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: 5YV2Z

Calculation Name: 5O5C-D-Xray547

Preferred Name:

Target Type:

Ligand Name: pyridoxal-5'-phosphate

Ligand 3-letter code: PLP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5O5C

Chain ID: D

ChEMBL ID:

UniProt ID: D4I245

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 476
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -8771347.149578
FMO2-HF: Nuclear repulsion 8586218.067692
FMO2-HF: Total energy -185129.081885
FMO2-MP2: Total energy -185668.124897


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:22:PRO)


Summations of interaction energy for fragment #1(A:22: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.
-124.478-122.066-0.014-0.931-1.467-0.003
Interaction energy analysis for fragmet #1(A:22:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / 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].
3A24ASP-1-0.857-0.9253.682-59.621-57.367-0.013-0.918-1.323-0.003
4A25PHE0-0.020-0.0105.1855.2215.379-0.001-0.013-0.1440.000
5A26ILE0-0.037-0.0066.0593.8433.8430.0000.0000.0000.000
6A27PHE00.0160.0097.832-1.632-1.6320.0000.0000.0000.000
7A28ASN00.0330.0015.5710.9730.9730.0000.0000.0000.000
8A29ASP-1-0.864-0.94410.051-26.155-26.1550.0000.0000.0000.000
9A30HIS0-0.049-0.0206.7300.8470.8470.0000.0000.0000.000
10A31GLN00.0090.0045.2281.5561.5560.0000.0000.0000.000
11A32LEU0-0.0280.0099.7712.5512.5510.0000.0000.0000.000
12A33SER00.008-0.00912.9962.0412.0410.0000.0000.0000.000
13A34ALA0-0.010-0.00411.4721.1701.1700.0000.0000.0000.000
14A35TRP0-0.003-0.00313.4451.3481.3480.0000.0000.0000.000
15A36ALA00.0420.02315.1091.0371.0370.0000.0000.0000.000
16A37ARG11.0111.01916.31218.94818.9480.0000.0000.0000.000
17A38GLN00.0370.02615.1580.1960.1960.0000.0000.0000.000
18A39THR0-0.079-0.04718.4160.9310.9310.0000.0000.0000.000
19A40GLU-1-0.919-0.97020.913-13.838-13.8380.0000.0000.0000.000
20A41GLN0-0.050-0.04319.3540.3510.3510.0000.0000.0000.000
21A42VAL00.0170.00821.7620.6530.6530.0000.0000.0000.000
22A43LEU0-0.010-0.00324.2170.6490.6490.0000.0000.0000.000
23A44ALA0-0.0060.01426.3050.5800.5800.0000.0000.0000.000
24A45LEU00.0340.01325.7250.4670.4670.0000.0000.0000.000
25A46MET00.0060.00127.5170.4050.4050.0000.0000.0000.000
26A47THR0-0.064-0.04230.0130.5560.5560.0000.0000.0000.000
27A48GLU-1-0.990-0.99331.697-9.753-9.7530.0000.0000.0000.000
28A49THR00.014-0.01331.3880.2010.2010.0000.0000.0000.000
29A50VAL0-0.055-0.02433.1980.2880.2880.0000.0000.0000.000
30A51LYS10.8920.94935.6129.1259.1250.0000.0000.0000.000
31A52GLY00.0250.02737.0820.2380.2380.0000.0000.0000.000
32A53VAL0-0.066-0.01937.4440.1300.1300.0000.0000.0000.000
33A54GLU-1-0.912-0.95840.062-7.134-7.1340.0000.0000.0000.000
34A55LYS10.7800.89242.9567.3227.3220.0000.0000.0000.000
35A56PRO0-0.0280.00142.114-0.203-0.2030.0000.0000.0000.000
36A57PHE0-0.0260.00239.757-0.169-0.1690.0000.0000.0000.000
37A58SER00.019-0.02240.0880.2270.2270.0000.0000.0000.000
38A59GLY00.0420.01942.2200.1980.1980.0000.0000.0000.000
39A60ILE0-0.061-0.00539.0490.1990.1990.0000.0000.0000.000
40A61LEU0-0.008-0.02042.7550.0510.0510.0000.0000.0000.000
41A62PRO00.031-0.00339.937-0.112-0.1120.0000.0000.0000.000
42A63HIS00.0240.01239.543-0.249-0.2490.0000.0000.0000.000
43A64GLU-1-0.807-0.86441.417-7.206-7.2060.0000.0000.0000.000
44A65LEU00.0880.04134.710-0.061-0.0610.0000.0000.0000.000
45A66ALA00.0120.00335.871-0.247-0.2470.0000.0000.0000.000
46A67ARG10.8460.93535.9187.4227.4220.0000.0000.0000.000
47A68GLU-1-0.940-0.96134.217-9.032-9.0320.0000.0000.0000.000
48A69PHE00.015-0.00829.418-0.241-0.2410.0000.0000.0000.000
49A70SER0-0.066-0.04131.070-0.205-0.2050.0000.0000.0000.000
50A71GLY0-0.043-0.00731.3700.0240.0240.0000.0000.0000.000
51A72VAL0-0.037-0.01225.694-0.243-0.2430.0000.0000.0000.000
52A73ASP-1-0.858-0.92624.589-12.462-12.4620.0000.0000.0000.000
53A74LEU0-0.012-0.02422.782-0.560-0.5600.0000.0000.0000.000
54A75ASP-1-0.916-0.94720.223-14.534-14.5340.0000.0000.0000.000
55A76GLN0-0.115-0.05219.409-0.666-0.6660.0000.0000.0000.000
56A77SER0-0.030-0.02418.086-0.950-0.9500.0000.0000.0000.000
57A78LEU0-0.0170.01019.4710.0230.0230.0000.0000.0000.000
58A79GLY0-0.022-0.00316.169-0.902-0.9020.0000.0000.0000.000
59A80SER0-0.041-0.03016.125-0.317-0.3170.0000.0000.0000.000
60A81ASN00.0310.02015.6520.3090.3090.0000.0000.0000.000
61A82GLU-1-0.854-0.92818.486-16.378-16.3780.0000.0000.0000.000
62A83ALA00.0040.00221.1170.7860.7860.0000.0000.0000.000
63A84ALA00.0290.01420.1700.6340.6340.0000.0000.0000.000
64A85LEU0-0.005-0.01021.8660.7110.7110.0000.0000.0000.000
65A86GLU-1-0.871-0.93224.352-10.257-10.2570.0000.0000.0000.000
66A87GLU-1-0.876-0.94325.242-11.976-11.9760.0000.0000.0000.000
67A88LEU00.0090.01124.6690.5400.5400.0000.0000.0000.000
68A89LYS10.8420.90327.55211.38811.3880.0000.0000.0000.000
69A90LYS10.8360.92830.37910.20910.2090.0000.0000.0000.000
70A91LEU00.0600.02828.5390.3260.3260.0000.0000.0000.000
71A92TYR0-0.026-0.01528.8030.0010.0010.0000.0000.0000.000
72A93LEU0-0.022-0.02128.2610.3340.3340.0000.0000.0000.000
73A94ARG10.9340.98432.4489.1189.1180.0000.0000.0000.000
74A95ASP-1-0.798-0.88635.284-8.251-8.2510.0000.0000.0000.000
75A96ALA00.0030.01333.8720.1020.1020.0000.0000.0000.000
76A97VAL0-0.054-0.02735.9390.2700.2700.0000.0000.0000.000
77A98TRP00.0110.00032.889-0.226-0.2260.0000.0000.0000.000
78A99PHE0-0.013-0.02736.3790.1930.1930.0000.0000.0000.000
79A100HIS00.0270.01637.6320.0780.0780.0000.0000.0000.000
80A101HIS00.0120.01540.0940.1740.1740.0000.0000.0000.000
81A102PRO00.0110.00542.6880.0430.0430.0000.0000.0000.000
82A103LYS10.8520.92346.2036.4956.4950.0000.0000.0000.000
83A104TYR0-0.027-0.02642.7250.0610.0610.0000.0000.0000.000
84A105VAL00.0120.00945.2700.0120.0120.0000.0000.0000.000
85A106ALA00.0210.02945.5250.1460.1460.0000.0000.0000.000
86A107HIS0-0.023-0.01543.6020.1530.1530.0000.0000.0000.000
87A108LEU00.0090.00544.086-0.039-0.0390.0000.0000.0000.000
88A109ASN0-0.0030.00638.7440.0170.0170.0000.0000.0000.000
89A110CYS0-0.0240.00539.1780.0860.0860.0000.0000.0000.000
90A111PRO00.0310.02238.494-0.235-0.2350.0000.0000.0000.000
91A112VAL0-0.013-0.00733.0980.0680.0680.0000.0000.0000.000
92A113VAL00.0370.01236.2830.0010.0010.0000.0000.0000.000
93A114LEU00.0420.01133.245-0.245-0.2450.0000.0000.0000.000
94A115PRO0-0.010-0.01231.923-0.352-0.3520.0000.0000.0000.000
95A116SER00.0430.01431.469-0.323-0.3230.0000.0000.0000.000
96A117LEU00.014-0.00128.973-0.337-0.3370.0000.0000.0000.000
97A118LEU0-0.0130.00427.287-0.454-0.4540.0000.0000.0000.000
98A119ALA0-0.0120.00226.650-0.422-0.4220.0000.0000.0000.000
99A120GLU-1-0.688-0.82825.791-12.183-12.1830.0000.0000.0000.000
100A121GLN0-0.0290.00021.615-0.127-0.1270.0000.0000.0000.000
101A122ILE0-0.015-0.00721.501-0.710-0.7100.0000.0000.0000.000
102A123MET0-0.063-0.02721.563-0.425-0.4250.0000.0000.0000.000
103A124ALA0-0.010-0.00519.639-0.449-0.4490.0000.0000.0000.000
104A125ALA0-0.0280.00517.037-0.944-0.9440.0000.0000.0000.000
105A126VAL0-0.040-0.03316.887-0.812-0.8120.0000.0000.0000.000
106A127ASN0-0.053-0.02017.5720.4640.4640.0000.0000.0000.000
107A128SER0-0.0130.00020.1170.1490.1490.0000.0000.0000.000
108A129SER0-0.007-0.02522.7720.3240.3240.0000.0000.0000.000
109A130VAL0-0.044-0.03324.7010.1000.1000.0000.0000.0000.000
110A131ASP-1-0.795-0.88126.817-11.153-11.1530.0000.0000.0000.000
111A132THR0-0.008-0.03026.5450.3490.3490.0000.0000.0000.000
112A133TRP00.0340.02327.643-0.393-0.3930.0000.0000.0000.000
113A134ASP-1-0.846-0.91024.724-12.048-12.0480.0000.0000.0000.000
114A135GLN0-0.040-0.01222.529-1.126-1.1260.0000.0000.0000.000
115A136SER0-0.023-0.02223.487-0.121-0.1210.0000.0000.0000.000
116A137ALA00.0260.01125.7000.0500.0500.0000.0000.0000.000
117A138GLY0-0.013-0.00427.8860.4190.4190.0000.0000.0000.000
118A139GLY00.022-0.00228.1050.3390.3390.0000.0000.0000.000
119A140THR00.0140.00329.1450.3800.3800.0000.0000.0000.000
120A141LEU0-0.028-0.01831.5370.3740.3740.0000.0000.0000.000
121A142ILE0-0.041-0.01530.1860.3320.3320.0000.0000.0000.000
122A143GLU-1-0.749-0.87132.730-9.280-9.2800.0000.0000.0000.000
123A144GLN0-0.012-0.01234.4940.0830.0830.0000.0000.0000.000
124A145LYS10.9440.98036.9558.1068.1060.0000.0000.0000.000
125A146VAL0-0.034-0.02035.8540.2370.2370.0000.0000.0000.000
126A147ILE0-0.0130.01137.3720.2250.2250.0000.0000.0000.000
127A148ASP-1-0.820-0.90340.503-7.486-7.4860.0000.0000.0000.000
128A149TRP0-0.034-0.01041.8070.2220.2220.0000.0000.0000.000
129A150THR0-0.036-0.02941.4430.1680.1680.0000.0000.0000.000
130A151LEU00.0220.01944.1320.1810.1810.0000.0000.0000.000
131A152SER0-0.088-0.06146.5690.2000.2000.0000.0000.0000.000
132A153ARG10.8440.91446.0266.8736.8730.0000.0000.0000.000
133A154ILE0-0.013-0.00246.0250.1170.1170.0000.0000.0000.000
134A155GLY00.0100.01349.9900.1390.1390.0000.0000.0000.000
135A156LEU0-0.026-0.00748.1190.1170.1170.0000.0000.0000.000
136A157PRO0-0.019-0.00651.365-0.008-0.0080.0000.0000.0000.000
137A158ALA00.033-0.00550.470-0.104-0.1040.0000.0000.0000.000
138A159GLY0-0.034-0.00849.093-0.109-0.1090.0000.0000.0000.000
139A160ALA00.0140.01547.775-0.068-0.0680.0000.0000.0000.000
140A161ASP-1-0.784-0.88941.546-7.895-7.8950.0000.0000.0000.000
141A162GLY0-0.007-0.02341.5580.1550.1550.0000.0000.0000.000
142A163ILE0-0.0300.00634.510-0.126-0.1260.0000.0000.0000.000
143A164PHE00.032-0.00234.2070.1640.1640.0000.0000.0000.000
144A165THR0-0.042-0.02834.624-0.228-0.2280.0000.0000.0000.000
145A166SER0-0.013-0.02833.174-0.063-0.0630.0000.0000.0000.000
146A167GLY00.0420.00034.346-0.068-0.0680.0000.0000.0000.000
147A168GLY00.010-0.00437.9160.0560.0560.0000.0000.0000.000
148A169THR0-0.041-0.02940.1140.1840.1840.0000.0000.0000.000
149A170GLN00.0560.03934.946-0.006-0.0060.0000.0000.0000.000
150A171SER00.000-0.00739.592-0.012-0.0120.0000.0000.0000.000
151A172ASN00.0000.00341.7270.1540.1540.0000.0000.0000.000
152A173LEU00.0090.01739.9380.1380.1380.0000.0000.0000.000
153A174MET0-0.012-0.00237.4960.0900.0900.0000.0000.0000.000
154A175ALA00.0230.01642.9880.1210.1210.0000.0000.0000.000
155A176MET0-0.041-0.01646.5730.1940.1940.0000.0000.0000.000
156A177LEU0-0.0030.00142.1430.1190.1190.0000.0000.0000.000
157A178LEU00.0040.00243.9310.0980.0980.0000.0000.0000.000
158A179ALA0-0.0010.03347.5010.1400.1400.0000.0000.0000.000
159A180ARG10.8240.88845.7176.8676.8670.0000.0000.0000.000
160A181ASP-1-0.791-0.89547.047-6.620-6.6200.0000.0000.0000.000
161A182SER0-0.039-0.03449.8480.1330.1330.0000.0000.0000.000
162A183TRP00.0280.02351.8200.1260.1260.0000.0000.0000.000
163A184CYS0-0.0100.00852.4410.1280.1280.0000.0000.0000.000
164A185ALA0-0.014-0.00351.9100.0990.0990.0000.0000.0000.000
165A186ALA0-0.032-0.00554.0370.0770.0770.0000.0000.0000.000
166A187HIS10.7860.88957.1775.5465.5460.0000.0000.0000.000
167A188HIS0-0.022-0.02356.4120.0560.0560.0000.0000.0000.000
168A189PRO00.0120.00956.640-0.107-0.1070.0000.0000.0000.000
169A190GLY00.0300.01854.5040.0030.0030.0000.0000.0000.000
170A191HIS0-0.059-0.04052.6080.0160.0160.0000.0000.0000.000
171A192LEU00.0420.02147.7390.0030.0030.0000.0000.0000.000
172A193ILE00.0090.00047.494-0.033-0.0330.0000.0000.0000.000
173A194LYS10.8030.89641.9677.3567.3560.0000.0000.0000.000
174A195HIS0-0.016-0.00144.146-0.151-0.1510.0000.0000.0000.000
175A196ARG10.8530.91546.5105.9855.9850.0000.0000.0000.000
176A197GLY00.0370.03548.3240.0900.0900.0000.0000.0000.000
177A198LEU00.006-0.00749.4630.0680.0680.0000.0000.0000.000
178A199PRO00.0030.01952.3700.0410.0410.0000.0000.0000.000
179A200HIS00.029-0.00655.924-0.014-0.0140.0000.0000.0000.000
180A201ASP-1-0.818-0.88558.916-5.366-5.3660.0000.0000.0000.000
181A202ALA00.0540.02454.5410.0200.0200.0000.0000.0000.000
182A203ALA00.0300.01356.655-0.029-0.0290.0000.0000.0000.000
183A204LYS10.8460.92357.9445.0235.0230.0000.0000.0000.000
184A205TRP0-0.043-0.02053.054-0.012-0.0120.0000.0000.0000.000
185A206ARG10.8640.94257.4545.4005.4000.0000.0000.0000.000
186A207VAL00.0120.00552.9800.0040.0040.0000.0000.0000.000
187A208PHE00.0100.00356.2010.0360.0360.0000.0000.0000.000
188A209THR0-0.009-0.00653.460-0.120-0.1200.0000.0000.0000.000
189A210SER00.1030.05256.0680.1340.1340.0000.0000.0000.000
190A211LYS10.8070.88556.1535.0255.0250.0000.0000.0000.000
191A212LEU0-0.0200.00355.248-0.046-0.0460.0000.0000.0000.000
192A213SER00.010-0.00852.238-0.063-0.0630.0000.0000.0000.000
193A214HIS00.0120.03244.3710.0000.0000.0000.0000.0000.000
194A215PHE00.0490.01347.623-0.027-0.0270.0000.0000.0000.000
195A216SER0-0.025-0.02244.404-0.022-0.0220.0000.0000.0000.000
196A217ILE00.0180.03546.033-0.078-0.0780.0000.0000.0000.000
197A218GLN00.1010.04548.940-0.120-0.1200.0000.0000.0000.000
198A219LYS10.9360.96441.9837.4717.4710.0000.0000.0000.000
199A220SER0-0.001-0.01345.002-0.140-0.1400.0000.0000.0000.000
200A221MET00.0200.01646.003-0.063-0.0630.0000.0000.0000.000
201A222ALA0-0.039-0.01147.2670.0550.0550.0000.0000.0000.000
202A223ILE0-0.021-0.01141.410-0.016-0.0160.0000.0000.0000.000
203A224LEU0-0.052-0.01644.799-0.046-0.0460.0000.0000.0000.000
204A225GLY00.0080.00646.7920.0900.0900.0000.0000.0000.000
205A226LEU0-0.027-0.01649.0380.1300.1300.0000.0000.0000.000
206A227GLY00.0090.00950.7650.1200.1200.0000.0000.0000.000
207A228TYR0-0.027-0.04248.826-0.070-0.0700.0000.0000.0000.000
208A229ASP-1-0.875-0.93053.533-5.585-5.5850.0000.0000.0000.000
209A230ALA0-0.011-0.00253.9860.1050.1050.0000.0000.0000.000
210A231VAL0-0.058-0.03752.704-0.004-0.0040.0000.0000.0000.000
211A232ILE00.0440.02256.0070.0580.0580.0000.0000.0000.000
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