L6GLN0-0.029-0.02411.6060.0580.0580.0000.0000.0000.000
7L7SER0-0.0430.01014.638-0.427-0.4270.0000.0000.0000.000
8L8PRO00.0600.01018.132-0.119-0.1190.0000.0000.0000.000
9L9SER00.0910.04318.4250.0650.0650.0000.0000.0000.000
10L10SER0-0.0090.00319.502-0.086-0.0860.0000.0000.0000.000
11L11LEU0-0.014-0.01923.068-0.120-0.1200.0000.0000.0000.000
12L12ALA0-0.0010.01625.706-0.056-0.0560.0000.0000.0000.000
13L13VAL0-0.029-0.01828.117-0.107-0.1070.0000.0000.0000.000
14L14SER0-0.028-0.05130.931-0.222-0.2220.0000.0000.0000.000
15L15VAL0-0.036-0.02934.0880.1060.1060.0000.0000.0000.000
16L16GLY0-0.0050.00034.935-0.233-0.2330.0000.0000.0000.000
17L17GLU-1-0.769-0.84232.4449.1249.1240.0000.0000.0000.000
18L18LYS10.9640.99129.424-9.754-9.7540.0000.0000.0000.000
19L19VAL0-0.028-0.01225.5110.0100.0100.0000.0000.0000.000
20L20SER0-0.026-0.01524.572-0.061-0.0610.0000.0000.0000.000
21L21MET0-0.0240.01119.6180.1360.1360.0000.0000.0000.000
22L22SER00.0090.01418.3140.2530.2530.0000.0000.0000.000
23L23CYS0-0.023-0.00912.5400.5190.5190.0000.0000.0000.000
24L24LYS10.9020.96713.377-16.401-16.4010.0000.0000.0000.000
25L25SER00.026-0.0039.1760.7580.7580.0000.0000.0000.000
26L26SER00.0050.0085.714-1.140-1.1400.0000.0000.0000.000
27L27GLN00.017-0.0015.6432.8122.8120.0000.0000.0000.000
28L28SER0-0.0020.0059.430-0.313-0.3130.0000.0000.0000.000
29L29LEU0-0.0070.0039.0281.4061.4060.0000.0000.0000.000
30L30PHE00.0060.01612.284-0.631-0.6310.0000.0000.0000.000
31L31TYR00.0350.01015.1740.4080.4080.0000.0000.0000.000
32L32SER00.038-0.00916.720-0.545-0.5450.0000.0000.0000.000
33L33SER0-0.0230.00819.728-0.730-0.7300.0000.0000.0000.000
34L34TYR0-0.015-0.01218.212-0.252-0.2520.0000.0000.0000.000
35L35GLN0-0.065-0.03121.317-0.618-0.6180.0000.0000.0000.000
36L36LYS10.9610.99319.710-13.000-13.0000.0000.0000.0000.000
37L37ASP-1-0.721-0.83815.92717.13117.1310.0000.0000.0000.000
38L38LEU0-0.056-0.01212.603-0.696-0.6960.0000.0000.0000.000
39L39LEU00.0160.00512.0921.9941.9940.0000.0000.0000.000
40L40ALA00.0070.01013.750-1.469-1.4690.0000.0000.0000.000
41L41TRP0-0.009-0.01514.6971.0651.0650.0000.0000.0000.000
42L42TYR00.015-0.00614.174-1.176-1.1760.0000.0000.0000.000
43L43GLN00.0340.02718.496-0.225-0.2250.0000.0000.0000.000
44L44GLN0-0.005-0.01818.8220.6030.6030.0000.0000.0000.000
45L45LYS10.8520.92621.744-11.134-11.1340.0000.0000.0000.000
46L46PRO00.0650.01724.4970.3190.3190.0000.0000.0000.000
47L47GLY00.0090.00325.267-0.362-0.3620.0000.0000.0000.000
48L48GLN0-0.0210.00824.937-0.117-0.1170.0000.0000.0000.000
49L49SER00.0550.03821.1980.2730.2730.0000.0000.0000.000
50L50PRO0-0.009-0.01217.070-0.568-0.5680.0000.0000.0000.000
51L51LYS10.8910.94820.027-11.755-11.7550.0000.0000.0000.000
52L52LEU00.0370.01918.3380.3210.3210.0000.0000.0000.000
53L53LEU0-0.062-0.02420.269-0.727-0.7270.0000.0000.0000.000
54L54ILE0-0.012-0.01219.779-0.615-0.6150.0000.0000.0000.000
55L55TYR00.0550.03118.2451.0151.0150.0000.0000.0000.000
56L56TRP00.001-0.01517.865-1.008-1.0080.0000.0000.0000.000
57L57ALA00.0170.01617.584-0.715-0.7150.0000.0000.0000.000
58L58SER0-0.083-0.05018.791-0.501-0.5010.0000.0000.0000.000
59L59THR0-0.034-0.00522.234-0.762-0.7620.0000.0000.0000.000
60L60ARG10.8620.94423.049-10.005-10.0050.0000.0000.0000.000
61L61GLU-1-0.825-0.92223.43712.11112.1110.0000.0000.0000.000
62L62SER0-0.035-0.01625.360-0.467-0.4670.0000.0000.0000.000
63L63GLY00.001-0.00128.6630.1250.1250.0000.0000.0000.000
64L64VAL0-0.035-0.00925.076-0.108-0.1080.0000.0000.0000.000
65L65PRO0-0.033-0.02628.448-0.180-0.1800.0000.0000.0000.000
66L66ASP-1-0.872-0.96429.3259.4269.4260.0000.0000.0000.000
67L67ARG10.7450.84829.759-9.710-9.7100.0000.0000.0000.000
68L68PHE0-0.0130.00324.8660.1940.1940.0000.0000.0000.000
69L69THR0-0.002-0.00525.722-0.159-0.1590.0000.0000.0000.000
70L70GLY00.0160.02221.6990.2220.2220.0000.0000.0000.000
71L71SER0-0.026-0.02621.308-0.533-0.5330.0000.0000.0000.000
72L72GLY00.0430.01519.6450.5520.5520.0000.0000.0000.000
73L73SER0-0.056-0.05318.307-0.114-0.1140.0000.0000.0000.000
74L74GLY0-0.0010.00115.762-0.326-0.3260.0000.0000.0000.000
75L75THR00.013-0.01612.1921.0341.0340.0000.0000.0000.000
76L76ASP-1-0.876-0.92414.19617.40217.4020.0000.0000.0000.000
77L77PHE0-0.0070.00513.677-0.893-0.8930.0000.0000.0000.000
78L78THR0-0.057-0.04417.593-0.090-0.0900.0000.0000.0000.000
79L79LEU0-0.0060.01719.955-0.167-0.1670.0000.0000.0000.000
80L80THR0-0.020-0.03321.579-0.267-0.2670.0000.0000.0000.000
81L81ILE00.0030.00925.303-0.059-0.0590.0000.0000.0000.000
82L82SER0-0.032-0.03127.842-0.173-0.1730.0000.0000.0000.000
83L83SER00.009-0.00331.190-0.270-0.2700.0000.0000.0000.000
84L84VAL0-0.0380.00429.3620.0030.0030.0000.0000.0000.000
85L85LYS11.0100.99631.680-8.956-8.9560.0000.0000.0000.000
86L86ALA00.0710.02231.7890.2560.2560.0000.0000.0000.000
87L87GLU-1-0.862-0.90931.8299.5249.5240.0000.0000.0000.000
88L88ASP-1-0.766-0.84927.88110.50310.5030.0000.0000.0000.000
89L89LEU00.0030.02826.8150.4980.4980.0000.0000.0000.000
90L90ALA0-0.018-0.02423.799-0.078-0.0780.0000.0000.0000.000
91L91VAL0-0.0080.00518.358-0.100-0.1000.0000.0000.0000.000
92L92TYR0-0.008-0.02519.168-0.016-0.0160.0000.0000.0000.000
93L93PHE00.0030.01113.8050.2610.2610.0000.0000.0000.000
94L95GLN00.0300.0069.785-0.444-0.4440.0000.0000.0000.000
95L96GLN00.0470.0235.106-6.018-6.0180.0000.0000.0000.000
96L97TYR00.007-0.0209.0251.3961.3960.0000.0000.0000.000
97L98TYR0-0.0060.0058.421-1.652-1.6520.0000.0000.0000.000
98L99THR0-0.014-0.0144.830-3.244-3.2440.0000.0000.0000.000
99L100TYR0-0.0480.0076.6591.1291.1290.0000.0000.0000.000
100L101PRO00.0600.0252.715-10.319-6.6392.452-2.468-3.6650.030
101L102LEU0-0.031-0.0154.7400.3920.471-0.001-0.005-0.0730.000
102L103THR0-0.011-0.0142.5040.5591.1440.407-0.246-0.7470.000
103L104PHE00.009-0.0075.856-4.069-4.0690.0000.0000.0000.000
104L105GLY00.0180.0168.3851.6191.6190.0000.0000.0000.000
105L106ALA0-0.020-0.02610.675-0.191-0.1910.0000.0000.0000.000
106L107GLY00.0030.00412.948-0.976-0.9760.0000.0000.0000.000
107L108THR0-0.078-0.04915.9350.0310.0310.0000.0000.0000.000
108L109LYS10.8900.94019.223-11.961-11.9610.0000.0000.0000.000
109L110LEU0-0.059-0.01822.235-0.256-0.2560.0000.0000.0000.000
110L111GLU-1-0.789-0.84025.57010.50810.5080.0000.0000.0000.000
111L112LEU00.0200.00028.616-0.041-0.0410.0000.0000.0000.000
112L113LYS10.8350.91232.227-9.038-9.0380.0000.0000.0000.000
113L114ARG10.8560.93133.835-8.201-8.2010.0000.0000.0000.000
114L115ALA00.0000.00936.7280.1060.1060.0000.0000.0000.000
115L116ASP-1-0.807-0.88935.9898.6368.6360.0000.0000.0000.000
116L117ALA0-0.030-0.02138.096-0.248-0.2480.0000.0000.0000.000
117L118ALA00.0420.03338.5330.2150.2150.0000.0000.0000.000
118L119PRO0-0.0210.00838.270-0.067-0.0670.0000.0000.0000.000
119L120THR00.0140.00640.287-0.236-0.2360.0000.0000.0000.000
120L121VAL0-0.024-0.02140.8030.1150.1150.0000.0000.0000.000
121L122SER0-0.036-0.01943.150-0.219-0.2190.0000.0000.0000.000
122L123ILE0-0.009-0.00443.4580.1990.1990.0000.0000.0000.000
123L124PHE0-0.019-0.01544.626-0.186-0.1860.0000.0000.0000.000
124L125PRO00.0360.02045.5190.1550.1550.0000.0000.0000.000
125L126PRO0-0.0130.00145.7270.0120.0120.0000.0000.0000.000
126L127SER0-0.0100.00047.444-0.102-0.1020.0000.0000.0000.000
127L128SER00.047-0.00149.7670.0110.0110.0000.0000.0000.000
128L129GLU-1-0.850-0.90350.0356.2346.2340.0000.0000.0000.000
129L130GLN00.0430.01442.564-0.036-0.0360.0000.0000.0000.000
130L131LEU00.0440.03147.9810.0520.0520.0000.0000.0000.000
131L132THR0-0.080-0.04049.890-0.045-0.0450.0000.0000.0000.000
132L133SER0-0.094-0.04747.341-0.001-0.0010.0000.0000.0000.000
133L134GLY00.010-0.00247.5180.1020.1020.0000.0000.0000.000
134L135GLY0-0.035-0.01744.3750.1400.1400.0000.0000.0000.000
135L136ALA0-0.006-0.01443.733-0.179-0.1790.0000.0000.0000.000
136L137SER0-0.035-0.01040.2150.1570.1570.0000.0000.0000.000
137L138VAL0-0.0110.01141.768-0.178-0.1780.0000.0000.0000.000
138L139VAL00.0020.00939.7710.2510.2510.0000.0000.0000.000
139L140CYS0-0.050-0.01439.3250.0180.0180.0000.0000.0000.000
140L141PHE00.0010.00539.0360.2830.2830.0000.0000.0000.000
141L142LEU0-0.003-0.01436.147-0.194-0.1940.0000.0000.0000.000
142L143ASN00.032-0.00437.6380.4150.4150.0000.0000.0000.000
143L144ASN0-0.002-0.00938.757-0.186-0.1860.0000.0000.0000.000
144L145PHE0-0.024-0.00432.725-0.172-0.1720.0000.0000.0000.000
145L146TYR00.017-0.02331.2100.1350.1350.0000.0000.0000.000
146L147PRO0-0.019-0.01330.783-0.256-0.2560.0000.0000.0000.000
147L148LYS10.9190.93125.929-11.518-11.5180.0000.0000.0000.000
148L149ASP-1-0.964-0.95426.53111.35011.3500.0000.0000.0000.000
149L150ILE0-0.020-0.01529.578-0.394-0.3940.0000.0000.0000.000
150L151ASN0-0.048-0.01129.8090.4920.4920.0000.0000.0000.000
151L152VAL00.0280.00832.525-0.306-0.3060.0000.0000.0000.000
152L153LYS10.8140.90534.035-8.429-8.4290.0000.0000.0000.000
153L154TRP00.0350.00636.364-0.347-0.3470.0000.0000.0000.000
154L155LYS10.8750.94038.977-7.476-7.4760.0000.0000.0000.000
155L156ILE0-0.002-0.00641.850-0.084-0.0840.0000.0000.0000.000
156L157ASP-1-0.768-0.88244.5186.5756.5750.0000.0000.0000.000
157L158GLY00.000-0.01445.842-0.101-0.1010.0000.0000.0000.000
158L159SER0-0.064-0.02641.2820.0800.0800.0000.0000.0000.000
159L160GLU-1-0.851-0.91035.0798.7368.7360.0000.0000.0000.000
160L161ARG10.8560.92437.604-8.060-8.0600.0000.0000.0000.000
161L162GLN00.0410.01831.892-0.023-0.0230.0000.0000.0000.000
162L163ASN0-0.010-0.00733.2820.3000.3000.0000.0000.0000.000
163L164GLY00.0590.02233.766-0.281-0.2810.0000.0000.0000.000
164L165VAL0-0.0230.01033.336-0.217-0.2170.0000.0000.0000.000
165L166LEU00.0040.00330.2530.3760.3760.0000.0000.0000.000
166L167ASN00.0180.01430.191-0.640-0.6400.0000.0000.0000.000
167L168SER0-0.0050.01130.0320.4480.4480.0000.0000.0000.000
168L169TRP00.0380.00527.433-0.225-0.2250.0000.0000.0000.000
169L170THR00.0050.00930.5060.1270.1270.0000.0000.0000.000
170L171ASP-1-0.843-0.93227.98811.37211.3720.0000.0000.0000.000
171L172GLN0-0.081-0.03630.191-0.121-0.1210.0000.0000.0000.000
172L173ASP-1-0.806-0.90632.1348.1518.1510.0000.0000.0000.000
173L174SER0-0.053-0.02935.672-0.086-0.0860.0000.0000.0000.000
174L175LYS10.8720.93236.516-7.466-7.4660.0000.0000.0000.000
175L176ASP-1-0.779-0.86638.9907.8467.8460.0000.0000.0000.000
176L177SER00.0000.00435.2440.0370.0370.0000.0000.0000.000
177L178THR0-0.107-0.06734.9820.2310.2310.0000.0000.0000.000
178L179TYR0-0.018-0.03029.0610.2780.2780.0000.0000.0000.000
179L180SER00.0480.02834.330-0.382-0.3820.0000.0000.0000.000
180L181MET0-0.060-0.01231.4850.3140.3140.0000.0000.0000.000
181L182SER0-0.0130.00734.570-0.303-0.3030.0000.0000.0000.000
182L183SER0-0.001-0.01534.4440.2620.2620.0000.0000.0000.000
183L184THR00.0230.00235.637-0.386-0.3860.0000.0000.0000.000
184L185LEU0-0.0050.00936.2710.2570.2570.0000.0000.0000.000
185L186THR0-0.015-0.02437.567-0.278-0.2780.0000.0000.0000.000
186L187LEU0-0.061-0.02939.0190.1350.1350.0000.0000.0000.000
187L188THR00.0650.02241.783-0.052-0.0520.0000.0000.0000.000
188L189LYS10.8890.92844.232-6.158-6.1580.0000.0000.0000.000
189L190ASP-1-0.901-0.94947.7146.4356.4350.0000.0000.0000.000
190L191GLU-1-0.869-0.92242.8597.2487.2480.0000.0000.0000.000
191L192TYR00.0560.01845.958-0.048-0.0480.0000.0000.0000.000
192L193GLU-1-0.789-0.89547.2656.0506.0500.0000.0000.0000.000
193L194ARG10.8530.93845.583-6.914-6.9140.0000.0000.0000.000
194L195HIS10.7690.89045.707-6.891-6.8910.0000.0000.0000.000
195L196ASN0-0.005-0.01449.812-0.073-0.0730.0000.0000.0000.000
196L197SER00.0200.04748.7100.0090.0090.0000.0000.0000.000
197L198TYR0-0.030-0.01044.3100.2500.2500.0000.0000.0000.000
198L199THR00.008-0.00443.383-0.154-0.1540.0000.0000.0000.000
199L201GLU-1-0.868-0.95939.3237.4847.4840.0000.0000.0000.000
200L202ALA00.0130.01137.2620.2690.2690.0000.0000.0000.000
201L203THR0-0.003-0.00335.010-0.246-0.2460.0000.0000.0000.000
202L204HIS00.0470.01434.1930.0740.0740.0000.0000.0000.000
203L205LYS10.8680.90733.346-9.036-9.0360.0000.0000.0000.000
204L206THR0-0.035-0.03735.742-0.175-0.1750.0000.0000.0000.000
205L207SER0-0.048-0.03239.062-0.308-0.3080.0000.0000.0000.000
206L208THR00.0040.00339.4350.1540.1540.0000.0000.0000.000
207L209SER00.0080.01340.7290.0250.0250.0000.0000.0000.000
208L210PRO0-0.0040.01239.7590.0090.0090.0000.0000.0000.000
209L211ILE0-0.0010.00941.128-0.222-0.2220.0000.0000.0000.000
210L212VAL00.0120.00142.1580.1610.1610.0000.0000.0000.000
211L213LYS10.8820.94944.238-6.860-6.8600.0000.0000.0000.000
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