FMO DATABASE

FMODB ID: MVL7Z

Calculation Name: 1CDC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CDC

Chain ID: B

ChEMBL ID:

UniProt ID: P08921

Base Structure: X-ray

Registration Date: 2023-06-26

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-568766.958216
FMO2-HF: Nuclear repulsion	531250.015689
FMO2-HF: Total energy	-37516.942527
FMO2-MP2: Total energy	-37627.044922

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(B:4:GLY)

Summations of interaction energy for fragment #1(B:4:GLY)

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.
1.613	2.862	-0.005	-0.56	-0.683	0.001

Interaction energy analysis for fragmet #1(B:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.008

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

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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	B	6	VAL	0	-0.007	0.010	3.864	2.032	3.064	-0.011	-0.498	-0.523	0.001
4	B	7	TRP	0	0.025	0.009	6.433	-0.478	-0.478	0.000	0.000	0.000	0.000
5	B	8	GLY	0	0.023	0.003	10.193	0.075	0.075	0.000	0.000	0.000	0.000
6	B	9	ALA	0	-0.002	0.016	13.397	-0.030	-0.030	0.000	0.000	0.000	0.000
7	B	10	LEU	0	0.056	0.008	17.180	-0.016	-0.016	0.000	0.000	0.000	0.000
8	B	11	GLY	0	-0.009	0.001	19.388	0.018	0.018	0.000	0.000	0.000	0.000
9	B	12	HIS	0	-0.057	-0.020	18.209	0.020	0.020	0.000	0.000	0.000	0.000
10	B	13	GLY	0	0.007	0.010	17.276	-0.023	-0.023	0.000	0.000	0.000	0.000
11	B	14	ILE	0	-0.022	-0.021	10.565	0.031	0.031	0.000	0.000	0.000	0.000
12	B	15	ASN	0	0.009	0.012	11.839	-0.070	-0.070	0.000	0.000	0.000	0.000
13	B	16	LEU	0	0.004	0.002	7.675	0.085	0.085	0.000	0.000	0.000	0.000
14	B	17	ASN	0	-0.004	-0.014	8.153	-0.119	-0.119	0.000	0.000	0.000	0.000
15	B	18	ILE	0	0.014	0.017	6.219	-0.078	-0.078	0.000	0.000	0.000	0.000
16	B	19	PRO	0	-0.015	-0.004	3.533	0.049	0.266	0.006	-0.062	-0.160	0.000
17	B	20	ASN	0	-0.038	-0.032	6.204	-0.052	-0.052	0.000	0.000	0.000	0.000
18	B	21	PHE	0	0.037	0.018	9.151	-0.067	-0.067	0.000	0.000	0.000	0.000
19	B	22	GLN	0	0.003	0.001	11.595	0.065	0.065	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.045	0.001	14.955	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	24	THR	0	0.010	-0.024	17.421	0.018	0.018	0.000	0.000	0.000	0.000
22	B	25	ASP	-1	-0.862	-0.949	20.421	-0.027	-0.027	0.000	0.000	0.000	0.000
23	B	26	ASP	-1	-0.880	-0.902	20.484	-0.041	-0.041	0.000	0.000	0.000	0.000
24	B	27	ILE	0	-0.025	-0.008	16.789	-0.016	-0.016	0.000	0.000	0.000	0.000
25	B	28	ASP	-1	-0.743	-0.870	19.884	-0.064	-0.064	0.000	0.000	0.000	0.000
26	B	29	GLU	-1	-0.874	-0.920	18.740	-0.159	-0.159	0.000	0.000	0.000	0.000
27	B	30	VAL	0	-0.017	0.003	13.413	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	31	ARG	1	0.836	0.902	14.589	0.236	0.236	0.000	0.000	0.000	0.000
29	B	32	TRP	0	0.031	0.023	8.305	-0.082	-0.082	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.773	-0.861	13.060	-0.253	-0.253	0.000	0.000	0.000	0.000
31	B	34	ARG	1	0.937	0.970	12.591	0.218	0.218	0.000	0.000	0.000	0.000
32	B	35	GLY	0	0.036	0.020	13.670	0.046	0.046	0.000	0.000	0.000	0.000
33	B	36	SER	0	0.033	0.015	15.479	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	37	THR	0	-0.065	-0.042	17.737	0.039	0.039	0.000	0.000	0.000	0.000
35	B	38	LEU	0	-0.004	0.015	17.334	-0.043	-0.043	0.000	0.000	0.000	0.000
36	B	39	VAL	0	-0.070	-0.035	15.618	0.017	0.017	0.000	0.000	0.000	0.000
37	B	40	ALA	0	0.014	0.001	16.021	0.028	0.028	0.000	0.000	0.000	0.000
38	B	41	GLU	-1	-0.815	-0.899	16.916	-0.188	-0.188	0.000	0.000	0.000	0.000
39	B	42	PHE	0	-0.031	-0.001	17.845	0.019	0.019	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.816	0.875	19.686	0.133	0.133	0.000	0.000	0.000	0.000
41	B	44	ARG	1	0.831	0.924	21.415	0.055	0.055	0.000	0.000	0.000	0.000
42	B	45	LYS	1	0.782	0.865	24.541	0.068	0.068	0.000	0.000	0.000	0.000
43	B	46	MET	0	0.045	0.026	27.004	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.868	0.935	29.503	0.060	0.060	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.069	0.031	28.291	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	49	PHE	0	0.041	0.021	25.896	0.007	0.007	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.010	-0.017	27.992	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	51	LYS	1	0.964	1.002	26.453	0.077	0.077	0.000	0.000	0.000	0.000
49	B	52	SER	0	0.050	0.013	29.956	0.004	0.004	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.051	0.021	33.684	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	54	ALA	0	0.023	0.029	35.695	0.001	0.001	0.000	0.000	0.000	0.000
52	B	55	PHE	0	0.027	0.023	32.607	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	56	GLU	-1	-0.840	-0.930	35.343	-0.047	-0.047	0.000	0.000	0.000	0.000
54	B	57	ILE	0	-0.012	0.020	31.460	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	58	LEU	0	0.011	0.001	34.373	0.004	0.004	0.000	0.000	0.000	0.000
56	B	59	ALA	0	-0.021	-0.021	35.712	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	60	ASN	0	-0.051	-0.044	36.738	0.000	0.000	0.000	0.000	0.000	0.000
58	B	61	GLY	0	-0.005	-0.002	32.750	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	62	ASP	-1	-0.859	-0.897	32.183	-0.078	-0.078	0.000	0.000	0.000	0.000
60	B	63	LEU	0	-0.026	-0.021	30.071	0.002	0.002	0.000	0.000	0.000	0.000
61	B	64	LYS	1	0.826	0.903	33.713	0.051	0.051	0.000	0.000	0.000	0.000
62	B	65	ILE	0	0.014	-0.002	33.355	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.788	0.888	37.011	0.050	0.050	0.000	0.000	0.000	0.000
64	B	67	ASN	0	-0.025	-0.019	39.646	0.004	0.004	0.000	0.000	0.000	0.000
65	B	68	LEU	0	-0.004	0.017	36.945	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	69	THR	0	-0.046	-0.041	36.769	0.004	0.004	0.000	0.000	0.000	0.000
67	B	70	ARG	1	0.838	0.843	37.316	0.031	0.031	0.000	0.000	0.000	0.000
68	B	71	ASP	-1	-0.928	-0.944	32.417	-0.053	-0.053	0.000	0.000	0.000	0.000
69	B	72	ASP	-1	-0.850	-0.892	32.288	-0.057	-0.057	0.000	0.000	0.000	0.000
70	B	73	SER	0	-0.033	-0.013	33.073	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.045	0.029	29.992	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	75	THR	0	-0.069	-0.052	26.245	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.067	-0.035	26.459	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	77	ASN	0	-0.016	-0.021	22.226	0.006	0.006	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.000	0.004	24.676	0.004	0.004	0.000	0.000	0.000	0.000
76	B	79	THR	0	-0.014	-0.011	20.840	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	80	VAL	0	-0.001	0.005	24.251	0.010	0.010	0.000	0.000	0.000	0.000
78	B	81	TYR	0	-0.047	-0.055	18.887	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	82	SER	0	0.024	0.008	25.463	0.009	0.009	0.000	0.000	0.000	0.000
80	B	83	THR	0	0.001	-0.022	26.557	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	84	ASN	0	0.016	0.033	26.355	0.003	0.003	0.000	0.000	0.000	0.000
82	B	85	GLY	0	0.053	0.038	22.484	-0.009	-0.009	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.031	-0.020	21.941	-0.022	-0.022	0.000	0.000	0.000	0.000
84	B	87	ARG	1	0.813	0.877	16.058	0.301	0.301	0.000	0.000	0.000	0.000
85	B	88	ILE	0	-0.035	-0.016	22.712	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.016	-0.002	25.339	0.006	0.006	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.815	-0.909	20.212	-0.223	-0.223	0.000	0.000	0.000	0.000
88	B	91	LYS	1	0.857	0.926	23.782	0.147	0.147	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.047	0.028	24.891	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	93	LEU	0	-0.009	0.003	26.794	0.005	0.005	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.787	-0.883	29.570	-0.080	-0.080	0.000	0.000	0.000	0.000
92	B	95	LEU	0	-0.026	0.005	31.516	0.005	0.005	0.000	0.000	0.000	0.000
93	B	96	ARG	1	0.851	0.902	33.146	0.067	0.067	0.000	0.000	0.000	0.000
94	B	97	ILE	0	0.025	0.012	36.477	0.000	0.000	0.000	0.000	0.000	0.000
95	B	98	LEU	0	-0.035	-0.016	39.546	0.001	0.001	0.000	0.000	0.000	0.000
96	B	99	GLU	-1	-0.793	-0.843	42.180	-0.034	-0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:GLY)