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: 65NRZ

Calculation Name: 7LXJ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: methyl (8r)-8-{[(4p)-6-amino-3h-purin-3-yl]methyl}-4-hydroxy-6-(5,6,7-trimethoxy-1h-indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carboxylate | 2-deoxy-5-phosphono-ribose | calcium ion

Ligand 3-letter code: YNY | ORP | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7LXJ

Chain ID: A

ChEMBL ID:

UniProt ID:

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3044554.828505
FMO2-HF: Nuclear repulsion 2951129.402381
FMO2-HF: Total energy -93425.426124
FMO2-MP2: Total energy -93703.607788


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:VAL)


Summations of interaction energy for fragment #1(A:-1:VAL)
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.
-21.204-17.8070.58-1.466-2.512-0.015
Interaction energy analysis for fragmet #1(A:-1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.913
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].
3A1MET0-0.023-0.0322.661-0.1382.8170.584-1.435-2.105-0.015
4A2HIS00.0430.0055.2874.2914.378-0.001-0.004-0.0820.000
8A6LYS10.8540.9274.28837.47337.590-0.001-0.010-0.1060.000
11A9GLN00.008-0.0044.785-2.451-2.346-0.001-0.004-0.1000.000
73A71LEU0-0.081-0.0344.378-1.776-1.643-0.001-0.013-0.1190.000
5A3PRO00.004-0.0107.931-1.310-1.3100.0000.0000.0000.000
6A4PHE00.0320.0199.9080.4240.4240.0000.0000.0000.000
7A5VAL00.0070.0067.1860.9150.9150.0000.0000.0000.000
9A7ALA00.0280.0227.2250.8760.8760.0000.0000.0000.000
10A8LEU0-0.0100.00010.9411.3591.3590.0000.0000.0000.000
12A10GLU-1-0.931-0.9509.140-18.730-18.7300.0000.0000.0000.000
13A11HIS00.0230.00310.4870.7980.7980.0000.0000.0000.000
14A12PHE0-0.037-0.02712.3181.4761.4760.0000.0000.0000.000
15A13THR0-0.005-0.0239.9560.5580.5580.0000.0000.0000.000
16A14ALA0-0.015-0.00212.4600.9700.9700.0000.0000.0000.000
17A15HIS10.8110.89315.34816.59616.5960.0000.0000.0000.000
18A16GLN0-0.056-0.01213.3540.6630.6630.0000.0000.0000.000
19A17ASN0-0.005-0.01417.2290.8230.8230.0000.0000.0000.000
20A18PRO00.0700.01719.2060.0380.0380.0000.0000.0000.000
21A19GLU-1-0.884-0.93621.068-11.645-11.6450.0000.0000.0000.000
22A20LYS10.8290.91922.48612.64112.6410.0000.0000.0000.000
23A21ALA00.0180.00118.665-0.001-0.0010.0000.0000.0000.000
24A22GLU-1-0.917-0.93720.539-12.209-12.2090.0000.0000.0000.000
25A23PRO0-0.018-0.01422.8320.0330.0330.0000.0000.0000.000
26A24MET0-0.082-0.02820.3910.2850.2850.0000.0000.0000.000
27A25ALA00.0570.02919.376-0.102-0.1020.0000.0000.0000.000
28A26ARG10.9790.99020.92311.14911.1490.0000.0000.0000.000
29A27TYR0-0.067-0.02724.5120.5470.5470.0000.0000.0000.000
30A28MET0-0.070-0.02320.7180.4870.4870.0000.0000.0000.000
31A29LYS10.9020.94021.95110.82010.8200.0000.0000.0000.000
32A30ASN0-0.008-0.00820.7400.0900.0900.0000.0000.0000.000
33A31HIS0-0.0050.01218.704-0.716-0.7160.0000.0000.0000.000
34A32PHE0-0.022-0.01314.860-0.935-0.9350.0000.0000.0000.000
35A33LEU00.0470.03611.6311.1231.1230.0000.0000.0000.000
36A34PHE0-0.020-0.02114.956-0.134-0.1340.0000.0000.0000.000
37A35LEU00.0230.01312.0280.1010.1010.0000.0000.0000.000
38A36GLY00.0230.00915.9430.7580.7580.0000.0000.0000.000
39A37ILE0-0.021-0.01015.9950.8310.8310.0000.0000.0000.000
40A38GLN00.0510.01619.745-0.006-0.0060.0000.0000.0000.000
41A39THR00.006-0.01422.202-0.296-0.2960.0000.0000.0000.000
42A40PRO0-0.016-0.01023.211-0.220-0.2200.0000.0000.0000.000
43A41GLU-1-0.847-0.91520.966-13.581-13.5810.0000.0000.0000.000
44A42ARG10.8510.91417.06715.36515.3650.0000.0000.0000.000
45A43ARG10.8370.89319.35512.60512.6050.0000.0000.0000.000
46A44GLN0-0.0230.00121.916-0.042-0.0420.0000.0000.0000.000
47A45LEU00.0360.02117.411-0.034-0.0340.0000.0000.0000.000
48A46LEU00.004-0.00616.542-0.506-0.5060.0000.0000.0000.000
49A47LYS10.9040.95718.47911.39411.3940.0000.0000.0000.000
50A48ASP-1-0.798-0.88719.253-13.636-13.6360.0000.0000.0000.000
51A49ILE0-0.007-0.00214.1270.1090.1090.0000.0000.0000.000
52A50ILE0-0.034-0.02617.2300.0350.0350.0000.0000.0000.000
53A51GLN0-0.078-0.03919.6800.4860.4860.0000.0000.0000.000
54A52ILE0-0.0190.00417.7670.4890.4890.0000.0000.0000.000
55A53HIS00.002-0.00114.3590.2920.2920.0000.0000.0000.000
56A54THR0-0.052-0.01018.1930.3110.3110.0000.0000.0000.000
57A55LEU0-0.021-0.02118.771-0.777-0.7770.0000.0000.0000.000
58A56PRO00.0230.01515.3870.4590.4590.0000.0000.0000.000
59A57ASP-1-0.762-0.86918.349-13.443-13.4430.0000.0000.0000.000
60A58GLN00.006-0.00819.152-0.712-0.7120.0000.0000.0000.000
61A59LYS10.8420.91419.41013.62413.6240.0000.0000.0000.000
62A60ASP-1-0.796-0.88014.815-20.222-20.2220.0000.0000.0000.000
63A61PHE0-0.057-0.02014.864-1.612-1.6120.0000.0000.0000.000
64A62GLN00.0200.00015.284-0.258-0.2580.0000.0000.0000.000
65A63ILE00.0010.00710.457-1.353-1.3530.0000.0000.0000.000
66A64ILE0-0.013-0.01410.383-2.787-2.7870.0000.0000.0000.000
67A65ILE0-0.004-0.01111.040-1.514-1.5140.0000.0000.0000.000
68A66ARG10.8160.8749.33622.64122.6410.0000.0000.0000.000
69A67GLU-1-0.758-0.8706.097-46.301-46.3010.0000.0000.0000.000
70A68LEU0-0.055-0.0276.807-2.590-2.5900.0000.0000.0000.000
71A69TRP00.004-0.0159.5721.5831.5830.0000.0000.0000.000
72A70ASP-1-0.896-0.9325.124-37.703-37.7030.0000.0000.0000.000
74A72PRO0-0.029-0.0166.0983.5713.5710.0000.0000.0000.000
75A73GLU-1-0.876-0.9439.317-26.354-26.3540.0000.0000.0000.000
76A74ARG10.7780.86311.91017.37317.3730.0000.0000.0000.000
77A75GLU-1-0.758-0.89214.665-18.124-18.1240.0000.0000.0000.000
78A76PHE00.0130.0139.7140.3560.3560.0000.0000.0000.000
79A77GLN00.0560.03311.3161.8561.8560.0000.0000.0000.000
80A78ALA0-0.006-0.01014.4341.0691.0690.0000.0000.0000.000
81A79ALA0-0.002-0.00614.6050.9490.9490.0000.0000.0000.000
82A80ALA00.0350.01813.6300.6000.6000.0000.0000.0000.000
83A81LEU00.0150.01415.6190.8720.8720.0000.0000.0000.000
84A82ASP-1-0.820-0.88319.195-13.852-13.8520.0000.0000.0000.000
85A83ILE0-0.017-0.01315.1580.8570.8570.0000.0000.0000.000
86A84MET00.0140.02318.8420.4460.4460.0000.0000.0000.000
87A85GLN0-0.021-0.01720.3521.1191.1190.0000.0000.0000.000
88A86LYS10.8600.93421.24314.39714.3970.0000.0000.0000.000
89A87TYR00.014-0.01418.3690.1780.1780.0000.0000.0000.000
90A88LYS10.8640.95023.19511.37911.3790.0000.0000.0000.000
91A89LYS10.9220.95525.74910.69410.6940.0000.0000.0000.000
92A90HIS00.0290.01424.2720.4650.4650.0000.0000.0000.000
93A91ILE0-0.048-0.00521.939-0.156-0.1560.0000.0000.0000.000
94A92ASN0-0.0060.00825.2030.6250.6250.0000.0000.0000.000
95A93GLU-1-0.756-0.88126.011-10.911-10.9110.0000.0000.0000.000
96A94THR0-0.070-0.04924.961-0.356-0.3560.0000.0000.0000.000
97A95HIS00.0190.01320.831-0.210-0.2100.0000.0000.0000.000
98A96ILE00.0110.02522.055-0.529-0.5290.0000.0000.0000.000
99A97PRO00.0380.01321.710-0.353-0.3530.0000.0000.0000.000
100A98PHE00.0020.00314.325-0.544-0.5440.0000.0000.0000.000
101A99LEU0-0.001-0.01618.233-0.689-0.6890.0000.0000.0000.000
102A100GLU-1-0.770-0.86820.607-12.673-12.6730.0000.0000.0000.000
103A101GLU-1-0.785-0.84914.209-20.937-20.9370.0000.0000.0000.000
104A102LEU0-0.012-0.00414.266-0.752-0.7520.0000.0000.0000.000
105A103ILE0-0.034-0.00316.9240.0510.0510.0000.0000.0000.000
106A104VAL0-0.0380.00117.7610.2650.2650.0000.0000.0000.000
107A105THR0-0.0030.00712.253-0.488-0.4880.0000.0000.0000.000
108A106LYS10.7880.8908.77230.38430.3840.0000.0000.0000.000
109A107SER0-0.005-0.02215.3910.2050.2050.0000.0000.0000.000
110A108TRP00.0280.00019.1160.5600.5600.0000.0000.0000.000
111A109TRP00.0340.01121.453-0.111-0.1110.0000.0000.0000.000
112A110ASP-1-0.782-0.85720.093-15.382-15.3820.0000.0000.0000.000
113A111SER00.0440.03118.2790.2020.2020.0000.0000.0000.000
114A112VAL00.0270.00820.3040.2110.2110.0000.0000.0000.000
115A113ASP-1-0.766-0.86822.809-11.145-11.1450.0000.0000.0000.000
116A114SER0-0.081-0.04622.1450.5750.5750.0000.0000.0000.000
117A115ILE0-0.024-0.01118.6350.1310.1310.0000.0000.0000.000
118A116VAL00.0160.01622.9960.3500.3500.0000.0000.0000.000
119A117PRO00.0040.00526.2900.2860.2860.0000.0000.0000.000
120A118THR0-0.049-0.03525.7400.3910.3910.0000.0000.0000.000
121A119PHE00.0000.01123.1780.1790.1790.0000.0000.0000.000
122A120LEU00.0480.02524.7760.1960.1960.0000.0000.0000.000
123A121GLY00.0410.03627.6340.3740.3740.0000.0000.0000.000
124A122ASP-1-0.872-0.95429.354-10.105-10.1050.0000.0000.0000.000
125A123ILE0-0.044-0.02025.5570.2710.2710.0000.0000.0000.000
126A124PHE0-0.008-0.01829.2780.1980.1980.0000.0000.0000.000
127A125LEU0-0.042-0.01032.7810.3480.3480.0000.0000.0000.000
128A126LYS10.8990.95932.5789.8899.8890.0000.0000.0000.000
129A127HIS10.7680.86431.7009.7739.7730.0000.0000.0000.000
130A128PRO00.0950.04834.611-0.188-0.1880.0000.0000.0000.000
131A129GLU-1-0.801-0.90536.108-8.842-8.8420.0000.0000.0000.000
132A130LEU0-0.031-0.01731.346-0.079-0.0790.0000.0000.0000.000
133A131ILE00.0210.01932.902-0.285-0.2850.0000.0000.0000.000
134A132SER00.0110.00133.588-0.252-0.2520.0000.0000.0000.000
135A133ALA00.0080.00931.4690.0100.0100.0000.0000.0000.000
136A134TYR0-0.065-0.03526.090-0.460-0.4600.0000.0000.0000.000
137A135ILE00.0470.03030.244-0.116-0.1160.0000.0000.0000.000
138A136PRO00.013-0.00432.323-0.029-0.0290.0000.0000.0000.000
139A137LYS10.8530.92925.93611.84711.8470.0000.0000.0000.000
140A138TRP0-0.060-0.06126.028-0.127-0.1270.0000.0000.0000.000
141A139ILE00.0170.01729.403-0.144-0.1440.0000.0000.0000.000
142A140ALA00.0100.00532.6050.0140.0140.0000.0000.0000.000
143A141SER0-0.038-0.02327.015-0.219-0.2190.0000.0000.0000.000
144A142ASP-1-0.894-0.94127.955-10.165-10.1650.0000.0000.0000.000
145A143ASN0-0.0070.00021.870-0.130-0.1300.0000.0000.0000.000
146A144ILE00.0510.01125.6810.1100.1100.0000.0000.0000.000
147A145TRP00.002-0.00422.7880.3660.3660.0000.0000.0000.000
148A146LEU00.0150.01523.1200.0300.0300.0000.0000.0000.000
149A147GLN0-0.033-0.01026.2670.2620.2620.0000.0000.0000.000
150A148ARG10.7420.81227.17811.23811.2380.0000.0000.0000.000
151A149ALA0-0.010-0.01125.9360.2080.2080.0000.0000.0000.000
152A150ALA00.0040.00228.0390.2080.2080.0000.0000.0000.000
153A151ILE00.0030.00331.3780.2770.2770.0000.0000.0000.000
154A152LEU0-0.033-0.02129.3080.2430.2430.0000.0000.0000.000
155A153PHE00.000-0.00529.932-0.030-0.0300.0000.0000.0000.000
156A154GLN00.0600.02831.1020.0990.0990.0000.0000.0000.000
157A155LEU0-0.0260.00332.0940.2390.2390.0000.0000.0000.000
158A156LYS10.8820.92430.11110.52010.5200.0000.0000.0000.000
159A157TYR0-0.037-0.01833.3030.1200.1200.0000.0000.0000.000
160A158LYS10.9160.97437.7948.3878.3870.0000.0000.0000.000
161A159GLN00.0690.02541.002-0.040-0.0400.0000.0000.0000.000
162A160LYS10.8940.94537.7328.4688.4680.0000.0000.0000.000
163A161MET0-0.056-0.00138.004-0.214-0.2140.0000.0000.0000.000
164A162ASP-1-0.814-0.89639.875-7.484-7.4840.0000.0000.0000.000
165A163GLU-1-0.776-0.89441.096-6.945-6.9450.0000.0000.0000.000
166A164GLU-1-0.880-0.93743.603-6.908-6.9080.0000.0000.0000.000
167A165LEU0-0.012-0.00236.756-0.129-0.1290.0000.0000.0000.000
168A166LEU0-0.046-0.03538.127-0.190-0.1900.0000.0000.0000.000
169A167PHE00.002-0.01439.988-0.142-0.1420.0000.0000.0000.000
170A168TRP00.0330.02936.981-0.085-0.0850.0000.0000.0000.000
171A169ILE0-0.027-0.02234.895-0.100-0.1000.0000.0000.0000.000
172A170ILE0-0.035-0.02837.623-0.154-0.1540.0000.0000.0000.000
173A171GLY00.0430.02439.2720.0050.0050.0000.0000.0000.000
174A172GLN0-0.054-0.01937.630-0.012-0.0120.0000.0000.0000.000
175A173LEU0-0.023-0.01133.435-0.140-0.1400.0000.0000.0000.000
176A174HIS0-0.025-0.01337.213-0.058-0.0580.0000.0000.0000.000
177A175SER00.000-0.00340.0400.0560.0560.0000.0000.0000.000
178A176SER0-0.0190.01033.609-0.087-0.0870.0000.0000.0000.000
179A177LYS10.9070.93431.8679.8009.8000.0000.0000.0000.000
180A178GLU-1-0.833-0.89630.395-10.361-10.3610.0000.0000.0000.000
181A179PHE00.0240.00830.6500.1730.1730.0000.0000.0000.000
182A180PHE0-0.001-0.01627.1890.1480.1480.0000.0000.0000.000
183A181ILE00.0560.05330.382-0.095-0.0950.0000.0000.0000.000
184A182GLN00.0360.00532.9960.2380.2380.0000.0000.0000.000
185A183LYS10.8470.92133.0789.0149.0140.0000.0000.0000.000
186A184ALA0-0.0180.00531.7400.0520.0520.0000.0000.0000.000
187A185ILE00.0690.03533.7840.1160.1160.0000.0000.0000.000
188A186GLY00.0240.00137.2200.1810.1810.0000.0000.0000.000
189A187TRP0-0.130-0.05330.1310.1260.1260.0000.0000.0000.000
190A188VAL00.0460.00735.6390.1260.1260.0000.0000.0000.000
191A189LEU00.0460.03637.4040.1500.1500.0000.0000.0000.000
192A190ARG10.8370.91737.0678.3588.3580.0000.0000.0000.000
193A191GLU-1-0.891-0.93437.162-8.199-8.1990.0000.0000.0000.000
194A192TYR0-0.033-0.03640.0540.0670.0670.0000.0000.0000.000
195A193ALA00.0550.02742.0630.1640.1640.0000.0000.0000.000
196A194LYS10.7780.87239.6378.1148.1140.0000.0000.0000.000
197A195THR0-0.099-0.04443.2620.0130.0130.0000.0000.0000.000
198A196ASN00.002-0.00845.7430.2550.2550.0000.0000.0000.000
199A197PRO00.0250.02247.438-0.088-0.0880.0000.0000.0000.000
200A198ASP-1-0.825-0.89048.952-6.062-6.0620.0000.0000.0000.000
201A199VAL0-0.0010.00946.9980.0330.0330.0000.0000.0000.000
202A200VAL0-0.034-0.01144.593-0.087-0.0870.0000.0000.0000.000
203A201TRP0-0.009-0.00947.180-0.116-0.1160.0000.0000.0000.000
204A202GLU-1-0.869-0.92850.255-6.208-6.2080.0000.0000.0000.000
205A203TYR00.0490.02443.491-0.062-0.0620.0000.0000.0000.000
206A204VAL0-0.043-0.04045.282-0.035-0.0350.0000.0000.0000.000
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