FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1NN5Z

Calculation Name: 4NZP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NZP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PHK7

Base Structure: X-ray

Registration Date: 2023-09-21

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 385
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6231958.218994
FMO2-HF: Nuclear repulsion 6081050.358499
FMO2-HF: Total energy -150907.860496
FMO2-MP2: Total energy -151350.746479


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
3.2011.66419.253-8.199-9.5170.094
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.894 / q_NPA : -0.954
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].
3A6LYS10.8090.9021.888-116.031-118.08119.255-8.168-9.0380.094
4A7LYS10.8410.9285.462-26.982-26.9820.0000.0000.0000.000
5A8VAL00.0240.0218.668-1.165-1.1650.0000.0000.0000.000
6A9VAL00.0040.01611.041-1.522-1.5220.0000.0000.0000.000
7A10LEU0-0.031-0.01814.837-0.024-0.0240.0000.0000.0000.000
8A11ALA0-0.0060.00216.524-0.826-0.8260.0000.0000.0000.000
9A12TYR0-0.024-0.03119.794-0.096-0.0960.0000.0000.0000.000
10A13SER00.0740.04221.527-0.280-0.2800.0000.0000.0000.000
11A14GLY00.0500.03323.755-0.499-0.4990.0000.0000.0000.000
12A15GLY00.0080.01425.229-0.290-0.2900.0000.0000.0000.000
13A16LEU0-0.0060.00324.2930.5090.5090.0000.0000.0000.000
14A17ASP-1-0.842-0.93822.87613.20613.2060.0000.0000.0000.000
15A18THR00.0560.01520.0850.7240.7240.0000.0000.0000.000
16A19SER0-0.048-0.03019.2590.7690.7690.0000.0000.0000.000
17A20ILE0-0.011-0.00119.1030.6460.6460.0000.0000.0000.000
18A21ILE0-0.0080.00415.2400.8800.8800.0000.0000.0000.000
19A22LEU0-0.005-0.00114.8111.4971.4970.0000.0000.0000.000
20A23LYS10.8400.90814.139-17.536-17.5360.0000.0000.0000.000
21A24TRP00.001-0.00110.8931.5021.5020.0000.0000.0000.000
22A25LEU0-0.004-0.00210.4042.0972.0970.0000.0000.0000.000
23A26GLN00.007-0.0039.0222.8902.8900.0000.0000.0000.000
24A27ASP-1-0.880-0.9359.52326.79026.7900.0000.0000.0000.000
25A28GLU-1-0.851-0.9119.20126.13126.1310.0000.0000.0000.000
26A29TYR0-0.051-0.0584.2102.0292.245-0.001-0.015-0.2000.000
27A30ASN0-0.075-0.0174.1929.5299.7110.000-0.015-0.1660.000
28A31CYS0-0.073-0.0215.4124.9375.052-0.001-0.001-0.1130.000
29A32GLU-1-0.770-0.8677.11218.93318.9330.0000.0000.0000.000
30A33VAL0-0.008-0.01110.4520.4430.4430.0000.0000.0000.000
31A34VAL0-0.014-0.00512.747-1.308-1.3080.0000.0000.0000.000
32A35THR0-0.013-0.00315.6030.0370.0370.0000.0000.0000.000
33A36PHE00.009-0.00318.706-0.529-0.5290.0000.0000.0000.000
34A37THR0-0.014-0.01921.3350.0740.0740.0000.0000.0000.000
35A38ALA0-0.015-0.01324.755-0.175-0.1750.0000.0000.0000.000
36A39ASP-1-0.786-0.88127.6009.3709.3700.0000.0000.0000.000
37A40ILE0-0.023-0.03329.934-0.095-0.0950.0000.0000.0000.000
38A41GLY00.036-0.01632.818-0.242-0.2420.0000.0000.0000.000
39A42GLN0-0.0360.00829.749-0.352-0.3520.0000.0000.0000.000
40A43GLY0-0.0180.00034.395-0.148-0.1480.0000.0000.0000.000
41A44GLU-1-0.941-0.97030.85410.45710.4570.0000.0000.0000.000
42A45GLU-1-0.934-0.97333.6279.1209.1200.0000.0000.0000.000
43A46LEU00.0260.00029.5700.3400.3400.0000.0000.0000.000
44A47GLU-1-0.792-0.87829.15411.08111.0810.0000.0000.0000.000
45A48PRO00.001-0.00829.2270.3520.3520.0000.0000.0000.000
46A49ALA00.0490.04125.5300.3390.3390.0000.0000.0000.000
47A50ARG10.8490.90024.789-10.951-10.9510.0000.0000.0000.000
48A51LYS10.8880.93224.869-10.000-10.0000.0000.0000.0000.000
49A52LYS10.8770.93924.070-12.540-12.5400.0000.0000.0000.000
50A53ALA00.0310.01120.8990.4930.4930.0000.0000.0000.000
51A54LEU0-0.010-0.00520.8730.6500.6500.0000.0000.0000.000
52A55SER0-0.119-0.05222.4020.2260.2260.0000.0000.0000.000
53A56LEU00.004-0.00519.4170.1370.1370.0000.0000.0000.000
54A57GLY0-0.004-0.00317.9981.1661.1660.0000.0000.0000.000
55A58ILE0-0.073-0.01316.0271.0651.0650.0000.0000.0000.000
56A59LYS10.8800.93314.789-22.004-22.0040.0000.0000.0000.000
57A60GLU-1-0.757-0.89819.16612.52012.5200.0000.0000.0000.000
58A61GLU-1-0.912-0.95519.03516.39616.3960.0000.0000.0000.000
59A62ASN0-0.068-0.04215.1650.1100.1100.0000.0000.0000.000
60A63ILE0-0.0120.01018.6360.3980.3980.0000.0000.0000.000
61A64PHE0-0.037-0.01419.106-0.840-0.8400.0000.0000.0000.000
62A65ILE00.0090.00223.088-0.003-0.0030.0000.0000.0000.000
63A66LYS10.9250.96124.155-12.817-12.8170.0000.0000.0000.000
64A67ASP-1-0.778-0.85728.4879.2639.2630.0000.0000.0000.000
65A68LEU0-0.026-0.01627.3350.0150.0150.0000.0000.0000.000
66A69ARG10.8560.90332.088-9.128-9.1280.0000.0000.0000.000
67A70ASP-1-0.797-0.89235.3937.9837.9830.0000.0000.0000.000
68A71GLU-1-0.813-0.89330.39910.38110.3810.0000.0000.0000.000
69A72PHE00.0130.01132.743-0.021-0.0210.0000.0000.0000.000
70A73VAL00.0250.00634.048-0.088-0.0880.0000.0000.0000.000
71A74LYS10.8110.89736.294-8.686-8.6860.0000.0000.0000.000
72A75ASP-1-0.834-0.90733.6768.6808.6800.0000.0000.0000.000
73A76TYR0-0.042-0.04128.9800.3250.3250.0000.0000.0000.000
74A77VAL0-0.0080.00334.520-0.159-0.1590.0000.0000.0000.000
75A78PHE0-0.013-0.02537.463-0.172-0.1720.0000.0000.0000.000
76A79PRO00.0150.00936.636-0.148-0.1480.0000.0000.0000.000
77A80MET00.0270.03236.549-0.054-0.0540.0000.0000.0000.000
78A81PHE0-0.002-0.02338.519-0.174-0.1740.0000.0000.0000.000
79A82ARG10.7820.87639.989-7.742-7.7420.0000.0000.0000.000
80A83ALA00.0000.00041.004-0.186-0.1860.0000.0000.0000.000
81A84ASN0-0.103-0.06542.957-0.089-0.0890.0000.0000.0000.000
82A85ALA0-0.015-0.01339.083-0.047-0.0470.0000.0000.0000.000
83A86ILE0-0.011-0.00441.1140.0240.0240.0000.0000.0000.000
84A87TYR0-0.040-0.04535.247-0.051-0.0510.0000.0000.0000.000
85A88GLU-1-0.816-0.91739.1177.7837.7830.0000.0000.0000.000
86A89GLY0-0.031-0.00542.030-0.120-0.1200.0000.0000.0000.000
87A90GLU-1-0.892-0.94443.1986.5566.5560.0000.0000.0000.000
88A91TYR00.0140.01334.8190.0970.0970.0000.0000.0000.000
89A92LEU00.0280.00339.9660.0560.0560.0000.0000.0000.000
90A93LEU0-0.033-0.02534.6040.1340.1340.0000.0000.0000.000
91A94GLY00.0650.03034.7770.1940.1940.0000.0000.0000.000
92A95THR0-0.036-0.02929.9260.0880.0880.0000.0000.0000.000
93A96SER0-0.031-0.03430.1360.3790.3790.0000.0000.0000.000
94A97ILE0-0.0080.00730.1480.2810.2810.0000.0000.0000.000
95A98ALA00.0180.01230.6180.1340.1340.0000.0000.0000.000
96A99ARG10.7430.85125.619-10.784-10.7840.0000.0000.0000.000
97A100PRO00.0070.01125.3110.5070.5070.0000.0000.0000.000
98A101LEU00.0360.03025.5070.3500.3500.0000.0000.0000.000
99A102ILE0-0.0120.00323.1510.3570.3570.0000.0000.0000.000
100A103ALA00.0210.00521.0850.5260.5260.0000.0000.0000.000
101A104LYS10.8630.94120.668-10.562-10.5620.0000.0000.0000.000
102A105THR0-0.024-0.02622.2020.2200.2200.0000.0000.0000.000
103A106GLN0-0.039-0.01516.813-0.521-0.5210.0000.0000.0000.000
104A107ALA00.0230.01217.5310.8970.8970.0000.0000.0000.000
105A108GLN00.003-0.00618.1550.3180.3180.0000.0000.0000.000
106A109ILE0-0.0080.00718.0830.0040.0040.0000.0000.0000.000
107A110ALA00.0220.01314.3090.4700.4700.0000.0000.0000.000
108A111LEU00.0110.01014.8390.6960.6960.0000.0000.0000.000
109A112GLN0-0.084-0.03816.8010.1180.1180.0000.0000.0000.000
110A113THR0-0.080-0.06315.4740.4140.4140.0000.0000.0000.000
111A114GLY0-0.0080.00513.3700.6880.6880.0000.0000.0000.000
112A115ALA0-0.080-0.02510.8251.8631.8630.0000.0000.0000.000
113A116ASP-1-0.765-0.8826.00138.75138.7510.0000.0000.0000.000
114A117ALA00.020-0.0018.0760.2100.2100.0000.0000.0000.000
115A118VAL0-0.0210.00210.120-1.213-1.2130.0000.0000.0000.000
116A119SER0-0.030-0.02812.5130.8860.8860.0000.0000.0000.000
117A120HIS0-0.008-0.01914.518-1.271-1.2710.0000.0000.0000.000
118A121GLY00.0550.01317.5890.5140.5140.0000.0000.0000.000
119A122ALA0-0.042-0.00620.068-0.707-0.7070.0000.0000.0000.000
120A123THR00.0360.00720.9410.5250.5250.0000.0000.0000.000
121A124GLY00.0800.03220.5970.1180.1180.0000.0000.0000.000
122A125LYS10.8930.93821.395-11.322-11.3220.0000.0000.0000.000
123A126GLY00.0730.05524.473-0.501-0.5010.0000.0000.0000.000
124A127ASN00.0570.00425.0600.3530.3530.0000.0000.0000.000
125A128ASP-1-0.788-0.89624.68111.45911.4590.0000.0000.0000.000
126A129GLN0-0.0090.01719.7410.8780.8780.0000.0000.0000.000
127A130VAL00.0310.01320.3620.4390.4390.0000.0000.0000.000
128A131ARG10.8200.90322.099-10.280-10.2800.0000.0000.0000.000
129A132PHE0-0.014-0.00819.650-0.060-0.0600.0000.0000.0000.000
130A133GLU-1-0.725-0.82516.44116.95616.9560.0000.0000.0000.000
131A134LEU00.0000.00918.4750.2420.2420.0000.0000.0000.000
132A135GLY00.0060.00221.080-0.104-0.1040.0000.0000.0000.000
133A136TYR0-0.035-0.04915.9900.1060.1060.0000.0000.0000.000
134A137LEU00.0120.01114.3230.1210.1210.0000.0000.0000.000
135A138ALA0-0.0370.00017.916-0.291-0.2910.0000.0000.0000.000
136A139PHE0-0.069-0.04220.304-0.394-0.3940.0000.0000.0000.000
137A140SER00.000-0.01615.3430.0190.0190.0000.0000.0000.000
138A141PRO0-0.0020.00315.2990.8100.8100.0000.0000.0000.000
139A142ASP-1-0.916-0.95211.91818.10218.1020.0000.0000.0000.000
140A143LEU0-0.087-0.02410.4801.6291.6290.0000.0000.0000.000
141A144LYS10.8880.9586.111-31.397-31.3970.0000.0000.0000.000
142A145ILE00.002-0.0158.877-0.489-0.4890.0000.0000.0000.000
143A146ILE0-0.032-0.0097.8280.5890.5890.0000.0000.0000.000
144A147ALA00.0310.03111.395-1.351-1.3510.0000.0000.0000.000
145A148PRO00.0490.02913.817-0.277-0.2770.0000.0000.0000.000
146A149TRP0-0.024-0.01614.692-0.413-0.4130.0000.0000.0000.000
147A150ARG10.7140.81014.989-17.591-17.5910.0000.0000.0000.000
148A151GLU-1-0.834-0.88810.16326.72226.7220.0000.0000.0000.000
149A152TRP00.0240.01814.1100.3970.3970.0000.0000.0000.000
150A153ASP-1-0.838-0.92115.08914.83814.8380.0000.0000.0000.000
151A154LEU0-0.048-0.01717.725-1.036-1.0360.0000.0000.0000.000
152A155ASN0-0.007-0.00919.221-0.431-0.4310.0000.0000.0000.000
153A156SER0-0.029-0.02022.502-0.499-0.4990.0000.0000.0000.000
154A157ARG11.0041.00324.646-11.115-11.1150.0000.0000.0000.000
155A158GLU-1-0.811-0.90526.83211.11411.1140.0000.0000.0000.000
156A159LYS10.8050.87620.727-14.600-14.6000.0000.0000.0000.000
157A160LEU00.0090.02521.4120.5620.5620.0000.0000.0000.000
158A161LEU0-0.024-0.02023.3770.2510.2510.0000.0000.0000.000
159A162ALA0-0.0040.00824.2690.0600.0600.0000.0000.0000.000
160A163TYR0-0.032-0.03914.380-0.275-0.2750.0000.0000.0000.000
161A164ALA00.004-0.00320.8970.3920.3920.0000.0000.0000.000
162A165GLN0-0.047-0.03922.651-0.257-0.2570.0000.0000.0000.000
163A166LYS10.8740.96316.540-18.854-18.8540.0000.0000.0000.000
164A167HIS0-0.046-0.01215.060-0.609-0.6090.0000.0000.0000.000
165A168GLY0-0.083-0.03120.010-0.374-0.3740.0000.0000.0000.000
166A177LYS10.9440.96532.975-9.429-9.4290.0000.0000.0000.000
167A178SER0-0.010-0.02137.918-0.159-0.1590.0000.0000.0000.000
168A179PRO0-0.0050.00436.7730.3360.3360.0000.0000.0000.000
169A180TYR0-0.022-0.03636.6890.1710.1710.0000.0000.0000.000
170A181SER0-0.038-0.01231.7800.3350.3350.0000.0000.0000.000
171A182MET0-0.026-0.01633.075-0.220-0.2200.0000.0000.0000.000
172A183ASP-1-0.791-0.85930.61210.60310.6030.0000.0000.0000.000
173A184ALA00.0410.02432.846-0.330-0.3300.0000.0000.0000.000
174A185ASN0-0.009-0.01832.9370.1180.1180.0000.0000.0000.000
175A186LEU00.0150.01535.104-0.215-0.2150.0000.0000.0000.000
176A187LEU0-0.069-0.01036.875-0.281-0.2810.0000.0000.0000.000
177A188HIS0-0.023-0.02033.992-0.339-0.3390.0000.0000.0000.000
178A189ILE00.0410.03137.1030.2280.2280.0000.0000.0000.000
179A190SER0-0.038-0.01434.612-0.290-0.2900.0000.0000.0000.000
180A191TYR00.007-0.03636.4790.1720.1720.0000.0000.0000.000
181A192GLU-1-0.727-0.84933.1799.2229.2220.0000.0000.0000.000
182A193GLY00.0450.02536.2450.1320.1320.0000.0000.0000.000
183A194LEU0-0.015-0.03436.913-0.211-0.2110.0000.0000.0000.000
184A195VAL00.0550.02339.7910.0090.0090.0000.0000.0000.000
185A196LEU0-0.035-0.00839.507-0.107-0.1070.0000.0000.0000.000
186A197GLU-1-0.946-0.97136.6068.7058.7050.0000.0000.0000.000
187A198ASP-1-0.855-0.92140.0626.8716.8710.0000.0000.0000.000
188A199PRO0-0.026-0.02542.112-0.085-0.0850.0000.0000.0000.000
189A200ALA0-0.068-0.02844.344-0.131-0.1310.0000.0000.0000.000
190A201HIS0-0.074-0.02846.185-0.243-0.2430.0000.0000.0000.000
191A202ALA00.0000.00146.8330.1090.1090.0000.0000.0000.000
192A203PRO00.0440.02845.1080.0510.0510.0000.0000.0000.000
193A204GLU-1-0.853-0.88444.2847.0267.0260.0000.0000.0000.000
194A205GLU-1-0.823-0.92346.9666.5366.5360.0000.0000.0000.000
195A206ASP-1-0.902-0.95445.8767.0547.0540.0000.0000.0000.000
196A207MET00.0050.02841.8280.2050.2050.0000.0000.0000.000
197A208TRP0-0.055-0.03442.8590.2540.2540.0000.0000.0000.000
198A209ARG10.8170.88941.160-7.563-7.5630.0000.0000.0000.000
199A210TRP0-0.046-0.00441.032-0.037-0.0370.0000.0000.0000.000
200A211SER0-0.047-0.05244.284-0.176-0.1760.0000.0000.0000.000
201A212LYS10.8830.93647.551-5.932-5.9320.0000.0000.0000.000
202A213SER00.030-0.00750.7410.0070.0070.0000.0000.0000.000
203A214PRO00.013-0.02152.101-0.083-0.0830.0000.0000.0000.000
204A215LYS10.9320.95955.128-5.791-5.7910.0000.0000.0000.000
205A216ASP-1-0.852-0.88154.2805.8295.8290.0000.0000.0000.000
206A217ALA0-0.0410.01154.923-0.009-0.0090.0000.0000.0000.000
207A218PRO00.0050.01256.441-0.097-0.0970.0000.0000.0000.000
208A219ASN0-0.041-0.01559.6070.0470.0470.0000.0000.0000.000
209A220GLU-1-0.891-0.94962.2485.0685.0680.0000.0000.0000.000
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