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

tag_button

FMODB ID: V5651

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2282547.38043
FMO2-HF: Nuclear repulsion 2196813.588348
FMO2-HF: Total energy -85733.792082
FMO2-MP2: Total energy -85982.876587


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.
-39.881-34.4112.678-3.22-4.9260.032
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 : -0.910 / q_NPA : -0.967
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].
3L3VAL00.0410.0313.863-0.7701.018-0.008-0.773-1.0060.005
4L4MET0-0.0190.0005.309-3.425-3.380-0.001-0.004-0.0400.000
5L5SER00.0290.0018.449-0.979-0.9790.0000.0000.0000.000
6L6GLN0-0.029-0.03011.377-0.053-0.0530.0000.0000.0000.000
7L7SER0-0.050-0.00114.326-0.382-0.3820.0000.0000.0000.000
8L8PRO00.0270.00917.761-0.245-0.2450.0000.0000.0000.000
9L9SER00.0850.03817.7750.1390.1390.0000.0000.0000.000
10L10SER00.0130.00819.072-0.130-0.1300.0000.0000.0000.000
11L11LEU0-0.026-0.01922.820-0.113-0.1130.0000.0000.0000.000
12L12ALA00.0330.02625.485-0.089-0.0890.0000.0000.0000.000
13L13VAL0-0.047-0.02328.196-0.070-0.0700.0000.0000.0000.000
14L14SER00.000-0.03331.006-0.155-0.1550.0000.0000.0000.000
15L15VAL0-0.035-0.02434.2030.1280.1280.0000.0000.0000.000
16L16GLY00.0240.01935.160-0.250-0.2500.0000.0000.0000.000
17L17GLU-1-0.758-0.83732.6249.1339.1330.0000.0000.0000.000
18L18LYS10.9460.98628.434-10.234-10.2340.0000.0000.0000.000
19L19VAL0-0.0040.00525.7850.1100.1100.0000.0000.0000.000
20L20SER0-0.021-0.04124.758-0.129-0.1290.0000.0000.0000.000
21L21MET0-0.0140.01320.0550.0510.0510.0000.0000.0000.000
22L22SER0-0.0190.00018.3580.2340.2340.0000.0000.0000.000
23L23CYS0-0.034-0.01412.7790.4330.4330.0000.0000.0000.000
24L24LYS10.8920.96613.050-16.808-16.8080.0000.0000.0000.000
25L25SER00.0500.0159.0970.7710.7710.0000.0000.0000.000
26L26SER0-0.028-0.0105.927-0.654-0.6540.0000.0000.0000.000
27L27GLN00.009-0.0015.4793.5263.512-0.001-0.0050.0210.000
28L28SER00.0090.0039.433-0.685-0.6850.0000.0000.0000.000
29L29LEU00.0140.0068.7821.5571.5570.0000.0000.0000.000
30L30PHE0-0.0140.01412.329-0.498-0.4980.0000.0000.0000.000
31L31TYR00.0240.00415.1410.3290.3290.0000.0000.0000.000
32L32SER00.0420.00016.904-0.532-0.5320.0000.0000.0000.000
33L33SER0-0.019-0.00119.823-0.757-0.7570.0000.0000.0000.000
34L34TYR0-0.018-0.01018.032-0.147-0.1470.0000.0000.0000.000
35L35GLN0-0.053-0.02621.798-0.473-0.4730.0000.0000.0000.000
36L36LYS10.9240.97119.402-13.204-13.2040.0000.0000.0000.000
37L37ASP-1-0.721-0.83515.42417.31217.3120.0000.0000.0000.000
38L38LEU0-0.055-0.01312.420-0.667-0.6670.0000.0000.0000.000
39L39LEU00.0010.00412.0721.9651.9650.0000.0000.0000.000
40L40ALA0-0.014-0.00613.957-1.532-1.5320.0000.0000.0000.000
41L41TRP00.014-0.00815.2921.0071.0070.0000.0000.0000.000
42L42TYR0-0.005-0.01214.905-1.217-1.2170.0000.0000.0000.000
43L43GLN00.0340.01919.291-0.218-0.2180.0000.0000.0000.000
44L44GLN00.003-0.01818.7260.8440.8440.0000.0000.0000.000
45L45LYS10.8470.91422.052-11.395-11.3950.0000.0000.0000.000
46L46PRO00.0610.01024.5960.3210.3210.0000.0000.0000.000
47L47GLY00.0120.01025.729-0.319-0.3190.0000.0000.0000.000
48L48GLN0-0.0240.00724.832-0.213-0.2130.0000.0000.0000.000
49L49SER00.0400.02320.9560.2650.2650.0000.0000.0000.000
50L50PRO00.000-0.00516.969-0.591-0.5910.0000.0000.0000.000
51L51LYS10.8930.95420.069-12.118-12.1180.0000.0000.0000.000
52L52LEU00.0290.01918.8930.2390.2390.0000.0000.0000.000
53L53LEU0-0.054-0.01220.948-0.702-0.7020.0000.0000.0000.000
54L54ILE0-0.030-0.02320.061-0.594-0.5940.0000.0000.0000.000
55L55TYR00.0440.01218.3051.0411.0410.0000.0000.0000.000
56L56TRP00.0230.00917.676-1.027-1.0270.0000.0000.0000.000
57L57ALA00.0170.00717.253-0.745-0.7450.0000.0000.0000.000
58L58SER0-0.085-0.04018.693-0.539-0.5390.0000.0000.0000.000
59L59THR0-0.045-0.01822.087-0.771-0.7710.0000.0000.0000.000
60L60ARG10.8810.94223.143-10.122-10.1220.0000.0000.0000.000
61L61GLU-1-0.791-0.88323.75212.37712.3770.0000.0000.0000.000
62L62SER0-0.044-0.03225.626-0.519-0.5190.0000.0000.0000.000
63L63GLY00.0100.00529.1790.0910.0910.0000.0000.0000.000
64L64VAL0-0.063-0.01425.518-0.114-0.1140.0000.0000.0000.000
65L65PRO0-0.021-0.01928.887-0.198-0.1980.0000.0000.0000.000
66L66ASP-1-0.856-0.94529.8369.4879.4870.0000.0000.0000.000
67L67ARG10.7500.85030.053-9.735-9.7350.0000.0000.0000.000
68L68PHE0-0.0040.00625.3640.2030.2030.0000.0000.0000.000
69L69THR00.0160.00225.928-0.133-0.1330.0000.0000.0000.000
70L70GLY00.0050.01621.6580.1920.1920.0000.0000.0000.000
71L71SER0-0.024-0.02421.295-0.610-0.6100.0000.0000.0000.000
72L72GLY00.0570.01419.3480.5570.5570.0000.0000.0000.000
73L73SER0-0.069-0.06218.001-0.316-0.3160.0000.0000.0000.000
74L74GLY00.0000.00715.642-0.207-0.2070.0000.0000.0000.000
75L75THR00.004-0.02412.3651.1481.1480.0000.0000.0000.000
76L76ASP-1-0.870-0.91113.97417.66217.6620.0000.0000.0000.000
77L77PHE00.0110.00613.611-0.991-0.9910.0000.0000.0000.000
78L78THR0-0.049-0.02917.883-0.003-0.0030.0000.0000.0000.000
79L79LEU0-0.0060.02620.254-0.298-0.2980.0000.0000.0000.000
80L80THR0-0.011-0.01821.818-0.328-0.3280.0000.0000.0000.000
81L81ILE0-0.0030.01325.5670.0170.0170.0000.0000.0000.000
82L82SER0-0.015-0.02028.348-0.182-0.1820.0000.0000.0000.000
83L83SER0-0.027-0.02131.687-0.281-0.2810.0000.0000.0000.000
84L84VAL0-0.0100.01529.547-0.048-0.0480.0000.0000.0000.000
85L85LYS10.9260.94931.889-9.243-9.2430.0000.0000.0000.000
86L86ALA00.0720.02732.1050.2630.2630.0000.0000.0000.000
87L87GLU-1-0.833-0.90632.1389.5969.5960.0000.0000.0000.000
88L88ASP-1-0.795-0.86928.26010.66910.6690.0000.0000.0000.000
89L89LEU00.0080.02427.2050.4810.4810.0000.0000.0000.000
90L90ALA0-0.011-0.01624.155-0.068-0.0680.0000.0000.0000.000
91L91VAL0-0.0100.00718.655-0.093-0.0930.0000.0000.0000.000
92L92TYR0-0.013-0.02219.576-0.144-0.1440.0000.0000.0000.000
93L93PHE00.0260.01914.1380.2750.2750.0000.0000.0000.000
94L95GLN00.0130.00010.388-0.511-0.5110.0000.0000.0000.000
95L96GLN00.0460.0215.173-6.080-6.0800.0000.0000.0000.000
96L97TYR00.014-0.0179.3101.2261.2260.0000.0000.0000.000
97L98TYR0-0.0040.0028.651-1.563-1.5630.0000.0000.0000.000
98L99THR0-0.022-0.0204.550-3.103-3.060-0.001-0.004-0.0380.000
99L100TYR0-0.0250.0086.5110.5770.5770.0000.0000.0000.000
100L101PRO00.0520.0272.655-9.380-6.4342.659-2.267-3.3390.026
101L102LEU0-0.019-0.0024.5280.2730.308-0.001-0.010-0.0230.000
102L103THR0-0.023-0.0183.213-0.0720.5550.031-0.157-0.5010.001
103L104PHE00.016-0.0086.689-4.322-4.3220.0000.0000.0000.000
104L105GLY00.0270.0098.5021.9061.9060.0000.0000.0000.000
105L106ALA0-0.031-0.02410.852-0.398-0.3980.0000.0000.0000.000
106L107GLY00.0080.00912.467-0.951-0.9510.0000.0000.0000.000
107L108THR0-0.053-0.04615.7660.0260.0260.0000.0000.0000.000
108L109LYS10.8270.91219.166-12.172-12.1720.0000.0000.0000.000
109L110LEU0-0.043-0.01422.327-0.223-0.2230.0000.0000.0000.000
110L111GLU-1-0.787-0.85025.68410.68510.6850.0000.0000.0000.000
111L112LEU00.010-0.00528.774-0.086-0.0860.0000.0000.0000.000
112L113LYS10.8160.89632.068-9.178-9.1780.0000.0000.0000.000
113L114ARG10.8230.91133.598-8.317-8.3170.0000.0000.0000.000
114L115ALA00.0190.01136.3490.1140.1140.0000.0000.0000.000
115L116ASP-1-0.816-0.88135.8008.6388.6380.0000.0000.0000.000
116L117ALA0-0.019-0.01137.683-0.238-0.2380.0000.0000.0000.000
117L118ALA00.0460.02738.0790.2220.2220.0000.0000.0000.000
118L119PRO0-0.0220.00037.882-0.079-0.0790.0000.0000.0000.000
119L120THR00.0210.00439.834-0.234-0.2340.0000.0000.0000.000
120L121VAL0-0.053-0.02540.3140.0600.0600.0000.0000.0000.000
121L122SER0-0.041-0.02242.593-0.231-0.2310.0000.0000.0000.000
122L123ILE00.003-0.00942.9990.2030.2030.0000.0000.0000.000
123L124PHE0-0.007-0.00544.264-0.185-0.1850.0000.0000.0000.000
124L125PRO00.0180.00645.2580.1630.1630.0000.0000.0000.000
125L126PRO0-0.0020.01145.1470.0210.0210.0000.0000.0000.000
126L127SER0-0.027-0.02347.006-0.105-0.1050.0000.0000.0000.000
127L128SER00.041-0.00849.6650.0130.0130.0000.0000.0000.000
128L129GLU-1-0.822-0.86649.7926.2656.2650.0000.0000.0000.000
129L130GLN00.0420.01742.402-0.041-0.0410.0000.0000.0000.000
130L131LEU00.0430.02447.7800.0460.0460.0000.0000.0000.000
131L132THR0-0.078-0.04649.879-0.074-0.0740.0000.0000.0000.000
132L133SER0-0.111-0.06246.9400.0190.0190.0000.0000.0000.000
133L134GLY00.0320.02047.4100.0950.0950.0000.0000.0000.000
134L135GLY0-0.033-0.01744.2980.1050.1050.0000.0000.0000.000
135L136ALA0-0.010-0.01243.658-0.160-0.1600.0000.0000.0000.000
136L137SER0-0.021-0.01439.9320.1530.1530.0000.0000.0000.000
137L138VAL0-0.0040.01341.968-0.148-0.1480.0000.0000.0000.000
138L139VAL0-0.0050.00339.7320.2500.2500.0000.0000.0000.000
139L140CYS0-0.071-0.02339.1950.0360.0360.0000.0000.0000.000
140L141PHE00.0050.00438.8270.2750.2750.0000.0000.0000.000
141L142LEU00.013-0.00836.168-0.193-0.1930.0000.0000.0000.000
142L143ASN00.026-0.00237.2810.4290.4290.0000.0000.0000.000
143L144ASN0-0.016-0.02038.703-0.181-0.1810.0000.0000.0000.000
144L145PHE00.0030.01732.465-0.144-0.1440.0000.0000.0000.000
145L146TYR00.003-0.03130.6860.1360.1360.0000.0000.0000.000
146L147PRO00.0110.00230.215-0.255-0.2550.0000.0000.0000.000
147L148LYS10.8780.92425.615-11.528-11.5280.0000.0000.0000.000
148L149ASP-1-0.924-0.95426.33711.35111.3510.0000.0000.0000.000
149L150ILE0-0.032-0.01229.286-0.375-0.3750.0000.0000.0000.000
150L151ASN0-0.046-0.02029.2310.4360.4360.0000.0000.0000.000
151L152VAL00.0100.01332.316-0.303-0.3030.0000.0000.0000.000
152L153LYS10.8090.89833.780-8.505-8.5050.0000.0000.0000.000
153L154TRP00.0390.00636.254-0.318-0.3180.0000.0000.0000.000
154L155LYS10.8410.92238.924-7.491-7.4910.0000.0000.0000.000
155L156ILE00.0140.01341.831-0.064-0.0640.0000.0000.0000.000
156L157ASP-1-0.786-0.89544.6026.5696.5690.0000.0000.0000.000
157L158GLY00.000-0.00445.717-0.133-0.1330.0000.0000.0000.000
158L159SER0-0.035-0.00841.4060.1230.1230.0000.0000.0000.000
159L160GLU-1-0.833-0.90535.2828.7658.7650.0000.0000.0000.000
160L161ARG10.8380.90037.730-8.095-8.0950.0000.0000.0000.000
161L162GLN00.0280.01932.197-0.002-0.0020.0000.0000.0000.000
162L163ASN00.005-0.00733.7720.2140.2140.0000.0000.0000.000
163L164GLY00.0840.03634.087-0.326-0.3260.0000.0000.0000.000
164L165VAL0-0.0470.00033.320-0.137-0.1370.0000.0000.0000.000
165L166LEU00.0010.01030.6670.3700.3700.0000.0000.0000.000
166L167ASN00.0160.01129.979-0.629-0.6290.0000.0000.0000.000
167L168SER0-0.0040.00430.1810.4270.4270.0000.0000.0000.000
168L169TRP00.0430.00727.625-0.236-0.2360.0000.0000.0000.000
169L170THR0-0.010-0.00830.6440.0870.0870.0000.0000.0000.000
170L171ASP-1-0.803-0.89627.68911.59411.5940.0000.0000.0000.000
171L172GLN0-0.046-0.02229.961-0.141-0.1410.0000.0000.0000.000
172L173ASP-1-0.778-0.88931.9378.2358.2350.0000.0000.0000.000
173L174SER0-0.073-0.03735.532-0.051-0.0510.0000.0000.0000.000
174L175LYS10.8580.92236.776-7.579-7.5790.0000.0000.0000.000
175L176ASP-1-0.760-0.84538.6717.9007.9000.0000.0000.0000.000
176L177SER0-0.030-0.00834.9980.0350.0350.0000.0000.0000.000
177L178THR0-0.095-0.06034.7150.2370.2370.0000.0000.0000.000
178L179TYR0-0.023-0.03428.5160.3160.3160.0000.0000.0000.000
179L180SER00.0220.01433.883-0.400-0.4000.0000.0000.0000.000
180L181MET0-0.062-0.00731.4920.2940.2940.0000.0000.0000.000
181L182SER0-0.0180.00134.273-0.321-0.3210.0000.0000.0000.000
182L183SER00.0350.00334.1670.2630.2630.0000.0000.0000.000
183L184THR0-0.028-0.03235.652-0.326-0.3260.0000.0000.0000.000
184L185LEU00.0230.04036.3770.2520.2520.0000.0000.0000.000
185L186THR0-0.017-0.01337.504-0.299-0.2990.0000.0000.0000.000
186L187LEU0-0.061-0.02839.0330.1330.1330.0000.0000.0000.000
187L188THR00.033-0.00941.7960.0290.0290.0000.0000.0000.000
188L189LYS10.8490.90544.425-6.144-6.1440.0000.0000.0000.000
189L190ASP-1-0.798-0.87647.6716.7436.7430.0000.0000.0000.000
190L191GLU-1-0.829-0.91043.0897.2367.2360.0000.0000.0000.000
191L192TYR00.0320.00846.123-0.033-0.0330.0000.0000.0000.000
192L193GLU-1-0.783-0.89047.3236.0556.0550.0000.0000.0000.000
193L194ARG10.7930.90445.744-6.922-6.9220.0000.0000.0000.000
194L195HIS10.7930.91645.814-6.871-6.8710.0000.0000.0000.000
195L196ASN0-0.042-0.04250.077-0.074-0.0740.0000.0000.0000.000
196L197SER0-0.0020.01648.8620.0500.0500.0000.0000.0000.000
197L198TYR0-0.013-0.02644.4830.2430.2430.0000.0000.0000.000
198L199THR00.0080.01043.560-0.140-0.1400.0000.0000.0000.000
199L201GLU-1-0.857-0.94939.1817.5257.5250.0000.0000.0000.000
200L202ALA00.015-0.00237.1710.2690.2690.0000.0000.0000.000
201L203THR00.0090.00534.735-0.245-0.2450.0000.0000.0000.000
202L204HIS00.0240.00433.7460.0540.0540.0000.0000.0000.000
203L205LYS10.8640.90933.179-9.018-9.0180.0000.0000.0000.000
204L206THR0-0.036-0.03635.382-0.180-0.1800.0000.0000.0000.000
205L207SER0-0.040-0.02938.692-0.293-0.2930.0000.0000.0000.000
206L208THR00.0000.00339.1230.1650.1650.0000.0000.0000.000
207L209SER00.0040.01140.799-0.020-0.0200.0000.0000.0000.000
208L210PRO0-0.0220.00939.239-0.011-0.0110.0000.0000.0000.000
209L211ILE00.0260.01640.760-0.225-0.2250.0000.0000.0000.000
210L212VAL00.004-0.00341.7670.1680.1680.0000.0000.0000.000
211L213LYS10.8700.93844.083-6.932-6.9320.0000.0000.0000.000
212L214SER00.019-0.01145.0300.0980.0980.0000.0000.0000.000
213L215PHE00.0060.00546.347-0.096-0.0960.0000.0000.0000.000
214L216ASN00.000-0.00549.7840.2330.2330.0000.0000.0000.000
215L217ARG10.8330.91950.592-6.148-6.1480.0000.0000.0000.000
216L218ASN0-0.025-0.00752.726-0.035-0.0350.0000.0000.0000.000
217L219GLU-1-0.824-0.88255.4985.6245.6240.0000.0000.0000.000