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: 46MNN

Calculation Name: 1AMF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: molybdate ion

Ligand 3-letter code: MOO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AMF

Chain ID: A

ChEMBL ID:

UniProt ID: P37329

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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2670658.203105
FMO2-HF: Nuclear repulsion 2585634.840677
FMO2-HF: Total energy -85023.362428
FMO2-MP2: Total energy -85277.025032


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:3:GLY)


Summations of interaction energy for fragment #1(A:3: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.
-13.189-10.810.507-1.01-1.875-0.009
Interaction energy analysis for fragmet #1(A:3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.924
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].
3A5ILE00.0220.0303.8520.8231.655-0.011-0.303-0.518-0.001
28A30VAL0-0.061-0.0342.389-8.003-7.1680.373-0.466-0.742-0.006
29A31ASP-1-0.812-0.8884.674-31.763-31.534-0.001-0.022-0.2060.000
206A208THR0-0.053-0.0222.867-6.824-6.3410.146-0.219-0.409-0.002
4A6THR0-0.0020.0076.5962.0692.0690.0000.0000.0000.000
5A7VAL00.0180.00410.0931.2621.2620.0000.0000.0000.000
6A8PHE00.0170.00313.1050.6470.6470.0000.0000.0000.000
7A9ALA00.0150.00216.5870.3460.3460.0000.0000.0000.000
8A10ALA00.0450.01619.1390.3600.3600.0000.0000.0000.000
9A11ALA00.0360.01922.738-0.227-0.2270.0000.0000.0000.000
10A12SER0-0.0090.02324.271-0.225-0.2250.0000.0000.0000.000
11A13LEU0-0.035-0.01420.3770.0900.0900.0000.0000.0000.000
12A14THR0-0.045-0.02620.940-0.666-0.6660.0000.0000.0000.000
13A15ASN00.0720.02920.278-0.592-0.5920.0000.0000.0000.000
14A16ALA00.0600.03520.686-0.440-0.4400.0000.0000.0000.000
15A17MET0-0.009-0.00314.156-0.643-0.6430.0000.0000.0000.000
16A18GLN00.0100.00615.799-0.881-0.8810.0000.0000.0000.000
17A19ASP-1-0.802-0.87316.440-16.104-16.1040.0000.0000.0000.000
18A20ILE00.000-0.00313.963-0.987-0.9870.0000.0000.0000.000
19A21ALA0-0.019-0.00511.912-1.518-1.5180.0000.0000.0000.000
20A22THR0-0.046-0.03311.781-2.152-2.1520.0000.0000.0000.000
21A23GLN00.0320.02113.800-0.806-0.8060.0000.0000.0000.000
22A24PHE00.0210.0106.578-0.942-0.9420.0000.0000.0000.000
23A25LYS10.8490.9166.99038.58238.5820.0000.0000.0000.000
24A26LYS10.8220.9059.80121.98221.9820.0000.0000.0000.000
25A27GLU-1-0.794-0.88112.349-20.876-20.8760.0000.0000.0000.000
26A28LYS10.8560.9287.67825.53725.5370.0000.0000.0000.000
27A29GLY00.0290.0346.661-5.064-5.0640.0000.0000.0000.000
30A32VAL0-0.006-0.0086.302-4.944-4.9440.0000.0000.0000.000
31A33VAL00.0010.0049.0212.8252.8250.0000.0000.0000.000
32A34SER0-0.008-0.00511.1870.0630.0630.0000.0000.0000.000
33A35SER0-0.026-0.00114.5170.8810.8810.0000.0000.0000.000
34A36PHE00.0130.00017.203-0.135-0.1350.0000.0000.0000.000
35A37ALA00.0610.03720.7120.3720.3720.0000.0000.0000.000
36A38SER00.0360.00723.870-0.099-0.0990.0000.0000.0000.000
37A39SER00.0330.00223.686-0.189-0.1890.0000.0000.0000.000
38A40SER0-0.0020.00924.619-0.378-0.3780.0000.0000.0000.000
39A41THR0-0.005-0.00724.1260.1680.1680.0000.0000.0000.000
40A42LEU0-0.0110.00219.215-0.173-0.1730.0000.0000.0000.000
41A43ALA00.0350.02021.133-0.428-0.4280.0000.0000.0000.000
42A44ARG10.9550.97623.15010.65510.6550.0000.0000.0000.000
43A45GLN0-0.019-0.00620.273-0.537-0.5370.0000.0000.0000.000
44A46ILE00.000-0.00117.454-0.364-0.3640.0000.0000.0000.000
45A47GLU-1-0.797-0.85919.887-11.334-11.3340.0000.0000.0000.000
46A48ALA0-0.047-0.02122.6620.1900.1900.0000.0000.0000.000
47A49GLY00.0230.02319.2350.0460.0460.0000.0000.0000.000
48A50ALA0-0.039-0.01717.310-0.796-0.7960.0000.0000.0000.000
49A51PRO0-0.021-0.01112.022-0.233-0.2330.0000.0000.0000.000
50A52ALA0-0.021-0.01411.571-2.241-2.2410.0000.0000.0000.000
51A53ASP-1-0.798-0.8958.172-33.398-33.3980.0000.0000.0000.000
52A54LEU0-0.023-0.01310.7560.7950.7950.0000.0000.0000.000
53A55PHE00.010-0.00113.6460.3270.3270.0000.0000.0000.000
54A56ILE0-0.007-0.00716.4760.1350.1350.0000.0000.0000.000
55A57SER00.0040.00719.7550.2230.2230.0000.0000.0000.000
56A58ALA00.019-0.00123.393-0.093-0.0930.0000.0000.0000.000
57A59ASP-1-0.797-0.89726.434-10.493-10.4930.0000.0000.0000.000
58A60GLN00.0260.00226.763-0.727-0.7270.0000.0000.0000.000
59A61LYS10.9651.00927.8219.5499.5490.0000.0000.0000.000
60A62TRP0-0.022-0.03125.8350.0900.0900.0000.0000.0000.000
61A63MET0-0.032-0.00120.131-0.440-0.4400.0000.0000.0000.000
62A64ASP-1-0.826-0.89324.795-10.888-10.8880.0000.0000.0000.000
63A65TYR0-0.076-0.06526.1310.1180.1180.0000.0000.0000.000
64A66ALA00.013-0.00721.952-0.012-0.0120.0000.0000.0000.000
65A67VAL0-0.027-0.01323.391-0.369-0.3690.0000.0000.0000.000
66A68ASP-1-0.900-0.94224.884-10.319-10.3190.0000.0000.0000.000
67A69LYS10.7680.87224.46610.88810.8880.0000.0000.0000.000
68A70LYS10.9160.95823.91010.82410.8240.0000.0000.0000.000
69A71ALA00.0570.03820.106-0.437-0.4370.0000.0000.0000.000
70A72ILE0-0.059-0.03618.549-0.956-0.9560.0000.0000.0000.000
71A73ASP-1-0.762-0.86416.994-16.380-16.3800.0000.0000.0000.000
72A74THR0-0.006-0.01218.935-0.183-0.1830.0000.0000.0000.000
73A75ALA00.0070.01620.5370.3880.3880.0000.0000.0000.000
74A76THR0-0.048-0.02716.022-0.395-0.3950.0000.0000.0000.000
75A77ARG10.8060.88219.20011.52511.5250.0000.0000.0000.000
76A78GLN00.0320.02321.4400.0770.0770.0000.0000.0000.000
77A79THR0-0.011-0.01022.612-0.400-0.4000.0000.0000.0000.000
78A80LEU0-0.0090.00719.4350.0040.0040.0000.0000.0000.000
79A81LEU00.0180.01122.1210.2280.2280.0000.0000.0000.000
80A82GLY00.007-0.00725.7920.2630.2630.0000.0000.0000.000
81A83ASN0-0.013-0.01628.6490.0700.0700.0000.0000.0000.000
82A84SER00.0420.03631.2980.1440.1440.0000.0000.0000.000
83A85LEU00.010-0.00334.054-0.269-0.2690.0000.0000.0000.000
84A86VAL0-0.003-0.00335.8100.2800.2800.0000.0000.0000.000
85A87VAL0-0.0040.00338.249-0.085-0.0850.0000.0000.0000.000
86A88VAL00.004-0.00536.5150.0460.0460.0000.0000.0000.000
87A89ALA00.0440.01839.8430.1250.1250.0000.0000.0000.000
88A90PRO00.0740.03240.838-0.159-0.1590.0000.0000.0000.000
89A91LYS10.8340.91437.5718.7518.7510.0000.0000.0000.000
90A92ALA00.004-0.00641.7560.1170.1170.0000.0000.0000.000
91A93SER00.0210.03044.9100.2500.2500.0000.0000.0000.000
92A94VAL00.0290.00946.864-0.031-0.0310.0000.0000.0000.000
93A95GLN0-0.041-0.01946.3600.1390.1390.0000.0000.0000.000
94A96LYS10.9290.95547.7346.0926.0920.0000.0000.0000.000
95A97ASP-1-0.851-0.92445.678-7.127-7.1270.0000.0000.0000.000
96A98PHE0-0.086-0.04245.6240.1890.1890.0000.0000.0000.000
97A99THR00.0180.01547.222-0.163-0.1630.0000.0000.0000.000
98A100ILE0-0.057-0.01843.6200.0810.0810.0000.0000.0000.000
99A101ASP-1-0.792-0.91147.493-6.317-6.3170.0000.0000.0000.000
100A102SER0-0.003-0.01249.960-0.058-0.0580.0000.0000.0000.000
101A103LYS10.8600.93652.0715.8795.8790.0000.0000.0000.000
102A104THR00.0500.03448.9240.0950.0950.0000.0000.0000.000
103A105ASN0-0.029-0.01852.145-0.071-0.0710.0000.0000.0000.000
104A106TRP00.1120.02544.187-0.018-0.0180.0000.0000.0000.000
105A107THR00.0060.00450.334-0.110-0.1100.0000.0000.0000.000
106A108SER0-0.018-0.01352.7500.0180.0180.0000.0000.0000.000
107A109LEU0-0.045-0.01248.8500.0140.0140.0000.0000.0000.000
108A110LEU0-0.0050.00745.689-0.083-0.0830.0000.0000.0000.000
109A111ASN0-0.040-0.01049.5280.0550.0550.0000.0000.0000.000
110A112GLY00.0080.00752.1910.0460.0460.0000.0000.0000.000
111A113GLY0-0.0040.00848.172-0.041-0.0410.0000.0000.0000.000
112A114ARG10.8390.89544.0387.0737.0730.0000.0000.0000.000
113A115LEU0-0.012-0.00641.408-0.056-0.0560.0000.0000.0000.000
114A116ALA00.0060.00837.845-0.059-0.0590.0000.0000.0000.000
115A117VAL0-0.023-0.01236.920-0.024-0.0240.0000.0000.0000.000
116A118GLY00.0590.02233.200-0.126-0.1260.0000.0000.0000.000
117A119ASP-1-0.780-0.91033.836-8.650-8.6500.0000.0000.0000.000
118A120PRO0-0.015-0.01434.585-0.210-0.2100.0000.0000.0000.000
119A121GLU-1-0.954-0.96036.434-7.961-7.9610.0000.0000.0000.000
120A122HIS0-0.079-0.04831.336-0.459-0.4590.0000.0000.0000.000
121A123VAL00.0010.01929.757-0.375-0.3750.0000.0000.0000.000
122A124PRO0-0.011-0.00527.7620.3030.3030.0000.0000.0000.000
123A125ALA00.0280.01331.1020.2770.2770.0000.0000.0000.000
124A126GLY00.0440.03032.9660.2900.2900.0000.0000.0000.000
125A127ILE0-0.030-0.01632.5600.3190.3190.0000.0000.0000.000
126A128TYR0-0.017-0.04030.2180.3430.3430.0000.0000.0000.000
127A129ALA00.0090.00736.5530.2540.2540.0000.0000.0000.000
128A130LYS10.9210.97738.8888.1138.1130.0000.0000.0000.000
129A131GLU-1-0.796-0.87938.178-8.176-8.1760.0000.0000.0000.000
130A132ALA00.0010.00540.6510.2120.2120.0000.0000.0000.000
131A133LEU0-0.020-0.02442.4330.2200.2200.0000.0000.0000.000
132A134GLN0-0.039-0.01343.9480.1120.1120.0000.0000.0000.000
133A135LYS10.8430.93344.6337.2217.2210.0000.0000.0000.000
134A136LEU0-0.041-0.02245.6360.1240.1240.0000.0000.0000.000
135A137GLY00.0030.00548.5220.1190.1190.0000.0000.0000.000
136A138ALA00.0010.00348.0820.0820.0820.0000.0000.0000.000
137A139TRP00.027-0.00142.011-0.076-0.0760.0000.0000.0000.000
138A140ASP-1-0.845-0.92747.403-6.433-6.4330.0000.0000.0000.000
139A141THR0-0.053-0.02650.2430.0930.0930.0000.0000.0000.000
140A142LEU0-0.015-0.01945.7340.0330.0330.0000.0000.0000.000
141A143SER0-0.0100.01745.516-0.061-0.0610.0000.0000.0000.000
142A144PRO00.0330.01645.889-0.121-0.1210.0000.0000.0000.000
143A145LYS10.8700.93447.2976.3196.3190.0000.0000.0000.000
144A146LEU00.0060.01641.389-0.110-0.1100.0000.0000.0000.000
145A147ALA00.0180.00940.5140.1320.1320.0000.0000.0000.000
146A148PRO00.0010.00737.258-0.158-0.1580.0000.0000.0000.000
147A149ALA00.0140.01633.5040.0130.0130.0000.0000.0000.000
148A150GLU-1-0.888-0.95029.385-10.088-10.0880.0000.0000.0000.000
149A151ASP-1-0.852-0.94626.822-12.028-12.0280.0000.0000.0000.000
150A152VAL00.001-0.00528.4430.3110.3110.0000.0000.0000.000
151A153ARG10.7870.88926.03712.32112.3210.0000.0000.0000.000
152A154GLY00.0360.02029.7820.1930.1930.0000.0000.0000.000
153A155ALA0-0.010-0.01031.8090.2970.2970.0000.0000.0000.000
154A156LEU00.008-0.00630.9150.2590.2590.0000.0000.0000.000
155A157ALA00.0260.01332.1900.2630.2630.0000.0000.0000.000
156A158LEU0-0.002-0.00134.2180.2210.2210.0000.0000.0000.000
157A159VAL0-0.0180.00837.2650.2680.2680.0000.0000.0000.000
158A160GLU-1-0.900-0.93633.056-9.790-9.7900.0000.0000.0000.000
159A161ARG10.8070.87334.2999.0719.0710.0000.0000.0000.000
160A162ASN0-0.060-0.02839.0650.2130.2130.0000.0000.0000.000
161A163GLU-1-0.826-0.87539.389-8.210-8.2100.0000.0000.0000.000
162A164ALA0-0.035-0.01240.8380.1310.1310.0000.0000.0000.000
163A165PRO0-0.025-0.01142.518-0.107-0.1070.0000.0000.0000.000
164A166LEU00.003-0.01042.754-0.011-0.0110.0000.0000.0000.000
165A167GLY00.0460.01638.898-0.013-0.0130.0000.0000.0000.000
166A168ILE0-0.061-0.01237.0290.0310.0310.0000.0000.0000.000
167A169VAL0-0.021-0.01033.181-0.211-0.2110.0000.0000.0000.000
168A170TYR00.012-0.00129.0220.2720.2720.0000.0000.0000.000
169A171GLY00.0320.01932.7650.0330.0330.0000.0000.0000.000
170A172SER00.0490.01927.6940.0870.0870.0000.0000.0000.000
171A173ASP-1-0.790-0.90628.920-11.382-11.3820.0000.0000.0000.000
172A174ALA0-0.009-0.00930.7020.0720.0720.0000.0000.0000.000
173A175VAL0-0.060-0.01729.6430.1220.1220.0000.0000.0000.000
174A176ALA0-0.029-0.01227.547-0.137-0.1370.0000.0000.0000.000
175A177SER0-0.066-0.03529.1900.0010.0010.0000.0000.0000.000
176A178LYS10.9510.96831.18210.36910.3690.0000.0000.0000.000
177A179GLY00.0090.00634.3100.3090.3090.0000.0000.0000.000
178A180VAL00.0260.02335.8030.2870.2870.0000.0000.0000.000
179A181LYS10.8250.91438.2017.1497.1490.0000.0000.0000.000
180A182VAL00.0220.00837.711-0.005-0.0050.0000.0000.0000.000
181A183VAL0-0.029-0.00740.1760.1500.1500.0000.0000.0000.000
182A184ALA00.0700.03942.3830.2050.2050.0000.0000.0000.000
183A185THR0-0.014-0.01439.296-0.324-0.3240.0000.0000.0000.000
184A186PHE00.008-0.00139.9610.2220.2220.0000.0000.0000.000
185A187PRO00.0540.03940.848-0.199-0.1990.0000.0000.0000.000
186A188GLU-1-0.853-0.94837.043-8.857-8.8570.0000.0000.0000.000
187A189ASP-1-0.848-0.92340.351-7.235-7.2350.0000.0000.0000.000
188A190SER0-0.092-0.06142.2950.0900.0900.0000.0000.0000.000
189A191HIS10.8230.91136.9738.5368.5360.0000.0000.0000.000
190A192LYS10.9200.93735.0638.4968.4960.0000.0000.0000.000
191A193LYS10.8920.97032.4949.6969.6960.0000.0000.0000.000
192A194VAL00.0140.01230.280-0.191-0.1910.0000.0000.0000.000
193A195GLU-1-0.865-0.92828.606-10.480-10.4800.0000.0000.0000.000
194A196TYR0-0.011-0.00723.5290.2060.2060.0000.0000.0000.000
195A197PRO0-0.0220.00623.430-0.257-0.2570.0000.0000.0000.000
196A198VAL00.006-0.00316.955-0.384-0.3840.0000.0000.0000.000
197A199ALA00.0130.00118.0990.6220.6220.0000.0000.0000.000
198A200VAL0-0.005-0.00412.485-1.099-1.0990.0000.0000.0000.000
199A201VAL0-0.017-0.00313.9311.2681.2680.0000.0000.0000.000
200A202GLU-1-0.886-0.95414.608-17.371-17.3710.0000.0000.0000.000
201A203GLY00.0190.01214.867-0.543-0.5430.0000.0000.0000.000
202A204HIS10.7710.8769.72223.12623.1260.0000.0000.0000.000
203A205ASN0-0.058-0.03410.145-3.863-3.8630.0000.0000.0000.000
204A206ASN00.0540.0286.589-3.167-3.1670.0000.0000.0000.000
205A207ALA00.0580.0108.639-0.599-0.5990.0000.0000.0000.000
207A209VAL00.0060.0046.1130.3700.3700.0000.0000.0000.000
208A210LYS10.8520.9188.17222.36722.3670.0000.0000.0000.000
209A211ALA00.0410.0168.0551.8991.8990.0000.0000.0000.000
210A212PHE0-0.001-0.0108.6741.6961.6960.0000.0000.0000.000
211A213TYR0-0.027-0.03110.4512.1232.1230.0000.0000.0000.000
212A214ASP-1-0.815-0.90713.241-18.592-18.5920.0000.0000.0000.000
213A215TYR0-0.079-0.05912.4141.0141.0140.0000.0000.0000.000
214A216LEU0-0.010-0.01214.3061.2661.2660.0000.0000.0000.000
215A217LYS10.8790.94816.40417.55817.5580.0000.0000.0000.000
216A218GLY00.0160.02817.5990.7070.7070.0000.0000.0000.000
217A219PRO0-0.006-0.01318.6690.3160.3160.0000.0000.0000.000
218A220GLN00.0370.01317.1890.4040.4040.0000.0000.0000.000
219A221ALA00.0350.02517.0380.2050.2050.0000.0000.0000.000
220A222ALA00.0250.01318.9490.6140.6140.0000.0000.0000.000
221A223GLU-1-0.916-0.94922.389-12.937-12.9370.0000.0000.0000.000
222A224ILE0-0.016-0.00118.3720.5060.5060.0000.0000.0000.000
223A225PHE00.023-0.00618.8510.3560.3560.0000.0000.0000.000
224A226LYS10.9730.98223.67011.42411.4240.0000.0000.0000.000
225A227ARG10.8100.91921.78314.35114.3510.0000.0000.0000.000
226A228TYR0-0.074-0.05922.4490.5240.5240.0000.0000.0000.000
227A229GLY00.0180.00427.0210.1290.1290.0000.0000.0000.000
228A230PHE0-0.048-0.02424.9580.1800.1800.0000.0000.0000.000
229A231THR0-0.071-0.04427.9150.1570.1570.0000.0000.0000.000
230A232ILE0-0.022-0.01824.357-0.192-0.1920.0000.0000.0000.000
231A233LYS0-0.055-0.01126.122-0.714-0.7140.0000.0000.0000.000