FMO DATABASE

FMODB ID: QVJMY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-842393.050017
FMO2-HF: Nuclear repulsion	798473.780239
FMO2-HF: Total energy	-43919.269777
FMO2-MP2: Total energy	-44042.992361

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.
-2.794	0.572	0.313	-1.645	-2.033	-0.01

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 : -0.018 / q_NPA : -0.031

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	0.888	0.946	3.817	-0.703	0.699	-0.021	-0.660	-0.720	0.001
4	A	7	VAL	0	-0.011	0.001	6.685	0.343	0.343	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.957	0.960	9.710	0.236	0.236	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.035	-0.005	12.852	0.033	0.033	0.000	0.000	0.000	0.000
7	A	10	CYS	0	-0.039	-0.021	14.738	0.041	0.041	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.027	0.027	17.307	-0.059	-0.059	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.043	0.001	18.911	0.005	0.005	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.954	-0.965	20.323	-0.140	-0.140	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.874	-0.934	21.871	-0.138	-0.138	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.112	-0.074	18.784	0.006	0.006	0.000	0.000	0.000	0.000
13	A	16	MET	0	-0.002	0.002	23.440	0.005	0.005	0.000	0.000	0.000	0.000
14	A	17	PRO	0	-0.011	-0.018	25.199	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	18	PHE	0	-0.003	-0.009	24.970	0.008	0.008	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.056	-0.026	26.042	0.009	0.009	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.016	0.020	23.703	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.000	0.011	21.946	0.011	0.011	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.052	-0.029	21.402	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.025	0.017	17.032	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.022	-0.025	18.130	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.007	0.003	11.670	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.942	-0.969	11.797	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.005	0.007	14.747	0.019	0.019	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.880	-0.928	15.531	-0.091	-0.091	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.857	0.923	18.010	0.060	0.060	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.023	0.025	15.283	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	ALA	0	0.000	-0.001	18.590	0.009	0.009	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.015	-0.011	15.867	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.060	0.015	19.274	0.021	0.021	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.023	0.008	19.929	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.017	0.004	20.505	0.019	0.019	0.000	0.000	0.000	0.000
33	A	36	PRO	0	-0.010	0.002	21.339	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.887	-0.947	22.235	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.087	-0.036	19.249	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.006	0.010	16.786	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.022	-0.019	15.467	0.021	0.021	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.036	-0.009	15.123	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.012	0.009	14.193	0.013	0.013	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.035	0.015	16.130	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.032	-0.022	18.257	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.775	-0.918	19.705	-0.089	-0.089	0.000	0.000	0.000	0.000
43	A	46	TRP	0	-0.030	-0.017	22.706	0.010	0.010	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.678	-0.765	24.385	-0.061	-0.061	0.000	0.000	0.000	0.000
45	A	48	PRO	0	-0.077	-0.036	25.055	0.006	0.006	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.009	0.007	27.421	0.007	0.007	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.071	0.010	30.874	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.742	0.887	29.195	0.038	0.038	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.085	0.021	29.365	0.003	0.003	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.082	-0.035	23.916	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.006	0.006	27.030	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.050	0.043	24.125	0.003	0.003	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.049	-0.021	24.760	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.894	0.936	25.628	0.075	0.075	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.009	0.020	27.979	0.006	0.006	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.031	-0.020	28.672	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.001	0.001	25.775	0.000	0.000	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.002	0.002	28.391	0.005	0.005	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.908	-0.963	28.429	-0.078	-0.078	0.000	0.000	0.000	0.000
60	A	63	ILE	0	-0.033	-0.012	28.918	0.006	0.006	0.000	0.000	0.000	0.000
61	A	64	ASN	0	-0.028	-0.018	28.557	0.000	0.000	0.000	0.000	0.000	0.000
62	A	65	GLY	0	-0.017	-0.006	28.316	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.949	-0.981	23.655	-0.088	-0.088	0.000	0.000	0.000	0.000
64	A	67	MET	0	0.055	0.041	23.874	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.024	-0.019	23.960	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	69	VAL	0	-0.035	-0.002	24.136	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.045	0.019	26.849	0.003	0.003	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.054	-0.085	29.324	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	72	PRO	0	-0.017	-0.024	29.901	0.005	0.005	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.056	-0.016	32.133	0.004	0.004	0.000	0.000	0.000	0.000
71	A	74	TYR	0	-0.066	-0.039	33.882	0.003	0.003	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.887	0.934	33.629	0.048	0.048	0.000	0.000	0.000	0.000
73	A	76	GLN	0	0.070	0.060	30.606	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	77	HIS	0	-0.029	-0.026	29.320	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	78	PHE	0	0.029	0.010	24.043	0.003	0.003	0.000	0.000	0.000	0.000
76	A	79	SER	0	0.038	0.033	22.141	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.019	0.005	20.346	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	81	LYS	1	0.921	0.977	13.301	0.208	0.208	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.040	-0.042	17.088	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.061	0.031	18.710	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	84	GLN	0	-0.012	-0.016	20.691	0.013	0.013	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.029	0.006	23.665	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.007	-0.015	26.993	0.004	0.004	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.823	-0.902	29.623	-0.048	-0.048	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.885	-0.972	30.719	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.953	-0.968	28.656	-0.033	-0.033	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.056	-0.002	27.695	0.000	0.000	0.000	0.000	0.000	0.000
88	A	91	HIS	0	-0.048	-0.025	26.397	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	92	CYS	0	-0.026	-0.016	20.273	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.074	-0.020	20.624	0.002	0.002	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.847	0.913	13.854	0.110	0.110	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.032	0.013	14.379	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	96	TRP	0	-0.003	-0.009	10.585	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.916	0.955	5.600	0.493	0.493	0.000	0.000	0.000	0.000
95	A	98	VAL	0	0.044	0.020	9.109	-0.148	-0.148	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.080	-0.031	8.161	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.046	0.000	10.855	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.927	-0.944	11.099	-0.681	-0.681	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.906	-0.945	13.857	-0.191	-0.191	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.009	-0.003	17.450	0.006	0.006	0.000	0.000	0.000	0.000
101	A	104	GLN	0	-0.036	-0.010	13.811	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.054	0.031	14.075	-0.055	-0.055	0.000	0.000	0.000	0.000
103	A	106	CYS	0	-0.036	-0.007	9.682	0.014	0.014	0.000	0.000	0.000	0.000
104	A	107	TYR	0	0.079	0.031	8.216	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	108	LEU	0	-0.067	-0.042	4.165	-0.208	-0.057	-0.001	-0.018	-0.133	0.000
106	A	109	ALA	0	0.017	0.012	4.295	0.288	0.413	-0.001	-0.018	-0.105	0.000
107	A	110	LYS	1	0.907	0.934	2.689	-4.234	-2.609	0.337	-0.946	-1.016	-0.011
108	A	111	GLU	-1	-0.888	-0.959	4.350	2.944	3.007	-0.001	-0.003	-0.059	0.000
109	A	112	LEU	0	-0.027	0.013	7.051	-0.447	-0.447	0.000	0.000	0.000	0.000

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