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: QM3ZY

Calculation Name: 7QI1-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoserine | [2-(2-methylphenyl)sulfanylphenyl]methanamine

Ligand 3-letter code: SEP | Q95

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7QI1

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-05

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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2928198.715561
FMO2-HF: Nuclear repulsion 2832585.023715
FMO2-HF: Total energy -95613.691847
FMO2-MP2: Total energy -95888.427219


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:-2:MET)


Summations of interaction energy for fragment #1(A:-2: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.
-111.583-108.806-0.004-1.14-1.633-0.002
Interaction energy analysis for fragmet #1(A:-2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.922
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].
3A0SER00.0100.0143.746-0.2771.530-0.017-0.806-0.9840.000
5A2THR0-0.032-0.0373.671-12.711-11.8550.014-0.330-0.540-0.002
6A3MET0-0.0170.0104.6691.2071.321-0.001-0.004-0.1090.000
4A1MET00.0110.0256.1843.4083.4080.0000.0000.0000.000
7A4ASP-1-0.798-0.8717.194-28.895-28.8950.0000.0000.0000.000
8A5LYS10.8930.9248.87721.87821.8780.0000.0000.0000.000
9A6SER0-0.063-0.04511.9522.3162.3160.0000.0000.0000.000
10A7GLU-1-0.849-0.9379.807-26.150-26.1500.0000.0000.0000.000
11A8LEU0-0.048-0.0309.3441.4801.4800.0000.0000.0000.000
12A9VAL00.0440.01613.3891.4101.4100.0000.0000.0000.000
13A10GLN00.0020.00816.4301.2121.2120.0000.0000.0000.000
14A11LYS10.9520.97014.70120.32020.3200.0000.0000.0000.000
15A12ALA00.001-0.00217.3870.7900.7900.0000.0000.0000.000
16A13LYS10.8860.93419.16815.25415.2540.0000.0000.0000.000
17A14LEU0-0.041-0.02719.3230.6750.6750.0000.0000.0000.000
18A15ALA0-0.038-0.01820.4090.5200.5200.0000.0000.0000.000
19A16GLU-1-0.888-0.96022.378-11.748-11.7480.0000.0000.0000.000
20A17GLN0-0.047-0.02025.0060.8170.8170.0000.0000.0000.000
21A18ALA0-0.053-0.01524.9740.3980.3980.0000.0000.0000.000
22A19GLU-1-0.932-0.96127.010-9.727-9.7270.0000.0000.0000.000
23A20ARG10.7940.88221.60813.57913.5790.0000.0000.0000.000
24A21TYR00.0600.00322.993-0.845-0.8450.0000.0000.0000.000
25A22ASP-1-0.753-0.86022.451-13.186-13.1860.0000.0000.0000.000
26A23ASP-1-0.860-0.90919.033-16.168-16.1680.0000.0000.0000.000
27A24MET0-0.088-0.01518.119-0.985-0.9850.0000.0000.0000.000
28A25ALA00.0260.01418.918-0.661-0.6610.0000.0000.0000.000
29A26ALA00.0180.00815.977-0.745-0.7450.0000.0000.0000.000
30A27ALA0-0.043-0.02014.168-1.573-1.5730.0000.0000.0000.000
31A28MET00.006-0.00314.184-1.462-1.4620.0000.0000.0000.000
32A29LYS10.8510.94714.29620.33620.3360.0000.0000.0000.000
33A30ALA00.0190.01110.212-1.082-1.0820.0000.0000.0000.000
34A31VAL0-0.032-0.02410.615-2.102-2.1020.0000.0000.0000.000
35A32THR0-0.017-0.01912.535-0.071-0.0710.0000.0000.0000.000
36A33GLU-1-0.865-0.93510.713-23.455-23.4550.0000.0000.0000.000
37A34GLN0-0.107-0.0426.803-0.188-0.1880.0000.0000.0000.000
38A35GLY0-0.017-0.0058.964-0.845-0.8450.0000.0000.0000.000
39A36HIS0-0.059-0.0319.9042.6762.6760.0000.0000.0000.000
40A37GLU-1-0.912-0.95013.846-13.944-13.9440.0000.0000.0000.000
41A38LEU0-0.056-0.02616.105-0.237-0.2370.0000.0000.0000.000
42A39SER00.0400.01918.8671.0351.0350.0000.0000.0000.000
43A40ASN00.034-0.00821.381-0.284-0.2840.0000.0000.0000.000
44A41GLU-1-0.844-0.89821.804-13.819-13.8190.0000.0000.0000.000
45A42GLU-1-0.794-0.88817.511-18.089-18.0890.0000.0000.0000.000
46A43ARG10.8430.92020.45911.86111.8610.0000.0000.0000.000
47A44ASN00.0040.00522.6640.5550.5550.0000.0000.0000.000
48A45LEU00.0150.00220.4260.1510.1510.0000.0000.0000.000
49A46LEU00.0250.01218.4560.1330.1330.0000.0000.0000.000
50A47SER0-0.011-0.00721.5020.3190.3190.0000.0000.0000.000
51A48VAL0-0.001-0.00525.1590.3430.3430.0000.0000.0000.000
52A49ALA00.0420.02022.1460.3280.3280.0000.0000.0000.000
53A50TYR00.0390.00618.5850.5240.5240.0000.0000.0000.000
54A51LYS10.9440.98724.87110.32510.3250.0000.0000.0000.000
55A52ASN0-0.047-0.02527.4810.7610.7610.0000.0000.0000.000
56A53VAL0-0.0140.01023.4140.3050.3050.0000.0000.0000.000
57A54VAL00.0170.00226.7690.2930.2930.0000.0000.0000.000
58A55GLY00.0100.01229.0020.4070.4070.0000.0000.0000.000
59A56ALA00.0280.02130.0330.4100.4100.0000.0000.0000.000
60A57ARG10.7880.88525.99312.12012.1200.0000.0000.0000.000
61A58ARG10.8650.89332.3279.6079.6070.0000.0000.0000.000
62A59SER0-0.037-0.02834.7920.3920.3920.0000.0000.0000.000
63A60SER0-0.026-0.02434.5890.3310.3310.0000.0000.0000.000
64A61TRP0-0.021-0.02136.0860.2700.2700.0000.0000.0000.000
65A62ARG10.8940.96137.8878.1928.1920.0000.0000.0000.000
66A63VAL0-0.022-0.00640.2900.2720.2720.0000.0000.0000.000
67A64ILE0-0.004-0.00739.1790.2520.2520.0000.0000.0000.000
68A65SER00.0450.01041.0440.1900.1900.0000.0000.0000.000
69A66SER0-0.047-0.01543.5440.2810.2810.0000.0000.0000.000
70A67ILE0-0.033-0.02643.8840.2230.2230.0000.0000.0000.000
71A68GLU-1-0.817-0.87944.529-7.221-7.2210.0000.0000.0000.000
72A69GLN0-0.004-0.01145.4610.2420.2420.0000.0000.0000.000
73A70LYS10.9180.97649.3626.5966.5960.0000.0000.0000.000
74A71THR0-0.096-0.05349.5230.1420.1420.0000.0000.0000.000
75A72GLU-1-0.919-0.94251.957-5.572-5.5720.0000.0000.0000.000
76A73ARG10.9850.98055.2445.3455.3450.0000.0000.0000.000
77A74ASN0-0.054-0.02852.185-0.008-0.0080.0000.0000.0000.000
78A75GLU-1-0.715-0.86050.664-6.608-6.6080.0000.0000.0000.000
79A76LYS10.8710.92849.2046.3866.3860.0000.0000.0000.000
80A77LYS10.9180.97047.7136.4556.4550.0000.0000.0000.000
81A78GLN0-0.015-0.01147.013-0.164-0.1640.0000.0000.0000.000
82A79GLN00.0040.01344.914-0.295-0.2950.0000.0000.0000.000
83A80MET00.0450.02642.737-0.147-0.1470.0000.0000.0000.000
84A81GLY0-0.025-0.01642.196-0.208-0.2080.0000.0000.0000.000
85A82LYS10.8420.91741.8877.4777.4770.0000.0000.0000.000
86A83GLU-1-0.928-0.97139.981-7.846-7.8460.0000.0000.0000.000
87A84TYR0-0.042-0.02735.603-0.285-0.2850.0000.0000.0000.000
88A85ARG10.7820.84936.9967.6237.6230.0000.0000.0000.000
89A86GLU-1-0.803-0.89936.799-8.229-8.2290.0000.0000.0000.000
90A87LYS10.8610.93030.72110.02110.0210.0000.0000.0000.000
91A88ILE0-0.031-0.01932.430-0.364-0.3640.0000.0000.0000.000
92A89GLU-1-0.810-0.88432.541-8.764-8.7640.0000.0000.0000.000
93A90ALA00.0150.01830.386-0.233-0.2330.0000.0000.0000.000
94A91GLU-1-0.812-0.90327.923-11.246-11.2460.0000.0000.0000.000
95A92LEU0-0.050-0.02227.634-0.407-0.4070.0000.0000.0000.000
96A93GLN0-0.002-0.00928.650-0.313-0.3130.0000.0000.0000.000
97A94ASP-1-0.885-0.93124.309-12.690-12.6900.0000.0000.0000.000
98A95ILE0-0.043-0.02623.943-0.525-0.5250.0000.0000.0000.000
99A96CYS0-0.080-0.05224.302-0.200-0.2000.0000.0000.0000.000
100A97ASN0-0.0180.00522.2860.3320.3320.0000.0000.0000.000
101A98ASP-1-0.844-0.93019.448-16.769-16.7690.0000.0000.0000.000
102A99VAL0-0.046-0.02220.315-0.550-0.5500.0000.0000.0000.000
103A100LEU0-0.039-0.02522.286-0.169-0.1690.0000.0000.0000.000
104A101GLU-1-0.853-0.90917.870-17.032-17.0320.0000.0000.0000.000
105A102LEU0-0.018-0.02115.707-0.715-0.7150.0000.0000.0000.000
106A103LEU0-0.021-0.02618.849-0.213-0.2130.0000.0000.0000.000
107A104ASP-1-0.893-0.93921.907-12.728-12.7280.0000.0000.0000.000
108A105LYS10.8500.92314.89319.33219.3320.0000.0000.0000.000
109A106TYR0-0.018-0.00411.805-0.281-0.2810.0000.0000.0000.000
110A107LEU0-0.0020.00117.5630.3800.3800.0000.0000.0000.000
111A108ILE00.0110.00220.3620.4860.4860.0000.0000.0000.000
112A109PRO0-0.048-0.00319.5630.5650.5650.0000.0000.0000.000
113A110ASN0-0.025-0.02416.7680.3080.3080.0000.0000.0000.000
114A111ALA0-0.0200.00620.6070.2440.2440.0000.0000.0000.000
115A112THR00.0110.01323.3220.6710.6710.0000.0000.0000.000
116A113GLN00.0260.02025.7660.4740.4740.0000.0000.0000.000
117A114PRO00.0540.00628.232-0.188-0.1880.0000.0000.0000.000
118A115GLU-1-0.820-0.90029.415-10.595-10.5950.0000.0000.0000.000
119A116SER00.0320.00324.7910.1040.1040.0000.0000.0000.000
120A117LYS10.8800.94725.32811.85411.8540.0000.0000.0000.000
121A118VAL00.0250.01328.3580.0130.0130.0000.0000.0000.000
122A119PHE0-0.025-0.01325.1960.0850.0850.0000.0000.0000.000
123A120TYR00.0510.00221.577-0.066-0.0660.0000.0000.0000.000
124A121LEU0-0.0040.01726.513-0.110-0.1100.0000.0000.0000.000
125A122LYS10.8830.93929.45910.02710.0270.0000.0000.0000.000
126A123MET0-0.051-0.00923.7960.0600.0600.0000.0000.0000.000
127A124LYS10.9150.95326.50711.56911.5690.0000.0000.0000.000
128A125GLY00.0570.02428.4750.1420.1420.0000.0000.0000.000
129A126ASP-1-0.782-0.83530.333-9.539-9.5390.0000.0000.0000.000
130A127TYR00.0290.00426.9940.1300.1300.0000.0000.0000.000
131A128PHE00.0540.02828.7210.0470.0470.0000.0000.0000.000
132A129ARG10.8800.95831.7249.3299.3290.0000.0000.0000.000
133A130TYR0-0.064-0.04729.9200.3310.3310.0000.0000.0000.000
134A131LEU00.0430.03029.0660.1460.1460.0000.0000.0000.000
135A132SER0-0.008-0.02533.1060.2840.2840.0000.0000.0000.000
136A133GLU-1-0.860-0.89636.275-8.670-8.6700.0000.0000.0000.000
137A134VAL0-0.015-0.00334.6860.1840.1840.0000.0000.0000.000
138A135ALA0-0.0150.02235.6280.0840.0840.0000.0000.0000.000
139A136SER0-0.012-0.02237.4860.2200.2200.0000.0000.0000.000
140A137GLY00.0340.00839.474-0.157-0.1570.0000.0000.0000.000
141A138ASP-1-0.814-0.91539.738-7.706-7.7060.0000.0000.0000.000
142A139ASN0-0.0070.01533.512-0.265-0.2650.0000.0000.0000.000
143A140LYS10.9540.99036.2927.5727.5720.0000.0000.0000.000
144A141GLN0-0.065-0.04138.5600.0560.0560.0000.0000.0000.000
145A142THR0-0.012-0.01133.545-0.036-0.0360.0000.0000.0000.000
146A143THR0-0.028-0.03132.622-0.120-0.1200.0000.0000.0000.000
147A144VAL00.0060.00034.810-0.094-0.0940.0000.0000.0000.000
148A145SER0-0.008-0.00737.0530.0970.0970.0000.0000.0000.000
149A146ASN0-0.010-0.01331.6380.0880.0880.0000.0000.0000.000
150A147SER0-0.065-0.03533.361-0.088-0.0880.0000.0000.0000.000
151A148GLN00.011-0.00234.625-0.021-0.0210.0000.0000.0000.000
152A149GLN00.0020.00634.7800.1510.1510.0000.0000.0000.000
153A150ALA00.0090.01531.067-0.002-0.0020.0000.0000.0000.000
154A151TYR00.006-0.03033.005-0.048-0.0480.0000.0000.0000.000
155A152GLN0-0.047-0.04335.4450.1120.1120.0000.0000.0000.000
156A153GLU-1-0.900-0.95031.744-9.920-9.9200.0000.0000.0000.000
157A154ALA00.001-0.00132.7590.0010.0010.0000.0000.0000.000
158A155PHE00.0330.00134.2570.1660.1660.0000.0000.0000.000
159A156GLU-1-0.883-0.93138.021-7.831-7.8310.0000.0000.0000.000
160A157ILE00.0230.01132.4410.1010.1010.0000.0000.0000.000
161A158SER0-0.057-0.04036.2440.1220.1220.0000.0000.0000.000
162A159LYS10.8840.94437.3177.6177.6170.0000.0000.0000.000
163A160LYS10.8300.92438.6858.3388.3380.0000.0000.0000.000
164A161GLU-1-0.882-0.94135.108-8.551-8.5510.0000.0000.0000.000
165A162MET0-0.086-0.02133.033-0.134-0.1340.0000.0000.0000.000
166A163GLN0-0.011-0.01038.4580.0900.0900.0000.0000.0000.000
167A164PRO0-0.018-0.01540.689-0.216-0.2160.0000.0000.0000.000
168A165THR00.001-0.02042.139-0.139-0.1390.0000.0000.0000.000
169A166HIS00.0090.02433.198-0.013-0.0130.0000.0000.0000.000
170A167PRO00.0580.02134.8740.0280.0280.0000.0000.0000.000
171A168ILE0-0.035-0.02130.412-0.091-0.0910.0000.0000.0000.000
172A169ARG10.9040.95734.4857.5757.5750.0000.0000.0000.000
173A170LEU0-0.0120.01037.5590.0730.0730.0000.0000.0000.000
174A171GLY00.0430.01435.8550.0920.0920.0000.0000.0000.000
175A172LEU0-0.067-0.02634.630-0.112-0.1120.0000.0000.0000.000
176A173ALA00.0130.00936.4400.0800.0800.0000.0000.0000.000
177A174LEU00.0140.02538.4280.1470.1470.0000.0000.0000.000
178A175ASN0-0.038-0.04533.9350.2260.2260.0000.0000.0000.000
179A176PHE00.0120.01437.7620.0370.0370.0000.0000.0000.000
180A177SER0-0.027-0.02239.3350.1690.1690.0000.0000.0000.000
181A178VAL00.0360.01039.5700.1410.1410.0000.0000.0000.000
182A179PHE0-0.011-0.01037.9230.0700.0700.0000.0000.0000.000
183A180TYR0-0.011-0.01640.3800.1470.1470.0000.0000.0000.000
184A181TYR00.0000.01143.8870.1320.1320.0000.0000.0000.000
185A182GLU-1-0.894-0.95140.670-7.835-7.8350.0000.0000.0000.000
186A183ILE0-0.075-0.03938.8420.0190.0190.0000.0000.0000.000
187A184LEU0-0.017-0.00642.1950.0620.0620.0000.0000.0000.000
188A185ASN0-0.055-0.00244.8490.1640.1640.0000.0000.0000.000
189A186SER0-0.007-0.01247.2690.2050.2050.0000.0000.0000.000
190A187PRO00.0490.01948.672-0.082-0.0820.0000.0000.0000.000
191A188GLU-1-0.850-0.91750.107-5.865-5.8650.0000.0000.0000.000
192A189LYS10.9290.97247.5076.7096.7090.0000.0000.0000.000
193A190ALA0-0.0090.00545.972-0.090-0.0900.0000.0000.0000.000
194A191CYS00.0150.00646.935-0.085-0.0850.0000.0000.0000.000
195A192SER0-0.014-0.02249.6290.0380.0380.0000.0000.0000.000
196A193LEU0-0.074-0.01342.286-0.003-0.0030.0000.0000.0000.000
197A194ALA00.0380.00745.179-0.058-0.0580.0000.0000.0000.000
198A195LYS10.8750.91746.1726.0206.0200.0000.0000.0000.000
199A196THR0-0.027-0.01747.5670.0700.0700.0000.0000.0000.000
200A197ALA0-0.022-0.02043.396-0.018-0.0180.0000.0000.0000.000
201A198PHE00.0090.01145.423-0.047-0.0470.0000.0000.0000.000
202A199ASP-1-0.815-0.90547.377-6.125-6.1250.0000.0000.0000.000
203A200GLU-1-0.938-0.97946.493-6.810-6.8100.0000.0000.0000.000
204A201ALA0-0.008-0.00844.677-0.018-0.0180.0000.0000.0000.000
205A202ILE0-0.022-0.01146.540-0.019-0.0190.0000.0000.0000.000
206A203ALA00.0220.01249.7470.0400.0400.0000.0000.0000.000
207A204GLU-1-0.752-0.83744.273-7.263-7.2630.0000.0000.0000.000
208A205LEU0-0.005-0.00744.659-0.037-0.0370.0000.0000.0000.000
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