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

tag_button

FMODB ID: N6Y6Q

Calculation Name: 1OCY-A-Xray549

Preferred Name:

Target Type:

Ligand Name: citric acid | sulfate ion | zinc ion

Ligand 3-letter code: CIT | SO4 | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1OCY

Chain ID: A

ChEMBL ID:

UniProt ID: P10930

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1659891.983852
FMO2-HF: Nuclear repulsion 1582630.478898
FMO2-HF: Total energy -77261.504954
FMO2-MP2: Total energy -77484.456507


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:330:ARG)


Summations of interaction energy for fragment #1(A:330:ARG)
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.
-135.311-139.21838.497-19.008-15.585-0.232
Interaction energy analysis for fragmet #1(A:330:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.618 / q_NPA : 1.757
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].
3A332VAL00.0140.0122.073-30.254-27.1126.956-4.359-5.739-0.049
4A333THR00.000-0.0203.0229.3559.7780.0110.044-0.479-0.001
5A334GLN00.007-0.0225.054-2.264-2.232-0.0010.000-0.0320.000
7A336GLU-1-0.789-0.8671.693-188.584-196.08831.531-14.693-9.335-0.182
6A335ASN00.0530.0485.4200.7060.7060.0000.0000.0000.000
8A337ILE00.0220.0286.1961.5691.5690.0000.0000.0000.000
9A338ASP-1-0.727-0.8259.446-34.892-34.8920.0000.0000.0000.000
10A339ARG10.9280.9635.65460.66060.6600.0000.0000.0000.000
11A340THR0-0.063-0.0347.300-1.004-1.0040.0000.0000.0000.000
12A341ILE0-0.025-0.0259.4812.8982.8980.0000.0000.0000.000
13A342PRO00.0020.02413.1300.6030.6030.0000.0000.0000.000
14A343VAL0-0.008-0.00714.7161.8751.8750.0000.0000.0000.000
15A344GLY0-0.005-0.00617.8400.2840.2840.0000.0000.0000.000
16A345ALA0-0.045-0.01117.4801.0561.0560.0000.0000.0000.000
17A346ILE00.001-0.01319.5400.3270.3270.0000.0000.0000.000
18A347MET0-0.040-0.01019.645-1.003-1.0030.0000.0000.0000.000
19A348MET0-0.001-0.00222.7711.0611.0610.0000.0000.0000.000
20A349TRP0-0.024-0.02422.590-1.385-1.3850.0000.0000.0000.000
21A350ALA00.007-0.00426.4880.7880.7880.0000.0000.0000.000
22A351ALA00.0300.02529.1550.4070.4070.0000.0000.0000.000
23A352ASP-1-0.876-0.94030.575-18.170-18.1700.0000.0000.0000.000
24A353SER0-0.048-0.02030.3520.0820.0820.0000.0000.0000.000
25A354LEU00.002-0.00224.545-0.489-0.4890.0000.0000.0000.000
26A355PRO0-0.0050.00222.3630.4640.4640.0000.0000.0000.000
27A356SER0-0.022-0.01719.906-0.203-0.2030.0000.0000.0000.000
28A357ASP-1-0.816-0.89922.497-25.089-25.0890.0000.0000.0000.000
29A358ALA00.0200.01618.2000.2210.2210.0000.0000.0000.000
30A359TRP00.008-0.00617.413-0.422-0.4220.0000.0000.0000.000
31A360ARG10.8840.93322.20421.66321.6630.0000.0000.0000.000
32A361PHE00.0450.02025.829-0.447-0.4470.0000.0000.0000.000
33A362CYS0-0.063-0.02427.5030.0550.0550.0000.0000.0000.000
34A363HIS0-0.028-0.02529.7280.5930.5930.0000.0000.0000.000
35A364GLY00.0080.00332.6670.4880.4880.0000.0000.0000.000
36A365GLY0-0.0100.01432.8720.3690.3690.0000.0000.0000.000
37A366THR00.000-0.00631.267-0.207-0.2070.0000.0000.0000.000
38A367VAL00.0330.01725.870-0.257-0.2570.0000.0000.0000.000
39A368SER00.0690.04028.0640.5560.5560.0000.0000.0000.000
40A369ALA00.005-0.01926.644-0.796-0.7960.0000.0000.0000.000
41A370SER0-0.047-0.02625.600-0.654-0.6540.0000.0000.0000.000
42A371ASP-1-0.833-0.90224.124-24.648-24.6480.0000.0000.0000.000
43A372CYS0-0.0270.00522.110-1.288-1.2880.0000.0000.0000.000
44A373PRO00.0560.03220.4520.3600.3600.0000.0000.0000.000
45A374LEU00.0240.01315.7930.5610.5610.0000.0000.0000.000
46A375TYR00.012-0.01820.4020.0910.0910.0000.0000.0000.000
47A376ALA0-0.024-0.02422.9500.7720.7720.0000.0000.0000.000
48A377SER0-0.052-0.03522.2860.3900.3900.0000.0000.0000.000
49A378ARG10.7540.84814.99632.49832.4980.0000.0000.0000.000
50A379ILE0-0.072-0.02322.9350.4560.4560.0000.0000.0000.000
51A380GLY00.0300.01625.8020.8280.8280.0000.0000.0000.000
52A381THR0-0.008-0.01728.493-0.104-0.1040.0000.0000.0000.000
53A382ARG10.8690.95027.48720.58920.5890.0000.0000.0000.000
54A383TYR0-0.008-0.01027.0270.3280.3280.0000.0000.0000.000
55A384GLY00.0460.03932.2680.1900.1900.0000.0000.0000.000
56A385GLY00.0150.00033.193-0.518-0.5180.0000.0000.0000.000
57A386SER0-0.032-0.03333.7500.2620.2620.0000.0000.0000.000
58A387SER00.0460.00131.425-0.268-0.2680.0000.0000.0000.000
59A388SER00.0000.00630.553-0.387-0.3870.0000.0000.0000.000
60A389ASN0-0.033-0.02031.051-0.702-0.7020.0000.0000.0000.000
61A390PRO00.0440.04127.5630.5130.5130.0000.0000.0000.000
62A391GLY00.0360.02930.278-0.080-0.0800.0000.0000.0000.000
63A392LEU0-0.0160.01327.006-0.742-0.7420.0000.0000.0000.000
64A393PRO00.0220.00027.8190.6600.6600.0000.0000.0000.000
65A394ASP-1-0.794-0.87030.901-16.852-16.8520.0000.0000.0000.000
66A395MET0-0.034-0.01928.280-0.062-0.0620.0000.0000.0000.000
67A396ARG10.8560.90633.12716.37616.3760.0000.0000.0000.000
68A397GLY00.0280.02135.6760.4000.4000.0000.0000.0000.000
69A398LEU0-0.038-0.00434.1160.2720.2720.0000.0000.0000.000
70A399PHE00.0360.01533.898-0.511-0.5110.0000.0000.0000.000
71A400VAL00.0110.01127.9700.0610.0610.0000.0000.0000.000
72A401ARG10.8910.94031.44816.64516.6450.0000.0000.0000.000
73A402GLY00.0030.00529.184-0.409-0.4090.0000.0000.0000.000
74A403SER00.0130.00329.2760.4360.4360.0000.0000.0000.000
75A404GLY0-0.007-0.00130.999-0.355-0.3550.0000.0000.0000.000
76A405ARG10.8240.88033.50315.10215.1020.0000.0000.0000.000
77A406GLY00.0700.03732.112-0.098-0.0980.0000.0000.0000.000
78A407SER00.0660.01832.3130.3360.3360.0000.0000.0000.000
79A408HIS0-0.014-0.01630.6590.9190.9190.0000.0000.0000.000
80A409LEU0-0.0070.00435.5740.3620.3620.0000.0000.0000.000
81A410THR0-0.0200.00035.9620.4340.4340.0000.0000.0000.000
82A411ASN00.0490.03938.0410.6120.6120.0000.0000.0000.000
83A412PRO00.0630.02339.6320.2220.2220.0000.0000.0000.000
84A413ASN0-0.021-0.00640.7330.1580.1580.0000.0000.0000.000
85A414VAL00.0000.00840.1020.1910.1910.0000.0000.0000.000
86A415ASN0-0.046-0.03841.2710.1760.1760.0000.0000.0000.000
87A416GLY00.0630.03845.1680.1630.1630.0000.0000.0000.000
88A417ASN00.0210.00448.855-0.230-0.2300.0000.0000.0000.000
89A418ASP-1-0.811-0.91351.544-11.591-11.5910.0000.0000.0000.000
90A419GLN00.0070.00052.8940.2250.2250.0000.0000.0000.000
91A420PHE0-0.0140.00355.5540.2330.2330.0000.0000.0000.000
92A421GLY00.0000.01056.4280.1420.1420.0000.0000.0000.000
93A422LYS10.8470.90953.43710.81610.8160.0000.0000.0000.000
94A423PRO00.0180.01049.772-0.128-0.1280.0000.0000.0000.000
95A424ARG10.8490.93946.12512.57312.5730.0000.0000.0000.000
96A425LEU00.0490.01044.279-0.095-0.0950.0000.0000.0000.000
97A426GLY00.0640.04541.703-0.274-0.2740.0000.0000.0000.000
98A427VAL0-0.045-0.01442.400-0.207-0.2070.0000.0000.0000.000
99A428GLY0-0.0120.00344.5780.1090.1090.0000.0000.0000.000
100A429CYS0-0.045-0.01640.107-0.156-0.1560.0000.0000.0000.000
101A430THR00.000-0.01837.244-0.281-0.2810.0000.0000.0000.000
102A431GLY0-0.0070.01534.3780.1560.1560.0000.0000.0000.000
103A432GLY00.0330.02135.2750.2810.2810.0000.0000.0000.000
104A433TYR00.013-0.00732.887-0.687-0.6870.0000.0000.0000.000
105A434VAL00.004-0.01526.8210.0330.0330.0000.0000.0000.000
106A435GLY00.0270.01330.175-0.111-0.1110.0000.0000.0000.000
107A436GLU-1-0.926-0.93531.697-15.419-15.4190.0000.0000.0000.000
108A437VAL00.0090.00735.161-0.164-0.1640.0000.0000.0000.000
109A438GLN0-0.0130.00037.2210.3370.3370.0000.0000.0000.000
110A439LYS10.9650.97639.58913.46813.4680.0000.0000.0000.000
111A440GLN00.0440.02942.464-0.115-0.1150.0000.0000.0000.000
112A441GLN0-0.023-0.02343.8490.2080.2080.0000.0000.0000.000
113A442MET00.0390.02645.226-0.137-0.1370.0000.0000.0000.000
114A443SER0-0.014-0.00947.6570.0350.0350.0000.0000.0000.000
115A444TYR00.0350.02649.0370.2650.2650.0000.0000.0000.000
116A445HIS0-0.023-0.01852.2600.0050.0050.0000.0000.0000.000
117A446LYS10.8540.90854.55210.48910.4890.0000.0000.0000.000
118A447HIS00.0510.03056.088-0.042-0.0420.0000.0000.0000.000
119A448ALA0-0.022-0.01160.1460.1120.1120.0000.0000.0000.000
120A449GLY00.0410.02563.492-0.013-0.0130.0000.0000.0000.000
121A450GLY0-0.008-0.01166.4610.0460.0460.0000.0000.0000.000
122A451PHE0-0.015-0.01668.8030.1550.1550.0000.0000.0000.000
123A452GLY0-0.0030.00670.723-0.133-0.1330.0000.0000.0000.000
124A453GLU0-0.003-0.03872.7120.1370.1370.0000.0000.0000.000
125A454TYR0-0.047-0.03674.711-0.080-0.0800.0000.0000.0000.000
126A455ASP-1-0.864-0.92076.028-8.097-8.0970.0000.0000.0000.000
127A456ASP-1-0.926-0.94470.211-9.088-9.0880.0000.0000.0000.000
128A457SER0-0.005-0.01771.8030.0490.0490.0000.0000.0000.000
129A458GLY00.0120.01669.1190.0290.0290.0000.0000.0000.000
130A459ALA00.0310.01468.228-0.107-0.1070.0000.0000.0000.000
131A460PHE0-0.036-0.01362.985-0.140-0.1400.0000.0000.0000.000
132A461GLY00.0280.02563.359-0.230-0.2300.0000.0000.0000.000
133A462ASN0-0.042-0.04265.6390.0730.0730.0000.0000.0000.000
134A463THR00.0010.00065.246-0.120-0.1200.0000.0000.0000.000
135A464ARG10.9960.99867.0779.4219.4210.0000.0000.0000.000
136A465ARG10.9450.98469.4858.1958.1950.0000.0000.0000.000
137A466SER00.0160.00370.267-0.013-0.0130.0000.0000.0000.000
138A467ASN0-0.024-0.00272.6570.2010.2010.0000.0000.0000.000
139A468PHE0-0.006-0.00867.544-0.132-0.1320.0000.0000.0000.000
140A469VAL00.0070.01573.1140.1250.1250.0000.0000.0000.000
141A470GLY00.0900.04174.504-0.112-0.1120.0000.0000.0000.000
142A471THR0-0.022-0.00277.1130.1380.1380.0000.0000.0000.000
143A472ARG10.9520.98580.4217.4237.4230.0000.0000.0000.000
144A473LYS10.9210.94883.1747.3037.3030.0000.0000.0000.000
145A474GLY00.0290.01483.131-0.067-0.0670.0000.0000.0000.000
146A475LEU0-0.0170.00578.518-0.065-0.0650.0000.0000.0000.000
147A476ASP-1-0.836-0.90880.355-7.718-7.7180.0000.0000.0000.000
148A477TRP0-0.037-0.03172.844-0.152-0.1520.0000.0000.0000.000
149A478ASP-1-0.923-0.94776.218-7.973-7.9730.0000.0000.0000.000
150A479ASN0-0.079-0.03975.403-0.021-0.0210.0000.0000.0000.000
151A480ARG10.9310.96572.1418.3458.3450.0000.0000.0000.000
152A481SER00.0010.00566.8130.0230.0230.0000.0000.0000.000
153A482TYR0-0.017-0.02069.1060.0130.0130.0000.0000.0000.000
154A483PHE0-0.024-0.01263.845-0.070-0.0700.0000.0000.0000.000
155A484THR0-0.0020.00061.3390.1130.1130.0000.0000.0000.000
156A485ASN0-0.034-0.02461.7740.0550.0550.0000.0000.0000.000
157A486ASP-1-0.828-0.92457.841-10.510-10.5100.0000.0000.0000.000
158A487GLY00.0110.01957.233-0.213-0.2130.0000.0000.0000.000
159A488TYR0-0.019-0.01054.510-0.176-0.1760.0000.0000.0000.000
160A489GLU-1-0.815-0.91859.102-10.280-10.2800.0000.0000.0000.000
161A490ILE00.0040.01161.6730.0330.0330.0000.0000.0000.000
162A491ASP-1-0.869-0.92865.237-9.083-9.0830.0000.0000.0000.000
163A492PRO00.0070.00365.131-0.202-0.2020.0000.0000.0000.000
164A493ALA00.019-0.01462.3730.0610.0610.0000.0000.0000.000
165A494SER0-0.039-0.01764.441-0.013-0.0130.0000.0000.0000.000
166A495GLN00.0040.00167.6120.1640.1640.0000.0000.0000.000
167A496ARG10.8660.94261.08910.18310.1830.0000.0000.0000.000
168A497ASN00.0460.01166.318-0.082-0.0820.0000.0000.0000.000
169A498SER00.0260.00463.666-0.021-0.0210.0000.0000.0000.000
170A499ARG10.9380.96864.2428.9828.9820.0000.0000.0000.000
171A500TYR0-0.026-0.00866.5880.1050.1050.0000.0000.0000.000
172A501THR0-0.055-0.00660.364-0.025-0.0250.0000.0000.0000.000
173A502LEU0-0.055-0.01660.3220.0200.0200.0000.0000.0000.000
174A503ASN0-0.049-0.03355.797-0.186-0.1860.0000.0000.0000.000
175A504ARG10.9300.96248.93512.44012.4400.0000.0000.0000.000
176A505PRO00.0220.00153.1790.0040.0040.0000.0000.0000.000
177A506GLU-1-0.937-0.98050.264-12.596-12.5960.0000.0000.0000.000
178A507LEU0-0.070-0.01449.491-0.198-0.1980.0000.0000.0000.000
179A508ILE0-0.034-0.00850.682-0.173-0.1730.0000.0000.0000.000
180A509GLY00.0630.02150.9770.0720.0720.0000.0000.0000.000
181A510ASN0-0.033-0.01849.6780.1540.1540.0000.0000.0000.000
182A511GLU-1-0.891-0.93042.847-14.382-14.3820.0000.0000.0000.000
183A512THR0-0.028-0.00645.0170.0750.0750.0000.0000.0000.000
184A513ARG10.8800.92941.00513.65613.6560.0000.0000.0000.000
185A514PRO0-0.0200.00138.4090.2670.2670.0000.0000.0000.000
186A515TRP00.0400.00939.834-0.091-0.0910.0000.0000.0000.000
187A516ASN0-0.076-0.04636.282-0.510-0.5100.0000.0000.0000.000
188A517ILE00.0380.02432.6980.3040.3040.0000.0000.0000.000
189A518SER0-0.0020.00534.211-0.167-0.1670.0000.0000.0000.000
190A519LEU0-0.009-0.00828.925-0.165-0.1650.0000.0000.0000.000
191A520ASN00.0160.01729.3210.6210.6210.0000.0000.0000.000
192A521TYR0-0.017-0.01827.193-0.877-0.8770.0000.0000.0000.000
193A522ILE0-0.017-0.00922.1490.5120.5120.0000.0000.0000.000
194A523ILE0-0.002-0.00622.551-0.493-0.4930.0000.0000.0000.000
195A524LYS10.8310.93915.01935.03835.0380.0000.0000.0000.000
196A525VAL0-0.023-0.02619.9710.3810.3810.0000.0000.0000.000
197A526LYS10.8290.88618.89525.82025.8200.0000.0000.0000.000
198A527GLU-2-1.729-1.84512.864-75.422-75.4220.0000.0000.0000.000