FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N65ZQ

Calculation Name: 1VKW-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VKW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1S2

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2793792.92207
FMO2-HF: Nuclear repulsion 2705337.257672
FMO2-HF: Total energy -88455.664397
FMO2-MP2: Total energy -88715.500669


3D Structure Molmil
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:-10:GLY)


Summations of interaction energy for fragment #1(A:-10:GLY)
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.
26.70527.712-0.013-0.378-0.615-0.002
Interaction energy analysis for fragmet #1(A:-10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.915
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].
3A-8ASP-1-0.787-0.8723.842-29.937-28.930-0.013-0.378-0.615-0.002
4A-7LYS10.9190.9526.97121.93021.9300.0000.0000.0000.000
5A-6ILE00.0060.00510.232-0.801-0.8010.0000.0000.0000.000
6A-5HIS00.0360.01412.089-0.027-0.0270.0000.0000.0000.000
7A-4HIS0-0.107-0.05410.3092.2872.2870.0000.0000.0000.000
8A-3HIS00.0070.00315.110-0.058-0.0580.0000.0000.0000.000
9A-2HIS0-0.001-0.00415.6870.3790.3790.0000.0000.0000.000
10A-1HIS0-0.019-0.00720.7300.0870.0870.0000.0000.0000.000
11A0HIS00.0000.00524.460-0.046-0.0460.0000.0000.0000.000
12A1MET0-0.0460.00726.1000.5370.5370.0000.0000.0000.000
13A2ASN00.0490.01628.8600.1540.1540.0000.0000.0000.000
14A3ILE00.0430.01331.929-0.029-0.0290.0000.0000.0000.000
15A4PHE00.0660.01134.2400.1230.1230.0000.0000.0000.000
16A5GLU-1-0.805-0.89631.654-9.898-9.8980.0000.0000.0000.000
17A6ALA00.0220.01730.717-0.114-0.1140.0000.0000.0000.000
18A7ILE0-0.014-0.01331.9000.0150.0150.0000.0000.0000.000
19A8GLU-1-0.951-0.96135.217-8.337-8.3370.0000.0000.0000.000
20A9ASN0-0.048-0.04530.2660.0650.0650.0000.0000.0000.000
21A10ARG10.8830.97731.5638.5768.5760.0000.0000.0000.000
22A11HIS10.8370.91431.7199.6499.6490.0000.0000.0000.000
23A12SER00.0130.00132.527-0.224-0.2240.0000.0000.0000.000
24A13VAL0-0.039-0.01728.9930.1210.1210.0000.0000.0000.000
25A14ARG10.9720.97331.7369.2459.2450.0000.0000.0000.000
26A15ASP-1-0.863-0.90530.524-10.197-10.1970.0000.0000.0000.000
27A16PHE0-0.003-0.00125.578-0.093-0.0930.0000.0000.0000.000
28A17LEU0-0.024-0.01121.815-0.018-0.0180.0000.0000.0000.000
29A18GLU-1-0.874-0.95020.369-13.685-13.6850.0000.0000.0000.000
30A19ARG10.8600.92616.70514.74014.7400.0000.0000.0000.000
31A20LYS10.9730.99013.83518.01518.0150.0000.0000.0000.000
32A21MET0-0.0150.00915.9430.8440.8440.0000.0000.0000.000
33A22PRO0-0.0020.01813.467-0.008-0.0080.0000.0000.0000.000
34A23GLU-1-0.707-0.86115.602-14.617-14.6170.0000.0000.0000.000
35A24ARG10.8700.93813.97519.56619.5660.0000.0000.0000.000
36A25VAL0-0.054-0.04716.3260.4120.4120.0000.0000.0000.000
37A26LYS10.8550.92518.98714.66614.6660.0000.0000.0000.000
38A27ASP-1-0.834-0.92617.568-16.685-16.6850.0000.0000.0000.000
39A28ASP-1-0.861-0.92618.981-16.030-16.0300.0000.0000.0000.000
40A29ILE0-0.060-0.02921.5000.6750.6750.0000.0000.0000.000
41A30GLU-1-0.961-0.98224.209-12.092-12.0920.0000.0000.0000.000
42A31ASN0-0.061-0.02723.7430.1960.1960.0000.0000.0000.000
43A32LEU0-0.030-0.00425.7270.2160.2160.0000.0000.0000.000
44A33LEU0-0.016-0.00827.9140.3010.3010.0000.0000.0000.000
45A34VAL0-0.053-0.01831.3090.1610.1610.0000.0000.0000.000
46A35LYS10.8550.92333.6187.8997.8990.0000.0000.0000.000
47A36PHE0-0.012-0.02137.374-0.091-0.0910.0000.0000.0000.000
48A37ILE0-0.034-0.02139.8840.0880.0880.0000.0000.0000.000
49A38THR0-0.019-0.00743.6050.1900.1900.0000.0000.0000.000
50A39LYS10.9250.95041.1287.6967.6960.0000.0000.0000.000
51A40LYS10.9841.01232.4639.5819.5810.0000.0000.0000.000
52A41LEU0-0.037-0.02536.6820.1630.1630.0000.0000.0000.000
53A42ASP-1-0.832-0.91333.836-9.671-9.6710.0000.0000.0000.000
54A43TRP0-0.057-0.04531.184-0.046-0.0460.0000.0000.0000.000
55A44LYS10.8190.91829.4329.4999.4990.0000.0000.0000.000
56A45ILE00.0520.01523.9200.1740.1740.0000.0000.0000.000
57A46ASN0-0.0070.01125.966-0.619-0.6190.0000.0000.0000.000
58A47LEU00.016-0.00719.3590.2480.2480.0000.0000.0000.000
59A48SER0-0.034-0.01821.910-0.422-0.4220.0000.0000.0000.000
60A49SER0-0.047-0.02924.1260.3320.3320.0000.0000.0000.000
61A50PHE00.0150.03424.100-0.320-0.3200.0000.0000.0000.000
62A51PRO0-0.048-0.04025.9990.4350.4350.0000.0000.0000.000
63A52SER00.0910.04622.5420.1500.1500.0000.0000.0000.000
64A53TYR0-0.067-0.03825.6920.4010.4010.0000.0000.0000.000
65A54ILE00.0250.02826.479-0.200-0.2000.0000.0000.0000.000
66A55TYR0-0.019-0.01429.9420.4560.4560.0000.0000.0000.000
67A56ALA00.0800.04032.944-0.218-0.2180.0000.0000.0000.000
68A57LYS10.8210.88835.7048.0118.0110.0000.0000.0000.000
69A58ALA0-0.006-0.01339.065-0.021-0.0210.0000.0000.0000.000
70A59GLU-1-0.879-0.92642.067-6.726-6.7260.0000.0000.0000.000
71A60LYS10.8310.90543.3137.2317.2310.0000.0000.0000.000
72A61HIS00.0170.02047.9810.2420.2420.0000.0000.0000.000
73A62PHE00.0150.00048.130-0.156-0.1560.0000.0000.0000.000
74A63ASP-1-0.723-0.83147.705-6.492-6.4920.0000.0000.0000.000
75A64GLU-1-0.791-0.90844.244-6.922-6.9220.0000.0000.0000.000
76A65LEU0-0.030-0.01443.038-0.269-0.2690.0000.0000.0000.000
77A66VAL0-0.0090.01043.168-0.165-0.1650.0000.0000.0000.000
78A67GLU-1-0.704-0.83340.554-7.910-7.9100.0000.0000.0000.000
79A68TYR0-0.023-0.03236.322-0.291-0.2910.0000.0000.0000.000
80A69GLY0-0.018-0.01938.185-0.252-0.2520.0000.0000.0000.000
81A70PHE0-0.017-0.00238.492-0.209-0.2090.0000.0000.0000.000
82A71GLN0-0.030-0.00935.476-0.422-0.4220.0000.0000.0000.000
83A72GLY00.0400.01834.062-0.303-0.3030.0000.0000.0000.000
84A73GLU-1-0.785-0.89433.419-9.100-9.1000.0000.0000.0000.000
85A74GLN0-0.017-0.02133.183-0.287-0.2870.0000.0000.0000.000
86A75ILE00.0300.02528.342-0.348-0.3480.0000.0000.0000.000
87A76VAL0-0.049-0.01529.027-0.405-0.4050.0000.0000.0000.000
88A77LEU0-0.018-0.00229.920-0.239-0.2390.0000.0000.0000.000
89A78PHE00.0410.02723.346-0.154-0.1540.0000.0000.0000.000
90A79LEU0-0.004-0.01024.373-0.482-0.4820.0000.0000.0000.000
91A80THR0-0.070-0.04025.214-0.314-0.3140.0000.0000.0000.000
92A81ALA00.012-0.00526.331-0.185-0.1850.0000.0000.0000.000
93A82GLN0-0.051-0.01020.277-0.107-0.1070.0000.0000.0000.000
94A83GLY0-0.020-0.00321.297-0.710-0.7100.0000.0000.0000.000
95A84PHE0-0.078-0.05319.297-0.112-0.1120.0000.0000.0000.000
96A85GLY00.0000.00124.5990.4730.4730.0000.0000.0000.000
97A86THR00.0490.00727.498-0.098-0.0980.0000.0000.0000.000
98A87CYS0-0.068-0.03730.1950.4250.4250.0000.0000.0000.000
99A88TRP00.0220.02133.466-0.116-0.1160.0000.0000.0000.000
100A89MET0-0.035-0.02933.9210.2130.2130.0000.0000.0000.000
101A90ALA00.0270.02137.207-0.079-0.0790.0000.0000.0000.000
102A91ARG10.9270.95833.4389.0789.0780.0000.0000.0000.000
103A92SER00.0530.01436.205-0.001-0.0010.0000.0000.0000.000
104A93PRO0-0.0170.00633.8640.1400.1400.0000.0000.0000.000
105A94HIS00.0360.01937.1030.1970.1970.0000.0000.0000.000
106A95PRO00.0670.03739.066-0.058-0.0580.0000.0000.0000.000
107A96ASP-1-0.793-0.88841.374-7.277-7.2770.0000.0000.0000.000
108A97VAL0-0.086-0.04136.513-0.030-0.0300.0000.0000.0000.000
109A98PRO0-0.057-0.01539.4920.0880.0880.0000.0000.0000.000
110A99TYR00.0230.00137.7960.1390.1390.0000.0000.0000.000
111A100ILE0-0.0390.00832.666-0.114-0.1140.0000.0000.0000.000
112A101ILE00.0020.01230.5240.1800.1800.0000.0000.0000.000
113A102VAL0-0.017-0.00929.589-0.336-0.3360.0000.0000.0000.000
114A103PHE00.001-0.01922.6240.2100.2100.0000.0000.0000.000
115A104GLY00.0700.03823.344-0.296-0.2960.0000.0000.0000.000
116A105TYR00.0500.02917.839-0.109-0.1090.0000.0000.0000.000
117A106PRO00.0210.00223.0870.1880.1880.0000.0000.0000.000
118A107ARG10.8540.92925.40910.02010.0200.0000.0000.0000.000
119A108THR00.0180.01627.0800.0480.0480.0000.0000.0000.000
120A109ARG10.8890.91723.41811.76811.7680.0000.0000.0000.000
121A110ASN00.0020.02130.191-0.082-0.0820.0000.0000.0000.000
122A111PHE00.0390.00530.081-0.060-0.0600.0000.0000.0000.000
123A112THR0-0.0060.00136.1850.2060.2060.0000.0000.0000.000
124A113ARG10.8150.88236.5558.2268.2260.0000.0000.0000.000
125A114LYS10.9781.00141.3736.8566.8560.0000.0000.0000.000
126A115ARG10.7960.88040.8937.2947.2940.0000.0000.0000.000
127A116ARG10.8920.95146.7116.3306.3300.0000.0000.0000.000
128A117PRO00.0650.02249.530-0.118-0.1180.0000.0000.0000.000
129A118ILE00.0610.04348.6940.0330.0330.0000.0000.0000.000
130A119THR00.0760.02251.149-0.033-0.0330.0000.0000.0000.000
131A120SER0-0.094-0.04752.7080.0750.0750.0000.0000.0000.000
132A121PHE0-0.078-0.04648.799-0.019-0.0190.0000.0000.0000.000
133A122LEU0-0.040-0.00952.578-0.024-0.0240.0000.0000.0000.000
134A123GLU-1-0.802-0.90154.564-5.437-5.4370.0000.0000.0000.000
135A124ASN0-0.039-0.01056.474-0.016-0.0160.0000.0000.0000.000
136A125ASP-1-0.825-0.89557.738-5.251-5.2510.0000.0000.0000.000
137A126LEU0-0.057-0.04952.227-0.085-0.0850.0000.0000.0000.000
138A127GLU-1-0.911-0.97055.566-5.487-5.4870.0000.0000.0000.000
139A128GLU-1-0.906-0.94458.135-5.284-5.2840.0000.0000.0000.000
140A129LEU0-0.085-0.04251.598-0.053-0.0530.0000.0000.0000.000
141A130PRO00.0200.02052.111-0.018-0.0180.0000.0000.0000.000
142A131PRO00.0370.00849.505-0.094-0.0940.0000.0000.0000.000
143A132GLU-1-0.895-0.95446.844-6.571-6.5710.0000.0000.0000.000
144A133ILE0-0.003-0.00946.801-0.164-0.1640.0000.0000.0000.000
145A134VAL00.0160.02048.551-0.068-0.0680.0000.0000.0000.000
146A135LYS10.9440.99740.1557.6257.6250.0000.0000.0000.000
147A136ILE0-0.0030.00043.853-0.168-0.1680.0000.0000.0000.000
148A137VAL00.0090.02244.539-0.122-0.1220.0000.0000.0000.000
149A138GLU-1-0.902-0.95944.368-6.987-6.9870.0000.0000.0000.000
150A139MET0-0.036-0.02439.651-0.254-0.2540.0000.0000.0000.000
151A140THR0-0.015-0.01440.797-0.246-0.2460.0000.0000.0000.000
152A141ILE00.0070.01342.986-0.082-0.0820.0000.0000.0000.000
153A142LEU0-0.0020.00839.227-0.073-0.0730.0000.0000.0000.000
154A143ALA00.0260.02938.996-0.311-0.3110.0000.0000.0000.000
155A144PRO0-0.054-0.01636.7770.1630.1630.0000.0000.0000.000
156A145SER00.0670.02539.7290.1860.1860.0000.0000.0000.000
157A146ALA0-0.003-0.00442.200-0.077-0.0770.0000.0000.0000.000
158A147LEU0-0.029-0.03043.0810.1530.1530.0000.0000.0000.000
159A148ASN0-0.036-0.00643.0380.0010.0010.0000.0000.0000.000
160A149ARG10.8920.94544.3626.9016.9010.0000.0000.0000.000
161A150GLN00.0100.00945.6210.1910.1910.0000.0000.0000.000
162A151PRO0-0.034-0.00146.6060.1310.1310.0000.0000.0000.000
163A152TRP0-0.019-0.00943.4230.0480.0480.0000.0000.0000.000
164A153LYS10.9270.96750.0885.5585.5580.0000.0000.0000.000
165A154ILE00.006-0.00348.379-0.085-0.0850.0000.0000.0000.000
166A155LYS10.8960.95452.4705.5935.5930.0000.0000.0000.000
167A156TYR00.0110.00752.936-0.089-0.0890.0000.0000.0000.000
168A157THR0-0.014-0.02154.6650.1170.1170.0000.0000.0000.000
169A158GLY00.0420.03156.0620.0980.0980.0000.0000.0000.000
170A159GLY0-0.004-0.00354.589-0.093-0.0930.0000.0000.0000.000
171A160GLU-1-0.803-0.87451.990-6.068-6.0680.0000.0000.0000.000
172A161LEU0-0.008-0.00147.5100.0770.0770.0000.0000.0000.000
173A162CYS0-0.078-0.02250.354-0.040-0.0400.0000.0000.0000.000
174A163ILE00.012-0.01046.385-0.011-0.0110.0000.0000.0000.000
175A164SER00.0290.00450.525-0.020-0.0200.0000.0000.0000.000
176A165SER0-0.078-0.08049.485-0.097-0.0970.0000.0000.0000.000
177A166GLU-1-0.820-0.90251.490-5.801-5.8010.0000.0000.0000.000
178A167ARG10.8300.91047.5716.2086.2080.0000.0000.0000.000
179A168PRO00.0780.05046.803-0.133-0.1330.0000.0000.0000.000
180A169VAL0-0.0120.00440.976-0.109-0.1090.0000.0000.0000.000
181A170ASP-1-0.699-0.86942.532-7.299-7.2990.0000.0000.0000.000
182A171LEU0-0.0160.02144.130-0.084-0.0840.0000.0000.0000.000
183A172GLY00.0250.01942.664-0.040-0.0400.0000.0000.0000.000
184A173ILE0-0.028-0.01438.686-0.141-0.1410.0000.0000.0000.000
185A174ALA00.0140.01740.277-0.156-0.1560.0000.0000.0000.000
186A175LEU00.0440.01142.755-0.050-0.0500.0000.0000.0000.000
187A176SER0-0.031-0.01737.986-0.098-0.0980.0000.0000.0000.000
188A177HIS10.7780.86137.0368.1418.1410.0000.0000.0000.000
189A178ALA00.0580.05139.999-0.048-0.0480.0000.0000.0000.000
190A179TYR0-0.010-0.03937.817-0.122-0.1220.0000.0000.0000.000
191A180LEU0-0.015-0.01535.061-0.054-0.0540.0000.0000.0000.000
192A181THR0-0.028-0.03838.627-0.029-0.0290.0000.0000.0000.000
193A182ALA00.0350.02440.3610.0420.0420.0000.0000.0000.000
194A183ARG10.9070.95234.4488.7888.7880.0000.0000.0000.000
195A184GLU-1-0.904-0.94136.807-8.660-8.6600.0000.0000.0000.000
196A185ILE0-0.059-0.03039.284-0.012-0.0120.0000.0000.0000.000
197A186PHE00.0330.00342.6380.0720.0720.0000.0000.0000.000
198A187LYS10.7800.89737.8608.3468.3460.0000.0000.0000.000
199A188ARG10.8410.90741.9976.7736.7730.0000.0000.0000.000
200A189GLU-1-0.746-0.85340.310-8.163-8.1630.0000.0000.0000.000
201A190PRO0-0.035-0.01042.1680.1540.1540.0000.0000.0000.000
202A191VAL0-0.0060.00144.472-0.118-0.1180.0000.0000.0000.000
203A192ILE0-0.021-0.00542.8690.0700.0700.0000.0000.0000.000
204A193GLN00.0270.01447.3720.1130.1130.0000.0000.0000.000
205A194LYS10.8420.92850.6326.1316.1310.0000.0000.0000.000
206A195ARG10.7350.80652.1165.9795.9790.0000.0000.0000.000
207A196GLY00.0370.02355.6030.0130.0130.0000.0000.0000.000
208A197GLU-1-0.937-0.97255.926-5.481-5.4810.0000.0000.0000.000
209A198ASP-1-0.820-0.90953.249-5.925-5.9250.0000.0000.0000.000
210A199THR0-0.019-0.01752.423-0.112-0.1120.0000.0000.0000.000
211A200TYR0-0.075-0.06248.281-0.033-0.0330.0000.0000.0000.000
212A202LEU0-0.020-0.00744.697-0.112-0.1120.0000.0000.0000.000
213A203ILE00.0480.01048.7880.0770.0770.0000.0000.0000.000
214A204LEU0-0.023-0.01247.437-0.169-0.1690.0000.0000.0000.000
215A205ASN0-0.005-0.01246.971-0.283-0.2830.0000.0000.0000.000
216A206PRO-1-0.838-0.86447.282-6.490-6.4900.0000.0000.0000.000