FMO DATABASE

FMODB ID: 1NJ5Z

Calculation Name: 3KP8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KP8

Chain ID: A

ChEMBL ID:

UniProt ID: Q2JJF6

Base Structure: X-ray

Registration Date: 2023-09-20

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-624652.485286
FMO2-HF: Nuclear repulsion	588814.755987
FMO2-HF: Total energy	-35837.7293
FMO2-MP2: Total energy	-35940.058443

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:186:SER)

Summations of interaction energy for fragment #1(A:186:SER)

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.
-15.25	-9.126	4.926	-4.595	-6.454	0.026

Interaction energy analysis for fragmet #1(A:186:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.093 / q_NPA : 0.051

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	188	LEU	0	0.007	0.021	2.738	-3.660	-0.535	0.744	-1.656	-2.213	0.012
4	A	189	ALA	0	0.049	0.028	2.254	-7.614	-6.215	4.064	-2.412	-3.051	0.015
5	A	190	VAL	0	0.024	0.002	3.532	-0.892	-0.232	0.011	-0.236	-0.434	0.000
6	A	191	GLY	0	0.001	0.006	5.972	0.199	0.199	0.000	0.000	0.000	0.000
7	A	192	LEU	0	-0.004	0.006	6.975	-0.091	-0.091	0.000	0.000	0.000	0.000
8	A	193	ALA	0	0.019	0.008	7.696	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	194	ALA	0	-0.046	-0.020	9.415	0.059	0.059	0.000	0.000	0.000	0.000
10	A	195	HIS	0	-0.043	-0.036	11.498	0.045	0.045	0.000	0.000	0.000	0.000
11	A	196	LEU	0	0.009	-0.002	10.535	0.014	0.014	0.000	0.000	0.000	0.000
12	A	197	ARG	1	0.831	0.915	13.124	0.415	0.415	0.000	0.000	0.000	0.000
13	A	198	GLN	0	-0.055	-0.025	15.400	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	199	ILE	0	-0.041	-0.007	15.974	0.023	0.023	0.000	0.000	0.000	0.000
15	A	200	GLY	0	0.010	0.014	18.668	0.011	0.011	0.000	0.000	0.000	0.000
16	A	201	GLY	0	-0.031	-0.015	16.317	0.009	0.009	0.000	0.000	0.000	0.000
17	A	202	THR	0	-0.019	-0.014	15.752	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	203	MET	0	-0.077	-0.020	14.524	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	204	TYR	0	0.067	0.015	17.269	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	205	GLY	0	0.015	-0.025	19.409	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	206	ALA	0	0.008	0.009	20.459	0.012	0.012	0.000	0.000	0.000	0.000
22	A	207	TYR	0	-0.048	-0.036	19.437	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	208	TRP	0	0.007	0.006	19.701	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	209	CYS	0	-0.061	-0.013	20.602	0.011	0.011	0.000	0.000	0.000	0.000
25	A	210	PRO	0	0.068	0.020	18.996	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	211	HIS	0	0.078	0.045	17.126	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	212	CYS	0	-0.068	-0.008	15.877	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	213	GLN	0	-0.028	0.001	14.727	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	214	ASP	-1	-0.846	-0.926	12.810	-0.316	-0.316	0.000	0.000	0.000	0.000
30	A	215	GLN	0	-0.020	-0.017	10.509	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	216	LYS	1	0.894	0.958	10.156	0.219	0.219	0.000	0.000	0.000	0.000
32	A	217	GLU	-1	-0.878	-0.955	8.614	-0.461	-0.461	0.000	0.000	0.000	0.000
33	A	218	LEU	0	-0.066	-0.030	7.297	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	219	PHE	0	-0.051	-0.029	4.426	-1.018	-0.871	-0.001	-0.007	-0.139	0.000
35	A	220	GLY	0	0.019	0.014	4.582	-0.702	-0.629	-0.001	-0.009	-0.063	0.000
36	A	221	ALA	0	0.021	-0.001	6.482	-0.085	-0.085	0.000	0.000	0.000	0.000
37	A	222	ALA	0	-0.046	-0.011	4.128	-0.116	-0.057	-0.001	-0.015	-0.043	0.000
38	A	223	PHE	0	0.016	-0.020	6.148	0.349	0.349	0.000	0.000	0.000	0.000
39	A	224	ASP	-1	-0.891	-0.933	9.252	-0.569	-0.569	0.000	0.000	0.000	0.000
40	A	225	GLN	0	-0.034	-0.008	8.731	0.267	0.267	0.000	0.000	0.000	0.000
41	A	226	VAL	0	-0.019	-0.009	10.152	0.086	0.086	0.000	0.000	0.000	0.000
42	A	227	PRO	0	-0.003	0.007	12.897	0.020	0.020	0.000	0.000	0.000	0.000
43	A	228	TYR	0	0.003	-0.031	15.709	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	229	VAL	0	0.006	0.006	17.652	0.016	0.016	0.000	0.000	0.000	0.000
45	A	230	GLU	-1	-0.735	-0.857	21.010	-0.206	-0.206	0.000	0.000	0.000	0.000
46	A	231	CYS	0	-0.035	-0.008	22.374	0.009	0.009	0.000	0.000	0.000	0.000
47	A	232	SER	0	-0.003	0.013	24.480	0.015	0.015	0.000	0.000	0.000	0.000
48	A	233	PRO	0	0.052	0.019	25.729	0.000	0.000	0.000	0.000	0.000	0.000
49	A	234	ASN	0	-0.029	-0.023	26.662	0.003	0.003	0.000	0.000	0.000	0.000
50	A	235	GLY	0	0.028	0.032	27.525	0.007	0.007	0.000	0.000	0.000	0.000
51	A	236	PRO	0	0.003	-0.003	27.139	0.002	0.002	0.000	0.000	0.000	0.000
52	A	237	GLY	0	-0.018	-0.006	29.188	0.006	0.006	0.000	0.000	0.000	0.000
53	A	238	THR	0	-0.062	-0.031	30.418	0.004	0.004	0.000	0.000	0.000	0.000
54	A	239	PRO	0	-0.017	-0.022	31.504	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	240	GLN	0	-0.013	0.015	27.667	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	241	ALA	0	0.010	-0.003	27.387	0.007	0.007	0.000	0.000	0.000	0.000
57	A	242	GLN	0	-0.042	-0.032	29.463	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	243	GLU	-1	-0.912	-0.960	27.105	-0.139	-0.139	0.000	0.000	0.000	0.000
59	A	245	THR	0	0.004	0.003	27.387	0.001	0.001	0.000	0.000	0.000	0.000
60	A	246	GLU	-1	-0.857	-0.922	30.957	-0.077	-0.077	0.000	0.000	0.000	0.000
61	A	247	ALA	0	-0.060	-0.016	26.680	0.003	0.003	0.000	0.000	0.000	0.000
62	A	248	GLY	0	-0.012	-0.002	27.966	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	249	ILE	0	-0.059	-0.028	23.648	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	250	THR	0	0.011	0.000	26.656	0.004	0.004	0.000	0.000	0.000	0.000
65	A	251	SER	0	-0.069	-0.026	23.619	0.004	0.004	0.000	0.000	0.000	0.000
66	A	252	TYR	0	-0.009	-0.003	21.475	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	253	PRO	0	0.043	-0.004	16.193	0.008	0.008	0.000	0.000	0.000	0.000
68	A	254	THR	0	-0.056	-0.052	19.146	0.023	0.023	0.000	0.000	0.000	0.000
69	A	255	TRP	0	0.003	-0.006	11.722	0.002	0.002	0.000	0.000	0.000	0.000
70	A	256	ILE	0	0.001	-0.002	18.461	0.026	0.026	0.000	0.000	0.000	0.000
71	A	257	ILE	0	0.004	0.009	14.783	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	258	ASN	0	-0.010	-0.001	18.304	0.011	0.011	0.000	0.000	0.000	0.000
73	A	259	GLY	0	0.018	0.013	21.396	0.012	0.012	0.000	0.000	0.000	0.000
74	A	260	ARG	1	0.919	0.972	21.059	0.075	0.075	0.000	0.000	0.000	0.000
75	A	261	THR	0	0.051	0.018	21.238	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	262	TYR	0	-0.077	-0.040	17.820	0.019	0.019	0.000	0.000	0.000	0.000
77	A	263	THR	0	0.045	0.027	18.894	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	264	GLY	0	0.046	0.034	19.038	0.004	0.004	0.000	0.000	0.000	0.000
79	A	265	VAL	0	0.017	0.008	13.074	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	266	ARG	1	0.803	0.894	13.060	0.234	0.234	0.000	0.000	0.000	0.000
81	A	267	SER	0	0.031	-0.004	8.794	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	268	LEU	0	0.041	0.015	2.969	-0.880	-0.219	0.110	-0.260	-0.511	-0.001
83	A	269	GLU	-1	-0.811	-0.892	6.460	-0.407	-0.407	0.000	0.000	0.000	0.000
84	A	270	ALA	0	-0.027	-0.012	9.240	0.080	0.080	0.000	0.000	0.000	0.000
85	A	271	LEU	0	0.028	0.013	9.706	0.053	0.053	0.000	0.000	0.000	0.000
86	A	272	ALA	0	-0.006	0.022	9.170	0.033	0.033	0.000	0.000	0.000	0.000
87	A	273	VAL	0	-0.002	-0.007	11.134	0.011	0.011	0.000	0.000	0.000	0.000
88	A	274	ALA	0	-0.054	-0.015	14.252	0.006	0.006	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.024	-0.050	12.743	0.012	0.012	0.000	0.000	0.000	0.000
90	A	276	GLY	0	0.000	0.012	15.223	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	277	TYR	0	-0.028	0.002	8.148	-0.075	-0.075	0.000	0.000	0.000	0.000
92	A	278	PRO	0	-0.005	-0.014	12.290	0.009	0.009	0.000	0.000	0.000	0.000
93	A	279	LEU	0	-0.001	0.010	8.216	0.087	0.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:186:SER)