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: 1YG5Z

Calculation Name: 7MCI-B-Xray547

Preferred Name:

Target Type:

Ligand Name: iron-sulfur-molybdenum cluster with interstitial carbon | fe(8)-s(7) cluster | 3-hydroxy-3-carboxy-adipic acid | glycerol | calcium ion | molybdenum atom | hydrosulfuric acid

Ligand 3-letter code: ICS | CLF | HCA | GOL | CA | MO | H2S

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7MCI

Chain ID: B

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 522
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -10655103.07902
FMO2-HF: Nuclear repulsion 10444215.519774
FMO2-HF: Total energy -210887.559246
FMO2-MP2: Total energy -211493.525547


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:SER)


Summations of interaction energy for fragment #1(A:2: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.
-92.448-85.3951.554-4.355-4.25-0.043
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.925
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].
3A4GLN00.0550.0423.727-0.7110.898-0.008-0.810-0.791-0.003
8A9LYS10.7730.8764.69455.35655.439-0.001-0.005-0.0770.000
13A14LEU0-0.010-0.0023.574-1.829-1.6540.002-0.051-0.1250.000
16A17ASP-1-0.756-0.8523.529-62.650-61.9680.002-0.428-0.255-0.003
18A19ASP-1-0.853-0.9242.354-95.031-91.2061.474-2.777-2.522-0.034
19A20TYR00.025-0.0072.8047.5818.2600.085-0.284-0.480-0.003
4A5VAL00.0250.0076.3220.8630.8630.0000.0000.0000.000
5A6ASP-1-0.870-0.9359.473-20.988-20.9880.0000.0000.0000.000
6A7LYS10.8400.9098.92631.56831.5680.0000.0000.0000.000
7A8ILE0-0.0040.0158.251-3.930-3.9300.0000.0000.0000.000
9A10ALA00.0770.0418.406-2.358-2.3580.0000.0000.0000.000
10A11SER00.0230.0009.559-1.822-1.8220.0000.0000.0000.000
11A12TYR00.0130.03710.200-1.736-1.7360.0000.0000.0000.000
12A13PRO00.031-0.0089.8510.7370.7370.0000.0000.0000.000
14A15PHE0-0.018-0.0225.942-4.233-4.2330.0000.0000.0000.000
15A16LEU0-0.066-0.0388.2443.3663.3660.0000.0000.0000.000
17A18GLN0-0.019-0.0366.0561.3391.3390.0000.0000.0000.000
20A21LYS10.8930.9667.19630.88930.8890.0000.0000.0000.000
21A22ASP-1-0.842-0.9099.690-23.856-23.8560.0000.0000.0000.000
22A23MET0-0.059-0.0239.0141.8781.8780.0000.0000.0000.000
23A24LEU0-0.020-0.01810.8882.4542.4540.0000.0000.0000.000
24A25ALA0-0.0050.00413.0601.7681.7680.0000.0000.0000.000
25A26LYS10.9730.97712.00924.84224.8420.0000.0000.0000.000
26A27LYS10.8660.93314.72418.56918.5690.0000.0000.0000.000
27A28ARG10.8180.86116.56317.52617.5260.0000.0000.0000.000
28A29ASP-1-0.813-0.88119.007-15.075-15.0750.0000.0000.0000.000
29A30GLY0-0.0280.00519.6300.6650.6650.0000.0000.0000.000
30A31PHE0-0.050-0.03818.1270.4210.4210.0000.0000.0000.000
31A32GLU-1-0.929-0.95518.585-16.315-16.3150.0000.0000.0000.000
32A33GLU-1-0.951-0.96522.705-10.742-10.7420.0000.0000.0000.000
33A34LYS10.9170.97520.76915.12715.1270.0000.0000.0000.000
34A35TYR00.0160.00625.4960.1170.1170.0000.0000.0000.000
35A36PRO00.0350.00526.562-0.443-0.4430.0000.0000.0000.000
36A37GLN0-0.028-0.02524.032-0.242-0.2420.0000.0000.0000.000
37A38ASP-1-0.834-0.91326.671-10.618-10.6180.0000.0000.0000.000
38A39LYS10.7940.88530.1709.3049.3040.0000.0000.0000.000
39A40ILE0-0.038-0.01925.4930.1770.1770.0000.0000.0000.000
40A41ASP-1-0.821-0.90527.670-11.507-11.5070.0000.0000.0000.000
41A42GLU-1-0.863-0.90930.295-8.599-8.5990.0000.0000.0000.000
42A43VAL00.003-0.00432.4970.2770.2770.0000.0000.0000.000
43A44PHE00.0060.00930.0740.1430.1430.0000.0000.0000.000
44A45GLN00.0550.04032.2290.0630.0630.0000.0000.0000.000
45A46TRP0-0.013-0.01434.8330.1070.1070.0000.0000.0000.000
46A47THR0-0.078-0.04734.0910.1610.1610.0000.0000.0000.000
47A48THR0-0.059-0.03234.6690.0770.0770.0000.0000.0000.000
48A49THR0-0.050-0.03037.5100.2830.2830.0000.0000.0000.000
49A50LYS11.0030.97441.0646.8846.8840.0000.0000.0000.000
50A51GLU-1-0.870-0.91043.586-7.299-7.2990.0000.0000.0000.000
51A52TYR00.0450.03436.791-0.008-0.0080.0000.0000.0000.000
52A53GLN00.0410.02441.949-0.174-0.1740.0000.0000.0000.000
53A54GLU-1-0.925-0.96643.393-6.638-6.6380.0000.0000.0000.000
54A55LEU0-0.0020.00243.3270.0550.0550.0000.0000.0000.000
55A56ASN0-0.061-0.02739.8550.0280.0280.0000.0000.0000.000
56A57PHE0-0.016-0.04242.9100.0080.0080.0000.0000.0000.000
57A58GLN0-0.0250.00246.0990.0950.0950.0000.0000.0000.000
58A59ARG10.6750.80440.4757.8577.8570.0000.0000.0000.000
59A60GLU-1-0.930-0.95345.626-6.250-6.2500.0000.0000.0000.000
60A61ALA0-0.014-0.01645.8540.0030.0030.0000.0000.0000.000
61A62LEU0-0.0160.00538.289-0.116-0.1160.0000.0000.0000.000
62A63THR0-0.024-0.01039.2050.1040.1040.0000.0000.0000.000
63A64VAL00.011-0.01334.625-0.170-0.1700.0000.0000.0000.000
64A65ASN0-0.0080.00132.049-0.016-0.0160.0000.0000.0000.000
65A66PRO00.0410.01435.3660.1730.1730.0000.0000.0000.000
66A67ALA0-0.0060.00337.377-0.186-0.1860.0000.0000.0000.000
67A68LYS10.8890.95539.6587.3637.3630.0000.0000.0000.000
68A69ALA00.0310.02539.368-0.200-0.2000.0000.0000.0000.000
69A70CYS0-0.029-0.01940.9790.1970.1970.0000.0000.0000.000
70A71GLN00.0330.01143.635-0.018-0.0180.0000.0000.0000.000
71A72PRO00.0420.01843.8830.0010.0010.0000.0000.0000.000
72A73LEU0-0.0140.01139.127-0.033-0.0330.0000.0000.0000.000
73A74GLY00.034-0.00342.900-0.048-0.0480.0000.0000.0000.000
74A75ALA00.0020.00345.8690.0850.0850.0000.0000.0000.000
75A76VAL0-0.002-0.01341.9390.0580.0580.0000.0000.0000.000
76A77LEU0-0.015-0.00242.8020.0160.0160.0000.0000.0000.000
77A78CYS0-0.0490.00345.0880.1110.1110.0000.0000.0000.000
78A79ALA00.0430.00947.7410.1020.1020.0000.0000.0000.000
79A80LEU0-0.017-0.01842.4280.0460.0460.0000.0000.0000.000
80A81GLY0-0.0050.01946.928-0.026-0.0260.0000.0000.0000.000
81A82PHE0-0.022-0.02049.6170.1540.1540.0000.0000.0000.000
82A83GLU-1-0.869-0.93451.099-5.890-5.8900.0000.0000.0000.000
83A84LYS10.8370.92250.4866.2446.2440.0000.0000.0000.000
84A85THR00.0090.01650.2300.0740.0740.0000.0000.0000.000
85A86MET0-0.038-0.01044.669-0.227-0.2270.0000.0000.0000.000
86A87PRO00.001-0.00444.8000.1170.1170.0000.0000.0000.000
87A88TYR00.003-0.02646.058-0.150-0.1500.0000.0000.0000.000
88A89VAL0-0.040-0.02243.9070.0720.0720.0000.0000.0000.000
89A90HIS10.7640.84346.1186.1956.1950.0000.0000.0000.000
90A91GLY00.041-0.00347.0420.0180.0180.0000.0000.0000.000
91A92SER00.017-0.00242.286-0.046-0.0460.0000.0000.0000.000
92A93GLN00.0900.04638.970-0.016-0.0160.0000.0000.0000.000
93A94GLY00.0090.00437.059-0.158-0.1580.0000.0000.0000.000
94A95CYS0-0.050-0.02137.087-0.152-0.1520.0000.0000.0000.000
95A96VAL00.0610.03238.828-0.119-0.1190.0000.0000.0000.000
96A97ALA00.0060.00934.277-0.118-0.1180.0000.0000.0000.000
97A98TYR0-0.0110.00331.646-0.364-0.3640.0000.0000.0000.000
98A99PHE00.031-0.01035.346-0.124-0.1240.0000.0000.0000.000
99A100ARG10.9000.95936.3688.4468.4460.0000.0000.0000.000
100A101SER00.0150.00331.431-0.237-0.2370.0000.0000.0000.000
101A102TYR0-0.063-0.02832.549-0.348-0.3480.0000.0000.0000.000
102A103PHE00.0370.01234.498-0.067-0.0670.0000.0000.0000.000
103A104ASN0-0.050-0.02732.315-0.076-0.0760.0000.0000.0000.000
104A105ARG10.8980.94927.94810.84310.8430.0000.0000.0000.000
105A106HIS0-0.0180.00031.337-0.447-0.4470.0000.0000.0000.000
106A107PHE00.0500.01034.130-0.035-0.0350.0000.0000.0000.000
107A108ARG10.8010.90327.56710.90510.9050.0000.0000.0000.000
108A109GLU-1-0.754-0.83533.174-8.670-8.6700.0000.0000.0000.000
109A110PRO0-0.011-0.01535.379-0.183-0.1830.0000.0000.0000.000
110A111VAL00.0330.01936.9410.1660.1660.0000.0000.0000.000
111A112SER0-0.0150.00338.773-0.206-0.2060.0000.0000.0000.000
112A113CYS00.0120.00141.2480.1340.1340.0000.0000.0000.000
113A114VAL0-0.017-0.00341.692-0.193-0.1930.0000.0000.0000.000
114A115SER0-0.025-0.01942.8580.0030.0030.0000.0000.0000.000
115A116ASP-1-0.706-0.81544.665-6.522-6.5220.0000.0000.0000.000
116A117SER0-0.044-0.03342.4250.0920.0920.0000.0000.0000.000
117A118MET0-0.0360.02944.7560.0470.0470.0000.0000.0000.000
118A119THR0-0.047-0.05243.707-0.201-0.2010.0000.0000.0000.000
119A120GLU-1-0.938-0.97845.156-6.865-6.8650.0000.0000.0000.000
120A121ASP-1-0.816-0.87647.289-6.424-6.4240.0000.0000.0000.000
121A122ALA00.0460.01849.6580.1510.1510.0000.0000.0000.000
122A123ALA0-0.066-0.03649.4310.0850.0850.0000.0000.0000.000
123A124VAL0-0.054-0.01951.4850.0840.0840.0000.0000.0000.000
124A125PHE0-0.044-0.03253.9820.1370.1370.0000.0000.0000.000
125A126GLY00.0190.03254.5810.0970.0970.0000.0000.0000.000
126A127GLY0-0.010-0.03452.411-0.050-0.0500.0000.0000.0000.000
127A128GLN0-0.017-0.01453.1600.0130.0130.0000.0000.0000.000
128A129GLN0-0.024-0.02953.8320.1200.1200.0000.0000.0000.000
129A130ASN00.013-0.00848.3520.0770.0770.0000.0000.0000.000
130A131MET0-0.0140.00651.400-0.086-0.0860.0000.0000.0000.000
131A132LYS10.8660.93953.4745.3685.3680.0000.0000.0000.000
132A133ASP-1-0.795-0.89551.612-6.006-6.0060.0000.0000.0000.000
133A134GLY0-0.014-0.00749.478-0.088-0.0880.0000.0000.0000.000
134A135LEU0-0.018-0.01650.361-0.075-0.0750.0000.0000.0000.000
135A136GLN00.0340.03052.970-0.053-0.0530.0000.0000.0000.000
136A137ASN00.002-0.00448.5520.0030.0030.0000.0000.0000.000
137A138CYS0-0.054-0.00148.366-0.124-0.1240.0000.0000.0000.000
138A139LYS10.9600.98649.3915.6515.6510.0000.0000.0000.000
139A140ALA0-0.014-0.00251.8620.0290.0290.0000.0000.0000.000
140A141THR0-0.066-0.03645.523-0.011-0.0110.0000.0000.0000.000
141A142TYR00.012-0.01642.827-0.088-0.0880.0000.0000.0000.000
142A143LYS10.8550.95847.8996.2646.2640.0000.0000.0000.000
143A144PRO00.0110.01949.8170.0130.0130.0000.0000.0000.000
144A145ASP-1-0.858-0.95151.724-5.796-5.7960.0000.0000.0000.000
145A146MET0-0.043-0.00953.6420.1790.1790.0000.0000.0000.000
146A147ILE0-0.032-0.01350.626-0.163-0.1630.0000.0000.0000.000
147A148ALA00.0260.01850.4910.1070.1070.0000.0000.0000.000
148A149VAL0-0.023-0.00850.155-0.166-0.1660.0000.0000.0000.000
149A150SER00.0100.00347.8940.0350.0350.0000.0000.0000.000
150A151THR0-0.020-0.05248.907-0.038-0.0380.0000.0000.0000.000
151A152THR00.0120.00143.718-0.058-0.0580.0000.0000.0000.000
152A153CYS0-0.028-0.03044.8920.0810.0810.0000.0000.0000.000
153A154MET00.0260.02846.0690.0430.0430.0000.0000.0000.000
154A155ALA00.0660.03047.9910.1150.1150.0000.0000.0000.000
155A156GLU-1-0.839-0.87650.508-5.943-5.9430.0000.0000.0000.000
156A157VAL0-0.037-0.02249.4170.1110.1110.0000.0000.0000.000
157A158ILE0-0.0210.00051.4800.0720.0720.0000.0000.0000.000
158A159GLY0-0.0170.01054.1280.1080.1080.0000.0000.0000.000
159A160ASP-1-0.719-0.86353.014-5.928-5.9280.0000.0000.0000.000
160A161ASP-1-0.873-0.94856.021-5.280-5.2800.0000.0000.0000.000
161A162LEU0-0.004-0.01953.6410.0150.0150.0000.0000.0000.000
162A163ASN00.0030.02357.3040.0060.0060.0000.0000.0000.000
163A164ALA00.0110.01160.8540.0370.0370.0000.0000.0000.000
164A165PHE0-0.017-0.00655.0360.0190.0190.0000.0000.0000.000
165A166ILE00.0160.02555.921-0.014-0.0140.0000.0000.0000.000
166A167ASN00.0050.00259.1200.0100.0100.0000.0000.0000.000
167A168ASN0-0.002-0.00861.5160.1400.1400.0000.0000.0000.000
168A169SER0-0.022-0.03257.979-0.016-0.0160.0000.0000.0000.000
169A170LYS10.7880.90660.0555.2285.2280.0000.0000.0000.000
170A171LYS10.8160.90362.5084.9864.9860.0000.0000.0000.000
171A172GLU-1-0.851-0.91662.243-5.097-5.0970.0000.0000.0000.000
172A173GLY00.0060.01462.719-0.024-0.0240.0000.0000.0000.000
173A174PHE0-0.027-0.00856.459-0.041-0.0410.0000.0000.0000.000
174A175ILE0-0.062-0.04156.261-0.122-0.1220.0000.0000.0000.000
175A176PRO00.010-0.00259.1910.0620.0620.0000.0000.0000.000
176A177ASP-1-0.842-0.92761.843-4.967-4.9670.0000.0000.0000.000
177A178GLU-1-0.868-0.93764.181-4.978-4.9780.0000.0000.0000.000
178A179PHE0-0.059-0.02254.691-0.047-0.0470.0000.0000.0000.000
179A180PRO00.016-0.00157.5390.0110.0110.0000.0000.0000.000
180A181VAL00.0090.00655.033-0.132-0.1320.0000.0000.0000.000
181A182PRO00.0200.02455.1090.0650.0650.0000.0000.0000.000
182A183PHE0-0.008-0.01654.668-0.127-0.1270.0000.0000.0000.000
183A184ALA0-0.005-0.00652.9940.0890.0890.0000.0000.0000.000
184A185HIS10.8400.90952.9625.7255.7250.0000.0000.0000.000
185A186THR0-0.003-0.00448.6210.0330.0330.0000.0000.0000.000
186A187PRO00.0340.02448.661-0.166-0.1660.0000.0000.0000.000
187A188SER0-0.010-0.02644.3330.0430.0430.0000.0000.0000.000
188A189PHE00.0320.01345.978-0.120-0.1200.0000.0000.0000.000
189A190VAL0-0.0040.00847.8770.0930.0930.0000.0000.0000.000
190A191GLY00.0170.01849.553-0.015-0.0150.0000.0000.0000.000
191A192SER0-0.004-0.01445.174-0.155-0.1550.0000.0000.0000.000
192A193HIS0-0.024-0.02243.1010.1170.1170.0000.0000.0000.000
193A194VAL00.0510.02345.2410.1070.1070.0000.0000.0000.000
194A195THR0-0.013-0.01047.9370.0850.0850.0000.0000.0000.000
195A196GLY00.0070.00048.6750.1290.1290.0000.0000.0000.000
196A197TRP00.0360.03547.1420.1140.1140.0000.0000.0000.000
197A198ASP-1-0.753-0.85449.945-5.685-5.6850.0000.0000.0000.000
198A199ASN0-0.026-0.02652.5610.2320.2320.0000.0000.0000.000
199A200MET0-0.0390.00050.4650.0550.0550.0000.0000.0000.000
200A201PHE00.0580.01953.0390.0860.0860.0000.0000.0000.000
201A202GLU-1-0.862-0.93354.883-5.291-5.2910.0000.0000.0000.000
202A203GLY00.0020.00056.6990.1120.1120.0000.0000.0000.000
203A204ILE00.001-0.01452.9700.0920.0920.0000.0000.0000.000
204A205ALA0-0.0010.00157.5620.0870.0870.0000.0000.0000.000
205A206ARG10.9080.96760.3505.2635.2630.0000.0000.0000.000
206A207TYR0-0.019-0.00460.0960.0860.0860.0000.0000.0000.000
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