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: R94G8

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2020448.500186
FMO2-HF: Nuclear repulsion 1941384.946759
FMO2-HF: Total energy -79063.553428
FMO2-MP2: Total energy -79295.457038


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.
-4.416-1.816-0.006-1.329-1.2650.004
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 : -0.025 / q_NPA : -0.020
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].
3L3ALA00.0270.0093.8800.0421.927-0.017-0.989-0.8790.001
4L4LEU0-0.0240.0146.546-0.192-0.1920.0000.0000.0000.000
5L5THR0-0.006-0.0059.6280.2600.2600.0000.0000.0000.000
6L6GLN00.010-0.01212.163-0.106-0.1060.0000.0000.0000.000
7L7PRO0-0.0180.00815.9400.0600.0600.0000.0000.0000.000
8L8ALA00.0770.04618.446-0.011-0.0110.0000.0000.0000.000
9L9SER0-0.018-0.00519.5500.0020.0020.0000.0000.0000.000
10L11VAL0-0.0070.00523.036-0.010-0.0100.0000.0000.0000.000
11L12SER0-0.020-0.03225.5870.0110.0110.0000.0000.0000.000
12L13GLY00.0150.01829.434-0.010-0.0100.0000.0000.0000.000
13L14SER00.0010.00332.5400.0090.0090.0000.0000.0000.000
14L15PRO00.021-0.00235.838-0.005-0.0050.0000.0000.0000.000
15L16GLY0-0.028-0.00537.842-0.002-0.0020.0000.0000.0000.000
16L17GLN0-0.0020.01334.0970.0000.0000.0000.0000.0000.000
17L18SER00.007-0.00531.8240.0040.0040.0000.0000.0000.000
18L19ILE0-0.033-0.00727.0900.0010.0010.0000.0000.0000.000
19L20THR00.013-0.01223.121-0.004-0.0040.0000.0000.0000.000
20L21ILE0-0.030-0.00420.0680.0140.0140.0000.0000.0000.000
21L22SER00.0340.02117.854-0.014-0.0140.0000.0000.0000.000
22L23CYS0-0.073-0.04814.4780.0400.0400.0000.0000.0000.000
23L24THR00.0220.02312.103-0.042-0.0420.0000.0000.0000.000
24L25GLY00.020-0.0048.8660.1370.1370.0000.0000.0000.000
25L26THR0-0.088-0.0648.356-0.205-0.2050.0000.0000.0000.000
26L27SER0-0.036-0.0448.823-0.162-0.1620.0000.0000.0000.000
27L27THR00.0810.0259.2630.1420.1420.0000.0000.0000.000
28L27ASP-1-0.821-0.8448.758-1.734-1.7340.0000.0000.0000.000
29L27VAL00.0270.01011.6050.1760.1760.0000.0000.0000.000
30L28ASN0-0.030-0.02214.5940.0930.0930.0000.0000.0000.000
31L29GLY00.0000.00212.7530.0990.0990.0000.0000.0000.000
32L30TYR0-0.0180.00713.7980.0470.0470.0000.0000.0000.000
33L31ASN00.0520.00914.6490.0230.0230.0000.0000.0000.000
34L32TYR0-0.0150.00514.5890.0540.0540.0000.0000.0000.000
35L33VAL00.0260.00214.410-0.031-0.0310.0000.0000.0000.000
36L34SER0-0.016-0.00916.7070.0370.0370.0000.0000.0000.000
37L35TRP00.0090.00218.5150.0110.0110.0000.0000.0000.000
38L36TYR0-0.010-0.01119.2400.0120.0120.0000.0000.0000.000
39L37GLN00.0540.03422.966-0.002-0.0020.0000.0000.0000.000
40L38GLN00.013-0.00423.3260.0130.0130.0000.0000.0000.000
41L39TYR00.0120.00326.375-0.002-0.0020.0000.0000.0000.000
42L40ALA00.0700.02228.9810.0110.0110.0000.0000.0000.000
43L41GLY00.0200.01929.070-0.007-0.0070.0000.0000.0000.000
44L42LYS10.8330.91529.126-0.108-0.1080.0000.0000.0000.000
45L43ALA00.0620.03527.1620.0120.0120.0000.0000.0000.000
46L44PRO0-0.003-0.00122.876-0.012-0.0120.0000.0000.0000.000
47L45LYS10.8960.95825.309-0.032-0.0320.0000.0000.0000.000
48L46LEU0-0.0040.00523.128-0.004-0.0040.0000.0000.0000.000
49L47ILE0-0.047-0.03124.943-0.003-0.0030.0000.0000.0000.000
50L48ILE0-0.008-0.00622.325-0.011-0.0110.0000.0000.0000.000
51L49PHE00.0330.00421.5720.0140.0140.0000.0000.0000.000
52L50ASP-1-0.782-0.87720.365-0.144-0.1440.0000.0000.0000.000
53L51VAL0-0.017-0.00618.135-0.013-0.0130.0000.0000.0000.000
54L52SER0-0.060-0.03020.5390.0160.0160.0000.0000.0000.000
55L53LYS10.8220.91424.3360.1520.1520.0000.0000.0000.000
56L54ARG10.9290.96926.1040.0680.0680.0000.0000.0000.000
57L55PRO0-0.0090.00127.236-0.001-0.0010.0000.0000.0000.000
58L56SER00.0040.00030.178-0.001-0.0010.0000.0000.0000.000
59L57GLY00.0230.01334.0270.0080.0080.0000.0000.0000.000
60L58VAL0-0.056-0.01429.4200.0040.0040.0000.0000.0000.000
61L59SER00.0450.02032.751-0.011-0.0110.0000.0000.0000.000
62L60ASN00.013-0.01632.6180.0010.0010.0000.0000.0000.000
63L61ARG10.7810.87133.2750.0050.0050.0000.0000.0000.000
64L62PHE0-0.0190.00428.189-0.004-0.0040.0000.0000.0000.000
65L63SER0-0.023-0.02327.597-0.009-0.0090.0000.0000.0000.000
66L64GLY00.0230.01423.4240.0100.0100.0000.0000.0000.000
67L65SER0-0.021-0.01022.001-0.008-0.0080.0000.0000.0000.000
68L66LYS10.8260.88213.1100.7130.7130.0000.0000.0000.000
69L67SER0-0.0220.00518.0810.0320.0320.0000.0000.0000.000
70L68GLY00.0250.01815.213-0.007-0.0070.0000.0000.0000.000
71L69ASP-1-0.737-0.87410.545-0.812-0.8120.0000.0000.0000.000
72L70THR0-0.0390.00712.3550.1160.1160.0000.0000.0000.000
73L71ALA00.0220.02015.2890.0300.0300.0000.0000.0000.000
74L72SER0-0.040-0.04417.1820.0390.0390.0000.0000.0000.000
75L73LEU0-0.0070.02520.541-0.005-0.0050.0000.0000.0000.000
76L74THR00.0100.00023.1450.0090.0090.0000.0000.0000.000
77L75ILE0-0.0030.01426.6570.0010.0010.0000.0000.0000.000
78L76SER0-0.004-0.01129.647-0.001-0.0010.0000.0000.0000.000
79L77GLY00.0270.01533.1910.0050.0050.0000.0000.0000.000
80L78LEU0-0.038-0.01230.9440.0050.0050.0000.0000.0000.000
81L79GLN00.0080.00235.057-0.004-0.0040.0000.0000.0000.000
82L80ALA00.0300.00635.1950.0030.0030.0000.0000.0000.000
83L81GLU-1-0.860-0.92935.1980.0220.0220.0000.0000.0000.000
84L82ASP-1-0.743-0.83131.1680.0040.0040.0000.0000.0000.000
85L83GLU-1-0.809-0.87630.0700.0660.0660.0000.0000.0000.000
86L84ALA0-0.056-0.02527.9240.0060.0060.0000.0000.0000.000
87L85ASP-1-0.885-0.94323.1660.1270.1270.0000.0000.0000.000
88L86TYR0-0.055-0.04922.539-0.014-0.0140.0000.0000.0000.000
89L87HIS00.0220.00818.0100.0100.0100.0000.0000.0000.000
90L89SER0-0.019-0.02114.6670.0490.0490.0000.0000.0000.000
91L90SER00.000-0.02710.845-0.112-0.1120.0000.0000.0000.000
92L91TYR00.0130.03010.3040.1800.1800.0000.0000.0000.000
93L92THR00.0270.0245.789-0.738-0.7380.0000.0000.0000.000
94L93SER0-0.009-0.0385.9460.2420.2420.0000.0000.0000.000
95L94SER0-0.036-0.0073.327-2.629-1.9140.011-0.340-0.3860.003
96L95THR00.0320.0216.317-0.648-0.6480.0000.0000.0000.000
97L95PRO00.0320.0137.1580.5830.5830.0000.0000.0000.000
98L95TYR0-0.041-0.0219.240-0.054-0.0540.0000.0000.0000.000
99L96VAL0-0.031-0.02310.800-0.261-0.2610.0000.0000.0000.000
100L97LEU00.0050.0146.6950.1220.1220.0000.0000.0000.000
101L98PHE00.009-0.01611.419-0.114-0.1140.0000.0000.0000.000
102L99GLY00.0330.02111.7520.0560.0560.0000.0000.0000.000
103L100GLY0-0.053-0.02913.3930.0270.0270.0000.0000.0000.000
104L101GLY00.0050.01714.713-0.002-0.0020.0000.0000.0000.000
105L102THR0-0.061-0.05218.211-0.001-0.0010.0000.0000.0000.000
106L103LYS10.8160.90420.947-0.100-0.1000.0000.0000.0000.000
107L104LEU0-0.018-0.00724.346-0.009-0.0090.0000.0000.0000.000
108L105THR0-0.034-0.01626.9910.0090.0090.0000.0000.0000.000
109L106VAL00.0220.00530.175-0.009-0.0090.0000.0000.0000.000
110L106LEU0-0.028-0.02933.2520.0050.0050.0000.0000.0000.000
111L107GLY00.002-0.00235.820-0.006-0.0060.0000.0000.0000.000
112L108GLN0-0.088-0.04638.255-0.001-0.0010.0000.0000.0000.000
113L109PRO00.0170.00739.4490.0000.0000.0000.0000.0000.000
114L110LYS10.8550.91836.198-0.032-0.0320.0000.0000.0000.000
115L111ALA0-0.041-0.02339.083-0.003-0.0030.0000.0000.0000.000
116L112ALA00.0540.02938.9050.0040.0040.0000.0000.0000.000
117L113PRO0-0.025-0.00336.927-0.001-0.0010.0000.0000.0000.000
118L114SER00.0120.01539.488-0.004-0.0040.0000.0000.0000.000
119L115VAL00.000-0.00539.2480.0050.0050.0000.0000.0000.000
120L116THR0-0.022-0.00541.774-0.007-0.0070.0000.0000.0000.000
121L117LEU0-0.028-0.00840.6300.0050.0050.0000.0000.0000.000
122L118PHE0-0.0020.00343.289-0.005-0.0050.0000.0000.0000.000
123L119PRO00.0040.00743.7930.0040.0040.0000.0000.0000.000
124L120PRO00.0320.02344.0200.0010.0010.0000.0000.0000.000
125L121SER00.0230.02345.991-0.005-0.0050.0000.0000.0000.000
126L122SER00.021-0.00749.0060.0020.0020.0000.0000.0000.000
127L123GLU-1-0.922-0.96050.7140.0740.0740.0000.0000.0000.000
128L124GLU-1-0.803-0.88942.7830.1060.1060.0000.0000.0000.000
129L125LEU0-0.020-0.00546.8300.0020.0020.0000.0000.0000.000
130L126GLN0-0.045-0.02848.637-0.001-0.0010.0000.0000.0000.000
131L127ALA0-0.040-0.00447.4730.0000.0000.0000.0000.0000.000
132L128ASN0-0.058-0.03346.2430.0040.0040.0000.0000.0000.000
133L129LYS10.9200.95041.100-0.112-0.1120.0000.0000.0000.000
134L130ALA00.0220.00342.127-0.006-0.0060.0000.0000.0000.000
135L131THR0-0.021-0.02738.5130.0090.0090.0000.0000.0000.000
136L132LEU0-0.0470.00139.568-0.006-0.0060.0000.0000.0000.000
137L133VAL00.0260.01139.1590.0070.0070.0000.0000.0000.000
138L134CYS0-0.050-0.01237.4190.0000.0000.0000.0000.0000.000
139L135LEU00.0010.00037.8900.0070.0070.0000.0000.0000.000
140L136ILE00.0130.00134.678-0.006-0.0060.0000.0000.0000.000
141L137SER00.013-0.01938.1530.0040.0040.0000.0000.0000.000
142L138ASP-1-0.811-0.90140.0660.0590.0590.0000.0000.0000.000
143L139PHE00.0280.03633.103-0.005-0.0050.0000.0000.0000.000
144L140TYR00.0390.00334.9310.0020.0020.0000.0000.0000.000
145L141PRO00.0870.02532.379-0.004-0.0040.0000.0000.0000.000
146L142GLY00.0030.00532.5110.0020.0020.0000.0000.0000.000
147L143ALA0-0.020-0.01628.2980.0110.0110.0000.0000.0000.000
148L144VAL0-0.0100.00129.798-0.010-0.0100.0000.0000.0000.000
149L145THR0-0.0100.00327.1990.0130.0130.0000.0000.0000.000
150L146VAL00.016-0.00329.878-0.012-0.0120.0000.0000.0000.000
151L147ALA0-0.046-0.02130.6740.0120.0120.0000.0000.0000.000
152L148TRP00.0520.01632.888-0.013-0.0130.0000.0000.0000.000
153L149LYS10.7770.86134.903-0.078-0.0780.0000.0000.0000.000
154L150ALA00.0690.03737.638-0.002-0.0020.0000.0000.0000.000
155L151ASP-1-0.767-0.85939.6650.0670.0670.0000.0000.0000.000
156L152SER0-0.023-0.01441.310-0.003-0.0030.0000.0000.0000.000
157L153SER0-0.0240.00037.114-0.003-0.0030.0000.0000.0000.000
158L154PRO0-0.019-0.01932.6750.0030.0030.0000.0000.0000.000
159L155VAL0-0.0050.00633.4570.0020.0020.0000.0000.0000.000
160L156LYS10.9680.96426.184-0.179-0.1790.0000.0000.0000.000
161L157ALA00.0170.01630.0270.0110.0110.0000.0000.0000.000
162L158GLY00.0580.02431.517-0.009-0.0090.0000.0000.0000.000
163L159VAL0-0.054-0.01230.224-0.007-0.0070.0000.0000.0000.000
164L160GLU-1-0.873-0.92829.2520.2220.2220.0000.0000.0000.000
165L161THR0-0.047-0.02829.058-0.019-0.0190.0000.0000.0000.000
166L162THR0-0.0150.01128.9090.0100.0100.0000.0000.0000.000
167L163THR00.0210.00725.9990.0030.0030.0000.0000.0000.000
168L164PRO0-0.011-0.00528.209-0.009-0.0090.0000.0000.0000.000
169L165SER0-0.030-0.00230.6570.0060.0060.0000.0000.0000.000
170L166LYS10.8810.93133.313-0.079-0.0790.0000.0000.0000.000
171L167GLN00.0330.00435.8570.0040.0040.0000.0000.0000.000
172L168SER00.031-0.00239.537-0.001-0.0010.0000.0000.0000.000
173L169ASN0-0.0070.00742.3690.0000.0000.0000.0000.0000.000
174L170ASN0-0.005-0.00539.3830.0010.0010.0000.0000.0000.000
175L171LYS10.9041.00238.444-0.051-0.0510.0000.0000.0000.000
176L172TYR0-0.032-0.01832.2060.0060.0060.0000.0000.0000.000
177L173ALA00.0170.00835.817-0.004-0.0040.0000.0000.0000.000
178L174ALA0-0.019-0.01932.9100.0070.0070.0000.0000.0000.000
179L175SER0-0.0060.00333.974-0.007-0.0070.0000.0000.0000.000
180L176SER0-0.003-0.01332.4540.0080.0080.0000.0000.0000.000
181L177TYR00.014-0.00134.135-0.012-0.0120.0000.0000.0000.000
182L178LEU0-0.0200.00134.4130.0080.0080.0000.0000.0000.000
183L179SER0-0.0080.00035.208-0.007-0.0070.0000.0000.0000.000
184L180LEU0-0.027-0.01636.8420.0030.0030.0000.0000.0000.000
185L181THR0-0.023-0.04139.5880.0000.0000.0000.0000.0000.000
186L182PRO00.0320.00542.365-0.003-0.0030.0000.0000.0000.000
187L183GLU-1-0.792-0.88345.4860.0860.0860.0000.0000.0000.000
188L184GLN00.0310.04437.959-0.001-0.0010.0000.0000.0000.000
189L185TRP00.0510.01643.254-0.002-0.0020.0000.0000.0000.000
190L186LYS10.8360.90544.922-0.083-0.0830.0000.0000.0000.000
191L187SER0-0.048-0.02745.140-0.004-0.0040.0000.0000.0000.000
192L188HIS0-0.087-0.03641.8490.0030.0030.0000.0000.0000.000
193L189ARG10.8330.88745.717-0.062-0.0620.0000.0000.0000.000
194L190SER0-0.016-0.01344.840-0.003-0.0030.0000.0000.0000.000
195L191TYR00.0120.00438.9620.0050.0050.0000.0000.0000.000
196L192SER00.0180.02040.258-0.005-0.0050.0000.0000.0000.000
197L194GLN00.0330.02834.635-0.009-0.0090.0000.0000.0000.000
198L195VAL00.0130.00234.4840.0090.0090.0000.0000.0000.000
199L196THR0-0.014-0.02231.901-0.010-0.0100.0000.0000.0000.000
200L197HIS00.001-0.01632.7120.0050.0050.0000.0000.0000.000
201L198GLU-1-0.845-0.90932.8240.0410.0410.0000.0000.0000.000
202L199GLY00.0040.00833.014-0.007-0.0070.0000.0000.0000.000
203L200SER0-0.035-0.00734.168-0.006-0.0060.0000.0000.0000.000
204L201THR0-0.013-0.01935.5300.0070.0070.0000.0000.0000.000
205L202VAL0-0.025-0.00337.861-0.006-0.0060.0000.0000.0000.000
206L203GLU-1-0.809-0.89439.0800.0830.0830.0000.0000.0000.000
207L204LYS10.8350.92041.004-0.067-0.0670.0000.0000.0000.000
208L205THR00.029-0.01242.2020.0040.0040.0000.0000.0000.000
209L206VAL0-0.022-0.00644.046-0.003-0.0030.0000.0000.0000.000
210L207ALA00.0510.01346.0730.0020.0020.0000.0000.0000.000
211L208PRO00.0040.01147.708-0.001-0.0010.0000.0000.0000.000
212L209THR0-0.0230.00450.471-0.003-0.0030.0000.0000.0000.000