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: 52QJZ

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2279192.080024
FMO2-HF: Nuclear repulsion 2193460.026693
FMO2-HF: Total energy -85732.053331
FMO2-MP2: Total energy -85981.114828


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.
-35.434-28.9771.287-3.092-4.6510.023
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 : -0.912 / q_NPA : -0.957
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].
3L3VAL00.0090.0133.5270.1672.5600.021-1.111-1.3030.005
4L4MET0-0.021-0.0045.518-3.295-3.2950.0000.0000.0000.000
5L5SER00.007-0.0108.507-0.186-0.1860.0000.0000.0000.000
6L6GLN0-0.020-0.01911.575-0.006-0.0060.0000.0000.0000.000
7L7SER0-0.0400.01914.681-0.399-0.3990.0000.0000.0000.000
8L8PRO00.0710.01318.140-0.124-0.1240.0000.0000.0000.000
9L9SER00.1050.05818.2100.0860.0860.0000.0000.0000.000
10L10SER0-0.013-0.00819.472-0.099-0.0990.0000.0000.0000.000
11L11LEU0-0.028-0.01723.112-0.088-0.0880.0000.0000.0000.000
12L12ALA0-0.0020.01725.749-0.053-0.0530.0000.0000.0000.000
13L13VAL0-0.032-0.01128.182-0.106-0.1060.0000.0000.0000.000
14L14SER0-0.010-0.00730.967-0.288-0.2880.0000.0000.0000.000
15L15VAL0-0.014-0.02334.1190.1070.1070.0000.0000.0000.000
16L16GLY0-0.015-0.00834.956-0.231-0.2310.0000.0000.0000.000
17L17GLU-1-0.897-0.94432.3889.1809.1800.0000.0000.0000.000
18L18LYS10.9520.98429.539-9.581-9.5810.0000.0000.0000.000
19L19VAL0-0.021-0.00725.4030.0120.0120.0000.0000.0000.000
20L20SER0-0.020-0.01524.659-0.063-0.0630.0000.0000.0000.000
21L21MET0-0.0270.00919.6510.1450.1450.0000.0000.0000.000
22L22SER0-0.0060.00517.9370.2490.2490.0000.0000.0000.000
23L23CYS0-0.020-0.01912.5650.5420.5420.0000.0000.0000.000
24L24LYS10.9420.99113.410-16.383-16.3830.0000.0000.0000.000
25L25SER00.0430.0149.1950.8380.8380.0000.0000.0000.000
26L26SER0-0.015-0.0035.661-1.136-1.1360.0000.0000.0000.000
27L27GLN00.0290.0135.8512.7282.7280.0000.0000.0000.000
28L28SER0-0.024-0.0139.430-0.308-0.3080.0000.0000.0000.000
29L29LEU0-0.0060.0009.0861.3771.3770.0000.0000.0000.000
30L30PHE00.0000.01412.290-0.668-0.6680.0000.0000.0000.000
31L31TYR00.0290.01215.2140.5180.5180.0000.0000.0000.000
32L32SER00.048-0.00916.729-0.510-0.5100.0000.0000.0000.000
33L33SER0-0.0240.00619.747-0.672-0.6720.0000.0000.0000.000
34L34TYR0-0.010-0.00117.941-0.644-0.6440.0000.0000.0000.000
35L35GLN0-0.074-0.04021.299-0.688-0.6880.0000.0000.0000.000
36L36LYS10.9660.99019.862-12.692-12.6920.0000.0000.0000.000
37L37ASP-1-0.719-0.82215.85516.88416.8840.0000.0000.0000.000
38L38LEU0-0.047-0.01412.631-0.627-0.6270.0000.0000.0000.000
39L39LEU00.0120.00712.1111.9361.9360.0000.0000.0000.000
40L40ALA00.0110.01413.740-1.441-1.4410.0000.0000.0000.000
41L41TRP0-0.012-0.01714.6951.0951.0950.0000.0000.0000.000
42L42TYR00.008-0.02314.055-1.080-1.0800.0000.0000.0000.000
43L43GLN0-0.011-0.00418.498-0.060-0.0600.0000.0000.0000.000
44L44GLN0-0.001-0.01219.0360.5300.5300.0000.0000.0000.000
45L45LYS10.8890.94821.753-10.839-10.8390.0000.0000.0000.000
46L46PRO00.0590.01424.5080.3260.3260.0000.0000.0000.000
47L47GLY00.0180.00825.287-0.359-0.3590.0000.0000.0000.000
48L48GLN0-0.043-0.00724.9520.0030.0030.0000.0000.0000.000
49L49SER00.0290.01821.1790.2970.2970.0000.0000.0000.000
50L50PRO0-0.004-0.00417.160-0.541-0.5410.0000.0000.0000.000
51L51LYS10.9560.98220.024-11.557-11.5570.0000.0000.0000.000
52L52LEU00.0430.02218.4700.3480.3480.0000.0000.0000.000
53L53LEU0-0.060-0.02820.260-0.716-0.7160.0000.0000.0000.000
54L54ILE0-0.018-0.01019.750-0.610-0.6100.0000.0000.0000.000
55L55TYR00.0520.02418.2270.9570.9570.0000.0000.0000.000
56L56TRP00.011-0.01317.837-0.948-0.9480.0000.0000.0000.000
57L57ALA00.0060.01417.640-0.683-0.6830.0000.0000.0000.000
58L58SER0-0.085-0.05318.783-0.496-0.4960.0000.0000.0000.000
59L59THR0-0.0180.00622.213-0.728-0.7280.0000.0000.0000.000
60L60ARG10.8540.93723.034-10.046-10.0460.0000.0000.0000.000
61L61GLU-1-0.877-0.94723.44012.15412.1540.0000.0000.0000.000
62L62SER0-0.017-0.00725.342-0.452-0.4520.0000.0000.0000.000
63L63GLY00.0190.00628.6460.1250.1250.0000.0000.0000.000
64L64VAL0-0.032-0.00525.071-0.108-0.1080.0000.0000.0000.000
65L65PRO0-0.041-0.02928.441-0.205-0.2050.0000.0000.0000.000
66L66ASP-1-0.884-0.96329.3269.3609.3600.0000.0000.0000.000
67L67ARG10.8060.89029.770-9.723-9.7230.0000.0000.0000.000
68L68PHE0-0.0190.00024.8550.1730.1730.0000.0000.0000.000
69L69THR00.0130.00025.582-0.166-0.1660.0000.0000.0000.000
70L70GLY00.0120.02121.7030.2240.2240.0000.0000.0000.000
71L71SER0-0.025-0.02521.318-0.509-0.5090.0000.0000.0000.000
72L72GLY00.0460.01619.6570.5560.5560.0000.0000.0000.000
73L73SER0-0.053-0.06018.309-0.117-0.1170.0000.0000.0000.000
74L74GLY0-0.011-0.00615.772-0.297-0.2970.0000.0000.0000.000
75L75THR00.007-0.01512.3200.9870.9870.0000.0000.0000.000
76L76ASP-1-0.885-0.92714.21617.34417.3440.0000.0000.0000.000
77L77PHE0-0.027-0.00513.642-0.862-0.8620.0000.0000.0000.000
78L78THR0-0.048-0.04117.610-0.034-0.0340.0000.0000.0000.000
79L79LEU0-0.0140.00920.002-0.166-0.1660.0000.0000.0000.000
80L80THR0-0.033-0.03621.597-0.249-0.2490.0000.0000.0000.000
81L81ILE00.0040.01225.322-0.061-0.0610.0000.0000.0000.000
82L82SER0-0.032-0.03227.860-0.164-0.1640.0000.0000.0000.000
83L83SER00.0150.00431.208-0.255-0.2550.0000.0000.0000.000
84L84VAL0-0.0320.00229.371-0.001-0.0010.0000.0000.0000.000
85L85LYS11.0291.00331.686-8.927-8.9270.0000.0000.0000.000
86L86ALA00.0720.02331.8100.2550.2550.0000.0000.0000.000
87L87GLU-1-0.984-0.97931.7189.4809.4800.0000.0000.0000.000
88L88ASP-1-0.733-0.83727.96510.43910.4390.0000.0000.0000.000
89L89LEU00.0020.02826.8360.4960.4960.0000.0000.0000.000
90L90ALA0-0.021-0.02423.796-0.076-0.0760.0000.0000.0000.000
91L91VAL0-0.0160.00218.324-0.110-0.1100.0000.0000.0000.000
92L92TYR00.001-0.02019.188-0.066-0.0660.0000.0000.0000.000
93L93PHE0-0.0080.00213.7950.2910.2910.0000.0000.0000.000
94L95GLN00.0420.0319.855-0.511-0.5110.0000.0000.0000.000
95L96GLN00.0550.0325.167-5.931-5.9310.0000.0000.0000.000
96L97TYR0-0.004-0.0268.9961.3061.3060.0000.0000.0000.000
97L98TYR00.0100.0078.219-1.746-1.7460.0000.0000.0000.000
98L99THR0-0.010-0.0074.798-3.238-3.199-0.001-0.003-0.0350.000
99L100TYR0-0.0460.0016.6410.8570.8570.0000.0000.0000.000
100L101PRO00.0630.0222.959-8.542-5.1140.831-1.736-2.5220.018
101L102LEU0-0.028-0.0164.6860.3450.417-0.001-0.005-0.0660.000
102L103THR0-0.013-0.0082.4910.3840.9090.437-0.237-0.7250.000
103L104PHE00.010-0.0075.848-3.977-3.9770.0000.0000.0000.000
104L105GLY00.0130.0138.4141.7041.7040.0000.0000.0000.000
105L106ALA0-0.020-0.02510.707-0.179-0.1790.0000.0000.0000.000
106L107GLY0-0.0030.00412.988-0.995-0.9950.0000.0000.0000.000
107L108THR0-0.082-0.06315.9680.0380.0380.0000.0000.0000.000
108L109LYS10.9540.97519.260-12.176-12.1760.0000.0000.0000.000
109L110LEU0-0.044-0.01722.270-0.227-0.2270.0000.0000.0000.000
110L111GLU-1-0.849-0.88125.60310.27110.2710.0000.0000.0000.000
111L112LEU00.0340.00228.652-0.038-0.0380.0000.0000.0000.000
112L113LYS10.9290.98032.263-8.842-8.8420.0000.0000.0000.000
113L114ARG10.8650.92933.877-8.170-8.1700.0000.0000.0000.000
114L115ALA0-0.023-0.00336.7350.1050.1050.0000.0000.0000.000
115L116ASP-1-0.858-0.94435.9088.6598.6590.0000.0000.0000.000
116L117ALA0-0.039-0.02337.959-0.250-0.2500.0000.0000.0000.000
117L118ALA00.0420.02938.4090.2210.2210.0000.0000.0000.000
118L119PRO0-0.0370.00538.109-0.070-0.0700.0000.0000.0000.000
119L120THR00.0310.00840.183-0.236-0.2360.0000.0000.0000.000
120L121VAL0-0.020-0.01740.7840.1190.1190.0000.0000.0000.000
121L122SER0-0.046-0.02443.074-0.222-0.2220.0000.0000.0000.000
122L123ILE00.0110.00443.3950.2020.2020.0000.0000.0000.000
123L124PHE0-0.030-0.02044.380-0.192-0.1920.0000.0000.0000.000
124L125PRO00.0260.01645.3380.1540.1540.0000.0000.0000.000
125L126PRO00.0030.01045.6810.0170.0170.0000.0000.0000.000
126L127SER00.0450.03947.272-0.121-0.1210.0000.0000.0000.000
127L128SER00.0510.01149.6130.0050.0050.0000.0000.0000.000
128L129GLU-1-0.899-0.96150.0276.1786.1780.0000.0000.0000.000
129L130GLN00.0330.00242.442-0.042-0.0420.0000.0000.0000.000
130L131LEU00.0340.03247.8380.0470.0470.0000.0000.0000.000
131L132THR0-0.090-0.03149.729-0.046-0.0460.0000.0000.0000.000
132L133SER0-0.096-0.05347.228-0.003-0.0030.0000.0000.0000.000
133L134GLY00.005-0.00547.3780.1000.1000.0000.0000.0000.000
134L135GLY0-0.029-0.01444.2200.1400.1400.0000.0000.0000.000
135L136ALA0-0.003-0.01643.564-0.180-0.1800.0000.0000.0000.000
136L137SER0-0.0190.01040.2010.1530.1530.0000.0000.0000.000
137L138VAL0-0.0060.01241.574-0.181-0.1810.0000.0000.0000.000
138L139VAL00.0100.01139.7960.2580.2580.0000.0000.0000.000
139L140CYS0-0.061-0.01439.0980.0130.0130.0000.0000.0000.000
140L141PHE0-0.017-0.00438.9290.2840.2840.0000.0000.0000.000
141L142LEU0-0.004-0.01635.861-0.196-0.1960.0000.0000.0000.000
142L143ASN00.0410.00037.5510.4280.4280.0000.0000.0000.000
143L144ASN00.0150.00238.695-0.241-0.2410.0000.0000.0000.000
144L145PHE0-0.017-0.00232.568-0.166-0.1660.0000.0000.0000.000
145L146TYR0-0.009-0.03531.3720.1390.1390.0000.0000.0000.000
146L147PRO0-0.007-0.00330.692-0.230-0.2300.0000.0000.0000.000
147L148LYS11.0020.97325.442-11.628-11.6280.0000.0000.0000.000
148L149ASP-1-0.963-0.94826.58311.53211.5320.0000.0000.0000.000
149L150ILE0-0.023-0.01229.464-0.399-0.3990.0000.0000.0000.000
150L151ASN0-0.033-0.00429.7370.5390.5390.0000.0000.0000.000
151L152VAL00.0310.01232.443-0.312-0.3120.0000.0000.0000.000
152L153LYS10.9140.96733.978-8.301-8.3010.0000.0000.0000.000
153L154TRP00.0250.00336.280-0.355-0.3550.0000.0000.0000.000
154L155LYS10.8830.94238.937-7.556-7.5560.0000.0000.0000.000
155L156ILE00.0130.00441.609-0.089-0.0890.0000.0000.0000.000
156L157ASP-1-0.784-0.89044.4956.5856.5850.0000.0000.0000.000
157L158GLY00.004-0.01645.805-0.101-0.1010.0000.0000.0000.000
158L159SER0-0.087-0.03942.2270.1270.1270.0000.0000.0000.000
159L160GLU-1-0.918-0.96134.8438.8378.8370.0000.0000.0000.000
160L161ARG10.8860.95037.585-8.090-8.0900.0000.0000.0000.000
161L162GLN00.0560.02531.695-0.096-0.0960.0000.0000.0000.000
162L163ASN0-0.005-0.00533.0580.4320.4320.0000.0000.0000.000
163L164GLY00.0330.01033.556-0.278-0.2780.0000.0000.0000.000
164L165VAL0-0.0140.01433.014-0.226-0.2260.0000.0000.0000.000
165L166LEU0-0.003-0.00429.2870.3780.3780.0000.0000.0000.000
166L167ASN00.0230.01129.974-0.663-0.6630.0000.0000.0000.000
167L168SER0-0.0120.00529.8690.4690.4690.0000.0000.0000.000
168L169TRP00.0240.00127.058-0.218-0.2180.0000.0000.0000.000
169L170THR00.0290.02130.3880.1170.1170.0000.0000.0000.000
170L171ASP-1-0.928-0.96328.50411.13111.1310.0000.0000.0000.000
171L172GLN0-0.105-0.06630.256-0.075-0.0750.0000.0000.0000.000
172L173ASP-1-0.809-0.89532.1708.1428.1420.0000.0000.0000.000
173L174SER0-0.030-0.02635.645-0.073-0.0730.0000.0000.0000.000
174L175LYS10.8750.93236.545-7.446-7.4460.0000.0000.0000.000
175L176ASP-1-0.807-0.88439.0867.8477.8470.0000.0000.0000.000
176L177SER00.0000.00135.3120.0250.0250.0000.0000.0000.000
177L178THR0-0.095-0.05435.0220.2320.2320.0000.0000.0000.000
178L179TYR0-0.054-0.05429.4860.3510.3510.0000.0000.0000.000
179L180SER00.0470.02834.307-0.381-0.3810.0000.0000.0000.000
180L181MET0-0.044-0.00431.6400.3380.3380.0000.0000.0000.000
181L182SER0-0.0100.01234.437-0.250-0.2500.0000.0000.0000.000
182L183SER00.009-0.00634.2730.2510.2510.0000.0000.0000.000
183L184THR00.009-0.00235.452-0.387-0.3870.0000.0000.0000.000
184L185LEU0-0.0010.01136.0810.2610.2610.0000.0000.0000.000
185L186THR0-0.026-0.03337.389-0.276-0.2760.0000.0000.0000.000
186L187LEU0-0.054-0.02438.8210.1410.1410.0000.0000.0000.000
187L188THR00.0550.02241.586-0.075-0.0750.0000.0000.0000.000
188L189LYS10.9800.99044.043-6.212-6.2120.0000.0000.0000.000
189L190ASP-1-0.877-0.93847.5296.3886.3880.0000.0000.0000.000
190L191GLU-1-0.988-1.00442.5007.4487.4480.0000.0000.0000.000
191L192TYR00.0610.01345.720-0.044-0.0440.0000.0000.0000.000
192L193GLU-1-0.876-0.95347.0556.0586.0580.0000.0000.0000.000
193L194ARG10.8870.96645.387-6.930-6.9300.0000.0000.0000.000
194L195HIS10.7970.90645.442-6.900-6.9000.0000.0000.0000.000
195L196ASN00.0470.02349.591-0.106-0.1060.0000.0000.0000.000
196L197SER00.0150.05648.7570.0110.0110.0000.0000.0000.000
197L198TYR0-0.027-0.02144.2700.2410.2410.0000.0000.0000.000
198L199THR00.0380.02843.128-0.159-0.1590.0000.0000.0000.000
199L201GLU-1-0.893-0.97139.3837.4257.4250.0000.0000.0000.000
200L202ALA00.0180.01337.1800.2720.2720.0000.0000.0000.000
201L203THR0-0.006-0.00334.857-0.241-0.2410.0000.0000.0000.000
202L204HIS00.0490.01534.0550.0640.0640.0000.0000.0000.000
203L205LYS10.9580.97532.007-9.409-9.4090.0000.0000.0000.000
204L206THR0-0.032-0.03535.614-0.167-0.1670.0000.0000.0000.000
205L207SER0-0.034-0.01638.938-0.303-0.3030.0000.0000.0000.000
206L208THR0-0.021-0.00639.3190.1590.1590.0000.0000.0000.000
207L209SER00.0220.01840.6200.0350.0350.0000.0000.0000.000
208L210PRO0-0.010-0.00339.6860.0070.0070.0000.0000.0000.000
209L211ILE00.0000.01440.917-0.221-0.2210.0000.0000.0000.000
210L212VAL00.0150.00442.0770.1630.1630.0000.0000.0000.000
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