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: RMY78

Calculation Name: 3PCC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: p-hydroxybenzoic acid | beta-mercaptoethanol | fe (iii) ion

Ligand 3-letter code: PHB | BME | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PCC

Chain ID: A

ChEMBL ID:

UniProt ID: P00436

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2190352.570771
FMO2-HF: Nuclear repulsion 2113094.423436
FMO2-HF: Total energy -77258.147335
FMO2-MP2: Total energy -77486.878606


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:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-189.294-181.9360.873-3.851-4.379-0.039
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.903
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].
3A3GLU-1-0.888-0.9392.665-82.866-75.5570.874-3.844-4.339-0.039
4A4LEU0-0.003-0.0094.9054.5454.594-0.001-0.007-0.0400.000
5A5LEU0-0.028-0.0158.400-0.080-0.0800.0000.0000.0000.000
6A6PRO0-0.018-0.01511.1410.2560.2560.0000.0000.0000.000
7A7GLU-1-0.905-0.93612.581-16.412-16.4120.0000.0000.0000.000
8A8THR0-0.048-0.03415.419-0.260-0.2600.0000.0000.0000.000
9A9PRO0-0.025-0.01217.4610.3010.3010.0000.0000.0000.000
10A10SER00.0220.00719.4070.7530.7530.0000.0000.0000.000
11A11GLN0-0.023-0.01722.153-0.028-0.0280.0000.0000.0000.000
12A12THR0-0.014-0.00425.4420.3040.3040.0000.0000.0000.000
13A13ALA00.0230.01528.6160.1040.1040.0000.0000.0000.000
14A14GLY0-0.016-0.00631.2220.2430.2430.0000.0000.0000.000
15A15PRO00.000-0.01734.0000.0460.0460.0000.0000.0000.000
16A16TYR0-0.009-0.01436.9810.1850.1850.0000.0000.0000.000
17A17VAL00.0500.04633.7650.0850.0850.0000.0000.0000.000
18A18HIS00.0590.01436.108-0.041-0.0410.0000.0000.0000.000
19A19ILE0-0.032-0.01938.8770.1090.1090.0000.0000.0000.000
20A20GLY0-0.0190.00336.8830.0880.0880.0000.0000.0000.000
21A21LEU0-0.054-0.03832.501-0.009-0.0090.0000.0000.0000.000
22A22ALA00.0060.00637.0570.0030.0030.0000.0000.0000.000
23A23LEU0-0.0240.00040.3870.1190.1190.0000.0000.0000.000
24A24GLU-1-0.870-0.93643.150-6.637-6.6370.0000.0000.0000.000
25A25ALA0-0.0060.00242.7110.1200.1200.0000.0000.0000.000
26A26ALA0-0.059-0.03242.5660.0140.0140.0000.0000.0000.000
27A27GLY0-0.025-0.00144.5290.0720.0720.0000.0000.0000.000
28A28ASN0-0.056-0.02643.7860.2200.2200.0000.0000.0000.000
29A29PRO0-0.031-0.01647.3580.0150.0150.0000.0000.0000.000
30A30THR00.0100.00144.959-0.110-0.1100.0000.0000.0000.000
31A31ARG10.7750.85438.7287.9207.9200.0000.0000.0000.000
32A32ASP-1-0.915-0.95945.520-6.544-6.5440.0000.0000.0000.000
33A33GLN0-0.058-0.03042.808-0.089-0.0890.0000.0000.0000.000
34A34GLU-1-0.747-0.84241.215-7.714-7.7140.0000.0000.0000.000
35A35ILE0-0.0140.00635.5630.0510.0510.0000.0000.0000.000
36A36TRP00.017-0.00438.853-0.208-0.2080.0000.0000.0000.000
37A37ASN00.0070.00140.169-0.024-0.0240.0000.0000.0000.000
38A38ARG10.9080.95742.0076.6576.6570.0000.0000.0000.000
39A39LEU00.0280.03337.545-0.035-0.0350.0000.0000.0000.000
40A40ALA0-0.034-0.00841.649-0.007-0.0070.0000.0000.0000.000
41A41LYS10.8100.90644.9526.7336.7330.0000.0000.0000.000
42A42PRO0-0.016-0.03248.399-0.029-0.0290.0000.0000.0000.000
43A43ASP-1-0.937-0.96050.640-6.195-6.1950.0000.0000.0000.000
44A44ALA0-0.0120.00945.992-0.021-0.0210.0000.0000.0000.000
45A45PRO0-0.0090.00245.7270.0920.0920.0000.0000.0000.000
46A46GLY00.0660.01445.858-0.187-0.1870.0000.0000.0000.000
47A47GLU-1-0.886-0.92446.757-6.286-6.2860.0000.0000.0000.000
48A48HIS0-0.017-0.02046.590-0.182-0.1820.0000.0000.0000.000
49A49ILE0-0.015-0.01642.5090.1250.1250.0000.0000.0000.000
50A50LEU0-0.078-0.04046.381-0.026-0.0260.0000.0000.0000.000
51A51LEU00.0010.00640.038-0.042-0.0420.0000.0000.0000.000
52A52LEU00.0200.00243.3830.0290.0290.0000.0000.0000.000
53A53GLY00.0530.03241.700-0.049-0.0490.0000.0000.0000.000
54A54GLN0-0.038-0.00742.087-0.007-0.0070.0000.0000.0000.000
55A55VAL00.0200.01436.029-0.151-0.1510.0000.0000.0000.000
56A56TYR0-0.034-0.01738.0020.1790.1790.0000.0000.0000.000
57A57ASP-1-0.777-0.90136.198-8.253-8.2530.0000.0000.0000.000
58A58GLY00.0070.00336.1230.0980.0980.0000.0000.0000.000
59A59ASN0-0.145-0.06636.8840.1270.1270.0000.0000.0000.000
60A60GLY00.0110.01840.0200.2080.2080.0000.0000.0000.000
61A61HIS0-0.056-0.03141.1860.2550.2550.0000.0000.0000.000
62A62LEU0-0.033-0.01240.749-0.180-0.1800.0000.0000.0000.000
63A63VAL0-0.010-0.00936.2530.0340.0340.0000.0000.0000.000
64A64ARG10.8710.93539.5936.8566.8560.0000.0000.0000.000
65A65ASP-1-0.822-0.88738.238-8.146-8.1460.0000.0000.0000.000
66A66SER0-0.051-0.03435.860-0.296-0.2960.0000.0000.0000.000
67A67PHE00.015-0.01532.8290.2690.2690.0000.0000.0000.000
68A68LEU00.008-0.00133.655-0.296-0.2960.0000.0000.0000.000
69A69GLU-1-0.849-0.91530.244-9.734-9.7340.0000.0000.0000.000
70A70VAL0-0.016-0.01632.284-0.156-0.1560.0000.0000.0000.000
71A71TRP00.0360.00728.9930.1670.1670.0000.0000.0000.000
72A72GLN0-0.0030.00632.500-0.094-0.0940.0000.0000.0000.000
73A73ALA00.0560.05134.6790.0000.0000.0000.0000.0000.000
74A74ASP-1-0.734-0.86436.059-7.689-7.6890.0000.0000.0000.000
75A75ALA00.014-0.01139.630-0.075-0.0750.0000.0000.0000.000
76A76ASN0-0.075-0.03240.7850.2210.2210.0000.0000.0000.000
77A77GLY0-0.024-0.00237.316-0.034-0.0340.0000.0000.0000.000
78A78GLU-1-0.953-0.97535.546-8.208-8.2080.0000.0000.0000.000
79A79TYR0-0.046-0.02831.7230.0330.0330.0000.0000.0000.000
80A80GLN0-0.048-0.03134.148-0.169-0.1690.0000.0000.0000.000
81A81ASP-1-0.887-0.96631.667-9.403-9.4030.0000.0000.0000.000
82A82ALA0-0.0270.00433.767-0.054-0.0540.0000.0000.0000.000
83A83TYR0-0.030-0.02335.6590.3140.3140.0000.0000.0000.000
84A84ASN00.009-0.01037.4530.0630.0630.0000.0000.0000.000
85A85LEU00.0240.02841.0820.0820.0820.0000.0000.0000.000
86A86GLU-1-0.890-0.93843.936-6.579-6.5790.0000.0000.0000.000
87A87ASN0-0.053-0.01740.4510.2840.2840.0000.0000.0000.000
88A88ALA00.0250.00944.6490.0460.0460.0000.0000.0000.000
89A89PHE0-0.001-0.01938.4910.0750.0750.0000.0000.0000.000
90A90ASN0-0.0010.00538.408-0.169-0.1690.0000.0000.0000.000
91A91SER00.0410.01334.4000.0930.0930.0000.0000.0000.000
92A92PHE0-0.027-0.00431.094-0.154-0.1540.0000.0000.0000.000
93A93GLY00.0150.00535.1870.2910.2910.0000.0000.0000.000
94A94ARG10.8200.91633.0068.7818.7810.0000.0000.0000.000
95A95THR0-0.005-0.02837.2080.2960.2960.0000.0000.0000.000
96A96ALA00.004-0.00237.857-0.254-0.2540.0000.0000.0000.000
97A97THR0-0.050-0.01539.8190.1180.1180.0000.0000.0000.000
98A98THR0-0.0040.00741.787-0.036-0.0360.0000.0000.0000.000
99A99PHE0-0.005-0.00641.981-0.008-0.0080.0000.0000.0000.000
100A100ASP-1-0.844-0.91145.826-6.461-6.4610.0000.0000.0000.000
101A101ALA0-0.032-0.03248.235-0.041-0.0410.0000.0000.0000.000
102A102GLY00.0100.01144.043-0.026-0.0260.0000.0000.0000.000
103A103GLU-1-0.856-0.92043.116-6.908-6.9080.0000.0000.0000.000
104A104TRP00.0060.02039.1740.0510.0510.0000.0000.0000.000
105A105THR00.000-0.02242.6370.1140.1140.0000.0000.0000.000
106A106LEU00.0150.02339.009-0.112-0.1120.0000.0000.0000.000
107A107HIS0-0.032-0.01442.8290.1850.1850.0000.0000.0000.000
108A108THR00.029-0.01340.448-0.055-0.0550.0000.0000.0000.000
109A109VAL00.0220.01942.4940.1890.1890.0000.0000.0000.000
110A110LYS10.8070.88841.9476.8716.8710.0000.0000.0000.000
111A111PRO0-0.053-0.00437.6180.0800.0800.0000.0000.0000.000
112A112GLY00.0450.01939.3980.1190.1190.0000.0000.0000.000
113A113VAL0-0.070-0.04136.559-0.194-0.1940.0000.0000.0000.000
114A114VAL00.0510.03131.7460.0030.0030.0000.0000.0000.000
115A115ASN0-0.017-0.00831.1970.0700.0700.0000.0000.0000.000
116A116ASN00.0570.02926.671-0.139-0.1390.0000.0000.0000.000
117A117ALA00.0350.00123.6250.1810.1810.0000.0000.0000.000
118A118ALA0-0.048-0.01525.515-0.099-0.0990.0000.0000.0000.000
119A119GLY0-0.018-0.00626.9030.2820.2820.0000.0000.0000.000
120A120VAL0-0.035-0.01529.7640.3740.3740.0000.0000.0000.000
121A121PRO00.0030.00631.237-0.211-0.2110.0000.0000.0000.000
122A122MET0-0.018-0.00628.750-0.205-0.2050.0000.0000.0000.000
123A123ALA0-0.0030.00133.1890.2060.2060.0000.0000.0000.000
124A124PRO00.0050.00835.342-0.243-0.2430.0000.0000.0000.000
125A125HIS0-0.030-0.03131.615-0.171-0.1710.0000.0000.0000.000
126A126ILE0-0.0110.00534.538-0.003-0.0030.0000.0000.0000.000
127A127ASN0-0.028-0.01729.081-0.303-0.3030.0000.0000.0000.000
128A128ILE0-0.004-0.00130.5450.2200.2200.0000.0000.0000.000
129A129SER00.0110.01026.929-0.310-0.3100.0000.0000.0000.000
130A130LEU0-0.035-0.01029.4480.3270.3270.0000.0000.0000.000
131A131PHE00.0420.00527.494-0.380-0.3800.0000.0000.0000.000
132A132ALA00.0720.02331.3910.3760.3760.0000.0000.0000.000
133A133ARG10.8600.92031.7627.9277.9270.0000.0000.0000.000
134A134GLY0-0.026-0.00930.9920.1450.1450.0000.0000.0000.000
135A135ILE0-0.0060.01128.003-0.255-0.2550.0000.0000.0000.000
136A136ASN0-0.006-0.02224.6140.3210.3210.0000.0000.0000.000
137A137ILE00.0400.02820.361-0.323-0.3230.0000.0000.0000.000
138A138HIS0-0.0200.00923.0830.5030.5030.0000.0000.0000.000
139A139LEU0-0.0040.00425.079-0.377-0.3770.0000.0000.0000.000
140A140HIS00.0880.05321.9431.0441.0440.0000.0000.0000.000
141A141THR0-0.006-0.02826.9290.0600.0600.0000.0000.0000.000
142A142ARG10.8460.89428.54010.28110.2810.0000.0000.0000.000
143A143LEU0-0.0150.02532.0910.1310.1310.0000.0000.0000.000
144A144TYR00.021-0.06431.832-0.146-0.1460.0000.0000.0000.000
145A145PHE00.0500.01637.3720.1190.1190.0000.0000.0000.000
146A146ASP-1-0.794-0.89741.234-6.950-6.9500.0000.0000.0000.000
147A147ASP-1-0.812-0.86943.553-6.832-6.8320.0000.0000.0000.000
148A148GLU-1-0.817-0.89540.917-7.204-7.2040.0000.0000.0000.000
149A149ALA0-0.024-0.00441.432-0.173-0.1730.0000.0000.0000.000
150A150GLN0-0.040-0.03641.536-0.154-0.1540.0000.0000.0000.000
151A151ALA00.0250.02038.949-0.087-0.0870.0000.0000.0000.000
152A152ASN00.015-0.02237.139-0.365-0.3650.0000.0000.0000.000
153A153ALA0-0.023-0.01436.478-0.217-0.2170.0000.0000.0000.000
154A154LYS10.8880.93835.9747.6657.6650.0000.0000.0000.000
155A155CYS-1-0.814-0.74732.236-9.813-9.8130.0000.0000.0000.000
156A156PRO0-0.016-0.01428.378-0.107-0.1070.0000.0000.0000.000
157A157VAL00.009-0.02126.673-0.362-0.3620.0000.0000.0000.000
158A158LEU00.033-0.01228.731-0.132-0.1320.0000.0000.0000.000
159A159ASN0-0.084-0.06731.2470.1680.1680.0000.0000.0000.000
160A160LEU0-0.0180.00424.096-0.072-0.0720.0000.0000.0000.000
161A161ILE0-0.0290.01526.646-0.294-0.2940.0000.0000.0000.000
162A162GLU-1-0.927-0.96426.169-10.690-10.6900.0000.0000.0000.000
163A163GLN00.0140.00329.5860.5610.5610.0000.0000.0000.000
164A164PRO00.001-0.00532.599-0.017-0.0170.0000.0000.0000.000
165A165GLN00.0740.02235.316-0.112-0.1120.0000.0000.0000.000
166A166ARG10.8670.91928.77010.06410.0640.0000.0000.0000.000
167A167ARG10.8580.95331.7489.2379.2370.0000.0000.0000.000
168A168GLU-1-0.936-0.96534.763-7.634-7.6340.0000.0000.0000.000
169A169THR0-0.080-0.05334.3570.1170.1170.0000.0000.0000.000
170A170LEU00.0180.01130.886-0.005-0.0050.0000.0000.0000.000
171A171ILE0-0.065-0.00235.4960.0610.0610.0000.0000.0000.000
172A172ALA00.0360.02238.9600.1250.1250.0000.0000.0000.000
173A173LYS10.8240.90241.0647.6027.6020.0000.0000.0000.000
174A174ARG10.8640.92444.9326.4126.4120.0000.0000.0000.000
175A175CYS0-0.098-0.04547.5920.0900.0900.0000.0000.0000.000
176A176GLU-1-0.925-0.96150.584-5.752-5.7520.0000.0000.0000.000
177A177VAL0-0.027-0.01750.4060.0330.0330.0000.0000.0000.000
178A178ASP-1-0.935-0.97153.338-5.725-5.7250.0000.0000.0000.000
179A179GLY0-0.035-0.00656.4110.0610.0610.0000.0000.0000.000
180A180LYS10.8770.96148.3616.4386.4380.0000.0000.0000.000
181A181THR00.003-0.01348.0880.0080.0080.0000.0000.0000.000
182A182ALA0-0.005-0.00647.635-0.093-0.0930.0000.0000.0000.000
183A183TYR0-0.033-0.05643.4100.0120.0120.0000.0000.0000.000
184A184ARG10.7510.85244.1206.8686.8680.0000.0000.0000.000
185A185PHE0-0.004-0.01834.689-0.025-0.0250.0000.0000.0000.000
186A186ASP-1-0.799-0.87939.746-7.319-7.3190.0000.0000.0000.000
187A187ILE0-0.0140.00033.917-0.130-0.1300.0000.0000.0000.000
188A188ARG10.9130.96235.9837.8837.8830.0000.0000.0000.000
189A189ILE00.0290.00031.097-0.226-0.2260.0000.0000.0000.000
190A190GLN0-0.015-0.01631.149-0.095-0.0950.0000.0000.0000.000
191A191GLY00.0100.01433.4030.2850.2850.0000.0000.0000.000
192A192GLU-1-0.962-0.98135.416-7.452-7.4520.0000.0000.0000.000
193A193GLY0-0.005-0.01337.9050.0670.0670.0000.0000.0000.000
194A194GLU-1-0.895-0.93130.221-10.046-10.0460.0000.0000.0000.000
195A195THR00.0390.01532.657-0.016-0.0160.0000.0000.0000.000
196A196VAL0-0.0190.00228.175-0.254-0.2540.0000.0000.0000.000
197A197PHE00.0210.00426.8020.1910.1910.0000.0000.0000.000
198A198PHE0-0.059-0.03924.290-0.056-0.0560.0000.0000.0000.000
199A199ASP-1-0.921-0.97218.062-16.286-16.2860.0000.0000.0000.000
200A200PHE-1-0.980-0.97017.896-15.617-15.6170.0000.0000.0000.000