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: 22KMR

Calculation Name: 4R3O-I-Xray322

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2332955.665966
FMO2-HF: Nuclear repulsion 2248230.644857
FMO2-HF: Total energy -84725.021109
FMO2-MP2: Total energy -84966.546167


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.
-34.677-32.87235.928-16.65-21.085-0.049
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 : -0.011 / q_NPA : -0.010
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].
3I3ILE 0-0.035-0.0142.620-0.1122.5570.704-1.224-2.1500.003
4I4ALA 00.009-0.0044.690-0.386-0.3670.000-0.005-0.0140.000
5I5GLY 0-0.014-0.0058.3200.2850.2850.0000.0000.0000.000
6I6VAL 00.0240.01711.610-0.080-0.0800.0000.0000.0000.000
7I7VAL 0-0.009-0.00515.2170.0740.0740.0000.0000.0000.000
8I8TYR 0-0.032-0.02118.705-0.021-0.0210.0000.0000.0000.000
9I9LYS 10.8590.93221.4420.0850.0850.0000.0000.0000.000
10I10ASP -1-0.919-0.96324.166-0.010-0.0100.0000.0000.0000.000
11I11GLY 0-0.025-0.03721.6330.0290.0290.0000.0000.0000.000
12I12ILE 0-0.0260.00615.485-0.029-0.0290.0000.0000.0000.000
13I13VAL 0-0.0120.00913.6840.0480.0480.0000.0000.0000.000
14I14LEU 0-0.009-0.00710.479-0.068-0.0680.0000.0000.0000.000
15I15GLY 00.0510.0089.0850.0500.0500.0000.0000.0000.000
16I16ALA 00.000-0.0104.538-0.113-0.0660.000-0.004-0.0420.000
17I17ASP -1-0.684-0.8282.424-3.712-0.7383.304-3.220-3.059-0.039
18I18THR 00.001-0.0165.0081.0541.1390.000-0.004-0.0810.000
19I19ARG 10.8570.9664.4511.1851.3210.000-0.011-0.1260.000
20I20ALA 00.0300.0093.8403.3173.7430.005-0.089-0.3430.000
21I21THR 0-0.024-0.0154.790-1.003-0.9390.000-0.004-0.0600.000
22I22GLU -1-0.893-0.9356.6911.0861.0860.0000.0000.0000.000
23I23GLY 00.0060.0059.264-0.228-0.2280.0000.0000.0000.000
24I24MET 0-0.030-0.0268.847-0.034-0.0340.0000.0000.0000.000
25I25VAL 00.0160.01210.675-0.122-0.1220.0000.0000.0000.000
26I26VAL 0-0.061-0.0338.0550.1760.1760.0000.0000.0000.000
27I27ALA 00.0140.0159.045-0.113-0.1130.0000.0000.0000.000
28I28ASP -1-0.811-0.9198.5161.6061.6060.0000.0000.0000.000
29I29LYS 10.8790.9338.604-0.250-0.2500.0000.0000.0000.000
30I30ASN 0-0.041-0.02810.060-0.107-0.1070.0000.0000.0000.000
31I31CYS 00.0710.0546.5870.2830.2830.0000.0000.0000.000
32I32SER 0-0.025-0.0747.850-0.036-0.0360.0000.0000.0000.000
33I33LYS 10.8480.9041.811-21.390-29.11818.758-5.548-5.4810.042
34I34ILE 00.0010.0046.348-0.329-0.3290.0000.0000.0000.000
35I35HIS 10.8830.9427.197-2.183-2.1830.0000.0000.0000.000
36I36PHE 00.0560.02611.461-0.136-0.1360.0000.0000.0000.000
37I37ILE 0-0.054-0.01313.7050.0380.0380.0000.0000.0000.000
38I38SER 00.001-0.03016.668-0.026-0.0260.0000.0000.0000.000
39I39PRO 00.0270.01119.2420.0100.0100.0000.0000.0000.000
40I40ASN 0-0.0020.01821.2530.0170.0170.0000.0000.0000.000
41I41ILE 0-0.036-0.02116.305-0.033-0.0330.0000.0000.0000.000
42I42TYR 00.0870.03613.1870.0700.0700.0000.0000.0000.000
43I43CYS 0-0.024-0.01511.057-0.112-0.1120.0000.0000.0000.000
44I44CYS 0-0.0120.0246.1670.2660.2660.0000.0000.0000.000
45I45GLY 00.0070.0015.353-0.447-0.4070.000-0.011-0.0280.000
46I46ALA 0-0.001-0.0032.4340.2821.1651.558-0.830-1.612-0.003
47I47GLY 00.0070.0063.308-0.887-1.0290.0350.310-0.2030.000
48I48THR 0-0.004-0.0166.0291.0261.0260.0000.0000.0000.000
49I49ALA 00.0420.0226.685-0.160-0.1600.0000.0000.0000.000
50I50ALA 00.1020.0527.954-0.279-0.2790.0000.0000.0000.000
51I51ASP -1-0.785-0.89310.8840.8150.8150.0000.0000.0000.000
52I52THR 0-0.114-0.0226.331-0.033-0.0330.0000.0000.0000.000
53I53ASP -1-0.864-0.9339.5031.7941.7940.0000.0000.0000.000
54I54MET 0-0.015-0.01911.438-0.204-0.2040.0000.0000.0000.000
55I55THR 0-0.042-0.06112.529-0.174-0.1740.0000.0000.0000.000
56I56THR 0-0.010-0.01611.391-0.137-0.1370.0000.0000.0000.000
57I57GLN 0-0.016-0.00713.559-0.003-0.0030.0000.0000.0000.000
58I58LEU 0-0.0210.00416.274-0.092-0.0920.0000.0000.0000.000
59I59ILE 0-0.034-0.03416.541-0.078-0.0780.0000.0000.0000.000
60I60SER 0-0.028-0.00917.093-0.054-0.0540.0000.0000.0000.000
61I61SER 00.0280.01918.864-0.061-0.0610.0000.0000.0000.000
62I62ASN 00.020-0.00621.721-0.047-0.0470.0000.0000.0000.000
63I63LEU 0-0.038-0.03119.543-0.045-0.0450.0000.0000.0000.000
64I64GLU -1-0.933-0.94623.0600.3030.3030.0000.0000.0000.000
65I65LEU 00.0490.01224.770-0.030-0.0300.0000.0000.0000.000
66I66HIS 0-0.036-0.01225.923-0.020-0.0200.0000.0000.0000.000
67I67SER 0-0.071-0.02626.284-0.021-0.0210.0000.0000.0000.000
68I68LEU 00.0340.01828.178-0.019-0.0190.0000.0000.0000.000
69I69SER 0-0.055-0.01230.422-0.018-0.0180.0000.0000.0000.000
70I70THR 0-0.101-0.06829.923-0.014-0.0140.0000.0000.0000.000
71I71GLY 00.0310.01931.928-0.013-0.0130.0000.0000.0000.000
72I72ARG 10.8600.93230.547-0.116-0.1160.0000.0000.0000.000
73I73LEU 00.0390.01725.2070.0140.0140.0000.0000.0000.000
74I74PRO 0-0.013-0.00622.798-0.016-0.0160.0000.0000.0000.000
75I75ARG 10.9700.98624.164-0.103-0.1030.0000.0000.0000.000
76I76VAL 00.0530.01218.2630.0240.0240.0000.0000.0000.000
77I77VAL 0-0.039-0.02420.0120.0120.0120.0000.0000.0000.000
78I78THR 00.0000.00122.083-0.005-0.0050.0000.0000.0000.000
79I79ALA 00.0810.04817.4180.0120.0120.0000.0000.0000.000
80I80ASN 00.0170.00717.3360.0310.0310.0000.0000.0000.000
81I81ARG 10.9060.95018.559-0.094-0.0940.0000.0000.0000.000
82I82MET 0-0.006-0.00119.9830.0090.0090.0000.0000.0000.000
83I83LEU 00.0490.02513.7730.0110.0110.0000.0000.0000.000
84I84LYS 10.9120.97017.205-0.059-0.0590.0000.0000.0000.000
85I85GLN 0-0.047-0.02518.327-0.038-0.0380.0000.0000.0000.000
86I86MET 0-0.0130.00417.492-0.009-0.0090.0000.0000.0000.000
87I87LEU 0-0.005-0.01013.2990.0000.0000.0000.0000.0000.000
88I88PHE 00.0260.02017.501-0.015-0.0150.0000.0000.0000.000
89I89ARG 10.8930.95620.364-0.270-0.2700.0000.0000.0000.000
90I90TYR 0-0.032-0.02318.672-0.008-0.0080.0000.0000.0000.000
91I91GLN 0-0.015-0.00119.8520.0100.0100.0000.0000.0000.000
92I92GLY 00.0240.01516.018-0.028-0.0280.0000.0000.0000.000
93I93TYR 0-0.071-0.03515.3690.0330.0330.0000.0000.0000.000
94I94ILE 0-0.0010.01913.2400.0610.0610.0000.0000.0000.000
95I95GLY 00.0330.03011.120-0.063-0.0630.0000.0000.0000.000
96I96ALA 0-0.021-0.0258.8530.3480.3480.0000.0000.0000.000
97I97ALA 0-0.006-0.0016.492-0.323-0.3230.0000.0000.0000.000
98I98LEU 0-0.031-0.0276.6640.3500.3500.0000.0000.0000.000
99I99VAL 00.0240.0197.297-0.265-0.2650.0000.0000.0000.000
100I100LEU 0-0.008-0.0059.5620.1500.1500.0000.0000.0000.000
101I101GLY 00.0360.01113.007-0.103-0.1030.0000.0000.0000.000
102I102GLY 00.0180.00515.2540.0680.0680.0000.0000.0000.000
103I103VAL 0-0.0140.00418.700-0.045-0.0450.0000.0000.0000.000
104I104ASP -1-0.813-0.88922.3220.1490.1490.0000.0000.0000.000
105I105VAL 0-0.014-0.02825.246-0.009-0.0090.0000.0000.0000.000
106I106THR 0-0.053-0.03726.326-0.007-0.0070.0000.0000.0000.000
107I107GLY 00.0420.03325.791-0.016-0.0160.0000.0000.0000.000
108I108PRO 00.0370.03720.9350.0260.0260.0000.0000.0000.000
109I109HIS 0-0.033-0.02219.867-0.031-0.0310.0000.0000.0000.000
110I110LEU 00.0300.02312.6760.0500.0500.0000.0000.0000.000
111I111TYR 0-0.026-0.02514.958-0.045-0.0450.0000.0000.0000.000
112I112SER 00.0110.02511.1440.0170.0170.0000.0000.0000.000
113I113ILE 0-0.016-0.03111.231-0.008-0.0080.0000.0000.0000.000
114I114TYR 00.0690.03110.9660.0510.0510.0000.0000.0000.000
115I115PRO 00.0320.02010.6630.0190.0190.0000.0000.0000.000
116I116HIS 00.0270.00713.1750.0290.0290.0000.0000.0000.000
117I117GLY 00.0090.00615.844-0.004-0.0040.0000.0000.0000.000
118I118SER 0-0.038-0.01416.4850.0030.0030.0000.0000.0000.000
119I119THR 0-0.018-0.03215.6040.0330.0330.0000.0000.0000.000
120I120ASP -1-0.877-0.92015.513-0.222-0.2220.0000.0000.0000.000
121I121LYS 10.8540.92016.1190.0320.0320.0000.0000.0000.000
122I122LEU 00.0210.01215.312-0.012-0.0120.0000.0000.0000.000
123I123PRO 00.0140.01216.9120.0220.0220.0000.0000.0000.000
124I124TYR 00.0220.00314.4520.0350.0350.0000.0000.0000.000
125I125VAL 0-0.0180.00210.602-0.013-0.0130.0000.0000.0000.000
126I126THR 00.012-0.0087.9620.0400.0400.0000.0000.0000.000
127I127MET 0-0.0100.0015.2210.2220.2220.0000.0000.0000.000
128I128GLY 00.0270.0033.049-0.997-0.6130.054-0.161-0.2770.000
129I129SER 0-0.053-0.0312.132-4.125-3.2123.316-1.845-2.384-0.020
130I130GLY 00.0480.0343.3711.8222.1190.001-0.075-0.2230.000
131I131SER 0-0.073-0.0915.1271.4071.4800.000-0.003-0.0690.000
132I132LEU 00.0330.0087.5590.5990.5990.0000.0000.0000.000
133I133ALA 00.0350.0299.1750.3110.3110.0000.0000.0000.000
134I134ALA 00.009-0.0028.8550.3470.3470.0000.0000.0000.000
135I135MET 0-0.010-0.00610.7550.3130.3130.0000.0000.0000.000
136I136ALA 00.0140.01512.7190.1830.1830.0000.0000.0000.000
137I137VAL 0-0.008-0.00513.8350.1300.1300.0000.0000.0000.000
138I138PHE 0-0.067-0.04311.6120.1070.1070.0000.0000.0000.000
139I139GLU -1-0.906-0.98115.994-0.443-0.4430.0000.0000.0000.000
140I140ASP -1-0.984-0.95818.402-0.455-0.4550.0000.0000.0000.000
141I141LYS 10.8310.91219.1550.6030.6030.0000.0000.0000.000
142I142PHE 00.0130.00218.2370.0440.0440.0000.0000.0000.000
143I143ARG 10.8770.93320.2780.2130.2130.0000.0000.0000.000
144I144PRO 0-0.002-0.00522.5490.0030.0030.0000.0000.0000.000
145I145ASP -1-0.950-0.97324.212-0.105-0.1050.0000.0000.0000.000
146I146MET 0-0.0450.00118.868-0.002-0.0020.0000.0000.0000.000
147I147GLU -1-0.756-0.88224.091-0.055-0.0550.0000.0000.0000.000
148I148GLU -1-0.818-0.89721.007-0.004-0.0040.0000.0000.0000.000
149I149GLU -1-0.830-0.91720.498-0.078-0.0780.0000.0000.0000.000
150I150GLU -1-0.832-0.90520.705-0.233-0.2330.0000.0000.0000.000
151I151ALA 00.0350.00518.346-0.047-0.0470.0000.0000.0000.000
152I152LYS 10.8160.88816.212-0.024-0.0240.0000.0000.0000.000
153I153ASN 0-0.0050.01015.782-0.018-0.0180.0000.0000.0000.000
154I154LEU 00.0530.03815.966-0.075-0.0750.0000.0000.0000.000
155I155VAL 00.0060.00111.101-0.131-0.1310.0000.0000.0000.000
156I156SER 0-0.079-0.04111.671-0.144-0.1440.0000.0000.0000.000
157I157GLU -1-0.830-0.92612.407-0.670-0.6700.0000.0000.0000.000
158I158ALA 00.0080.02011.301-0.177-0.1770.0000.0000.0000.000
159I159ILE 0-0.050-0.0336.514-0.426-0.4260.0000.0000.0000.000
160I160ALA 00.0050.0048.078-0.441-0.4410.0000.0000.0000.000
161I161ALA 0-0.0020.00810.379-0.155-0.1550.0000.0000.0000.000
162I162GLY 00.0410.0237.098-0.093-0.0930.0000.0000.0000.000
163I163ILE 0-0.084-0.0456.199-0.597-0.5970.0000.0000.0000.000
164I164PHE 0-0.050-0.0387.2130.0970.0970.0000.0000.0000.000
165I165ASN 0-0.079-0.0429.1300.4050.4050.0000.0000.0000.000
166I166ASP -1-0.740-0.8133.216-11.459-10.4840.050-0.550-0.474-0.004
167I167LEU 0-0.011-0.0075.886-0.065-0.0650.0000.0000.0000.000
168I168GLY 0-0.0040.0043.1900.9541.4900.082-0.255-0.364-0.001
169I169SER 0-0.0520.0122.095-3.500-4.2587.991-3.353-3.881-0.028
170I170GLY 00.000-0.0203.0392.1482.0600.0700.232-0.2140.001
171I171SER 0-0.109-0.0496.5480.3730.3730.0000.0000.0000.000
172I172ASN 00.0150.0059.362-0.379-0.3790.0000.0000.0000.000
173I173ILE 00.0590.0348.314-0.037-0.0370.0000.0000.0000.000
174I174ASP -1-0.805-0.8928.7021.0351.0350.0000.0000.0000.000
175I175LEU 0-0.020-0.0189.749-0.125-0.1250.0000.0000.0000.000
176I176CYS 0-0.057-0.00912.3580.0800.0800.0000.0000.0000.000
177I177VAL 00.0140.01814.165-0.060-0.0600.0000.0000.0000.000
178I178ILE 00.0060.00915.8290.0340.0340.0000.0000.0000.000
179I179SER 00.0230.01219.427-0.037-0.0370.0000.0000.0000.000
180I180LYS 10.8600.89822.9760.0160.0160.0000.0000.0000.000
181I181ASN 0-0.080-0.03426.0390.0060.0060.0000.0000.0000.000
182I182LYS 10.8910.93722.710-0.052-0.0520.0000.0000.0000.000
183I183LEU 0-0.018-0.00517.9200.0020.0020.0000.0000.0000.000
184I184ASP -1-0.852-0.93319.0900.1420.1420.0000.0000.0000.000
185I185PHE 0-0.016-0.01012.5990.0010.0010.0000.0000.0000.000
186I186LEU 0-0.012-0.00915.5970.0270.0270.0000.0000.0000.000
187I187ARG 10.8721.0289.815-1.241-1.2410.0000.0000.0000.000
188I188PRO 0-0.083-0.05412.5710.0050.0050.0000.0000.0000.000
189I189TYR 00.044-0.00413.019-0.046-0.0460.0000.0000.0000.000
190I190THR 0-0.010-0.02913.886-0.036-0.0360.0000.0000.0000.000
191I191VAL 0-0.044-0.00913.218-0.060-0.0600.0000.0000.0000.000
192I192PRO 0-0.0390.00112.1710.0330.0330.0000.0000.0000.000
193I193ASN 0-0.020-0.00511.170-0.033-0.0330.0000.0000.0000.000
194I194LYS 11.0040.98814.3640.1390.1390.0000.0000.0000.000
195I195LYS 10.9150.97716.909-0.090-0.0900.0000.0000.0000.000
196I196GLY 00.0490.02718.1220.0080.0080.0000.0000.0000.000
197I197THR 00.020-0.00121.3600.0270.0270.0000.0000.0000.000
198I198ARG 10.9250.94623.858-0.103-0.1030.0000.0000.0000.000
199I199LEU 00.0660.04226.0690.0040.0040.0000.0000.0000.000
200I200GLY 00.0280.03028.6000.0000.0000.0000.0000.0000.000
201I201ARG 10.9130.94029.571-0.031-0.0310.0000.0000.0000.000
202I202TYR 00.0180.00727.411-0.002-0.0020.0000.0000.0000.000
203I203ARG 10.9350.96931.155-0.082-0.0820.0000.0000.0000.000
204I204CYS 00.0170.01932.581-0.008-0.0080.0000.0000.0000.000
205I205GLU -1-0.890-0.94534.8990.0830.0830.0000.0000.0000.000
206I206LYS 10.9920.97838.189-0.098-0.0980.0000.0000.0000.000
207I207GLY 00.0160.00439.557-0.006-0.0060.0000.0000.0000.000
208I208THR 0-0.023-0.00336.543-0.005-0.0050.0000.0000.0000.000
209I209THR 0-0.047-0.01535.3940.0010.0010.0000.0000.0000.000
210I210ALA 00.0030.00537.9000.0010.0010.0000.0000.0000.000
211I211VAL 00.0170.00338.7990.0060.0060.0000.0000.0000.000
212I212LEU 00.0010.00340.373-0.005-0.0050.0000.0000.0000.000
213I213THR 0-0.044-0.03441.262-0.004-0.0040.0000.0000.0000.000
214I214GLU -1-0.873-0.91540.4830.1380.1380.0000.0000.0000.000
215I215LYS 10.8860.91841.318-0.127-0.1270.0000.0000.0000.000
216I216ILE 00.0190.02240.8830.0070.0070.0000.0000.0000.000
217I217THR 0-0.030-0.02840.141-0.009-0.0090.0000.0000.0000.000
218I218PRO 0-0.039-0.01540.8850.0070.0070.0000.0000.0000.000
219I219LEU 0-0.056-0.02837.0220.0040.0040.0000.0000.0000.000
220I220GLU -2-1.872-1.91840.7220.2890.2890.0000.0000.0000.000