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: G6VM1

Calculation Name: 1GGI-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GGI

Chain ID: L

ChEMBL ID:

UniProt ID: P05877

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2188845.868501
FMO2-HF: Nuclear repulsion 2105723.143086
FMO2-HF: Total energy -83122.725415
FMO2-MP2: Total energy -83365.66765


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.
68.69874.8513.052-3.637-5.5690.036
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 : -0.914 / q_NPA : -0.975
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].
3L3VAL00.0020.0113.7430.1061.538-0.003-0.573-0.8560.004
4L4LEU00.0060.0015.192-4.859-4.810-0.001-0.004-0.0440.000
5L5THR00.0020.0008.491-1.162-1.1620.0000.0000.0000.000
6L6GLN00.006-0.01311.218-0.363-0.3630.0000.0000.0000.000
7L7SER0-0.026-0.00714.271-0.236-0.2360.0000.0000.0000.000
8L8PRO00.0280.01517.861-0.158-0.1580.0000.0000.0000.000
9L9GLY00.0680.05018.5440.6500.6500.0000.0000.0000.000
10L10SER0-0.071-0.03619.430-0.159-0.1590.0000.0000.0000.000
11L11LEU00.0170.00123.098-0.129-0.1290.0000.0000.0000.000
12L12ALA00.0150.02425.782-0.146-0.1460.0000.0000.0000.000
13L13VAL0-0.028-0.01328.398-0.163-0.1630.0000.0000.0000.000
14L14SER0-0.019-0.02531.102-0.209-0.2090.0000.0000.0000.000
15L15LEU00.0640.03233.4560.2030.2030.0000.0000.0000.000
16L16GLY00.0020.00735.321-0.172-0.1720.0000.0000.0000.000
17L17GLN0-0.025-0.00531.425-0.252-0.2520.0000.0000.0000.000
18L18ARG10.9470.97427.856-10.257-10.2570.0000.0000.0000.000
19L19ALA0-0.017-0.00126.944-0.060-0.0600.0000.0000.0000.000
20L20THR0-0.013-0.02223.606-0.232-0.2320.0000.0000.0000.000
21L21ILE00.0010.01518.635-0.030-0.0300.0000.0000.0000.000
22L22SER00.0020.00718.397-0.388-0.3880.0000.0000.0000.000
23L23CYS0-0.071-0.01712.5640.2660.2660.0000.0000.0000.000
24L24ARG10.8500.93012.784-18.871-18.8710.0000.0000.0000.000
25L25ALA00.0260.0248.9051.3131.3130.0000.0000.0000.000
26L26SER0-0.051-0.0536.083-1.223-1.2230.0000.0000.0000.000
27L27GLU-1-0.820-0.8875.76333.93333.9330.0000.0000.0000.000
28L27SER0-0.036-0.0349.342-0.340-0.3400.0000.0000.0000.000
29L27VAL0-0.0120.0058.5191.4831.4830.0000.0000.0000.000
30L27ASP-1-0.728-0.85711.10716.60916.6090.0000.0000.0000.000
31L27ASP-1-0.873-0.93814.16016.90616.9060.0000.0000.0000.000
32L28ASP-1-0.980-0.98716.37514.91614.9160.0000.0000.0000.000
33L29GLY0-0.015-0.01318.435-0.807-0.8070.0000.0000.0000.000
34L30ASN0-0.100-0.04817.864-0.950-0.9500.0000.0000.0000.000
35L31SER00.021-0.00115.3820.2990.2990.0000.0000.0000.000
36L32PHE0-0.053-0.02512.113-0.729-0.7290.0000.0000.0000.000
37L33LEU00.0080.00911.3231.4431.4430.0000.0000.0000.000
38L34HIS0-0.023-0.00513.350-2.898-2.8980.0000.0000.0000.000
39L35TRP00.016-0.00215.0821.1761.1760.0000.0000.0000.000
40L36TYR0-0.010-0.03015.082-1.207-1.2070.0000.0000.0000.000
41L37GLN00.0250.01119.064-0.096-0.0960.0000.0000.0000.000
42L38GLN00.001-0.00318.9140.7470.7470.0000.0000.0000.000
43L39LYS10.8790.93821.959-10.917-10.9170.0000.0000.0000.000
44L40PRO00.0350.00224.6590.3090.3090.0000.0000.0000.000
45L41GLY0-0.0030.00824.584-0.461-0.4610.0000.0000.0000.000
46L42GLN0-0.025-0.00124.7430.0420.0420.0000.0000.0000.000
47L43PRO00.0280.01620.7960.5030.5030.0000.0000.0000.000
48L44PRO0-0.010-0.01316.538-0.557-0.5570.0000.0000.0000.000
49L45LYS10.8820.95919.515-12.173-12.1730.0000.0000.0000.000
50L46LEU00.0180.00617.892-0.014-0.0140.0000.0000.0000.000
51L47LEU0-0.070-0.03320.707-0.822-0.8220.0000.0000.0000.000
52L48ILE0-0.0020.00120.246-0.637-0.6370.0000.0000.0000.000
53L49TYR00.0140.00118.1960.8730.8730.0000.0000.0000.000
54L50ARG10.9120.94217.100-14.763-14.7630.0000.0000.0000.000
55L51SER0-0.0180.00017.283-0.940-0.9400.0000.0000.0000.000
56L52SER0-0.049-0.02418.599-0.485-0.4850.0000.0000.0000.000
57L53ASN0-0.044-0.01621.815-0.499-0.4990.0000.0000.0000.000
58L54LEU00.0410.02123.0280.5260.5260.0000.0000.0000.000
59L55ILE0-0.019-0.00222.032-0.227-0.2270.0000.0000.0000.000
60L56SER0-0.002-0.01325.718-0.394-0.3940.0000.0000.0000.000
61L57GLY00.0190.00729.3060.1310.1310.0000.0000.0000.000
62L58ILE0-0.074-0.02625.719-0.082-0.0820.0000.0000.0000.000
63L59PRO0-0.009-0.01129.134-0.151-0.1510.0000.0000.0000.000
64L60ASP-1-0.843-0.93029.6869.5229.5220.0000.0000.0000.000
65L61ARG10.8030.89730.588-9.733-9.7330.0000.0000.0000.000
66L62PHE0-0.054-0.01824.8960.2710.2710.0000.0000.0000.000
67L63SER00.0040.00126.002-0.083-0.0830.0000.0000.0000.000
68L64GLY00.0180.00121.8970.3670.3670.0000.0000.0000.000
69L65SER0-0.018-0.01521.333-0.430-0.4300.0000.0000.0000.000
70L66GLY00.0540.01619.0580.5970.5970.0000.0000.0000.000
71L67SER00.0160.00917.615-0.413-0.4130.0000.0000.0000.000
72L68ARG10.9050.93514.111-17.223-17.2230.0000.0000.0000.000
73L69THR00.024-0.00211.8990.9450.9450.0000.0000.0000.000
74L70ASP-1-0.894-0.91413.82317.74117.7410.0000.0000.0000.000
75L71PHE00.0000.01013.352-0.883-0.8830.0000.0000.0000.000
76L72THR0-0.113-0.07417.720-0.157-0.1570.0000.0000.0000.000
77L73LEU00.0290.03320.103-0.102-0.1020.0000.0000.0000.000
78L74THR0-0.019-0.02021.745-0.262-0.2620.0000.0000.0000.000
79L75ILE00.0190.02324.075-0.062-0.0620.0000.0000.0000.000
80L76ASN0-0.040-0.01627.868-0.214-0.2140.0000.0000.0000.000
81L77PRO00.0340.01431.531-0.088-0.0880.0000.0000.0000.000
82L78VAL00.0030.00229.6910.2360.2360.0000.0000.0000.000
83L79GLU-1-0.896-0.96831.4318.2628.2620.0000.0000.0000.000
84L80ALA0-0.007-0.01932.0730.2910.2910.0000.0000.0000.000
85L81ASP-1-0.868-0.91631.37210.19310.1930.0000.0000.0000.000
86L82ASP-1-0.766-0.86227.97810.91010.9100.0000.0000.0000.000
87L83VAL0-0.013-0.00227.0530.4960.4960.0000.0000.0000.000
88L84ALA0-0.0030.00324.224-0.063-0.0630.0000.0000.0000.000
89L85THR0-0.0060.00018.549-0.288-0.2880.0000.0000.0000.000
90L86TYR0-0.031-0.03019.436-0.148-0.1480.0000.0000.0000.000
91L87TYR00.006-0.01314.1140.3420.3420.0000.0000.0000.000
92L89GLN00.0530.03410.817-0.500-0.5000.0000.0000.0000.000
93L90GLN00.0410.0025.045-6.710-6.7100.0000.0000.0000.000
94L91SER0-0.022-0.0209.0121.1941.1940.0000.0000.0000.000
95L92ASN00.0110.0198.667-3.317-3.3170.0000.0000.0000.000
96L93GLU-1-0.931-0.9615.73330.92630.9260.0000.0000.0000.000
97L94ASP-1-0.943-0.9496.07234.77434.7740.0000.0000.0000.000
98L95PRO0-0.009-0.0092.599-7.803-4.1742.990-2.670-3.9490.030
99L96LEU00.0110.0034.6060.0690.130-0.001-0.006-0.0540.000
100L97THR0-0.050-0.0303.161-4.636-3.6540.067-0.384-0.6660.002
101L98PHE0-0.017-0.0276.341-6.303-6.3030.0000.0000.0000.000
102L99GLY00.0380.0178.2172.2982.2980.0000.0000.0000.000
103L100ALA0-0.065-0.04010.659-0.644-0.6440.0000.0000.0000.000
104L101GLY00.0130.01612.481-0.945-0.9450.0000.0000.0000.000
105L102THR0-0.063-0.04815.818-0.019-0.0190.0000.0000.0000.000
106L103LYS10.8070.89219.137-12.252-12.2520.0000.0000.0000.000
107L104LEU0-0.0050.00522.431-0.324-0.3240.0000.0000.0000.000
108L105GLU-1-0.780-0.86725.67611.46811.4680.0000.0000.0000.000
109L106ILE00.0530.03828.769-0.090-0.0900.0000.0000.0000.000
110L107LYS10.8380.92232.436-8.781-8.7810.0000.0000.0000.000
111L108ARG10.7910.89634.165-8.213-8.2130.0000.0000.0000.000
112L109ALA00.009-0.00137.5230.0740.0740.0000.0000.0000.000
113L110ASP-1-0.801-0.88839.0618.1158.1150.0000.0000.0000.000
114L111ALA0-0.019-0.00640.024-0.184-0.1840.0000.0000.0000.000
115L112ALA00.0480.02640.5100.1890.1890.0000.0000.0000.000
116L113PRO0-0.0210.00640.175-0.035-0.0350.0000.0000.0000.000
117L114THR00.008-0.00442.079-0.229-0.2290.0000.0000.0000.000
118L115VAL0-0.012-0.01043.0140.0590.0590.0000.0000.0000.000
119L116SER0-0.032-0.01244.633-0.306-0.3060.0000.0000.0000.000
120L117ILE0-0.0180.00044.9410.1840.1840.0000.0000.0000.000
121L118PHE0-0.010-0.00445.304-0.164-0.1640.0000.0000.0000.000
122L119PRO00.0130.00446.7260.1310.1310.0000.0000.0000.000
123L120PRO00.0230.02446.9980.0380.0380.0000.0000.0000.000
124L121SER00.0330.02248.193-0.137-0.1370.0000.0000.0000.000
125L122SER00.015-0.01550.2220.0670.0670.0000.0000.0000.000
126L123GLU-1-0.892-0.93549.1606.5126.5120.0000.0000.0000.000
127L124GLN00.0590.03443.249-0.050-0.0500.0000.0000.0000.000
128L125LEU00.0030.00548.2930.0070.0070.0000.0000.0000.000
129L126THR0-0.090-0.06150.845-0.070-0.0700.0000.0000.0000.000
130L127SER0-0.046-0.02147.8020.0050.0050.0000.0000.0000.000
131L128GLY00.0130.01347.8470.1150.1150.0000.0000.0000.000
132L129GLY0-0.025-0.00945.2200.0710.0710.0000.0000.0000.000
133L130ALA0-0.013-0.01745.197-0.147-0.1470.0000.0000.0000.000
134L131SER0-0.016-0.01641.2980.1030.1030.0000.0000.0000.000
135L132VAL0-0.0110.00843.592-0.136-0.1360.0000.0000.0000.000
136L133VAL00.0020.00240.6280.2050.2050.0000.0000.0000.000
137L134CYS0-0.031-0.00441.322-0.041-0.0410.0000.0000.0000.000
138L135PHE00.0170.02039.2930.2770.2770.0000.0000.0000.000
139L136LEU00.028-0.01038.449-0.226-0.2260.0000.0000.0000.000
140L137ASN0-0.007-0.02439.0840.2270.2270.0000.0000.0000.000
141L138ASN00.011-0.00439.690-0.054-0.0540.0000.0000.0000.000
142L139PHE0-0.0210.01334.713-0.171-0.1710.0000.0000.0000.000
143L140TYR00.0370.01032.6570.2580.2580.0000.0000.0000.000
144L141PRO00.004-0.00632.829-0.263-0.2630.0000.0000.0000.000
145L142LYS10.9090.92926.314-11.636-11.6360.0000.0000.0000.000
146L143ASP-1-0.914-0.94729.60110.36110.3610.0000.0000.0000.000
147L144ILE0-0.026-0.00832.415-0.360-0.3600.0000.0000.0000.000
148L145ASN0-0.0080.00033.8070.0270.0270.0000.0000.0000.000
149L146VAL00.011-0.01136.058-0.259-0.2590.0000.0000.0000.000
150L147LYS10.8230.92037.890-7.820-7.8200.0000.0000.0000.000
151L148TRP00.013-0.01839.309-0.257-0.2570.0000.0000.0000.000
152L149LYS10.8300.89642.687-6.978-6.9780.0000.0000.0000.000
153L150ILE00.0170.00145.416-0.056-0.0560.0000.0000.0000.000
154L151ASP-1-0.898-0.92948.6616.2346.2340.0000.0000.0000.000
155L152GLY0-0.028-0.01950.204-0.128-0.1280.0000.0000.0000.000
156L153SER0-0.046-0.03347.6600.1210.1210.0000.0000.0000.000
157L154GLU-1-0.882-0.95840.7867.9557.9550.0000.0000.0000.000
158L155ARG10.7850.89141.405-7.601-7.6010.0000.0000.0000.000
159L156GLN00.0570.02836.0240.2640.2640.0000.0000.0000.000
160L157ASN0-0.039-0.02037.0910.1900.1900.0000.0000.0000.000
161L158GLY00.0670.02836.608-0.230-0.2300.0000.0000.0000.000
162L159VAL0-0.0140.00935.535-0.127-0.1270.0000.0000.0000.000
163L160LEU0-0.0170.00831.7050.3210.3210.0000.0000.0000.000
164L161ASN00.000-0.02532.291-0.521-0.5210.0000.0000.0000.000
165L162SER0-0.015-0.00330.9450.4730.4730.0000.0000.0000.000
166L163TRP00.0490.01629.952-0.319-0.3190.0000.0000.0000.000
167L164THR0-0.024-0.01230.7440.1120.1120.0000.0000.0000.000
168L165ASP-1-0.787-0.87927.54911.61911.6190.0000.0000.0000.000
169L166GLN0-0.022-0.03129.838-0.593-0.5930.0000.0000.0000.000
170L167ASP-1-0.765-0.86931.6978.5888.5880.0000.0000.0000.000
171L168SER0-0.057-0.03134.035-0.252-0.2520.0000.0000.0000.000
172L169LYS10.7490.85835.294-8.321-8.3210.0000.0000.0000.000
173L170ASP-1-0.753-0.88038.7787.8097.8090.0000.0000.0000.000
174L171SER00.0080.00934.918-0.130-0.1300.0000.0000.0000.000
175L172THR0-0.052-0.01135.3260.2270.2270.0000.0000.0000.000
176L173TYR0-0.035-0.02729.3440.1990.1990.0000.0000.0000.000
177L174SER00.0180.01235.001-0.436-0.4360.0000.0000.0000.000
178L175MET0-0.0530.02533.9580.3210.3210.0000.0000.0000.000
179L176SER0-0.012-0.00235.460-0.305-0.3050.0000.0000.0000.000
180L177SER00.0250.00135.6740.2450.2450.0000.0000.0000.000
181L178THR00.013-0.00137.295-0.338-0.3380.0000.0000.0000.000
182L179LEU00.0160.03338.2300.1980.1980.0000.0000.0000.000
183L180THR0-0.018-0.01039.567-0.233-0.2330.0000.0000.0000.000
184L181LEU0-0.034-0.00541.4800.0570.0570.0000.0000.0000.000
185L182THR00.0450.01944.169-0.003-0.0030.0000.0000.0000.000
186L183LYS10.8180.89146.487-6.054-6.0540.0000.0000.0000.000
187L184ASP-1-0.796-0.88549.8366.1956.1950.0000.0000.0000.000
188L185GLU-1-0.841-0.92245.4057.0847.0840.0000.0000.0000.000
189L186TYR00.0320.01448.311-0.065-0.0650.0000.0000.0000.000
190L187GLU-1-0.831-0.90949.9125.8645.8640.0000.0000.0000.000
191L188ARG10.8390.90749.691-6.465-6.4650.0000.0000.0000.000
192L189HIS00.0120.02749.644-0.076-0.0760.0000.0000.0000.000
193L190ASN0-0.0010.00153.545-0.014-0.0140.0000.0000.0000.000
194L191SER0-0.016-0.00253.1320.0130.0130.0000.0000.0000.000
195L192TYR00.013-0.01247.3870.1380.1380.0000.0000.0000.000
196L193THR00.004-0.00547.505-0.041-0.0410.0000.0000.0000.000
197L195GLU-1-0.821-0.90243.1286.9366.9360.0000.0000.0000.000
198L196ALA00.0500.03540.4470.2380.2380.0000.0000.0000.000
199L197THR0-0.019-0.00138.605-0.222-0.2220.0000.0000.0000.000
200L198HIS00.0360.01736.5200.0230.0230.0000.0000.0000.000
201L199LYS10.8510.90536.438-8.282-8.2820.0000.0000.0000.000
202L200THR0-0.008-0.01939.172-0.184-0.1840.0000.0000.0000.000
203L201SER0-0.059-0.03142.536-0.247-0.2470.0000.0000.0000.000
204L202THR00.0020.00943.7660.0930.0930.0000.0000.0000.000
205L203SER0-0.033-0.00846.271-0.090-0.0900.0000.0000.0000.000
206L204PRO00.0180.00244.1860.1380.1380.0000.0000.0000.000
207L205ILE0-0.0090.00443.658-0.190-0.1900.0000.0000.0000.000
208L206VAL00.004-0.00744.9410.1580.1580.0000.0000.0000.000
209L207LYS10.8300.90247.021-6.684-6.6840.0000.0000.0000.000
210L208SER00.0410.01847.9730.1360.1360.0000.0000.0000.000
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