FMO DATABASE

FMODB ID: 94R62

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

Total energy (hartree)

FMO2-HF: Electronic energy	-568592.230143
FMO2-HF: Nuclear repulsion	531075.566927
FMO2-HF: Total energy	-37516.663216
FMO2-MP2: Total energy	-37626.715535

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.
1.856	2.802	-0.011	-0.37	-0.566	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 : 0.020 / q_NPA : 0.002

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	-0.002	0.009	3.833	2.041	2.898	-0.010	-0.356	-0.492	0.001
4	B	7	TRP	0	0.012	0.003	6.130	-0.376	-0.376	0.000	0.000	0.000	0.000
5	B	8	GLY	0	0.029	0.016	9.796	0.051	0.051	0.000	0.000	0.000	0.000
6	B	9	ALA	0	-0.005	0.002	12.799	0.001	0.001	0.000	0.000	0.000	0.000
7	B	10	LEU	0	0.030	-0.007	16.517	-0.019	-0.019	0.000	0.000	0.000	0.000
8	B	11	GLY	0	0.016	0.013	18.971	0.021	0.021	0.000	0.000	0.000	0.000
9	B	12	HIS	0	-0.063	-0.025	17.813	0.024	0.024	0.000	0.000	0.000	0.000
10	B	13	GLY	0	-0.001	0.015	17.318	-0.025	-0.025	0.000	0.000	0.000	0.000
11	B	14	ILE	0	-0.011	-0.010	10.364	0.027	0.027	0.000	0.000	0.000	0.000
12	B	15	ASN	0	0.004	0.003	11.933	-0.037	-0.037	0.000	0.000	0.000	0.000
13	B	16	LEU	0	-0.001	0.001	7.768	0.009	0.009	0.000	0.000	0.000	0.000
14	B	17	ASN	0	0.000	-0.013	7.642	0.021	0.021	0.000	0.000	0.000	0.000
15	B	18	ILE	0	0.012	0.014	6.203	-0.292	-0.292	0.000	0.000	0.000	0.000
16	B	19	PRO	0	0.004	0.008	4.188	0.140	0.229	-0.001	-0.014	-0.074	0.000
17	B	20	ASN	0	-0.040	-0.027	6.592	0.058	0.058	0.000	0.000	0.000	0.000
18	B	21	PHE	0	0.028	0.002	9.572	-0.035	-0.035	0.000	0.000	0.000	0.000
19	B	22	GLN	0	0.012	0.011	11.976	0.031	0.031	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.022	0.006	15.315	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	24	THR	0	0.004	-0.025	17.436	0.018	0.018	0.000	0.000	0.000	0.000
22	B	25	ASP	-1	-0.864	-0.947	20.495	-0.058	-0.058	0.000	0.000	0.000	0.000
23	B	26	ASP	-1	-0.928	-0.927	20.964	-0.069	-0.069	0.000	0.000	0.000	0.000
24	B	27	ILE	0	-0.018	0.010	17.291	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	28	ASP	-1	-0.735	-0.866	20.381	-0.086	-0.086	0.000	0.000	0.000	0.000
26	B	29	GLU	-1	-0.857	-0.916	19.067	-0.176	-0.176	0.000	0.000	0.000	0.000
27	B	30	VAL	0	-0.013	0.008	13.693	-0.011	-0.011	0.000	0.000	0.000	0.000
28	B	31	ARG	1	0.859	0.928	15.209	0.249	0.249	0.000	0.000	0.000	0.000
29	B	32	TRP	0	0.013	0.015	8.391	-0.081	-0.081	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.785	-0.882	12.745	-0.261	-0.261	0.000	0.000	0.000	0.000
31	B	34	ARG	1	0.960	0.982	12.180	0.266	0.266	0.000	0.000	0.000	0.000
32	B	35	GLY	0	0.015	0.008	13.152	0.056	0.056	0.000	0.000	0.000	0.000
33	B	36	SER	0	0.017	0.004	15.015	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	37	THR	0	-0.047	-0.019	17.458	0.037	0.037	0.000	0.000	0.000	0.000
35	B	38	LEU	0	-0.005	0.006	17.065	-0.046	-0.046	0.000	0.000	0.000	0.000
36	B	39	VAL	0	-0.068	-0.034	15.463	0.017	0.017	0.000	0.000	0.000	0.000
37	B	40	ALA	0	0.015	0.000	16.645	0.028	0.028	0.000	0.000	0.000	0.000
38	B	41	GLU	-1	-0.822	-0.909	17.434	-0.211	-0.211	0.000	0.000	0.000	0.000
39	B	42	PHE	0	-0.023	0.010	18.144	0.017	0.017	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.823	0.877	19.812	0.157	0.157	0.000	0.000	0.000	0.000
41	B	44	ARG	1	0.831	0.911	21.810	0.090	0.090	0.000	0.000	0.000	0.000
42	B	45	LYS	1	0.770	0.863	24.727	0.090	0.090	0.000	0.000	0.000	0.000
43	B	46	MET	0	0.035	0.017	27.433	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.857	0.930	29.912	0.070	0.070	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.089	0.042	28.816	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	49	PHE	0	0.032	0.017	26.319	0.008	0.008	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.014	-0.018	28.345	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	51	LYS	1	0.953	0.999	26.344	0.078	0.078	0.000	0.000	0.000	0.000
49	B	52	SER	0	0.053	0.012	29.944	0.004	0.004	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.061	0.031	33.675	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	54	ALA	0	0.028	0.019	35.288	0.002	0.002	0.000	0.000	0.000	0.000
52	B	55	PHE	0	0.018	0.016	32.400	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	56	GLU	-1	-0.865	-0.931	35.389	-0.051	-0.051	0.000	0.000	0.000	0.000
54	B	57	ILE	0	-0.008	0.015	31.144	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	58	LEU	0	0.006	0.002	34.381	0.005	0.005	0.000	0.000	0.000	0.000
56	B	59	ALA	0	-0.002	-0.007	35.647	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	60	ASN	0	-0.066	-0.061	36.809	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	61	GLY	0	-0.014	-0.007	32.849	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	62	ASP	-1	-0.859	-0.890	32.142	-0.078	-0.078	0.000	0.000	0.000	0.000
60	B	63	LEU	0	-0.020	-0.019	30.372	0.001	0.001	0.000	0.000	0.000	0.000
61	B	64	LYS	1	0.841	0.910	33.887	0.055	0.055	0.000	0.000	0.000	0.000
62	B	65	ILE	0	0.029	0.005	33.612	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.807	0.893	36.974	0.052	0.052	0.000	0.000	0.000	0.000
64	B	67	ASN	0	-0.016	-0.015	39.670	0.003	0.003	0.000	0.000	0.000	0.000
65	B	68	LEU	0	-0.014	0.000	37.111	0.000	0.000	0.000	0.000	0.000	0.000
66	B	69	THR	0	-0.041	-0.031	36.806	0.004	0.004	0.000	0.000	0.000	0.000
67	B	70	ARG	1	0.835	0.852	37.537	0.026	0.026	0.000	0.000	0.000	0.000
68	B	71	ASP	-1	-0.953	-0.977	32.657	-0.046	-0.046	0.000	0.000	0.000	0.000
69	B	72	ASP	-1	-0.857	-0.887	32.557	-0.055	-0.055	0.000	0.000	0.000	0.000
70	B	73	SER	0	-0.041	0.000	32.996	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.068	0.033	29.905	0.000	0.000	0.000	0.000	0.000	0.000
72	B	75	THR	0	-0.064	-0.044	26.092	0.000	0.000	0.000	0.000	0.000	0.000
73	B	76	TYR	0	-0.048	-0.025	26.874	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	77	ASN	0	-0.010	-0.023	22.491	0.008	0.008	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.014	0.019	24.903	0.000	0.000	0.000	0.000	0.000	0.000
76	B	79	THR	0	0.005	-0.008	20.703	0.000	0.000	0.000	0.000	0.000	0.000
77	B	80	VAL	0	0.006	0.013	24.039	0.006	0.006	0.000	0.000	0.000	0.000
78	B	81	TYR	0	-0.059	-0.066	18.543	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	82	SER	0	0.019	0.019	25.209	0.009	0.009	0.000	0.000	0.000	0.000
80	B	83	THR	0	0.045	-0.004	26.480	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	84	ASN	0	-0.027	0.006	26.341	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	85	GLY	0	0.068	0.048	22.473	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.056	-0.038	21.717	-0.024	-0.024	0.000	0.000	0.000	0.000
84	B	87	ARG	1	0.836	0.906	16.276	0.293	0.293	0.000	0.000	0.000	0.000
85	B	88	ILE	0	-0.039	-0.025	22.847	0.001	0.001	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.034	-0.013	25.372	0.007	0.007	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.812	-0.911	20.165	-0.210	-0.210	0.000	0.000	0.000	0.000
88	B	91	LYS	1	0.853	0.927	23.791	0.137	0.137	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.048	0.028	24.930	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	93	LEU	0	-0.022	-0.012	26.816	0.005	0.005	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.825	-0.893	29.653	-0.065	-0.065	0.000	0.000	0.000	0.000
92	B	95	LEU	0	-0.035	-0.006	31.652	0.003	0.003	0.000	0.000	0.000	0.000
93	B	96	ARG	1	0.871	0.913	33.863	0.055	0.055	0.000	0.000	0.000	0.000
94	B	97	ILE	0	0.034	0.015	36.743	0.000	0.000	0.000	0.000	0.000	0.000
95	B	98	LEU	0	-0.031	-0.011	39.805	0.002	0.002	0.000	0.000	0.000	0.000
96	B	99	GLU	-1	-0.796	-0.849	42.406	-0.030	-0.030	0.000	0.000	0.000	0.000

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