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: 434LN

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 OptHSide
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 -2334626.489224
FMO2-HF: Nuclear repulsion 2249899.708976
FMO2-HF: Total energy -84726.780248
FMO2-MP2: Total energy -84968.321468


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.
-33.807-29.72732.402-15.312-21.166-0.039
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 : -0.001 / q_NPA : 0.003
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].
3I3ILE0-0.045-0.0202.464-0.3062.3930.939-1.386-2.2530.004
4I4ALA00.016-0.0014.695-0.353-0.339-0.001-0.005-0.0070.000
5I5GLY0-0.019-0.0048.3500.2750.2750.0000.0000.0000.000
6I6VAL00.0410.01611.610-0.077-0.0770.0000.0000.0000.000
7I7VAL0-0.017-0.01015.2310.0750.0750.0000.0000.0000.000
8I8TYR0-0.041-0.02418.707-0.020-0.0200.0000.0000.0000.000
9I9LYS10.8470.92321.4380.1040.1040.0000.0000.0000.000
10I10ASP-1-0.912-0.95824.187-0.033-0.0330.0000.0000.0000.000
11I11GLY0-0.015-0.03121.6640.0300.0300.0000.0000.0000.000
12I12ILE0-0.0390.00515.314-0.029-0.0290.0000.0000.0000.000
13I13VAL00.0010.01113.8760.0500.0500.0000.0000.0000.000
14I14LEU0-0.012-0.00610.574-0.073-0.0730.0000.0000.0000.000
15I15GLY00.0580.0099.1860.0630.0630.0000.0000.0000.000
16I16ALA00.005-0.0064.623-0.135-0.096-0.001-0.003-0.0340.000
17I17ASP-1-0.654-0.8042.390-2.3040.1583.399-2.921-2.939-0.035
18I18THR0-0.025-0.0154.9330.8930.989-0.001-0.004-0.0920.000
19I19ARG10.8490.9624.4640.7440.893-0.001-0.009-0.1380.000
20I20ALA00.0350.0153.8893.5763.9970.003-0.083-0.3410.000
21I21THR0-0.008-0.0114.820-0.918-0.9180.0000.0000.0000.000
22I22GLU-1-0.907-0.9406.6971.3051.3050.0000.0000.0000.000
23I23GLY00.0030.0029.275-0.258-0.2580.0000.0000.0000.000
24I24MET0-0.028-0.0249.009-0.012-0.0120.0000.0000.0000.000
25I25VAL00.0090.00710.667-0.140-0.1400.0000.0000.0000.000
26I26VAL0-0.051-0.0288.1900.2140.2140.0000.0000.0000.000
27I27ALA00.0100.0159.075-0.174-0.1740.0000.0000.0000.000
28I28ASP-1-0.809-0.9158.6531.6991.6990.0000.0000.0000.000
29I29LYS10.8810.9338.648-0.307-0.3070.0000.0000.0000.000
30I30ASN0-0.040-0.04510.049-0.181-0.1810.0000.0000.0000.000
31I31CYS00.0660.0536.6510.2220.2220.0000.0000.0000.000
32I32SER0-0.012-0.0137.681-0.063-0.0630.0000.0000.0000.000
33I33LYS10.8010.8701.863-22.748-26.81413.782-4.489-5.2270.046
34I34ILE0-0.009-0.0066.204-0.310-0.3100.0000.0000.0000.000
35I35HIS10.8760.9376.794-2.167-2.1670.0000.0000.0000.000
36I36PHE00.0520.03111.445-0.131-0.1310.0000.0000.0000.000
37I37ILE0-0.049-0.01313.9070.0370.0370.0000.0000.0000.000
38I38SER00.016-0.00516.669-0.019-0.0190.0000.0000.0000.000
39I39PRO00.0230.01119.2710.0070.0070.0000.0000.0000.000
40I40ASN0-0.014-0.00821.2300.0170.0170.0000.0000.0000.000
41I41ILE0-0.037-0.02116.342-0.037-0.0370.0000.0000.0000.000
42I42TYR00.0810.03413.1740.0690.0690.0000.0000.0000.000
43I43CYS0-0.031-0.01610.924-0.102-0.1020.0000.0000.0000.000
44I44CYS0-0.0050.0286.1450.2680.2680.0000.0000.0000.000
45I45GLY00.0190.0035.352-0.440-0.396-0.001-0.011-0.0330.000
46I46ALA0-0.006-0.0052.3990.1481.0201.628-0.832-1.668-0.003
47I47GLY00.0110.0073.286-0.806-1.0080.0360.374-0.2080.000
48I48THR0-0.007-0.0135.9661.1661.1660.0000.0000.0000.000
49I49ALA00.0390.0206.712-0.209-0.2090.0000.0000.0000.000
50I50ALA00.0850.0377.781-0.303-0.3030.0000.0000.0000.000
51I51ASP-1-0.782-0.89110.6550.8350.8350.0000.0000.0000.000
52I52THR0-0.097-0.0366.180-0.075-0.0750.0000.0000.0000.000
53I53ASP-1-0.857-0.9339.4051.8331.8330.0000.0000.0000.000
54I54MET0-0.032-0.01111.317-0.195-0.1950.0000.0000.0000.000
55I55THR0-0.025-0.02812.462-0.178-0.1780.0000.0000.0000.000
56I56THR00.006-0.01011.043-0.143-0.1430.0000.0000.0000.000
57I57GLN0-0.018-0.01813.507-0.142-0.1420.0000.0000.0000.000
58I58LEU0-0.0040.00816.196-0.089-0.0890.0000.0000.0000.000
59I59ILE0-0.030-0.03416.562-0.075-0.0750.0000.0000.0000.000
60I60SER0-0.024-0.01417.005-0.053-0.0530.0000.0000.0000.000
61I61SER00.0230.01918.831-0.053-0.0530.0000.0000.0000.000
62I62ASN00.011-0.01121.491-0.052-0.0520.0000.0000.0000.000
63I63LEU0-0.026-0.02219.412-0.044-0.0440.0000.0000.0000.000
64I64GLU-1-0.935-0.94123.0310.3000.3000.0000.0000.0000.000
65I65LEU00.0390.01024.747-0.028-0.0280.0000.0000.0000.000
66I66HIS0-0.023-0.00325.880-0.019-0.0190.0000.0000.0000.000
67I67SER0-0.044-0.03325.736-0.019-0.0190.0000.0000.0000.000
68I68LEU00.0050.01228.061-0.019-0.0190.0000.0000.0000.000
69I69SER0-0.039-0.00330.410-0.014-0.0140.0000.0000.0000.000
70I70THR0-0.103-0.07429.989-0.015-0.0150.0000.0000.0000.000
71I71GLY00.0230.01531.941-0.014-0.0140.0000.0000.0000.000
72I72ARG10.8410.92630.802-0.106-0.1060.0000.0000.0000.000
73I73LEU00.0290.01425.2400.0140.0140.0000.0000.0000.000
74I74PRO00.0050.00022.820-0.016-0.0160.0000.0000.0000.000
75I75ARG10.9620.98824.227-0.085-0.0850.0000.0000.0000.000
76I76VAL00.0550.01518.2130.0230.0230.0000.0000.0000.000
77I77VAL0-0.042-0.02520.0460.0120.0120.0000.0000.0000.000
78I78THR00.0060.00322.139-0.005-0.0050.0000.0000.0000.000
79I79ALA00.0820.05117.5360.0130.0130.0000.0000.0000.000
80I80ASN00.0220.00417.1390.0340.0340.0000.0000.0000.000
81I81ARG10.8760.93618.612-0.081-0.0810.0000.0000.0000.000
82I82MET0-0.0040.00020.0460.0090.0090.0000.0000.0000.000
83I83LEU00.0480.02513.8840.0140.0140.0000.0000.0000.000
84I84LYS10.8870.94717.206-0.024-0.0240.0000.0000.0000.000
85I85GLN0-0.015-0.00618.346-0.032-0.0320.0000.0000.0000.000
86I86MET0-0.0060.00916.749-0.014-0.0140.0000.0000.0000.000
87I87LEU0-0.004-0.01213.2930.0030.0030.0000.0000.0000.000
88I88PHE00.0150.01617.472-0.012-0.0120.0000.0000.0000.000
89I89ARG10.8750.94920.351-0.268-0.2680.0000.0000.0000.000
90I90TYR0-0.013-0.01518.656-0.009-0.0090.0000.0000.0000.000
91I91GLN0-0.0100.00119.7870.0080.0080.0000.0000.0000.000
92I92GLY00.0320.01615.981-0.029-0.0290.0000.0000.0000.000
93I93TYR0-0.079-0.03715.3740.0360.0360.0000.0000.0000.000
94I94ILE0-0.0140.01213.2620.0630.0630.0000.0000.0000.000
95I95GLY00.0410.03111.070-0.080-0.0800.0000.0000.0000.000
96I96ALA0-0.026-0.0288.7940.3540.3540.0000.0000.0000.000
97I97ALA0-0.007-0.0016.479-0.318-0.3180.0000.0000.0000.000
98I98LEU0-0.015-0.0216.6900.3360.3360.0000.0000.0000.000
99I99VAL00.0150.0157.226-0.250-0.2500.0000.0000.0000.000
100I100LEU0-0.018-0.0029.5240.1470.1470.0000.0000.0000.000
101I101GLY00.0490.01412.939-0.099-0.0990.0000.0000.0000.000
102I102GLY00.0190.00415.1840.0690.0690.0000.0000.0000.000
103I103VAL0-0.0140.00218.614-0.044-0.0440.0000.0000.0000.000
104I104ASP-1-0.832-0.90022.2410.1240.1240.0000.0000.0000.000
105I105VAL0-0.010-0.02525.166-0.008-0.0080.0000.0000.0000.000
106I106THR0-0.038-0.02626.430-0.008-0.0080.0000.0000.0000.000
107I107GLY00.0440.03525.741-0.016-0.0160.0000.0000.0000.000
108I108PRO00.0390.03620.8190.0260.0260.0000.0000.0000.000
109I109HIS0-0.004-0.00319.836-0.034-0.0340.0000.0000.0000.000
110I110LEU00.0300.02012.6370.0480.0480.0000.0000.0000.000
111I111TYR0-0.023-0.02614.942-0.040-0.0400.0000.0000.0000.000
112I112SER00.0590.04511.3500.0090.0090.0000.0000.0000.000
113I113ILE0-0.057-0.04511.241-0.002-0.0020.0000.0000.0000.000
114I114TYR00.0470.02510.9780.0430.0430.0000.0000.0000.000
115I115PRO00.0270.01610.7100.0190.0190.0000.0000.0000.000
116I116HIS00.0300.01213.1680.0420.0420.0000.0000.0000.000
117I117GLY00.0070.00615.8690.0000.0000.0000.0000.0000.000
118I118SER0-0.025-0.00816.6810.0070.0070.0000.0000.0000.000
119I119THR0-0.016-0.02115.6400.0310.0310.0000.0000.0000.000
120I120ASP-1-0.870-0.92515.558-0.263-0.2630.0000.0000.0000.000
121I121LYS10.8190.90416.1590.0520.0520.0000.0000.0000.000
122I122LEU00.0230.01315.479-0.007-0.0070.0000.0000.0000.000
123I123PRO00.0030.00816.9480.0220.0220.0000.0000.0000.000
124I124TYR0-0.024-0.05014.6230.0380.0380.0000.0000.0000.000
125I125VAL0-0.0160.00510.387-0.014-0.0140.0000.0000.0000.000
126I126THR00.010-0.0208.0350.0290.0290.0000.0000.0000.000
127I127MET0-0.0150.0025.2810.2460.2460.0000.0000.0000.000
128I128GLY00.0190.0013.246-0.922-0.5740.030-0.143-0.2350.000
129I129SER0-0.037-0.0352.025-3.617-4.1065.293-2.222-2.582-0.021
130I130GLY00.0370.0253.4951.8562.1470.000-0.072-0.2180.000
131I131SER0-0.063-0.0405.2741.3861.452-0.001-0.002-0.0620.000
132I132LEU00.0470.0187.7460.6000.6000.0000.0000.0000.000
133I133ALA00.0310.0259.3070.3180.3180.0000.0000.0000.000
134I134ALA00.003-0.0018.9660.3590.3590.0000.0000.0000.000
135I135MET00.001-0.00210.8930.3160.3160.0000.0000.0000.000
136I136ALA00.0020.01112.8710.1880.1880.0000.0000.0000.000
137I137VAL00.003-0.00413.9850.1330.1330.0000.0000.0000.000
138I138PHE0-0.054-0.04111.8320.1020.1020.0000.0000.0000.000
139I139GLU-1-0.862-0.92316.106-0.488-0.4880.0000.0000.0000.000
140I140ASP-1-0.989-0.97118.534-0.499-0.4990.0000.0000.0000.000
141I141LYS10.8340.90719.1260.6580.6580.0000.0000.0000.000
142I142PHE00.0220.01118.2840.0430.0430.0000.0000.0000.000
143I143ARG10.8110.89020.3630.2360.2360.0000.0000.0000.000
144I144PRO00.0100.00522.603-0.001-0.0010.0000.0000.0000.000
145I145ASP-1-0.927-0.97324.260-0.136-0.1360.0000.0000.0000.000
146I146MET0-0.0560.00318.900-0.003-0.0030.0000.0000.0000.000
147I147GLU-1-0.769-0.88324.109-0.074-0.0740.0000.0000.0000.000
148I148GLU-1-0.777-0.88221.039-0.033-0.0330.0000.0000.0000.000
149I149GLU-1-0.824-0.91020.618-0.098-0.0980.0000.0000.0000.000
150I150GLU-1-0.802-0.88320.837-0.251-0.2510.0000.0000.0000.000
151I151ALA00.0470.01718.489-0.048-0.0480.0000.0000.0000.000
152I152LYS10.7920.87416.330-0.002-0.0020.0000.0000.0000.000
153I153ASN0-0.0440.00415.916-0.029-0.0290.0000.0000.0000.000
154I154LEU00.0360.02616.027-0.072-0.0720.0000.0000.0000.000
155I155VAL00.0100.00311.295-0.135-0.1350.0000.0000.0000.000
156I156SER0-0.052-0.04811.844-0.171-0.1710.0000.0000.0000.000
157I157GLU-1-0.824-0.90112.431-0.726-0.7260.0000.0000.0000.000
158I158ALA00.0000.01411.432-0.176-0.1760.0000.0000.0000.000
159I159ILE0-0.056-0.0406.661-0.433-0.4330.0000.0000.0000.000
160I160ALA00.0030.0058.099-0.451-0.4510.0000.0000.0000.000
161I161ALA0-0.0030.00710.215-0.146-0.1460.0000.0000.0000.000
162I162GLY00.0430.0186.896-0.061-0.0610.0000.0000.0000.000
163I163ILE0-0.077-0.0476.086-0.585-0.5850.0000.0000.0000.000
164I164PHE0-0.061-0.0377.0850.1230.1230.0000.0000.0000.000
165I165ASN0-0.080-0.0348.9350.4310.4310.0000.0000.0000.000
166I166ASP-1-0.745-0.8193.313-12.126-11.0630.066-0.638-0.491-0.004
167I167LEU0-0.009-0.0045.776-0.036-0.0360.0000.0000.0000.000
168I168GLY0-0.021-0.0123.1671.1401.5670.080-0.173-0.3340.000
169I169SER0-0.050-0.0162.276-2.048-2.0977.074-2.937-4.087-0.026
170I170GLY0-0.002-0.0193.0221.9961.8910.0780.244-0.2170.000
171I171SER0-0.104-0.0496.5920.3240.3240.0000.0000.0000.000
172I172ASN00.0330.0149.371-0.400-0.4000.0000.0000.0000.000
173I173ILE00.0500.0338.324-0.050-0.0500.0000.0000.0000.000
174I174ASP-1-0.778-0.8648.5811.0951.0950.0000.0000.0000.000
175I175LEU0-0.004-0.0089.792-0.134-0.1340.0000.0000.0000.000
176I176CYS0-0.062-0.01012.3970.0840.0840.0000.0000.0000.000
177I177VAL00.0160.02014.186-0.061-0.0610.0000.0000.0000.000
178I178ILE00.0010.00515.7410.0380.0380.0000.0000.0000.000
179I179SER00.0250.01219.468-0.036-0.0360.0000.0000.0000.000
180I180LYS10.8770.90623.0320.0360.0360.0000.0000.0000.000
181I181ASN0-0.076-0.03226.1060.0050.0050.0000.0000.0000.000
182I182LYS10.8360.90422.895-0.031-0.0310.0000.0000.0000.000
183I183LEU0-0.018-0.00417.8970.0000.0000.0000.0000.0000.000
184I184ASP-1-0.826-0.90219.4400.1090.1090.0000.0000.0000.000
185I185PHE00.007-0.00512.687-0.009-0.0090.0000.0000.0000.000
186I186LEU0-0.024-0.01015.5920.0330.0330.0000.0000.0000.000
187I187ARG10.8190.9349.350-1.212-1.2120.0000.0000.0000.000
188I188PRO0-0.057-0.04612.6430.0100.0100.0000.0000.0000.000
189I189TYR00.029-0.01513.019-0.040-0.0400.0000.0000.0000.000
190I190THR0-0.004-0.02113.900-0.022-0.0220.0000.0000.0000.000
191I191VAL0-0.0260.00513.222-0.072-0.0720.0000.0000.0000.000
192I192PRO0-0.0050.01912.1910.0510.0510.0000.0000.0000.000
193I193ASN0-0.020-0.01410.885-0.044-0.0440.0000.0000.0000.000
194I194LYS10.9450.95314.3720.1620.1620.0000.0000.0000.000
195I195LYS10.8890.95916.990-0.097-0.0970.0000.0000.0000.000
196I196GLY00.0700.04018.2360.0040.0040.0000.0000.0000.000
197I197THR00.0330.00521.4550.0300.0300.0000.0000.0000.000
198I198ARG10.9010.94024.612-0.133-0.1330.0000.0000.0000.000
199I199LEU00.0800.04726.2080.0020.0020.0000.0000.0000.000
200I200GLY00.0310.02828.745-0.001-0.0010.0000.0000.0000.000
201I201ARG10.9160.94429.732-0.043-0.0430.0000.0000.0000.000
202I202TYR00.0130.00127.636-0.001-0.0010.0000.0000.0000.000
203I203ARG10.9270.97131.344-0.098-0.0980.0000.0000.0000.000
204I204CYS00.0130.02132.828-0.009-0.0090.0000.0000.0000.000
205I205GLU-1-0.868-0.94434.9310.1020.1020.0000.0000.0000.000
206I206LYS10.9860.97438.219-0.111-0.1110.0000.0000.0000.000
207I207GLY00.0190.00739.604-0.007-0.0070.0000.0000.0000.000
208I208THR0-0.022-0.00336.640-0.005-0.0050.0000.0000.0000.000
209I209THR0-0.059-0.02035.3300.0020.0020.0000.0000.0000.000
210I210ALA00.0120.00937.9400.0000.0000.0000.0000.0000.000
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