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: 98GR2

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 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 281
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3388688.689106
FMO2-HF: Nuclear repulsion 3279331.941727
FMO2-HF: Total energy -109356.747379
FMO2-MP2: Total energy -109675.115041


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.
17.54926.99816.164-9.661-15.948-0.089
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 : 0.948 / q_NPA : 0.978
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].
3C190SER0-0.096-0.0562.656-4.764-1.4100.654-1.524-2.484-0.003
4C191PRO0-0.0100.0113.5493.6604.1070.037-0.012-0.471-0.001
5C192MET00.0740.0676.914-1.051-1.0510.0000.0000.0000.000
6C193LEU00.003-0.0116.5322.1742.1740.0000.0000.0000.000
7C194CYS0-0.055-0.0329.6872.3062.3060.0000.0000.0000.000
8C195GLY0-0.0370.00011.8341.5701.5700.0000.0000.0000.000
9C196GLN00.0460.02313.206-0.302-0.3020.0000.0000.0000.000
10C197TYR0-0.018-0.0199.799-0.436-0.4360.0000.0000.0000.000
11C198PRO0-0.0180.00913.6700.5280.5280.0000.0000.0000.000
12C199VAL00.0730.04014.092-0.933-0.9330.0000.0000.0000.000
13C200LYS10.9930.96615.31411.54411.5440.0000.0000.0000.000
14C201SER0-0.032-0.03815.4370.4030.4030.0000.0000.0000.000
15C202GLU-1-0.805-0.88815.060-16.294-16.2940.0000.0000.0000.000
16C203GLY0-0.0080.00617.585-0.068-0.0680.0000.0000.0000.000
17C204LYS10.8280.91413.15815.78115.7810.0000.0000.0000.000
18C205GLU-1-0.886-0.94816.415-12.943-12.9430.0000.0000.0000.000
19C206LEU0-0.0230.02010.870-0.266-0.2660.0000.0000.0000.000
20C207LYS10.8990.94814.88712.40912.4090.0000.0000.0000.000
21C208ILE0-0.018-0.00816.697-0.315-0.3150.0000.0000.0000.000
22C209VAL0-0.022-0.00618.6590.5620.5620.0000.0000.0000.000
23C210VAL00.0000.00420.6070.5650.5650.0000.0000.0000.000
24C211GLN00.0430.02020.582-0.814-0.8140.0000.0000.0000.000
25C212PRO00.0110.01919.8280.2570.2570.0000.0000.0000.000
26C213GLU-1-0.745-0.87721.953-11.890-11.8900.0000.0000.0000.000
27C214THR0-0.003-0.01424.457-0.327-0.3270.0000.0000.0000.000
28C215GLN0-0.061-0.05226.3770.2110.2110.0000.0000.0000.000
29C216HIS0-0.0170.00622.154-0.312-0.3120.0000.0000.0000.000
30C217ARG10.8870.96524.52110.38910.3890.0000.0000.0000.000
31C218ALA00.0100.00922.257-0.232-0.2320.0000.0000.0000.000
32C219ARG10.8570.97118.89415.48015.4800.0000.0000.0000.000
33C220TYR00.0340.00922.470-0.513-0.5130.0000.0000.0000.000
34C221LEU00.0470.00619.514-0.025-0.0250.0000.0000.0000.000
35C222THR00.000-0.00822.466-0.011-0.0110.0000.0000.0000.000
36C223GLU-1-0.807-0.86525.083-11.053-11.0530.0000.0000.0000.000
37C224GLY00.0440.01924.311-0.526-0.5260.0000.0000.0000.000
38C225SER00.000-0.01721.150-0.319-0.3190.0000.0000.0000.000
39C226ARG10.8640.87322.27811.93311.9330.0000.0000.0000.000
40C227GLY0-0.0050.01622.5030.3310.3310.0000.0000.0000.000
41C228SER00.0130.00519.510-0.623-0.6230.0000.0000.0000.000
42C229VAL0-0.071-0.02419.0180.6650.6650.0000.0000.0000.000
43C230LYS10.9941.00420.66411.57511.5750.0000.0000.0000.000
44C231ASP-1-0.730-0.79522.638-11.659-11.6590.0000.0000.0000.000
45C232ARG10.9120.93124.28311.38811.3880.0000.0000.0000.000
46C233THR0-0.056-0.07627.5790.3070.3070.0000.0000.0000.000
47C234GLN0-0.112-0.06127.6600.1540.1540.0000.0000.0000.000
48C235GLN00.0420.01528.504-0.230-0.2300.0000.0000.0000.000
49C236GLY0-0.0110.00124.9890.0280.0280.0000.0000.0000.000
50C237PHE0-0.032-0.01719.847-0.126-0.1260.0000.0000.0000.000
51C238PRO0-0.0180.00917.7230.2210.2210.0000.0000.0000.000
52C239THR0-0.012-0.00817.974-0.439-0.4390.0000.0000.0000.000
53C240VAL0-0.0350.00013.0780.4000.4000.0000.0000.0000.000
54C241LYS10.9100.96016.10712.95412.9540.0000.0000.0000.000
55C242LEU0-0.046-0.01911.018-0.372-0.3720.0000.0000.0000.000
56C243GLU-1-0.849-0.92515.148-11.962-11.9620.0000.0000.0000.000
57C244GLY00.0430.00916.745-0.374-0.3740.0000.0000.0000.000
58C245HIS00.026-0.01111.654-0.035-0.0350.0000.0000.0000.000
59C246ASN0-0.025-0.00915.821-0.054-0.0540.0000.0000.0000.000
60C247GLU-1-0.857-0.90212.633-15.056-15.0560.0000.0000.0000.000
61C248PRO00.0380.02110.732-0.387-0.3870.0000.0000.0000.000
62C249VAL0-0.029-0.0186.549-0.869-0.8690.0000.0000.0000.000
63C250VAL0-0.017-0.0082.682-0.2210.5560.161-0.234-0.7030.000
64C251LEU0-0.015-0.0045.770-0.296-0.2960.0000.0000.0000.000
65C252GLN0-0.041-0.0232.0215.6481.9168.940-1.841-3.367-0.007
66C253VAL00.0430.0116.2223.2733.2730.0000.0000.0000.000
67C254PHE00.0410.0188.449-1.935-1.9350.0000.0000.0000.000
68C255VAL00.0450.03910.8061.5141.5140.0000.0000.0000.000
69C256GLY00.0400.01714.348-0.690-0.6900.0000.0000.0000.000
70C257ASN0-0.046-0.04115.6310.8400.8400.0000.0000.0000.000
71C258ASP-1-0.814-0.92319.167-12.927-12.9270.0000.0000.0000.000
72C259SER0-0.034-0.01121.9000.3670.3670.0000.0000.0000.000
73C260GLY00.0320.02821.968-0.139-0.1390.0000.0000.0000.000
74C261ARG10.8630.90917.82214.74914.7490.0000.0000.0000.000
75C262VAL00.0420.01213.4960.1660.1660.0000.0000.0000.000
76C263LYS10.9500.98014.97014.84214.8420.0000.0000.0000.000
77C264PRO00.0430.04612.0921.0121.0120.0000.0000.0000.000
78C265HIS0-0.046-0.02414.1800.6840.6840.0000.0000.0000.000
79C266GLY00.0290.01816.604-0.690-0.6900.0000.0000.0000.000
80C267PHE0-0.053-0.04119.0340.2170.2170.0000.0000.0000.000
81C268TYR0-0.0010.00018.3340.8050.8050.0000.0000.0000.000
82C269GLN00.0800.06312.860-1.765-1.7650.0000.0000.0000.000
83C270ALA00.0020.00511.7191.2001.2000.0000.0000.0000.000
84C271CYS00.0070.00712.980-0.370-0.3700.0000.0000.0000.000
85C272ARG10.9641.00111.93323.14523.1450.0000.0000.0000.000
86C273VAL0-0.065-0.03113.9611.0531.0530.0000.0000.0000.000
87C274THR0-0.051-0.02416.4760.0020.0020.0000.0000.0000.000
88C275GLY00.0820.02218.6020.6840.6840.0000.0000.0000.000
89C276ARG10.9340.96821.17212.05912.0590.0000.0000.0000.000
90C277ASN0-0.013-0.00822.4430.2860.2860.0000.0000.0000.000
91C278THR0-0.0030.01518.6610.0030.0030.0000.0000.0000.000
92C279THR0-0.010-0.01114.163-0.078-0.0780.0000.0000.0000.000
93C280PRO0-0.052-0.01113.769-0.711-0.7110.0000.0000.0000.000
94C281CYS0-0.016-0.03910.199-0.483-0.4830.0000.0000.0000.000
95C282LYS10.9040.9595.12544.99944.9990.0000.0000.0000.000
96C283GLU-1-0.828-0.9357.815-25.182-25.1820.0000.0000.0000.000
97C284VAL0-0.054-0.0102.345-3.787-3.1471.642-0.546-1.736-0.007
98C285ASP-1-0.867-0.9345.081-30.427-30.365-0.001-0.003-0.0580.000
99C286ILE0-0.013-0.0252.759-10.393-9.4700.196-0.269-0.850-0.003
100C287GLU-1-0.840-0.9226.058-25.618-25.6180.0000.0000.0000.000
101C288GLY0-0.0160.0068.9823.4363.4360.0000.0000.0000.000
102C289THR0-0.083-0.0389.3072.9912.9910.0000.0000.0000.000
103C290THR00.026-0.0058.708-3.265-3.2650.0000.0000.0000.000
104C291VAL0-0.062-0.0414.9381.9471.9470.0000.0000.0000.000
105C292ILE0-0.004-0.0086.591-2.771-2.7710.0000.0000.0000.000
106C293GLU-1-0.913-0.9702.277-90.870-85.0904.295-4.727-5.347-0.064
107C294VAL00.0400.0176.6322.0762.0760.0000.0000.0000.000
108C295GLY00.020-0.0027.912-2.204-2.2040.0000.0000.0000.000
109C296LEU0-0.0290.0049.7321.5711.5710.0000.0000.0000.000
110C297ASP-1-0.723-0.84911.488-17.243-17.2430.0000.0000.0000.000
111C298PRO00.0310.02714.1710.6220.6220.0000.0000.0000.000
112C299SER0-0.073-0.06117.0330.8430.8430.0000.0000.0000.000
113C300ASN0-0.039-0.02417.9180.8790.8790.0000.0000.0000.000
114C301ASN0-0.022-0.01619.537-0.194-0.1940.0000.0000.0000.000
115C302MET0-0.019-0.00812.2810.0280.0280.0000.0000.0000.000
116C303THR0-0.036-0.03416.324-0.229-0.2290.0000.0000.0000.000
117C304LEU00.0070.00613.146-0.199-0.1990.0000.0000.0000.000
118C305ALA00.031-0.00716.391-0.021-0.0210.0000.0000.0000.000
119C306VAL0-0.026-0.02513.512-0.321-0.3210.0000.0000.0000.000
120C307ASP-1-0.756-0.86415.953-15.483-15.4830.0000.0000.0000.000
121C308CYS0-0.0280.00413.631-0.141-0.1410.0000.0000.0000.000
122C309VAL00.005-0.00612.920-1.246-1.2460.0000.0000.0000.000
123C310GLY00.0440.02015.6891.2971.2970.0000.0000.0000.000
124C311ILE0-0.017-0.01616.317-1.164-1.1640.0000.0000.0000.000
125C312LEU0-0.014-0.00716.9871.0111.0110.0000.0000.0000.000
126C313LYS10.8480.93118.93212.53712.5370.0000.0000.0000.000
127C314LEU00.0130.00317.6570.0600.0600.0000.0000.0000.000
128C315ARG10.8440.89021.43812.52812.5280.0000.0000.0000.000
129C316ASN00.029-0.00224.635-0.533-0.5330.0000.0000.0000.000
130C317ALA00.0610.04725.991-0.271-0.2710.0000.0000.0000.000
131C318ASP-1-0.799-0.87523.103-12.819-12.8190.0000.0000.0000.000
132C319VAL0-0.053-0.02821.130-0.363-0.3630.0000.0000.0000.000
133C320GLU-1-0.962-1.01123.117-10.724-10.7240.0000.0000.0000.000
134C321ALA0-0.0280.00226.1270.0610.0610.0000.0000.0000.000
135C322ARG10.9610.99114.73818.45518.4550.0000.0000.0000.000
136C323ILE0-0.050-0.02819.161-0.148-0.1480.0000.0000.0000.000
137C324GLY00.1350.06723.1100.2370.2370.0000.0000.0000.000
138C325ILE0-0.095-0.04924.0680.3280.3280.0000.0000.0000.000
139C326ALA0-0.035-0.01723.6970.0860.0860.0000.0000.0000.000
140C327GLY00.0870.01725.8260.0650.0650.0000.0000.0000.000
141C328SER0-0.021-0.00729.110-0.044-0.0440.0000.0000.0000.000
142C329LYS10.9450.99228.51010.04610.0460.0000.0000.0000.000
143C330LYS10.9450.95221.61213.52413.5240.0000.0000.0000.000
144C331LYS11.0021.03926.4239.9729.9720.0000.0000.0000.000
145C332SER0-0.020-0.00723.7130.1700.1700.0000.0000.0000.000
146C333THR00.022-0.00624.643-0.353-0.3530.0000.0000.0000.000
147C334ARG10.9720.99624.14910.79810.7980.0000.0000.0000.000
148C335ALA0-0.002-0.00718.707-0.303-0.3030.0000.0000.0000.000
149C336ARG10.8660.95117.93115.53215.5320.0000.0000.0000.000
150C337LEU00.0280.02615.077-0.979-0.9790.0000.0000.0000.000
151C338VAL0-0.042-0.03010.8980.9180.9180.0000.0000.0000.000
152C339PHE00.0490.03310.566-1.900-1.9000.0000.0000.0000.000
153C340ARG10.8520.8994.36135.92836.020-0.001-0.006-0.0840.000
154C341VAL00.0300.0306.641-2.594-2.5940.0000.0000.0000.000
155C342ASN0-0.044-0.0352.8750.6901.7050.242-0.494-0.763-0.004
156C343ILE00.0430.0324.744-0.788-0.697-0.001-0.005-0.0850.000
157C344MET00.0290.0167.238-0.995-0.9950.0000.0000.0000.000
158C345ARG10.7850.8578.67718.62818.6280.0000.0000.0000.000
159C346LYS10.9040.95312.43915.66015.6600.0000.0000.0000.000
160C347ASP-1-0.773-0.88315.148-16.243-16.2430.0000.0000.0000.000
161C348GLY00.0360.01012.120-0.696-0.6960.0000.0000.0000.000
162C349SER0-0.0670.00110.792-1.837-1.8370.0000.0000.0000.000
163C350THR00.016-0.0226.286-1.366-1.3660.0000.0000.0000.000
164C351LEU0-0.071-0.0038.8930.0790.0790.0000.0000.0000.000
165C352THR0-0.037-0.0327.185-0.995-0.9950.0000.0000.0000.000
166C353LEU0-0.0250.0109.2351.0281.0280.0000.0000.0000.000
167C354GLN00.039-0.0159.928-3.249-3.2490.0000.0000.0000.000
168C355THR0-0.042-0.01211.6691.3611.3610.0000.0000.0000.000
169C356PRO0-0.008-0.00214.370-0.635-0.6350.0000.0000.0000.000
170C357SER00.0450.02016.1250.4960.4960.0000.0000.0000.000
171C358SER0-0.055-0.03718.8940.3620.3620.0000.0000.0000.000
172C359PRO0-0.038-0.03121.539-0.460-0.4600.0000.0000.0000.000
173C360ILE00.0020.02420.0920.3720.3720.0000.0000.0000.000
174C361LEU0-0.068-0.04123.694-0.268-0.2680.0000.0000.0000.000
175C362CYS00.023-0.00722.220-0.189-0.1890.0000.0000.0000.000
176C363THR0-0.0050.00424.840-0.110-0.1100.0000.0000.0000.000
177C364GLN00.0270.00128.151-0.363-0.3630.0000.0000.0000.000
178C365PRO00.003-0.00729.8340.2150.2150.0000.0000.0000.000
179C366ALA00.0050.00032.8690.0760.0760.0000.0000.0000.000
180C367GLY00.0110.02936.6040.1030.1030.0000.0000.0000.000
181C368VAL00.003-0.00738.2590.0750.0750.0000.0000.0000.000
182C369PRO0-0.026-0.00441.240-0.005-0.0050.0000.0000.0000.000
183C370GLU-1-0.886-0.96144.630-6.925-6.9250.0000.0000.0000.000
184C371ILE00.0000.00847.4440.0340.0340.0000.0000.0000.000
185C372LEU0-0.004-0.00148.7880.0140.0140.0000.0000.0000.000
186C373LYS10.9280.95352.4215.5295.5290.0000.0000.0000.000
187C374LYS10.9080.97156.0435.3915.3910.0000.0000.0000.000
188C375SER0-0.025-0.01658.4540.0260.0260.0000.0000.0000.000
189C376LEU00.0290.04061.8080.0720.0720.0000.0000.0000.000
190C377HIS0-0.030-0.03661.303-0.127-0.1270.0000.0000.0000.000
191C378SER0-0.017-0.00563.9340.0050.0050.0000.0000.0000.000
192C379CYS00.0670.05666.6060.0070.0070.0000.0000.0000.000
193C380SER00.0280.03768.373-0.002-0.0020.0000.0000.0000.000
194C381VAL00.0410.01469.077-0.078-0.0780.0000.0000.0000.000
195C382LYS10.9510.98668.7464.2734.2730.0000.0000.0000.000
196C383GLY0-0.044-0.02366.671-0.051-0.0510.0000.0000.0000.000
197C384GLU-1-0.906-0.97665.747-4.812-4.8120.0000.0000.0000.000
198C385GLU-1-0.986-0.97766.387-4.678-4.6780.0000.0000.0000.000
199C386GLU-1-0.929-0.96562.087-5.137-5.1370.0000.0000.0000.000
200C387VAL0-0.034-0.03059.0920.0330.0330.0000.0000.0000.000
201C388PHE0-0.005-0.00258.217-0.129-0.1290.0000.0000.0000.000
202C389LEU0-0.010-0.00553.7610.0070.0070.0000.0000.0000.000
203C390ILE00.0090.01152.154-0.087-0.0870.0000.0000.0000.000
204C391GLY00.010-0.03549.9500.0440.0440.0000.0000.0000.000
205C392LYS10.8930.95643.8797.0457.0450.0000.0000.0000.000
206C393ASN00.0010.00740.5530.0360.0360.0000.0000.0000.000
207C394PHE0-0.0050.00943.633-0.075-0.0750.0000.0000.0000.000
208C395LEU0-0.018-0.02540.100-0.023-0.0230.0000.0000.0000.000
209C396LYS10.9760.96742.6117.0607.0600.0000.0000.0000.000
210C397GLY0-0.013-0.00743.3000.1210.1210.0000.0000.0000.000
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