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: 7NMGK

Calculation Name: 3M4F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 3-cyclohexyl-1-propylsulfonic acid

Ligand 3-letter code: CXS

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3M4F

Chain ID: A

ChEMBL ID:

UniProt ID: Q6VAY1

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1862177.341187
FMO2-HF: Nuclear repulsion 1793693.82098
FMO2-HF: Total energy -68483.520207
FMO2-MP2: Total energy -68683.412615


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:25:ASN)


Summations of interaction energy for fragment #1(A:25:ASN)
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.
-294.278-283.77816.535-12.062-14.973-0.102
Interaction energy analysis for fragmet #1(A:25:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.795 / q_NPA : 0.892
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].
3A27GLY00.1120.0543.715-5.522-4.3390.010-0.464-0.7290.000
4A28GLY0-0.096-0.0323.6876.1936.5080.004-0.064-0.2550.000
5A29ILE0-0.065-0.0172.3611.6103.7500.922-1.086-1.976-0.007
6A30ASP-1-0.829-0.8941.854-74.089-74.18810.912-5.780-5.034-0.074
7A31TYR00.0080.0103.6906.9327.1000.001-0.053-0.116-0.001
22A46GLU-1-0.832-0.9262.637-53.838-52.7551.711-1.034-1.760-0.002
23A47GLY0-0.053-0.0222.570-18.758-14.3682.845-2.979-4.257-0.009
24A48ALA0-0.060-0.0463.042-8.517-7.1870.132-0.585-0.877-0.009
25A49GLY00.0300.0254.5140.9500.927-0.001-0.0160.0410.000
26A50THR0-0.040-0.0205.1783.7193.732-0.001-0.001-0.0100.000
8A32VAL00.0020.0016.508-1.037-1.0370.0000.0000.0000.000
9A33GLN0-0.032-0.0068.5141.3671.3670.0000.0000.0000.000
10A34ASN00.004-0.02111.9600.9050.9050.0000.0000.0000.000
11A35TYR0-0.0350.00014.5890.5130.5130.0000.0000.0000.000
12A36ASN00.006-0.01418.2430.0090.0090.0000.0000.0000.000
13A37GLY00.0750.02217.4880.2570.2570.0000.0000.0000.000
14A38ASP-1-0.975-0.98318.545-13.299-13.2990.0000.0000.0000.000
15A39VAL0-0.045-0.02521.1100.4520.4520.0000.0000.0000.000
16A40ALA0-0.026-0.00519.9410.3380.3380.0000.0000.0000.000
17A41ASP-1-0.878-0.92819.979-15.105-15.1050.0000.0000.0000.000
18A42PHE00.0000.00211.179-0.636-0.6360.0000.0000.0000.000
19A43GLN0-0.059-0.01914.192-1.238-1.2380.0000.0000.0000.000
20A44TYR0-0.013-0.0237.2310.1860.1860.0000.0000.0000.000
21A45ASN0-0.023-0.0206.652-2.227-2.2270.0000.0000.0000.000
27A51TYR0-0.009-0.0248.755-0.611-0.6110.0000.0000.0000.000
28A52THR0-0.065-0.02311.4111.2001.2000.0000.0000.0000.000
29A53CYS00.0120.01115.250-0.469-0.4690.0000.0000.0000.000
30A54GLY00.013-0.00218.2320.2870.2870.0000.0000.0000.000
31A55TRP0-0.0080.00620.648-0.271-0.2710.0000.0000.0000.000
32A56ASP-1-0.898-0.97824.690-9.710-9.7100.0000.0000.0000.000
33A57GLY0-0.0230.00528.4520.0690.0690.0000.0000.0000.000
34A58SER0-0.083-0.04429.7560.0530.0530.0000.0000.0000.000
35A59THR0-0.035-0.01725.8120.3350.3350.0000.0000.0000.000
36A60ASP-1-0.831-0.92624.324-12.787-12.7870.0000.0000.0000.000
37A61PHE0-0.0080.01419.458-0.117-0.1170.0000.0000.0000.000
38A62VAL00.0530.03016.961-0.140-0.1400.0000.0000.0000.000
39A63VAL0-0.0160.00114.798-0.604-0.6040.0000.0000.0000.000
40A64GLY00.0490.01212.1040.5800.5800.0000.0000.0000.000
41A65LEU0-0.034-0.0045.723-1.575-1.5750.0000.0000.0000.000
42A66GLY00.015-0.0056.9922.5732.5730.0000.0000.0000.000
43A67TRP0-0.043-0.0395.983-4.437-4.4370.0000.0000.0000.000
44A68SER0-0.039-0.0437.8884.7844.7840.0000.0000.0000.000
45A69THR0-0.026-0.0059.7583.1073.1070.0000.0000.0000.000
46A70GLY00.0180.00611.807-1.802-1.8020.0000.0000.0000.000
47A71ALA0-0.013-0.02013.6830.6320.6320.0000.0000.0000.000
48A72ALA00.0160.01415.413-0.043-0.0430.0000.0000.0000.000
49A73ARG10.7940.9039.50528.66328.6630.0000.0000.0000.000
50A74ASP-1-0.857-0.94614.311-17.997-17.9970.0000.0000.0000.000
51A75ILE0-0.0400.00010.889-1.788-1.7880.0000.0000.0000.000
52A76THR0-0.015-0.00411.2463.0553.0550.0000.0000.0000.000
53A77TYR0-0.022-0.02610.848-2.592-2.5920.0000.0000.0000.000
54A78SER0-0.053-0.04012.7682.0412.0410.0000.0000.0000.000
55A79ALA00.0450.02314.086-1.172-1.1720.0000.0000.0000.000
56A80THR0-0.071-0.01716.6021.1881.1880.0000.0000.0000.000
57A81TYR00.012-0.02418.885-0.641-0.6410.0000.0000.0000.000
58A82ASN0-0.066-0.02721.0670.7470.7470.0000.0000.0000.000
59A83ALA00.0750.03624.172-0.077-0.0770.0000.0000.0000.000
60A84GLY00.0070.01426.1760.2110.2110.0000.0000.0000.000
61A85GLY0-0.030-0.01729.8280.0600.0600.0000.0000.0000.000
62A86SER0-0.051-0.04027.288-0.085-0.0850.0000.0000.0000.000
63A87GLY0-0.0110.00428.679-0.050-0.0500.0000.0000.0000.000
64A88SER0-0.006-0.02522.959-0.336-0.3360.0000.0000.0000.000
65A89TYR00.014-0.00721.4120.5430.5430.0000.0000.0000.000
66A90LEU0-0.0070.01616.404-0.601-0.6010.0000.0000.0000.000
67A91ALA00.020-0.01317.6440.6140.6140.0000.0000.0000.000
68A92VAL00.0020.00814.557-1.167-1.1670.0000.0000.0000.000
69A93TYR0-0.016-0.02815.3410.6600.6600.0000.0000.0000.000
70A94GLY00.0280.00715.180-1.751-1.7510.0000.0000.0000.000
71A95TRP00.0120.00816.7861.3221.3220.0000.0000.0000.000
72A96VAL0-0.040-0.00718.425-0.877-0.8770.0000.0000.0000.000
73A97ASN0-0.0020.00018.8520.5690.5690.0000.0000.0000.000
74A98SER0-0.061-0.02322.6640.6930.6930.0000.0000.0000.000
75A99PRO00.0590.01025.766-0.213-0.2130.0000.0000.0000.000
76A100GLN00.0010.03224.074-0.019-0.0190.0000.0000.0000.000
77A101ALA0-0.008-0.00923.9910.4890.4890.0000.0000.0000.000
78A102GLU-1-0.783-0.85221.248-14.049-14.0490.0000.0000.0000.000
79A103TYR0-0.033-0.03716.4450.1490.1490.0000.0000.0000.000
80A104TYR00.007-0.02620.017-0.848-0.8480.0000.0000.0000.000
81A105ILE0-0.064-0.03218.3210.6230.6230.0000.0000.0000.000
82A106VAL00.0110.00619.684-0.715-0.7150.0000.0000.0000.000
83A107GLU-1-0.734-0.81518.213-14.798-14.7980.0000.0000.0000.000
84A108SER0-0.012-0.02021.4540.5110.5110.0000.0000.0000.000
85A109TYR0-0.043-0.01522.807-0.376-0.3760.0000.0000.0000.000
86A110GLY00.0330.03625.2930.0970.0970.0000.0000.0000.000
87A111ASP-1-0.884-0.94927.797-9.462-9.4620.0000.0000.0000.000
88A112TYR0-0.047-0.02228.9640.4660.4660.0000.0000.0000.000
89A113ASN00.0370.01828.835-0.435-0.4350.0000.0000.0000.000
90A114PRO00.0280.02626.4840.4020.4020.0000.0000.0000.000
91A115CYS0-0.105-0.04229.0990.4740.4740.0000.0000.0000.000
92A116SER0-0.062-0.03831.8770.3500.3500.0000.0000.0000.000
93A117ASN0-0.071-0.04334.3390.1220.1220.0000.0000.0000.000
94A118ALA00.0260.03832.2010.0920.0920.0000.0000.0000.000
95A119GLU-1-0.967-0.97934.213-8.495-8.4950.0000.0000.0000.000
96A120GLY00.009-0.00333.779-0.331-0.3310.0000.0000.0000.000
97A121LEU0-0.016-0.01430.4920.1880.1880.0000.0000.0000.000
98A122GLY0-0.0220.01633.9280.0080.0080.0000.0000.0000.000
99A123THR00.007-0.00331.523-0.051-0.0510.0000.0000.0000.000
100A124LEU0-0.059-0.00725.4650.1510.1510.0000.0000.0000.000
101A125GLU-1-0.839-0.89928.704-10.439-10.4390.0000.0000.0000.000
102A126SER00.005-0.03222.237-0.218-0.2180.0000.0000.0000.000
103A127ASP-1-0.811-0.83820.655-15.211-15.2110.0000.0000.0000.000
104A128GLY0-0.014-0.00323.138-0.067-0.0670.0000.0000.0000.000
105A129SER0-0.041-0.04526.0570.3380.3380.0000.0000.0000.000
106A130THR00.0070.00127.312-0.238-0.2380.0000.0000.0000.000
107A131TYR0-0.061-0.03821.685-0.161-0.1610.0000.0000.0000.000
108A132THR00.0120.00328.1820.3390.3390.0000.0000.0000.000
109A133VAL0-0.0190.00428.006-0.389-0.3890.0000.0000.0000.000
110A135THR0-0.008-0.01629.127-0.405-0.4050.0000.0000.0000.000
111A136ASP-1-0.804-0.88030.201-10.099-10.0990.0000.0000.0000.000
112A137THR0-0.022-0.01230.682-0.223-0.2230.0000.0000.0000.000
113A138ARG10.8640.93627.16810.96710.9670.0000.0000.0000.000
114A139THR00.004-0.02031.295-0.024-0.0240.0000.0000.0000.000
115A140ASN0-0.088-0.05832.4140.0060.0060.0000.0000.0000.000
116A141GLU-1-0.796-0.87529.482-9.694-9.6940.0000.0000.0000.000
117A142PRO00.013-0.00626.355-0.167-0.1670.0000.0000.0000.000
118A143SER00.0110.00023.893-0.248-0.2480.0000.0000.0000.000
119A144ILE00.0010.00918.822-0.037-0.0370.0000.0000.0000.000
120A145THR0-0.054-0.01921.392-0.233-0.2330.0000.0000.0000.000
121A146GLY0-0.0050.00924.0720.5180.5180.0000.0000.0000.000
122A147THR0-0.063-0.04725.8640.2460.2460.0000.0000.0000.000
123A148SER0-0.045-0.02027.0870.1240.1240.0000.0000.0000.000
124A149THR0-0.0060.00029.7500.1480.1480.0000.0000.0000.000
125A150PHE0-0.048-0.00725.831-0.064-0.0640.0000.0000.0000.000
126A151THR0-0.0070.00027.8600.3760.3760.0000.0000.0000.000
127A152GLN00.0290.00225.927-0.761-0.7610.0000.0000.0000.000
128A153TYR0-0.019-0.03124.7890.4270.4270.0000.0000.0000.000
129A154TRP00.025-0.00524.495-0.749-0.7490.0000.0000.0000.000
130A155SER0-0.024-0.01623.6760.6180.6180.0000.0000.0000.000
131A156VAL00.0230.00624.120-0.563-0.5630.0000.0000.0000.000
132A157ARG10.7640.87722.91513.61413.6140.0000.0000.0000.000
133A158GLN0-0.016-0.03026.0460.3140.3140.0000.0000.0000.000
134A159SER0-0.049-0.01528.1280.2820.2820.0000.0000.0000.000
135A160GLU-1-0.834-0.91825.231-11.836-11.8360.0000.0000.0000.000
136A161ARG10.7540.84419.61815.53715.5370.0000.0000.0000.000
137A162THR00.0280.01619.753-0.111-0.1110.0000.0000.0000.000
138A163SER0-0.026-0.01717.144-0.820-0.8200.0000.0000.0000.000
139A164GLY0-0.0010.00516.5141.0671.0670.0000.0000.0000.000
140A165THR0-0.004-0.01115.453-0.845-0.8450.0000.0000.0000.000
141A166VAL0-0.0110.00615.9031.3391.3390.0000.0000.0000.000
142A167THR00.008-0.02716.652-1.089-1.0890.0000.0000.0000.000
143A168VAL0-0.015-0.00615.5411.0811.0810.0000.0000.0000.000
144A169GLY00.0150.00718.6910.7090.7090.0000.0000.0000.000
145A170ASN0-0.050-0.03120.9290.8310.8310.0000.0000.0000.000
146A171HIS00.0480.02421.1470.9530.9530.0000.0000.0000.000
147A172PHE00.0130.00617.8070.4550.4550.0000.0000.0000.000
148A173ASN0-0.005-0.00223.1420.4220.4220.0000.0000.0000.000
149A174TYR0-0.024-0.03326.1280.4910.4910.0000.0000.0000.000
150A175TRP00.0240.00321.2570.3160.3160.0000.0000.0000.000
151A176ALA00.0200.03526.3680.3470.3470.0000.0000.0000.000
152A177GLN0-0.109-0.05828.1800.3820.3820.0000.0000.0000.000
153A178HIS10.8200.89430.53410.29010.2900.0000.0000.0000.000
154A179GLY00.0320.03230.9100.0400.0400.0000.0000.0000.000
155A180PHE0-0.0260.00820.960-0.078-0.0780.0000.0000.0000.000
156A181GLY00.0230.00125.5100.1580.1580.0000.0000.0000.000
157A182ASP-1-0.897-0.96222.101-13.366-13.3660.0000.0000.0000.000
158A183SER0-0.029-0.01020.810-0.781-0.7810.0000.0000.0000.000
159A184TYR0-0.026-0.01516.6570.0410.0410.0000.0000.0000.000
160A185ASN0-0.038-0.01615.965-0.953-0.9530.0000.0000.0000.000
161A186PHE00.0440.01911.799-0.803-0.8030.0000.0000.0000.000
162A187GLN0-0.011-0.00511.6560.2350.2350.0000.0000.0000.000
163A188VAL0-0.025-0.0059.795-2.912-2.9120.0000.0000.0000.000
164A189MET00.0040.01910.6861.9451.9450.0000.0000.0000.000
165A190ALA0-0.031-0.02611.904-1.414-1.4140.0000.0000.0000.000
166A191VAL00.004-0.00814.6760.7490.7490.0000.0000.0000.000
167A192GLU-1-0.782-0.86717.645-13.889-13.8890.0000.0000.0000.000
168A193ALA0-0.0220.00420.7100.3510.3510.0000.0000.0000.000
169A194PHE00.0560.03524.1380.1130.1130.0000.0000.0000.000
170A195SER0-0.044-0.01727.2830.5390.5390.0000.0000.0000.000
171A196GLY00.0340.05029.015-0.186-0.1860.0000.0000.0000.000
172A197SER0-0.008-0.00927.675-0.236-0.2360.0000.0000.0000.000
173A198GLY00.0280.00525.1430.1180.1180.0000.0000.0000.000
174A199SER0-0.040-0.01821.762-0.157-0.1570.0000.0000.0000.000
175A200ALA00.008-0.00317.5360.1450.1450.0000.0000.0000.000
176A201SER0-0.048-0.01415.656-0.652-0.6520.0000.0000.0000.000
177A202VAL00.0230.01711.7360.7570.7570.0000.0000.0000.000
178A203SER0-0.028-0.0169.686-2.401-2.4010.0000.0000.0000.000
179A204VAL0-0.002-0.0047.2802.7002.7000.0000.0000.0000.000
180A205SER-1-0.823-0.9296.584-37.968-37.9680.0000.0000.0000.000