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: 4Y93N

Calculation Name: 1TC1-B-Xray547

Preferred Name:

Target Type:

Ligand Name: formycin b | 2-(n-morpholino)-ethanesulfonic acid

Ligand 3-letter code: FMB | MES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TC1

Chain ID: B

ChEMBL ID:

UniProt ID: Q4DRC4

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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2111589.208906
FMO2-HF: Nuclear repulsion 2036505.231715
FMO2-HF: Total energy -75083.977191
FMO2-MP2: Total energy -75303.028267


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:5:TYR)


Summations of interaction energy for fragment #1(A:5:TYR)
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.
-84.921-81.11827.31-13.877-17.24-0.092
Interaction energy analysis for fragmet #1(A:5:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.848
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].
3A7PHE00.0390.0162.499-0.2803.7342.173-2.196-3.991-0.020
4A8ALA0-0.0020.0002.2075.3475.6622.450-0.980-1.785-0.006
5A9GLU-1-0.941-0.9753.805-25.776-25.7280.0000.002-0.0510.000
7A11ILE00.0190.0162.983-2.324-1.2600.314-0.294-1.0850.002
175A179LEU0-0.063-0.0142.201-3.057-2.1692.558-0.822-2.6240.003
176A180ARG10.8970.9203.72025.36325.8070.006-0.111-0.3390.000
177A181ASP-1-0.829-0.8821.628-71.686-76.33319.562-9.063-5.852-0.074
178A182ILE0-0.0090.0013.9101.0141.217-0.001-0.010-0.1930.000
179A183VAL0-0.010-0.0183.393-2.644-1.1700.248-0.403-1.3200.003
6A10LYS10.9250.9566.25923.75723.7570.0000.0000.0000.000
8A12LEU0-0.085-0.0357.0692.7332.7330.0000.0000.0000.000
9A13PHE0-0.001-0.0138.0542.1712.1710.0000.0000.0000.000
10A14THR0-0.004-0.0225.589-1.610-1.6100.0000.0000.0000.000
11A15GLU-1-0.747-0.8705.583-20.327-20.3270.0000.0000.0000.000
12A16GLU-1-0.845-0.9187.290-16.967-16.9670.0000.0000.0000.000
13A17GLU-1-0.845-0.8829.910-20.887-20.8870.0000.0000.0000.000
14A18ILE0-0.007-0.0029.1811.6331.6330.0000.0000.0000.000
15A19ARG10.8120.89010.07021.19321.1930.0000.0000.0000.000
16A20THR0-0.042-0.02013.3541.2311.2310.0000.0000.0000.000
17A21ARG10.9430.97213.46217.12717.1270.0000.0000.0000.000
18A22ILE0-0.017-0.00313.5380.9040.9040.0000.0000.0000.000
19A23LYS10.8790.93616.99913.63313.6330.0000.0000.0000.000
20A24GLU-1-0.922-0.96318.904-12.617-12.6170.0000.0000.0000.000
21A25VAL0-0.035-0.02119.5460.6380.6380.0000.0000.0000.000
22A26ALA00.002-0.00321.0140.5200.5200.0000.0000.0000.000
23A27LYS10.8930.94422.84010.13710.1370.0000.0000.0000.000
24A28ARG10.9080.95923.72711.03711.0370.0000.0000.0000.000
25A29ILE00.0090.01323.4930.4020.4020.0000.0000.0000.000
26A30ALA00.006-0.00727.0240.3650.3650.0000.0000.0000.000
27A31ASP-1-0.865-0.91828.972-8.707-8.7070.0000.0000.0000.000
28A32ASP-1-0.811-0.87129.489-8.889-8.8890.0000.0000.0000.000
29A33TYR0-0.045-0.05629.0950.4460.4460.0000.0000.0000.000
30A34LYS10.8870.95532.7408.5198.5190.0000.0000.0000.000
31A35GLY00.0120.00834.6950.1520.1520.0000.0000.0000.000
32A36LYS10.8410.92135.0128.0358.0350.0000.0000.0000.000
33A37GLY00.0250.02037.5980.0450.0450.0000.0000.0000.000
34A38LEU0-0.0020.01431.9550.0500.0500.0000.0000.0000.000
35A39ARG10.9410.96036.0237.0937.0930.0000.0000.0000.000
36A40PRO00.0550.01934.035-0.042-0.0420.0000.0000.0000.000
37A41TYR0-0.022-0.00234.8580.2050.2050.0000.0000.0000.000
38A42VAL0-0.009-0.01336.563-0.047-0.0470.0000.0000.0000.000
39A43ASN0-0.003-0.01237.027-0.025-0.0250.0000.0000.0000.000
40A44PRO0-0.0020.01431.561-0.031-0.0310.0000.0000.0000.000
41A45LEU00.0210.01127.5610.0900.0900.0000.0000.0000.000
42A46VAL0-0.031-0.02829.274-0.211-0.2110.0000.0000.0000.000
43A47LEU00.0120.00823.190-0.048-0.0480.0000.0000.0000.000
44A48ILE00.000-0.00525.962-0.023-0.0230.0000.0000.0000.000
45A49SER0-0.032-0.01320.420-0.180-0.1800.0000.0000.0000.000
46A50VAL00.0280.01721.3370.3430.3430.0000.0000.0000.000
47A51LEU0-0.0460.01519.608-0.670-0.6700.0000.0000.0000.000
48A52LYS10.8510.88216.33115.07415.0740.0000.0000.0000.000
49A53GLY00.0810.03814.737-0.191-0.1910.0000.0000.0000.000
50A54SER0-0.021-0.00814.716-0.496-0.4960.0000.0000.0000.000
51A55PHE00.0190.02212.3780.3090.3090.0000.0000.0000.000
52A56MET0-0.0130.0188.9820.2910.2910.0000.0000.0000.000
53A57PHE00.0770.02414.0460.3050.3050.0000.0000.0000.000
54A58THR0-0.001-0.01815.1270.7130.7130.0000.0000.0000.000
55A59ALA00.0050.00616.0730.5810.5810.0000.0000.0000.000
56A60ASP-1-0.807-0.85812.812-16.215-16.2150.0000.0000.0000.000
57A61LEU0-0.0070.00516.4390.4990.4990.0000.0000.0000.000
58A62CYS0-0.079-0.04519.0870.5460.5460.0000.0000.0000.000
59A63ARG10.8590.90615.51914.52914.5290.0000.0000.0000.000
60A64ALA00.0380.02518.7180.3410.3410.0000.0000.0000.000
61A65LEU0-0.026-0.02420.7470.4200.4200.0000.0000.0000.000
62A66CYS0-0.065-0.01923.7920.5500.5500.0000.0000.0000.000
63A67ASP-1-0.815-0.89721.198-11.524-11.5240.0000.0000.0000.000
64A68PHE0-0.065-0.03522.6140.3320.3320.0000.0000.0000.000
65A69ASN0-0.065-0.03427.2240.3950.3950.0000.0000.0000.000
66A70VAL00.0160.01327.4440.3310.3310.0000.0000.0000.000
67A71PRO0-0.052-0.00928.433-0.171-0.1710.0000.0000.0000.000
68A72VAL00.0320.01025.3710.0800.0800.0000.0000.0000.000
69A73ARG10.8480.92128.6478.2918.2910.0000.0000.0000.000
70A74MET00.0080.01423.4900.0110.0110.0000.0000.0000.000
71A75GLU-1-0.820-0.92026.578-8.552-8.5520.0000.0000.0000.000
72A76PHE00.004-0.00221.053-0.235-0.2350.0000.0000.0000.000
73A77ILE0-0.0230.00524.7000.3310.3310.0000.0000.0000.000
74A78CYS0-0.011-0.00424.060-0.537-0.5370.0000.0000.0000.000
75A79VAL00.0530.01724.1080.4730.4730.0000.0000.0000.000
76A80SER00.0280.01424.730-0.259-0.2590.0000.0000.0000.000
77A81SER00.0260.01625.9970.1830.1830.0000.0000.0000.000
78A82TYR0-0.039-0.01827.6520.1910.1910.0000.0000.0000.000
79A83GLY00.0540.01929.209-0.297-0.2970.0000.0000.0000.000
80A84GLU-1-0.901-0.95329.649-9.269-9.2690.0000.0000.0000.000
81A85GLY0-0.006-0.01030.8490.2630.2630.0000.0000.0000.000
82A86LEU0-0.033-0.00732.9850.2520.2520.0000.0000.0000.000
83A87THR0-0.054-0.05030.9050.1170.1170.0000.0000.0000.000
84A88SER00.0000.00232.323-0.216-0.2160.0000.0000.0000.000
85A89SER0-0.023-0.01933.239-0.002-0.0020.0000.0000.0000.000
86A90GLY00.0190.00929.193-0.038-0.0380.0000.0000.0000.000
87A91GLN0-0.0190.02929.574-0.176-0.1760.0000.0000.0000.000
88A92VAL00.0360.01026.541-0.142-0.1420.0000.0000.0000.000
89A93ARG10.9160.96329.8988.6848.6840.0000.0000.0000.000
90A94MET0-0.0080.00628.945-0.341-0.3410.0000.0000.0000.000
91A95LEU0-0.042-0.02726.4710.2520.2520.0000.0000.0000.000
92A96LEU0-0.038-0.01626.5960.1780.1780.0000.0000.0000.000
93A97ASP-1-0.723-0.82128.738-8.837-8.8370.0000.0000.0000.000
94A98THR0-0.018-0.01830.5990.0130.0130.0000.0000.0000.000
95A99ARG10.9100.96130.9678.5668.5660.0000.0000.0000.000
96A100HIS10.8180.90331.5368.6728.6720.0000.0000.0000.000
97A101SER00.0520.03435.338-0.162-0.1620.0000.0000.0000.000
98A102ILE00.026-0.00832.905-0.126-0.1260.0000.0000.0000.000
99A103GLU-1-0.918-0.94136.087-6.749-6.7490.0000.0000.0000.000
100A104GLY0-0.019-0.00939.5680.0230.0230.0000.0000.0000.000
101A105HIS0-0.049-0.01534.922-0.021-0.0210.0000.0000.0000.000
102A106HIS00.0060.02133.112-0.111-0.1110.0000.0000.0000.000
103A107VAL0-0.003-0.00330.311-0.126-0.1260.0000.0000.0000.000
104A108LEU0-0.019-0.00624.7630.0560.0560.0000.0000.0000.000
105A109ILE00.0090.00724.674-0.134-0.1340.0000.0000.0000.000
106A110VAL0-0.022-0.01519.515-0.117-0.1170.0000.0000.0000.000
107A111GLU-1-0.850-0.94419.789-12.248-12.2480.0000.0000.0000.000
108A112ASP-1-0.839-0.94614.100-16.118-16.1180.0000.0000.0000.000
109A113ILE00.012-0.00515.231-0.632-0.6320.0000.0000.0000.000
110A114VAL0-0.0280.00317.4750.6920.6920.0000.0000.0000.000
111A115ASP-1-0.776-0.88319.214-13.704-13.7040.0000.0000.0000.000
112A116THR0-0.032-0.03621.5440.6860.6860.0000.0000.0000.000
113A117ALA00.013-0.00823.9330.4760.4760.0000.0000.0000.000
114A118LEU0-0.0010.00325.5890.3070.3070.0000.0000.0000.000
115A119THR00.0660.02224.0120.4260.4260.0000.0000.0000.000
116A120LEU00.0490.03123.5920.3150.3150.0000.0000.0000.000
117A121ASN00.0270.01826.3210.4220.4220.0000.0000.0000.000
118A122TYR0-0.0010.00529.6950.4030.4030.0000.0000.0000.000
119A123LEU00.017-0.00325.9420.2880.2880.0000.0000.0000.000
120A124TYR0-0.0030.00229.8800.2840.2840.0000.0000.0000.000
121A125HIS00.009-0.00931.2770.3820.3820.0000.0000.0000.000
122A126MET0-0.030-0.00431.3520.2940.2940.0000.0000.0000.000
123A127TYR0-0.004-0.04429.1140.1020.1020.0000.0000.0000.000
124A128PHE00.0240.00834.1840.2330.2330.0000.0000.0000.000
125A129THR0-0.017-0.01436.4380.2300.2300.0000.0000.0000.000
126A130ARG10.7900.88934.2878.3428.3420.0000.0000.0000.000
127A131ARG10.8860.94138.9867.0987.0980.0000.0000.0000.000
128A132PRO00.0430.04035.2610.0920.0920.0000.0000.0000.000
129A133ALA0-0.037-0.01537.6600.1000.1000.0000.0000.0000.000
130A134SER0-0.099-0.07434.533-0.036-0.0360.0000.0000.0000.000
131A135LEU00.0060.01730.986-0.092-0.0920.0000.0000.0000.000
132A136LYS10.8760.95728.7758.7658.7650.0000.0000.0000.000
133A137THR0-0.011-0.01625.423-0.151-0.1510.0000.0000.0000.000
134A138VAL0-0.013-0.02120.4880.0460.0460.0000.0000.0000.000
135A139VAL00.0000.00619.523-0.077-0.0770.0000.0000.0000.000
136A140LEU00.0020.01611.5440.1040.1040.0000.0000.0000.000
137A141LEU00.015-0.00211.911-0.297-0.2970.0000.0000.0000.000
138A142ASP-1-0.787-0.89116.503-11.509-11.5090.0000.0000.0000.000
139A143LYS10.8500.93915.92016.33116.3310.0000.0000.0000.000
140A144ARG10.8830.93120.36911.70111.7010.0000.0000.0000.000
141A145GLU-1-0.835-0.92521.130-13.181-13.1810.0000.0000.0000.000
142A146GLY0-0.014-0.00322.6910.2330.2330.0000.0000.0000.000
143A147ARG10.7190.85423.11111.60711.6070.0000.0000.0000.000
144A148ARG10.9220.95324.57111.39311.3930.0000.0000.0000.000
145A149VAL0-0.0090.01328.9220.3750.3750.0000.0000.0000.000
146A150PRO00.001-0.00729.456-0.291-0.2910.0000.0000.0000.000
147A151PHE00.0520.02126.8060.1330.1330.0000.0000.0000.000
148A152SER0-0.020-0.00827.418-0.309-0.3090.0000.0000.0000.000
149A153ALA00.0400.03323.7530.1760.1760.0000.0000.0000.000
150A154ASP-1-0.836-0.90525.736-9.518-9.5180.0000.0000.0000.000
151A155TYR0-0.122-0.10722.8400.0660.0660.0000.0000.0000.000
152A156VAL00.0180.01219.184-0.117-0.1170.0000.0000.0000.000
153A157VAL0-0.0290.01414.2010.1760.1760.0000.0000.0000.000
154A158ALA00.0180.00414.616-0.216-0.2160.0000.0000.0000.000
155A159ASN0-0.0060.00116.5870.2830.2830.0000.0000.0000.000
156A160ILE0-0.004-0.00713.909-0.665-0.6650.0000.0000.0000.000
157A161PRO00.0340.02515.9940.7070.7070.0000.0000.0000.000
158A162ASN00.007-0.01016.722-1.253-1.2530.0000.0000.0000.000
159A163ALA00.0110.02112.6370.1190.1190.0000.0000.0000.000
160A164PHE00.0290.01911.1490.6980.6980.0000.0000.0000.000
161A165VAL0-0.050-0.0249.973-1.773-1.7730.0000.0000.0000.000
162A166ILE00.0190.0085.3220.8060.8060.0000.0000.0000.000
163A167GLY00.0290.0175.730-2.027-2.0270.0000.0000.0000.000
164A168TYR0-0.074-0.0946.4232.5432.5430.0000.0000.0000.000
165A169GLY0-0.016-0.0048.8681.4991.4990.0000.0000.0000.000
166A170LEU00.0040.00610.0390.7560.7560.0000.0000.0000.000
167A171ASP-1-0.867-0.9269.198-18.978-18.9780.0000.0000.0000.000
168A172TYR0-0.005-0.01710.3100.5640.5640.0000.0000.0000.000
169A173ASP-1-0.889-0.93712.080-16.928-16.9280.0000.0000.0000.000
170A174ASP-1-0.819-0.88814.126-15.804-15.8040.0000.0000.0000.000
171A175THR0-0.0180.0029.146-0.128-0.1280.0000.0000.0000.000
172A176TYR00.025-0.0125.610-0.416-0.4160.0000.0000.0000.000
173A177ARG10.7640.8816.66016.86716.8670.0000.0000.0000.000
174A178GLU-1-0.903-0.9696.770-24.537-24.5370.0000.0000.0000.000
180A184VAL0-0.023-0.0126.5182.4552.4550.0000.0000.0000.000
181A185LEU0-0.016-0.0026.377-4.736-4.7360.0000.0000.0000.000
182A186ARG10.8410.9166.18839.15939.1590.0000.0000.0000.000
183A187PRO00.0190.0038.9470.7840.7840.0000.0000.0000.000
184A188GLU-1-0.857-0.92110.685-25.761-25.7610.0000.0000.0000.000
185A189VAL0-0.075-0.0418.929-0.569-0.5690.0000.0000.0000.000
186A190TYR-1-0.936-0.94511.409-16.311-16.3110.0000.0000.0000.000