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: V5Y41

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184776.619403
FMO2-HF: Nuclear repulsion 2101657.768544
FMO2-HF: Total energy -83118.850859
FMO2-MP2: Total energy -83361.813495


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.
68.90375.7171.937-3.502-5.2480.033
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 : -0.887 / q_NPA : -0.951
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].
3L3VAL0-0.018-0.0153.1020.5713.4450.120-1.343-1.6500.009
4L4LEU0-0.002-0.0084.853-5.379-5.331-0.001-0.006-0.0410.000
5L5THR0-0.016-0.0168.182-0.363-0.3630.0000.0000.0000.000
6L6GLN00.020-0.01711.203-0.306-0.3060.0000.0000.0000.000
7L7SER0-0.117-0.01814.310-0.353-0.3530.0000.0000.0000.000
8L8PRO00.0910.03017.7750.0520.0520.0000.0000.0000.000
9L9GLY00.0760.04618.4260.5250.5250.0000.0000.0000.000
10L10SER0-0.028-0.03619.360-0.206-0.2060.0000.0000.0000.000
11L11LEU0-0.015-0.00322.885-0.149-0.1490.0000.0000.0000.000
12L12ALA00.0180.03425.447-0.129-0.1290.0000.0000.0000.000
13L13VAL0-0.023-0.00328.205-0.127-0.1270.0000.0000.0000.000
14L14SER0-0.017-0.03330.869-0.186-0.1860.0000.0000.0000.000
15L15LEU00.0470.00633.6020.1570.1570.0000.0000.0000.000
16L16GLY0-0.007-0.00434.851-0.148-0.1480.0000.0000.0000.000
17L17GLN0-0.0150.00831.177-0.257-0.2570.0000.0000.0000.000
18L18ARG10.9640.98528.748-9.911-9.9110.0000.0000.0000.000
19L19ALA0-0.031-0.01026.529-0.011-0.0110.0000.0000.0000.000
20L20THR0-0.018-0.00622.944-0.091-0.0910.0000.0000.0000.000
21L21ILE0-0.018-0.00218.3330.0360.0360.0000.0000.0000.000
22L22SER0-0.007-0.01817.981-0.228-0.2280.0000.0000.0000.000
23L23CYS0-0.0430.01512.2800.3040.3040.0000.0000.0000.000
24L24ARG10.8900.93612.832-18.287-18.2870.0000.0000.0000.000
25L25ALA0-0.0070.0048.8251.3431.3430.0000.0000.0000.000
26L26SER0-0.0250.0095.066-0.149-0.1490.0000.0000.0000.000
27L27GLU-1-0.908-0.9635.46328.35128.3510.0000.0000.0000.000
28L27SER0-0.037-0.0319.036-0.296-0.2960.0000.0000.0000.000
29L27VAL00.0030.0118.6911.3561.3560.0000.0000.0000.000
30L27ASP-1-0.769-0.89511.03616.43716.4370.0000.0000.0000.000
31L27ASP-1-0.875-0.93314.01016.85916.8590.0000.0000.0000.000
32L28ASP-1-0.981-0.98416.09014.87514.8750.0000.0000.0000.000
33L29GLY00.0150.00618.704-0.708-0.7080.0000.0000.0000.000
34L30ASN0-0.157-0.08517.841-0.339-0.3390.0000.0000.0000.000
35L31SER00.0720.03115.2230.2350.2350.0000.0000.0000.000
36L32PHE0-0.102-0.05011.993-0.709-0.7090.0000.0000.0000.000
37L33LEU00.0470.03011.4851.7031.7030.0000.0000.0000.000
38L34HIS0-0.014-0.02913.212-3.102-3.1020.0000.0000.0000.000
39L35TRP0-0.004-0.00214.8551.1531.1530.0000.0000.0000.000
40L36TYR0-0.008-0.02814.361-1.270-1.2700.0000.0000.0000.000
41L37GLN0-0.006-0.02018.371-0.049-0.0490.0000.0000.0000.000
42L38GLN0-0.008-0.02518.8930.6590.6590.0000.0000.0000.000
43L39LYS10.8800.94621.617-10.987-10.9870.0000.0000.0000.000
44L40PRO00.0300.00024.5150.3250.3250.0000.0000.0000.000
45L41GLY00.0380.03124.749-0.497-0.4970.0000.0000.0000.000
46L42GLN0-0.039-0.01824.9060.1060.1060.0000.0000.0000.000
47L43PRO00.0180.01321.0660.5240.5240.0000.0000.0000.000
48L44PRO0-0.004-0.00917.012-0.562-0.5620.0000.0000.0000.000
49L45LYS10.9620.99719.933-12.097-12.0970.0000.0000.0000.000
50L46LEU0-0.021-0.01817.7200.0450.0450.0000.0000.0000.000
51L47LEU0-0.060-0.02720.552-0.785-0.7850.0000.0000.0000.000
52L48ILE00.0340.03020.169-0.658-0.6580.0000.0000.0000.000
53L49TYR0-0.015-0.02318.6040.8560.8560.0000.0000.0000.000
54L50ARG10.9520.96317.136-15.103-15.1030.0000.0000.0000.000
55L51SER0-0.0430.01217.984-0.791-0.7910.0000.0000.0000.000
56L52SER00.003-0.00618.973-0.415-0.4150.0000.0000.0000.000
57L53ASN0-0.037-0.00622.497-0.334-0.3340.0000.0000.0000.000
58L54LEU00.0470.03123.1610.5770.5770.0000.0000.0000.000
59L55ILE0-0.0230.00322.448-0.196-0.1960.0000.0000.0000.000
60L56SER0-0.035-0.03425.622-0.425-0.4250.0000.0000.0000.000
61L57GLY00.0420.01829.2240.1320.1320.0000.0000.0000.000
62L58ILE0-0.069-0.02325.578-0.092-0.0920.0000.0000.0000.000
63L59PRO0-0.012-0.02428.721-0.174-0.1740.0000.0000.0000.000
64L60ASP-1-0.818-0.91729.1059.5129.5120.0000.0000.0000.000
65L61ARG10.8510.94130.089-9.649-9.6490.0000.0000.0000.000
66L62PHE0-0.042-0.00624.3690.2410.2410.0000.0000.0000.000
67L63SER00.001-0.00525.328-0.034-0.0340.0000.0000.0000.000
68L64GLY00.0300.00721.5190.3460.3460.0000.0000.0000.000
69L65SER0-0.019-0.00721.132-0.506-0.5060.0000.0000.0000.000
70L66GLY00.017-0.00619.1290.6320.6320.0000.0000.0000.000
71L67SER0-0.0020.00417.792-0.260-0.2600.0000.0000.0000.000
72L68ARG10.9920.99413.858-16.726-16.7260.0000.0000.0000.000
73L69THR0-0.008-0.00811.5540.7060.7060.0000.0000.0000.000
74L70ASP-1-0.930-0.96113.71817.37917.3790.0000.0000.0000.000
75L71PHE00.0490.03113.720-0.918-0.9180.0000.0000.0000.000
76L72THR0-0.073-0.03117.0430.1390.1390.0000.0000.0000.000
77L73LEU00.0500.03419.658-0.212-0.2120.0000.0000.0000.000
78L74THR0-0.052-0.03721.256-0.268-0.2680.0000.0000.0000.000
79L75ILE00.0460.02424.295-0.064-0.0640.0000.0000.0000.000
80L76ASN0-0.064-0.04427.334-0.310-0.3100.0000.0000.0000.000
81L77PRO00.0140.03730.905-0.039-0.0390.0000.0000.0000.000
82L78VAL0-0.023-0.03129.4730.0930.0930.0000.0000.0000.000
83L79GLU-1-0.860-0.92631.3348.1868.1860.0000.0000.0000.000
84L80ALA00.006-0.03031.6140.3190.3190.0000.0000.0000.000
85L81ASP-1-0.952-0.95931.3609.9059.9050.0000.0000.0000.000
86L82ASP-1-0.785-0.88827.18410.90110.9010.0000.0000.0000.000
87L83VAL0-0.060-0.03026.3430.5260.5260.0000.0000.0000.000
88L84ALA0-0.004-0.00123.890-0.095-0.0950.0000.0000.0000.000
89L85THR00.0200.00318.366-0.324-0.3240.0000.0000.0000.000
90L86TYR0-0.031-0.01018.987-0.012-0.0120.0000.0000.0000.000
91L87TYR00.0250.02113.6550.3430.3430.0000.0000.0000.000
92L89GLN00.0390.02510.345-0.096-0.0960.0000.0000.0000.000
93L90GLN00.0420.0145.130-7.024-7.0240.0000.0000.0000.000
94L91SER0-0.058-0.0359.1971.4011.4010.0000.0000.0000.000
95L92ASN0-0.0020.0098.487-2.953-2.9530.0000.0000.0000.000
96L93GLU-1-0.933-0.9614.91832.17232.1720.0000.0000.0000.000
97L94ASP-1-0.959-0.9545.59934.13234.1320.0000.0000.0000.000
98L95PRO0-0.010-0.0252.692-7.553-4.3301.758-1.997-2.9840.023
99L96LEU00.0040.0114.885-0.855-0.809-0.001-0.003-0.0420.000
100L97THR0-0.0030.0123.010-2.096-1.4730.061-0.153-0.5310.001
101L98PHE00.001-0.0196.200-6.035-6.0350.0000.0000.0000.000
102L99GLY00.0280.0218.2912.3352.3350.0000.0000.0000.000
103L100ALA0-0.051-0.04810.394-0.825-0.8250.0000.0000.0000.000
104L101GLY00.0330.03412.804-0.901-0.9010.0000.0000.0000.000
105L102THR0-0.056-0.04215.811-0.183-0.1830.0000.0000.0000.000
106L103LYS10.8670.95018.936-12.613-12.6130.0000.0000.0000.000
107L104LEU0-0.010-0.00622.167-0.283-0.2830.0000.0000.0000.000
108L105GLU-1-0.883-0.94825.34411.52111.5210.0000.0000.0000.000
109L106ILE00.0560.02428.400-0.083-0.0830.0000.0000.0000.000
110L107LYS10.9200.96831.956-8.607-8.6070.0000.0000.0000.000
111L108ARG10.8430.92234.002-8.156-8.1560.0000.0000.0000.000
112L109ALA0-0.025-0.00937.6530.0580.0580.0000.0000.0000.000
113L110ASP-1-0.883-0.95239.1928.0888.0880.0000.0000.0000.000
114L111ALA0-0.0110.00140.380-0.211-0.2110.0000.0000.0000.000
115L112ALA00.0390.01640.7420.1910.1910.0000.0000.0000.000
116L113PRO0-0.0260.00940.352-0.068-0.0680.0000.0000.0000.000
117L114THR0-0.029-0.02842.386-0.200-0.2000.0000.0000.0000.000
118L115VAL00.0430.00842.8390.0710.0710.0000.0000.0000.000
119L116SER0-0.061-0.03644.725-0.283-0.2830.0000.0000.0000.000
120L117ILE0-0.030-0.01145.3020.1620.1620.0000.0000.0000.000
121L118PHE00.0020.01545.114-0.155-0.1550.0000.0000.0000.000
122L119PRO00.009-0.01146.8680.1180.1180.0000.0000.0000.000
123L120PRO00.0210.01247.1670.0440.0440.0000.0000.0000.000
124L121SER00.0310.04248.548-0.132-0.1320.0000.0000.0000.000
125L122SER00.026-0.02850.2430.1130.1130.0000.0000.0000.000
126L123GLU-1-0.889-0.93449.8186.4276.4270.0000.0000.0000.000
127L124GLN00.0400.00643.765-0.069-0.0690.0000.0000.0000.000
128L125LEU0-0.0070.01348.412-0.002-0.0020.0000.0000.0000.000
129L126THR0-0.113-0.07050.902-0.022-0.0220.0000.0000.0000.000
130L127SER0-0.004-0.00348.0240.0020.0020.0000.0000.0000.000
131L128GLY00.0170.00647.8570.1350.1350.0000.0000.0000.000
132L129GLY0-0.0070.00345.2630.0680.0680.0000.0000.0000.000
133L130ALA0-0.030-0.01645.588-0.106-0.1060.0000.0000.0000.000
134L131SER00.0120.02441.7290.1130.1130.0000.0000.0000.000
135L132VAL0-0.0200.01643.768-0.170-0.1700.0000.0000.0000.000
136L133VAL0-0.022-0.01440.8370.2100.2100.0000.0000.0000.000
137L134CYS0-0.008-0.02941.402-0.050-0.0500.0000.0000.0000.000
138L135PHE0-0.0210.00239.6940.2470.2470.0000.0000.0000.000
139L136LEU00.0130.01038.436-0.220-0.2200.0000.0000.0000.000
140L137ASN00.024-0.02139.3220.1290.1290.0000.0000.0000.000
141L138ASN00.0190.00939.720-0.026-0.0260.0000.0000.0000.000
142L139PHE0-0.0610.00235.276-0.177-0.1770.0000.0000.0000.000
143L140TYR00.0820.03632.4820.2630.2630.0000.0000.0000.000
144L141PRO0-0.049-0.03733.156-0.215-0.2150.0000.0000.0000.000
145L142LYS10.9820.96625.811-11.916-11.9160.0000.0000.0000.000
146L143ASP-1-0.952-0.95529.98610.37710.3770.0000.0000.0000.000
147L144ILE0-0.0080.00432.698-0.363-0.3630.0000.0000.0000.000
148L145ASN0-0.026-0.03134.3430.2080.2080.0000.0000.0000.000
149L146VAL00.0540.01736.520-0.247-0.2470.0000.0000.0000.000
150L147LYS10.9010.95738.569-8.014-8.0140.0000.0000.0000.000
151L148TRP00.0060.00239.194-0.332-0.3320.0000.0000.0000.000
152L149LYS10.8710.91842.557-6.909-6.9090.0000.0000.0000.000
153L150ILE00.003-0.00644.687-0.074-0.0740.0000.0000.0000.000
154L151ASP-1-0.973-0.99348.2856.1826.1820.0000.0000.0000.000
155L152GLY00.0110.01650.125-0.118-0.1180.0000.0000.0000.000
156L153SER0-0.049-0.03347.7350.0900.0900.0000.0000.0000.000
157L154GLU-1-0.983-0.99740.4768.0808.0800.0000.0000.0000.000
158L155ARG10.8670.93941.254-7.656-7.6560.0000.0000.0000.000
159L156GLN00.0440.01535.9930.2590.2590.0000.0000.0000.000
160L157ASN0-0.034-0.01636.8530.3790.3790.0000.0000.0000.000
161L158GLY00.0510.02336.278-0.245-0.2450.0000.0000.0000.000
162L159VAL0-0.0080.01235.883-0.204-0.2040.0000.0000.0000.000
163L160LEU0-0.026-0.00832.1400.3490.3490.0000.0000.0000.000
164L161ASN00.0450.01232.322-0.377-0.3770.0000.0000.0000.000
165L162SER0-0.0130.00331.1720.4010.4010.0000.0000.0000.000
166L163TRP00.0230.00229.867-0.274-0.2740.0000.0000.0000.000
167L164THR00.0310.03230.5230.1330.1330.0000.0000.0000.000
168L165ASP-1-0.964-0.99128.03611.05311.0530.0000.0000.0000.000
169L166GLN00.004-0.02529.980-0.506-0.5060.0000.0000.0000.000
170L167ASP-1-0.860-0.91731.8738.5208.5200.0000.0000.0000.000
171L168SER0-0.055-0.03333.994-0.270-0.2700.0000.0000.0000.000
172L169LYS10.8430.92235.241-8.180-8.1800.0000.0000.0000.000
173L170ASP-1-0.776-0.89838.6607.8977.8970.0000.0000.0000.000
174L171SER0-0.116-0.06035.296-0.015-0.0150.0000.0000.0000.000
175L172THR00.0260.02735.6180.1580.1580.0000.0000.0000.000
176L173TYR0-0.027-0.00229.6570.2310.2310.0000.0000.0000.000
177L174SER00.022-0.00134.989-0.449-0.4490.0000.0000.0000.000
178L175MET0-0.058-0.01333.6910.3210.3210.0000.0000.0000.000
179L176SER00.0230.02035.493-0.403-0.4030.0000.0000.0000.000
180L177SER0-0.034-0.02235.9600.1890.1890.0000.0000.0000.000
181L178THR00.0480.02437.149-0.336-0.3360.0000.0000.0000.000
182L179LEU00.0300.02638.2150.1860.1860.0000.0000.0000.000
183L180THR0-0.028-0.03039.642-0.213-0.2130.0000.0000.0000.000
184L181LEU0-0.0240.00341.2620.0890.0890.0000.0000.0000.000
185L182THR00.0230.01144.001-0.011-0.0110.0000.0000.0000.000
186L183LYS10.8930.94346.249-6.139-6.1390.0000.0000.0000.000
187L184ASP-1-0.885-0.96049.6196.0706.0700.0000.0000.0000.000
188L185GLU-1-0.931-0.96945.5427.0697.0690.0000.0000.0000.000
189L186TYR00.0430.02548.546-0.071-0.0710.0000.0000.0000.000
190L187GLU-1-0.951-1.02450.0125.8525.8520.0000.0000.0000.000
191L188ARG10.9460.99250.083-6.504-6.5040.0000.0000.0000.000
192L189HIS00.0030.01349.721-0.043-0.0430.0000.0000.0000.000
193L190ASN0-0.032-0.03353.512-0.006-0.0060.0000.0000.0000.000
194L191SER00.0110.00952.6710.0080.0080.0000.0000.0000.000
195L192TYR00.0850.07146.9600.1430.1430.0000.0000.0000.000
196L193THR00.000-0.00447.714-0.049-0.0490.0000.0000.0000.000
197L195GLU-1-0.853-0.90843.5726.9766.9760.0000.0000.0000.000
198L196ALA00.0740.05140.8130.2410.2410.0000.0000.0000.000
199L197THR0-0.046-0.00739.095-0.180-0.1800.0000.0000.0000.000
200L198HIS00.0290.00236.8730.0470.0470.0000.0000.0000.000
201L199LYS10.9700.98037.157-8.330-8.3300.0000.0000.0000.000
202L200THR0-0.020-0.01339.446-0.170-0.1700.0000.0000.0000.000
203L201SER0-0.029-0.02242.619-0.270-0.2700.0000.0000.0000.000
204L202THR0-0.0040.01744.0270.0810.0810.0000.0000.0000.000
205L203SER0-0.0390.00046.629-0.095-0.0950.0000.0000.0000.000
206L204PRO00.010-0.01144.7580.1530.1530.0000.0000.0000.000
207L205ILE00.0030.01243.889-0.191-0.1910.0000.0000.0000.000
208L206VAL00.026-0.00145.3120.1540.1540.0000.0000.0000.000
209L207LYS10.8810.93346.751-6.697-6.6970.0000.0000.0000.000
210L208SER00.0220.00448.3320.1170.1170.0000.0000.0000.000
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