FMO DATABASE

FMODB ID: KGM83

Calculation Name: 3C0D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q87HB1

Base Structure: X-ray

Registration Date: 2023-09-23

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-842702.948079
FMO2-HF: Nuclear repulsion	798782.954854
FMO2-HF: Total energy	-43919.993225
FMO2-MP2: Total energy	-44043.659859

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:4:LEU)

Summations of interaction energy for fragment #1(A:4:LEU)

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.
-9.4	-5.718	0.308	-1.816	-2.174	-0.011

Interaction energy analysis for fragmet #1(A:4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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 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	6	LYS	1	0.796	0.884	3.817	0.183	1.811	-0.024	-0.809	-0.795	0.001
4	A	7	VAL	0	-0.004	0.005	6.665	0.263	0.263	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.960	0.965	9.690	0.798	0.798	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.033	-0.008	13.013	0.018	0.018	0.000	0.000	0.000	0.000
7	A	10	CYS	0	-0.045	-0.019	14.724	0.060	0.060	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.000	0.007	17.297	-0.090	-0.090	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.044	0.001	18.705	0.016	0.016	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.931	-0.960	20.316	-0.216	-0.216	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.854	-0.915	21.799	-0.270	-0.270	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.118	-0.077	18.732	0.013	0.013	0.000	0.000	0.000	0.000
13	A	16	MET	0	0.008	0.005	23.424	0.009	0.009	0.000	0.000	0.000	0.000
14	A	17	PRO	0	-0.010	-0.016	25.183	0.001	0.001	0.000	0.000	0.000	0.000
15	A	18	PHE	0	-0.012	-0.013	24.951	0.007	0.007	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.059	-0.027	26.022	0.010	0.010	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.016	0.024	23.705	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.003	0.004	22.026	0.004	0.004	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.028	-0.012	21.399	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.004	-0.003	16.893	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.025	-0.025	18.123	0.033	0.033	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.001	0.009	11.607	-0.057	-0.057	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.870	-0.920	11.628	-0.588	-0.588	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.006	0.006	14.739	0.052	0.052	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.837	-0.898	15.247	-0.089	-0.089	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.857	0.934	18.008	0.130	0.130	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.043	0.022	15.249	0.025	0.025	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.024	-0.009	18.591	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.012	-0.006	15.766	0.001	0.001	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.060	0.015	19.271	0.014	0.014	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.014	0.007	19.910	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.023	0.007	20.492	0.014	0.014	0.000	0.000	0.000	0.000
33	A	36	PRO	0	-0.013	0.000	21.331	0.000	0.000	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.884	-0.943	22.234	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.084	-0.040	19.354	0.020	0.020	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.011	0.013	16.780	0.005	0.005	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.022	-0.021	15.503	0.002	0.002	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.046	-0.011	15.105	0.010	0.010	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.013	0.009	14.164	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.040	0.015	16.140	0.037	0.037	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.016	0.002	18.265	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.796	-0.928	19.712	-0.101	-0.101	0.000	0.000	0.000	0.000
43	A	46	TRP	0	-0.026	-0.016	22.710	0.006	0.006	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.713	-0.828	24.394	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	48	PRO	0	-0.062	-0.019	25.033	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.028	0.026	27.432	0.004	0.004	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.050	0.010	30.886	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.740	0.876	29.630	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.086	0.026	29.360	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.077	-0.037	24.070	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.008	0.000	27.032	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.051	0.051	24.129	0.004	0.004	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.035	-0.013	24.371	0.004	0.004	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.865	0.921	25.630	0.084	0.084	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.018	0.025	27.986	0.006	0.006	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.036	-0.022	28.678	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	60	VAL	0	0.003	0.003	25.677	0.006	0.006	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.013	0.008	28.364	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.947	-0.975	28.408	0.010	0.010	0.000	0.000	0.000	0.000
60	A	63	ILE	0	0.008	0.004	28.900	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	64	ASN	0	-0.049	-0.034	28.562	0.004	0.004	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.000	0.009	28.100	0.010	0.010	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.868	-0.908	23.245	0.067	0.067	0.000	0.000	0.000	0.000
64	A	67	MET	0	0.047	0.032	23.776	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.051	0.004	23.958	0.007	0.007	0.000	0.000	0.000	0.000
66	A	69	VAL	0	-0.024	-0.015	24.105	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.057	0.028	26.860	0.007	0.007	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.028	-0.047	29.342	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.020	-0.010	29.854	0.005	0.005	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.044	-0.012	32.087	0.000	0.000	0.000	0.000	0.000	0.000
71	A	74	TYR	0	-0.045	-0.030	33.868	0.001	0.001	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.798	0.885	33.606	0.025	0.025	0.000	0.000	0.000	0.000
73	A	76	GLN	0	0.072	0.065	30.434	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	77	HIS	0	-0.040	-0.039	29.316	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	78	PHE	0	0.015	-0.001	24.120	0.009	0.009	0.000	0.000	0.000	0.000
76	A	79	SER	0	0.006	-0.038	22.359	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.000	-0.004	20.376	0.003	0.003	0.000	0.000	0.000	0.000
78	A	81	LYS	1	0.882	0.947	14.094	-0.171	-0.171	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.033	-0.021	17.075	0.021	0.021	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.064	0.031	18.729	0.009	0.009	0.000	0.000	0.000	0.000
81	A	84	GLN	0	0.000	-0.009	20.707	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.023	0.005	23.684	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.011	-0.015	27.010	0.009	0.009	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.825	-0.894	29.642	0.027	0.027	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.874	-0.967	30.767	0.042	0.042	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.971	-0.971	28.640	0.089	0.089	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.051	-0.005	27.716	0.011	0.011	0.000	0.000	0.000	0.000
88	A	91	HIS	0	-0.059	-0.033	26.398	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	92	CYS	0	-0.002	-0.004	20.317	0.013	0.013	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.082	-0.019	20.643	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.810	0.878	14.008	0.098	0.098	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.021	0.005	14.547	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	96	TRP	0	-0.002	-0.005	10.701	0.049	0.049	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.931	0.961	4.772	-1.276	-1.209	-0.001	-0.001	-0.064	0.000
95	A	98	VAL	0	0.041	0.016	9.113	-0.254	-0.254	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.050	-0.018	7.999	0.020	0.020	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.027	-0.010	10.849	-0.081	-0.081	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.868	-0.897	10.981	-0.861	-0.861	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.909	-0.945	13.869	-0.303	-0.303	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.007	-0.006	17.463	0.044	0.044	0.000	0.000	0.000	0.000
101	A	104	GLN	0	-0.027	-0.003	13.854	-0.051	-0.051	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.048	0.030	14.079	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	106	CYS	0	-0.040	-0.007	9.725	-0.071	-0.071	0.000	0.000	0.000	0.000
104	A	107	TYR	0	0.030	-0.008	8.199	0.046	0.046	0.000	0.000	0.000	0.000
105	A	108	LEU	0	-0.065	-0.040	4.123	-0.394	-0.228	-0.001	-0.020	-0.145	0.000
106	A	109	ALA	0	0.015	0.011	4.301	0.902	1.029	-0.001	-0.021	-0.105	0.000
107	A	110	LYS	1	0.914	0.937	2.689	-4.356	-2.716	0.336	-0.950	-1.027	-0.012
108	A	111	GLU	-1	-0.830	-0.903	4.347	-3.595	-3.541	-0.001	-0.015	-0.038	0.000
109	A	112	LEU	0	-0.050	-0.003	6.339	0.358	0.358	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LEU)