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: 6N5VZ

Calculation Name: 3GHE-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHE

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2018346.293958
FMO2-HF: Nuclear repulsion 1939283.818681
FMO2-HF: Total energy -79062.475277
FMO2-MP2: Total energy -79294.374158


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:GLN)


Summations of interaction energy for fragment #1(L:1:GLN)
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.
0.3513.04-0.035-1.396-1.2570.001
Interaction energy analysis for fragmet #1(L:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.013
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].
3L3ALA00.0420.0083.8020.3152.857-0.034-1.388-1.1190.001
4L4LEU0-0.0280.0096.467-0.608-0.6080.0000.0000.0000.000
5L5THR0-0.009-0.0018.9240.1770.1770.0000.0000.0000.000
6L6GLN00.0190.00211.349-0.018-0.0180.0000.0000.0000.000
7L7PRO0-0.0260.00415.1130.0410.0410.0000.0000.0000.000
8L8ALA00.0950.04317.5420.0300.0300.0000.0000.0000.000
9L9SER0-0.063-0.03018.9090.0200.0200.0000.0000.0000.000
10L11VAL00.0080.01722.088-0.028-0.0280.0000.0000.0000.000
11L12SER00.0500.00924.6780.0220.0220.0000.0000.0000.000
12L13GLY0-0.0060.00328.478-0.016-0.0160.0000.0000.0000.000
13L14SER0-0.0070.00331.2420.0120.0120.0000.0000.0000.000
14L15PRO00.0420.00834.996-0.005-0.0050.0000.0000.0000.000
15L16GLY0-0.0110.01036.847-0.005-0.0050.0000.0000.0000.000
16L17GLN0-0.018-0.00632.728-0.002-0.0020.0000.0000.0000.000
17L18SER00.002-0.00330.7600.0080.0080.0000.0000.0000.000
18L19ILE0-0.027-0.01025.957-0.008-0.0080.0000.0000.0000.000
19L20THR00.019-0.00522.3900.0040.0040.0000.0000.0000.000
20L21ILE0-0.0300.01319.119-0.007-0.0070.0000.0000.0000.000
21L22SER00.0130.00517.2370.0130.0130.0000.0000.0000.000
22L23CYS0-0.044-0.02414.2470.0570.0570.0000.0000.0000.000
23L24THR00.0030.01610.8900.0290.0290.0000.0000.0000.000
24L25GLY00.0370.0058.5210.1250.1250.0000.0000.0000.000
25L26THR0-0.089-0.0488.4060.0750.0750.0000.0000.0000.000
26L27SER00.0220.0148.933-0.275-0.2750.0000.0000.0000.000
27L27THR00.0360.0059.5930.1020.1020.0000.0000.0000.000
28L27ASP-1-0.884-0.9249.753-0.587-0.5870.0000.0000.0000.000
29L27VAL00.039-0.00511.9780.1150.1150.0000.0000.0000.000
30L28ASN0-0.040-0.03514.9280.0520.0520.0000.0000.0000.000
31L29GLY00.0250.01613.1690.0950.0950.0000.0000.0000.000
32L30TYR0-0.0370.00514.0130.0100.0100.0000.0000.0000.000
33L31ASN00.025-0.00914.979-0.015-0.0150.0000.0000.0000.000
34L32TYR0-0.0050.02114.5910.0260.0260.0000.0000.0000.000
35L33VAL00.0230.00414.8880.0020.0020.0000.0000.0000.000
36L34SER0-0.019-0.02416.9790.0130.0130.0000.0000.0000.000
37L35TRP00.0440.02118.4070.0120.0120.0000.0000.0000.000
38L36TYR0-0.004-0.00819.469-0.001-0.0010.0000.0000.0000.000
39L37GLN0-0.014-0.00723.047-0.001-0.0010.0000.0000.0000.000
40L38GLN00.017-0.00123.7250.0250.0250.0000.0000.0000.000
41L39TYR00.0180.01926.562-0.002-0.0020.0000.0000.0000.000
42L40ALA00.0520.01228.8520.0170.0170.0000.0000.0000.000
43L41GLY0-0.006-0.00229.131-0.010-0.0100.0000.0000.0000.000
44L42LYS10.8840.95030.036-0.152-0.1520.0000.0000.0000.000
45L43ALA00.0310.01427.8730.0160.0160.0000.0000.0000.000
46L44PRO00.000-0.00823.713-0.022-0.0220.0000.0000.0000.000
47L45LYS10.9891.00626.105-0.116-0.1160.0000.0000.0000.000
48L46LEU0-0.0120.01022.930-0.011-0.0110.0000.0000.0000.000
49L47ILE0-0.036-0.03025.023-0.017-0.0170.0000.0000.0000.000
50L48ILE0-0.012-0.01022.301-0.023-0.0230.0000.0000.0000.000
51L49PHE00.0260.01521.5070.0290.0290.0000.0000.0000.000
52L50ASP-1-0.824-0.91320.5300.0650.0650.0000.0000.0000.000
53L51VAL0-0.027-0.00618.366-0.035-0.0350.0000.0000.0000.000
54L52SER0-0.088-0.06020.694-0.008-0.0080.0000.0000.0000.000
55L53LYS10.8860.96724.427-0.037-0.0370.0000.0000.0000.000
56L54ARG10.9600.98026.2670.0000.0000.0000.0000.0000.000
57L55PRO0-0.0050.01727.431-0.003-0.0030.0000.0000.0000.000
58L56SER00.0230.00430.332-0.008-0.0080.0000.0000.0000.000
59L57GLY00.006-0.00134.1200.0100.0100.0000.0000.0000.000
60L58VAL0-0.056-0.01629.474-0.001-0.0010.0000.0000.0000.000
61L59SER00.0420.02432.786-0.011-0.0110.0000.0000.0000.000
62L60ASN0-0.028-0.02032.395-0.003-0.0030.0000.0000.0000.000
63L61ARG10.8340.89333.090-0.024-0.0240.0000.0000.0000.000
64L62PHE0-0.021-0.00127.625-0.008-0.0080.0000.0000.0000.000
65L63SER0-0.016-0.01627.638-0.001-0.0010.0000.0000.0000.000
66L64GLY00.0350.01923.5090.0010.0010.0000.0000.0000.000
67L65SER0-0.002-0.00322.325-0.012-0.0120.0000.0000.0000.000
68L66LYS10.8410.89913.4160.3980.3980.0000.0000.0000.000
69L67SER0-0.0180.00818.1720.0280.0280.0000.0000.0000.000
70L68GLY00.0170.02215.577-0.032-0.0320.0000.0000.0000.000
71L69ASP-1-0.809-0.91210.672-1.100-1.1000.0000.0000.0000.000
72L70THR0-0.0080.00612.7300.0760.0760.0000.0000.0000.000
73L71ALA00.0050.01415.1930.0450.0450.0000.0000.0000.000
74L72SER0-0.029-0.03917.303-0.001-0.0010.0000.0000.0000.000
75L73LEU0-0.0160.01220.4870.0160.0160.0000.0000.0000.000
76L74THR0-0.014-0.01723.028-0.015-0.0150.0000.0000.0000.000
77L75ILE0-0.0050.00326.4300.0120.0120.0000.0000.0000.000
78L76SER00.0110.00729.296-0.004-0.0040.0000.0000.0000.000
79L77GLY00.0200.00432.7350.0100.0100.0000.0000.0000.000
80L78LEU0-0.041-0.01429.9050.0080.0080.0000.0000.0000.000
81L79GLN00.0390.01133.9800.0040.0040.0000.0000.0000.000
82L80ALA00.0350.00634.3030.0030.0030.0000.0000.0000.000
83L81GLU-1-0.940-0.96234.6470.0620.0620.0000.0000.0000.000
84L82ASP-1-0.742-0.85230.6490.0390.0390.0000.0000.0000.000
85L83GLU-1-0.927-0.94729.5920.0690.0690.0000.0000.0000.000
86L84ALA0-0.055-0.04527.5850.0130.0130.0000.0000.0000.000
87L85ASP-1-0.900-0.93922.7060.1640.1640.0000.0000.0000.000
88L86TYR0-0.045-0.04822.1780.0010.0010.0000.0000.0000.000
89L87HIS00.0250.01918.0850.0040.0040.0000.0000.0000.000
90L89SER0-0.017-0.00615.0450.0740.0740.0000.0000.0000.000
91L90SER00.014-0.02411.170-0.191-0.1910.0000.0000.0000.000
92L91TYR00.0150.03310.5970.2630.2630.0000.0000.0000.000
93L92THR0-0.014-0.0085.494-0.610-0.6100.0000.0000.0000.000
94L93SER00.0090.0056.1790.7060.7060.0000.0000.0000.000
95L94SER0-0.0090.0044.3971.2841.431-0.001-0.008-0.1380.000
96L95THR00.0230.0316.704-0.548-0.5480.0000.0000.0000.000
97L95PRO00.0250.0017.6020.7890.7890.0000.0000.0000.000
98L95TYR0-0.016-0.0209.515-0.315-0.3150.0000.0000.0000.000
99L96VAL0-0.018-0.01210.969-0.287-0.2870.0000.0000.0000.000
100L97LEU0-0.016-0.0057.1550.0970.0970.0000.0000.0000.000
101L98PHE00.012-0.01511.867-0.229-0.2290.0000.0000.0000.000
102L99GLY00.0130.01112.3870.0900.0900.0000.0000.0000.000
103L100GLY0-0.033-0.01513.4670.0720.0720.0000.0000.0000.000
104L101GLY00.0050.01014.8100.0010.0010.0000.0000.0000.000
105L102THR0-0.087-0.05318.085-0.028-0.0280.0000.0000.0000.000
106L103LYS10.9600.98820.282-0.108-0.1080.0000.0000.0000.000
107L104LEU0-0.041-0.02523.709-0.023-0.0230.0000.0000.0000.000
108L105THR0-0.026-0.02026.2950.0160.0160.0000.0000.0000.000
109L106VAL0-0.008-0.00529.501-0.015-0.0150.0000.0000.0000.000
110L106LEU0-0.028-0.02732.3230.0060.0060.0000.0000.0000.000
111L107GLY00.0060.01234.895-0.005-0.0050.0000.0000.0000.000
112L108GLN0-0.077-0.04137.675-0.003-0.0030.0000.0000.0000.000
113L109PRO0-0.017-0.00538.480-0.003-0.0030.0000.0000.0000.000
114L110LYS10.9670.98736.0010.0200.0200.0000.0000.0000.000
115L111ALA0-0.051-0.02737.938-0.001-0.0010.0000.0000.0000.000
116L112ALA00.0210.01138.0280.0020.0020.0000.0000.0000.000
117L113PRO0-0.0050.00436.3440.0030.0030.0000.0000.0000.000
118L114SER00.0110.01338.884-0.006-0.0060.0000.0000.0000.000
119L115VAL00.000-0.01438.6830.0050.0050.0000.0000.0000.000
120L116THR0-0.022-0.00841.289-0.006-0.0060.0000.0000.0000.000
121L117LEU0-0.043-0.02240.0740.0040.0040.0000.0000.0000.000
122L118PHE0-0.0010.00042.749-0.004-0.0040.0000.0000.0000.000
123L119PRO0-0.012-0.00543.2710.0030.0030.0000.0000.0000.000
124L120PRO00.0490.02743.2720.0020.0020.0000.0000.0000.000
125L121SER00.0330.02745.503-0.004-0.0040.0000.0000.0000.000
126L122SER00.0470.00648.6140.0020.0020.0000.0000.0000.000
127L123GLU-1-0.933-0.96650.7400.0660.0660.0000.0000.0000.000
128L124GLU-1-0.801-0.87142.7050.0900.0900.0000.0000.0000.000
129L125LEU0-0.029-0.01646.2000.0010.0010.0000.0000.0000.000
130L126GLN0-0.094-0.04648.263-0.002-0.0020.0000.0000.0000.000
131L127ALA0-0.0210.00647.4680.0000.0000.0000.0000.0000.000
132L128ASN0-0.086-0.05745.5610.0020.0020.0000.0000.0000.000
133L129LYS10.9430.96140.324-0.106-0.1060.0000.0000.0000.000
134L130ALA00.0230.00441.997-0.006-0.0060.0000.0000.0000.000
135L131THR0-0.013-0.02838.4890.0060.0060.0000.0000.0000.000
136L132LEU0-0.068-0.00639.076-0.006-0.0060.0000.0000.0000.000
137L133VAL00.0350.01138.6960.0060.0060.0000.0000.0000.000
138L134CYS0-0.069-0.00536.680-0.005-0.0050.0000.0000.0000.000
139L135LEU00.003-0.00637.4100.0070.0070.0000.0000.0000.000
140L136ILE00.0140.00434.142-0.008-0.0080.0000.0000.0000.000
141L137SER0-0.013-0.01737.7690.0060.0060.0000.0000.0000.000
142L138ASP-1-0.808-0.89439.3790.0420.0420.0000.0000.0000.000
143L139PHE00.0000.01932.404-0.005-0.0050.0000.0000.0000.000
144L140TYR00.0580.01834.2460.0070.0070.0000.0000.0000.000
145L141PRO00.0970.02831.346-0.006-0.0060.0000.0000.0000.000
146L142GLY00.0100.00731.795-0.001-0.0010.0000.0000.0000.000
147L143ALA0-0.020-0.01627.6450.0120.0120.0000.0000.0000.000
148L144VAL0-0.0010.00628.948-0.011-0.0110.0000.0000.0000.000
149L145THR0-0.022-0.00626.0980.0100.0100.0000.0000.0000.000
150L146VAL00.0340.01028.924-0.008-0.0080.0000.0000.0000.000
151L147ALA0-0.062-0.02229.8760.0040.0040.0000.0000.0000.000
152L148TRP00.0600.00531.939-0.007-0.0070.0000.0000.0000.000
153L149LYS10.8320.89634.186-0.010-0.0100.0000.0000.0000.000
154L150ALA00.0860.05136.8950.0030.0030.0000.0000.0000.000
155L151ASP-1-0.818-0.93639.2420.0170.0170.0000.0000.0000.000
156L152SER0-0.022-0.01939.913-0.001-0.0010.0000.0000.0000.000
157L153SER0-0.054-0.02236.359-0.008-0.0080.0000.0000.0000.000
158L154PRO0-0.013-0.01031.6960.0060.0060.0000.0000.0000.000
159L155VAL00.0210.03533.0010.0000.0000.0000.0000.0000.000
160L156LYS10.9630.96025.004-0.042-0.0420.0000.0000.0000.000
161L157ALA0-0.0120.00529.2170.0130.0130.0000.0000.0000.000
162L158GLY00.0630.03230.670-0.007-0.0070.0000.0000.0000.000
163L159VAL0-0.027-0.00529.663-0.007-0.0070.0000.0000.0000.000
164L160GLU-1-0.885-0.92728.9350.1960.1960.0000.0000.0000.000
165L161THR0-0.027-0.01928.581-0.020-0.0200.0000.0000.0000.000
166L162THR00.0010.01628.4090.0110.0110.0000.0000.0000.000
167L163THR00.0100.00825.710-0.005-0.0050.0000.0000.0000.000
168L164PRO0-0.020-0.01927.901-0.003-0.0030.0000.0000.0000.000
169L165SER0-0.018-0.00130.3570.0110.0110.0000.0000.0000.000
170L166LYS10.8900.93832.988-0.094-0.0940.0000.0000.0000.000
171L167GLN00.0190.00535.6020.0060.0060.0000.0000.0000.000
172L168SER00.044-0.00539.2500.0010.0010.0000.0000.0000.000
173L169ASN0-0.058-0.02941.7830.0020.0020.0000.0000.0000.000
174L170ASN00.0250.01139.1390.0020.0020.0000.0000.0000.000
175L171LYS10.9461.02437.995-0.036-0.0360.0000.0000.0000.000
176L172TYR0-0.047-0.03332.0540.0110.0110.0000.0000.0000.000
177L173ALA00.0440.01835.423-0.007-0.0070.0000.0000.0000.000
178L174ALA0-0.027-0.01832.3480.0080.0080.0000.0000.0000.000
179L175SER0-0.0050.00533.517-0.007-0.0070.0000.0000.0000.000
180L176SER00.0040.00532.0340.0070.0070.0000.0000.0000.000
181L177TYR00.0210.00233.632-0.010-0.0100.0000.0000.0000.000
182L178LEU0-0.0010.01133.9220.0050.0050.0000.0000.0000.000
183L179SER0-0.033-0.02135.211-0.002-0.0020.0000.0000.0000.000
184L180LEU0-0.044-0.02336.658-0.002-0.0020.0000.0000.0000.000
185L181THR00.0320.01539.3350.0030.0030.0000.0000.0000.000
186L182PRO00.0260.00942.117-0.005-0.0050.0000.0000.0000.000
187L183GLU-1-0.866-0.94244.0730.0620.0620.0000.0000.0000.000
188L184GLN00.0420.05037.566-0.002-0.0020.0000.0000.0000.000
189L185TRP00.0270.00143.034-0.005-0.0050.0000.0000.0000.000
190L186LYS10.9210.94144.429-0.054-0.0540.0000.0000.0000.000
191L187SER0-0.044-0.03144.507-0.004-0.0040.0000.0000.0000.000
192L188HIS0-0.130-0.03940.6310.0000.0000.0000.0000.0000.000
193L189ARG10.9300.96644.201-0.009-0.0090.0000.0000.0000.000
194L190SER0-0.006-0.01944.119-0.001-0.0010.0000.0000.0000.000
195L191TYR0-0.0090.02338.5630.0000.0000.0000.0000.0000.000
196L192SER00.0380.02239.148-0.001-0.0010.0000.0000.0000.000
197L194GLN00.025-0.00333.249-0.009-0.0090.0000.0000.0000.000
198L195VAL00.0120.00633.6510.0050.0050.0000.0000.0000.000
199L196THR0-0.019-0.01130.797-0.011-0.0110.0000.0000.0000.000
200L197HIS0-0.039-0.04231.7880.0030.0030.0000.0000.0000.000
201L198GLU-1-0.923-0.96531.026-0.013-0.0130.0000.0000.0000.000
202L199GLY0-0.020-0.00831.634-0.006-0.0060.0000.0000.0000.000
203L200SER0-0.035-0.00932.886-0.005-0.0050.0000.0000.0000.000
204L201THR0-0.008-0.01034.2770.0050.0050.0000.0000.0000.000
205L202VAL00.0070.02336.762-0.003-0.0030.0000.0000.0000.000
206L203GLU-1-0.877-0.95038.3080.0160.0160.0000.0000.0000.000
207L204LYS10.8710.95439.990-0.031-0.0310.0000.0000.0000.000
208L205THR00.036-0.00541.4920.0010.0010.0000.0000.0000.000
209L206VAL0-0.044-0.01243.4410.0000.0000.0000.0000.0000.000
210L207ALA00.0460.00045.4430.0000.0000.0000.0000.0000.000
211L208PRO0-0.0160.00447.0010.0010.0010.0000.0000.0000.000
212L209THR0-0.0080.01249.793-0.003-0.0030.0000.0000.0000.000