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: Y1Q62

Calculation Name: 2PQ7-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | (4s)-2-methyl-2,4-pentanediol | fe (iii) ion | chloride ion

Ligand 3-letter code: PO4 | MPD | FE | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PQ7

Chain ID: A

ChEMBL ID:

UniProt ID: Q1EM40

Base Structure: X-ray

Registration Date: 2025-10-04

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1894720.627662
FMO2-HF: Nuclear repulsion 1823849.561398
FMO2-HF: Total energy -70871.066263
FMO2-MP2: Total energy -71077.815132


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-170.792-160.92721.813-11.854-19.826-0.081
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.793 / q_NPA : 0.907
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].
3A3LEU00.0870.0142.827-3.048-0.3700.290-1.411-1.558-0.010
5A5GLU-1-0.804-0.8992.232-86.301-82.0146.810-5.165-5.932-0.062
6A6LEU0-0.041-0.0282.2984.2496.0493.644-1.266-4.178-0.008
7A7MET0-0.035-0.0374.3814.4734.5760.0080.040-0.1520.000
9A9ARG10.9010.9492.61030.29528.1998.152-2.091-3.9650.018
10A10ILE0-0.033-0.0064.5391.0761.163-0.001-0.006-0.0800.000
42A42GLU-1-0.876-0.9523.473-73.601-72.8080.002-0.531-0.264-0.004
45A45SER0-0.0100.0002.609-1.0500.2960.811-0.794-1.363-0.009
46A46GLU-1-0.844-0.8884.385-47.654-47.3980.000-0.019-0.2370.000
49A49SER0-0.031-0.0203.1811.3122.0350.109-0.330-0.501-0.003
55A55LEU00.0280.0082.223-0.188-0.3951.989-0.275-1.507-0.003
59A59ILE00.0050.0024.395-0.0470.048-0.001-0.006-0.0890.000
4A4THR0-0.0130.0065.5133.4343.4340.0000.0000.0000.000
8A8GLU-1-0.934-0.9576.585-27.485-27.4850.0000.0000.0000.000
11A11PRO00.0370.0238.460-0.115-0.1150.0000.0000.0000.000
12A12HIS00.0390.00812.330-0.833-0.8330.0000.0000.0000.000
13A13LEU00.0310.0287.3470.3530.3530.0000.0000.0000.000
14A14ARG10.9710.97211.56317.46517.4650.0000.0000.0000.000
15A15GLU-1-0.928-0.96112.885-14.352-14.3520.0000.0000.0000.000
16A16ILE00.0220.01112.9570.3950.3950.0000.0000.0000.000
17A17LEU00.001-0.0149.2060.2170.2170.0000.0000.0000.000
18A18ASN0-0.086-0.02413.864-0.009-0.0090.0000.0000.0000.000
19A19ILE00.0840.03717.2160.4340.4340.0000.0000.0000.000
20A20VAL0-0.009-0.00615.1370.5480.5480.0000.0000.0000.000
21A21ARG10.8690.91515.23018.39118.3910.0000.0000.0000.000
22A22GLU-1-0.929-0.96218.828-13.336-13.3360.0000.0000.0000.000
23A23ALA0-0.023-0.01221.1170.5620.5620.0000.0000.0000.000
24A24PHE00.003-0.02018.5100.1430.1430.0000.0000.0000.000
25A25LYS10.9240.97322.04611.80311.8030.0000.0000.0000.000
26A26ASP-1-0.933-0.96524.302-10.431-10.4310.0000.0000.0000.000
27A27TYR0-0.040-0.01523.1170.2150.2150.0000.0000.0000.000
28A28ASP-1-0.925-0.96623.435-13.717-13.7170.0000.0000.0000.000
29A29ASP-1-0.793-0.88524.515-12.080-12.0800.0000.0000.0000.000
30A30PRO00.0330.01222.156-0.698-0.6980.0000.0000.0000.000
31A31ALA0-0.067-0.03221.582-0.643-0.6430.0000.0000.0000.000
32A32HIS0-0.150-0.09921.057-0.562-0.5620.0000.0000.0000.000
33A33ASP-1-0.738-0.81918.373-17.390-17.3900.0000.0000.0000.000
34A34ILE00.0280.00215.684-0.917-0.9170.0000.0000.0000.000
35A35SER0-0.069-0.05614.363-1.903-1.9030.0000.0000.0000.000
36A36HIS10.8350.91113.58316.30616.3060.0000.0000.0000.000
37A37THR0-0.036-0.01313.743-1.306-1.3060.0000.0000.0000.000
38A38PHE0-0.009-0.01110.319-1.660-1.6600.0000.0000.0000.000
39A39ARG10.8400.8899.19817.78617.7860.0000.0000.0000.000
40A40VAL0-0.038-0.0019.716-1.802-1.8020.0000.0000.0000.000
41A41MET0-0.0130.0016.659-2.069-2.0690.0000.0000.0000.000
43A43ASN0-0.065-0.0336.036-3.978-3.9780.0000.0000.0000.000
44A44ALA00.0270.0008.3850.7070.7070.0000.0000.0000.000
47A47ILE00.012-0.0146.3093.8253.8250.0000.0000.0000.000
48A48ALA0-0.017-0.0065.9922.0222.0220.0000.0000.0000.000
50A50ARG10.7970.8895.57632.89332.8930.0000.0000.0000.000
51A51GLU-1-0.800-0.9058.856-18.107-18.1070.0000.0000.0000.000
52A52LYS10.8940.9649.48924.97424.9740.0000.0000.0000.000
53A53CYS0-0.027-0.0069.2761.9871.9870.0000.0000.0000.000
54A54ASP-1-0.803-0.9158.244-21.168-21.1680.0000.0000.0000.000
56A56GLN0-0.025-0.0106.196-0.033-0.0330.0000.0000.0000.000
57A57LYS10.8570.9318.29816.61816.6180.0000.0000.0000.000
58A58ALA0-0.016-0.0107.9150.3380.3380.0000.0000.0000.000
60A60ILE00.0280.0198.2990.6910.6910.0000.0000.0000.000
61A61ALA00.002-0.00411.6551.1241.1240.0000.0000.0000.000
62A62ALA0-0.017-0.01210.0380.9580.9580.0000.0000.0000.000
63A63LEU0-0.020-0.00210.5140.6520.6520.0000.0000.0000.000
64A64LEU00.0300.00613.1511.1081.1080.0000.0000.0000.000
65A65HIS10.7610.86615.13720.07220.0720.0000.0000.0000.000
66A66ASP-1-0.730-0.86517.623-15.397-15.3970.0000.0000.0000.000
67A67ILE0-0.0240.00018.4760.4340.4340.0000.0000.0000.000
68A68LYS10.9100.96720.41512.12512.1250.0000.0000.0000.000
69A69ARG10.9040.94922.10213.31213.3120.0000.0000.0000.000
70A70PRO00.0470.02823.2460.5050.5050.0000.0000.0000.000
71A71HIS00.0000.00626.4350.2690.2690.0000.0000.0000.000
72A72GLU-1-0.785-0.85827.607-11.086-11.0860.0000.0000.0000.000
73A73ALA0-0.023-0.01228.3640.4170.4170.0000.0000.0000.000
74A74LEU0-0.0080.00630.2090.3460.3460.0000.0000.0000.000
75A75THR0-0.068-0.05431.6830.3670.3670.0000.0000.0000.000
76A76GLY00.0030.01132.8890.2740.2740.0000.0000.0000.000
77A77VAL0-0.082-0.04130.1610.0380.0380.0000.0000.0000.000
78A78ASP-1-0.757-0.90427.860-11.597-11.5970.0000.0000.0000.000
79A79HIS0-0.052-0.04922.145-0.672-0.6720.0000.0000.0000.000
80A80ALA0-0.038-0.04622.022-0.572-0.5720.0000.0000.0000.000
81A81GLU-1-0.832-0.85823.907-10.731-10.7310.0000.0000.0000.000
82A82SER00.0550.02425.996-0.223-0.2230.0000.0000.0000.000
83A83GLY00.0300.00822.179-0.142-0.1420.0000.0000.0000.000
84A84ALA0-0.057-0.02921.548-0.475-0.4750.0000.0000.0000.000
85A85GLU-1-0.968-0.97522.730-10.348-10.3480.0000.0000.0000.000
86A86TYR00.000-0.00520.4440.1880.1880.0000.0000.0000.000
87A87ALA0-0.016-0.00918.787-0.196-0.1960.0000.0000.0000.000
88A88SER0-0.025-0.04020.458-0.011-0.0110.0000.0000.0000.000
89A89GLY0-0.0090.00922.9090.2850.2850.0000.0000.0000.000
90A90LEU00.0000.00118.6750.0830.0830.0000.0000.0000.000
91A91LEU0-0.0010.00515.945-0.096-0.0960.0000.0000.0000.000
92A92PRO00.0220.00219.348-0.163-0.1630.0000.0000.0000.000
93A93THR0-0.075-0.03822.0840.1640.1640.0000.0000.0000.000
94A94MET0-0.0140.00317.459-0.316-0.3160.0000.0000.0000.000
95A95GLY00.0010.00618.513-0.419-0.4190.0000.0000.0000.000
96A96PHE0-0.042-0.01612.861-0.208-0.2080.0000.0000.0000.000
97A97ASP-1-0.824-0.91018.033-12.744-12.7440.0000.0000.0000.000
98A98ILE00.0570.00519.784-0.334-0.3340.0000.0000.0000.000
99A99SER0-0.015-0.00219.7600.1400.1400.0000.0000.0000.000
100A100PHE0-0.016-0.01911.704-0.301-0.3010.0000.0000.0000.000
101A101VAL00.0240.01616.877-0.543-0.5430.0000.0000.0000.000
102A102ALA00.0300.03219.016-0.072-0.0720.0000.0000.0000.000
103A103GLU-1-0.845-0.90515.620-16.007-16.0070.0000.0000.0000.000
104A104VAL00.0190.01013.888-0.284-0.2840.0000.0000.0000.000
105A105SER00.0260.00416.575-0.103-0.1030.0000.0000.0000.000
106A106LYS10.8840.93320.13612.52412.5240.0000.0000.0000.000
107A107ALA0-0.050-0.02016.3440.1510.1510.0000.0000.0000.000
108A108ILE00.0030.00416.923-0.061-0.0610.0000.0000.0000.000
109A109ARG10.9000.93819.40511.34511.3450.0000.0000.0000.000
110A110SER0-0.061-0.00721.5700.7470.7470.0000.0000.0000.000
111A111HIS10.7940.89218.97014.70614.7060.0000.0000.0000.000
112A112ARG10.9410.95520.51414.11914.1190.0000.0000.0000.000
113A113TYR0-0.089-0.03722.5930.2720.2720.0000.0000.0000.000
114A114SER0-0.022-0.00125.0020.4340.4340.0000.0000.0000.000
115A115GLY00.0510.03227.1640.3750.3750.0000.0000.0000.000
116A116GLY0-0.010-0.00526.6860.2800.2800.0000.0000.0000.000
117A117LEU00.0080.00925.807-0.383-0.3830.0000.0000.0000.000
118A118THR00.010-0.00325.166-0.213-0.2130.0000.0000.0000.000
119A119PRO0-0.0010.00519.7230.1400.1400.0000.0000.0000.000
120A120THR00.0360.02321.816-0.015-0.0150.0000.0000.0000.000
121A121SER0-0.041-0.01517.5520.0830.0830.0000.0000.0000.000
122A122LEU00.0510.02014.132-0.122-0.1220.0000.0000.0000.000
123A123THR00.019-0.01512.570-0.999-0.9990.0000.0000.0000.000
124A124GLY00.0250.00314.022-0.617-0.6170.0000.0000.0000.000
125A125LYS10.8320.93816.69013.55013.5500.0000.0000.0000.000
126A126ILE00.0290.01010.000-0.187-0.1870.0000.0000.0000.000
127A127LEU0-0.0080.01413.049-0.988-0.9880.0000.0000.0000.000
128A128GLN0-0.009-0.00714.138-0.163-0.1630.0000.0000.0000.000
129A129ASP-1-0.735-0.85214.689-17.422-17.4220.0000.0000.0000.000
130A130ALA00.005-0.00311.478-0.075-0.0750.0000.0000.0000.000
131A131ASP-1-0.776-0.91313.235-17.952-17.9520.0000.0000.0000.000
132A132ARG10.8370.90815.94715.51315.5130.0000.0000.0000.000
133A133LEU00.0070.00612.4370.4300.4300.0000.0000.0000.000
134A134ASP-1-0.779-0.83914.300-20.756-20.7560.0000.0000.0000.000
135A135ALA0-0.0150.00815.5690.6890.6890.0000.0000.0000.000
136A136ILE0-0.025-0.00217.1620.8170.8170.0000.0000.0000.000
137A137GLY00.0740.03016.609-1.282-1.2820.0000.0000.0000.000
138A138ALA00.0180.00516.1400.4980.4980.0000.0000.0000.000
139A139VAL00.0090.00113.7580.5710.5710.0000.0000.0000.000
140A140ALA0-0.0070.01217.0450.6310.6310.0000.0000.0000.000
141A141ILE00.0170.00719.5170.6790.6790.0000.0000.0000.000
142A142ALA00.002-0.00419.6200.6020.6020.0000.0000.0000.000
143A143ARG10.8680.93617.11817.25517.2550.0000.0000.0000.000
144A144VAL0-0.028-0.00822.4180.4980.4980.0000.0000.0000.000
145A145PHE0-0.021-0.01425.0860.4730.4730.0000.0000.0000.000
146A146SER0-0.088-0.04723.9900.2020.2020.0000.0000.0000.000
147A147TYR-1-0.980-0.96526.427-10.400-10.4000.0000.0000.0000.000
148A186PRO10.8320.89421.12513.95113.9510.0000.0000.0000.000
149A187GLU-1-0.741-0.87521.409-13.195-13.1950.0000.0000.0000.000
150A188THR0-0.0300.00523.670-0.257-0.2570.0000.0000.0000.000
151A189PHE0-0.0210.00517.238-0.145-0.1450.0000.0000.0000.000
152A190TRP0-0.026-0.03317.9840.8040.8040.0000.0000.0000.000
153A191THR0-0.053-0.04913.8040.0010.0010.0000.0000.0000.000
154A192GLU-1-0.790-0.89616.103-16.123-16.1230.0000.0000.0000.000
155A193THR0-0.098-0.05510.288-0.394-0.3940.0000.0000.0000.000
156A194ALA00.0410.01713.726-0.496-0.4960.0000.0000.0000.000
157A195ARG10.8460.93215.13715.21215.2120.0000.0000.0000.000
158A196LYS10.8420.90815.44818.86518.8650.0000.0000.0000.000
159A197MET0-0.0120.0039.316-0.092-0.0920.0000.0000.0000.000
160A198ALA00.001-0.00614.5690.2430.2430.0000.0000.0000.000
161A199GLU-1-0.885-0.94117.653-13.400-13.4000.0000.0000.0000.000
162A200ASP-1-0.931-0.95314.771-20.201-20.2010.0000.0000.0000.000
163A201ARG10.8720.91810.60625.51625.5160.0000.0000.0000.000
164A202TYR0-0.040-0.01117.7340.6580.6580.0000.0000.0000.000
165A203SER00.020-0.02121.3640.7980.7980.0000.0000.0000.000
166A204PHE0-0.0020.00919.0280.3630.3630.0000.0000.0000.000
167A205VAL0-0.013-0.01620.7250.3750.3750.0000.0000.0000.000
168A206VAL0-0.030-0.00823.0410.6000.6000.0000.0000.0000.000
169A207GLU-1-0.827-0.89223.976-12.591-12.5910.0000.0000.0000.000
170A208PHE00.011-0.00123.2780.3510.3510.0000.0000.0000.000
171A209VAL0-0.005-0.00525.5470.4270.4270.0000.0000.0000.000
172A210GLN0-0.038-0.02428.6050.3290.3290.0000.0000.0000.000
173A211ARG10.8240.90025.96712.24712.2470.0000.0000.0000.000
174A212PHE00.0300.01629.1490.3190.3190.0000.0000.0000.000
175A213LEU0-0.040-0.02830.8950.3240.3240.0000.0000.0000.000
176A214ALA0-0.036-0.02033.2050.2910.2910.0000.0000.0000.000
177A215GLU-1-0.988-1.00029.973-10.585-10.5850.0000.0000.0000.000
178A216TRP0-0.117-0.03734.4860.0700.0700.0000.0000.0000.000
179A217GLY-1-0.951-0.96836.564-7.856-7.8560.0000.0000.0000.000