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: 179QZ

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 OptHSide
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 -2186534.714359
FMO2-HF: Nuclear repulsion 2103413.592533
FMO2-HF: Total energy -83121.121826
FMO2-MP2: Total energy -83364.076463


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.
72.28477.8483.497-3.423-5.6370.035
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 : -0.902 / q_NPA : -0.972
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].
3L3VAL0-0.031-0.0173.4490.6542.4340.042-0.725-1.0960.004
4L4LEU00.0040.0004.908-5.388-5.360-0.001-0.005-0.0220.000
5L5THR0-0.016-0.0108.227-0.767-0.7670.0000.0000.0000.000
6L6GLN00.005-0.01611.245-0.314-0.3140.0000.0000.0000.000
7L7SER0-0.0400.01114.345-0.281-0.2810.0000.0000.0000.000
8L8PRO00.0440.01417.8120.0250.0250.0000.0000.0000.000
9L9GLY00.0710.03818.4450.5120.5120.0000.0000.0000.000
10L10SER0-0.039-0.03119.380-0.111-0.1110.0000.0000.0000.000
11L11LEU00.009-0.00222.902-0.150-0.1500.0000.0000.0000.000
12L12ALA0-0.0020.02525.470-0.134-0.1340.0000.0000.0000.000
13L13VAL0-0.020-0.00428.194-0.125-0.1250.0000.0000.0000.000
14L14SER0-0.021-0.02830.894-0.169-0.1690.0000.0000.0000.000
15L15LEU00.0570.01533.6270.1500.1500.0000.0000.0000.000
16L16GLY0-0.002-0.00134.871-0.153-0.1530.0000.0000.0000.000
17L17GLN0-0.0040.01931.432-0.255-0.2550.0000.0000.0000.000
18L18ARG10.9310.96627.714-10.165-10.1650.0000.0000.0000.000
19L19ALA0-0.034-0.01526.634-0.008-0.0080.0000.0000.0000.000
20L20THR0-0.023-0.00923.005-0.099-0.0990.0000.0000.0000.000
21L21ILE00.0080.00818.4060.0280.0280.0000.0000.0000.000
22L22SER0-0.029-0.02017.903-0.200-0.2000.0000.0000.0000.000
23L23CYS0-0.055-0.00212.2610.3710.3710.0000.0000.0000.000
24L24ARG10.8600.92412.879-18.627-18.6270.0000.0000.0000.000
25L25ALA0-0.0010.0028.9601.2631.2630.0000.0000.0000.000
26L26SER0-0.020-0.0165.717-0.665-0.6650.0000.0000.0000.000
27L27GLU-1-0.838-0.9015.47633.14733.1470.0000.0000.0000.000
28L27SER0-0.037-0.0429.092-0.602-0.6020.0000.0000.0000.000
29L27VAL0-0.0120.0078.5461.3951.3950.0000.0000.0000.000
30L27ASP-1-0.712-0.83611.01816.86216.8620.0000.0000.0000.000
31L27ASP-1-0.878-0.94213.97917.23917.2390.0000.0000.0000.000
32L28ASP-1-0.975-0.98016.06114.91514.9150.0000.0000.0000.000
33L29GLY00.0110.00718.673-0.743-0.7430.0000.0000.0000.000
34L30ASN0-0.141-0.08218.047-0.168-0.1680.0000.0000.0000.000
35L31SER00.0470.00715.3110.1700.1700.0000.0000.0000.000
36L32PHE0-0.093-0.04711.982-0.691-0.6910.0000.0000.0000.000
37L33LEU00.0300.01511.3191.7071.7070.0000.0000.0000.000
38L34HIS0-0.025-0.01313.512-3.013-3.0130.0000.0000.0000.000
39L35TRP00.001-0.00814.8771.1911.1910.0000.0000.0000.000
40L36TYR00.000-0.02514.729-1.248-1.2480.0000.0000.0000.000
41L37GLN00.014-0.00218.376-0.035-0.0350.0000.0000.0000.000
42L38GLN00.007-0.00818.9350.6290.6290.0000.0000.0000.000
43L39LYS10.8450.93821.609-10.934-10.9340.0000.0000.0000.000
44L40PRO00.0430.00524.5460.3030.3030.0000.0000.0000.000
45L41GLY00.0210.02024.772-0.497-0.4970.0000.0000.0000.000
46L42GLN0-0.060-0.03024.8760.0650.0650.0000.0000.0000.000
47L43PRO00.0470.02921.0220.5090.5090.0000.0000.0000.000
48L44PRO0-0.005-0.01116.915-0.537-0.5370.0000.0000.0000.000
49L45LYS10.9070.96619.918-12.160-12.1600.0000.0000.0000.000
50L46LEU0-0.021-0.01017.7510.0620.0620.0000.0000.0000.000
51L47LEU0-0.052-0.02320.561-0.787-0.7870.0000.0000.0000.000
52L48ILE00.0350.01820.162-0.646-0.6460.0000.0000.0000.000
53L49TYR0-0.014-0.02518.6240.8600.8600.0000.0000.0000.000
54L50ARG10.9330.95017.192-14.896-14.8960.0000.0000.0000.000
55L51SER0-0.0320.01717.915-0.825-0.8250.0000.0000.0000.000
56L52SER00.002-0.00619.013-0.433-0.4330.0000.0000.0000.000
57L53ASN0-0.057-0.01422.462-0.288-0.2880.0000.0000.0000.000
58L54LEU00.0410.03923.1850.5760.5760.0000.0000.0000.000
59L55ILE00.0020.00422.072-0.186-0.1860.0000.0000.0000.000
60L56SER0-0.036-0.03625.636-0.429-0.4290.0000.0000.0000.000
61L57GLY00.0380.01829.2310.1210.1210.0000.0000.0000.000
62L58ILE0-0.069-0.01725.381-0.103-0.1030.0000.0000.0000.000
63L59PRO0-0.015-0.02128.734-0.194-0.1940.0000.0000.0000.000
64L60ASP-1-0.843-0.93329.1289.5279.5270.0000.0000.0000.000
65L61ARG10.8470.92529.976-9.714-9.7140.0000.0000.0000.000
66L62PHE0-0.045-0.01024.2290.2710.2710.0000.0000.0000.000
67L63SER00.0290.01025.364-0.163-0.1630.0000.0000.0000.000
68L64GLY0-0.008-0.00821.5610.3480.3480.0000.0000.0000.000
69L65SER0-0.018-0.01021.172-0.471-0.4710.0000.0000.0000.000
70L66GLY00.015-0.00819.1870.6490.6490.0000.0000.0000.000
71L67SER00.0270.01017.778-0.450-0.4500.0000.0000.0000.000
72L68ARG10.9000.93614.300-17.344-17.3440.0000.0000.0000.000
73L69THR00.0080.00511.5840.7210.7210.0000.0000.0000.000
74L70ASP-1-0.925-0.94313.75617.72317.7230.0000.0000.0000.000
75L71PHE00.0500.03213.399-1.011-1.0110.0000.0000.0000.000
76L72THR0-0.082-0.03717.097-0.081-0.0810.0000.0000.0000.000
77L73LEU00.0250.02219.680-0.253-0.2530.0000.0000.0000.000
78L74THR0-0.046-0.04021.295-0.268-0.2680.0000.0000.0000.000
79L75ILE00.0440.03623.945-0.059-0.0590.0000.0000.0000.000
80L76ASN0-0.043-0.02727.365-0.237-0.2370.0000.0000.0000.000
81L77PRO00.0500.03830.939-0.038-0.0380.0000.0000.0000.000
82L78VAL0-0.027-0.03529.5880.0940.0940.0000.0000.0000.000
83L79GLU-1-0.857-0.92131.3598.2498.2490.0000.0000.0000.000
84L80ALA0-0.007-0.03431.6280.3250.3250.0000.0000.0000.000
85L81ASP-1-0.888-0.93531.3579.9769.9760.0000.0000.0000.000
86L82ASP-1-0.786-0.87627.26210.97710.9770.0000.0000.0000.000
87L83VAL0-0.054-0.02026.3540.5130.5130.0000.0000.0000.000
88L84ALA00.0070.00623.968-0.099-0.0990.0000.0000.0000.000
89L85THR00.0280.01218.312-0.285-0.2850.0000.0000.0000.000
90L86TYR0-0.033-0.02518.998-0.025-0.0250.0000.0000.0000.000
91L87TYR00.0050.01113.7000.3960.3960.0000.0000.0000.000
92L89GLN00.0510.02310.3610.0110.0110.0000.0000.0000.000
93L90GLN00.0550.0095.310-6.727-6.7270.0000.0000.0000.000
94L91SER0-0.047-0.0339.2151.1841.1840.0000.0000.0000.000
95L92ASN00.0050.0158.589-2.931-2.9310.0000.0000.0000.000
96L93GLU-1-0.942-0.9665.19631.95931.9590.0000.0000.0000.000
97L94ASP-1-0.947-0.9385.60234.40134.4010.0000.0000.0000.000
98L95PRO0-0.002-0.0212.707-8.119-5.0933.350-2.505-3.8710.030
99L96LEU0-0.0060.0084.913-0.715-0.669-0.001-0.003-0.0420.000
100L97THR0-0.023-0.0142.859-2.445-1.7610.107-0.185-0.6060.001
101L98PHE00.012-0.0146.191-5.746-5.7460.0000.0000.0000.000
102L99GLY00.0290.0178.2952.2372.2370.0000.0000.0000.000
103L100ALA0-0.057-0.04810.409-0.865-0.8650.0000.0000.0000.000
104L101GLY00.0290.02512.809-0.919-0.9190.0000.0000.0000.000
105L102THR0-0.062-0.03915.818-0.148-0.1480.0000.0000.0000.000
106L103LYS10.7940.89018.952-12.218-12.2180.0000.0000.0000.000
107L104LEU0-0.037-0.01022.177-0.282-0.2820.0000.0000.0000.000
108L105GLU-1-0.819-0.89125.35811.33211.3320.0000.0000.0000.000
109L106ILE00.0630.03128.411-0.081-0.0810.0000.0000.0000.000
110L107LYS10.8930.94731.970-8.716-8.7160.0000.0000.0000.000
111L108ARG10.7790.88934.020-8.142-8.1420.0000.0000.0000.000
112L109ALA0-0.016-0.00537.6690.0570.0570.0000.0000.0000.000
113L110ASP-1-0.833-0.93538.9618.1498.1490.0000.0000.0000.000
114L111ALA0-0.022-0.00340.372-0.211-0.2110.0000.0000.0000.000
115L112ALA00.0530.02240.7480.1950.1950.0000.0000.0000.000
116L113PRO0-0.0290.00940.417-0.057-0.0570.0000.0000.0000.000
117L114THR0-0.024-0.02342.383-0.220-0.2200.0000.0000.0000.000
118L115VAL00.0440.00443.1820.0700.0700.0000.0000.0000.000
119L116SER0-0.040-0.01744.881-0.296-0.2960.0000.0000.0000.000
120L117ILE0-0.025-0.00245.4550.1640.1640.0000.0000.0000.000
121L118PHE00.0010.01345.666-0.149-0.1490.0000.0000.0000.000
122L119PRO00.0170.00647.0190.1190.1190.0000.0000.0000.000
123L120PRO00.0190.01547.6720.0550.0550.0000.0000.0000.000
124L121SER00.0160.02548.680-0.147-0.1470.0000.0000.0000.000
125L122SER00.025-0.02050.3680.0960.0960.0000.0000.0000.000
126L123GLU-1-0.898-0.93049.7146.4426.4420.0000.0000.0000.000
127L124GLN00.0600.02243.535-0.052-0.0520.0000.0000.0000.000
128L125LEU0-0.0110.00348.532-0.002-0.0020.0000.0000.0000.000
129L126THR0-0.100-0.06751.034-0.040-0.0400.0000.0000.0000.000
130L127SER0-0.030-0.01148.2820.0030.0030.0000.0000.0000.000
131L128GLY00.0260.01147.9780.1300.1300.0000.0000.0000.000
132L129GLY0-0.0040.00445.3980.0650.0650.0000.0000.0000.000
133L130ALA0-0.038-0.01945.754-0.108-0.1080.0000.0000.0000.000
134L131SER00.0030.00041.6760.1260.1260.0000.0000.0000.000
135L132VAL0-0.0160.01643.945-0.164-0.1640.0000.0000.0000.000
136L133VAL0-0.024-0.02440.7880.2000.2000.0000.0000.0000.000
137L134CYS0-0.038-0.01941.491-0.016-0.0160.0000.0000.0000.000
138L135PHE00.0120.00239.7240.2590.2590.0000.0000.0000.000
139L136LEU00.0200.01238.721-0.224-0.2240.0000.0000.0000.000
140L137ASN0-0.003-0.03039.4700.1540.1540.0000.0000.0000.000
141L138ASN0-0.015-0.02239.691-0.031-0.0310.0000.0000.0000.000
142L139PHE0-0.0580.00235.229-0.173-0.1730.0000.0000.0000.000
143L140TYR00.0770.04132.4330.2720.2720.0000.0000.0000.000
144L141PRO0-0.037-0.02833.214-0.213-0.2130.0000.0000.0000.000
145L142LYS10.9320.94426.271-11.721-11.7210.0000.0000.0000.000
146L143ASP-1-0.923-0.95329.93410.33310.3330.0000.0000.0000.000
147L144ILE00.0060.00932.702-0.360-0.3600.0000.0000.0000.000
148L145ASN0-0.013-0.00834.3750.0350.0350.0000.0000.0000.000
149L146VAL00.0800.02736.642-0.250-0.2500.0000.0000.0000.000
150L147LYS10.8060.90538.771-7.925-7.9250.0000.0000.0000.000
151L148TRP00.0150.00639.501-0.323-0.3230.0000.0000.0000.000
152L149LYS10.8700.91542.757-6.953-6.9530.0000.0000.0000.000
153L150ILE00.006-0.00945.205-0.074-0.0740.0000.0000.0000.000
154L151ASP-1-0.963-0.97948.4876.1996.1990.0000.0000.0000.000
155L152GLY00.0140.01750.345-0.119-0.1190.0000.0000.0000.000
156L153SER0-0.054-0.03547.8900.0960.0960.0000.0000.0000.000
157L154GLU-1-0.937-0.99241.1107.9647.9640.0000.0000.0000.000
158L155ARG10.8280.91941.323-7.599-7.5990.0000.0000.0000.000
159L156GLN00.0430.02036.1570.2440.2440.0000.0000.0000.000
160L157ASN0-0.043-0.02737.0550.2430.2430.0000.0000.0000.000
161L158GLY00.0590.02636.468-0.236-0.2360.0000.0000.0000.000
162L159VAL00.0110.02135.791-0.187-0.1870.0000.0000.0000.000
163L160LEU0-0.032-0.00831.9880.3420.3420.0000.0000.0000.000
164L161ASN00.006-0.00632.286-0.416-0.4160.0000.0000.0000.000
165L162SER0-0.0100.00331.3190.4340.4340.0000.0000.0000.000
166L163TRP00.0310.00629.955-0.273-0.2730.0000.0000.0000.000
167L164THR00.0310.03330.6440.1380.1380.0000.0000.0000.000
168L165ASP-1-0.872-0.95028.14811.20011.2000.0000.0000.0000.000
169L166GLN00.0150.00229.976-0.600-0.6000.0000.0000.0000.000
170L167ASP-1-0.792-0.87431.8708.4918.4910.0000.0000.0000.000
171L168SER0-0.012-0.02033.863-0.288-0.2880.0000.0000.0000.000
172L169LYS10.7530.87335.238-8.343-8.3430.0000.0000.0000.000
173L170ASP-1-0.799-0.92138.6817.7637.7630.0000.0000.0000.000
174L171SER0-0.086-0.02835.182-0.012-0.0120.0000.0000.0000.000
175L172THR00.0290.02835.6240.1490.1490.0000.0000.0000.000
176L173TYR0-0.019-0.01529.4650.2180.2180.0000.0000.0000.000
177L174SER00.0350.02235.074-0.439-0.4390.0000.0000.0000.000
178L175MET0-0.065-0.01633.9340.3160.3160.0000.0000.0000.000
179L176SER00.0220.02135.637-0.344-0.3440.0000.0000.0000.000
180L177SER0-0.015-0.01936.1120.1820.1820.0000.0000.0000.000
181L178THR00.0440.01537.308-0.334-0.3340.0000.0000.0000.000
182L179LEU00.0230.02438.3800.1780.1780.0000.0000.0000.000
183L180THR00.002-0.00539.758-0.218-0.2180.0000.0000.0000.000
184L181LEU0-0.0380.00341.4300.0860.0860.0000.0000.0000.000
185L182THR00.0320.00544.169-0.019-0.0190.0000.0000.0000.000
186L183LYS10.8000.88146.409-6.088-6.0880.0000.0000.0000.000
187L184ASP-1-0.837-0.91149.7736.0826.0820.0000.0000.0000.000
188L185GLU-1-0.821-0.92245.6137.0597.0590.0000.0000.0000.000
189L186TYR00.0380.02448.562-0.078-0.0780.0000.0000.0000.000
190L187GLU-1-0.866-0.94150.1845.8485.8480.0000.0000.0000.000
191L188ARG10.8620.93850.277-6.440-6.4400.0000.0000.0000.000
192L189HIS00.0110.02149.848-0.062-0.0620.0000.0000.0000.000
193L190ASN0-0.017-0.02453.7020.0060.0060.0000.0000.0000.000
194L191SER0-0.0160.00352.8800.0120.0120.0000.0000.0000.000
195L192TYR00.0730.05247.2750.1380.1380.0000.0000.0000.000
196L193THR00.0250.01147.897-0.064-0.0640.0000.0000.0000.000
197L195GLU-1-0.848-0.91143.5696.9726.9720.0000.0000.0000.000
198L196ALA00.0400.03840.9370.2440.2440.0000.0000.0000.000
199L197THR0-0.0050.00339.110-0.192-0.1920.0000.0000.0000.000
200L198HIS00.0070.00836.7530.0190.0190.0000.0000.0000.000
201L199LYS10.9570.97336.931-8.345-8.3450.0000.0000.0000.000
202L200THR0-0.034-0.03339.458-0.200-0.2000.0000.0000.0000.000
203L201SER0-0.066-0.03642.630-0.265-0.2650.0000.0000.0000.000
204L202THR00.0140.01744.0380.0810.0810.0000.0000.0000.000
205L203SER0-0.0160.01046.639-0.096-0.0960.0000.0000.0000.000
206L204PRO00.0260.00544.7600.1550.1550.0000.0000.0000.000
207L205ILE0-0.017-0.00743.965-0.195-0.1950.0000.0000.0000.000
208L206VAL00.012-0.00445.4130.1520.1520.0000.0000.0000.000
209L207LYS10.8300.90046.931-6.715-6.7150.0000.0000.0000.000
210L208SER00.0090.00648.5140.1150.1150.0000.0000.0000.000
211L209PHE00.0290.01649.046-0.069-0.0690.0000.0000.0000.000
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