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: R91N8

Calculation Name: 5GNG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNG

Chain ID: A

ChEMBL ID:

UniProt ID: P44251

Base Structure: X-ray

Registration Date: 2023-06-21

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2843391.102392
FMO2-HF: Nuclear repulsion 2755875.796966
FMO2-HF: Total energy -87515.305426
FMO2-MP2: Total energy -87772.530563


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-40.717-36.79444.679-18.831-29.77-0.128
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.111 / q_NPA : -0.041
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].
3A3THR00.031-0.0082.867-2.4570.9880.274-1.838-1.881-0.003
4A4LYS10.8410.9305.142-0.329-0.290-0.001-0.005-0.0330.000
5A5PHE00.0270.0148.7900.2360.2360.0000.0000.0000.000
6A6TYR0-0.066-0.03810.949-0.068-0.0680.0000.0000.0000.000
7A7ASP-1-0.831-0.89914.4530.1270.1270.0000.0000.0000.000
8A8TYR0-0.039-0.03416.739-0.026-0.0260.0000.0000.0000.000
9A9GLN0-0.084-0.05519.226-0.021-0.0210.0000.0000.0000.000
10A10GLY0-0.037-0.00119.209-0.010-0.0100.0000.0000.0000.000
11A11GLU-1-0.738-0.83619.3560.1230.1230.0000.0000.0000.000
12A12HIS0-0.059-0.02918.5100.0080.0080.0000.0000.0000.000
13A13LEU00.0210.02911.0770.0010.0010.0000.0000.0000.000
14A14ILE0-0.046-0.02112.9040.0200.0200.0000.0000.0000.000
15A15LEU00.0340.0217.3360.0250.0250.0000.0000.0000.000
16A16TYR00.038-0.0049.028-0.058-0.0580.0000.0000.0000.000
17A17PHE00.0420.0152.683-0.4920.4640.993-0.408-1.541-0.001
18A18ALA00.0160.0146.757-0.937-0.9370.0000.0000.0000.000
19A19GLY00.0720.0468.0410.3410.3410.0000.0000.0000.000
20A20TRP0-0.009-0.0148.6290.1180.1180.0000.0000.0000.000
21A21GLY0-0.028-0.0278.815-0.105-0.1050.0000.0000.0000.000
22A22THR0-0.112-0.05410.229-0.104-0.1040.0000.0000.0000.000
23A23PRO00.0250.01510.2560.0840.0840.0000.0000.0000.000
24A24PRO00.0460.0098.9030.0570.0570.0000.0000.0000.000
25A25ASP-1-0.863-0.94611.3400.3570.3570.0000.0000.0000.000
26A26ALA0-0.0290.00014.205-0.044-0.0440.0000.0000.0000.000
27A27VAL00.0040.00212.808-0.024-0.0240.0000.0000.0000.000
28A28ASN0-0.034-0.01715.824-0.009-0.0090.0000.0000.0000.000
29A29HIS0-0.057-0.01817.103-0.032-0.0320.0000.0000.0000.000
30A30LEU0-0.072-0.01516.541-0.033-0.0330.0000.0000.0000.000
31A31ILE00.0230.00119.431-0.001-0.0010.0000.0000.0000.000
32A32LEU0-0.015-0.00716.5920.0330.0330.0000.0000.0000.000
33A33PRO0-0.060-0.02019.715-0.033-0.0330.0000.0000.0000.000
34A34GLU-1-0.799-0.90621.8530.1790.1790.0000.0000.0000.000
35A35ASN0-0.039-0.03322.8030.0170.0170.0000.0000.0000.000
36A36HIS0-0.122-0.08017.8900.0300.0300.0000.0000.0000.000
37A37ASP-1-0.683-0.80014.5280.2040.2040.0000.0000.0000.000
38A38LEU0-0.067-0.03511.9860.0810.0810.0000.0000.0000.000
39A39LEU00.0020.0116.776-0.081-0.0810.0000.0000.0000.000
40A40ILE0-0.050-0.0197.6150.4180.4180.0000.0000.0000.000
41A41CYS00.0070.0062.832-2.285-2.0081.817-0.598-1.4960.004
42A42TYR00.012-0.0193.206-0.3660.5920.080-0.244-0.7940.000
43A43ASP-1-0.804-0.8902.385-3.732-2.7052.081-1.149-1.960-0.017
44A44TYR0-0.006-0.0332.405-5.081-3.2906.750-2.512-6.028-0.008
45A45GLN0-0.004-0.0243.584-0.665-0.3940.0080.012-0.2910.000
46A46ASP-1-0.827-0.8851.851-12.847-16.29810.316-3.611-3.253-0.034
47A47LEU0-0.032-0.0432.382-4.736-2.0522.777-2.332-3.128-0.022
48A48ASN0-0.056-0.0352.7461.3182.5910.560-0.009-1.824-0.003
49A49LEU00.008-0.0011.800-8.866-14.20815.559-5.575-4.642-0.042
50A50ASP-1-0.940-0.9583.717-0.0750.3260.006-0.028-0.3800.000
51A51PHE0-0.015-0.0276.2510.4280.4280.0000.0000.0000.000
52A52ASP-1-0.836-0.8838.516-0.118-0.1180.0000.0000.0000.000
53A53LEU0-0.004-0.0188.8320.1350.1350.0000.0000.0000.000
54A54SER0-0.089-0.06712.6820.0640.0640.0000.0000.0000.000
55A55ALA0-0.013-0.00316.0570.0140.0140.0000.0000.0000.000
56A56TYR0-0.036-0.03013.9240.0250.0250.0000.0000.0000.000
57A57ARG10.7780.85917.970-0.141-0.1410.0000.0000.0000.000
58A58HIS0-0.053-0.03118.9580.0140.0140.0000.0000.0000.000
59A59ILE00.0950.04712.1880.0150.0150.0000.0000.0000.000
60A60ARG10.8650.92915.012-0.425-0.4250.0000.0000.0000.000
61A61LEU00.0360.0338.7720.0800.0800.0000.0000.0000.000
62A62VAL0-0.014-0.00611.464-0.186-0.1860.0000.0000.0000.000
63A63ALA00.0250.0209.1490.3460.3460.0000.0000.0000.000
64A64TRP0-0.030-0.01910.357-0.314-0.3140.0000.0000.0000.000
65A65SER00.007-0.00310.6160.2060.2060.0000.0000.0000.000
66A66MET0-0.028-0.0299.341-0.007-0.0070.0000.0000.0000.000
67A67GLY00.0350.0256.5290.0340.0340.0000.0000.0000.000
68A68VAL0-0.049-0.0137.0320.1700.1700.0000.0000.0000.000
69A69TRP00.0100.0006.546-0.021-0.0210.0000.0000.0000.000
70A70VAL00.0160.0102.520-0.825-0.7021.105-0.183-1.0450.000
71A71ALA00.0280.0114.888-0.383-0.333-0.001-0.004-0.0440.000
72A72GLU-1-0.869-0.9256.2030.0600.0600.0000.0000.0000.000
73A73ARG10.7560.8615.592-0.192-0.1920.0000.0000.0000.000
74A74VAL0-0.028-0.0162.126-0.189-0.7682.355-0.347-1.430-0.002
75A75LEU0-0.004-0.0055.501-0.075-0.0750.0000.0000.0000.000
76A76GLN00.0100.0158.689-0.006-0.0060.0000.0000.0000.000
77A77GLY0-0.021-0.01011.198-0.098-0.0980.0000.0000.0000.000
78A78ILE0-0.0190.00010.509-0.027-0.0270.0000.0000.0000.000
79A79ARG10.8580.92813.619-0.159-0.1590.0000.0000.0000.000
80A80LEU00.0510.02911.4780.0240.0240.0000.0000.0000.000
81A81LYS10.8380.93015.769-0.293-0.2930.0000.0000.0000.000
82A82SER00.007-0.00917.009-0.061-0.0610.0000.0000.0000.000
83A83ALA00.0250.03613.4900.0650.0650.0000.0000.0000.000
84A84THR0-0.020-0.02814.330-0.093-0.0930.0000.0000.0000.000
85A85ALA00.0090.01413.7580.1480.1480.0000.0000.0000.000
86A86VAL0-0.005-0.00514.113-0.109-0.1090.0000.0000.0000.000
87A87ASN0-0.013-0.02014.9310.0510.0510.0000.0000.0000.000
88A88GLY00.0400.01013.6670.0370.0370.0000.0000.0000.000
89A89THR0-0.049-0.03614.243-0.009-0.0090.0000.0000.0000.000
90A90GLY00.0800.03412.7450.0600.0600.0000.0000.0000.000
91A91LEU0-0.053-0.02613.714-0.058-0.0580.0000.0000.0000.000
92A92PRO00.0270.01211.360-0.009-0.0090.0000.0000.0000.000
93A93CYS0-0.038-0.00514.542-0.013-0.0130.0000.0000.0000.000
94A94ASP-1-0.796-0.90116.8490.0820.0820.0000.0000.0000.000
95A95ASP-1-0.868-0.94519.9500.1110.1110.0000.0000.0000.000
96A96SER0-0.066-0.01822.7840.0010.0010.0000.0000.0000.000
97A97PHE0-0.035-0.01719.4960.0080.0080.0000.0000.0000.000
98A98GLY0-0.0100.01917.6070.0450.0450.0000.0000.0000.000
99A99ILE0-0.055-0.01915.565-0.014-0.0140.0000.0000.0000.000
100A100PRO00.0350.01418.961-0.023-0.0230.0000.0000.0000.000
101A101TYR00.0390.01019.7200.0090.0090.0000.0000.0000.000
102A102ALA0-0.013-0.01421.261-0.006-0.0060.0000.0000.0000.000
103A103ILE0-0.0080.00020.747-0.006-0.0060.0000.0000.0000.000
104A104PHE00.0350.02112.5340.0040.0040.0000.0000.0000.000
105A105LYS10.8400.89518.455-0.004-0.0040.0000.0000.0000.000
106A106GLY0-0.0120.00220.456-0.011-0.0110.0000.0000.0000.000
107A107THR0-0.033-0.03617.5910.0010.0010.0000.0000.0000.000
108A108LEU00.0200.01015.1780.0020.0020.0000.0000.0000.000
109A109GLU-1-0.840-0.89718.239-0.026-0.0260.0000.0000.0000.000
110A110ASN0-0.091-0.04621.539-0.011-0.0110.0000.0000.0000.000
111A111LEU0-0.0190.02515.3020.0130.0130.0000.0000.0000.000
112A112THR00.006-0.00519.869-0.018-0.0180.0000.0000.0000.000
113A113GLU-1-0.735-0.87918.7450.1400.1400.0000.0000.0000.000
114A114ASN0-0.029-0.01221.0580.0260.0260.0000.0000.0000.000
115A115THR0-0.027-0.04321.9850.0150.0150.0000.0000.0000.000
116A116ARG10.8710.93714.848-0.190-0.1900.0000.0000.0000.000
117A117LEU00.0370.02219.2890.0300.0300.0000.0000.0000.000
118A118LYS10.8430.92021.659-0.093-0.0930.0000.0000.0000.000
119A119PHE00.0410.01316.0600.0000.0000.0000.0000.0000.000
120A120GLU-1-0.765-0.88516.5260.3140.3140.0000.0000.0000.000
121A121ARG10.8310.90419.699-0.158-0.1580.0000.0000.0000.000
122A122ARG10.8550.92521.897-0.199-0.1990.0000.0000.0000.000
123A123ILE0-0.0010.01215.9300.0030.0030.0000.0000.0000.000
124A124CYS0-0.026-0.00720.2010.0190.0190.0000.0000.0000.000
125A125GLY00.0580.04422.638-0.011-0.0110.0000.0000.0000.000
126A126ASP-1-0.850-0.89025.8290.1780.1780.0000.0000.0000.000
127A127LYS10.8500.90627.098-0.126-0.1260.0000.0000.0000.000
128A128ALA00.0480.02927.9740.0030.0030.0000.0000.0000.000
129A129SER0-0.054-0.06524.6070.0080.0080.0000.0000.0000.000
130A130PHE0-0.031-0.01522.1690.0140.0140.0000.0000.0000.000
131A131GLU-1-0.806-0.91723.6580.1500.1500.0000.0000.0000.000
132A132ARG10.9070.96123.885-0.247-0.2470.0000.0000.0000.000
133A133TYR00.0220.00615.4830.0350.0350.0000.0000.0000.000
134A134GLN0-0.040-0.02419.905-0.002-0.0020.0000.0000.0000.000
135A135LEU0-0.045-0.01021.833-0.020-0.0200.0000.0000.0000.000
136A136PHE0-0.060-0.01516.8140.0040.0040.0000.0000.0000.000
137A137PRO00.0140.00815.621-0.018-0.0180.0000.0000.0000.000
138A138ALA00.0160.01815.4530.0480.0480.0000.0000.0000.000
139A139ARG10.7650.8727.422-0.570-0.5700.0000.0000.0000.000
140A140PRO00.0590.01711.2930.0060.0060.0000.0000.0000.000
141A141PHE00.0190.01112.8360.0130.0130.0000.0000.0000.000
142A142ASP-1-0.857-0.94213.841-0.032-0.0320.0000.0000.0000.000
143A143GLU-1-0.881-0.9178.385-0.218-0.2180.0000.0000.0000.000
144A144ILE00.0030.0139.258-0.009-0.0090.0000.0000.0000.000
145A145HIS00.0150.01511.0490.0080.0080.0000.0000.0000.000
146A146GLN00.001-0.0019.490-0.058-0.0580.0000.0000.0000.000
147A147GLU-1-0.731-0.8416.0911.0411.0410.0000.0000.0000.000
148A148LEU0-0.036-0.0098.569-0.008-0.0080.0000.0000.0000.000
149A149THR0-0.013-0.02111.629-0.016-0.0160.0000.0000.0000.000
150A150ALA00.0220.0208.2790.0000.0000.0000.0000.0000.000
151A151LEU0-0.013-0.0056.408-0.006-0.0060.0000.0000.0000.000
152A152PHE00.0310.0109.4960.0100.0100.0000.0000.0000.000
153A153ALA0-0.0220.00012.4790.0140.0140.0000.0000.0000.000
154A154MET00.0380.0115.733-0.037-0.0370.0000.0000.0000.000
155A155ILE00.0010.00610.1300.0460.0460.0000.0000.0000.000
156A156GLN0-0.101-0.07112.4530.0450.0450.0000.0000.0000.000
157A157GLN0-0.028-0.01413.744-0.032-0.0320.0000.0000.0000.000
158A158ASP-1-0.791-0.83411.377-0.255-0.2550.0000.0000.0000.000
159A159LYS10.9220.95613.3040.0660.0660.0000.0000.0000.000
160A160ARG10.8510.91011.4220.3200.3200.0000.0000.0000.000
161A161ILE00.0080.00314.2520.0290.0290.0000.0000.0000.000
162A162ASP-1-0.813-0.86315.4550.1590.1590.0000.0000.0000.000
163A163LEU0-0.015-0.00511.027-0.043-0.0430.0000.0000.0000.000
164A164ILE0-0.030-0.00710.205-0.013-0.0130.0000.0000.0000.000
165A165HIS0-0.021-0.00213.909-0.016-0.0160.0000.0000.0000.000
166A166TRP0-0.028-0.03710.3040.0950.0950.0000.0000.0000.000
167A167ALA0-0.052-0.03116.851-0.050-0.0500.0000.0000.0000.000
168A168ASN0-0.0040.00218.456-0.006-0.0060.0000.0000.0000.000
169A169ALA00.0660.03517.8740.0680.0680.0000.0000.0000.000
170A170TRP0-0.038-0.02418.597-0.073-0.0730.0000.0000.0000.000
171A171VAL00.0180.00919.3970.0360.0360.0000.0000.0000.000
172A172SER0-0.039-0.04021.576-0.023-0.0230.0000.0000.0000.000
173A173SER0-0.005-0.01323.456-0.003-0.0030.0000.0000.0000.000
174A174ARG10.8390.90826.145-0.229-0.2290.0000.0000.0000.000
175A175ASP-1-0.706-0.84119.7050.3970.3970.0000.0000.0000.000
176A176LYS10.7660.84822.786-0.243-0.2430.0000.0000.0000.000
177A177ILE0-0.069-0.02516.963-0.031-0.0310.0000.0000.0000.000
178A178PHE00.0510.02913.486-0.015-0.0150.0000.0000.0000.000
179A179THR00.0220.01919.4540.0090.0090.0000.0000.0000.000
180A180PRO00.0620.02222.5470.0080.0080.0000.0000.0000.000
181A181ALA0-0.0130.00324.3260.0010.0010.0000.0000.0000.000
182A182ASN0-0.009-0.00521.456-0.017-0.0170.0000.0000.0000.000
183A183GLN0-0.047-0.02819.0080.0290.0290.0000.0000.0000.000
184A184HIS0-0.038-0.04421.0650.0090.0090.0000.0000.0000.000
185A185GLN0-0.041-0.01423.918-0.012-0.0120.0000.0000.0000.000
186A186TYR00.0120.00916.149-0.018-0.0180.0000.0000.0000.000
187A187TRP00.043-0.01114.768-0.021-0.0210.0000.0000.0000.000
188A188ALA0-0.0050.02221.346-0.005-0.0050.0000.0000.0000.000
189A189LEU0-0.040-0.02824.586-0.007-0.0070.0000.0000.0000.000
190A190ARG10.7230.83418.548-0.207-0.2070.0000.0000.0000.000
191A191CYS0-0.047-0.01920.0320.0130.0130.0000.0000.0000.000
192A192ALA0-0.0080.01322.154-0.015-0.0150.0000.0000.0000.000
193A193VAL00.0300.00722.2500.0330.0330.0000.0000.0000.000
194A194GLN0-0.0110.00321.980-0.039-0.0390.0000.0000.0000.000
195A195GLU-1-0.864-0.91523.8020.2260.2260.0000.0000.0000.000
196A196ILE0-0.025-0.01823.103-0.012-0.0120.0000.0000.0000.000
197A197GLU-1-0.857-0.92526.0360.2000.2000.0000.0000.0000.000
198A198GLY0-0.017-0.01825.4980.0060.0060.0000.0000.0000.000
199A199GLU-1-0.776-0.85323.6110.2200.2200.0000.0000.0000.000
200A200HIS00.0130.02016.0160.0780.0780.0000.0000.0000.000
201A201TYR0-0.009-0.01017.0080.0360.0360.0000.0000.0000.000
202A202VAL00.0190.00319.007-0.054-0.0540.0000.0000.0000.000
203A203PHE00.0900.02714.408-0.036-0.0360.0000.0000.0000.000
204A204SER0-0.039-0.01319.622-0.026-0.0260.0000.0000.0000.000
205A205ARG10.8430.92322.772-0.286-0.2860.0000.0000.0000.000
206A206PHE0-0.0140.00320.877-0.009-0.0090.0000.0000.0000.000
207A207THR00.031-0.00822.7430.0030.0030.0000.0000.0000.000
208A208HIS00.0420.04322.2410.0030.0030.0000.0000.0000.000
209A209TRP00.0910.02613.0280.0440.0440.0000.0000.0000.000
210A210SER00.0230.00519.2140.0270.0270.0000.0000.0000.000
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