FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: VRG21

Calculation Name: 3NXH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXH

Chain ID: A

ChEMBL ID:

UniProt ID: P96499

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2689383.116148
FMO2-HF: Nuclear repulsion 2601971.395372
FMO2-HF: Total energy -87411.720776
FMO2-MP2: Total energy -87667.453123


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:72:MET)


Summations of interaction energy for fragment #1(A:72: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.
-7.836-3.38511.1-3.692-11.857-0.023
Interaction energy analysis for fragmet #1(A:72:MET)
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 : 0.012
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].
3A74LYS10.9620.9612.527-2.0850.6921.455-1.880-2.353-0.014
4A75LYS10.9070.9494.6461.2731.480-0.001-0.014-0.1920.000
5A76PRO00.0870.0495.600-0.538-0.5380.0000.0000.0000.000
6A77PHE0-0.055-0.0244.2720.0060.2320.000-0.019-0.2070.000
7A78SER00.0560.0038.520-0.067-0.0670.0000.0000.0000.000
8A79ILE0-0.033-0.0167.7940.1240.1240.0000.0000.0000.000
9A80LEU00.0170.00811.917-0.050-0.0500.0000.0000.0000.000
10A81PHE00.003-0.01311.5580.0550.0550.0000.0000.0000.000
11A82MET0-0.068-0.03516.739-0.017-0.0170.0000.0000.0000.000
12A83GLY00.0350.03220.2520.0140.0140.0000.0000.0000.000
13A84ILE0-0.039-0.04022.735-0.009-0.0090.0000.0000.0000.000
14A85GLU-1-0.800-0.89725.6810.0090.0090.0000.0000.0000.000
15A86ASP-1-0.816-0.90228.2210.0470.0470.0000.0000.0000.000
16A87TYR00.0920.05921.7150.0050.0050.0000.0000.0000.000
17A88ALA0-0.010-0.01127.1040.0070.0070.0000.0000.0000.000
18A89THR0-0.0620.03728.372-0.005-0.0050.0000.0000.0000.000
19A90LYS10.8870.92231.065-0.064-0.0640.0000.0000.0000.000
20A91GLY00.0550.03533.819-0.001-0.0010.0000.0000.0000.000
21A92GLN0-0.009-0.01734.532-0.003-0.0030.0000.0000.0000.000
22A93LYS10.8500.89433.187-0.038-0.0380.0000.0000.0000.000
23A94GLY00.000-0.02131.2290.0010.0010.0000.0000.0000.000
24A95ARG10.7880.88029.329-0.002-0.0020.0000.0000.0000.000
25A96SER00.0810.05024.8470.0040.0040.0000.0000.0000.000
26A97ASP-1-0.989-0.99026.089-0.036-0.0360.0000.0000.0000.000
27A98SER0-0.009-0.01322.058-0.012-0.0120.0000.0000.0000.000
28A99LEU0-0.013-0.00921.0820.0160.0160.0000.0000.0000.000
29A100ILE00.0130.01616.886-0.018-0.0180.0000.0000.0000.000
30A101VAL00.0210.02015.1340.0190.0190.0000.0000.0000.000
31A102VAL00.0020.00610.625-0.026-0.0260.0000.0000.0000.000
32A103THR0-0.008-0.01711.2960.0530.0530.0000.0000.0000.000
33A104LEU0-0.009-0.0105.785-0.069-0.0690.0000.0000.0000.000
34A105ASP-1-0.778-0.8868.008-1.495-1.4950.0000.0000.0000.000
35A106PRO00.0280.0123.567-0.343-0.0510.007-0.048-0.2520.000
36A107LYS10.9090.9586.0011.3701.3700.0000.0000.0000.000
37A108ASN0-0.065-0.0288.2930.2810.2810.0000.0000.0000.000
38A109LYS10.8480.9408.6861.6851.6850.0000.0000.0000.000
39A110THR00.0160.0149.9110.2200.2200.0000.0000.0000.000
40A111MET0-0.0030.0169.191-0.152-0.1520.0000.0000.0000.000
41A112LYS10.8520.94612.1180.5770.5770.0000.0000.0000.000
42A113MET00.0190.00814.174-0.003-0.0030.0000.0000.0000.000
43A114LEU00.0040.01216.6470.0180.0180.0000.0000.0000.000
44A115SER00.0190.00219.4690.0080.0080.0000.0000.0000.000
45A116ILE0-0.056-0.02021.315-0.001-0.0010.0000.0000.0000.000
46A117PRO00.0480.03324.2790.0110.0110.0000.0000.0000.000
47A118ARG10.9871.03727.6650.0430.0430.0000.0000.0000.000
48A119ASP-1-0.908-0.97528.823-0.034-0.0340.0000.0000.0000.000
49A120THR0-0.024-0.07228.434-0.003-0.0030.0000.0000.0000.000
50A121ARG10.8200.89730.6240.0490.0490.0000.0000.0000.000
51A122VAL00.0180.00627.831-0.006-0.0060.0000.0000.0000.000
52A123GLN0-0.026-0.02330.9480.0020.0020.0000.0000.0000.000
53A124LEU0-0.038-0.02529.239-0.002-0.0020.0000.0000.0000.000
54A125ALA00.0530.05726.093-0.002-0.0020.0000.0000.0000.000
55A126GLY00.0130.01028.1560.0030.0030.0000.0000.0000.000
56A127ASP-1-0.816-0.88031.121-0.004-0.0040.0000.0000.0000.000
57A128THR0-0.053-0.03733.4340.0010.0010.0000.0000.0000.000
58A129THR0-0.087-0.03635.0670.0020.0020.0000.0000.0000.000
59A130GLY0-0.027-0.02637.515-0.001-0.0010.0000.0000.0000.000
60A131SER0-0.052-0.03835.266-0.001-0.0010.0000.0000.0000.000
61A132LYS10.8360.91637.717-0.007-0.0070.0000.0000.0000.000
62A133THR00.0140.01534.4700.0000.0000.0000.0000.0000.000
63A134LYS10.8410.92934.0590.0060.0060.0000.0000.0000.000
64A135ILE00.0510.03432.030-0.002-0.0020.0000.0000.0000.000
65A136ASN00.0740.03625.2360.0060.0060.0000.0000.0000.000
66A137ALA0-0.039-0.02028.2600.0020.0020.0000.0000.0000.000
67A138ALA00.032-0.00726.4840.0060.0060.0000.0000.0000.000
68A139TYR0-0.0070.02522.7440.0020.0020.0000.0000.0000.000
69A140SER0-0.062-0.01927.0150.0070.0070.0000.0000.0000.000
70A141LYS10.8920.94130.389-0.012-0.0120.0000.0000.0000.000
71A142GLY00.0900.03128.191-0.004-0.0040.0000.0000.0000.000
72A143GLY0-0.0060.01925.7740.0120.0120.0000.0000.0000.000
73A144LYS10.9480.94117.533-0.225-0.2250.0000.0000.0000.000
74A145ASP-1-0.848-0.93720.4350.1500.1500.0000.0000.0000.000
75A146GLU-1-0.780-0.87322.1270.0220.0220.0000.0000.0000.000
76A147THR0-0.089-0.05322.237-0.018-0.0180.0000.0000.0000.000
77A148VAL00.029-0.00417.769-0.019-0.0190.0000.0000.0000.000
78A149GLU-1-0.871-0.91720.3940.0130.0130.0000.0000.0000.000
79A150THR0-0.059-0.03622.549-0.017-0.0170.0000.0000.0000.000
80A151VAL0-0.023-0.02719.615-0.017-0.0170.0000.0000.0000.000
81A152GLU-1-0.810-0.88517.587-0.031-0.0310.0000.0000.0000.000
82A153ASN00.0040.00220.688-0.022-0.0220.0000.0000.0000.000
83A154PHE0-0.041-0.01624.050-0.012-0.0120.0000.0000.0000.000
84A155LEU0-0.015-0.02518.899-0.011-0.0110.0000.0000.0000.000
85A156GLN0-0.104-0.05221.156-0.028-0.0280.0000.0000.0000.000
86A157ILE0-0.007-0.00115.603-0.027-0.0270.0000.0000.0000.000
87A158PRO00.0250.02214.4650.0280.0280.0000.0000.0000.000
88A159ILE0-0.028-0.00614.412-0.063-0.0630.0000.0000.0000.000
89A160ASP-1-0.898-0.9419.811-0.170-0.1700.0000.0000.0000.000
90A161LYS10.7930.9026.612-0.943-0.9430.0000.0000.0000.000
91A162TYR00.0410.02511.010-0.091-0.0910.0000.0000.0000.000
92A163VAL0-0.016-0.01212.8190.0800.0800.0000.0000.0000.000
93A164THR0-0.029-0.00215.330-0.057-0.0570.0000.0000.0000.000
94A165VAL00.0090.01319.0230.0220.0220.0000.0000.0000.000
95A166ASP-1-0.795-0.90320.9130.0510.0510.0000.0000.0000.000
96A167PHE00.014-0.01124.341-0.010-0.0100.0000.0000.0000.000
97A168ASP-1-0.853-0.92526.8450.0360.0360.0000.0000.0000.000
98A169GLY00.0300.00623.103-0.004-0.0040.0000.0000.0000.000
99A170PHE0-0.0060.02621.282-0.001-0.0010.0000.0000.0000.000
100A171LYS10.9190.96222.711-0.029-0.0290.0000.0000.0000.000
101A172ASP-1-0.910-0.94022.6590.0760.0760.0000.0000.0000.000
102A173VAL00.0580.02517.480-0.005-0.0050.0000.0000.0000.000
103A174ILE0-0.030-0.00520.215-0.013-0.0130.0000.0000.0000.000
104A175ASN00.0170.00021.948-0.023-0.0230.0000.0000.0000.000
105A176GLU-1-0.893-0.94519.9260.0610.0610.0000.0000.0000.000
106A177VAL0-0.091-0.03516.723-0.008-0.0080.0000.0000.0000.000
107A178GLY0-0.046-0.02219.551-0.024-0.0240.0000.0000.0000.000
108A179GLY0-0.0040.01022.624-0.003-0.0030.0000.0000.0000.000
109A180ILE0-0.098-0.06120.422-0.014-0.0140.0000.0000.0000.000
110A181ASP-1-0.862-0.93023.326-0.122-0.1220.0000.0000.0000.000
111A182VAL0-0.096-0.08023.948-0.014-0.0140.0000.0000.0000.000
112A184VAL00.0440.02529.8220.0010.0010.0000.0000.0000.000
113A185PRO0-0.055-0.02931.3380.0030.0030.0000.0000.0000.000
114A206GLU-1-0.916-0.90828.919-0.132-0.1320.0000.0000.0000.000
115A207MET0-0.050-0.03329.5150.0070.0070.0000.0000.0000.000
116A208HIS0-0.025-0.01525.1600.0030.0030.0000.0000.0000.000
117A209LEU00.0240.00026.6910.0040.0040.0000.0000.0000.000
118A210ASN00.0010.00926.7750.0030.0030.0000.0000.0000.000
119A211GLY00.0850.04325.934-0.002-0.0020.0000.0000.0000.000
120A212GLU-1-0.949-0.98626.915-0.006-0.0060.0000.0000.0000.000
121A213GLU-1-0.914-0.95429.713-0.050-0.0500.0000.0000.0000.000
122A214ALA00.0730.01625.240-0.003-0.0030.0000.0000.0000.000
123A215LEU0-0.038-0.04226.565-0.002-0.0020.0000.0000.0000.000
124A216ALA0-0.014-0.01127.5980.0010.0010.0000.0000.0000.000
125A217TYR0-0.149-0.04126.858-0.003-0.0030.0000.0000.0000.000
126A218ALA0-0.057-0.03127.100-0.008-0.0080.0000.0000.0000.000
127A228ASP-1-0.830-0.94729.497-0.068-0.0680.0000.0000.0000.000
128A229PHE0-0.022-0.02728.396-0.001-0.0010.0000.0000.0000.000
129A230GLY00.0320.03930.283-0.006-0.0060.0000.0000.0000.000
130A231ARG10.8880.92629.3250.0390.0390.0000.0000.0000.000
131A232ASN00.0040.01125.902-0.013-0.0130.0000.0000.0000.000
132A233ASP-1-0.897-0.94624.654-0.157-0.1570.0000.0000.0000.000
133A234ARG10.9130.95525.0810.0640.0640.0000.0000.0000.000
134A235GLN00.0740.04022.649-0.014-0.0140.0000.0000.0000.000
135A236LYS10.9850.99720.1390.1760.1760.0000.0000.0000.000
136A237GLN0-0.0250.01020.167-0.024-0.0240.0000.0000.0000.000
137A238ILE00.0420.02720.447-0.012-0.0120.0000.0000.0000.000
138A239LEU0-0.016-0.00715.087-0.006-0.0060.0000.0000.0000.000
139A240ASN00.015-0.02516.742-0.054-0.0540.0000.0000.0000.000
140A241ALA00.0150.03417.650-0.027-0.0270.0000.0000.0000.000
141A242LEU00.0170.00615.133-0.005-0.0050.0000.0000.0000.000
142A243ILE0-0.030-0.03512.205-0.024-0.0240.0000.0000.0000.000
143A244ASP-1-0.763-0.87913.849-0.398-0.3980.0000.0000.0000.000
144A245ARG10.7830.89216.5510.1260.1260.0000.0000.0000.000
145A246MET0-0.100-0.02911.9690.0370.0370.0000.0000.0000.000
146A247SER0-0.108-0.11012.0640.0050.0050.0000.0000.0000.000
147A256ASP-1-0.870-0.94313.6250.1160.1160.0000.0000.0000.000
148A257LYS10.8710.91714.690-0.219-0.2190.0000.0000.0000.000
149A258ILE00.0780.04015.6830.0170.0170.0000.0000.0000.000
150A259ALA0-0.0170.00012.1520.0060.0060.0000.0000.0000.000
151A260GLU-1-0.928-0.97814.1410.4650.4650.0000.0000.0000.000
152A261LYS10.7630.88115.885-0.111-0.1110.0000.0000.0000.000
153A262ALA00.0430.00416.0760.0040.0040.0000.0000.0000.000
154A263SER0-0.075-0.03513.4370.0200.0200.0000.0000.0000.000
155A264GLU-1-0.950-0.96515.5050.3520.3520.0000.0000.0000.000
156A265ASN00.0060.01118.469-0.018-0.0180.0000.0000.0000.000
157A266VAL0-0.040-0.01815.309-0.035-0.0350.0000.0000.0000.000
158A267GLU-1-0.871-0.92517.6550.1930.1930.0000.0000.0000.000
159A268THR00.010-0.02012.1900.0200.0200.0000.0000.0000.000
160A269ASN00.0000.00911.4750.0310.0310.0000.0000.0000.000
161A270ILE0-0.040-0.0206.6510.2280.2280.0000.0000.0000.000
162A271ARG10.9170.9643.682-2.696-2.4990.000-0.025-0.1720.000
163A272ILE00.1260.0537.3970.3050.3050.0000.0000.0000.000
164A273THR0-0.040-0.0274.6040.1710.271-0.001-0.010-0.0880.000
165A274GLU-1-0.830-0.9362.6180.9401.4704.021-1.763-2.7880.002
166A275GLY00.0780.0473.790-0.295-1.1540.0541.536-0.730-0.006
167A276LEU00.0240.0086.459-0.578-0.5780.0000.0000.0000.000
168A277ALA0-0.049-0.0332.672-1.206-1.3972.912-0.815-1.9050.000
169A278LEU0-0.028-0.0202.280-3.454-2.8352.154-0.477-2.296-0.005
170A279GLN00.1150.0644.014-0.0940.0330.002-0.043-0.0860.000
171A280GLN0-0.022-0.0046.605-0.062-0.0620.0000.0000.0000.000
172A281ILE0-0.092-0.0512.666-0.464-0.0380.497-0.134-0.7880.000
173A282TYR0-0.085-0.0985.1900.0710.0710.0000.0000.0000.000
174A283SER00.0510.0568.4810.2170.2170.0000.0000.0000.000
175A284GLY00.0040.03911.4270.1260.1260.0000.0000.0000.000
176A285PHE00.017-0.03212.015-0.094-0.0940.0000.0000.0000.000
177A286THR00.0240.01511.5590.0360.0360.0000.0000.0000.000
178A287SER0-0.0100.02613.8770.0390.0390.0000.0000.0000.000
179A288LYS10.9490.97916.6740.2670.2670.0000.0000.0000.000
180A289LYS10.8160.91115.9750.5780.5780.0000.0000.0000.000
181A290ILE0-0.0290.00114.004-0.023-0.0230.0000.0000.0000.000
182A291ASP-1-0.834-0.90116.289-0.329-0.3290.0000.0000.0000.000
183A292THR0-0.023-0.01418.099-0.002-0.0020.0000.0000.0000.000
184A293LEU0-0.0050.00619.1450.0210.0210.0000.0000.0000.000
185A294SER0-0.015-0.04221.9580.0160.0160.0000.0000.0000.000
186A295ILE00.0180.03024.202-0.003-0.0030.0000.0000.0000.000
187A296THR0-0.039-0.03826.8070.0060.0060.0000.0000.0000.000
188A297GLY00.0660.03930.3950.0010.0010.0000.0000.0000.000
189A298SER0-0.082-0.01833.3180.0000.0000.0000.0000.0000.000
190A299ASP-1-0.854-0.94036.282-0.060-0.0600.0000.0000.0000.000
191A300LEU0-0.029-0.00438.4850.0010.0010.0000.0000.0000.000
192A301TYR0-0.0110.00139.7110.0020.0020.0000.0000.0000.000
193A302LEU0-0.022-0.01440.2270.0010.0010.0000.0000.0000.000
194A303GLY0-0.007-0.00743.8240.0020.0020.0000.0000.0000.000
195A304PRO00.013-0.00946.776-0.001-0.0010.0000.0000.0000.000
196A305ASN0-0.028-0.02043.631-0.002-0.0020.0000.0000.0000.000
197A306ASN00.0010.01344.784-0.002-0.0020.0000.0000.0000.000
198A307THR0-0.023-0.00739.3720.0000.0000.0000.0000.0000.000
199A308TYR0-0.020-0.01034.780-0.001-0.0010.0000.0000.0000.000
200A309TYR0-0.034-0.01435.4670.0050.0050.0000.0000.0000.000
201A310PHE00.0120.01629.865-0.003-0.0030.0000.0000.0000.000
202A311GLU-1-0.785-0.88633.180-0.053-0.0530.0000.0000.0000.000
203A312PRO0-0.048-0.00929.946-0.005-0.0050.0000.0000.0000.000
204A313ASP-1-0.816-0.95331.869-0.098-0.0980.0000.0000.0000.000
205A314ALA00.0100.00731.118-0.008-0.0080.0000.0000.0000.000
206A315THR00.0180.02530.656-0.012-0.0120.0000.0000.0000.000
207A316ASN00.015-0.01727.037-0.009-0.0090.0000.0000.0000.000
208A317LEU00.0490.04025.558-0.017-0.0170.0000.0000.0000.000
209A318GLU-1-0.922-0.96725.603-0.129-0.1290.0000.0000.0000.000
210A319LYS10.8700.94325.8680.1340.1340.0000.0000.0000.000
211A320VAL00.0020.03821.565-0.027-0.0270.0000.0000.0000.000
212A321ARG10.8820.94821.2570.0960.0960.0000.0000.0000.000
213A322LYS10.9931.01220.7190.1890.1890.0000.0000.0000.000
214A323THR0-0.033-0.06219.196-0.026-0.0260.0000.0000.0000.000
215A324LEU0-0.012-0.01316.139-0.048-0.0480.0000.0000.0000.000
216A325GLN0-0.024-0.01115.954-0.056-0.0560.0000.0000.0000.000
217A326GLU-1-0.955-0.97616.602-0.402-0.4020.0000.0000.0000.000
218A327HIS0-0.049-0.00411.5550.0140.0140.0000.0000.0000.000
219A328LEU0-0.035-0.02611.042-0.145-0.1450.0000.0000.0000.000
220A329ASP-1-1.031-0.99512.627-0.616-0.6160.0000.0000.0000.000
221A330TYR0-0.012-0.01614.7710.0410.0410.0000.0000.0000.000
222A331THR0-0.021-0.01016.7710.0320.0320.0000.0000.0000.000