Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K3623

Calculation Name: 4R3O-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: I

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-06-20

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333122.713339
FMO2-HF: Nuclear repulsion 2248396.949489
FMO2-HF: Total energy -84725.76385
FMO2-MP2: Total energy -84967.313


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(I:1:THR)


Summations of interaction energy for fragment #1(I:1:THR)
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.
-35.201-33.29935.84-16.559-21.181-0.046
Interaction energy analysis for fragmet #1(I:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.009
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].
3I3ILE0-0.030-0.0132.621-0.2122.5240.696-1.242-2.1900.003
4I4ALA00.012-0.0034.690-0.396-0.378-0.001-0.005-0.0110.000
5I5GLY0-0.019-0.0068.3200.2790.2790.0000.0000.0000.000
6I6VAL00.0240.01711.610-0.080-0.0800.0000.0000.0000.000
7I7VAL0-0.010-0.00515.2170.0730.0730.0000.0000.0000.000
8I8TYR0-0.033-0.02118.705-0.021-0.0210.0000.0000.0000.000
9I9LYS10.8610.93221.4420.0870.0870.0000.0000.0000.000
10I10ASP-1-0.918-0.96224.167-0.012-0.0120.0000.0000.0000.000
11I11GLY0-0.022-0.03721.6340.0290.0290.0000.0000.0000.000
12I12ILE0-0.0260.00715.485-0.029-0.0290.0000.0000.0000.000
13I13VAL0-0.0130.00913.6850.0490.0490.0000.0000.0000.000
14I14LEU0-0.009-0.00710.479-0.069-0.0690.0000.0000.0000.000
15I15GLY00.0530.0099.0860.0520.0520.0000.0000.0000.000
16I16ALA0-0.002-0.0104.539-0.113-0.068-0.001-0.003-0.0410.000
17I17ASP-1-0.680-0.8272.424-3.630-0.7333.346-3.192-3.050-0.038
18I18THR0-0.005-0.0185.0081.0191.114-0.001-0.003-0.0910.000
19I19ARG10.8630.9684.4471.1461.289-0.001-0.009-0.1330.000
20I20ALA00.0270.0093.8463.2883.7120.004-0.087-0.3410.000
21I21THR0-0.024-0.0164.794-0.972-0.906-0.001-0.004-0.0610.000
22I22GLU-1-0.892-0.9356.6931.1021.1020.0000.0000.0000.000
23I23GLY00.0070.0059.263-0.220-0.2200.0000.0000.0000.000
24I24MET0-0.030-0.0268.850-0.025-0.0250.0000.0000.0000.000
25I25VAL00.0160.01210.679-0.126-0.1260.0000.0000.0000.000
26I26VAL0-0.060-0.0338.0550.1740.1740.0000.0000.0000.000
27I27ALA00.0130.0159.049-0.122-0.1220.0000.0000.0000.000
28I28ASP-1-0.813-0.9208.5221.6181.6180.0000.0000.0000.000
29I29LYS10.8790.9338.610-0.252-0.2520.0000.0000.0000.000
30I30ASN0-0.040-0.02910.060-0.113-0.1130.0000.0000.0000.000
31I31CYS00.0690.0556.5870.2690.2690.0000.0000.0000.000
32I32SER0-0.027-0.0717.851-0.035-0.0350.0000.0000.0000.000
33I33LYS10.8470.9001.810-21.739-29.37018.712-5.566-5.5150.043
34I34ILE0-0.0040.0036.348-0.302-0.3020.0000.0000.0000.000
35I35HIS10.8890.9457.197-2.201-2.2010.0000.0000.0000.000
36I36PHE00.0540.02511.461-0.130-0.1300.0000.0000.0000.000
37I37ILE0-0.053-0.01313.7050.0400.0400.0000.0000.0000.000
38I38SER00.001-0.03016.668-0.024-0.0240.0000.0000.0000.000
39I39PRO00.0260.01019.2420.0110.0110.0000.0000.0000.000
40I40ASN0-0.0030.01621.2530.0180.0180.0000.0000.0000.000
41I41ILE0-0.033-0.01916.306-0.034-0.0340.0000.0000.0000.000
42I42TYR00.0850.03513.1880.0690.0690.0000.0000.0000.000
43I43CYS0-0.028-0.01511.057-0.116-0.1160.0000.0000.0000.000
44I44CYS0-0.0160.0226.1680.2590.2590.0000.0000.0000.000
45I45GLY00.0140.0035.353-0.475-0.429-0.001-0.011-0.0340.000
46I46ALA00.000-0.0012.4340.2931.1661.545-0.807-1.611-0.003
47I47GLY00.0060.0063.308-0.886-1.0230.0340.308-0.2050.000
48I48THR0-0.003-0.0156.0291.0251.0250.0000.0000.0000.000
49I49ALA00.0420.0226.686-0.172-0.1720.0000.0000.0000.000
50I50ALA00.0990.0507.954-0.258-0.2580.0000.0000.0000.000
51I51ASP-1-0.786-0.89410.8840.8280.8280.0000.0000.0000.000
52I52THR0-0.110-0.0216.331-0.032-0.0320.0000.0000.0000.000
53I53ASP-1-0.868-0.9349.5031.8161.8160.0000.0000.0000.000
54I54MET0-0.016-0.01911.438-0.196-0.1960.0000.0000.0000.000
55I55THR0-0.043-0.06112.529-0.172-0.1720.0000.0000.0000.000
56I56THR0-0.009-0.01611.391-0.137-0.1370.0000.0000.0000.000
57I57GLN0-0.016-0.00613.5590.0000.0000.0000.0000.0000.000
58I58LEU0-0.0170.00516.274-0.089-0.0890.0000.0000.0000.000
59I59ILE0-0.034-0.03416.541-0.076-0.0760.0000.0000.0000.000
60I60SER0-0.027-0.00917.093-0.054-0.0540.0000.0000.0000.000
61I61SER00.0240.01718.864-0.059-0.0590.0000.0000.0000.000
62I62ASN00.021-0.00521.721-0.046-0.0460.0000.0000.0000.000
63I63LEU0-0.037-0.03019.543-0.045-0.0450.0000.0000.0000.000
64I64GLU-1-0.935-0.94723.0600.3060.3060.0000.0000.0000.000
65I65LEU00.0480.01124.770-0.030-0.0300.0000.0000.0000.000
66I66HIS0-0.034-0.01125.923-0.020-0.0200.0000.0000.0000.000
67I67SER0-0.069-0.02626.284-0.021-0.0210.0000.0000.0000.000
68I68LEU00.0310.01628.178-0.019-0.0190.0000.0000.0000.000
69I69SER0-0.053-0.01130.422-0.018-0.0180.0000.0000.0000.000
70I70THR0-0.094-0.06529.921-0.014-0.0140.0000.0000.0000.000
71I71GLY00.0250.01631.928-0.013-0.0130.0000.0000.0000.000
72I72ARG10.8630.93430.547-0.116-0.1160.0000.0000.0000.000
73I73LEU00.0360.01725.2060.0140.0140.0000.0000.0000.000
74I74PRO0-0.014-0.00622.798-0.016-0.0160.0000.0000.0000.000
75I75ARG10.9720.98824.164-0.102-0.1020.0000.0000.0000.000
76I76VAL00.0550.01318.2630.0240.0240.0000.0000.0000.000
77I77VAL0-0.038-0.02320.0120.0130.0130.0000.0000.0000.000
78I78THR0-0.0010.00222.083-0.005-0.0050.0000.0000.0000.000
79I79ALA00.0810.04717.4180.0110.0110.0000.0000.0000.000
80I80ASN00.0150.00617.3360.0310.0310.0000.0000.0000.000
81I81ARG10.9050.94918.559-0.094-0.0940.0000.0000.0000.000
82I82MET0-0.006-0.00119.9830.0080.0080.0000.0000.0000.000
83I83LEU00.0520.02613.7730.0100.0100.0000.0000.0000.000
84I84LYS10.9110.97017.205-0.056-0.0560.0000.0000.0000.000
85I85GLN0-0.050-0.02618.327-0.038-0.0380.0000.0000.0000.000
86I86MET0-0.0110.00517.491-0.010-0.0100.0000.0000.0000.000
87I87LEU0-0.003-0.01013.299-0.001-0.0010.0000.0000.0000.000
88I88PHE00.0230.02017.501-0.013-0.0130.0000.0000.0000.000
89I89ARG10.8930.95520.364-0.272-0.2720.0000.0000.0000.000
90I90TYR0-0.031-0.02218.672-0.009-0.0090.0000.0000.0000.000
91I91GLN0-0.015-0.00219.8520.0110.0110.0000.0000.0000.000
92I92GLY00.0220.01516.018-0.029-0.0290.0000.0000.0000.000
93I93TYR0-0.067-0.03415.3690.0320.0320.0000.0000.0000.000
94I94ILE0-0.0030.01813.2400.0580.0580.0000.0000.0000.000
95I95GLY00.0320.03011.120-0.068-0.0680.0000.0000.0000.000
96I96ALA0-0.019-0.0258.8530.3460.3460.0000.0000.0000.000
97I97ALA0-0.0060.0006.491-0.319-0.3190.0000.0000.0000.000
98I98LEU0-0.028-0.0266.6640.3530.3530.0000.0000.0000.000
99I99VAL00.0220.0187.297-0.261-0.2610.0000.0000.0000.000
100I100LEU0-0.009-0.0059.5620.1500.1500.0000.0000.0000.000
101I101GLY00.0380.01213.007-0.102-0.1020.0000.0000.0000.000
102I102GLY00.0140.00415.2540.0690.0690.0000.0000.0000.000
103I103VAL0-0.0100.00518.700-0.045-0.0450.0000.0000.0000.000
104I104ASP-1-0.815-0.88922.3220.1500.1500.0000.0000.0000.000
105I105VAL0-0.016-0.02825.246-0.009-0.0090.0000.0000.0000.000
106I106THR0-0.050-0.03626.326-0.007-0.0070.0000.0000.0000.000
107I107GLY00.0420.03225.791-0.016-0.0160.0000.0000.0000.000
108I108PRO00.0370.03620.9350.0260.0260.0000.0000.0000.000
109I109HIS0-0.034-0.02219.867-0.032-0.0320.0000.0000.0000.000
110I110LEU00.0290.02312.6760.0500.0500.0000.0000.0000.000
111I111TYR0-0.028-0.02414.958-0.045-0.0450.0000.0000.0000.000
112I112SER00.0140.02611.1440.0170.0170.0000.0000.0000.000
113I113ILE0-0.017-0.03111.231-0.010-0.0100.0000.0000.0000.000
114I114TYR00.0700.03210.9660.0500.0500.0000.0000.0000.000
115I115PRO00.0320.01910.6630.0170.0170.0000.0000.0000.000
116I116HIS00.0240.00513.1750.0320.0320.0000.0000.0000.000
117I117GLY00.0090.00615.844-0.004-0.0040.0000.0000.0000.000
118I118SER0-0.036-0.01316.4890.0050.0050.0000.0000.0000.000
119I119THR0-0.021-0.03315.6040.0340.0340.0000.0000.0000.000
120I120ASP-1-0.875-0.91915.513-0.226-0.2260.0000.0000.0000.000
121I121LYS10.8550.92016.1190.0330.0330.0000.0000.0000.000
122I122LEU00.0200.01215.312-0.011-0.0110.0000.0000.0000.000
123I123PRO00.0150.01316.9120.0230.0230.0000.0000.0000.000
124I124TYR00.0220.00214.4520.0370.0370.0000.0000.0000.000
125I125VAL0-0.0210.00210.602-0.009-0.0090.0000.0000.0000.000
126I126THR00.011-0.0097.9620.0480.0480.0000.0000.0000.000
127I127MET0-0.0070.0035.2210.2390.2390.0000.0000.0000.000
128I128GLY00.0260.0033.049-0.973-0.5880.052-0.161-0.2760.000
129I129SER0-0.052-0.0312.133-4.048-3.1253.311-1.837-2.397-0.020
130I130GLY00.0500.0353.3661.8472.1460.000-0.075-0.2250.000
131I131SER0-0.075-0.0925.1201.3731.445-0.001-0.002-0.0690.000
132I132LEU00.0310.0077.5590.5850.5850.0000.0000.0000.000
133I133ALA00.0420.0329.1660.3110.3110.0000.0000.0000.000
134I134ALA00.004-0.0048.8550.3460.3460.0000.0000.0000.000
135I135MET0-0.012-0.00610.7550.3090.3090.0000.0000.0000.000
136I136ALA00.0150.01512.7190.1810.1810.0000.0000.0000.000
137I137VAL0-0.003-0.00313.8350.1290.1290.0000.0000.0000.000
138I138PHE0-0.069-0.04511.6120.1040.1040.0000.0000.0000.000
139I139GLU-1-0.905-0.98115.994-0.454-0.4540.0000.0000.0000.000
140I140ASP-1-0.985-0.96018.402-0.464-0.4640.0000.0000.0000.000
141I141LYS10.8300.91219.1550.6100.6100.0000.0000.0000.000
142I142PHE00.0190.00518.2370.0430.0430.0000.0000.0000.000
143I143ARG10.8700.93120.2780.2150.2150.0000.0000.0000.000
144I144PRO0-0.001-0.00522.5490.0020.0020.0000.0000.0000.000
145I145ASP-1-0.949-0.97324.212-0.108-0.1080.0000.0000.0000.000
146I146MET0-0.0430.00218.867-0.002-0.0020.0000.0000.0000.000
147I147GLU-1-0.759-0.88224.091-0.058-0.0580.0000.0000.0000.000
148I148GLU-1-0.817-0.89721.008-0.005-0.0050.0000.0000.0000.000
149I149GLU-1-0.828-0.91720.499-0.080-0.0800.0000.0000.0000.000
150I150GLU-1-0.835-0.90620.705-0.236-0.2360.0000.0000.0000.000
151I151ALA00.0370.00618.347-0.047-0.0470.0000.0000.0000.000
152I152LYS10.8150.88716.213-0.023-0.0230.0000.0000.0000.000
153I153ASN0-0.0070.00915.782-0.016-0.0160.0000.0000.0000.000
154I154LEU00.0520.03715.966-0.073-0.0730.0000.0000.0000.000
155I155VAL00.0070.00111.101-0.130-0.1300.0000.0000.0000.000
156I156SER0-0.077-0.04011.671-0.146-0.1460.0000.0000.0000.000
157I157GLU-1-0.832-0.92612.407-0.676-0.6760.0000.0000.0000.000
158I158ALA00.0110.02111.301-0.172-0.1720.0000.0000.0000.000
159I159ILE0-0.053-0.0336.514-0.420-0.4200.0000.0000.0000.000
160I160ALA00.0060.0058.078-0.447-0.4470.0000.0000.0000.000
161I161ALA0-0.0040.00710.378-0.149-0.1490.0000.0000.0000.000
162I162GLY00.0400.0227.088-0.070-0.0700.0000.0000.0000.000
163I163ILE0-0.082-0.0456.198-0.592-0.5920.0000.0000.0000.000
164I164PHE0-0.049-0.0397.2120.0890.0890.0000.0000.0000.000
165I165ASN0-0.081-0.0439.1310.4150.4150.0000.0000.0000.000
166I166ASP-1-0.737-0.8113.210-11.505-10.5300.050-0.551-0.473-0.004
167I167LEU0-0.013-0.0075.889-0.064-0.0640.0000.0000.0000.000
168I168GLY0-0.0070.0023.1960.9901.5310.079-0.253-0.367-0.001
169I169SER0-0.0470.0142.097-3.435-4.2127.947-3.295-3.875-0.027
170I170GLY0-0.003-0.0213.0392.0251.9340.0710.236-0.2160.001
171I171SER0-0.111-0.0506.5460.3550.3550.0000.0000.0000.000
172I172ASN00.0180.0079.361-0.383-0.3830.0000.0000.0000.000
173I173ILE00.0590.0338.314-0.036-0.0360.0000.0000.0000.000
174I174ASP-1-0.805-0.8928.7031.0421.0420.0000.0000.0000.000
175I175LEU0-0.017-0.0169.750-0.123-0.1230.0000.0000.0000.000
176I176CYS0-0.058-0.01012.3580.0800.0800.0000.0000.0000.000
177I177VAL00.0140.01814.166-0.058-0.0580.0000.0000.0000.000
178I178ILE00.0020.00715.8300.0350.0350.0000.0000.0000.000
179I179SER00.0250.01419.428-0.036-0.0360.0000.0000.0000.000
180I180LYS10.8610.89822.9760.0170.0170.0000.0000.0000.000
181I181ASN0-0.082-0.03626.0400.0060.0060.0000.0000.0000.000
182I182LYS10.8890.93722.710-0.052-0.0520.0000.0000.0000.000
183I183LEU0-0.023-0.00617.9200.0010.0010.0000.0000.0000.000
184I184ASP-1-0.851-0.93219.0900.1420.1420.0000.0000.0000.000
185I185PHE0-0.012-0.00912.600-0.001-0.0010.0000.0000.0000.000
186I186LEU0-0.012-0.00915.5970.0270.0270.0000.0000.0000.000
187I187ARG10.8721.0279.816-1.256-1.2560.0000.0000.0000.000
188I188PRO0-0.085-0.05312.5720.0070.0070.0000.0000.0000.000
189I189TYR00.047-0.00413.020-0.044-0.0440.0000.0000.0000.000
190I190THR0-0.010-0.03013.886-0.034-0.0340.0000.0000.0000.000
191I191VAL0-0.048-0.00913.218-0.060-0.0600.0000.0000.0000.000
192I192PRO0-0.0350.00112.1710.0370.0370.0000.0000.0000.000
193I193ASN0-0.019-0.00511.170-0.033-0.0330.0000.0000.0000.000
194I194LYS11.0060.98914.3610.1370.1370.0000.0000.0000.000
195I195LYS10.9130.97616.906-0.093-0.0930.0000.0000.0000.000
196I196GLY00.0500.02818.1200.0080.0080.0000.0000.0000.000
197I197THR00.020-0.00121.3590.0260.0260.0000.0000.0000.000
198I198ARG10.9240.94623.857-0.105-0.1050.0000.0000.0000.000
199I199LEU00.0670.04226.0680.0040.0040.0000.0000.0000.000
200I200GLY00.0290.03028.5990.0000.0000.0000.0000.0000.000
201I201ARG10.9130.94029.570-0.032-0.0320.0000.0000.0000.000
202I202TYR00.0190.00727.411-0.002-0.0020.0000.0000.0000.000
203I203ARG10.9340.96831.154-0.084-0.0840.0000.0000.0000.000
204I204CYS00.0170.02032.581-0.008-0.0080.0000.0000.0000.000
205I205GLU-1-0.889-0.94434.8980.0850.0850.0000.0000.0000.000
206I206LYS10.9900.97638.195-0.099-0.0990.0000.0000.0000.000
207I207GLY00.0140.00339.563-0.006-0.0060.0000.0000.0000.000
208I208THR0-0.020-0.00236.549-0.005-0.0050.0000.0000.0000.000
209I209THR0-0.048-0.01535.3990.0010.0010.0000.0000.0000.000
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