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: NL9YQ

Calculation Name: 1VIZ-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VIZ

Chain ID: A

ChEMBL ID:

UniProt ID: O34790

Base Structure: X-ray

Registration Date: 2025-10-05

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2822557.900339
FMO2-HF: Nuclear repulsion 2733150.492938
FMO2-HF: Total energy -89407.407401
FMO2-MP2: Total energy -89664.326462


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-380.615-376.1963.717-3.693-4.441-0.032
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.905
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].
3A2TYR00.010-0.0033.869-0.1711.512-0.005-0.773-0.905-0.004
4A3ASP-1-0.873-0.9262.179-54.775-53.4562.773-2.096-1.995-0.017
5A4VAL00.0430.0044.078-3.164-3.1060.001-0.013-0.0450.000
7A6GLU-1-1.003-1.0022.403-63.581-62.2710.949-0.809-1.450-0.011
8A7TRP0-0.086-0.0335.2495.7735.822-0.001-0.002-0.0460.000
6A5THR0-0.0100.0005.2013.6673.6670.0000.0000.0000.000
9A8LYS10.9410.9607.87727.60327.6030.0000.0000.0000.000
10A9HIS0-0.022-0.00911.5221.4361.4360.0000.0000.0000.000
11A10VAL00.0380.03511.758-1.664-1.6640.0000.0000.0000.000
12A11PHE00.0030.00714.2881.6861.6860.0000.0000.0000.000
13A12LYS10.7730.88917.21715.12615.1260.0000.0000.0000.000
14A13LEU0-0.016-0.01919.5350.8690.8690.0000.0000.0000.000
15A14ASP-1-0.766-0.87622.133-11.464-11.4640.0000.0000.0000.000
16A15PRO0-0.005-0.00423.7980.2130.2130.0000.0000.0000.000
17A16ASN0-0.068-0.02826.0520.4830.4830.0000.0000.0000.000
18A17LYS10.7220.85927.62911.83611.8360.0000.0000.0000.000
19A18ASP-1-0.918-0.96228.406-10.782-10.7820.0000.0000.0000.000
20A19LEU00.001-0.00524.370-0.057-0.0570.0000.0000.0000.000
21A20PRO00.0000.00927.529-0.164-0.1640.0000.0000.0000.000
22A21ASP-1-0.807-0.89826.318-12.241-12.2410.0000.0000.0000.000
23A22GLU-1-0.926-0.95225.199-11.466-11.4660.0000.0000.0000.000
24A23GLN00.0130.00225.003-0.384-0.3840.0000.0000.0000.000
25A24LEU00.001-0.00621.048-0.551-0.5510.0000.0000.0000.000
26A25GLU-1-0.905-0.94820.838-14.359-14.3590.0000.0000.0000.000
27A26ILE00.004-0.00420.079-0.877-0.8770.0000.0000.0000.000
28A27LEU0-0.019-0.01619.389-0.583-0.5830.0000.0000.0000.000
29A28CYS0-0.092-0.02416.421-1.278-1.2780.0000.0000.0000.000
30A29GLU-1-0.946-0.97715.293-18.258-18.2580.0000.0000.0000.000
31A30SER0-0.076-0.04916.426-0.679-0.6790.0000.0000.0000.000
32A31GLY00.0350.02412.7430.2590.2590.0000.0000.0000.000
33A32THR0-0.063-0.03811.994-1.953-1.9530.0000.0000.0000.000
34A33ASP-1-0.762-0.8668.216-35.834-35.8340.0000.0000.0000.000
35A34ALA0-0.009-0.0109.265-2.396-2.3960.0000.0000.0000.000
36A35VAL0-0.0070.00111.7331.7651.7650.0000.0000.0000.000
37A36ILE0-0.0040.00314.465-0.115-0.1150.0000.0000.0000.000
38A37ILE0-0.015-0.00516.6821.0751.0750.0000.0000.0000.000
39A38GLY00.0770.01919.770-0.170-0.1700.0000.0000.0000.000
40A39GLY00.0220.01021.9840.4420.4420.0000.0000.0000.000
41A40SER0-0.010-0.02025.2470.1440.1440.0000.0000.0000.000
42A41ASP-1-0.839-0.91127.187-9.851-9.8510.0000.0000.0000.000
43A42GLY0-0.0140.00028.4540.3560.3560.0000.0000.0000.000
44A43VAL0-0.008-0.00222.8400.1370.1370.0000.0000.0000.000
45A44THR0-0.005-0.01326.2210.3260.3260.0000.0000.0000.000
46A45GLU-1-0.877-0.94126.737-11.071-11.0710.0000.0000.0000.000
47A46ASP-1-0.779-0.86227.061-10.176-10.1760.0000.0000.0000.000
48A47ASN0-0.019-0.02227.454-0.417-0.4170.0000.0000.0000.000
49A48VAL00.0320.02122.012-0.405-0.4050.0000.0000.0000.000
50A49LEU00.0110.01723.146-0.570-0.5700.0000.0000.0000.000
51A50ARG10.7690.85724.0939.9799.9790.0000.0000.0000.000
52A51MET00.0020.02821.945-0.134-0.1340.0000.0000.0000.000
53A52MET00.0320.02418.526-0.524-0.5240.0000.0000.0000.000
54A53SER0-0.102-0.06219.908-0.407-0.4070.0000.0000.0000.000
55A54LYS10.8370.90622.40311.87211.8720.0000.0000.0000.000
56A55VAL00.0760.03116.137-0.043-0.0430.0000.0000.0000.000
57A56ARG10.9280.95015.14418.27218.2720.0000.0000.0000.000
58A57ARG10.7800.89917.69213.61313.6130.0000.0000.0000.000
59A58PHE0-0.023-0.00816.2000.2280.2280.0000.0000.0000.000
60A59LEU0-0.036-0.03111.191-0.213-0.2130.0000.0000.0000.000
61A60VAL0-0.0070.02210.647-2.629-2.6290.0000.0000.0000.000
62A61PRO0-0.028-0.0137.8181.6531.6530.0000.0000.0000.000
63A62CYS0-0.0380.00010.5621.7661.7660.0000.0000.0000.000
64A63VAL00.0290.00311.517-0.265-0.2650.0000.0000.0000.000
65A64LEU0-0.0280.00014.1761.1591.1590.0000.0000.0000.000
66A65GLU-1-0.795-0.89717.093-15.993-15.9930.0000.0000.0000.000
67A66VAL0-0.041-0.03119.1840.8420.8420.0000.0000.0000.000
68A67SER0-0.012-0.01321.6730.1090.1090.0000.0000.0000.000
69A68ALA00.0190.00025.0910.5370.5370.0000.0000.0000.000
70A69ILE00.0190.00825.393-0.410-0.4100.0000.0000.0000.000
71A70GLU-1-0.936-0.98726.678-10.406-10.4060.0000.0000.0000.000
72A71ALA0-0.029-0.00925.7130.1660.1660.0000.0000.0000.000
73A72ILE0-0.0250.00321.135-0.496-0.4960.0000.0000.0000.000
74A73VAL0-0.0020.01321.3770.4500.4500.0000.0000.0000.000
75A74PRO00.0020.00520.015-0.633-0.6330.0000.0000.0000.000
76A75GLY0-0.020-0.00117.5850.3180.3180.0000.0000.0000.000
77A76PHE00.006-0.01514.946-0.120-0.1200.0000.0000.0000.000
78A77ASP-1-0.842-0.9149.813-25.169-25.1690.0000.0000.0000.000
79A78LEU0-0.029-0.0127.792-1.453-1.4530.0000.0000.0000.000
80A79TYR0-0.052-0.04211.9421.2531.2530.0000.0000.0000.000
81A80PHE00.0120.01411.075-0.514-0.5140.0000.0000.0000.000
82A81ILE00.0230.00015.9951.0651.0650.0000.0000.0000.000
83A82PRO00.0140.01219.363-0.077-0.0770.0000.0000.0000.000
84A83SER0-0.059-0.02221.1740.4810.4810.0000.0000.0000.000
85A84VAL0-0.035-0.03323.122-0.237-0.2370.0000.0000.0000.000
86A85LEU0-0.017-0.01022.4920.5900.5900.0000.0000.0000.000
87A86ASN0-0.014-0.01726.428-0.010-0.0100.0000.0000.0000.000
88A87SER0-0.009-0.01429.1720.4220.4220.0000.0000.0000.000
89A88LYS10.8600.92630.9058.8948.8940.0000.0000.0000.000
90A89ASN0-0.033-0.02332.8940.1420.1420.0000.0000.0000.000
91A90ALA00.0550.01431.210-0.304-0.3040.0000.0000.0000.000
92A91ASP-1-0.854-0.93529.859-9.835-9.8350.0000.0000.0000.000
93A92TRP0-0.0100.00026.295-0.480-0.4800.0000.0000.0000.000
94A93ILE0-0.0400.01526.357-0.429-0.4290.0000.0000.0000.000
95A94VAL00.0230.00225.187-0.466-0.4660.0000.0000.0000.000
96A95GLY0-0.025-0.00726.532-0.070-0.0700.0000.0000.0000.000
97A96MET00.0000.02024.1030.2340.2340.0000.0000.0000.000
98A97HIS00.0710.02020.5480.5870.5870.0000.0000.0000.000
99A98GLN0-0.060-0.03123.8960.0820.0820.0000.0000.0000.000
100A99LYS10.8860.94427.09810.09610.0960.0000.0000.0000.000
101A100ALA00.0390.02022.7380.1100.1100.0000.0000.0000.000
102A101MET0-0.030-0.01419.7720.0370.0370.0000.0000.0000.000
103A102LYS10.7720.88625.0119.5049.5040.0000.0000.0000.000
104A103GLU-1-0.880-0.94228.244-9.438-9.4380.0000.0000.0000.000
105A104TYR0-0.034-0.01024.3280.2850.2850.0000.0000.0000.000
106A105GLY00.0790.04823.711-0.546-0.5460.0000.0000.0000.000
107A106GLU-1-0.947-0.97222.832-11.469-11.4690.0000.0000.0000.000
108A107LEU0-0.014-0.00820.455-0.381-0.3810.0000.0000.0000.000
109A108MET0-0.007-0.01919.144-0.874-0.8740.0000.0000.0000.000
110A109SER0-0.057-0.02818.317-0.515-0.5150.0000.0000.0000.000
111A110MET0-0.131-0.06317.385-0.141-0.1410.0000.0000.0000.000
112A111GLU-1-0.835-0.91215.157-17.819-17.8190.0000.0000.0000.000
113A112GLU-1-0.935-0.9609.078-24.892-24.8920.0000.0000.0000.000
114A113ILE0-0.032-0.02312.560-0.060-0.0600.0000.0000.0000.000
115A114VAL0-0.003-0.00110.907-0.378-0.3780.0000.0000.0000.000
116A115ALA0-0.029-0.01414.0580.9980.9980.0000.0000.0000.000
117A116GLU-1-0.831-0.93816.167-18.283-18.2830.0000.0000.0000.000
118A117GLY00.0450.02317.4721.0941.0940.0000.0000.0000.000
119A118TYR0-0.057-0.04319.457-0.412-0.4120.0000.0000.0000.000
120A119CYS0-0.050-0.01522.0010.7510.7510.0000.0000.0000.000
121A120ILE0-0.008-0.00524.733-0.229-0.2290.0000.0000.0000.000
122A121ALA00.0270.01227.0910.4170.4170.0000.0000.0000.000
123A122ASN0-0.018-0.01128.9430.4930.4930.0000.0000.0000.000
124A123PRO00.0230.02131.124-0.137-0.1370.0000.0000.0000.000
125A124ASP-1-0.913-0.94834.243-8.399-8.3990.0000.0000.0000.000
126A125CYS0-0.095-0.04830.152-0.289-0.2890.0000.0000.0000.000
127A126LYS10.8750.91431.6899.3579.3570.0000.0000.0000.000
128A127ALA00.0580.03027.5720.1240.1240.0000.0000.0000.000
129A128ALA00.0540.03529.674-0.049-0.0490.0000.0000.0000.000
130A129ALA0-0.020-0.00831.5580.1690.1690.0000.0000.0000.000
131A130LEU0-0.047-0.03231.1920.1610.1610.0000.0000.0000.000
132A131THR00.005-0.00627.719-0.014-0.0140.0000.0000.0000.000
133A132GLU-1-0.891-0.92731.105-8.680-8.6800.0000.0000.0000.000
134A133ALA0-0.0020.01530.4070.1290.1290.0000.0000.0000.000
135A134ASP-1-1.012-1.00932.252-8.439-8.4390.0000.0000.0000.000
136A135ALA00.0320.00631.551-0.242-0.2420.0000.0000.0000.000
137A136ASP-1-0.966-0.97232.503-8.618-8.6180.0000.0000.0000.000
138A137LEU0-0.0260.00029.5560.1220.1220.0000.0000.0000.000
139A138ASN0-0.078-0.04233.3700.1070.1070.0000.0000.0000.000
140A139MET0-0.017-0.00929.435-0.368-0.3680.0000.0000.0000.000
141A140ASP-1-0.892-0.95130.043-9.796-9.7960.0000.0000.0000.000
142A141ASP-1-0.822-0.89930.749-9.380-9.3800.0000.0000.0000.000
143A142ILE00.0230.01225.849-0.275-0.2750.0000.0000.0000.000
144A143VAL00.0020.00226.116-0.402-0.4020.0000.0000.0000.000
145A144ALA0-0.037-0.01426.479-0.286-0.2860.0000.0000.0000.000
146A145TYR00.015-0.01025.784-0.209-0.2090.0000.0000.0000.000
147A146ALA00.0420.03422.370-0.401-0.4010.0000.0000.0000.000
148A147ARG10.9670.96822.29311.04411.0440.0000.0000.0000.000
149A148VAL0-0.058-0.01824.400-0.001-0.0010.0000.0000.0000.000
150A149SER00.0450.00318.743-0.016-0.0160.0000.0000.0000.000
151A150GLU-1-0.727-0.84018.159-17.404-17.4040.0000.0000.0000.000
152A151LEU0-0.098-0.03920.470-0.064-0.0640.0000.0000.0000.000
153A152LEU0-0.071-0.04421.7460.2270.2270.0000.0000.0000.000
154A153GLN0-0.081-0.03316.910-0.911-0.9110.0000.0000.0000.000
155A154LEU00.0020.02116.240-0.737-0.7370.0000.0000.0000.000
156A155PRO00.0410.02411.485-0.115-0.1150.0000.0000.0000.000
157A156ILE0-0.0200.01012.107-1.397-1.3970.0000.0000.0000.000
158A157PHE0-0.0010.00114.6271.4131.4130.0000.0000.0000.000
159A158TYR00.0310.00817.357-0.537-0.5370.0000.0000.0000.000
160A159LEU0-0.031-0.00818.9620.8650.8650.0000.0000.0000.000
161A160GLU-1-0.812-0.91021.917-13.802-13.8020.0000.0000.0000.000
162A161TYR00.0480.01824.0420.5250.5250.0000.0000.0000.000
163A162SER00.004-0.00425.4410.7000.7000.0000.0000.0000.000
164A163GLY0-0.027-0.00926.572-0.225-0.2250.0000.0000.0000.000
165A164VAL0-0.049-0.02729.1970.1470.1470.0000.0000.0000.000
166A165LEU0-0.025-0.00726.626-0.326-0.3260.0000.0000.0000.000
167A166GLY00.0610.02326.8300.4170.4170.0000.0000.0000.000
168A167ASP-1-0.895-0.94328.054-10.490-10.4900.0000.0000.0000.000
169A168ILE00.0370.02324.219-0.310-0.3100.0000.0000.0000.000
170A169GLU-1-0.813-0.89325.954-11.486-11.4860.0000.0000.0000.000
171A170ALA00.027-0.00127.349-0.163-0.1630.0000.0000.0000.000
172A171VAL00.0060.02221.241-0.279-0.2790.0000.0000.0000.000
173A172LYS10.8400.91722.53610.94810.9480.0000.0000.0000.000
174A173LYS10.8400.89823.88510.22610.2260.0000.0000.0000.000
175A174THR0-0.032-0.02721.0150.1420.1420.0000.0000.0000.000
176A175LYS10.8710.92115.06119.35719.3570.0000.0000.0000.000
177A176ALA0-0.086-0.04220.354-0.309-0.3090.0000.0000.0000.000
178A177VAL0-0.134-0.06322.3740.4580.4580.0000.0000.0000.000
179A178LEU0-0.0270.00417.7080.2630.2630.0000.0000.0000.000
180A179GLU-1-0.992-0.99416.386-15.397-15.3970.0000.0000.0000.000
181A180THR0-0.066-0.06013.409-1.666-1.6660.0000.0000.0000.000
182A181SER0-0.059-0.03313.462-0.765-0.7650.0000.0000.0000.000
183A182THR0-0.011-0.00110.364-0.142-0.1420.0000.0000.0000.000
184A183LEU0-0.050-0.02513.1630.9480.9480.0000.0000.0000.000
185A184PHE00.0280.01010.922-0.581-0.5810.0000.0000.0000.000
186A185TYR0-0.009-0.01116.0591.4381.4380.0000.0000.0000.000
187A186GLY00.0560.03019.152-0.556-0.5560.0000.0000.0000.000
188A187GLY00.0640.01621.4110.5700.5700.0000.0000.0000.000
189A188GLY0-0.046-0.00524.898-0.118-0.1180.0000.0000.0000.000
190A189ILE0-0.0100.00121.5220.3400.3400.0000.0000.0000.000
191A190LYS10.8390.88624.54311.02011.0200.0000.0000.0000.000
192A191ASP-1-0.862-0.88725.190-11.537-11.5370.0000.0000.0000.000
193A192ALA00.0520.01722.569-0.401-0.4010.0000.0000.0000.000
194A193GLU-1-0.886-0.94622.841-12.946-12.9460.0000.0000.0000.000
195A194THR0-0.021-0.04124.847-0.261-0.2610.0000.0000.0000.000
196A195ALA00.0180.00019.846-0.255-0.2550.0000.0000.0000.000
197A196LYS10.9400.96920.26014.29114.2910.0000.0000.0000.000
198A197GLN0-0.022-0.01321.243-0.178-0.1780.0000.0000.0000.000
199A198TYR0-0.027-0.05221.4480.0510.0510.0000.0000.0000.000
200A199ALA00.0110.01216.872-0.338-0.3380.0000.0000.0000.000
201A200GLU-1-0.975-0.95917.789-13.760-13.7600.0000.0000.0000.000
202A201HIS0-0.078-0.06019.763-0.301-0.3010.0000.0000.0000.000
203A202ALA0-0.013-0.00917.274-0.144-0.1440.0000.0000.0000.000
204A203ASP-1-0.817-0.87212.111-21.547-21.5470.0000.0000.0000.000
205A204VAL0-0.018-0.01110.761-1.534-1.5340.0000.0000.0000.000
206A205ILE0-0.043-0.01213.5751.7071.7070.0000.0000.0000.000
207A206VAL00.0210.00215.766-0.958-0.9580.0000.0000.0000.000
208A207VAL0-0.050-0.02017.9681.2641.2640.0000.0000.0000.000
209A208GLY00.0620.03420.363-0.253-0.2530.0000.0000.0000.000
210A209ASN00.006-0.03322.752-0.064-0.0640.0000.0000.0000.000
211A210ALA00.0330.03924.6690.3420.3420.0000.0000.0000.000
212A211VAL00.0230.01622.2990.3460.3460.0000.0000.0000.000
213A212TYR0-0.012-0.01625.0170.0490.0490.0000.0000.0000.000
214A213GLU-1-0.942-0.93828.924-10.472-10.4720.0000.0000.0000.000
215A214ASP-1-0.880-0.96629.158-10.319-10.3190.0000.0000.0000.000
216A215PHE00.0460.04123.594-0.326-0.3260.0000.0000.0000.000
217A216ASP-1-0.832-0.92525.479-11.975-11.9750.0000.0000.0000.000
218A217ARG10.7230.87126.11910.59610.5960.0000.0000.0000.000
219A218ALA00.0660.02923.916-0.378-0.3780.0000.0000.0000.000
220A219LEU00.0380.03020.142-0.791-0.7910.0000.0000.0000.000
221A220LYS10.8320.90020.36611.39111.3910.0000.0000.0000.000
222A221THR0-0.033-0.02619.893-0.570-0.5700.0000.0000.0000.000
223A222VAL00.0410.03214.352-0.360-0.3600.0000.0000.0000.000
224A223ALA00.0650.03116.065-0.676-0.6760.0000.0000.0000.000
225A224ALA0-0.088-0.03617.785-0.072-0.0720.0000.0000.0000.000
226A225VAL0-0.047-0.02114.3290.4270.4270.0000.0000.0000.000
227A226LYS10.7790.8639.02530.76730.7670.0000.0000.0000.000
228A227GLY0-0.068-0.01713.474-0.863-0.8630.0000.0000.0000.000
229A228GLU-2-1.933-1.96316.193-33.488-33.4880.0000.0000.0000.000