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: VN621

Calculation Name: 4RCI-B-Xray547

Preferred Name:

Target Type:

Ligand Name: unknown atom or ion

Ligand 3-letter code: UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4RCI

Chain ID: B

ChEMBL ID:

UniProt ID: Q9BYJ9

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2116851.947637
FMO2-HF: Nuclear repulsion 2041171.941888
FMO2-HF: Total energy -75680.005749
FMO2-MP2: Total energy -75902.429949


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:365:HIS)


Summations of interaction energy for fragment #1(A:365:HIS)
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.
30.73736.4264.868-3.41-7.1460.015
Interaction energy analysis for fragmet #1(A:365:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.938
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].
3A367VAL00.0210.0242.242-4.931-2.7454.689-2.367-4.5080.019
4A368LEU0-0.033-0.0062.5830.7082.6610.162-0.744-1.371-0.003
5A369GLU-1-0.952-0.9694.000-41.701-41.168-0.001-0.119-0.4120.000
161A536PHE0-0.051-0.0373.332-1.138-0.6320.013-0.101-0.418-0.001
162A537ALA00.018-0.0163.4930.5020.8640.007-0.072-0.2970.000
163A538HIS00.0220.0235.2923.2863.291-0.001-0.003-0.0010.000
165A540GLU-1-0.805-0.8535.155-28.638-28.494-0.001-0.004-0.1390.000
6A370LYS10.9900.9855.52929.99429.9940.0000.0000.0000.000
7A371LEU0-0.020-0.0027.3282.7362.7360.0000.0000.0000.000
8A372LYS10.9470.9676.00941.53641.5360.0000.0000.0000.000
9A373ALA0-0.0070.0089.4182.1392.1390.0000.0000.0000.000
10A374ALA0-0.037-0.00611.3891.9381.9380.0000.0000.0000.000
11A375HIS0-0.053-0.02612.4242.6692.6690.0000.0000.0000.000
12A376SER0-0.0060.00413.909-0.977-0.9770.0000.0000.0000.000
13A377TYR00.016-0.00510.2840.1350.1350.0000.0000.0000.000
14A378ASN0-0.056-0.04414.0630.5760.5760.0000.0000.0000.000
15A379PRO00.0230.03716.9090.1430.1430.0000.0000.0000.000
16A380LYS10.8520.90419.58512.40812.4080.0000.0000.0000.000
17A381GLU-1-0.888-0.93422.153-10.866-10.8660.0000.0000.0000.000
18A382PHE00.0330.00723.462-0.296-0.2960.0000.0000.0000.000
19A383GLU-1-0.854-0.92525.501-9.364-9.3640.0000.0000.0000.000
20A384TRP00.0940.03828.1790.2340.2340.0000.0000.0000.000
21A385ASN0-0.004-0.00529.5680.2810.2810.0000.0000.0000.000
22A386LEU00.004-0.00529.6560.1860.1860.0000.0000.0000.000
23A387LYS10.8690.92533.4989.1939.1930.0000.0000.0000.000
24A388SER0-0.018-0.01335.0070.1790.1790.0000.0000.0000.000
25A389GLY00.0520.02832.990-0.271-0.2710.0000.0000.0000.000
26A390ARG10.8460.91332.4068.6678.6670.0000.0000.0000.000
27A391VAL00.0100.00128.322-0.339-0.3390.0000.0000.0000.000
28A392PHE0-0.0130.00028.9660.3830.3830.0000.0000.0000.000
29A393ILE0-0.033-0.01227.100-0.434-0.4340.0000.0000.0000.000
30A394ILE0-0.0020.00722.9910.3280.3280.0000.0000.0000.000
31A395LYS10.8070.90224.44210.93910.9390.0000.0000.0000.000
32A396SER00.0290.00419.5870.4290.4290.0000.0000.0000.000
33A397TYR0-0.007-0.01522.6490.3140.3140.0000.0000.0000.000
34A398SER00.0140.02318.452-0.199-0.1990.0000.0000.0000.000
35A399GLU-1-0.808-0.90614.738-16.084-16.0840.0000.0000.0000.000
36A400ASP-1-0.792-0.86513.991-19.676-19.6760.0000.0000.0000.000
37A401ASP-1-0.817-0.92214.545-15.643-15.6430.0000.0000.0000.000
38A402ILE0-0.022-0.00314.4880.0780.0780.0000.0000.0000.000
39A403HIS10.8230.9036.85428.77628.7760.0000.0000.0000.000
40A404ARG10.8850.94811.62914.20114.2010.0000.0000.0000.000
41A405SER0-0.045-0.04113.850-0.023-0.0230.0000.0000.0000.000
42A406ILE0-0.033-0.02011.1740.0240.0240.0000.0000.0000.000
43A407LYS10.7970.8967.76926.26826.2680.0000.0000.0000.000
44A408TYR0-0.032-0.02911.224-0.535-0.5350.0000.0000.0000.000
45A409SER00.0020.02014.7760.8940.8940.0000.0000.0000.000
46A410ILE00.0310.03017.0890.9260.9260.0000.0000.0000.000
47A411TRP0-0.031-0.01518.901-0.812-0.8120.0000.0000.0000.000
48A412CYS00.0040.02221.6700.6790.6790.0000.0000.0000.000
49A413SER0-0.037-0.02324.319-0.046-0.0460.0000.0000.0000.000
50A414THR00.0460.01126.9610.2230.2230.0000.0000.0000.000
51A415GLU-1-0.782-0.89130.031-9.235-9.2350.0000.0000.0000.000
52A416HIS00.0140.00432.6340.1640.1640.0000.0000.0000.000
53A417GLY00.0420.01331.1250.1550.1550.0000.0000.0000.000
54A418ASN00.0620.00128.062-0.278-0.2780.0000.0000.0000.000
55A419LYS10.9380.98030.7418.2258.2250.0000.0000.0000.000
56A420ARG10.8120.90333.4569.0939.0930.0000.0000.0000.000
57A421LEU00.0250.01027.6740.1140.1140.0000.0000.0000.000
58A422ASP-1-0.747-0.85031.657-9.280-9.2800.0000.0000.0000.000
59A423SER0-0.033-0.00532.8820.1500.1500.0000.0000.0000.000
60A424ALA00.0140.00433.1940.1440.1440.0000.0000.0000.000
61A425PHE00.0200.00629.3250.1690.1690.0000.0000.0000.000
62A426ARG10.8940.92033.0329.0889.0880.0000.0000.0000.000
63A427CYS0-0.048-0.01336.0070.2340.2340.0000.0000.0000.000
64A428MET0-0.027-0.00135.5990.2870.2870.0000.0000.0000.000
65A429SER00.0230.02131.373-0.126-0.1260.0000.0000.0000.000
66A430SER0-0.001-0.00633.6570.0040.0040.0000.0000.0000.000
67A431LYS10.8090.90135.8978.2708.2700.0000.0000.0000.000
68A432GLY00.0210.02233.6960.1320.1320.0000.0000.0000.000
69A433PRO00.0340.04628.714-0.099-0.0990.0000.0000.0000.000
70A434VAL00.0340.00028.7120.3460.3460.0000.0000.0000.000
71A435TYR0-0.0090.00224.813-0.273-0.2730.0000.0000.0000.000
72A436LEU0-0.014-0.00423.7140.4410.4410.0000.0000.0000.000
73A437LEU00.008-0.00723.219-0.610-0.6100.0000.0000.0000.000
74A438PHE00.0420.01220.0270.3720.3720.0000.0000.0000.000
75A439SER0-0.028-0.02621.518-0.194-0.1940.0000.0000.0000.000
76A440VAL00.0450.03518.5640.3090.3090.0000.0000.0000.000
77A441ASN0-0.022-0.00721.9180.6000.6000.0000.0000.0000.000
78A442GLY00.0220.00724.368-0.196-0.1960.0000.0000.0000.000
79A443SER00.010-0.00421.0150.0240.0240.0000.0000.0000.000
80A444GLY00.0030.01322.960-0.216-0.2160.0000.0000.0000.000
81A445HIS0-0.054-0.04018.928-0.232-0.2320.0000.0000.0000.000
82A446PHE0-0.0090.01022.0670.2700.2700.0000.0000.0000.000
83A447CYS00.0490.02916.619-0.007-0.0070.0000.0000.0000.000
84A448GLY00.0330.01216.607-1.176-1.1760.0000.0000.0000.000
85A449VAL0-0.070-0.03018.5400.9860.9860.0000.0000.0000.000
86A450ALA00.0550.04119.341-0.742-0.7420.0000.0000.0000.000
87A451GLU-1-0.850-0.92121.032-11.054-11.0540.0000.0000.0000.000
88A452MET0-0.029-0.00223.520-0.390-0.3900.0000.0000.0000.000
89A453LYS10.8150.89023.65712.30212.3020.0000.0000.0000.000
90A454SER00.0210.01926.3400.0980.0980.0000.0000.0000.000
91A455PRO0-0.009-0.01328.0890.0170.0170.0000.0000.0000.000
92A456VAL0-0.094-0.03528.793-0.364-0.3640.0000.0000.0000.000
93A457ASP-1-0.851-0.91127.191-10.214-10.2140.0000.0000.0000.000
94A458TYR-1-0.885-0.93328.409-10.265-10.2650.0000.0000.0000.000
95A470TRP0-0.003-0.01318.693-0.243-0.2430.0000.0000.0000.000
96A471LYS10.8140.89724.2939.5369.5360.0000.0000.0000.000
97A472GLY00.0660.04027.3290.0850.0850.0000.0000.0000.000
98A473LYS10.7730.85723.31610.61310.6130.0000.0000.0000.000
99A474PHE00.0210.00024.1770.4590.4590.0000.0000.0000.000
100A475ASP-1-0.811-0.90022.134-13.385-13.3850.0000.0000.0000.000
101A476VAL0-0.089-0.05818.9700.5250.5250.0000.0000.0000.000
102A477GLN00.0500.02519.334-0.279-0.2790.0000.0000.0000.000
103A478TRP0-0.005-0.02115.7760.2700.2700.0000.0000.0000.000
104A479ILE0-0.034-0.00617.107-0.345-0.3450.0000.0000.0000.000
105A480PHE0-0.003-0.01317.107-0.488-0.4880.0000.0000.0000.000
106A481VAL00.0120.00311.8840.2940.2940.0000.0000.0000.000
107A482LYS10.7660.88313.74713.93413.9340.0000.0000.0000.000
108A483ASP-1-0.791-0.86215.731-18.299-18.2990.0000.0000.0000.000
109A484VAL0-0.043-0.03018.1010.4600.4600.0000.0000.0000.000
110A485PRO00.0360.02121.8430.3840.3840.0000.0000.0000.000
111A486ASN00.0720.01424.2690.2220.2220.0000.0000.0000.000
112A487ASN0-0.049-0.03427.4040.2590.2590.0000.0000.0000.000
113A488GLN00.0500.02225.7130.4930.4930.0000.0000.0000.000
114A489LEU00.0250.00725.7770.2540.2540.0000.0000.0000.000
115A490ARG10.8710.94029.9219.6719.6710.0000.0000.0000.000
116A491HIS0-0.0180.00131.7640.4930.4930.0000.0000.0000.000
117A492ILE00.0210.02131.2740.2750.2750.0000.0000.0000.000
118A493ARG10.8890.94034.6727.8067.8060.0000.0000.0000.000
119A494LEU00.0050.00533.5710.0500.0500.0000.0000.0000.000
120A495GLU-1-0.781-0.88137.847-7.898-7.8980.0000.0000.0000.000
121A496ASN0-0.050-0.03537.0220.1200.1200.0000.0000.0000.000
122A497ASN0-0.017-0.02235.8220.0570.0570.0000.0000.0000.000
123A498ASP-1-0.806-0.88739.460-7.583-7.5830.0000.0000.0000.000
124A499ASN0-0.0040.01140.617-0.015-0.0150.0000.0000.0000.000
125A500LYS10.8660.93136.9337.9207.9200.0000.0000.0000.000
126A501PRO0-0.018-0.01033.918-0.031-0.0310.0000.0000.0000.000
127A502VAL00.0490.03230.216-0.072-0.0720.0000.0000.0000.000
128A503THR0-0.0200.00428.350-0.098-0.0980.0000.0000.0000.000
129A504ASN0-0.071-0.02530.076-0.315-0.3150.0000.0000.0000.000
130A505SER00.0230.00230.4570.4390.4390.0000.0000.0000.000
131A506ARG10.9820.97830.4918.1778.1770.0000.0000.0000.000
132A507ASP-1-0.729-0.85627.018-11.258-11.2580.0000.0000.0000.000
133A508THR0-0.0250.00428.9390.5300.5300.0000.0000.0000.000
134A509GLN0-0.0380.00530.6330.3800.3800.0000.0000.0000.000
135A510GLU-1-0.878-0.94931.799-8.962-8.9620.0000.0000.0000.000
136A511VAL00.002-0.00330.7680.2050.2050.0000.0000.0000.000
137A512PRO00.0220.01333.927-0.045-0.0450.0000.0000.0000.000
138A513LEU00.0630.03534.385-0.154-0.1540.0000.0000.0000.000
139A514GLU-1-0.789-0.88835.015-8.403-8.4030.0000.0000.0000.000
140A515LYS10.8240.89734.9497.9787.9780.0000.0000.0000.000
141A516ALA00.0160.00231.325-0.303-0.3030.0000.0000.0000.000
142A517LYS10.8370.91930.5568.0358.0350.0000.0000.0000.000
143A518GLN0-0.056-0.02631.336-0.241-0.2410.0000.0000.0000.000
144A519VAL00.0300.00527.246-0.250-0.2500.0000.0000.0000.000
145A520LEU00.0340.02425.677-0.448-0.4480.0000.0000.0000.000
146A521LYS10.8980.98526.2028.9758.9750.0000.0000.0000.000
147A522ILE0-0.0080.02026.344-0.243-0.2430.0000.0000.0000.000
148A523ILE00.0150.00321.569-0.358-0.3580.0000.0000.0000.000
149A524SER0-0.016-0.01722.038-0.552-0.5520.0000.0000.0000.000
150A525SER0-0.066-0.05222.388-0.445-0.4450.0000.0000.0000.000
151A526TYR00.0430.01921.461-0.172-0.1720.0000.0000.0000.000
152A527LYS10.8690.93021.06112.30612.3060.0000.0000.0000.000
153A528HIS00.0270.02114.2631.3961.3960.0000.0000.0000.000
154A529THR0-0.012-0.01217.191-0.233-0.2330.0000.0000.0000.000
155A530THR00.0160.00313.612-0.441-0.4410.0000.0000.0000.000
156A531SER0-0.016-0.01611.3920.3140.3140.0000.0000.0000.000
157A532ILE00.0490.04011.015-1.575-1.5750.0000.0000.0000.000
158A533PHE0-0.061-0.0527.130-2.403-2.4030.0000.0000.0000.000
159A534ASP-1-0.849-0.9246.468-34.471-34.4710.0000.0000.0000.000
160A535ASP-1-0.890-0.9347.789-27.649-27.6490.0000.0000.0000.000
164A539TYR00.040-0.0058.7692.2462.2460.0000.0000.0000.000
166A541LYS10.8770.9207.66425.23825.2380.0000.0000.0000.000
167A542ARG10.8460.8928.82220.66820.6680.0000.0000.0000.000
168A543GLN0-0.056-0.03710.2122.5122.5120.0000.0000.0000.000
169A544GLU-1-0.948-0.9746.477-30.750-30.7500.0000.0000.0000.000
170A545GLU-1-0.807-0.89411.058-19.903-19.9030.0000.0000.0000.000
171A546GLU-1-0.911-0.94513.399-13.498-13.4980.0000.0000.0000.000
172A547GLU-1-0.758-0.83214.261-13.787-13.7870.0000.0000.0000.000
173A548VAL0-0.017-0.00713.6860.8630.8630.0000.0000.0000.000
174A549VAL00.0380.02216.4180.9640.9640.0000.0000.0000.000
175A550ARG10.7870.85518.99514.29914.2990.0000.0000.0000.000
176A551LYS10.8280.89015.90015.95915.9590.0000.0000.0000.000
177A552GLU-1-0.796-0.86320.569-11.499-11.4990.0000.0000.0000.000
178A553ARG10.9520.98322.44311.68911.6890.0000.0000.0000.000
179A554GLN00.0110.01124.1010.0770.0770.0000.0000.0000.000
180A555SER0-0.065-0.04624.4400.3890.3890.0000.0000.0000.000
181A556ARG10.8500.88924.58611.15111.1510.0000.0000.0000.000
182A557ASN0-0.061-0.03628.5570.4960.4960.0000.0000.0000.000
183A558LYS10.8720.94527.61010.07310.0730.0000.0000.0000.000
184A559GLN-1-0.918-0.93629.405-8.750-8.7500.0000.0000.0000.000