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: GN2Q1

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:


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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2696006.805542
FMO2-HF: Nuclear repulsion 2608591.238093
FMO2-HF: Total energy -87415.567448
FMO2-MP2: Total energy -87671.021888


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.
-6.326-0.3997.966-3.526-10.364-0.015
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 : 0.082 / q_NPA : 0.057
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].
3A74LYS10.9040.9442.528-0.2263.8851.149-2.404-2.856-0.009
4A75LYS10.8210.8824.7651.3291.552-0.001-0.018-0.2040.000
5A76PRO00.0600.0395.551-0.499-0.4990.0000.0000.0000.000
6A77PHE0-0.055-0.0144.249-0.1790.0540.000-0.031-0.2010.000
7A78SER00.0510.0048.273-0.085-0.0850.0000.0000.0000.000
8A79ILE0-0.014-0.0087.2380.1270.1270.0000.0000.0000.000
9A80LEU00.0110.01611.144-0.053-0.0530.0000.0000.0000.000
10A81PHE00.017-0.00111.1650.0770.0770.0000.0000.0000.000
11A82MET0-0.042-0.02215.988-0.022-0.0220.0000.0000.0000.000
12A83GLY00.0360.03419.4770.0250.0250.0000.0000.0000.000
13A84ILE0-0.042-0.03922.325-0.016-0.0160.0000.0000.0000.000
14A85GLU-1-0.790-0.86225.1400.0600.0600.0000.0000.0000.000
15A86ASP-1-0.801-0.90727.3290.0900.0900.0000.0000.0000.000
16A87TYR00.0590.03621.2940.0050.0050.0000.0000.0000.000
17A88ALA0-0.045-0.02526.7840.0030.0030.0000.0000.0000.000
18A89THR0-0.0260.01527.693-0.009-0.0090.0000.0000.0000.000
19A90LYS10.8610.91230.434-0.114-0.1140.0000.0000.0000.000
20A91GLY00.0840.04733.407-0.004-0.0040.0000.0000.0000.000
21A92GLN00.004-0.01233.852-0.004-0.0040.0000.0000.0000.000
22A93LYS10.8240.89132.401-0.084-0.0840.0000.0000.0000.000
23A94GLY0-0.0100.01831.071-0.001-0.0010.0000.0000.0000.000
24A95ARG10.7630.84228.766-0.040-0.0400.0000.0000.0000.000
25A96SER00.0780.03224.3670.0070.0070.0000.0000.0000.000
26A97ASP-1-0.887-0.90325.4750.0040.0040.0000.0000.0000.000
27A98SER0-0.027-0.01021.962-0.015-0.0150.0000.0000.0000.000
28A99LEU00.0050.00120.4520.0230.0230.0000.0000.0000.000
29A100ILE00.0060.01016.705-0.022-0.0220.0000.0000.0000.000
30A101VAL00.0190.01614.6100.0170.0170.0000.0000.0000.000
31A102VAL0-0.006-0.00310.956-0.020-0.0200.0000.0000.0000.000
32A103THR00.011-0.01710.9760.0460.0460.0000.0000.0000.000
33A104LEU0-0.011-0.0016.022-0.022-0.0220.0000.0000.0000.000
34A105ASP-1-0.742-0.8638.066-1.518-1.5180.0000.0000.0000.000
35A106PRO00.0270.0033.516-0.2170.0480.007-0.040-0.2320.000
36A107LYS10.8300.9106.2561.4291.4290.0000.0000.0000.000
37A108ASN0-0.071-0.0438.6680.2670.2670.0000.0000.0000.000
38A109LYS10.8790.9498.8731.5891.5890.0000.0000.0000.000
39A110THR00.0250.02310.5400.1990.1990.0000.0000.0000.000
40A111MET0-0.004-0.0049.111-0.162-0.1620.0000.0000.0000.000
41A112LYS10.8590.95012.2630.5840.5840.0000.0000.0000.000
42A113MET0-0.0010.00313.969-0.010-0.0100.0000.0000.0000.000
43A114LEU00.0020.00616.5080.0120.0120.0000.0000.0000.000
44A115SER00.025-0.00419.2380.0120.0120.0000.0000.0000.000
45A116ILE0-0.032-0.01320.573-0.008-0.0080.0000.0000.0000.000
46A117PRO0-0.0020.00723.6630.0150.0150.0000.0000.0000.000
47A118ARG10.8910.94227.0210.0110.0110.0000.0000.0000.000
48A119ASP-1-0.832-0.91627.990-0.011-0.0110.0000.0000.0000.000
49A120THR0-0.026-0.02927.457-0.005-0.0050.0000.0000.0000.000
50A121ARG10.7920.88829.8050.0430.0430.0000.0000.0000.000
51A122VAL00.0120.00227.254-0.008-0.0080.0000.0000.0000.000
52A123GLN00.008-0.00630.3820.0050.0050.0000.0000.0000.000
53A124LEU0-0.037-0.02128.288-0.002-0.0020.0000.0000.0000.000
54A125ALA00.0650.03625.675-0.004-0.0040.0000.0000.0000.000
55A126GLY00.0010.00927.7950.0020.0020.0000.0000.0000.000
56A127ASP-1-0.788-0.86130.511-0.005-0.0050.0000.0000.0000.000
57A128THR0-0.035-0.02532.8720.0020.0020.0000.0000.0000.000
58A129THR0-0.081-0.04635.2790.0010.0010.0000.0000.0000.000
59A130GLY0-0.011-0.01537.925-0.001-0.0010.0000.0000.0000.000
60A131SER0-0.055-0.05234.9160.0000.0000.0000.0000.0000.000
61A132LYS10.8490.92136.136-0.015-0.0150.0000.0000.0000.000
62A133THR0-0.0220.00733.3080.0010.0010.0000.0000.0000.000
63A134LYS10.9040.94833.281-0.015-0.0150.0000.0000.0000.000
64A135ILE00.0380.03131.484-0.003-0.0030.0000.0000.0000.000
65A136ASN00.0890.04225.1090.0000.0000.0000.0000.0000.000
66A137ALA0-0.055-0.02226.9970.0070.0070.0000.0000.0000.000
67A138ALA00.007-0.00925.7220.0080.0080.0000.0000.0000.000
68A139TYR00.0230.00022.0510.0010.0010.0000.0000.0000.000
69A140SER0-0.059-0.02526.6380.0080.0080.0000.0000.0000.000
70A141LYS10.7870.87529.665-0.037-0.0370.0000.0000.0000.000
71A142GLY00.001-0.00427.701-0.002-0.0020.0000.0000.0000.000
72A143GLY00.0020.02525.2560.0140.0140.0000.0000.0000.000
73A144LYS10.8650.90717.320-0.307-0.3070.0000.0000.0000.000
74A145ASP-1-0.828-0.90319.9010.2150.2150.0000.0000.0000.000
75A146GLU-1-0.724-0.84621.7320.0250.0250.0000.0000.0000.000
76A147THR0-0.037-0.02621.857-0.026-0.0260.0000.0000.0000.000
77A148VAL0-0.003-0.00417.310-0.025-0.0250.0000.0000.0000.000
78A149GLU-1-0.803-0.89519.862-0.001-0.0010.0000.0000.0000.000
79A150THR0-0.061-0.02721.999-0.027-0.0270.0000.0000.0000.000
80A151VAL0-0.022-0.01618.829-0.021-0.0210.0000.0000.0000.000
81A152GLU-1-0.839-0.91517.207-0.028-0.0280.0000.0000.0000.000
82A153ASN0-0.079-0.04720.348-0.035-0.0350.0000.0000.0000.000
83A154PHE0-0.0070.00723.586-0.016-0.0160.0000.0000.0000.000
84A155LEU00.025-0.00818.488-0.012-0.0120.0000.0000.0000.000
85A156GLN0-0.085-0.03920.899-0.036-0.0360.0000.0000.0000.000
86A157ILE00.0020.00615.476-0.037-0.0370.0000.0000.0000.000
87A158PRO00.0330.01913.6840.0350.0350.0000.0000.0000.000
88A159ILE0-0.031-0.00213.681-0.071-0.0710.0000.0000.0000.000
89A160ASP-1-0.834-0.8929.077-0.281-0.2810.0000.0000.0000.000
90A161LYS10.7780.8715.919-1.834-1.8340.0000.0000.0000.000
91A162TYR00.0270.02910.624-0.143-0.1430.0000.0000.0000.000
92A163VAL0-0.009-0.00211.9910.1170.1170.0000.0000.0000.000
93A164THR0-0.065-0.03114.644-0.069-0.0690.0000.0000.0000.000
94A165VAL00.0090.01018.3430.0390.0390.0000.0000.0000.000
95A166ASP-1-0.807-0.90920.1270.1110.1110.0000.0000.0000.000
96A167PHE00.0400.00323.730-0.004-0.0040.0000.0000.0000.000
97A168ASP-1-0.839-0.92826.0550.1120.1120.0000.0000.0000.000
98A169GLY0-0.001-0.00522.6110.0070.0070.0000.0000.0000.000
99A170PHE0-0.013-0.01020.7200.0110.0110.0000.0000.0000.000
100A171LYS10.8490.93922.199-0.105-0.1050.0000.0000.0000.000
101A172ASP-1-0.863-0.90922.2230.2310.2310.0000.0000.0000.000
102A173VAL00.0480.01716.9920.0030.0030.0000.0000.0000.000
103A174ILE0-0.020-0.00819.725-0.007-0.0070.0000.0000.0000.000
104A175ASN00.0290.00021.563-0.023-0.0230.0000.0000.0000.000
105A176GLU-1-0.913-0.95219.9930.2500.2500.0000.0000.0000.000
106A177VAL0-0.091-0.03516.8130.0080.0080.0000.0000.0000.000
107A178GLY0-0.029-0.01019.723-0.022-0.0220.0000.0000.0000.000
108A179GLY00.0260.02223.069-0.014-0.0140.0000.0000.0000.000
109A180ILE0-0.107-0.05920.266-0.005-0.0050.0000.0000.0000.000
110A181ASP-1-0.856-0.92023.237-0.030-0.0300.0000.0000.0000.000
111A182VAL0-0.077-0.07823.980-0.013-0.0130.0000.0000.0000.000
112A184VAL00.0590.04229.4340.0010.0010.0000.0000.0000.000
113A185PRO0-0.116-0.06631.0640.0060.0060.0000.0000.0000.000
114A206GLU-1-0.910-0.91729.194-0.083-0.0830.0000.0000.0000.000
115A207MET0-0.038-0.02929.7950.0060.0060.0000.0000.0000.000
116A208HIS0-0.025-0.01225.4140.0050.0050.0000.0000.0000.000
117A209LEU0-0.036-0.01426.0070.0000.0000.0000.0000.0000.000
118A210ASN00.0390.01326.2900.0100.0100.0000.0000.0000.000
119A211GLY00.0430.01425.397-0.007-0.0070.0000.0000.0000.000
120A212GLU-1-0.904-0.96826.3170.0710.0710.0000.0000.0000.000
121A213GLU-1-0.884-0.92729.5500.0130.0130.0000.0000.0000.000
122A214ALA00.0210.00624.646-0.009-0.0090.0000.0000.0000.000
123A215LEU0-0.0060.00026.191-0.007-0.0070.0000.0000.0000.000
124A216ALA0-0.025-0.00227.455-0.006-0.0060.0000.0000.0000.000
125A217TYR0-0.043-0.03026.808-0.005-0.0050.0000.0000.0000.000
126A218ALA0-0.043-0.02526.054-0.014-0.0140.0000.0000.0000.000
127A228ASP-1-0.709-0.85828.454-0.041-0.0410.0000.0000.0000.000
128A229PHE0-0.038-0.01727.942-0.001-0.0010.0000.0000.0000.000
129A230GLY00.001-0.00128.839-0.008-0.0080.0000.0000.0000.000
130A231ARG10.7400.84128.8460.0070.0070.0000.0000.0000.000
131A232ASN00.0660.01723.976-0.013-0.0130.0000.0000.0000.000
132A233ASP-1-0.842-0.89524.127-0.134-0.1340.0000.0000.0000.000
133A234ARG10.8740.93524.5210.0250.0250.0000.0000.0000.000
134A235GLN00.0170.01822.285-0.007-0.0070.0000.0000.0000.000
135A236LYS10.8950.93920.0170.1510.1510.0000.0000.0000.000
136A237GLN0-0.056-0.01920.139-0.008-0.0080.0000.0000.0000.000
137A238ILE00.0320.02320.419-0.009-0.0090.0000.0000.0000.000
138A239LEU0-0.0040.00314.3950.0020.0020.0000.0000.0000.000
139A240ASN00.010-0.01916.286-0.052-0.0520.0000.0000.0000.000
140A241ALA00.0260.03017.244-0.023-0.0230.0000.0000.0000.000
141A242LEU00.0110.00215.0300.0050.0050.0000.0000.0000.000
142A243ILE0-0.008-0.00912.040-0.007-0.0070.0000.0000.0000.000
143A244ASP-1-0.796-0.88014.203-0.264-0.2640.0000.0000.0000.000
144A245ARG10.8200.91816.948-0.032-0.0320.0000.0000.0000.000
145A246MET0-0.076-0.03111.9160.0570.0570.0000.0000.0000.000
146A247SER0-0.063-0.02112.5170.0300.0300.0000.0000.0000.000
147A256ASP-1-0.852-0.93513.4020.4970.4970.0000.0000.0000.000
148A257LYS10.7820.85414.451-0.667-0.6670.0000.0000.0000.000
149A258ILE00.0880.04516.1490.0100.0100.0000.0000.0000.000
150A259ALA0-0.0080.00511.971-0.006-0.0060.0000.0000.0000.000
151A260GLU-1-0.849-0.91313.9841.0421.0420.0000.0000.0000.000
152A261LYS10.8070.90315.580-0.285-0.2850.0000.0000.0000.000
153A262ALA00.0350.00915.289-0.025-0.0250.0000.0000.0000.000
154A263SER0-0.113-0.06613.3190.0160.0160.0000.0000.0000.000
155A264GLU-1-0.928-0.96515.1990.5610.5610.0000.0000.0000.000
156A265ASN0-0.0020.00918.272-0.045-0.0450.0000.0000.0000.000
157A266VAL0-0.051-0.01515.011-0.056-0.0560.0000.0000.0000.000
158A267GLU-1-0.755-0.83517.6110.2940.2940.0000.0000.0000.000
159A268THR00.025-0.02711.8690.0310.0310.0000.0000.0000.000
160A269ASN00.0140.00211.0000.0030.0030.0000.0000.0000.000
161A270ILE0-0.028-0.0026.3140.3940.3940.0000.0000.0000.000
162A271ARG10.8990.9264.313-3.741-3.632-0.001-0.012-0.0950.000
163A272ILE00.1010.0527.1530.5540.5540.0000.0000.0000.000
164A273THR00.004-0.0144.989-0.431-0.4310.0000.0000.0000.000
165A274GLU-1-0.838-0.8892.9513.8154.1063.882-1.637-2.5360.002
166A275GLY00.0560.0303.833-1.352-2.590-0.0291.675-0.407-0.003
167A276LEU00.0400.0236.520-0.646-0.6460.0000.0000.0000.000
168A277ALA0-0.028-0.0142.719-1.744-0.9951.267-0.512-1.504-0.001
169A278LEU0-0.039-0.0242.224-3.075-2.4461.563-0.402-1.790-0.004
170A279GLN00.0600.0264.2560.0830.1590.001-0.029-0.0480.000
171A280GLN00.0220.0176.948-0.196-0.1960.0000.0000.0000.000
172A281ILE0-0.111-0.0392.871-0.711-0.2320.128-0.116-0.4910.000
173A282TYR0-0.053-0.0515.524-0.109-0.1090.0000.0000.0000.000
174A283SER00.0350.0269.1850.1570.1570.0000.0000.0000.000
175A284GLY00.0350.02311.8750.0770.0770.0000.0000.0000.000
176A285PHE0-0.016-0.03212.928-0.073-0.0730.0000.0000.0000.000
177A286THR00.0180.01711.552-0.034-0.0340.0000.0000.0000.000
178A287SER00.0480.00314.4250.0540.0540.0000.0000.0000.000
179A288LYS10.8740.94216.9080.1610.1610.0000.0000.0000.000
180A289LYS10.7770.87316.4070.5400.5400.0000.0000.0000.000
181A290ILE0-0.0100.01314.011-0.050-0.0500.0000.0000.0000.000
182A291ASP-1-0.847-0.91816.516-0.334-0.3340.0000.0000.0000.000
183A292THR0-0.033-0.01918.068-0.004-0.0040.0000.0000.0000.000
184A293LEU00.0320.02719.3530.0290.0290.0000.0000.0000.000
185A294SER0-0.040-0.04721.7440.0230.0230.0000.0000.0000.000
186A295ILE00.0170.03223.721-0.004-0.0040.0000.0000.0000.000
187A296THR00.012-0.00726.1910.0050.0050.0000.0000.0000.000
188A297GLY00.0160.00029.8190.0000.0000.0000.0000.0000.000
189A298SER0-0.050-0.00932.940-0.002-0.0020.0000.0000.0000.000
190A299ASP-1-0.814-0.87836.090-0.041-0.0410.0000.0000.0000.000
191A300LEU0-0.047-0.00737.7830.0000.0000.0000.0000.0000.000
192A301TYR0-0.024-0.03439.1030.0040.0040.0000.0000.0000.000
193A302LEU0-0.029-0.01339.7630.0000.0000.0000.0000.0000.000
194A303GLY00.0260.01543.2000.0030.0030.0000.0000.0000.000
195A304PRO00.025-0.00846.078-0.001-0.0010.0000.0000.0000.000
196A305ASN0-0.046-0.03042.932-0.002-0.0020.0000.0000.0000.000
197A306ASN0-0.043-0.01044.202-0.002-0.0020.0000.0000.0000.000
198A307THR0-0.0020.00738.7610.0010.0010.0000.0000.0000.000
199A308TYR0-0.031-0.03234.130-0.002-0.0020.0000.0000.0000.000
200A309TYR0-0.040-0.02134.8070.0060.0060.0000.0000.0000.000
201A310PHE00.0170.01729.704-0.004-0.0040.0000.0000.0000.000
202A311GLU-1-0.766-0.88432.372-0.048-0.0480.0000.0000.0000.000
203A312PRO0-0.044-0.01029.473-0.005-0.0050.0000.0000.0000.000
204A313ASP-1-0.821-0.93531.439-0.111-0.1110.0000.0000.0000.000
205A314ALA00.0220.01030.604-0.009-0.0090.0000.0000.0000.000
206A315THR00.033-0.00230.312-0.013-0.0130.0000.0000.0000.000
207A316ASN0-0.048-0.02826.813-0.012-0.0120.0000.0000.0000.000
208A317LEU00.0300.02025.020-0.018-0.0180.0000.0000.0000.000
209A318GLU-1-0.913-0.94525.516-0.148-0.1480.0000.0000.0000.000
210A319LYS10.8680.93425.5090.1390.1390.0000.0000.0000.000
211A320VAL00.0050.01821.440-0.030-0.0300.0000.0000.0000.000
212A321ARG10.8520.92821.1510.1050.1050.0000.0000.0000.000
213A322LYS10.8900.95420.6130.2860.2860.0000.0000.0000.000
214A323THR0-0.032-0.03619.251-0.038-0.0380.0000.0000.0000.000
215A324LEU0-0.013-0.01516.022-0.058-0.0580.0000.0000.0000.000
216A325GLN0-0.043-0.03915.848-0.064-0.0640.0000.0000.0000.000
217A326GLU-1-0.864-0.92616.587-0.410-0.4100.0000.0000.0000.000
218A327HIS0-0.050-0.00511.7150.0050.0050.0000.0000.0000.000
219A328LEU0-0.052-0.03610.976-0.152-0.1520.0000.0000.0000.000
220A329ASP-1-0.999-0.98912.720-0.747-0.7470.0000.0000.0000.000
221A330TYR0-0.0050.00414.5720.0390.0390.0000.0000.0000.000
222A331THR0-0.033-0.01316.7360.0290.0290.0000.0000.0000.000