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: MVZMZ

Calculation Name: 1KCV-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KCV

Chain ID: L

ChEMBL ID:

UniProt ID: P18532

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079304.833704
FMO2-HF: Nuclear repulsion 1997237.244507
FMO2-HF: Total energy -82067.589197
FMO2-MP2: Total energy -82302.828879


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.
-3.5551.6942.147-2.752-4.6430.026
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 : -0.923 / q_NPA : -0.974
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].
3L3VAL00.0290.0253.868-0.8080.828-0.009-0.692-0.9340.004
4L4MET0-0.0240.0065.469-4.022-4.0220.0000.0000.0000.000
5L5THR0-0.014-0.0178.590-0.062-0.0620.0000.0000.0000.000
6L6GLN0-0.008-0.03411.4240.2760.2760.0000.0000.0000.000
7L7SER0-0.0290.00314.933-0.223-0.2230.0000.0000.0000.000
8L8PRO00.0420.01617.889-0.211-0.2110.0000.0000.0000.000
9L9LYS10.9030.96016.310-16.729-16.7290.0000.0000.0000.000
10L10SER0-0.024-0.01819.6160.0070.0070.0000.0000.0000.000
11L11MET00.0040.00623.188-0.176-0.1760.0000.0000.0000.000
12L12GLY00.0500.02926.111-0.035-0.0350.0000.0000.0000.000
13L13MET0-0.066-0.02928.982-0.203-0.2030.0000.0000.0000.000
14L14SER00.007-0.01831.912-0.047-0.0470.0000.0000.0000.000
15L15VAL0-0.010-0.01334.6240.1430.1430.0000.0000.0000.000
16L16GLY0-0.0030.01435.594-0.263-0.2630.0000.0000.0000.000
17L17GLU-1-0.803-0.86133.1918.8768.8760.0000.0000.0000.000
18L18ALA00.0190.02032.0630.2150.2150.0000.0000.0000.000
19L19VAL0-0.011-0.01426.6560.0470.0470.0000.0000.0000.000
20L20THR0-0.027-0.01723.8050.0610.0610.0000.0000.0000.000
21L21LEU00.0100.02520.2620.0390.0390.0000.0000.0000.000
22L22ASN0-0.077-0.06918.777-0.002-0.0020.0000.0000.0000.000
23L23CYS0-0.043-0.01713.2900.2480.2480.0000.0000.0000.000
24L24LYS10.8070.90313.477-16.617-16.6170.0000.0000.0000.000
25L25ALA00.0350.0179.1741.3641.3640.0000.0000.0000.000
26L26SER00.0120.0076.350-0.657-0.6570.0000.0000.0000.000
27L27GLU-1-0.948-0.9735.39935.18635.1860.0000.0000.0000.000
28L28ASN0-0.011-0.0129.407-1.107-1.1070.0000.0000.0000.000
29L29VAL00.0440.0168.6321.8771.8770.0000.0000.0000.000
30L30GLY0-0.004-0.00411.258-0.805-0.8050.0000.0000.0000.000
31L31THR00.0270.00015.029-0.463-0.4630.0000.0000.0000.000
32L32TYR0-0.0210.01312.598-0.752-0.7520.0000.0000.0000.000
33L33VAL00.0200.00511.9601.9781.9780.0000.0000.0000.000
34L34SER0-0.027-0.01213.909-1.563-1.5630.0000.0000.0000.000
35L35TRP0-0.014-0.00615.1691.2861.2860.0000.0000.0000.000
36L36TYR00.014-0.00214.324-0.970-0.9700.0000.0000.0000.000
37L37GLN0-0.009-0.01019.374-0.032-0.0320.0000.0000.0000.000
38L38GLN0-0.009-0.02519.3420.7770.7770.0000.0000.0000.000
39L39LYS10.8880.95622.583-10.760-10.7600.0000.0000.0000.000
40L40PRO00.0560.01925.5960.3040.3040.0000.0000.0000.000
41L41GLY0-0.018-0.00126.484-0.318-0.3180.0000.0000.0000.000
42L42GLN0-0.052-0.01625.681-0.239-0.2390.0000.0000.0000.000
43L43SER00.0190.01621.7090.3120.3120.0000.0000.0000.000
44L44PRO0-0.014-0.01717.584-0.405-0.4050.0000.0000.0000.000
45L45VAL0-0.0110.00920.523-0.242-0.2420.0000.0000.0000.000
46L46LEU0-0.021-0.00718.5270.3160.3160.0000.0000.0000.000
47L47LEU0-0.022-0.00620.993-0.678-0.6780.0000.0000.0000.000
48L48ILE0-0.009-0.00920.369-0.605-0.6050.0000.0000.0000.000
49L49TYR00.0340.01218.2471.0051.0050.0000.0000.0000.000
50L50GLY00.0320.02317.489-0.747-0.7470.0000.0000.0000.000
51L51ALA0-0.004-0.00417.556-0.677-0.6770.0000.0000.0000.000
52L52SER0-0.016-0.02218.751-0.128-0.1280.0000.0000.0000.000
53L53ASN0-0.095-0.03121.399-1.109-1.1090.0000.0000.0000.000
54L54ARG10.8350.90923.004-9.827-9.8270.0000.0000.0000.000
55L55TYR00.0050.00123.289-0.103-0.1030.0000.0000.0000.000
56L56THR00.024-0.00525.293-0.371-0.3710.0000.0000.0000.000
57L57GLY0-0.016-0.00128.5830.1280.1280.0000.0000.0000.000
58L58VAL0-0.0340.00525.522-0.173-0.1730.0000.0000.0000.000
59L59PRO00.0040.00328.939-0.181-0.1810.0000.0000.0000.000
60L60ASP-1-0.796-0.92430.2819.6919.6910.0000.0000.0000.000
61L61ARG10.7350.85829.939-9.798-9.7980.0000.0000.0000.000
62L62PHE00.0270.02225.7840.1770.1770.0000.0000.0000.000
63L63THR0-0.005-0.00226.298-0.164-0.1640.0000.0000.0000.000
64L64GLY00.0460.01522.1670.3100.3100.0000.0000.0000.000
65L65SER0-0.040-0.01321.493-0.530-0.5300.0000.0000.0000.000
66L66GLY00.0660.02318.9410.5380.5380.0000.0000.0000.000
67L67SER0-0.025-0.03217.337-0.221-0.2210.0000.0000.0000.000
68L68ALA00.0100.01815.055-0.046-0.0460.0000.0000.0000.000
69L69THR00.0140.00512.1841.1611.1610.0000.0000.0000.000
70L70ASP-1-0.769-0.86314.04616.08316.0830.0000.0000.0000.000
71L71PHE00.0380.02413.754-0.580-0.5800.0000.0000.0000.000
72L72THR0-0.028-0.01517.8940.1410.1410.0000.0000.0000.000
73L73LEU00.0090.02820.5260.0380.0380.0000.0000.0000.000
74L74THR0-0.005-0.02522.232-0.019-0.0190.0000.0000.0000.000
75L75ILE0-0.009-0.00425.657-0.082-0.0820.0000.0000.0000.000
76L76SER00.011-0.01128.657-0.148-0.1480.0000.0000.0000.000
77L77SER0-0.005-0.01432.083-0.358-0.3580.0000.0000.0000.000
78L78VAL0-0.0220.01629.4650.1520.1520.0000.0000.0000.000
79L79GLN00.016-0.00532.187-0.390-0.3900.0000.0000.0000.000
80L80ALA00.0390.01532.7830.2490.2490.0000.0000.0000.000
81L81ASP-1-0.822-0.90131.9279.9429.9420.0000.0000.0000.000
82L82ASP-1-0.775-0.86528.71110.70410.7040.0000.0000.0000.000
83L83ASP-1-0.805-0.89427.69811.37611.3760.0000.0000.0000.000
84L84ALA0-0.002-0.01324.1400.0230.0230.0000.0000.0000.000
85L85ASP-1-0.822-0.88219.64114.92614.9260.0000.0000.0000.000
86L86TYR0-0.044-0.03419.871-0.154-0.1540.0000.0000.0000.000
87L87TYR0-0.036-0.01614.1070.7550.7550.0000.0000.0000.000
88L89GLY00.0450.01110.5161.4861.4860.0000.0000.0000.000
89L90GLN0-0.021-0.0155.250-6.143-6.1430.0000.0000.0000.000
90L91SER00.015-0.0088.8961.5871.5870.0000.0000.0000.000
91L92TYR0-0.0420.0038.800-2.640-2.6400.0000.0000.0000.000
92L93SER00.001-0.0035.663-1.130-1.1300.0000.0000.0000.000
93L94SER0-0.035-0.0066.244-0.325-0.3250.0000.0000.0000.000
94L95PRO00.0530.0262.690-6.561-3.7202.117-1.848-3.1110.021
95L96LEU0-0.008-0.0054.421-0.419-0.356-0.001-0.015-0.0460.000
96L97THR0-0.045-0.0253.3370.2820.9910.040-0.197-0.5520.001
97L98PHE00.011-0.0156.505-4.852-4.8520.0000.0000.0000.000
98L99GLY00.0170.0228.5141.8551.8550.0000.0000.0000.000
99L100GLY0-0.017-0.02010.928-0.383-0.3830.0000.0000.0000.000
100L101GLY00.0240.01112.631-1.093-1.0930.0000.0000.0000.000
101L102THR0-0.085-0.05615.9470.0810.0810.0000.0000.0000.000
102L103LYS10.8200.92019.284-11.894-11.8940.0000.0000.0000.000
103L104LEU0-0.045-0.02022.581-0.156-0.1560.0000.0000.0000.000
104L105GLU-1-0.770-0.84925.82010.50310.5030.0000.0000.0000.000
105L106LEU00.002-0.01129.174-0.081-0.0810.0000.0000.0000.000
106L107LYS10.7780.88632.586-9.067-9.0670.0000.0000.0000.000
107L108ARG10.8370.89935.082-7.817-7.8170.0000.0000.0000.000
108L109ALA00.0380.02338.770-0.016-0.0160.0000.0000.0000.000
109L110ASP-1-0.787-0.87541.6567.4837.4830.0000.0000.0000.000
110L111ALA0-0.007-0.01042.551-0.120-0.1200.0000.0000.0000.000
111L112ALA00.0430.02443.5540.1250.1250.0000.0000.0000.000
112L113PRO0-0.0230.00043.7430.0100.0100.0000.0000.0000.000
113L114THR00.0150.01045.389-0.220-0.2200.0000.0000.0000.000
114L115SER00.0080.00246.6000.1220.1220.0000.0000.0000.000
115L116SER0-0.041-0.02947.732-0.189-0.1890.0000.0000.0000.000
116L117ILE0-0.039-0.01748.0360.1400.1400.0000.0000.0000.000
117L118PHE00.0170.00746.637-0.097-0.0970.0000.0000.0000.000
118L119PRO00.0210.01049.9390.0990.0990.0000.0000.0000.000
119L120PRO0-0.0200.01049.8780.0870.0870.0000.0000.0000.000
120L121SER00.006-0.02450.292-0.109-0.1090.0000.0000.0000.000
121L122SER00.032-0.01352.073-0.021-0.0210.0000.0000.0000.000
122L123GLU-1-0.807-0.85750.2766.1976.1970.0000.0000.0000.000
123L124GLN00.0430.02845.912-0.043-0.0430.0000.0000.0000.000
124L125LEU00.0180.01549.939-0.003-0.0030.0000.0000.0000.000
125L126SER0-0.036-0.03053.209-0.096-0.0960.0000.0000.0000.000
126L127SER0-0.102-0.05149.0190.0270.0270.0000.0000.0000.000
127L128GLY00.0490.02850.2800.0680.0680.0000.0000.0000.000
128L129GLY0-0.052-0.02448.4300.0190.0190.0000.0000.0000.000
129L130ALA00.007-0.02048.889-0.101-0.1010.0000.0000.0000.000
130L131SER0-0.040-0.02444.6070.0290.0290.0000.0000.0000.000
131L132VAL00.0050.01746.910-0.053-0.0530.0000.0000.0000.000
132L133VAL00.0020.00343.6860.1560.1560.0000.0000.0000.000
133L134CYS0-0.058-0.02444.934-0.061-0.0610.0000.0000.0000.000
134L135PHE00.0090.00040.3180.1970.1970.0000.0000.0000.000
135L136LEU0-0.011-0.00542.219-0.218-0.2180.0000.0000.0000.000
136L137ASN00.0420.00941.7300.3820.3820.0000.0000.0000.000
137L138SER00.0270.00841.099-0.216-0.2160.0000.0000.0000.000
138L139PHE0-0.0150.00438.171-0.141-0.1410.0000.0000.0000.000
139L140TYR00.0460.01034.6430.1710.1710.0000.0000.0000.000
140L141PRO0-0.004-0.00136.641-0.222-0.2220.0000.0000.0000.000
141L142LYS10.9050.93029.289-10.543-10.5430.0000.0000.0000.000
142L143SER0-0.041-0.00335.737-0.007-0.0070.0000.0000.0000.000
143L144ILE00.0080.00237.026-0.228-0.2280.0000.0000.0000.000
144L145ALA0-0.0040.01139.1160.1740.1740.0000.0000.0000.000
145L146VAL00.0260.00041.603-0.187-0.1870.0000.0000.0000.000
146L147LYS10.8380.91243.581-6.622-6.6220.0000.0000.0000.000
147L148TRP00.0420.00544.574-0.142-0.1420.0000.0000.0000.000
148L149LYS10.7730.86048.879-6.022-6.0220.0000.0000.0000.000
149L150VAL00.0130.00652.0200.0270.0270.0000.0000.0000.000
150L151ASP-1-0.751-0.84254.7315.3755.3750.0000.0000.0000.000
151L152GLY00.0220.01757.148-0.061-0.0610.0000.0000.0000.000
152L153SER0-0.021-0.00355.2310.0330.0330.0000.0000.0000.000
153L154LYN00.0530.03747.7530.1080.1080.0000.0000.0000.000
154L155ARG10.7940.89546.902-6.710-6.7100.0000.0000.0000.000
155L156ALA00.0110.00544.1520.0680.0680.0000.0000.0000.000
156L157ASN00.0540.02543.6200.2580.2580.0000.0000.0000.000
157L158GLY00.0550.02542.721-0.181-0.1810.0000.0000.0000.000
158L159THR0-0.0040.00541.846-0.110-0.1100.0000.0000.0000.000
159L160ALA0-0.0120.01137.8010.1620.1620.0000.0000.0000.000
160L161ASN00.0090.00537.165-0.351-0.3510.0000.0000.0000.000
161L162SER00.0160.01433.9910.3270.3270.0000.0000.0000.000
162L163TRP00.003-0.00933.090-0.314-0.3140.0000.0000.0000.000
163L164THR0-0.018-0.01233.0700.1140.1140.0000.0000.0000.000
164L165ASP-1-0.872-0.94028.34711.12011.1200.0000.0000.0000.000
165L166GLN0-0.038-0.01430.960-0.117-0.1170.0000.0000.0000.000
166L167ASP-1-0.787-0.85332.7648.4798.4790.0000.0000.0000.000
167L168SER00.000-0.00732.199-0.023-0.0230.0000.0000.0000.000
168L169ALA0-0.036-0.00534.490-0.044-0.0440.0000.0000.0000.000
169L170SER0-0.061-0.06338.252-0.127-0.1270.0000.0000.0000.000
170L171SER00.006-0.00135.231-0.157-0.1570.0000.0000.0000.000
171L172THR0-0.068-0.02336.5530.0490.0490.0000.0000.0000.000
172L173TYR0-0.013-0.03631.8160.1260.1260.0000.0000.0000.000
173L174SER00.0080.00237.040-0.295-0.2950.0000.0000.0000.000
174L175MET0-0.0580.00037.0970.2420.2420.0000.0000.0000.000
175L176SER00.0010.00238.562-0.221-0.2210.0000.0000.0000.000
176L177SER0-0.015-0.01939.3570.1320.1320.0000.0000.0000.000
177L178THR00.0320.00241.327-0.199-0.1990.0000.0000.0000.000
178L179LEU0-0.0080.02042.9090.1090.1090.0000.0000.0000.000
179L180THR00.0280.01643.526-0.122-0.1220.0000.0000.0000.000
180L181LEU0-0.083-0.03845.961-0.047-0.0470.0000.0000.0000.000
181L182THR00.0470.01748.8230.0820.0820.0000.0000.0000.000
182L183LYS10.8640.91951.055-5.703-5.7030.0000.0000.0000.000
183L184ASP-1-0.784-0.89254.0715.6425.6420.0000.0000.0000.000
184L185LYS10.8120.92249.570-6.500-6.5000.0000.0000.0000.000
185L186TYR00.0560.02153.195-0.008-0.0080.0000.0000.0000.000
186L187GLU-1-0.789-0.90155.0465.4815.4810.0000.0000.0000.000
187L188ARG10.8220.91257.461-5.668-5.6680.0000.0000.0000.000
188L189HIS10.8380.89956.385-5.620-5.6200.0000.0000.0000.000
189L190ASN00.0460.04259.0150.0530.0530.0000.0000.0000.000
190L191SER00.000-0.00258.3060.0190.0190.0000.0000.0000.000
191L192TYR0-0.040-0.02752.6540.1200.1200.0000.0000.0000.000
192L193THR0-0.018-0.02152.787-0.032-0.0320.0000.0000.0000.000
193L195GLU-1-0.794-0.89548.3976.0276.0270.0000.0000.0000.000
194L196ALA00.0310.01544.9810.1450.1450.0000.0000.0000.000
195L197THR0-0.030-0.01744.564-0.158-0.1580.0000.0000.0000.000
196L198HIS00.0710.02740.4050.0060.0060.0000.0000.0000.000
197L199LYS10.8200.90441.223-7.557-7.5570.0000.0000.0000.000
198L200THR0-0.012-0.02444.384-0.124-0.1240.0000.0000.0000.000
199L201SER0-0.020-0.01246.760-0.118-0.1180.0000.0000.0000.000
200L202SER0-0.021-0.00549.1060.0520.0520.0000.0000.0000.000
201L203SER00.0000.00551.113-0.098-0.0980.0000.0000.0000.000
202L204PRO0-0.034-0.01749.4030.0700.0700.0000.0000.0000.000
203L205VAL00.0410.02848.556-0.149-0.1490.0000.0000.0000.000
204L206VAL0-0.019-0.01149.6800.1180.1180.0000.0000.0000.000
205L207LYS10.9190.96150.774-6.098-6.0980.0000.0000.0000.000
206L208SER00.0410.01352.6240.0930.0930.0000.0000.0000.000
207L209PHE00.0120.01852.198-0.033-0.0330.0000.0000.0000.000
208L210ASN00.023-0.01256.9480.0500.0500.0000.0000.0000.000
209L211ARG10.8970.93157.761-5.382-5.3820.0000.0000.0000.000
210L212ASN0-0.063-0.03559.5470.0360.0360.0000.0000.0000.000
211L213GLU-1-0.874-0.91961.8025.0205.0200.0000.0000.0000.000
212L214CYS0-0.062-0.01457.2300.0760.0760.0000.0000.0000.000