FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 76GKK

Calculation Name: 1IMH-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IMH

Chain ID: C

ChEMBL ID:

UniProt ID: O94916

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 281
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3388456.941212
FMO2-HF: Nuclear repulsion 3279096.155253
FMO2-HF: Total energy -109360.785959
FMO2-MP2: Total energy -109678.733715


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(C:188:LYS)


Summations of interaction energy for fragment #1(C:188:LYS)
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.
-0.22710.16320.441-11.715-19.116-0.126
Interaction energy analysis for fragmet #1(C:188:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.958
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].
3C190SER0-0.0070.0021.973-24.608-22.2307.134-4.261-5.251-0.042
4C191PRO0-0.0080.0123.5225.0855.5220.032-0.065-0.4050.000
5C192MET00.0430.0406.761-2.757-2.7570.0000.0000.0000.000
6C193LEU00.0340.0026.9071.7811.7810.0000.0000.0000.000
7C194CYS0-0.074-0.03110.0872.5552.5550.0000.0000.0000.000
8C195GLY0-0.0110.00412.3151.8161.8160.0000.0000.0000.000
9C196GLN0-0.004-0.00113.598-0.140-0.1400.0000.0000.0000.000
10C197TYR0-0.014-0.02510.142-0.202-0.2020.0000.0000.0000.000
11C198PRO0-0.0020.01713.4440.4220.4220.0000.0000.0000.000
12C199VAL00.0660.02613.902-0.992-0.9920.0000.0000.0000.000
13C200LYS10.8650.91515.59412.25612.2560.0000.0000.0000.000
14C201SER00.007-0.01215.2760.4310.4310.0000.0000.0000.000
15C202GLU-1-0.780-0.86014.747-16.699-16.6990.0000.0000.0000.000
16C203GLY00.0210.02217.767-0.017-0.0170.0000.0000.0000.000
17C204LYS10.8130.89413.30815.86615.8660.0000.0000.0000.000
18C205GLU-1-0.820-0.91116.428-12.901-12.9010.0000.0000.0000.000
19C206LEU0-0.0130.01410.567-0.126-0.1260.0000.0000.0000.000
20C207LYS10.8250.88614.66412.96312.9630.0000.0000.0000.000
21C208ILE0-0.002-0.00716.510-0.209-0.2090.0000.0000.0000.000
22C209VAL0-0.0060.00618.5800.5890.5890.0000.0000.0000.000
23C210VAL00.0140.01420.8310.6000.6000.0000.0000.0000.000
24C211GLN00.0720.03220.600-0.824-0.8240.0000.0000.0000.000
25C212PRO00.0190.01919.6320.3090.3090.0000.0000.0000.000
26C213GLU-1-0.738-0.85322.185-12.316-12.3160.0000.0000.0000.000
27C214THR00.026-0.00224.336-0.403-0.4030.0000.0000.0000.000
28C215GLN0-0.063-0.03626.5640.2110.2110.0000.0000.0000.000
29C216HIS00.0030.00721.291-0.372-0.3720.0000.0000.0000.000
30C217ARG10.8160.89524.51110.96010.9600.0000.0000.0000.000
31C218ALA00.0190.01621.370-0.179-0.1790.0000.0000.0000.000
32C219ARG10.8510.93518.85415.96315.9630.0000.0000.0000.000
33C220TYR00.0450.00821.836-0.634-0.6340.0000.0000.0000.000
34C221LEU00.003-0.01019.094-0.030-0.0300.0000.0000.0000.000
35C222THR0-0.001-0.00122.075-0.087-0.0870.0000.0000.0000.000
36C223GLU-1-0.753-0.82824.774-11.189-11.1890.0000.0000.0000.000
37C224GLY00.0530.03324.279-0.504-0.5040.0000.0000.0000.000
38C225SER0-0.010-0.02020.966-0.428-0.4280.0000.0000.0000.000
39C226ARG10.8450.88622.04112.21812.2180.0000.0000.0000.000
40C227GLY00.0220.03221.9530.3480.3480.0000.0000.0000.000
41C228SER0-0.0060.00318.497-0.878-0.8780.0000.0000.0000.000
42C229VAL0-0.058-0.03418.5090.7190.7190.0000.0000.0000.000
43C230LYS10.8950.94920.65211.41211.4120.0000.0000.0000.000
44C231ASP-1-0.785-0.86923.048-11.720-11.7200.0000.0000.0000.000
45C232ARG10.8410.88124.61412.07812.0780.0000.0000.0000.000
46C233THR0-0.022-0.03027.9480.3700.3700.0000.0000.0000.000
47C234GLN0-0.050-0.02827.1170.3020.3020.0000.0000.0000.000
48C235GLN00.0230.02328.774-0.238-0.2380.0000.0000.0000.000
49C236GLY00.0040.00725.160-0.035-0.0350.0000.0000.0000.000
50C237PHE0-0.001-0.01420.163-0.018-0.0180.0000.0000.0000.000
51C238PRO0-0.0190.01117.9020.2460.2460.0000.0000.0000.000
52C239THR0-0.018-0.01118.062-0.698-0.6980.0000.0000.0000.000
53C240VAL0-0.062-0.02813.3650.3400.3400.0000.0000.0000.000
54C241LYS10.8820.94716.08813.45713.4570.0000.0000.0000.000
55C242LEU0-0.033-0.00711.268-0.456-0.4560.0000.0000.0000.000
56C243GLU-1-0.818-0.90715.181-12.246-12.2460.0000.0000.0000.000
57C244GLY00.0620.02116.739-0.443-0.4430.0000.0000.0000.000
58C245HIS0-0.0130.00111.3090.2650.2650.0000.0000.0000.000
59C246ASN00.016-0.01615.6740.1340.1340.0000.0000.0000.000
60C247GLU-1-0.838-0.90112.260-15.720-15.7200.0000.0000.0000.000
61C248PRO00.0150.00410.600-0.619-0.6190.0000.0000.0000.000
62C249VAL0-0.047-0.0246.477-0.912-0.9120.0000.0000.0000.000
63C250VAL0-0.026-0.0122.393-1.463-0.4630.732-0.477-1.2550.000
64C251LEU00.0040.0055.329-0.584-0.5840.0000.0000.0000.000
65C252GLN0-0.034-0.0272.2814.6034.8952.941-0.986-2.246-0.006
66C253VAL00.0360.0086.3623.7613.7610.0000.0000.0000.000
67C254PHE00.0170.0068.585-2.002-2.0020.0000.0000.0000.000
68C255VAL00.0260.02610.7021.8791.8790.0000.0000.0000.000
69C256GLY00.0480.01814.069-0.913-0.9130.0000.0000.0000.000
70C257ASN00.017-0.01215.4830.5580.5580.0000.0000.0000.000
71C258ASP-1-0.773-0.84318.920-13.450-13.4500.0000.0000.0000.000
72C259SER0-0.025-0.01521.9140.4140.4140.0000.0000.0000.000
73C260GLY00.0430.02321.662-0.359-0.3590.0000.0000.0000.000
74C261ARG10.9050.93817.60215.70515.7050.0000.0000.0000.000
75C262VAL00.0200.02413.4720.2280.2280.0000.0000.0000.000
76C263LYS10.9590.97814.72916.11016.1100.0000.0000.0000.000
77C264PRO00.0510.04011.9660.9140.9140.0000.0000.0000.000
78C265HIS0-0.077-0.04014.0021.0921.0920.0000.0000.0000.000
79C266GLY00.0330.01916.127-0.839-0.8390.0000.0000.0000.000
80C267PHE0-0.056-0.03718.6250.1680.1680.0000.0000.0000.000
81C268TYR0-0.038-0.03818.1010.9270.9270.0000.0000.0000.000
82C269GLN00.0850.05912.580-1.636-1.6360.0000.0000.0000.000
83C270ALA00.002-0.00311.0541.3621.3620.0000.0000.0000.000
84C271CYS0-0.030-0.01812.895-0.118-0.1180.0000.0000.0000.000
85C272ARG10.9200.95711.70323.89223.8920.0000.0000.0000.000
86C273VAL0-0.087-0.03613.6261.2531.2530.0000.0000.0000.000
87C274THR0-0.023-0.00816.649-0.516-0.5160.0000.0000.0000.000
88C275GLY00.0280.00018.8420.7110.7110.0000.0000.0000.000
89C276ARG10.9240.96121.49911.87511.8750.0000.0000.0000.000
90C277ASN00.014-0.01122.3060.6170.6170.0000.0000.0000.000
91C278THR0-0.0280.02218.1950.0060.0060.0000.0000.0000.000
92C279THR00.032-0.01314.214-0.163-0.1630.0000.0000.0000.000
93C280PRO0-0.0190.00614.097-0.978-0.9780.0000.0000.0000.000
94C281CYS0-0.019-0.01610.630-1.026-1.0260.0000.0000.0000.000
95C282LYS10.8880.9383.32557.52957.7490.002-0.034-0.1890.000
96C283GLU-1-0.821-0.9237.309-26.218-26.2180.0000.0000.0000.000
97C284VAL0-0.075-0.0332.173-4.654-4.1281.791-0.659-1.657-0.005
98C285ASP-1-0.832-0.9145.366-30.302-30.3020.0000.0000.0000.000
99C286ILE0-0.016-0.0262.589-14.667-13.5750.523-0.364-1.252-0.002
100C287GLU-1-0.828-0.9055.637-27.826-27.8260.0000.0000.0000.000
101C288GLY0-0.0010.0218.6903.6253.6250.0000.0000.0000.000
102C289THR0-0.097-0.0619.0173.5743.5740.0000.0000.0000.000
103C290THR00.0340.0138.102-3.650-3.6500.0000.0000.0000.000
104C291VAL0-0.047-0.0274.9202.2722.2720.0000.0000.0000.000
105C292ILE00.0240.0126.255-3.018-3.0180.0000.0000.0000.000
106C293GLU-1-0.827-0.9152.213-101.242-98.1946.864-4.217-5.695-0.064
107C294VAL00.0150.0106.6922.1462.1460.0000.0000.0000.000
108C295GLY00.0290.0187.911-1.800-1.8000.0000.0000.0000.000
109C296LEU0-0.023-0.00310.0091.1431.1430.0000.0000.0000.000
110C297ASP-1-0.750-0.87411.539-17.033-17.0330.0000.0000.0000.000
111C298PRO00.0440.02514.1090.5880.5880.0000.0000.0000.000
112C299SER0-0.058-0.04217.1860.7560.7560.0000.0000.0000.000
113C300ASN0-0.023-0.01417.5850.8670.8670.0000.0000.0000.000
114C301ASN00.000-0.01119.023-0.153-0.1530.0000.0000.0000.000
115C302MET0-0.064-0.00112.2980.1110.1110.0000.0000.0000.000
116C303THR00.004-0.00915.786-0.242-0.2420.0000.0000.0000.000
117C304LEU00.0150.00413.449-0.082-0.0820.0000.0000.0000.000
118C305ALA00.0240.01616.301-0.167-0.1670.0000.0000.0000.000
119C306VAL0-0.013-0.02113.761-0.459-0.4590.0000.0000.0000.000
120C307ASP-1-0.796-0.87516.294-15.742-15.7420.0000.0000.0000.000
121C308CYS0-0.040-0.01414.205-0.015-0.0150.0000.0000.0000.000
122C309VAL00.023-0.00412.399-1.565-1.5650.0000.0000.0000.000
123C310GLY00.0440.03815.0971.2491.2490.0000.0000.0000.000
124C311ILE0-0.048-0.02415.822-1.258-1.2580.0000.0000.0000.000
125C312LEU00.0030.00715.9981.0511.0510.0000.0000.0000.000
126C313LYS10.8170.89918.41313.07813.0780.0000.0000.0000.000
127C314LEU00.0340.01717.0130.1770.1770.0000.0000.0000.000
128C315ARG10.8560.88721.20412.72312.7230.0000.0000.0000.000
129C316ASN00.027-0.00224.017-0.699-0.6990.0000.0000.0000.000
130C317ALA00.0740.03825.430-0.189-0.1890.0000.0000.0000.000
131C318ASP-1-0.769-0.84122.198-13.085-13.0850.0000.0000.0000.000
132C319VAL0-0.043-0.01720.327-0.417-0.4170.0000.0000.0000.000
133C320GLU-1-0.809-0.88822.175-11.115-11.1150.0000.0000.0000.000
134C321ALA00.0010.00225.0180.1790.1790.0000.0000.0000.000
135C322ARG10.9040.97513.81919.76019.7600.0000.0000.0000.000
136C323ILE0-0.042-0.03318.864-0.254-0.2540.0000.0000.0000.000
137C324GLY00.0960.05422.7640.2090.2090.0000.0000.0000.000
138C325ILE0-0.030-0.02023.6060.3650.3650.0000.0000.0000.000
139C326ALA0-0.036-0.01422.7760.1930.1930.0000.0000.0000.000
140C327GLY00.0810.02024.9270.0320.0320.0000.0000.0000.000
141C328SER0-0.034-0.03028.589-0.117-0.1170.0000.0000.0000.000
142C329LYS10.9260.98328.29210.16410.1640.0000.0000.0000.000
143C330LYS10.8700.91123.54913.14613.1460.0000.0000.0000.000
144C331LYS10.8330.91826.36010.56810.5680.0000.0000.0000.000
145C332SER0-0.078-0.05324.0240.4440.4440.0000.0000.0000.000
146C333THR00.0620.02324.350-0.511-0.5110.0000.0000.0000.000
147C334ARG10.9831.00224.34110.81610.8160.0000.0000.0000.000
148C335ALA00.0130.01218.798-0.313-0.3130.0000.0000.0000.000
149C336ARG10.8380.91417.76916.33516.3350.0000.0000.0000.000
150C337LEU00.0440.03014.690-0.972-0.9720.0000.0000.0000.000
151C338VAL0-0.042-0.02211.5961.0941.0940.0000.0000.0000.000
152C339PHE00.0430.02610.668-2.027-2.0270.0000.0000.0000.000
153C340ARG10.8200.8875.01639.75439.7540.0000.0000.0000.000
154C341VAL00.0350.0336.190-2.360-2.3600.0000.0000.0000.000
155C342ASN0-0.048-0.0402.8620.1651.4210.423-0.640-1.038-0.007
156C343ILE00.0330.0314.559-0.875-0.734-0.001-0.012-0.1280.000
157C344MET00.000-0.0026.943-0.074-0.0740.0000.0000.0000.000
158C345ARG10.8070.8838.23318.69418.6940.0000.0000.0000.000
159C346LYS10.8630.92612.04716.17516.1750.0000.0000.0000.000
160C347ASP-1-0.705-0.82514.321-16.362-16.3620.0000.0000.0000.000
161C348GLY00.0240.00311.402-0.555-0.5550.0000.0000.0000.000
162C349SER0-0.092-0.05110.257-1.737-1.7370.0000.0000.0000.000
163C350THR00.002-0.0245.643-1.110-1.1100.0000.0000.0000.000
164C351LEU0-0.0340.0088.7870.4030.4030.0000.0000.0000.000
165C352THR0-0.038-0.0316.338-1.365-1.3650.0000.0000.0000.000
166C353LEU0-0.0240.0108.7861.5221.5220.0000.0000.0000.000
167C354GLN00.027-0.0159.625-3.938-3.9380.0000.0000.0000.000
168C355THR0-0.0130.00011.5431.6241.6240.0000.0000.0000.000
169C356PRO0-0.010-0.00214.333-0.808-0.8080.0000.0000.0000.000
170C357SER00.003-0.01416.3350.5490.5490.0000.0000.0000.000
171C358SER0-0.014-0.02219.0510.4360.4360.0000.0000.0000.000
172C359PRO0-0.038-0.01221.437-0.548-0.5480.0000.0000.0000.000
173C360ILE00.0140.03019.6680.3600.3600.0000.0000.0000.000
174C361LEU0-0.030-0.02523.515-0.335-0.3350.0000.0000.0000.000
175C362CYS0-0.044-0.00621.727-0.133-0.1330.0000.0000.0000.000
176C363THR00.015-0.00924.122-0.071-0.0710.0000.0000.0000.000
177C364GLN00.0540.02527.369-0.281-0.2810.0000.0000.0000.000
178C365PRO00.0160.00529.2980.1840.1840.0000.0000.0000.000
179C366ALA0-0.004-0.00832.3520.0780.0780.0000.0000.0000.000
180C367GLY00.0040.02135.8960.1550.1550.0000.0000.0000.000
181C368VAL00.0260.01137.6510.0420.0420.0000.0000.0000.000
182C369PRO0-0.0170.00840.785-0.015-0.0150.0000.0000.0000.000
183C370GLU-1-0.770-0.87444.211-7.046-7.0460.0000.0000.0000.000
184C371ILE0-0.010-0.01346.9620.0280.0280.0000.0000.0000.000
185C372LEU0-0.0060.01248.3730.1060.1060.0000.0000.0000.000
186C373LYS10.9110.95151.7915.5955.5950.0000.0000.0000.000
187C374LYS10.8430.91155.0715.4015.4010.0000.0000.0000.000
188C375SER0-0.018-0.00157.8380.0250.0250.0000.0000.0000.000
189C376LEU00.0170.02461.2600.0690.0690.0000.0000.0000.000
190C377HIS00.012-0.00860.223-0.129-0.1290.0000.0000.0000.000
191C378SER0-0.053-0.03463.5000.0270.0270.0000.0000.0000.000
192C379CYS0-0.033-0.00666.169-0.025-0.0250.0000.0000.0000.000
193C380SER00.0120.01868.0610.0270.0270.0000.0000.0000.000
194C381VAL0-0.025-0.01969.030-0.073-0.0730.0000.0000.0000.000
195C382LYS10.8480.89768.4354.3454.3450.0000.0000.0000.000
196C383GLY00.0020.00366.099-0.048-0.0480.0000.0000.0000.000
197C384GLU-1-0.858-0.93264.592-4.953-4.9530.0000.0000.0000.000
198C385GLU-1-0.792-0.87866.225-4.706-4.7060.0000.0000.0000.000
199C386GLU-1-0.922-0.96662.156-5.198-5.1980.0000.0000.0000.000
200C387VAL0-0.059-0.04258.8350.0330.0330.0000.0000.0000.000
201C388PHE00.0090.01557.614-0.126-0.1260.0000.0000.0000.000
202C389LEU0-0.012-0.01653.4530.0240.0240.0000.0000.0000.000
203C390ILE0-0.002-0.01151.923-0.073-0.0730.0000.0000.0000.000
204C391GLY00.008-0.00949.0600.0430.0430.0000.0000.0000.000
205C392LYS10.7620.87342.3117.1507.1500.0000.0000.0000.000
206C393ASN0-0.007-0.01540.4810.0010.0010.0000.0000.0000.000
207C394PHE00.0180.02142.824-0.078-0.0780.0000.0000.0000.000
208C395LEU0-0.044-0.03339.373-0.019-0.0190.0000.0000.0000.000
209C396LYS10.8970.96642.4046.9666.9660.0000.0000.0000.000
210C397GLY00.0080.01443.2110.1330.1330.0000.0000.0000.000
211C398THR0-0.049-0.03744.6230.0050.0050.0000.0000.0000.000
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