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: NNL1Q

Calculation Name: 2G5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G5X

Chain ID: A

ChEMBL ID:

UniProt ID: P85101

Base Structure: X-ray

Registration Date: 2023-09-23

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3003970.028151
FMO2-HF: Nuclear repulsion 2912789.260095
FMO2-HF: Total energy -91180.768056
FMO2-MP2: Total energy -91448.861972


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:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
-45.395-43.95541.311-19.083-23.662-0.188
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.894
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].
3A3SER0-0.017-0.0222.778-9.180-6.4340.360-1.363-1.743-0.007
4A4TRP00.0570.0295.2133.4993.556-0.001-0.005-0.0500.000
5A5THR0-0.020-0.0078.853-0.515-0.5150.0000.0000.0000.000
6A6VAL0-0.013-0.00211.6041.0601.0600.0000.0000.0000.000
7A7ASP-1-0.819-0.91413.766-14.869-14.8690.0000.0000.0000.000
8A8SER0-0.019-0.01816.520-0.295-0.2950.0000.0000.0000.000
9A9ASP-1-0.804-0.87816.488-15.570-15.5700.0000.0000.0000.000
10A10SER00.0790.00816.298-1.045-1.0450.0000.0000.0000.000
11A11ALA00.0420.04016.945-0.418-0.4180.0000.0000.0000.000
12A12LYS10.8330.90612.90216.62816.6280.0000.0000.0000.000
13A13TYR0-0.033-0.02812.243-1.196-1.1960.0000.0000.0000.000
14A14SER00.037-0.01212.707-0.814-0.8140.0000.0000.0000.000
15A15SER0-0.030-0.02511.317-0.307-0.3070.0000.0000.0000.000
16A16PHE0-0.064-0.0255.835-1.482-1.4820.0000.0000.0000.000
17A17LEU00.0110.0058.732-1.878-1.8780.0000.0000.0000.000
18A18ASP-1-0.834-0.90210.863-17.569-17.5690.0000.0000.0000.000
19A19SER0-0.034-0.0205.456-1.238-1.2380.0000.0000.0000.000
20A20LEU0-0.043-0.0236.437-1.792-1.7920.0000.0000.0000.000
21A21ARG10.7160.8157.71917.61617.6160.0000.0000.0000.000
22A22GLU-1-0.775-0.8838.764-16.763-16.7630.0000.0000.0000.000
23A23GLU-1-0.897-0.9503.920-33.635-33.1360.003-0.159-0.342-0.001
24A24PHE0-0.052-0.0417.3130.0590.0590.0000.0000.0000.000
25A25GLY00.0140.01710.4061.2941.2940.0000.0000.0000.000
26A26ARG10.8390.9375.32630.70930.7090.0000.0000.0000.000
27A27GLY00.012-0.00311.967-0.091-0.0910.0000.0000.0000.000
28A28THR0-0.033-0.01214.9570.5550.5550.0000.0000.0000.000
29A29PRO00.0090.00516.941-0.465-0.4650.0000.0000.0000.000
30A30LYS10.8270.92314.32915.65815.6580.0000.0000.0000.000
31A31VAL00.0440.01919.3270.5620.5620.0000.0000.0000.000
32A32CYS0-0.024-0.01221.830-0.367-0.3670.0000.0000.0000.000
33A33ASN0-0.020-0.01518.982-0.286-0.2860.0000.0000.0000.000
34A34ILE00.0200.03118.171-0.559-0.5590.0000.0000.0000.000
35A35PRO00.0080.01313.8190.3990.3990.0000.0000.0000.000
36A36VAL00.0360.01115.9140.3560.3560.0000.0000.0000.000
37A37THR00.0020.01214.208-0.247-0.2470.0000.0000.0000.000
38A38LYS10.8170.87914.28917.31217.3120.0000.0000.0000.000
39A39LYS10.9590.97417.29311.34911.3490.0000.0000.0000.000
40A40ALA00.0030.00619.2330.0240.0240.0000.0000.0000.000
41A41ASN0-0.005-0.00613.1750.0460.0460.0000.0000.0000.000
42A42ASN00.0420.02514.426-0.984-0.9840.0000.0000.0000.000
43A43ASP-1-0.838-0.90515.665-18.177-18.1770.0000.0000.0000.000
44A44LYS10.8490.92111.52516.96916.9690.0000.0000.0000.000
45A45PHE00.020-0.0038.4210.9480.9480.0000.0000.0000.000
46A46VAL00.0000.0144.788-1.167-1.050-0.001-0.005-0.1100.000
47A47LEU0-0.052-0.0152.319-1.763-0.0563.412-1.150-3.9690.006
48A48VAL00.013-0.0022.637-5.906-3.9981.754-1.240-2.422-0.016
49A49ASN00.0050.0132.225-18.254-15.7534.196-2.319-4.377-0.033
50A50LEU00.0410.0344.5764.5824.633-0.001-0.019-0.0300.000
51A51VAL0-0.023-0.0227.654-1.362-1.3620.0000.0000.0000.000
52A52LEU00.0300.02910.1321.8031.8030.0000.0000.0000.000
53A53PRO0-0.007-0.01613.859-0.485-0.4850.0000.0000.0000.000
54A54PHE00.002-0.01115.934-0.061-0.0610.0000.0000.0000.000
55A55ASN00.0350.01215.610-0.471-0.4710.0000.0000.0000.000
56A56ARG10.9010.96311.24422.37922.3790.0000.0000.0000.000
57A57ASN00.0360.03211.163-2.602-2.6020.0000.0000.0000.000
58A58THR0-0.026-0.0215.543-0.456-0.4560.0000.0000.0000.000
59A59ILE0-0.042-0.0107.6660.5100.5100.0000.0000.0000.000
60A60THR0-0.051-0.0302.509-2.522-1.0791.503-0.942-2.005-0.002
61A61LEU00.0370.0114.8163.8033.867-0.001-0.007-0.0550.000
62A62ALA00.0250.0115.267-6.001-6.0010.0000.0000.0000.000
63A63PHE00.0100.0007.6333.6613.6610.0000.0000.0000.000
64A64ARG10.8130.8729.37716.53716.5370.0000.0000.0000.000
65A65ALA00.011-0.00710.0330.5630.5630.0000.0000.0000.000
66A66SER0-0.015-0.03211.8040.5080.5080.0000.0000.0000.000
67A67ASP-1-0.840-0.91414.673-16.628-16.6280.0000.0000.0000.000
68A68ALA00.0440.04112.2500.5300.5300.0000.0000.0000.000
69A69TYR0-0.058-0.03113.2790.0960.0960.0000.0000.0000.000
70A70LEU0-0.023-0.00110.532-1.171-1.1710.0000.0000.0000.000
71A71VAL0-0.006-0.01111.3731.3521.3520.0000.0000.0000.000
72A72GLY00.011-0.00511.5831.3131.3130.0000.0000.0000.000
73A73PHE0-0.052-0.0258.685-1.511-1.5110.0000.0000.0000.000
74A74GLN00.0210.0062.8066.9097.5280.024-0.293-0.3500.000
75A75ASP-1-0.726-0.8497.417-25.381-25.3810.0000.0000.0000.000
76A76ARG10.8530.9158.51727.07927.0790.0000.0000.0000.000
77A77ASP-1-0.804-0.89411.519-15.829-15.8290.0000.0000.0000.000
78A78SER0-0.005-0.01714.9100.3510.3510.0000.0000.0000.000
79A79LYS10.9210.97917.98713.33413.3340.0000.0000.0000.000
80A80THR0-0.036-0.04816.5950.1120.1120.0000.0000.0000.000
81A81ASN00.0140.01414.273-0.881-0.8810.0000.0000.0000.000
82A82LYS10.9170.96912.38518.55818.5580.0000.0000.0000.000
83A83LEU0-0.037-0.0185.6780.1940.1940.0000.0000.0000.000
84A84ARG10.7840.8759.34820.77920.7790.0000.0000.0000.000
85A85ALA00.0170.0089.564-1.818-1.8180.0000.0000.0000.000
86A86ASN00.003-0.01610.4273.8253.8250.0000.0000.0000.000
87A87PHE00.0140.00311.842-1.437-1.4370.0000.0000.0000.000
88A88PHE00.0150.00614.7440.9700.9700.0000.0000.0000.000
89A89SER0-0.017-0.03117.6830.1840.1840.0000.0000.0000.000
90A90ASP-1-0.779-0.84620.115-14.809-14.8090.0000.0000.0000.000
91A91GLU-1-0.726-0.84916.400-17.668-17.6680.0000.0000.0000.000
92A92TYR0-0.058-0.03116.969-0.038-0.0380.0000.0000.0000.000
93A93ARG10.9430.96818.69212.28612.2860.0000.0000.0000.000
94A94ALA00.0180.02519.3490.3680.3680.0000.0000.0000.000
95A95LEU0-0.033-0.01513.692-0.489-0.4890.0000.0000.0000.000
96A96SER0-0.035-0.02314.916-0.965-0.9650.0000.0000.0000.000
97A97GLY00.0230.00515.630-0.696-0.6960.0000.0000.0000.000
98A98LYS10.9020.96413.03821.12621.1260.0000.0000.0000.000
99A99TYR00.0580.03110.357-1.488-1.4880.0000.0000.0000.000
100A100LYS10.8220.9086.96131.12931.1290.0000.0000.0000.000
101A101SER0-0.074-0.0538.418-1.813-1.8130.0000.0000.0000.000
102A102ILE0-0.035-0.0058.458-0.256-0.2560.0000.0000.0000.000
103A103PHE00.013-0.0065.666-5.413-5.4130.0000.0000.0000.000
104A104THR00.0410.0153.087-0.844-0.3100.060-0.138-0.4560.000
105A105ASP-1-0.746-0.8271.710-124.748-135.64830.004-11.405-7.699-0.135
106A106ALA0-0.040-0.0044.5186.5316.625-0.001-0.038-0.0540.000
107A107GLU-1-0.808-0.8837.753-23.177-23.1770.0000.0000.0000.000
108A108VAL0-0.028-0.00711.0032.1152.1150.0000.0000.0000.000
109A109LEU0-0.0070.00411.919-2.095-2.0950.0000.0000.0000.000
110A110ALA00.0230.02414.1751.2531.2530.0000.0000.0000.000
111A111PRO00.015-0.00816.0140.2000.2000.0000.0000.0000.000
112A112ALA0-0.0050.00317.533-0.884-0.8840.0000.0000.0000.000
113A113LEU00.0000.00914.3090.5120.5120.0000.0000.0000.000
114A114PRO0-0.024-0.00618.7620.5420.5420.0000.0000.0000.000
115A115CYS0-0.038-0.03019.4600.4500.4500.0000.0000.0000.000
116A116ALA0-0.0240.01220.620-0.584-0.5840.0000.0000.0000.000
117A117SER0-0.001-0.04117.652-0.091-0.0910.0000.0000.0000.000
118A118THR00.0240.02818.9780.0850.0850.0000.0000.0000.000
119A119TYR00.052-0.02319.7550.1710.1710.0000.0000.0000.000
120A120THR0-0.0070.00922.5780.2150.2150.0000.0000.0000.000
121A121ASP-1-0.770-0.86923.664-12.163-12.1630.0000.0000.0000.000
122A122LEU00.0210.01518.1840.0730.0730.0000.0000.0000.000
123A123GLN00.019-0.00422.3640.2370.2370.0000.0000.0000.000
124A124ASN0-0.023-0.00625.2040.4020.4020.0000.0000.0000.000
125A125LYS10.7750.88423.80412.41312.4130.0000.0000.0000.000
126A126ALA0-0.030-0.01722.9570.0900.0900.0000.0000.0000.000
127A127GLY0-0.032-0.01524.7830.1610.1610.0000.0000.0000.000
128A128VAL0-0.062-0.03125.1240.2980.2980.0000.0000.0000.000
129A129SER00.002-0.01626.212-0.329-0.3290.0000.0000.0000.000
130A130ARG10.8380.88022.93212.29612.2960.0000.0000.0000.000
131A131GLU-1-0.857-0.90425.212-10.735-10.7350.0000.0000.0000.000
132A132LYS10.8570.91827.99410.38310.3830.0000.0000.0000.000
133A133LEU0-0.0040.02220.8050.0470.0470.0000.0000.0000.000
134A134SER0-0.037-0.02324.550-0.134-0.1340.0000.0000.0000.000
135A135LEU0-0.0130.01319.536-0.619-0.6190.0000.0000.0000.000
136A136GLY00.0750.02019.8040.6720.6720.0000.0000.0000.000
137A137VAL0-0.0070.00717.064-0.700-0.7000.0000.0000.0000.000
138A138SER00.0640.02818.449-0.512-0.5120.0000.0000.0000.000
139A139SER0-0.034-0.00820.647-0.016-0.0160.0000.0000.0000.000
140A140LEU00.0080.00912.983-0.101-0.1010.0000.0000.0000.000
141A141GLN00.000-0.01816.433-0.111-0.1110.0000.0000.0000.000
142A142THR0-0.014-0.00917.569-0.080-0.0800.0000.0000.0000.000
143A143ALA0-0.028-0.02317.6340.0630.0630.0000.0000.0000.000
144A144PHE00.0160.01110.1550.1060.1060.0000.0000.0000.000
145A145THR0-0.004-0.01315.308-0.320-0.3200.0000.0000.0000.000
146A146ALA0-0.054-0.01217.7520.5360.5360.0000.0000.0000.000
147A147VAL0-0.033-0.00914.6390.6460.6460.0000.0000.0000.000
148A148TYR0-0.003-0.01910.484-0.567-0.5670.0000.0000.0000.000
149A149GLY00.0360.02614.1721.0591.0590.0000.0000.0000.000
150A150LYS10.8350.92615.56416.32616.3260.0000.0000.0000.000
151A151VAL00.0300.01418.336-0.555-0.5550.0000.0000.0000.000
152A152PHE0-0.027-0.00714.1460.5370.5370.0000.0000.0000.000
153A153THR00.0490.02220.0370.5140.5140.0000.0000.0000.000
154A154GLY00.0560.00921.419-0.521-0.5210.0000.0000.0000.000
155A155LYS10.9580.98722.12510.58110.5810.0000.0000.0000.000
156A156ASN0-0.045-0.02820.1940.2590.2590.0000.0000.0000.000
157A157VAL00.0290.01016.463-0.623-0.6230.0000.0000.0000.000
158A158ALA00.0480.02817.504-0.763-0.7630.0000.0000.0000.000
159A159LYS10.9480.97519.39212.59112.5910.0000.0000.0000.000
160A160PHE00.0160.01311.132-0.085-0.0850.0000.0000.0000.000
161A161ALA00.0160.01614.607-0.922-0.9220.0000.0000.0000.000
162A162LEU00.002-0.00215.672-0.342-0.3420.0000.0000.0000.000
163A163ILE00.0130.00216.7440.0840.0840.0000.0000.0000.000
164A164SER0-0.010-0.01011.996-0.729-0.7290.0000.0000.0000.000
165A165ILE0-0.027-0.01813.436-0.712-0.7120.0000.0000.0000.000
166A166GLN0-0.035-0.03215.3070.2450.2450.0000.0000.0000.000
167A167MET0-0.0060.00515.1410.3180.3180.0000.0000.0000.000
168A168VAL0-0.0080.0149.068-0.706-0.7060.0000.0000.0000.000
169A169ALA00.0130.01712.438-0.136-0.1360.0000.0000.0000.000
170A170GLU-1-0.771-0.86313.642-14.752-14.7520.0000.0000.0000.000
171A171ALA00.0170.01114.6470.5740.5740.0000.0000.0000.000
172A172ALA00.0080.01712.0680.3380.3380.0000.0000.0000.000
173A173ARG10.8120.89614.17016.98916.9890.0000.0000.0000.000
174A174PHE00.0070.00417.3310.6960.6960.0000.0000.0000.000
175A175LYS10.8690.92718.42913.74313.7430.0000.0000.0000.000
176A176TYR00.0510.03020.345-0.102-0.1020.0000.0000.0000.000
177A177ILE0-0.009-0.01018.9970.2410.2410.0000.0000.0000.000
178A178GLU-1-0.724-0.82316.696-15.924-15.9240.0000.0000.0000.000
179A179ASP-1-0.816-0.90818.581-12.937-12.9370.0000.0000.0000.000
180A180GLN0-0.0040.01221.9040.4060.4060.0000.0000.0000.000
181A181VAL0-0.008-0.00817.3310.2570.2570.0000.0000.0000.000
182A182ILE0-0.043-0.02618.3650.0440.0440.0000.0000.0000.000
183A183ASN0-0.060-0.04621.0180.4930.4930.0000.0000.0000.000
184A184ARG10.8560.93123.76811.38411.3840.0000.0000.0000.000
185A185GLY0-0.013-0.00121.5230.1740.1740.0000.0000.0000.000
186A186MET0-0.0390.00516.768-0.748-0.7480.0000.0000.0000.000
187A187TYR00.001-0.01721.158-0.100-0.1000.0000.0000.0000.000
188A188SER00.0050.01223.8710.4680.4680.0000.0000.0000.000
189A189SER0-0.027-0.01323.595-0.615-0.6150.0000.0000.0000.000
190A190PHE0-0.040-0.01621.4160.5360.5360.0000.0000.0000.000
191A191GLU-1-0.808-0.90825.011-10.797-10.7970.0000.0000.0000.000
192A192ALA00.0350.02323.9980.2550.2550.0000.0000.0000.000
193A193GLY00.0560.02125.9370.2770.2770.0000.0000.0000.000
194A194ALA00.021-0.00128.356-0.280-0.2800.0000.0000.0000.000
195A195ARG10.7740.85329.9299.0869.0860.0000.0000.0000.000
196A196ILE00.0300.02123.831-0.054-0.0540.0000.0000.0000.000
197A197THR00.0130.00125.278-0.382-0.3820.0000.0000.0000.000
198A198LEU0-0.020-0.01326.339-0.164-0.1640.0000.0000.0000.000
199A199LEU0-0.0020.00624.9190.0520.0520.0000.0000.0000.000
200A200GLU-1-0.760-0.86321.371-13.269-13.2690.0000.0000.0000.000
201A201ASN0-0.027-0.00723.543-0.610-0.6100.0000.0000.0000.000
202A202ASN0-0.043-0.03025.8820.4040.4040.0000.0000.0000.000
203A203TRP00.0010.00517.2380.1170.1170.0000.0000.0000.000
204A204SER0-0.013-0.02823.637-0.054-0.0540.0000.0000.0000.000
205A205LYS10.8460.90624.75110.11410.1140.0000.0000.0000.000
206A206ILE00.0550.03725.3260.3370.3370.0000.0000.0000.000
207A207SER00.0740.03022.303-0.008-0.0080.0000.0000.0000.000
208A208GLU-1-0.855-0.90224.332-10.195-10.1950.0000.0000.0000.000
209A209GLN0-0.017-0.01027.2910.5570.5570.0000.0000.0000.000
210A210TYR00.0530.00824.4520.2460.2460.0000.0000.0000.000
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