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: N847Q

Calculation Name: 6P8C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nadp nicotinamide-adenine-dinucleotide phosphate | glycerol | magnesium ion | chloride ion

Ligand 3-letter code: NAP | GOL | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6P8C

Chain ID: A

ChEMBL ID:

UniProt ID: O26337

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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2466823.561071
FMO2-HF: Nuclear repulsion 2382760.288508
FMO2-HF: Total energy -84063.272564
FMO2-MP2: Total energy -84303.700302


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.
-255.369-248.4410.709-3.248-4.389-0.024
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 : 0.850 / q_NPA : 0.914
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].
3A3PRO00.0570.0373.8660.8833.002-0.010-0.924-1.185-0.002
133A133GLU-1-0.953-0.9772.712-80.254-77.7530.312-1.384-1.429-0.012
134A134ARG10.8550.9204.41029.71529.798-0.001-0.011-0.0710.000
136A136HIS0-0.021-0.0033.347-5.686-3.4610.408-0.929-1.704-0.010
4A4TYR0-0.087-0.0656.231-0.105-0.1050.0000.0000.0000.000
5A5VAL0-0.037-0.0228.9811.3941.3940.0000.0000.0000.000
6A6ILE00.0320.01611.9250.9580.9580.0000.0000.0000.000
7A7LEU00.0000.00315.5990.1170.1170.0000.0000.0000.000
8A8ASN00.0380.01818.0810.8510.8510.0000.0000.0000.000
9A9ALA0-0.024-0.01921.189-0.016-0.0160.0000.0000.0000.000
10A10ALA00.0390.03024.5180.1490.1490.0000.0000.0000.000
11A11MET0-0.050-0.01528.271-0.225-0.2250.0000.0000.0000.000
12A12THR00.008-0.01830.6660.0720.0720.0000.0000.0000.000
13A13LEU00.0490.02533.207-0.222-0.2220.0000.0000.0000.000
14A14ASP-1-0.824-0.87934.954-8.730-8.7300.0000.0000.0000.000
15A15GLY00.0110.00031.392-0.015-0.0150.0000.0000.0000.000
16A16LYS10.7970.88630.6418.7108.7100.0000.0000.0000.000
17A17ILE00.0210.00226.374-0.030-0.0300.0000.0000.0000.000
18A18ALA00.0190.01030.2290.0260.0260.0000.0000.0000.000
19A19THR00.0160.01032.8300.0710.0710.0000.0000.0000.000
20A20ALA0-0.017-0.01535.286-0.156-0.1560.0000.0000.0000.000
21A21THR0-0.079-0.04736.9200.0700.0700.0000.0000.0000.000
22A22GLY0-0.010-0.00234.2550.0600.0600.0000.0000.0000.000
23A23SER0-0.082-0.04334.436-0.178-0.1780.0000.0000.0000.000
24A24SER00.0630.01231.7410.0050.0050.0000.0000.0000.000
25A25GLU-1-0.867-0.90532.980-8.914-8.9140.0000.0000.0000.000
26A26ILE0-0.052-0.02031.8130.2350.2350.0000.0000.0000.000
27A27SER0-0.046-0.04129.6800.0950.0950.0000.0000.0000.000
28A28GLY00.0980.05532.6100.1950.1950.0000.0000.0000.000
29A29GLU-1-0.929-0.97732.958-8.763-8.7630.0000.0000.0000.000
30A30GLU-1-0.905-0.97132.881-8.811-8.8110.0000.0000.0000.000
31A31ASP-1-0.697-0.81928.075-11.443-11.4430.0000.0000.0000.000
32A32LEU0-0.016-0.01028.207-0.430-0.4300.0000.0000.0000.000
33A33ARG10.8440.91928.3608.7898.7890.0000.0000.0000.000
34A34ARG10.9520.98622.79611.98111.9810.0000.0000.0000.000
35A35VAL00.001-0.01123.372-0.553-0.5530.0000.0000.0000.000
36A36HIS00.0330.00423.104-0.526-0.5260.0000.0000.0000.000
37A37GLU-1-0.915-0.96123.867-11.187-11.1870.0000.0000.0000.000
38A38LEU0-0.022-0.02119.951-0.462-0.4620.0000.0000.0000.000
39A39ARG10.7460.83118.95612.36912.3690.0000.0000.0000.000
40A40ARG10.8330.90018.90511.46111.4610.0000.0000.0000.000
41A41GLU-1-0.968-0.96718.295-14.752-14.7520.0000.0000.0000.000
42A42CYS0-0.096-0.04114.460-1.237-1.2370.0000.0000.0000.000
43A43ASP-1-0.745-0.85510.985-22.671-22.6710.0000.0000.0000.000
44A44ALA0-0.028-0.02612.3630.2610.2610.0000.0000.0000.000
45A45ILE00.0080.01314.2210.2080.2080.0000.0000.0000.000
46A46MET0-0.026-0.00712.458-0.352-0.3520.0000.0000.0000.000
47A47VAL00.0380.02116.6550.7240.7240.0000.0000.0000.000
48A48GLY00.0070.00119.526-0.596-0.5960.0000.0000.0000.000
49A49ILE0-0.038-0.02521.2920.7130.7130.0000.0000.0000.000
50A50ASN0-0.013-0.03023.8570.4730.4730.0000.0000.0000.000
51A51THR00.0650.05524.4600.3060.3060.0000.0000.0000.000
52A52VAL0-0.007-0.00423.6180.3780.3780.0000.0000.0000.000
53A53LEU0-0.063-0.05826.5970.4000.4000.0000.0000.0000.000
54A54ALA0-0.0430.00529.4290.3860.3860.0000.0000.0000.000
55A55ASP-1-0.850-0.93728.763-10.570-10.5700.0000.0000.0000.000
56A56ASP-1-0.897-0.92829.689-10.129-10.1290.0000.0000.0000.000
57A57PRO00.0180.02125.5010.1890.1890.0000.0000.0000.000
58A58ARG10.8370.86726.50810.27210.2720.0000.0000.0000.000
59A59LEU0-0.034-0.00621.105-0.289-0.2890.0000.0000.0000.000
60A60THR00.0340.00722.254-0.429-0.4290.0000.0000.0000.000
61A61VAL00.0000.01322.6860.1930.1930.0000.0000.0000.000
62A62HIS0-0.109-0.07425.3650.5520.5520.0000.0000.0000.000
63A63ARG10.9290.96728.81110.04110.0410.0000.0000.0000.000
64A64VAL0-0.0060.00327.2210.2590.2590.0000.0000.0000.000
65A65ASP-1-0.913-0.94029.505-9.374-9.3740.0000.0000.0000.000
66A66ALA0-0.004-0.00326.402-0.364-0.3640.0000.0000.0000.000
67A67ALA0-0.0170.00226.1540.4340.4340.0000.0000.0000.000
68A68PRO0-0.029-0.04225.977-0.288-0.2880.0000.0000.0000.000
69A69GLY0-0.013-0.00622.415-0.194-0.1940.0000.0000.0000.000
70A70ASP-1-0.786-0.86920.776-12.815-12.8150.0000.0000.0000.000
71A71ASN0-0.008-0.01221.227-0.183-0.1830.0000.0000.0000.000
72A72PRO00.0020.03016.725-0.277-0.2770.0000.0000.0000.000
73A73VAL0-0.018-0.01914.2260.6920.6920.0000.0000.0000.000
74A74ARG10.8150.90416.15712.76512.7650.0000.0000.0000.000
75A75VAL00.007-0.00413.369-0.049-0.0490.0000.0000.0000.000
76A76VAL00.0000.00116.7810.5490.5490.0000.0000.0000.000
77A77VAL00.0050.00715.791-0.591-0.5910.0000.0000.0000.000
78A78ASP-1-0.740-0.87818.323-12.358-12.3580.0000.0000.0000.000
79A79SER00.0310.00420.133-0.210-0.2100.0000.0000.0000.000
80A80MET0-0.0270.00921.112-0.055-0.0550.0000.0000.0000.000
81A81ALA00.0400.03123.0200.6390.6390.0000.0000.0000.000
82A82ARG10.8650.91824.31212.44912.4490.0000.0000.0000.000
83A83THR00.016-0.01023.6990.3370.3370.0000.0000.0000.000
84A84PRO0-0.0050.01126.2090.0450.0450.0000.0000.0000.000
85A85PRO00.0020.00129.032-0.166-0.1660.0000.0000.0000.000
86A86HIS0-0.008-0.01430.064-0.093-0.0930.0000.0000.0000.000
87A87PHE0-0.002-0.00128.8910.2540.2540.0000.0000.0000.000
88A88ARG10.8710.92528.7479.4859.4850.0000.0000.0000.000
89A89VAL00.0150.02022.540-0.147-0.1470.0000.0000.0000.000
90A90LEU0-0.057-0.02223.797-0.618-0.6180.0000.0000.0000.000
91A91ASN0-0.013-0.01426.171-0.088-0.0880.0000.0000.0000.000
92A92ASP-1-0.880-0.95025.964-10.920-10.9200.0000.0000.0000.000
93A93GLU-1-0.791-0.82326.011-11.172-11.1720.0000.0000.0000.000
94A94ALA00.0370.01421.084-0.095-0.0950.0000.0000.0000.000
95A95PRO00.0040.01817.9560.1950.1950.0000.0000.0000.000
96A96THR00.000-0.00419.153-0.409-0.4090.0000.0000.0000.000
97A97VAL00.0160.01113.9950.0100.0100.0000.0000.0000.000
98A98ILE0-0.023-0.01317.4240.1740.1740.0000.0000.0000.000
99A99GLY00.0470.02815.388-0.649-0.6490.0000.0000.0000.000
100A100VAL0-0.051-0.03316.0371.1331.1330.0000.0000.0000.000
101A101SER0-0.020-0.02617.161-0.757-0.7570.0000.0000.0000.000
102A102GLU-1-0.857-0.94417.646-16.495-16.4950.0000.0000.0000.000
103A103SER0-0.061-0.03920.7680.8680.8680.0000.0000.0000.000
104A104ALA0-0.046-0.01322.4210.6700.6700.0000.0000.0000.000
105A105PRO0-0.017-0.01224.2070.0630.0630.0000.0000.0000.000
106A106PRO00.0510.01225.863-0.090-0.0900.0000.0000.0000.000
107A107GLU-1-0.934-0.95426.947-9.719-9.7190.0000.0000.0000.000
108A108ARG10.8730.91527.37711.12911.1290.0000.0000.0000.000
109A109VAL00.0230.01221.969-0.218-0.2180.0000.0000.0000.000
110A110ALA0-0.004-0.00724.205-0.347-0.3470.0000.0000.0000.000
111A111GLU-1-0.822-0.88326.532-10.220-10.2200.0000.0000.0000.000
112A112LEU0-0.008-0.00522.646-0.021-0.0210.0000.0000.0000.000
113A113ARG10.8900.94218.49815.56515.5650.0000.0000.0000.000
114A114LYS10.7960.89823.71810.75210.7520.0000.0000.0000.000
115A115ARG10.8310.90825.24411.02111.0210.0000.0000.0000.000
116A116ALA00.0300.02820.513-0.097-0.0970.0000.0000.0000.000
117A117GLU-1-0.914-0.94214.815-20.282-20.2820.0000.0000.0000.000
118A118VAL0-0.053-0.03218.081-0.001-0.0010.0000.0000.0000.000
119A119VAL00.0260.01511.680-0.109-0.1090.0000.0000.0000.000
120A120VAL0-0.010-0.00415.0730.3160.3160.0000.0000.0000.000
121A121ALA00.0230.00612.241-1.170-1.1700.0000.0000.0000.000
122A122GLY00.1020.06914.1520.3430.3430.0000.0000.0000.000
123A123THR0-0.008-0.00815.9010.6780.6780.0000.0000.0000.000
124A124ARG10.9340.96419.58912.85512.8550.0000.0000.0000.000
125A125ARG10.9180.94718.87516.06716.0670.0000.0000.0000.000
126A126VAL0-0.0020.01214.260-0.311-0.3110.0000.0000.0000.000
127A127ASP-1-0.875-0.93310.657-27.352-27.3520.0000.0000.0000.000
128A128LEU00.025-0.00711.542-1.194-1.1940.0000.0000.0000.000
129A129HIS00.0340.0277.144-1.667-1.6670.0000.0000.0000.000
130A130LEU0-0.006-0.0086.533-5.443-5.4430.0000.0000.0000.000
131A131LEU0-0.043-0.0258.007-0.736-0.7360.0000.0000.0000.000
132A132LEU00.0160.0046.921-0.646-0.6460.0000.0000.0000.000
135A135LEU00.0170.0097.6062.7042.7040.0000.0000.0000.000
137A137GLY0-0.040-0.0185.4623.0053.0050.0000.0000.0000.000
138A138MET0-0.090-0.0437.5573.5363.5360.0000.0000.0000.000
139A139GLY0-0.015-0.0018.3902.5652.5650.0000.0000.0000.000
140A140ILE0-0.068-0.0278.3291.6871.6870.0000.0000.0000.000
141A141GLU-1-0.862-0.9325.321-45.231-45.2310.0000.0000.0000.000
142A142ARG10.8560.9207.66518.94718.9470.0000.0000.0000.000
143A143LEU0-0.009-0.00610.6770.6210.6210.0000.0000.0000.000
144A144MET00.0130.00912.3380.2940.2940.0000.0000.0000.000
145A145LEU0-0.041-0.02115.4500.2030.2030.0000.0000.0000.000
146A146GLU-1-0.760-0.85617.023-13.269-13.2690.0000.0000.0000.000
147A147GLY00.0160.03519.9030.7540.7540.0000.0000.0000.000
148A148GLY00.034-0.00521.499-0.252-0.2520.0000.0000.0000.000
149A149SER00.007-0.04222.331-0.800-0.8000.0000.0000.0000.000
150A150THR0-0.018-0.02422.352-0.149-0.1490.0000.0000.0000.000
151A151LEU0-0.0270.00416.196-0.397-0.3970.0000.0000.0000.000
152A152ASN00.0320.00418.062-1.436-1.4360.0000.0000.0000.000
153A153TYR00.0160.00418.657-0.996-0.9960.0000.0000.0000.000
154A154SER0-0.035-0.01816.860-0.313-0.3130.0000.0000.0000.000
155A155MET0-0.0150.00112.117-1.370-1.3700.0000.0000.0000.000
156A156LEU0-0.018-0.00414.048-1.174-1.1740.0000.0000.0000.000
157A157THR00.004-0.02015.694-0.725-0.7250.0000.0000.0000.000
158A158GLY0-0.0170.00612.913-0.193-0.1930.0000.0000.0000.000
159A159GLY00.0250.01411.244-2.191-2.1910.0000.0000.0000.000
160A160LEU0-0.094-0.0558.360-2.870-2.8700.0000.0000.0000.000
161A161VAL0-0.006-0.01310.8360.5190.5190.0000.0000.0000.000
162A162ASP-1-0.754-0.81910.231-27.711-27.7110.0000.0000.0000.000
163A163GLU-1-0.880-0.91313.277-15.988-15.9880.0000.0000.0000.000
164A164VAL0-0.011-0.01016.537-0.355-0.3550.0000.0000.0000.000
165A165ARG10.7910.88519.80112.75512.7550.0000.0000.0000.000
166A166VAL0-0.013-0.02222.497-0.142-0.1420.0000.0000.0000.000
167A167CYS0-0.037-0.00225.8070.3910.3910.0000.0000.0000.000
168A168ILE0-0.031-0.02328.937-0.055-0.0550.0000.0000.0000.000
169A169ALA00.1220.07031.8810.2270.2270.0000.0000.0000.000
170A170PRO0-0.033-0.00534.9870.0400.0400.0000.0000.0000.000
171A171MET0-0.039-0.01636.9810.2290.2290.0000.0000.0000.000
172A172ILE0-0.027-0.02937.842-0.204-0.2040.0000.0000.0000.000
173A173VAL0-0.012-0.00636.8800.1710.1710.0000.0000.0000.000
174A174GLY0-0.0210.00038.7640.1950.1950.0000.0000.0000.000
175A175GLY0-0.003-0.01538.078-0.171-0.1710.0000.0000.0000.000
176A176ARG10.8790.93137.3097.5587.5580.0000.0000.0000.000
177A177ASP-1-0.857-0.93635.703-8.507-8.5070.0000.0000.0000.000
178A178ALA0-0.042-0.01034.699-0.081-0.0810.0000.0000.0000.000
179A179ARG10.8730.95727.13710.94010.9400.0000.0000.0000.000
180A180THR00.037-0.01328.6700.0650.0650.0000.0000.0000.000
181A181LEU00.0400.00924.464-0.318-0.3180.0000.0000.0000.000
182A182VAL0-0.046-0.02722.261-0.737-0.7370.0000.0000.0000.000
183A183ASP-1-0.778-0.81924.754-10.836-10.8360.0000.0000.0000.000
184A184GLY0-0.039-0.03023.739-0.365-0.3650.0000.0000.0000.000
185A185GLU-1-0.993-0.99423.282-12.583-12.5830.0000.0000.0000.000
186A186GLY00.0230.02425.2010.4340.4340.0000.0000.0000.000
187A187ILE0-0.020-0.01121.962-0.457-0.4570.0000.0000.0000.000
188A188ASP-1-0.922-0.95126.120-10.489-10.4890.0000.0000.0000.000
189A189GLU-1-0.925-0.96228.464-9.292-9.2920.0000.0000.0000.000
190A190MET0-0.041-0.03528.068-0.453-0.4530.0000.0000.0000.000
191A191ALA0-0.076-0.03728.373-0.171-0.1710.0000.0000.0000.000
192A192ASP-1-0.891-0.93924.492-12.078-12.0780.0000.0000.0000.000
193A193ALA0-0.046-0.01723.524-0.550-0.5500.0000.0000.0000.000
194A194ILE00.0100.00318.4110.0320.0320.0000.0000.0000.000
195A195ARG10.8800.94420.60812.67112.6710.0000.0000.0000.000
196A196LEU00.0300.01619.834-0.753-0.7530.0000.0000.0000.000
197A197GLU-1-0.898-0.95520.682-12.755-12.7550.0000.0000.0000.000
198A198LEU0-0.036-0.00721.786-0.403-0.4030.0000.0000.0000.000
199A199LYS10.8350.90518.52814.45414.4540.0000.0000.0000.000
200A200ARG10.9270.96223.09911.31211.3120.0000.0000.0000.000
201A201SER00.0140.01426.253-0.250-0.2500.0000.0000.0000.000
202A202TYR0-0.103-0.07925.5170.2510.2510.0000.0000.0000.000
203A203THR00.0300.01631.421-0.174-0.1740.0000.0000.0000.000
204A204LEU0-0.041-0.01929.800-0.131-0.1310.0000.0000.0000.000
205A205GLY00.0440.04133.682-0.046-0.0460.0000.0000.0000.000
206A206GLU-1-1.005-1.00536.791-7.954-7.9540.0000.0000.0000.000
207A207ASP-1-0.820-0.90732.730-9.304-9.3040.0000.0000.0000.000
208A208LEU0-0.052-0.03231.9980.0640.0640.0000.0000.0000.000
209A209ILE0-0.025-0.00726.859-0.306-0.3060.0000.0000.0000.000
210A210VAL0-0.028-0.02026.5100.2180.2180.0000.0000.0000.000
211A211GLU-1-0.790-0.87322.025-12.780-12.7800.0000.0000.0000.000
212A212TYR00.018-0.00321.4510.5160.5160.0000.0000.0000.000
213A213THR00.0310.02816.270-0.337-0.3370.0000.0000.0000.000
214A214VAL0-0.015-0.02215.2131.0991.0990.0000.0000.0000.000
215A215LYS10.8160.90616.13713.09613.0960.0000.0000.0000.000
216A216GLY-1-0.809-0.88616.407-16.148-16.1480.0000.0000.0000.000