FMO DATABASE

FMODB ID: 5J54Z

Calculation Name: 3CPK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CPK

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W7N7

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	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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-895478.880286
FMO2-HF: Nuclear repulsion	852072.58331
FMO2-HF: Total energy	-43406.296976
FMO2-MP2: Total energy	-43533.670671

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:PRO)

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

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.
-1.808	0.98	-0.02	-1.341	-1.427	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.019

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].
3	A	9	THR	0	-0.030	-0.007	3.857	-1.033	1.685	-0.019	-1.336	-1.363
4	A	10	ALA	0	0.024	0.016	5.535	-0.841	-0.771	-0.001	-0.005	-0.064
5	A	11	LEU	0	0.027	0.018	9.147	0.008	0.008	0.000	0.000	0.000
6	A	12	ASN	0	-0.048	-0.011	11.503	-0.018	-0.018	0.000	0.000	0.000
7	A	13	THR	0	0.017	0.006	14.515	-0.057	-0.057	0.000	0.000	0.000
8	A	14	VAL	0	-0.037	-0.018	17.446	0.005	0.005	0.000	0.000	0.000
9	A	15	THR	0	-0.042	-0.013	20.347	0.001	0.001	0.000	0.000	0.000
10	A	16	ALA	0	0.014	0.005	22.308	-0.011	-0.011	0.000	0.000	0.000
11	A	17	TYR	0	0.034	0.000	25.916	0.004	0.004	0.000	0.000	0.000
12	A	18	GLY	0	0.020	0.018	28.818	-0.001	-0.001	0.000	0.000	0.000
13	A	19	ASP	-1	-0.848	-0.919	32.361	0.044	0.044	0.000	0.000	0.000
14	A	20	GLY	0	0.002	-0.006	34.479	0.002	0.002	0.000	0.000	0.000
15	A	21	TYR	0	-0.122	-0.064	28.517	0.002	0.002	0.000	0.000	0.000
16	A	22	ILE	0	0.013	0.007	24.569	-0.004	-0.004	0.000	0.000	0.000
17	A	23	GLU	-1	-0.841	-0.911	23.701	0.112	0.112	0.000	0.000	0.000
18	A	24	VAL	0	0.002	0.004	18.431	-0.003	-0.003	0.000	0.000	0.000
19	A	25	ASN	0	0.021	-0.004	15.248	-0.003	-0.003	0.000	0.000	0.000
20	A	26	GLN	0	-0.023	-0.014	18.323	0.003	0.003	0.000	0.000	0.000
21	A	27	VAL	0	0.005	0.021	20.138	-0.013	-0.013	0.000	0.000	0.000
22	A	28	ARG	1	0.826	0.899	22.639	-0.092	-0.092	0.000	0.000	0.000
23	A	29	PHE	0	0.005	0.006	20.880	-0.001	-0.001	0.000	0.000	0.000
24	A	30	SER	0	0.027	0.002	26.786	-0.004	-0.004	0.000	0.000	0.000
25	A	31	HIS	0	-0.038	-0.017	26.316	-0.002	-0.002	0.000	0.000	0.000
26	A	32	ALA	0	0.027	0.010	27.947	0.005	0.005	0.000	0.000	0.000
27	A	33	ILE	0	-0.017	0.001	22.319	0.003	0.003	0.000	0.000	0.000
28	A	34	ALA	0	-0.007	-0.009	22.301	-0.010	-0.010	0.000	0.000	0.000
29	A	35	PHE	0	-0.020	-0.013	16.998	0.011	0.011	0.000	0.000	0.000
30	A	36	ALA	0	0.082	0.051	14.887	-0.026	-0.026	0.000	0.000	0.000
31	A	37	PRO	0	0.047	0.030	12.427	0.043	0.043	0.000	0.000	0.000
32	A	38	GLU	-1	-0.827	-0.888	7.914	0.211	0.211	0.000	0.000	0.000
33	A	39	GLY	0	0.008	0.007	10.401	-0.082	-0.082	0.000	0.000	0.000
34	A	40	PRO	0	-0.013	-0.020	12.125	0.034	0.034	0.000	0.000	0.000
35	A	41	VAL	0	0.013	0.023	15.177	-0.019	-0.019	0.000	0.000	0.000
36	A	42	ALA	0	-0.005	0.001	18.139	-0.003	-0.003	0.000	0.000	0.000
37	A	43	SER	0	0.004	0.001	20.867	-0.006	-0.006	0.000	0.000	0.000
38	A	44	TRP	0	-0.019	-0.031	24.707	-0.003	-0.003	0.000	0.000	0.000
39	A	45	PRO	0	-0.019	-0.013	26.595	-0.002	-0.002	0.000	0.000	0.000
40	A	46	VAL	0	-0.036	-0.005	29.663	-0.005	-0.005	0.000	0.000	0.000
41	A	47	GLN	0	-0.017	-0.017	32.046	0.001	0.001	0.000	0.000	0.000
42	A	48	ARG	1	0.814	0.883	34.543	-0.036	-0.036	0.000	0.000	0.000
43	A	49	PRO	0	0.060	0.018	34.982	0.000	0.000	0.000	0.000	0.000
44	A	50	ALA	0	-0.029	-0.014	36.013	-0.002	-0.002	0.000	0.000	0.000
45	A	51	ASP	-1	-0.762	-0.864	35.609	0.036	0.036	0.000	0.000	0.000
46	A	52	ILE	0	0.015	0.031	31.757	0.001	0.001	0.000	0.000	0.000
47	A	53	THR	0	0.003	-0.007	32.672	-0.003	-0.003	0.000	0.000	0.000
48	A	54	ALA	0	0.080	0.040	31.665	0.002	0.002	0.000	0.000	0.000
49	A	55	SER	0	-0.017	0.003	30.024	0.002	0.002	0.000	0.000	0.000
50	A	56	LEU	0	0.016	0.020	28.645	0.002	0.002	0.000	0.000	0.000
51	A	57	LEU	0	0.040	0.019	27.081	0.006	0.006	0.000	0.000	0.000
52	A	58	GLN	0	-0.004	-0.011	25.744	0.002	0.002	0.000	0.000	0.000
53	A	59	GLN	0	-0.038	-0.018	24.380	0.004	0.004	0.000	0.000	0.000
54	A	60	ALA	0	-0.022	-0.007	22.703	0.006	0.006	0.000	0.000	0.000
55	A	61	ALA	0	0.010	-0.005	21.072	0.007	0.007	0.000	0.000	0.000
56	A	62	GLY	0	0.009	0.012	20.344	-0.004	-0.004	0.000	0.000	0.000
57	A	63	LEU	0	-0.031	0.014	15.127	-0.003	-0.003	0.000	0.000	0.000
58	A	64	ALA	0	-0.033	-0.035	14.417	-0.009	-0.009	0.000	0.000	0.000
59	A	88	ALA	0	0.013	0.011	18.325	-0.001	-0.001	0.000	0.000	0.000
60	A	89	PRO	0	-0.060	-0.024	18.785	-0.008	-0.008	0.000	0.000	0.000
61	A	90	GLU	-1	-0.872	-0.935	19.730	-0.019	-0.019	0.000	0.000	0.000
62	A	91	VAL	0	-0.025	-0.023	21.588	0.000	0.000	0.000	0.000	0.000
63	A	92	LEU	0	-0.012	0.003	22.064	0.008	0.008	0.000	0.000	0.000
64	A	93	LEU	0	0.007	-0.004	23.690	-0.004	-0.004	0.000	0.000	0.000
65	A	94	VAL	0	-0.003	-0.010	25.410	0.007	0.007	0.000	0.000	0.000
66	A	95	GLY	0	0.024	0.001	27.921	-0.004	-0.004	0.000	0.000	0.000
67	A	96	THR	0	-0.041	-0.042	29.571	0.002	0.002	0.000	0.000	0.000
68	A	97	GLY	0	0.052	0.034	32.429	-0.002	-0.002	0.000	0.000	0.000
69	A	98	ARG	1	0.795	0.852	34.115	-0.040	-0.040	0.000	0.000	0.000
70	A	99	ARG	1	0.911	0.949	36.341	-0.028	-0.028	0.000	0.000	0.000
71	A	100	GLN	0	0.035	0.040	35.339	0.002	0.002	0.000	0.000	0.000
72	A	101	HIS	0	-0.038	-0.027	35.846	-0.001	-0.001	0.000	0.000	0.000
73	A	102	LEU	0	0.003	0.008	36.019	0.001	0.001	0.000	0.000	0.000
74	A	103	LEU	0	0.032	0.022	32.026	0.001	0.001	0.000	0.000	0.000
75	A	104	GLY	0	0.037	0.023	36.278	-0.002	-0.002	0.000	0.000	0.000
76	A	105	PRO	0	-0.016	-0.021	36.636	0.000	0.000	0.000	0.000	0.000
77	A	106	GLU	-1	-0.856	-0.946	36.872	0.013	0.013	0.000	0.000	0.000
78	A	107	GLN	0	-0.017	-0.017	34.198	0.000	0.000	0.000	0.000	0.000
79	A	108	VAL	0	0.032	0.019	32.140	0.001	0.001	0.000	0.000	0.000
80	A	109	ARG	1	0.929	0.957	32.050	-0.006	-0.006	0.000	0.000	0.000
81	A	110	PRO	0	0.012	-0.001	31.188	-0.002	-0.002	0.000	0.000	0.000
82	A	111	LEU	0	0.021	0.023	26.041	-0.001	-0.001	0.000	0.000	0.000
83	A	112	LEU	0	0.023	0.015	28.235	-0.003	-0.003	0.000	0.000	0.000
84	A	113	ALA	0	-0.066	-0.028	30.588	-0.003	-0.003	0.000	0.000	0.000
85	A	114	MET	0	-0.068	-0.031	25.716	-0.002	-0.002	0.000	0.000	0.000
86	A	115	GLY	0	-0.014	-0.004	25.791	-0.003	-0.003	0.000	0.000	0.000
87	A	116	VAL	0	-0.042	0.001	23.309	0.000	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.047	0.024	25.637	0.001	0.001	0.000	0.000	0.000
89	A	118	VAL	0	-0.049	-0.039	26.147	0.004	0.004	0.000	0.000	0.000
90	A	119	GLU	-1	-0.899	-0.943	27.738	0.017	0.017	0.000	0.000	0.000
91	A	120	ALA	0	-0.017	-0.007	29.224	0.005	0.005	0.000	0.000	0.000
92	A	121	MET	0	-0.042	-0.018	28.968	-0.002	-0.002	0.000	0.000	0.000
93	A	122	ASP	-1	-0.833	-0.905	32.156	0.042	0.042	0.000	0.000	0.000
94	A	123	THR	0	0.021	-0.038	28.713	0.001	0.001	0.000	0.000	0.000
95	A	124	GLN	0	-0.022	-0.009	28.572	0.008	0.008	0.000	0.000	0.000
96	A	125	ALA	0	-0.033	-0.028	28.839	0.003	0.003	0.000	0.000	0.000
97	A	126	ALA	0	0.026	0.022	26.836	0.000	0.000	0.000	0.000	0.000
98	A	127	ALA	0	0.031	0.007	24.169	0.004	0.004	0.000	0.000	0.000
99	A	128	ARG	1	0.922	0.976	23.593	-0.039	-0.039	0.000	0.000	0.000
100	A	129	THR	0	0.007	-0.017	24.511	-0.001	-0.001	0.000	0.000	0.000
101	A	130	TYR	0	-0.011	-0.019	16.136	-0.009	-0.009	0.000	0.000	0.000
102	A	131	ASN	0	0.011	-0.007	19.697	0.014	0.014	0.000	0.000	0.000
103	A	132	ILE	0	-0.038	-0.002	19.897	0.000	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.034	0.008	20.854	-0.006	-0.006	0.000	0.000	0.000
105	A	134	MET	0	-0.039	-0.009	14.973	-0.009	-0.009	0.000	0.000	0.000
106	A	135	ALA	0	-0.013	-0.006	16.113	-0.008	-0.008	0.000	0.000	0.000
107	A	136	GLU	-1	-0.913	-0.937	17.407	-0.018	-0.018	0.000	0.000	0.000
108	A	137	GLY	0	-0.009	-0.005	15.104	-0.018	-0.018	0.000	0.000	0.000
109	A	138	ARG	1	0.763	0.874	15.546	-0.008	-0.008	0.000	0.000	0.000
110	A	139	ARG	1	0.814	0.895	10.960	-0.001	-0.001	0.000	0.000	0.000
111	A	140	VAL	0	0.008	0.007	16.835	-0.001	-0.001	0.000	0.000	0.000
112	A	141	VAL	0	-0.012	-0.015	17.463	0.016	0.016	0.000	0.000	0.000
113	A	142	VAL	0	-0.031	-0.008	19.707	-0.012	-0.012	0.000	0.000	0.000
114	A	143	ALA	0	0.035	0.020	22.006	0.010	0.010	0.000	0.000	0.000
115	A	144	LEU	0	-0.037	-0.021	24.018	-0.007	-0.007	0.000	0.000	0.000
116	A	145	LEU	0	0.027	0.019	27.104	0.003	0.003	0.000	0.000	0.000
117	A	146	PRO	0	-0.023	0.019	28.943	-0.003	-0.003	0.000	0.000	0.000
118	A	147	ASP	-1	-0.837	-0.878	31.058	0.039	0.039	0.000	0.000	0.000

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