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: 97GL2

Calculation Name: 2YUT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nadp nicotinamide-adenine-dinucleotide phosphate

Ligand 3-letter code: NAP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YUT

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W68

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2106014.329416
FMO2-HF: Nuclear repulsion 2031864.29828
FMO2-HF: Total energy -74150.031136
FMO2-MP2: Total energy -74371.913331


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.
-44.601-33.56714.371-10.481-14.922-0.097
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 : 0.788 / q_NPA : 0.887
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].
3A3VAL0-0.023-0.0202.690-1.7461.1721.097-1.327-2.688-0.009
4A4LEU00.0470.0364.5862.9142.969-0.001-0.014-0.0390.000
20A20LEU0-0.039-0.0233.257-2.967-2.5370.057-0.075-0.4110.000
23A23HIS10.8060.8862.91947.77550.5651.466-1.057-3.199-0.010
24A24ASP-1-0.730-0.8183.644-32.501-31.869-0.001-0.136-0.4950.000
68A68ASP-1-0.800-0.9032.039-86.023-83.67710.724-7.355-5.715-0.076
69A69LEU0-0.042-0.0272.5784.1655.5521.024-0.434-1.977-0.002
70A70LEU00.0370.0315.014-1.203-1.2070.000-0.0210.0250.000
115A115ARG10.8910.9385.16630.69030.819-0.001-0.017-0.1110.000
197A197PHE0-0.009-0.0093.630-2.780-2.4290.006-0.045-0.3120.000
5A5ILE0-0.035-0.0147.0230.9630.9630.0000.0000.0000.000
6A6THR00.0740.02210.4200.8150.8150.0000.0000.0000.000
7A7GLY0-0.003-0.00713.9910.2920.2920.0000.0000.0000.000
8A8ALA00.0100.00313.3350.4940.4940.0000.0000.0000.000
9A9THR0-0.056-0.01314.7900.6660.6660.0000.0000.0000.000
10A10GLY00.0170.00717.5511.0471.0470.0000.0000.0000.000
11A11GLY0-0.009-0.01317.226-0.569-0.5690.0000.0000.0000.000
12A12LEU00.0530.01513.636-0.301-0.3010.0000.0000.0000.000
13A13GLY00.0290.02812.897-1.071-1.0710.0000.0000.0000.000
14A14GLY00.0470.02112.507-1.323-1.3230.0000.0000.0000.000
15A15ALA0-0.029-0.00713.404-0.491-0.4910.0000.0000.0000.000
16A16PHE00.019-0.0108.051-0.639-0.6390.0000.0000.0000.000
17A17ALA00.0050.0048.444-2.313-2.3130.0000.0000.0000.000
18A18ARG10.8110.8599.64315.31915.3190.0000.0000.0000.000
19A19ALA0-0.020-0.0058.877-0.713-0.7130.0000.0000.0000.000
21A21LYS10.9050.9605.86416.93916.9390.0000.0000.0000.000
22A22GLY00.0120.0347.1230.6440.6440.0000.0000.0000.000
25A25LEU00.0140.0105.731-2.073-2.0730.0000.0000.0000.000
26A26LEU00.0110.0167.5423.4763.4760.0000.0000.0000.000
27A27LEU0-0.004-0.00310.1510.0110.0110.0000.0000.0000.000
28A28SER00.0450.00812.8901.2661.2660.0000.0000.0000.000
29A29GLY0-0.001-0.02215.626-0.013-0.0130.0000.0000.0000.000
30A30ARG11.0221.01018.91011.92511.9250.0000.0000.0000.000
31A31ARG10.8640.93721.85613.13213.1320.0000.0000.0000.000
32A32ALA00.1020.04021.844-0.348-0.3480.0000.0000.0000.000
33A33GLY00.0400.02622.089-0.403-0.4030.0000.0000.0000.000
34A34ALA0-0.016-0.01821.737-0.222-0.2220.0000.0000.0000.000
35A35LEU0-0.038-0.01715.976-0.439-0.4390.0000.0000.0000.000
36A36ALA00.0250.01817.728-0.981-0.9810.0000.0000.0000.000
37A37GLU-1-0.846-0.90219.136-14.733-14.7330.0000.0000.0000.000
38A38LEU0-0.010-0.00114.671-0.414-0.4140.0000.0000.0000.000
39A39ALA0-0.005-0.01414.445-1.021-1.0210.0000.0000.0000.000
40A40ARG10.8980.94014.86312.78612.7860.0000.0000.0000.000
41A41GLU-1-0.809-0.85116.593-17.418-17.4180.0000.0000.0000.000
42A42VAL0-0.079-0.06111.517-0.525-0.5250.0000.0000.0000.000
43A43GLY00.0390.02611.853-1.776-1.7760.0000.0000.0000.000
44A44ALA0-0.055-0.01510.859-1.640-1.6400.0000.0000.0000.000
45A45ARG10.9240.9439.19131.36431.3640.0000.0000.0000.000
46A46ALA0-0.009-0.00813.392-0.566-0.5660.0000.0000.0000.000
47A47LEU00.0400.02013.6800.5470.5470.0000.0000.0000.000
48A48PRO0-0.050-0.03316.967-0.168-0.1680.0000.0000.0000.000
49A49ALA00.0700.04019.0410.1030.1030.0000.0000.0000.000
50A50ASP-1-0.956-0.99120.943-12.117-12.1170.0000.0000.0000.000
51A51LEU0-0.028-0.01817.088-0.042-0.0420.0000.0000.0000.000
52A52ALA0-0.011-0.01321.214-0.048-0.0480.0000.0000.0000.000
53A53ASP-1-0.817-0.89524.268-11.120-11.1200.0000.0000.0000.000
54A54GLU-1-0.790-0.87223.138-12.683-12.6830.0000.0000.0000.000
55A55LEU0-0.012-0.00922.686-0.525-0.5250.0000.0000.0000.000
56A56GLU-1-0.846-0.91822.019-13.133-13.1330.0000.0000.0000.000
57A57ALA0-0.047-0.02718.854-0.869-0.8690.0000.0000.0000.000
58A58LYS10.8970.95517.88712.32212.3220.0000.0000.0000.000
59A59ALA00.0020.00018.433-0.758-0.7580.0000.0000.0000.000
60A60LEU0-0.035-0.01214.068-0.883-0.8830.0000.0000.0000.000
61A61LEU0-0.020-0.02512.384-1.698-1.6980.0000.0000.0000.000
62A62GLU-1-0.876-0.92414.197-15.894-15.8940.0000.0000.0000.000
63A63GLU-1-0.944-0.96215.109-20.002-20.0020.0000.0000.0000.000
64A64ALA0-0.067-0.03710.395-1.536-1.5360.0000.0000.0000.000
65A65GLY00.0110.01410.352-2.716-2.7160.0000.0000.0000.000
66A66PRO0-0.031-0.0338.478-0.740-0.7400.0000.0000.0000.000
67A67LEU00.0020.0086.041-5.161-5.1610.0000.0000.0000.000
71A71VAL0-0.026-0.0196.8501.0231.0230.0000.0000.0000.000
72A72HIS00.0770.0429.620-0.572-0.5720.0000.0000.0000.000
73A73ALA0-0.049-0.01813.1181.2041.2040.0000.0000.0000.000
74A74VAL0-0.048-0.02514.7780.6560.6560.0000.0000.0000.000
75A75GLY00.0550.03318.2020.2270.2270.0000.0000.0000.000
76A76LYS10.8200.90021.66212.00012.0000.0000.0000.0000.000
77A77ALA00.0520.01025.174-0.078-0.0780.0000.0000.0000.000
78A78GLY00.0560.02927.6690.0600.0600.0000.0000.0000.000
79A79ARG10.8430.92131.4908.3138.3130.0000.0000.0000.000
80A80ALA00.0270.02034.4520.1490.1490.0000.0000.0000.000
81A81SER0-0.050-0.03737.129-0.017-0.0170.0000.0000.0000.000
82A82VAL00.0330.00638.509-0.076-0.0760.0000.0000.0000.000
83A83ARG10.8450.90940.8086.6966.6960.0000.0000.0000.000
84A84GLU-1-0.807-0.88143.308-6.649-6.6490.0000.0000.0000.000
85A85ALA0-0.031-0.01238.772-0.153-0.1530.0000.0000.0000.000
86A86GLY00.0790.04838.1020.1000.1000.0000.0000.0000.000
87A87ARG10.7950.86737.2197.6617.6610.0000.0000.0000.000
88A88ASP-1-0.828-0.91836.409-7.974-7.9740.0000.0000.0000.000
89A89LEU00.0070.01731.751-0.297-0.2970.0000.0000.0000.000
90A90VAL0-0.037-0.03031.921-0.326-0.3260.0000.0000.0000.000
91A91GLU-1-0.776-0.86831.435-8.695-8.6950.0000.0000.0000.000
92A92GLU-1-0.908-0.94730.018-9.599-9.5990.0000.0000.0000.000
93A93MET0-0.100-0.04927.470-0.591-0.5910.0000.0000.0000.000
94A94LEU00.026-0.00126.344-0.493-0.4930.0000.0000.0000.000
95A95ALA00.0450.02926.214-0.412-0.4120.0000.0000.0000.000
96A96ALA0-0.016-0.01524.071-0.537-0.5370.0000.0000.0000.000
97A97HIS0-0.050-0.01421.638-1.087-1.0870.0000.0000.0000.000
98A98LEU00.0260.02221.233-0.530-0.5300.0000.0000.0000.000
99A99LEU00.0060.00922.546-0.412-0.4120.0000.0000.0000.000
100A100THR0-0.005-0.00719.853-0.643-0.6430.0000.0000.0000.000
101A101ALA0-0.020-0.00917.889-0.761-0.7610.0000.0000.0000.000
102A102ALA00.0130.00318.274-0.621-0.6210.0000.0000.0000.000
103A103PHE0-0.008-0.00420.297-0.218-0.2180.0000.0000.0000.000
104A104VAL00.006-0.00414.186-0.462-0.4620.0000.0000.0000.000
105A105LEU0-0.033-0.02614.969-0.882-0.8820.0000.0000.0000.000
106A106LYS10.8230.90516.57411.95811.9580.0000.0000.0000.000
107A107HIS0-0.011-0.02317.852-0.173-0.1730.0000.0000.0000.000
108A108ALA0-0.0060.01412.374-0.674-0.6740.0000.0000.0000.000
109A109ARG10.8280.90812.26218.51418.5140.0000.0000.0000.000
110A110PHE0-0.001-0.0058.914-2.258-2.2580.0000.0000.0000.000
111A111GLN00.0300.0215.5655.3235.3230.0000.0000.0000.000
112A112LYS10.9480.9658.68920.75320.7530.0000.0000.0000.000
113A113GLY00.0300.0148.461-2.162-2.1620.0000.0000.0000.000
114A114ALA0-0.0380.0076.400-1.060-1.0600.0000.0000.0000.000
116A116ALA00.0450.0207.794-1.893-1.8930.0000.0000.0000.000
117A117VAL0-0.0180.0007.8281.6271.6270.0000.0000.0000.000
118A118PHE00.0560.02410.8570.0100.0100.0000.0000.0000.000
119A119PHE0-0.012-0.00511.5490.4070.4070.0000.0000.0000.000
120A120GLY00.0560.03816.7070.4280.4280.0000.0000.0000.000
121A121ALA0-0.038-0.04420.0770.0850.0850.0000.0000.0000.000
122A122TYR00.0180.01320.2690.2840.2840.0000.0000.0000.000
123A123PRO00.0420.01624.9310.2800.2800.0000.0000.0000.000
124A124ARG10.9530.96228.1209.1639.1630.0000.0000.0000.000
125A125TYR0-0.0030.01027.1230.1800.1800.0000.0000.0000.000
126A126VAL00.0040.00326.2000.0320.0320.0000.0000.0000.000
127A127GLN0-0.038-0.00829.433-0.080-0.0800.0000.0000.0000.000
128A128VAL00.0110.01132.3070.2300.2300.0000.0000.0000.000
129A129PRO00.026-0.00534.778-0.087-0.0870.0000.0000.0000.000
130A130GLY00.0060.01536.109-0.069-0.0690.0000.0000.0000.000
131A131PHE00.014-0.00730.719-0.132-0.1320.0000.0000.0000.000
132A132ALA00.0400.02431.313-0.269-0.2690.0000.0000.0000.000
133A133ALA00.0560.02932.034-0.136-0.1360.0000.0000.0000.000
134A134TYR00.0120.00222.807-0.372-0.3720.0000.0000.0000.000
135A135ALA0-0.028-0.01927.112-0.343-0.3430.0000.0000.0000.000
136A136ALA00.0110.01228.134-0.210-0.2100.0000.0000.0000.000
137A137ALA00.0070.00826.198-0.188-0.1880.0000.0000.0000.000
138A138LYS10.8250.91019.79012.67412.6740.0000.0000.0000.000
139A139GLY00.0140.01023.751-0.323-0.3230.0000.0000.0000.000
140A140ALA00.0060.00125.890-0.098-0.0980.0000.0000.0000.000
141A141LEU0-0.009-0.00118.850-0.186-0.1860.0000.0000.0000.000
142A142GLU-1-0.762-0.86820.948-12.216-12.2160.0000.0000.0000.000
143A143ALA0-0.0020.00022.194-0.206-0.2060.0000.0000.0000.000
144A144TYR0-0.0050.00120.977-0.171-0.1710.0000.0000.0000.000
145A145LEU00.012-0.00616.876-0.286-0.2860.0000.0000.0000.000
146A146GLU-1-0.876-0.90619.711-13.122-13.1220.0000.0000.0000.000
147A147ALA0-0.034-0.01821.987-0.016-0.0160.0000.0000.0000.000
148A148ALA00.0570.02919.761-0.038-0.0380.0000.0000.0000.000
149A149ARG10.7930.88516.57013.69513.6950.0000.0000.0000.000
150A150LYS10.9380.94418.48810.92810.9280.0000.0000.0000.000
151A151GLU-1-0.976-0.97520.655-12.505-12.5050.0000.0000.0000.000
152A152LEU00.0770.02814.609-0.218-0.2180.0000.0000.0000.000
153A153LEU00.0090.01815.153-0.765-0.7650.0000.0000.0000.000
154A154ARG10.8890.94916.85212.55312.5530.0000.0000.0000.000
155A155GLU-1-0.931-0.95814.964-17.509-17.5090.0000.0000.0000.000
156A156GLY0-0.038-0.02113.498-1.212-1.2120.0000.0000.0000.000
157A157VAL0-0.032-0.01310.708-1.759-1.7590.0000.0000.0000.000
158A158HIS0-0.036-0.0229.8682.6572.6570.0000.0000.0000.000
159A159LEU00.0260.01911.196-1.192-1.1920.0000.0000.0000.000
160A160VAL0-0.016-0.01510.2080.8920.8920.0000.0000.0000.000
161A161LEU0-0.0250.00213.123-0.149-0.1490.0000.0000.0000.000
162A162VAL00.0180.00212.3300.3100.3100.0000.0000.0000.000
163A163ARG10.8170.87815.59211.88111.8810.0000.0000.0000.000
164A164LEU00.0250.01615.0200.0410.0410.0000.0000.0000.000
165A165PRO00.0050.00418.8060.5040.5040.0000.0000.0000.000
166A166ALA00.0160.00421.353-0.255-0.2550.0000.0000.0000.000
167A167VAL00.0020.00618.244-0.161-0.1610.0000.0000.0000.000
168A168ALA00.0220.00021.5040.1960.1960.0000.0000.0000.000
169A169THR0-0.001-0.00419.531-0.414-0.4140.0000.0000.0000.000
170A170GLY00.0410.00122.8330.3950.3950.0000.0000.0000.000
171A171LEU0-0.025-0.00221.8740.2720.2720.0000.0000.0000.000
172A172TRP00.0450.00823.9060.4290.4290.0000.0000.0000.000
173A173ALA00.0010.02127.7220.3490.3490.0000.0000.0000.000
174A174PRO00.0090.00428.8840.2930.2930.0000.0000.0000.000
175A175LEU0-0.060-0.02528.4130.2390.2390.0000.0000.0000.000
176A176GLY00.0330.02532.1140.2330.2330.0000.0000.0000.000
177A177GLY00.0030.01730.0130.1030.1030.0000.0000.0000.000
178A178PRO0-0.038-0.03526.0890.0030.0030.0000.0000.0000.000
179A179PRO00.0070.02426.9860.2370.2370.0000.0000.0000.000
180A180LYS10.9980.97728.4237.8617.8610.0000.0000.0000.000
181A181GLY00.0120.00327.7770.0750.0750.0000.0000.0000.000
182A182ALA0-0.056-0.00824.182-0.252-0.2520.0000.0000.0000.000
183A183LEU00.0050.00718.5350.0190.0190.0000.0000.0000.000
184A184SER00.0320.00818.8840.1360.1360.0000.0000.0000.000
185A185PRO00.010-0.01316.608-0.287-0.2870.0000.0000.0000.000
186A186GLU-1-0.808-0.91014.480-15.403-15.4030.0000.0000.0000.000
187A187GLU-1-0.772-0.85514.107-15.052-15.0520.0000.0000.0000.000
188A188ALA0-0.045-0.02515.314-0.203-0.2030.0000.0000.0000.000
189A189ALA00.000-0.00610.768-0.419-0.4190.0000.0000.0000.000
190A190ARG10.7860.85910.27514.52714.5270.0000.0000.0000.000
191A191LYS10.9410.96811.09312.78012.7800.0000.0000.0000.000
192A192VAL0-0.033-0.0048.8800.0370.0370.0000.0000.0000.000
193A193LEU0-0.013-0.0114.817-0.830-0.8300.0000.0000.0000.000
194A194GLU-1-0.858-0.9197.767-17.144-17.1440.0000.0000.0000.000
195A195GLY0-0.022-0.02010.5360.1940.1940.0000.0000.0000.000
196A196LEU0-0.028-0.0146.2420.0940.0940.0000.0000.0000.000
198A198ARG10.8460.9228.62817.63217.6320.0000.0000.0000.000
199A199GLU-1-0.886-0.9209.575-18.390-18.3900.0000.0000.0000.000
200A200PRO0-0.031-0.02612.250-0.795-0.7950.0000.0000.0000.000
201A201VAL00.0100.01510.9720.1920.1920.0000.0000.0000.000
202A202PRO0-0.026-0.00614.1170.5140.5140.0000.0000.0000.000
203A203ALA0-0.008-0.01317.086-0.535-0.5350.0000.0000.0000.000
204A204LEU0-0.0040.00419.0870.0460.0460.0000.0000.0000.000
205A205LEU0-0.053-0.02916.582-0.232-0.2320.0000.0000.0000.000
206A206GLU-1-0.959-0.97721.173-11.099-11.0990.0000.0000.0000.000
207A207VAL-1-0.956-0.96821.894-11.672-11.6720.0000.0000.0000.000