FMO DATABASE

FMODB ID: LZ5K9

Calculation Name: 1CM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CM9

Chain ID: A

ChEMBL ID:

UniProt ID: Q98157

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-410154.533005
FMO2-HF: Nuclear repulsion	381986.795689
FMO2-HF: Total energy	-28167.737315
FMO2-MP2: Total energy	-28247.521278

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
1.022	3.106	-0.011	-0.914	-1.159	0.003

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.018

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 ES EX CT+mix DI(MP2)

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].
3	A	9	HIS	0	0.033	0.018	3.681	-0.616	1.317	-0.010	-0.904	-1.019	0.003
4	A	10	ARG	1	0.853	0.934	5.282	0.633	0.784	-0.001	-0.010	-0.140	0.000
5	A	11	PRO	0	0.039	0.031	7.516	0.176	0.176	0.000	0.000	0.000	0.000
6	A	12	ASP	-1	-0.787	-0.907	10.462	-0.366	-0.366	0.000	0.000	0.000	0.000
7	A	13	LYS	1	0.838	0.914	13.981	0.298	0.298	0.000	0.000	0.000	0.000
8	A	14	CYS	0	-0.042	-0.013	17.411	0.008	0.008	0.000	0.000	0.000	0.000
9	A	15	CYS	0	0.017	0.028	19.375	0.015	0.015	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.061	0.037	20.316	0.013	0.013	0.000	0.000	0.000	0.000
11	A	17	GLY	0	0.016	0.013	23.857	0.015	0.015	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.044	-0.049	26.827	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	19	GLN	0	0.014	0.011	29.582	0.013	0.013	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.967	0.978	32.030	0.080	0.080	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.902	0.955	34.206	0.071	0.071	0.000	0.000	0.000	0.000
16	A	22	PRO	0	0.056	0.015	36.105	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.034	-0.011	32.221	0.002	0.002	0.000	0.000	0.000	0.000
18	A	24	PRO	0	0.046	0.028	36.754	0.000	0.000	0.000	0.000	0.000	0.000
19	A	25	GLN	0	0.056	-0.002	36.862	0.002	0.002	0.000	0.000	0.000	0.000
20	A	26	VAL	0	0.070	0.035	36.731	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.014	-0.006	35.275	0.003	0.003	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.069	-0.014	31.164	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	29	SER	0	-0.005	-0.004	30.007	0.010	0.010	0.000	0.000	0.000	0.000
24	A	30	SER	0	-0.008	-0.009	26.762	0.007	0.007	0.000	0.000	0.000	0.000
25	A	31	TRP	0	0.015	0.011	27.197	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	32	TYR	0	0.046	0.037	19.782	0.016	0.016	0.000	0.000	0.000	0.000
27	A	33	PRO	0	-0.002	-0.001	22.935	0.001	0.001	0.000	0.000	0.000	0.000
28	A	34	THR	0	0.002	0.001	20.291	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	35	SER	0	0.045	0.029	16.477	0.042	0.042	0.000	0.000	0.000	0.000
30	A	36	GLN	0	-0.019	-0.032	19.115	0.023	0.023	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.029	0.024	15.334	0.013	0.013	0.000	0.000	0.000	0.000
32	A	39	SER	0	0.012	0.008	19.855	0.029	0.029	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.895	0.949	22.212	0.208	0.208	0.000	0.000	0.000	0.000
34	A	41	PRO	0	0.046	0.044	23.780	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	42	GLY	0	0.036	0.014	24.633	0.016	0.016	0.000	0.000	0.000	0.000
36	A	43	VAL	0	-0.031	-0.014	25.321	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	44	ILE	0	0.008	-0.001	21.249	0.004	0.004	0.000	0.000	0.000	0.000
38	A	45	PHE	0	0.011	0.010	25.419	0.005	0.005	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.008	-0.006	23.895	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	47	THR	0	0.012	-0.023	27.559	0.011	0.011	0.000	0.000	0.000	0.000
41	A	48	LYS	1	0.881	0.928	29.755	0.035	0.035	0.000	0.000	0.000	0.000
42	A	49	ARG	1	0.970	0.991	31.226	0.030	0.030	0.000	0.000	0.000	0.000
43	A	50	GLY	0	0.044	0.026	27.073	0.003	0.003	0.000	0.000	0.000	0.000
44	A	51	ARG	1	0.903	0.951	25.461	0.033	0.033	0.000	0.000	0.000	0.000
45	A	52	GLN	0	0.051	0.039	20.792	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	53	VAL	0	-0.016	-0.015	25.194	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	55	ALA	0	-0.016	-0.015	26.559	0.013	0.013	0.000	0.000	0.000	0.000
48	A	56	ASP	-1	-0.729	-0.818	28.421	-0.135	-0.135	0.000	0.000	0.000	0.000
49	A	57	LYS	1	0.938	0.946	26.106	0.181	0.181	0.000	0.000	0.000	0.000
50	A	58	SER	0	-0.008	-0.023	31.351	0.008	0.008	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.861	0.907	34.193	0.112	0.112	0.000	0.000	0.000	0.000
52	A	60	ASP	-1	-0.787	-0.898	36.000	-0.077	-0.077	0.000	0.000	0.000	0.000
53	A	61	TRP	0	0.031	0.025	33.953	0.002	0.002	0.000	0.000	0.000	0.000
54	A	62	VAL	0	0.006	0.008	31.920	0.002	0.002	0.000	0.000	0.000	0.000
55	A	63	LYS	1	0.885	0.933	34.070	0.085	0.085	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.964	0.982	35.495	0.059	0.059	0.000	0.000	0.000	0.000
57	A	65	LEU	0	-0.032	-0.008	34.065	0.003	0.003	0.000	0.000	0.000	0.000
58	A	66	MET	0	-0.066	-0.033	30.078	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	67	GLN	0	-0.016	-0.004	33.122	0.002	0.002	0.000	0.000	0.000	0.000
60	A	68	GLN	0	0.006	0.022	36.234	0.004	0.004	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.043	-0.001	32.285	0.004	0.004	0.000	0.000	0.000	0.000
62	A	70	PRO	0	0.037	0.027	30.555	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	71	VAL	0	0.037	0.005	25.360	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	72	THR	0	-0.042	-0.041	23.256	0.014	0.014	0.000	0.000	0.000	0.000
65	A	73	ALA	0	0.047	0.035	23.732	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	74	ARG	1	0.949	0.981	19.093	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)