FMO DATABASE

FMODB ID: KGVJ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-896687.757649
FMO2-HF: Nuclear repulsion	853282.715124
FMO2-HF: Total energy	-43405.042525
FMO2-MP2: Total energy	-43532.605229

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.
-1.623	1.381	-0.012	-1.269	-1.724	0.002

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 : -0.018 / 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

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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	A	9	THR	0	-0.022	-0.008	3.782	-2.138	0.770	-0.011	-1.258	-1.640	0.002
4	A	10	ALA	0	0.009	0.013	4.734	-0.208	-0.112	-0.001	-0.011	-0.084	0.000
5	A	11	LEU	0	0.019	0.000	7.925	0.068	0.068	0.000	0.000	0.000	0.000
6	A	12	ASN	0	-0.064	-0.024	11.073	-0.062	-0.062	0.000	0.000	0.000	0.000
7	A	13	THR	0	0.023	0.020	14.328	0.000	0.000	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.029	-0.004	16.916	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	15	THR	0	-0.041	-0.025	19.163	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.007	0.012	21.342	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	17	TYR	0	-0.012	-0.015	25.122	0.004	0.004	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.011	-0.020	27.903	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.960	-0.967	31.034	0.017	0.017	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.061	0.014	33.383	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	21	TYR	0	-0.106	-0.038	27.385	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	22	ILE	0	0.017	0.023	23.742	0.000	0.000	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.927	-0.971	22.212	0.019	0.019	0.000	0.000	0.000	0.000
18	A	24	VAL	0	-0.007	-0.006	17.822	0.002	0.002	0.000	0.000	0.000	0.000
19	A	25	ASN	0	0.028	-0.006	14.690	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	26	GLN	0	-0.025	-0.019	17.321	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	27	VAL	0	0.010	0.023	19.235	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.933	0.968	21.828	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	29	PHE	0	0.000	0.011	20.112	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	30	SER	0	0.028	0.001	25.903	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	HIS	0	-0.036	-0.013	25.144	0.001	0.001	0.000	0.000	0.000	0.000
26	A	32	ALA	0	0.025	0.004	27.176	0.002	0.002	0.000	0.000	0.000	0.000
27	A	33	ILE	0	-0.030	0.000	21.718	0.000	0.000	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.003	-0.011	21.921	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	35	PHE	0	-0.042	-0.019	16.749	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	36	ALA	0	0.075	0.054	14.760	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	37	PRO	0	0.047	0.022	12.843	0.003	0.003	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.882	-0.929	7.867	0.881	0.881	0.000	0.000	0.000	0.000
33	A	39	GLY	0	0.002	0.003	10.102	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	40	PRO	0	-0.012	-0.015	11.830	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	41	VAL	0	0.018	0.020	14.530	0.006	0.006	0.000	0.000	0.000	0.000
36	A	42	ALA	0	-0.006	0.003	17.702	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.021	0.013	20.163	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	TRP	0	-0.036	-0.033	23.897	0.001	0.001	0.000	0.000	0.000	0.000
39	A	45	PRO	0	-0.001	-0.008	26.142	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	46	VAL	0	-0.029	-0.013	29.664	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	47	GLN	0	-0.006	-0.017	31.541	0.000	0.000	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.826	0.892	34.171	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	49	PRO	0	0.014	0.009	34.807	0.001	0.001	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.021	0.003	35.831	0.000	0.000	0.000	0.000	0.000	0.000
45	A	51	ASP	-1	-0.801	-0.883	35.982	0.021	0.021	0.000	0.000	0.000	0.000
46	A	52	ILE	0	0.028	0.047	32.061	0.001	0.001	0.000	0.000	0.000	0.000
47	A	53	THR	0	0.016	0.005	33.071	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	54	ALA	0	0.111	0.050	31.953	0.002	0.002	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.060	-0.020	30.579	0.004	0.004	0.000	0.000	0.000	0.000
50	A	56	LEU	0	0.001	-0.001	29.114	0.003	0.003	0.000	0.000	0.000	0.000
51	A	57	LEU	0	0.008	0.000	27.465	0.004	0.004	0.000	0.000	0.000	0.000
52	A	58	GLN	0	0.023	-0.006	26.254	0.003	0.003	0.000	0.000	0.000	0.000
53	A	59	GLN	0	-0.021	0.007	24.349	0.005	0.005	0.000	0.000	0.000	0.000
54	A	60	ALA	0	-0.021	-0.004	22.827	0.005	0.005	0.000	0.000	0.000	0.000
55	A	61	ALA	0	0.017	-0.001	21.433	0.008	0.008	0.000	0.000	0.000	0.000
56	A	62	GLY	0	-0.042	-0.019	20.808	0.009	0.009	0.000	0.000	0.000	0.000
57	A	63	LEU	0	-0.043	0.004	14.998	0.001	0.001	0.000	0.000	0.000	0.000
58	A	64	ALA	0	0.013	-0.008	14.942	0.010	0.010	0.000	0.000	0.000	0.000
59	A	88	ALA	0	0.077	0.027	18.381	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	89	PRO	0	-0.155	-0.063	19.017	0.012	0.012	0.000	0.000	0.000	0.000
61	A	90	GLU	-1	-0.886	-0.971	20.415	0.070	0.070	0.000	0.000	0.000	0.000
62	A	91	VAL	0	-0.011	-0.006	22.237	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	92	LEU	0	-0.030	-0.010	22.831	0.008	0.008	0.000	0.000	0.000	0.000
64	A	93	LEU	0	-0.013	-0.003	23.306	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	94	VAL	0	0.003	-0.019	25.729	0.002	0.002	0.000	0.000	0.000	0.000
66	A	95	GLY	0	0.027	0.003	28.040	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	96	THR	0	-0.050	-0.052	29.578	0.000	0.000	0.000	0.000	0.000	0.000
68	A	97	GLY	0	0.045	0.031	31.953	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	98	ARG	1	0.950	0.980	33.608	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	99	ARG	1	0.944	0.957	36.191	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	100	GLN	0	0.042	0.037	35.685	0.000	0.000	0.000	0.000	0.000	0.000
72	A	101	HIS	0	0.008	0.007	36.090	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	102	LEU	0	-0.020	-0.009	36.311	0.002	0.002	0.000	0.000	0.000	0.000
74	A	103	LEU	0	0.024	0.017	31.995	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	104	GLY	0	0.057	0.033	36.602	0.000	0.000	0.000	0.000	0.000	0.000
76	A	105	PRO	0	0.033	-0.005	37.137	0.002	0.002	0.000	0.000	0.000	0.000
77	A	106	GLU	-1	-0.881	-0.943	37.348	0.024	0.024	0.000	0.000	0.000	0.000
78	A	107	GLN	0	-0.133	-0.086	34.517	0.000	0.000	0.000	0.000	0.000	0.000
79	A	108	VAL	0	0.095	0.010	32.227	0.002	0.002	0.000	0.000	0.000	0.000
80	A	109	ARG	1	0.946	0.994	32.834	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	110	PRO	0	0.006	0.015	31.775	0.001	0.001	0.000	0.000	0.000	0.000
82	A	111	LEU	0	0.046	0.012	26.757	0.001	0.001	0.000	0.000	0.000	0.000
83	A	112	LEU	0	0.014	0.032	28.847	0.002	0.002	0.000	0.000	0.000	0.000
84	A	113	ALA	0	-0.072	-0.015	30.974	0.000	0.000	0.000	0.000	0.000	0.000
85	A	114	MET	0	-0.088	-0.048	26.245	0.000	0.000	0.000	0.000	0.000	0.000
86	A	115	GLY	0	-0.022	-0.014	26.407	0.004	0.004	0.000	0.000	0.000	0.000
87	A	116	VAL	0	-0.019	0.002	24.330	0.003	0.003	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.019	0.011	26.603	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	118	VAL	0	-0.030	-0.023	27.150	0.004	0.004	0.000	0.000	0.000	0.000
90	A	119	GLU	-1	-0.918	-0.960	28.537	0.040	0.040	0.000	0.000	0.000	0.000
91	A	120	ALA	0	-0.019	0.001	29.549	0.002	0.002	0.000	0.000	0.000	0.000
92	A	121	MET	0	-0.052	-0.013	29.287	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	122	ASP	-1	-0.901	-0.935	32.332	0.026	0.026	0.000	0.000	0.000	0.000
94	A	123	THR	0	0.017	-0.068	28.343	0.002	0.002	0.000	0.000	0.000	0.000
95	A	124	GLN	0	0.014	0.002	28.605	0.003	0.003	0.000	0.000	0.000	0.000
96	A	125	ALA	0	-0.010	0.001	28.587	0.001	0.001	0.000	0.000	0.000	0.000
97	A	126	ALA	0	0.040	0.027	26.860	0.002	0.002	0.000	0.000	0.000	0.000
98	A	127	ALA	0	0.034	0.005	24.221	0.005	0.005	0.000	0.000	0.000	0.000
99	A	128	ARG	1	0.951	0.980	23.438	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	129	THR	0	0.005	-0.012	24.573	0.000	0.000	0.000	0.000	0.000	0.000
101	A	130	TYR	0	-0.028	-0.043	16.055	0.008	0.008	0.000	0.000	0.000	0.000
102	A	131	ASN	0	0.012	-0.006	19.536	0.015	0.015	0.000	0.000	0.000	0.000
103	A	132	ILE	0	-0.014	0.005	19.673	0.003	0.003	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.032	0.016	20.777	0.003	0.003	0.000	0.000	0.000	0.000
105	A	134	MET	0	-0.054	-0.011	15.121	0.012	0.012	0.000	0.000	0.000	0.000
106	A	135	ALA	0	-0.008	-0.010	16.099	0.009	0.009	0.000	0.000	0.000	0.000
107	A	136	GLU	-1	-1.007	-0.999	17.151	0.045	0.045	0.000	0.000	0.000	0.000
108	A	137	GLY	0	-0.034	-0.019	15.217	0.000	0.000	0.000	0.000	0.000	0.000
109	A	138	ARG	1	0.919	0.985	15.945	-0.055	-0.055	0.000	0.000	0.000	0.000
110	A	139	ARG	1	0.862	0.940	11.367	-0.283	-0.283	0.000	0.000	0.000	0.000
111	A	140	VAL	0	0.019	0.016	17.624	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	141	VAL	0	0.008	0.007	18.089	0.015	0.015	0.000	0.000	0.000	0.000
113	A	142	VAL	0	-0.028	-0.012	20.164	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	143	ALA	0	0.026	0.019	22.160	0.002	0.002	0.000	0.000	0.000	0.000
115	A	144	LEU	0	-0.025	-0.015	23.627	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	145	LEU	0	0.033	0.031	26.991	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	146	PRO	0	-0.011	0.034	29.108	0.000	0.000	0.000	0.000	0.000	0.000
118	A	147	ASP	-1	-0.933	-0.964	30.743	0.018	0.018	0.000	0.000	0.000	0.000

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