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

tag_button

FMODB ID: Z695N

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2019724.776483
FMO2-HF: Nuclear repulsion 1940661.563214
FMO2-HF: Total energy -79063.213269
FMO2-MP2: Total energy -79295.087075


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.
-0.9381.873-0.034-1.49-1.2870.001
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 : -0.022 / q_NPA : -0.015
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].
3L3ALA00.0560.0173.802-0.7931.908-0.033-1.488-1.1800.001
4L4LEU0-0.0290.0076.741-0.208-0.2080.0000.0000.0000.000
5L5THR0-0.017-0.0079.6680.2610.2610.0000.0000.0000.000
6L6GLN00.014-0.01112.084-0.117-0.1170.0000.0000.0000.000
7L7PRO0-0.0110.01215.8450.0590.0590.0000.0000.0000.000
8L8ALA00.0830.04918.368-0.012-0.0120.0000.0000.0000.000
9L9SER0-0.014-0.00819.687-0.009-0.0090.0000.0000.0000.000
10L11VAL0-0.028-0.00522.856-0.008-0.0080.0000.0000.0000.000
11L12SER00.0230.00625.4870.0040.0040.0000.0000.0000.000
12L13GLY00.0140.01029.289-0.009-0.0090.0000.0000.0000.000
13L14SER0-0.006-0.00132.0360.0090.0090.0000.0000.0000.000
14L15PRO00.019-0.00435.781-0.005-0.0050.0000.0000.0000.000
15L16GLY0-0.0140.00837.537-0.003-0.0030.0000.0000.0000.000
16L17GLN0-0.0150.00333.598-0.003-0.0030.0000.0000.0000.000
17L18SER00.006-0.00631.2910.0030.0030.0000.0000.0000.000
18L19ILE0-0.031-0.00526.7630.0020.0020.0000.0000.0000.000
19L20THR00.0340.00222.862-0.006-0.0060.0000.0000.0000.000
20L21ILE0-0.0240.01719.8110.0150.0150.0000.0000.0000.000
21L22SER00.0440.01917.282-0.022-0.0220.0000.0000.0000.000
22L23CYS0-0.072-0.04014.5110.0420.0420.0000.0000.0000.000
23L24THR00.0340.03110.641-0.046-0.0460.0000.0000.0000.000
24L25GLY00.004-0.0108.5010.2080.2080.0000.0000.0000.000
25L26THR0-0.083-0.0558.487-0.199-0.1990.0000.0000.0000.000
26L27SER0-0.016-0.0168.993-0.190-0.1900.0000.0000.0000.000
27L27THR00.0670.0219.6190.1690.1690.0000.0000.0000.000
28L27ASP-1-0.886-0.9189.237-1.796-1.7960.0000.0000.0000.000
29L27VAL00.0540.00511.9960.1640.1640.0000.0000.0000.000
30L28ASN0-0.037-0.03114.9050.1220.1220.0000.0000.0000.000
31L29GLY00.0210.01313.2280.0930.0930.0000.0000.0000.000
32L30TYR0-0.0420.00914.0830.0340.0340.0000.0000.0000.000
33L31ASN00.034-0.00815.0330.0350.0350.0000.0000.0000.000
34L32TYR0-0.0150.00914.7020.0580.0580.0000.0000.0000.000
35L33VAL00.0250.00314.930-0.026-0.0260.0000.0000.0000.000
36L34SER0-0.010-0.01917.0740.0290.0290.0000.0000.0000.000
37L35TRP00.0200.01218.8380.0240.0240.0000.0000.0000.000
38L36TYR0-0.009-0.00819.524-0.002-0.0020.0000.0000.0000.000
39L37GLN00.0280.01623.1890.0050.0050.0000.0000.0000.000
40L38GLN00.025-0.00623.6150.0140.0140.0000.0000.0000.000
41L39TYR00.0090.01326.5850.0050.0050.0000.0000.0000.000
42L40ALA00.0710.02228.8880.0090.0090.0000.0000.0000.000
43L41GLY0-0.012-0.00629.043-0.010-0.0100.0000.0000.0000.000
44L42LYS10.8800.94729.916-0.113-0.1130.0000.0000.0000.000
45L43ALA00.0380.02627.4960.0150.0150.0000.0000.0000.000
46L44PRO00.002-0.00623.370-0.013-0.0130.0000.0000.0000.000
47L45LYS10.9150.96925.854-0.059-0.0590.0000.0000.0000.000
48L46LEU0-0.0050.01123.018-0.002-0.0020.0000.0000.0000.000
49L47ILE0-0.035-0.02625.129-0.008-0.0080.0000.0000.0000.000
50L48ILE0-0.006-0.01122.354-0.013-0.0130.0000.0000.0000.000
51L49PHE00.0350.01921.6110.0150.0150.0000.0000.0000.000
52L50ASP-1-0.796-0.87920.578-0.137-0.1370.0000.0000.0000.000
53L51VAL0-0.028-0.00618.338-0.012-0.0120.0000.0000.0000.000
54L52SER0-0.083-0.05320.7770.0210.0210.0000.0000.0000.000
55L53LYS10.8500.93024.5110.1390.1390.0000.0000.0000.000
56L54ARG10.9500.97626.3630.0520.0520.0000.0000.0000.000
57L55PRO0-0.0220.01127.555-0.003-0.0030.0000.0000.0000.000
58L56SER00.0250.00730.4370.0000.0000.0000.0000.0000.000
59L57GLY00.005-0.00334.2290.0070.0070.0000.0000.0000.000
60L58VAL0-0.055-0.01429.5110.0060.0060.0000.0000.0000.000
61L59SER00.0530.02332.892-0.011-0.0110.0000.0000.0000.000
62L60ASN0-0.021-0.01932.4920.0020.0020.0000.0000.0000.000
63L61ARG10.8140.87433.177-0.020-0.0200.0000.0000.0000.000
64L62PHE0-0.033-0.01127.948-0.002-0.0020.0000.0000.0000.000
65L63SER0-0.018-0.01627.724-0.010-0.0100.0000.0000.0000.000
66L64GLY00.0330.01823.5940.0110.0110.0000.0000.0000.000
67L65SER0-0.013-0.00722.394-0.016-0.0160.0000.0000.0000.000
68L66LYS10.8380.89313.5000.6350.6350.0000.0000.0000.000
69L67SER0-0.0100.01318.2230.0190.0190.0000.0000.0000.000
70L68GLY00.0130.01615.5910.0100.0100.0000.0000.0000.000
71L69ASP-1-0.770-0.89710.750-0.675-0.6750.0000.0000.0000.000
72L70THR0-0.0230.01312.7690.1190.1190.0000.0000.0000.000
73L71ALA00.0070.01415.1730.0010.0010.0000.0000.0000.000
74L72SER0-0.031-0.03617.3750.0550.0550.0000.0000.0000.000
75L73LEU0-0.0150.01220.621-0.011-0.0110.0000.0000.0000.000
76L74THR0-0.027-0.03123.2610.0040.0040.0000.0000.0000.000
77L75ILE0-0.0030.00426.741-0.001-0.0010.0000.0000.0000.000
78L76SER00.0100.00529.7210.0020.0020.0000.0000.0000.000
79L77GLY00.0210.01133.1580.0050.0050.0000.0000.0000.000
80L78LEU0-0.033-0.00930.5600.0050.0050.0000.0000.0000.000
81L79GLN00.010-0.01034.633-0.006-0.0060.0000.0000.0000.000
82L80ALA00.0350.00334.9220.0050.0050.0000.0000.0000.000
83L81GLU-1-0.896-0.93835.1650.0430.0430.0000.0000.0000.000
84L82ASP-1-0.736-0.83131.1790.0330.0330.0000.0000.0000.000
85L83GLU-1-0.841-0.87730.0850.1050.1050.0000.0000.0000.000
86L84ALA0-0.055-0.03527.9780.0030.0030.0000.0000.0000.000
87L85ASP-1-0.884-0.94022.9850.1860.1860.0000.0000.0000.000
88L86TYR0-0.042-0.05322.576-0.022-0.0220.0000.0000.0000.000
89L87HIS00.0260.02518.1540.0300.0300.0000.0000.0000.000
90L89SER0-0.013-0.01315.1210.0480.0480.0000.0000.0000.000
91L90SER00.013-0.01911.112-0.105-0.1050.0000.0000.0000.000
92L91TYR00.0010.02710.7260.1660.1660.0000.0000.0000.000
93L92THR0-0.009-0.0045.674-0.465-0.4650.0000.0000.0000.000
94L93SER00.0360.0116.4030.3320.3320.0000.0000.0000.000
95L94SER0-0.034-0.0084.9831.1091.219-0.001-0.002-0.1070.000
96L95THR00.0300.0327.252-0.281-0.2810.0000.0000.0000.000
97L95PRO00.0230.0037.8780.3980.3980.0000.0000.0000.000
98L95TYR0-0.035-0.0249.864-0.051-0.0510.0000.0000.0000.000
99L96VAL0-0.018-0.01011.070-0.212-0.2120.0000.0000.0000.000
100L97LEU0-0.0080.0027.2420.1110.1110.0000.0000.0000.000
101L98PHE00.011-0.01311.967-0.129-0.1290.0000.0000.0000.000
102L99GLY00.0190.01712.3110.0970.0970.0000.0000.0000.000
103L100GLY0-0.032-0.01513.6900.0250.0250.0000.0000.0000.000
104L101GLY00.0140.01115.086-0.023-0.0230.0000.0000.0000.000
105L102THR0-0.101-0.06518.4300.0070.0070.0000.0000.0000.000
106L103LYS10.8500.92320.894-0.152-0.1520.0000.0000.0000.000
107L104LEU0-0.042-0.02424.300-0.007-0.0070.0000.0000.0000.000
108L105THR0-0.023-0.02526.9820.0030.0030.0000.0000.0000.000
109L106VAL00.012-0.00230.227-0.009-0.0090.0000.0000.0000.000
110L106LEU0-0.025-0.02633.1420.0030.0030.0000.0000.0000.000
111L107GLY00.0130.01635.675-0.007-0.0070.0000.0000.0000.000
112L108GLN0-0.093-0.04438.567-0.005-0.0050.0000.0000.0000.000
113L109PRO00.0120.00439.2900.0010.0010.0000.0000.0000.000
114L110LYS10.8520.92035.770-0.063-0.0630.0000.0000.0000.000
115L111ALA0-0.045-0.02638.782-0.004-0.0040.0000.0000.0000.000
116L112ALA00.0350.01838.8680.0060.0060.0000.0000.0000.000
117L113PRO0-0.0050.00437.023-0.001-0.0010.0000.0000.0000.000
118L114SER0-0.0090.00739.699-0.005-0.0050.0000.0000.0000.000
119L115VAL00.010-0.00839.3920.0050.0050.0000.0000.0000.000
120L116THR0-0.0110.00641.990-0.008-0.0080.0000.0000.0000.000
121L117LEU0-0.039-0.01440.6040.0060.0060.0000.0000.0000.000
122L118PHE00.0070.00243.207-0.006-0.0060.0000.0000.0000.000
123L119PRO0-0.0030.00443.6860.0050.0050.0000.0000.0000.000
124L120PRO00.0380.02943.7970.0000.0000.0000.0000.0000.000
125L121SER00.0120.01645.775-0.005-0.0050.0000.0000.0000.000
126L122SER00.0500.00748.8170.0020.0020.0000.0000.0000.000
127L123GLU-1-0.933-0.96350.7490.0820.0820.0000.0000.0000.000
128L124GLU-1-0.798-0.88442.7300.1180.1180.0000.0000.0000.000
129L125LEU0-0.0010.00046.5500.0020.0020.0000.0000.0000.000
130L126GLN0-0.076-0.04048.3630.0000.0000.0000.0000.0000.000
131L127ALA0-0.0270.00147.528-0.001-0.0010.0000.0000.0000.000
132L128ASN0-0.084-0.05545.8810.0030.0030.0000.0000.0000.000
133L129LYS10.9300.95640.557-0.126-0.1260.0000.0000.0000.000
134L130ALA00.004-0.00242.081-0.006-0.0060.0000.0000.0000.000
135L131THR0-0.007-0.02538.6350.0100.0100.0000.0000.0000.000
136L132LEU0-0.060-0.00139.467-0.007-0.0070.0000.0000.0000.000
137L133VAL00.0220.00139.0360.0080.0080.0000.0000.0000.000
138L134CYS0-0.0600.00337.2450.0010.0010.0000.0000.0000.000
139L135LEU00.006-0.00237.8730.0070.0070.0000.0000.0000.000
140L136ILE00.009-0.00134.575-0.006-0.0060.0000.0000.0000.000
141L137SER0-0.002-0.02538.2950.0040.0040.0000.0000.0000.000
142L138ASP-1-0.807-0.88839.9690.0780.0780.0000.0000.0000.000
143L139PHE00.0070.02133.112-0.004-0.0040.0000.0000.0000.000
144L140TYR00.0580.01935.0270.0030.0030.0000.0000.0000.000
145L141PRO00.0960.02432.119-0.006-0.0060.0000.0000.0000.000
146L142GLY00.0020.00432.4370.0010.0010.0000.0000.0000.000
147L143ALA0-0.024-0.01928.4790.0130.0130.0000.0000.0000.000
148L144VAL0-0.0060.00329.715-0.012-0.0120.0000.0000.0000.000
149L145THR0-0.012-0.00227.1090.0150.0150.0000.0000.0000.000
150L146VAL00.005-0.00329.741-0.014-0.0140.0000.0000.0000.000
151L147ALA0-0.042-0.01130.6190.0130.0130.0000.0000.0000.000
152L148TRP00.0600.01232.709-0.015-0.0150.0000.0000.0000.000
153L149LYS10.7860.85934.802-0.098-0.0980.0000.0000.0000.000
154L150ALA00.0760.04937.490-0.003-0.0030.0000.0000.0000.000
155L151ASP-1-0.802-0.90039.7320.0820.0820.0000.0000.0000.000
156L152SER0-0.028-0.02140.500-0.002-0.0020.0000.0000.0000.000
157L153SER0-0.038-0.00636.721-0.001-0.0010.0000.0000.0000.000
158L154PRO0-0.013-0.01332.2720.0030.0030.0000.0000.0000.000
159L155VAL00.0220.01933.3640.0010.0010.0000.0000.0000.000
160L156LYS10.9600.96325.554-0.218-0.2180.0000.0000.0000.000
161L157ALA0-0.0140.00729.6400.0130.0130.0000.0000.0000.000
162L158GLY00.0700.03330.901-0.010-0.0100.0000.0000.0000.000
163L159VAL0-0.028-0.00330.106-0.011-0.0110.0000.0000.0000.000
164L160GLU-1-0.891-0.93128.9830.2530.2530.0000.0000.0000.000
165L161THR0-0.021-0.01328.995-0.022-0.0220.0000.0000.0000.000
166L162THR0-0.0010.01828.6920.0120.0120.0000.0000.0000.000
167L163THR00.0230.01425.8500.0020.0020.0000.0000.0000.000
168L164PRO0-0.021-0.02028.340-0.010-0.0100.0000.0000.0000.000
169L165SER0-0.021-0.00330.6940.0050.0050.0000.0000.0000.000
170L166LYS10.8670.92033.311-0.101-0.1010.0000.0000.0000.000
171L167GLN00.0340.00935.9670.0040.0040.0000.0000.0000.000
172L168SER00.0440.00039.6120.0000.0000.0000.0000.0000.000
173L169ASN0-0.045-0.01942.3830.0010.0010.0000.0000.0000.000
174L170ASN0-0.0030.00339.6040.0010.0010.0000.0000.0000.000
175L171LYS10.9581.02938.621-0.070-0.0700.0000.0000.0000.000
176L172TYR0-0.050-0.03632.4260.0060.0060.0000.0000.0000.000
177L173ALA00.0410.02435.878-0.005-0.0050.0000.0000.0000.000
178L174ALA0-0.023-0.02032.8270.0090.0090.0000.0000.0000.000
179L175SER0-0.0010.00433.897-0.009-0.0090.0000.0000.0000.000
180L176SER0-0.007-0.01532.3170.0090.0090.0000.0000.0000.000
181L177TYR00.0150.00233.947-0.015-0.0150.0000.0000.0000.000
182L178LEU00.0040.01134.2180.0100.0100.0000.0000.0000.000
183L179SER0-0.030-0.01735.455-0.008-0.0080.0000.0000.0000.000
184L180LEU0-0.033-0.01536.9020.0030.0030.0000.0000.0000.000
185L181THR0-0.019-0.03439.5660.0000.0000.0000.0000.0000.000
186L182PRO00.0310.00742.274-0.003-0.0030.0000.0000.0000.000
187L183GLU-1-0.838-0.91644.8350.0990.0990.0000.0000.0000.000
188L184GLN00.0320.04737.917-0.002-0.0020.0000.0000.0000.000
189L185TRP00.0340.00343.325-0.002-0.0020.0000.0000.0000.000
190L186LYS10.9060.94544.816-0.090-0.0900.0000.0000.0000.000
191L187SER0-0.039-0.02644.807-0.004-0.0040.0000.0000.0000.000
192L188HIS0-0.117-0.03841.1850.0030.0030.0000.0000.0000.000
193L189ARG10.9010.92144.869-0.076-0.0760.0000.0000.0000.000
194L190SER00.000-0.00544.761-0.003-0.0030.0000.0000.0000.000
195L191TYR0-0.0120.00938.7140.0050.0050.0000.0000.0000.000
196L192SER00.0310.01639.841-0.006-0.0060.0000.0000.0000.000
197L194GLN00.0260.00934.130-0.012-0.0120.0000.0000.0000.000
198L195VAL00.0220.00734.4970.0100.0100.0000.0000.0000.000
199L196THR0-0.021-0.01731.641-0.012-0.0120.0000.0000.0000.000
200L197HIS0-0.022-0.02832.6510.0060.0060.0000.0000.0000.000
201L198GLU-1-0.845-0.91632.2190.0750.0750.0000.0000.0000.000
202L199GLY0-0.005-0.00432.568-0.008-0.0080.0000.0000.0000.000
203L200SER0-0.0130.01133.840-0.007-0.0070.0000.0000.0000.000
204L201THR0-0.010-0.01735.1960.0050.0050.0000.0000.0000.000
205L202VAL0-0.0100.01337.665-0.007-0.0070.0000.0000.0000.000
206L203GLU-1-0.823-0.90539.1490.1040.1040.0000.0000.0000.000
207L204LYS10.8350.92340.829-0.085-0.0850.0000.0000.0000.000
208L205THR00.027-0.00842.2620.0040.0040.0000.0000.0000.000
209L206VAL0-0.032-0.00944.028-0.003-0.0030.0000.0000.0000.000
210L207ALA00.0420.00246.0750.0030.0030.0000.0000.0000.000
211L208PRO0-0.0100.00747.614-0.001-0.0010.0000.0000.0000.000
212L209THR0-0.0100.01250.296-0.003-0.0030.0000.0000.0000.000