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: 2M1ZR

Calculation Name: 6CI9-D-Xray547

Preferred Name:

Target Type:

Ligand Name: nadp nicotinamide-adenine-dinucleotide phosphate | 1-aminopropan-2-one | magnesium ion | chloride ion

Ligand 3-letter code: NAP | F3V | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6CI9

Chain ID: D

ChEMBL ID:

UniProt ID: A0QP46

Base Structure: X-ray

Registration Date: 2025-10-06

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 259
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3047223.297863
FMO2-HF: Nuclear repulsion 2953343.643384
FMO2-HF: Total energy -93879.654479
FMO2-MP2: Total energy -94154.418992


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:SER)


Summations of interaction energy for fragment #1(A:-1:SER)
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.
-117.537-115.455-0.013-1.059-1.011-0.004
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.893
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].
3A1MET0-0.053-0.0253.497-10.488-8.406-0.013-1.059-1.011-0.004
4A2PHE00.0280.0176.0264.1964.1960.0000.0000.0000.000
5A3THR0-0.038-0.0499.222-2.324-2.3240.0000.0000.0000.000
6A4SER0-0.025-0.00711.0721.4671.4670.0000.0000.0000.000
7A5LEU00.025-0.00412.3991.4381.4380.0000.0000.0000.000
8A6GLU-1-0.840-0.90614.840-18.185-18.1850.0000.0000.0000.000
9A7GLY0-0.051-0.02416.5030.0920.0920.0000.0000.0000.000
10A8ARG10.7590.87215.92318.80818.8080.0000.0000.0000.000
11A9SER00.005-0.00521.4200.0540.0540.0000.0000.0000.000
12A10ALA00.031-0.00123.313-0.072-0.0720.0000.0000.0000.000
13A11ILE00.0030.00925.3830.3910.3910.0000.0000.0000.000
14A12VAL0-0.018-0.01125.431-0.285-0.2850.0000.0000.0000.000
15A13THR00.0310.01528.5190.2110.2110.0000.0000.0000.000
16A14GLY00.0130.00731.516-0.119-0.1190.0000.0000.0000.000
17A15GLY00.0110.00329.676-0.149-0.1490.0000.0000.0000.000
18A16SER0-0.0040.00129.785-0.267-0.2670.0000.0000.0000.000
19A17LYS10.8980.95831.8118.5828.5820.0000.0000.0000.000
20A18GLY00.0660.03530.311-0.179-0.1790.0000.0000.0000.000
21A19ILE00.012-0.01226.509-0.408-0.4080.0000.0000.0000.000
22A20GLY00.0170.01126.462-0.454-0.4540.0000.0000.0000.000
23A21ARG10.8430.91326.58710.88910.8890.0000.0000.0000.000
24A22GLY00.0300.01323.968-0.434-0.4340.0000.0000.0000.000
25A23ILE0-0.020-0.00522.238-0.857-0.8570.0000.0000.0000.000
26A24ALA0-0.0030.00021.991-0.611-0.6110.0000.0000.0000.000
27A25GLU-1-0.856-0.93821.490-13.579-13.5790.0000.0000.0000.000
28A26THR0-0.055-0.04617.044-0.870-0.8700.0000.0000.0000.000
29A27PHE0-0.013-0.02117.588-1.057-1.0570.0000.0000.0000.000
30A28ALA00.0200.02818.622-0.612-0.6120.0000.0000.0000.000
31A29ASN0-0.015-0.01616.367-0.191-0.1910.0000.0000.0000.000
32A30ALA0-0.063-0.01914.264-1.325-1.3250.0000.0000.0000.000
33A31GLY00.0170.00115.286-0.482-0.4820.0000.0000.0000.000
34A32VAL0-0.062-0.02417.4930.4510.4510.0000.0000.0000.000
35A33ASP-1-0.817-0.89820.052-13.407-13.4070.0000.0000.0000.000
36A34VAL0-0.035-0.02923.3240.1190.1190.0000.0000.0000.000
37A35VAL0-0.0120.00525.9040.3420.3420.0000.0000.0000.000
38A36ILE0-0.0120.00528.163-0.094-0.0940.0000.0000.0000.000
39A37THR00.0190.00230.5900.2540.2540.0000.0000.0000.000
40A38GLY00.033-0.00434.011-0.164-0.1640.0000.0000.0000.000
41A39ARG10.9830.99036.7877.7447.7440.0000.0000.0000.000
42A40ASN0-0.0090.00639.4470.0750.0750.0000.0000.0000.000
43A41GLN0-0.006-0.03038.401-0.110-0.1100.0000.0000.0000.000
44A42ASP-1-0.877-0.92538.456-7.735-7.7350.0000.0000.0000.000
45A43ASP-1-0.819-0.90736.409-8.741-8.7410.0000.0000.0000.000
46A44LEU0-0.075-0.03633.628-0.359-0.3590.0000.0000.0000.000
47A45ASP-1-0.830-0.90733.662-8.775-8.7750.0000.0000.0000.000
48A46ARG10.8100.89832.5539.1229.1220.0000.0000.0000.000
49A47THR0-0.006-0.01929.059-0.248-0.2480.0000.0000.0000.000
50A48VAL0-0.025-0.01029.566-0.400-0.4000.0000.0000.0000.000
51A49ALA0-0.021-0.00930.114-0.243-0.2430.0000.0000.0000.000
52A50ASP-1-0.858-0.91129.158-10.267-10.2670.0000.0000.0000.000
53A51LEU0-0.047-0.02024.508-0.397-0.3970.0000.0000.0000.000
54A52SER0-0.065-0.03125.806-0.390-0.3900.0000.0000.0000.000
55A53GLY0-0.051-0.03024.872-0.026-0.0260.0000.0000.0000.000
56A54THR0-0.025-0.01021.273-0.434-0.4340.0000.0000.0000.000
57A55ARG10.8050.91016.99116.93716.9370.0000.0000.0000.000
58A56GLY0-0.0180.00220.0340.3820.3820.0000.0000.0000.000
59A57LYS10.9230.94121.57612.04212.0420.0000.0000.0000.000
60A58VAL00.0610.03624.6950.1630.1630.0000.0000.0000.000
61A59THR0-0.033-0.01526.9950.5010.5010.0000.0000.0000.000
62A60ALA00.0670.03330.664-0.127-0.1270.0000.0000.0000.000
63A61VAL0-0.030-0.01033.4960.1670.1670.0000.0000.0000.000
64A62ARG00.0820.05935.976-0.076-0.0760.0000.0000.0000.000
65A63ALA0-0.012-0.01737.5770.1300.1300.0000.0000.0000.000
66A64ASP-1-0.873-0.91939.080-7.716-7.7160.0000.0000.0000.000
67A65VAL0-0.029-0.01635.997-0.013-0.0130.0000.0000.0000.000
68A66THR0-0.047-0.04439.2170.0280.0280.0000.0000.0000.000
69A67ASP-1-0.830-0.90642.382-6.997-6.9970.0000.0000.0000.000
70A68PRO0-0.024-0.03241.800-0.198-0.1980.0000.0000.0000.000
71A69GLU-1-0.835-0.89641.945-7.382-7.3820.0000.0000.0000.000
72A70ASP-1-0.752-0.85140.359-7.782-7.7820.0000.0000.0000.000
73A71ALA0-0.0340.00537.547-0.267-0.2670.0000.0000.0000.000
74A72ARG10.8400.88637.1657.1627.1620.0000.0000.0000.000
75A73ARG10.8140.89038.2897.6577.6570.0000.0000.0000.000
76A74THR0-0.003-0.01933.420-0.166-0.1660.0000.0000.0000.000
77A75VAL0-0.0140.01033.253-0.324-0.3240.0000.0000.0000.000
78A76ALA0-0.0030.00134.140-0.205-0.2050.0000.0000.0000.000
79A77GLU-1-0.852-0.91435.348-8.603-8.6030.0000.0000.0000.000
80A78THR0-0.010-0.03129.346-0.218-0.2180.0000.0000.0000.000
81A79VAL0-0.060-0.02430.907-0.270-0.2700.0000.0000.0000.000
82A80SER0-0.052-0.03432.184-0.031-0.0310.0000.0000.0000.000
83A81ARG10.7390.85731.0389.3519.3510.0000.0000.0000.000
84A82HIS0-0.031-0.03326.581-0.043-0.0430.0000.0000.0000.000
85A83GLY00.0090.02627.381-0.334-0.3340.0000.0000.0000.000
86A84GLY00.003-0.00628.085-0.019-0.0190.0000.0000.0000.000
87A85LEU0-0.026-0.01227.2950.1210.1210.0000.0000.0000.000
88A86ASP-1-0.823-0.90722.935-13.401-13.4010.0000.0000.0000.000
89A87ILE00.005-0.00620.097-0.090-0.0900.0000.0000.0000.000
90A88VAL0-0.006-0.00624.6780.3070.3070.0000.0000.0000.000
91A89CYS00.0030.01024.769-0.256-0.2560.0000.0000.0000.000
92A90ALA00.0160.00627.3990.3420.3420.0000.0000.0000.000
93A91ASN0-0.006-0.00528.594-0.185-0.1850.0000.0000.0000.000
94A92ALA0-0.029-0.00730.6920.1280.1280.0000.0000.0000.000
95A93GLY00.009-0.01134.1980.0510.0510.0000.0000.0000.000
96A94ILE0-0.046-0.01936.520-0.018-0.0180.0000.0000.0000.000
97A95PHE00.0400.01435.2710.0120.0120.0000.0000.0000.000
98A96PRO00.0550.04540.5800.0250.0250.0000.0000.0000.000
99A97SER0-0.009-0.02144.0920.0300.0300.0000.0000.0000.000
100A98GLY00.0440.01445.9640.1140.1140.0000.0000.0000.000
101A99ARG10.8890.95749.1276.1626.1620.0000.0000.0000.000
102A100LEU0-0.017-0.00750.6590.0060.0060.0000.0000.0000.000
103A101GLU-1-0.901-0.97052.304-5.932-5.9320.0000.0000.0000.000
104A102ASP-1-0.899-0.94953.178-5.825-5.8250.0000.0000.0000.000
105A103LEU0-0.108-0.04148.4480.0030.0030.0000.0000.0000.000
106A104THR00.014-0.01652.4400.0810.0810.0000.0000.0000.000
107A105PRO0-0.014-0.03552.012-0.122-0.1220.0000.0000.0000.000
108A106ASP-1-0.869-0.92051.226-6.158-6.1580.0000.0000.0000.000
109A107ASP-1-0.807-0.87848.795-6.512-6.5120.0000.0000.0000.000
110A108ILE0-0.039-0.02647.098-0.229-0.2290.0000.0000.0000.000
111A109GLU-1-0.800-0.87246.415-7.019-7.0190.0000.0000.0000.000
112A110GLN0-0.031-0.01645.460-0.229-0.2290.0000.0000.0000.000
113A111VAL0-0.0090.01041.655-0.220-0.2200.0000.0000.0000.000
114A112LEU0-0.037-0.02841.553-0.255-0.2550.0000.0000.0000.000
115A113GLY00.0240.01642.053-0.156-0.1560.0000.0000.0000.000
116A114VAL0-0.005-0.01038.468-0.173-0.1730.0000.0000.0000.000
117A115ASN0-0.012-0.00137.308-0.247-0.2470.0000.0000.0000.000
118A116PHE0-0.046-0.01236.819-0.255-0.2550.0000.0000.0000.000
119A117LYS10.8170.88038.6286.8126.8120.0000.0000.0000.000
120A118GLY00.1000.05438.499-0.067-0.0670.0000.0000.0000.000
121A119THR0-0.072-0.04033.429-0.368-0.3680.0000.0000.0000.000
122A120VAL0-0.031-0.01135.117-0.207-0.2070.0000.0000.0000.000
123A121TYR0-0.010-0.01037.335-0.050-0.0500.0000.0000.0000.000
124A122ILE0-0.0030.00032.905-0.028-0.0280.0000.0000.0000.000
125A123VAL0-0.0010.00331.754-0.216-0.2160.0000.0000.0000.000
126A124GLN0-0.028-0.03133.986-0.010-0.0100.0000.0000.0000.000
127A125ALA0-0.016-0.00136.4040.0450.0450.0000.0000.0000.000
128A126ALA00.0440.03131.465-0.019-0.0190.0000.0000.0000.000
129A127LEU0-0.0170.00232.548-0.247-0.2470.0000.0000.0000.000
130A128GLN0-0.0090.00933.011-0.073-0.0730.0000.0000.0000.000
131A129ALA00.0260.01231.124-0.108-0.1080.0000.0000.0000.000
132A130LEU00.0250.01927.306-0.318-0.3180.0000.0000.0000.000
133A131THR0-0.030-0.03028.181-0.354-0.3540.0000.0000.0000.000
134A132ALA0-0.040-0.01629.391-0.194-0.1940.0000.0000.0000.000
135A133SER0-0.0150.00025.004-0.366-0.3660.0000.0000.0000.000
136A134GLY0-0.047-0.02224.581-0.499-0.4990.0000.0000.0000.000
137A135HIS10.8300.91419.99714.31414.3140.0000.0000.0000.000
138A136GLY00.0580.05023.005-0.406-0.4060.0000.0000.0000.000
139A137ARG10.7910.90319.28815.06715.0670.0000.0000.0000.000
140A138VAL00.0040.00324.6230.3160.3160.0000.0000.0000.000
141A139VAL00.0000.00422.729-0.186-0.1860.0000.0000.0000.000
142A140VAL0-0.015-0.01426.0920.3290.3290.0000.0000.0000.000
143A141THR0-0.012-0.01128.649-0.385-0.3850.0000.0000.0000.000
144A142SER00.0140.00029.7850.4530.4530.0000.0000.0000.000
145A143SER0-0.008-0.01231.7090.0620.0620.0000.0000.0000.000
146A144ILE00.0300.01231.0760.0270.0270.0000.0000.0000.000
147A145THR0-0.0150.00633.4870.2990.2990.0000.0000.0000.000
148A146GLY00.005-0.02036.918-0.020-0.0200.0000.0000.0000.000
149A147PRO0-0.122-0.05134.2980.1460.1460.0000.0000.0000.000
150A148ILE0-0.030-0.00232.047-0.037-0.0370.0000.0000.0000.000
151A149THR00.0350.02136.1380.1910.1910.0000.0000.0000.000
152A150GLY00.0210.01038.7020.0290.0290.0000.0000.0000.000
153A151TYR00.007-0.02140.979-0.022-0.0220.0000.0000.0000.000
154A152PRO0-0.028-0.02743.0210.0950.0950.0000.0000.0000.000
155A153GLY00.0150.02446.048-0.029-0.0290.0000.0000.0000.000
156A154TRP00.0200.00038.465-0.035-0.0350.0000.0000.0000.000
157A155SER00.0190.01443.256-0.139-0.1390.0000.0000.0000.000
158A156HIS00.0350.02344.808-0.123-0.1230.0000.0000.0000.000
159A157TYR00.0480.02435.595-0.162-0.1620.0000.0000.0000.000
160A158GLY00.0780.03639.580-0.210-0.2100.0000.0000.0000.000
161A159ALA00.002-0.00139.924-0.163-0.1630.0000.0000.0000.000
162A160SER0-0.051-0.03839.676-0.166-0.1660.0000.0000.0000.000
163A161LYS10.8620.95134.1549.0969.0960.0000.0000.0000.000
164A162ALA00.0290.01735.748-0.284-0.2840.0000.0000.0000.000
165A163ALA00.0050.00537.823-0.092-0.0920.0000.0000.0000.000
166A164GLN00.009-0.01033.252-0.006-0.0060.0000.0000.0000.000
167A165LEU0-0.008-0.00731.888-0.213-0.2130.0000.0000.0000.000
168A166GLY0-0.031-0.01134.807-0.053-0.0530.0000.0000.0000.000
169A167PHE00.012-0.00234.3190.0310.0310.0000.0000.0000.000
170A168LEU0-0.0040.00730.1760.0140.0140.0000.0000.0000.000
171A169ARG10.9630.98132.6619.2689.2680.0000.0000.0000.000
172A170THR00.0110.02034.2060.0140.0140.0000.0000.0000.000
173A171ALA00.0240.01233.830-0.061-0.0610.0000.0000.0000.000
174A172ALA00.0200.00530.415-0.119-0.1190.0000.0000.0000.000
175A173MET0-0.048-0.02431.629-0.145-0.1450.0000.0000.0000.000
176A174GLU-1-0.926-0.96034.249-8.370-8.3700.0000.0000.0000.000
177A175LEU0-0.042-0.02630.7820.0550.0550.0000.0000.0000.000
178A176ALA00.0780.04929.277-0.237-0.2370.0000.0000.0000.000
179A177PRO0-0.044-0.02729.775-0.253-0.2530.0000.0000.0000.000
180A178LYS10.8620.92631.2109.2019.2010.0000.0000.0000.000
181A179LYS10.8790.94825.65110.65410.6540.0000.0000.0000.000
182A180ILE0-0.0310.00625.870-0.469-0.4690.0000.0000.0000.000
183A181THR0-0.034-0.00922.9920.3730.3730.0000.0000.0000.000
184A182ILE00.000-0.00426.1240.0210.0210.0000.0000.0000.000
185A183ASN0-0.023-0.02323.9290.3730.3730.0000.0000.0000.000
186A184ALA00.0220.01126.9190.1280.1280.0000.0000.0000.000
187A185VAL00.0010.01223.565-0.342-0.3420.0000.0000.0000.000
188A186LEU0-0.026-0.02026.3460.4640.4640.0000.0000.0000.000
189A187PRO00.0130.00127.669-0.161-0.1610.0000.0000.0000.000
190A188GLY00.0340.01228.7940.3990.3990.0000.0000.0000.000
191A189ASN0-0.0010.00730.8250.3630.3630.0000.0000.0000.000
192A190ILE0-0.032-0.01226.852-0.311-0.3110.0000.0000.0000.000
193A191MET00.0490.02229.4570.3390.3390.0000.0000.0000.000
194A192THR0-0.051-0.03129.869-0.312-0.3120.0000.0000.0000.000
195A193GLU-1-0.762-0.88732.349-9.600-9.6000.0000.0000.0000.000
196A194GLY0-0.0010.00635.1740.2420.2420.0000.0000.0000.000
197A195LEU0-0.064-0.03433.6630.1600.1600.0000.0000.0000.000
198A196ASP-1-0.877-0.94035.978-8.793-8.7930.0000.0000.0000.000
199A197GLU-1-1.005-1.00338.204-7.651-7.6510.0000.0000.0000.000
200A198MET0-0.079-0.02539.6570.2720.2720.0000.0000.0000.000
201A199GLY0-0.0020.00641.4730.1600.1600.0000.0000.0000.000
202A200GLN0-0.048-0.05038.326-0.092-0.0920.0000.0000.0000.000
203A201ASP-1-0.881-0.94240.790-7.177-7.1770.0000.0000.0000.000
204A202TYR0-0.026-0.02536.880-0.018-0.0180.0000.0000.0000.000
205A203LEU0-0.008-0.00735.477-0.232-0.2320.0000.0000.0000.000
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207A205GLN00.0070.02038.664-0.101-0.1010.0000.0000.0000.000
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