Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 399ML

Calculation Name: 4RFS-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RFS

Chain ID: S

ChEMBL ID:

UniProt ID: Q03PY5

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1980503.51552
FMO2-HF: Nuclear repulsion 1908954.080167
FMO2-HF: Total energy -71549.435353
FMO2-MP2: Total energy -71759.757348


3D Structure
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(S:3:ARG)


Summations of interaction energy for fragment #1(S:3: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.
100.8297.6059.627-1.695-4.716-0.002
Interaction energy analysis for fragmet #1(S:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.031 / q_NPA : 0.990
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].
3S5LYS11.0011.0023.54021.79924.5970.009-1.291-1.5160.005
4S6THR0-0.0170.0252.1483.351-3.2589.618-0.156-2.853-0.008
5S7PHE00.0490.0114.1711.2991.8950.000-0.248-0.3470.001
6S8ARG10.8870.9405.72723.29623.2960.0000.0000.0000.000
7S9LEU0-0.0070.0057.8681.4021.4020.0000.0000.0000.000
8S10VAL00.0030.0028.2591.5071.5070.0000.0000.0000.000
9S11VAL00.0250.0069.4681.3341.3340.0000.0000.0000.000
10S12ASP-1-0.844-0.91511.838-16.838-16.8380.0000.0000.0000.000
11S13ALA00.015-0.01313.4621.0571.0570.0000.0000.0000.000
12S14LEU00.0130.00713.3880.7260.7260.0000.0000.0000.000
13S15LEU0-0.042-0.01815.4090.9090.9090.0000.0000.0000.000
14S16MET0-0.037-0.02815.9590.8680.8680.0000.0000.0000.000
15S17ALA00.0080.01018.9690.6620.6620.0000.0000.0000.000
16S18ILE00.0050.00219.3820.6040.6040.0000.0000.0000.000
17S19VAL00.0310.02622.0810.5730.5730.0000.0000.0000.000
18S20LEU00.0090.02522.9960.5580.5580.0000.0000.0000.000
19S21LEU0-0.019-0.00124.0550.4490.4490.0000.0000.0000.000
20S22GLN0-0.001-0.02825.8750.1480.1480.0000.0000.0000.000
21S23ASN0-0.117-0.07827.5980.6430.6430.0000.0000.0000.000
22S24LEU0-0.0020.00028.1180.3240.3240.0000.0000.0000.000
23S25VAL0-0.0150.01430.1060.3040.3040.0000.0000.0000.000
24S26PRO00.034-0.00331.723-0.137-0.1370.0000.0000.0000.000
25S27PHE0-0.023-0.01132.857-0.001-0.0010.0000.0000.0000.000
26S28LEU00.0180.01727.401-0.082-0.0820.0000.0000.0000.000
27S29GLY00.0440.02330.020-0.196-0.1960.0000.0000.0000.000
28S30TYR0-0.034-0.03631.126-0.071-0.0710.0000.0000.0000.000
29S31ILE00.0370.01534.114-0.006-0.0060.0000.0000.0000.000
30S32PRO0-0.040-0.04336.9390.0690.0690.0000.0000.0000.000
31S33PHE0-0.0060.02840.565-0.014-0.0140.0000.0000.0000.000
32S34GLY00.0230.02343.2870.0890.0890.0000.0000.0000.000
33S35PRO00.001-0.00344.457-0.070-0.0700.0000.0000.0000.000
34S36PHE00.0160.01742.111-0.077-0.0770.0000.0000.0000.000
35S37SER00.014-0.02638.2440.0320.0320.0000.0000.0000.000
36S38MET00.0220.05034.881-0.097-0.0970.0000.0000.0000.000
37S39THR0-0.030-0.01531.258-0.166-0.1660.0000.0000.0000.000
38S40LEU00.012-0.00329.207-0.071-0.0710.0000.0000.0000.000
39S41ILE0-0.018-0.02326.515-0.349-0.3490.0000.0000.0000.000
40S42GLY00.0330.02226.488-0.251-0.2510.0000.0000.0000.000
41S43LEU00.024-0.01025.935-0.329-0.3290.0000.0000.0000.000
42S44THR0-0.0560.00422.653-0.468-0.4680.0000.0000.0000.000
43S45VAL00.0670.02621.492-0.615-0.6150.0000.0000.0000.000
44S46ILE0-0.0140.01421.815-0.485-0.4850.0000.0000.0000.000
45S47VAL00.025-0.10718.710-0.475-0.4750.0000.0000.0000.000
46S48ALA00.078-0.00517.385-0.533-0.5330.0000.0000.0000.000
47S49GLY00.0360.00917.405-0.546-0.5460.0000.0000.0000.000
48S50SER0-0.097-0.04518.939-0.348-0.3480.0000.0000.0000.000
49S51ALA0-0.014-0.02915.9060.0110.0110.0000.0000.0000.000
50S52LEU0-0.068-0.01911.741-1.281-1.2810.0000.0000.0000.000
51S53GLY00.0280.01414.205-0.609-0.6090.0000.0000.0000.000
52S54PRO00.0270.00616.7640.1080.1080.0000.0000.0000.000
53S55ARG10.8780.94214.20415.75715.7570.0000.0000.0000.000
54S56ASP-1-0.727-0.87413.543-17.846-17.8460.0000.0000.0000.000
55S57GLY00.0170.01916.8450.4890.4890.0000.0000.0000.000
56S58LEU0-0.043-0.00519.5960.5470.5470.0000.0000.0000.000
57S59LEU00.0160.00815.6600.5430.5430.0000.0000.0000.000
58S60ILE0-0.010-0.00818.0590.4680.4680.0000.0000.0000.000
59S61GLY00.0300.01920.9030.4640.4640.0000.0000.0000.000
60S62GLY00.018-0.01623.0460.4930.4930.0000.0000.0000.000
61S63PHE0-0.034-0.02221.6610.3630.3630.0000.0000.0000.000
62S64TRP00.0290.02123.8070.2730.2730.0000.0000.0000.000
63S65GLY00.0300.01126.6860.3020.3020.0000.0000.0000.000
64S66LEU00.0200.02226.0780.3250.3250.0000.0000.0000.000
65S67ILE00.012-0.00425.5440.2890.2890.0000.0000.0000.000
66S68THR0-0.038-0.03329.4470.2110.2110.0000.0000.0000.000
67S69PHE0-0.0140.01331.7020.2450.2450.0000.0000.0000.000
68S70VAL00.0570.02630.6630.2370.2370.0000.0000.0000.000
69S71ARG10.8020.90532.3498.7168.7160.0000.0000.0000.000
70S72ALA0-0.0170.00234.8570.1900.1900.0000.0000.0000.000
71S73PHE0-0.043-0.01136.7580.2170.2170.0000.0000.0000.000
72S74THR0-0.041-0.04035.6020.1020.1020.0000.0000.0000.000
73S75TRP00.0320.02132.4970.0360.0360.0000.0000.0000.000
74S76PRO00.0480.03736.816-0.223-0.2230.0000.0000.0000.000
75S77SER0-0.025-0.01335.754-0.027-0.0270.0000.0000.0000.000
76S78SER00.0270.02137.7310.1280.1280.0000.0000.0000.000
77S79PRO00.0750.02440.762-0.020-0.0200.0000.0000.0000.000
78S80VAL00.009-0.00441.8650.0870.0870.0000.0000.0000.000
79S81ALA0-0.050-0.02838.711-0.089-0.0890.0000.0000.0000.000
80S82PRO00.012-0.00240.590-0.061-0.0610.0000.0000.0000.000
81S83LEU0-0.0240.00342.4100.0870.0870.0000.0000.0000.000
82S84ILE00.0580.03738.795-0.015-0.0150.0000.0000.0000.000
83S85PHE0-0.044-0.02335.856-0.115-0.1150.0000.0000.0000.000
84S86THR00.0770.02436.765-0.192-0.1920.0000.0000.0000.000
85S87ASN00.0010.00338.650-0.031-0.0310.0000.0000.0000.000
86S88PRO0-0.014-0.00333.303-0.069-0.0690.0000.0000.0000.000
87S89LEU00.0450.01733.310-0.254-0.2540.0000.0000.0000.000
88S90ILE00.0420.00434.444-0.209-0.2090.0000.0000.0000.000
89S91SER0-0.051-0.02933.253-0.181-0.1810.0000.0000.0000.000
90S92ILE00.0130.00428.669-0.234-0.2340.0000.0000.0000.000
91S93LEU0-0.007-0.00129.721-0.319-0.3190.0000.0000.0000.000
92S94PRO0-0.017-0.00430.456-0.257-0.2570.0000.0000.0000.000
93S95ARG10.9150.97127.6538.8518.8510.0000.0000.0000.000
94S96LEU00.0010.00124.138-0.397-0.3970.0000.0000.0000.000
95S97LEU0-0.013-0.01525.562-0.423-0.4230.0000.0000.0000.000
96S98MET0-0.0190.02226.8860.0460.0460.0000.0000.0000.000
97S99GLY00.0260.00623.516-0.193-0.1930.0000.0000.0000.000
98S100LEU0-0.039-0.03222.552-0.609-0.6090.0000.0000.0000.000
99S101VAL00.0360.02524.362-0.296-0.2960.0000.0000.0000.000
100S102ALA0-0.0240.00923.306-0.122-0.1220.0000.0000.0000.000
101S103GLY00.0330.00320.846-0.237-0.2370.0000.0000.0000.000
102S104SER00.007-0.01421.471-0.141-0.1410.0000.0000.0000.000
103S105LEU00.0080.01723.433-0.049-0.0490.0000.0000.0000.000
104S106TYR00.0140.01719.2800.3030.3030.0000.0000.0000.000
105S107LEU0-0.024-0.02418.248-0.097-0.0970.0000.0000.0000.000
106S108TRP00.004-0.00722.2190.0520.0520.0000.0000.0000.000
107S109GLY00.0170.00325.8700.2390.2390.0000.0000.0000.000
108S110ARG10.9290.96121.71113.29713.2970.0000.0000.0000.000
109S111HIS00.0080.02024.326-0.273-0.2730.0000.0000.0000.000
110S112ARG10.8650.94825.65110.28510.2850.0000.0000.0000.000
111S113GLN0-0.013-0.00625.7910.1200.1200.0000.0000.0000.000
112S114TRP00.0310.04127.8550.2050.2050.0000.0000.0000.000
113S115SER0-0.015-0.01926.558-0.576-0.5760.0000.0000.0000.000
114S116MET0-0.029-0.01718.3400.1020.1020.0000.0000.0000.000
115S117ARG10.9540.97024.17910.03010.0300.0000.0000.0000.000
116S118GLN00.0570.01326.825-0.025-0.0250.0000.0000.0000.000
117S119ALA00.0490.03824.7410.1990.1990.0000.0000.0000.000
118S120MET0-0.046-0.00419.8630.1340.1340.0000.0000.0000.000
119S121GLN0-0.016-0.00925.2980.1570.1570.0000.0000.0000.000
120S122VAL00.0440.02328.9400.1650.1650.0000.0000.0000.000
121S123ALA0-0.010-0.00925.2980.2290.2290.0000.0000.0000.000
122S124ALA00.0160.00426.879-0.153-0.1530.0000.0000.0000.000
123S125GLY00.0490.02228.2460.1510.1510.0000.0000.0000.000
124S126CYS0-0.046-0.00329.8710.2790.2790.0000.0000.0000.000
125S127ALA00.0130.00527.2220.1480.1480.0000.0000.0000.000
126S128ALA00.0640.03329.2610.0480.0480.0000.0000.0000.000
127S129LEU00.1940.07931.7610.1460.1460.0000.0000.0000.000
128S130THR0-0.117-0.06430.6630.0890.0890.0000.0000.0000.000
129S131ASN0-0.114-0.05230.898-0.377-0.3770.0000.0000.0000.000
130S132THR00.004-0.03532.7740.1250.1250.0000.0000.0000.000
131S133VAL00.004-0.00336.1960.1990.1990.0000.0000.0000.000
132S134LEU0-0.0100.00533.1670.1920.1920.0000.0000.0000.000
133S135VAL00.0700.05635.8470.1510.1510.0000.0000.0000.000
134S136LEU00.001-0.00238.0500.2010.2010.0000.0000.0000.000
135S137GLY00.0070.00639.8960.1840.1840.0000.0000.0000.000
136S138LEU0-0.071-0.03535.8660.1090.1090.0000.0000.0000.000
137S139VAL0-0.015-0.00840.0600.1090.1090.0000.0000.0000.000
138S140PHE00.003-0.00742.7860.1890.1890.0000.0000.0000.000
139S141LEU0-0.032-0.01840.9430.1360.1360.0000.0000.0000.000
140S142PHE00.007-0.00140.3800.0780.0780.0000.0000.0000.000
141S143TYR00.034-0.04745.0300.1560.1560.0000.0000.0000.000
142S144GLN0-0.073-0.04047.9370.0870.0870.0000.0000.0000.000
143S145THR0-0.026-0.01347.3880.0730.0730.0000.0000.0000.000
144S146PRO0-0.019-0.00248.346-0.063-0.0630.0000.0000.0000.000
145S147ALA00.002-0.01046.953-0.103-0.1030.0000.0000.0000.000
146S148VAL0-0.0070.01646.561-0.061-0.0610.0000.0000.0000.000
147S160LEU00.045-0.01750.8000.0430.0430.0000.0000.0000.000
148S161GLY00.1340.01251.411-0.107-0.1070.0000.0000.0000.000
149S162TYR00.002-0.00751.855-0.066-0.0660.0000.0000.0000.000
150S163VAL00.0170.03849.164-0.043-0.0430.0000.0000.0000.000
151S164LEU0-0.0460.11146.242-0.123-0.1230.0000.0000.0000.000
152S165MET00.015-0.01047.469-0.141-0.1410.0000.0000.0000.000
153S166ILE00.0260.01748.678-0.077-0.0770.0000.0000.0000.000
154S167SER0-0.038-0.02044.597-0.119-0.1190.0000.0000.0000.000
155S168LEU0-0.064-0.01443.835-0.155-0.1550.0000.0000.0000.000
156S169PHE00.0260.00544.379-0.113-0.1130.0000.0000.0000.000
157S170THR0-0.061-0.04543.625-0.025-0.0250.0000.0000.0000.000
158S171ASN00.0120.00340.075-0.217-0.2170.0000.0000.0000.000
159S172GLY0-0.007-0.00940.404-0.150-0.1500.0000.0000.0000.000
160S173ILE00.0070.01942.2210.0430.0430.0000.0000.0000.000
161S174PRO0-0.014-0.00438.876-0.099-0.0990.0000.0000.0000.000
162S175GLU-1-0.821-0.91735.434-8.557-8.5570.0000.0000.0000.000
163S176LEU0-0.0040.01436.757-0.165-0.1650.0000.0000.0000.000
164S177ILE00.0090.00736.902-0.038-0.0380.0000.0000.0000.000
165S178LEU00.001-0.00732.546-0.181-0.1810.0000.0000.0000.000
166S179ASP-1-0.918-0.94932.855-8.749-8.7490.0000.0000.0000.000
167S180VAL00.011-0.00534.051-0.163-0.1630.0000.0000.0000.000
168S181LEU0-0.073-0.02731.123-0.157-0.1570.0000.0000.0000.000
169S182VAL00.020-0.06528.629-0.240-0.2400.0000.0000.0000.000
170S183ALA00.0910.04429.279-0.293-0.2930.0000.0000.0000.000
171S184PRO0-0.0310.00230.428-0.240-0.2400.0000.0000.0000.000
172S185LEU00.008-0.01027.868-0.379-0.3790.0000.0000.0000.000
173S186ILE00.0150.05824.654-0.283-0.2830.0000.0000.0000.000
174S187ALA0-0.0220.00224.818-0.520-0.5200.0000.0000.0000.000
175S188MET0-0.088-0.03824.123-0.420-0.4200.0000.0000.0000.000
176S189PRO0-0.063-0.01922.528-0.581-0.5810.0000.0000.0000.000
177S190LEU00.0560.16718.371-0.381-0.3810.0000.0000.0000.000
178S191ARG10.9300.96619.02311.04811.0480.0000.0000.0000.000
179S192ARG10.9640.95819.23311.88111.8810.0000.0000.0000.000
180S193GLN00.0080.01515.454-1.448-1.4480.0000.0000.0000.000
181S194TRP00.0810.03613.558-0.666-0.6660.0000.0000.0000.000
182S195GLU-1-1.012-0.99014.607-16.026-16.0260.0000.0000.0000.000
183S196ARG10.9490.95712.56316.66016.6600.0000.0000.0000.000
184S197LEU00.0510.0258.839-2.027-2.0270.0000.0000.0000.000
185S198LYS10.8930.93310.17216.94716.9470.0000.0000.0000.000
186S199PRO0-0.177-0.03410.878-0.146-0.1460.0000.0000.0000.000
187S200GLN00.0350.0266.346-4.210-4.2100.0000.0000.0000.000