FMO DATABASE

FMODB ID: 1NK4Z

Calculation Name: 3FQ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FQ4

Chain ID: A

ChEMBL ID:

UniProt ID: P16144

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:

Apendix: None

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-865761.251519
FMO2-HF: Nuclear repulsion	822870.461835
FMO2-HF: Total energy	-42890.789685
FMO2-MP2: Total energy	-43018.65615

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:988:MET)

Summations of interaction energy for fragment #1(A:988:MET)

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.
-4.389	-2.268	7.465	-2.559	-7.026	-0.003

Interaction energy analysis for fragmet #1(A:988:MET)

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 : -0.031

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	990	ASP	-1	-0.852	-0.926	3.668	-0.354	1.665	-0.012	-0.944	-1.064	0.001
4	A	991	VAL	0	-0.052	-0.023	2.669	-0.366	0.209	0.496	-0.207	-0.864	-0.001
5	A	992	VAL	0	0.015	-0.004	5.233	0.015	0.053	-0.001	-0.002	-0.035	0.000
6	A	993	SER	0	-0.010	-0.001	8.645	-0.084	-0.084	0.000	0.000	0.000	0.000
7	A	994	PHE	0	-0.003	-0.003	11.020	0.085	0.085	0.000	0.000	0.000	0.000
8	A	995	GLU	-1	-0.949	-0.968	13.829	-0.467	-0.467	0.000	0.000	0.000	0.000
9	A	996	GLN	0	-0.017	-0.013	15.614	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	997	PRO	0	0.020	0.005	17.095	0.015	0.015	0.000	0.000	0.000	0.000
11	A	998	GLU	-1	-0.926	-0.956	18.522	-0.225	-0.225	0.000	0.000	0.000	0.000
12	A	999	PHE	0	0.019	0.017	18.927	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	1000	SER	0	0.000	-0.006	24.151	0.012	0.012	0.000	0.000	0.000	0.000
14	A	1001	VAL	0	0.000	0.010	27.616	0.000	0.000	0.000	0.000	0.000	0.000
15	A	1002	SER	0	0.039	0.027	30.243	0.002	0.002	0.000	0.000	0.000	0.000
16	A	1003	ARG	1	0.874	0.907	33.749	0.089	0.089	0.000	0.000	0.000	0.000
17	A	1004	GLY	0	0.014	0.006	35.340	0.004	0.004	0.000	0.000	0.000	0.000
18	A	1005	ASP	-1	-0.892	-0.939	32.480	-0.101	-0.101	0.000	0.000	0.000	0.000
19	A	1006	GLN	0	-0.070	-0.026	34.130	0.004	0.004	0.000	0.000	0.000	0.000
20	A	1007	VAL	0	-0.055	-0.034	28.420	0.004	0.004	0.000	0.000	0.000	0.000
21	A	1008	ALA	0	-0.005	0.010	26.314	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	1009	ARG	1	0.920	0.956	25.139	0.104	0.104	0.000	0.000	0.000	0.000
23	A	1010	ILE	0	-0.014	-0.011	19.468	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	1011	PRO	0	0.047	0.044	18.298	0.015	0.015	0.000	0.000	0.000	0.000
25	A	1012	VAL	0	-0.033	-0.023	13.424	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	1013	ILE	0	0.049	0.024	11.148	0.037	0.037	0.000	0.000	0.000	0.000
27	A	1014	ARG	1	0.791	0.870	8.685	-0.077	-0.077	0.000	0.000	0.000	0.000
28	A	1015	ARG	1	0.968	0.979	6.445	1.763	1.763	0.000	0.000	0.000	0.000
29	A	1016	VAL	0	-0.042	-0.034	4.657	-0.242	-0.142	-0.001	-0.016	-0.082	0.000
30	A	1017	LEU	0	0.024	0.020	6.874	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	1018	ASP	-1	-0.873	-0.933	7.456	1.391	1.391	0.000	0.000	0.000	0.000
32	A	1019	GLY	0	0.010	0.014	9.335	0.039	0.039	0.000	0.000	0.000	0.000
33	A	1020	GLY	0	0.006	0.010	11.839	-0.037	-0.037	0.000	0.000	0.000	0.000
34	A	1021	LYS	1	0.916	0.970	12.866	-0.441	-0.441	0.000	0.000	0.000	0.000
35	A	1022	SER	0	0.032	0.022	9.586	0.053	0.053	0.000	0.000	0.000	0.000
36	A	1023	GLN	0	-0.014	-0.014	11.561	-0.083	-0.083	0.000	0.000	0.000	0.000
37	A	1024	VAL	0	0.004	0.020	10.366	0.104	0.104	0.000	0.000	0.000	0.000
38	A	1025	SER	0	0.044	0.023	13.054	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	1026	TYR	0	-0.026	-0.023	15.430	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	1027	ARG	1	0.974	0.993	17.964	0.113	0.113	0.000	0.000	0.000	0.000
41	A	1028	THR	0	0.053	0.034	20.942	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	1029	GLN	0	-0.046	-0.016	22.762	0.006	0.006	0.000	0.000	0.000	0.000
43	A	1030	ASP	-1	-0.754	-0.846	24.852	-0.099	-0.099	0.000	0.000	0.000	0.000
44	A	1031	GLY	0	-0.017	-0.011	27.053	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	1032	THR	0	-0.011	-0.006	28.486	0.007	0.007	0.000	0.000	0.000	0.000
46	A	1033	ALA	0	-0.061	-0.025	30.019	0.009	0.009	0.000	0.000	0.000	0.000
47	A	1034	GLN	0	0.022	-0.014	30.599	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	1035	GLY	0	0.066	0.024	31.452	0.003	0.003	0.000	0.000	0.000	0.000
49	A	1036	ASN	0	-0.056	-0.042	32.254	0.003	0.003	0.000	0.000	0.000	0.000
50	A	1037	ARG	1	0.868	0.951	35.146	0.083	0.083	0.000	0.000	0.000	0.000
51	A	1038	ASP	-1	-0.768	-0.889	33.143	-0.087	-0.087	0.000	0.000	0.000	0.000
52	A	1039	TYR	0	-0.028	-0.035	27.561	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	1040	ILE	0	0.013	0.011	30.732	0.005	0.005	0.000	0.000	0.000	0.000
54	A	1041	PRO	0	-0.024	-0.010	27.978	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	1042	VAL	0	-0.017	-0.011	24.061	0.009	0.009	0.000	0.000	0.000	0.000
56	A	1043	GLU	-1	-0.964	-0.991	22.483	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	1044	GLY	0	0.094	0.068	21.064	0.005	0.005	0.000	0.000	0.000	0.000
58	A	1045	GLU	-1	-0.952	-0.984	17.870	0.079	0.079	0.000	0.000	0.000	0.000
59	A	1046	LEU	0	-0.041	-0.012	14.957	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	1047	LEU	0	-0.030	-0.024	15.011	0.043	0.043	0.000	0.000	0.000	0.000
61	A	1048	PHE	0	-0.013	-0.007	12.969	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	1049	GLN	0	0.049	0.004	14.841	0.083	0.083	0.000	0.000	0.000	0.000
63	A	1050	PRO	0	0.028	0.013	15.190	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	1051	GLY	0	0.016	0.012	14.976	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	1052	GLU	-1	-0.809	-0.879	15.750	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	1053	ALA	0	0.034	0.003	13.531	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	1054	TRP	0	-0.027	-0.017	14.117	-0.080	-0.080	0.000	0.000	0.000	0.000
68	A	1055	LYS	1	0.827	0.909	16.043	0.069	0.069	0.000	0.000	0.000	0.000
69	A	1056	GLU	-1	-0.830	-0.921	18.366	-0.157	-0.157	0.000	0.000	0.000	0.000
70	A	1057	LEU	0	-0.041	-0.011	18.680	0.024	0.024	0.000	0.000	0.000	0.000
71	A	1058	GLN	0	0.003	-0.006	22.000	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	1059	VAL	0	-0.024	0.010	24.435	0.011	0.011	0.000	0.000	0.000	0.000
73	A	1060	LYS	1	0.979	0.982	27.109	0.042	0.042	0.000	0.000	0.000	0.000
74	A	1061	LEU	0	-0.027	-0.014	29.592	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	1062	LEU	0	-0.004	0.004	32.831	0.006	0.006	0.000	0.000	0.000	0.000
76	A	1063	GLU	-1	-0.915	-0.959	36.265	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	1064	LEU	0	-0.049	-0.015	38.057	0.004	0.004	0.000	0.000	0.000	0.000
78	A	1074	ARG	1	0.959	0.974	41.113	0.070	0.070	0.000	0.000	0.000	0.000
79	A	1075	GLN	0	-0.038	-0.011	37.587	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	1076	VAL	0	0.024	0.004	32.449	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	1077	ARG	1	0.781	0.896	32.666	0.089	0.089	0.000	0.000	0.000	0.000
82	A	1078	ARG	1	0.983	0.999	26.998	0.179	0.179	0.000	0.000	0.000	0.000
83	A	1079	PHE	0	-0.007	0.015	25.088	0.008	0.008	0.000	0.000	0.000	0.000
84	A	1080	HIS	0	0.009	0.006	21.520	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	1081	VAL	0	0.010	0.007	19.211	0.026	0.026	0.000	0.000	0.000	0.000
86	A	1082	GLN	0	-0.018	-0.022	16.792	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	1083	LEU	0	0.019	0.019	11.955	0.040	0.040	0.000	0.000	0.000	0.000
88	A	1084	SER	0	-0.027	-0.023	12.926	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	1085	ASN	0	0.009	0.003	12.911	0.080	0.080	0.000	0.000	0.000	0.000
90	A	1086	PRO	0	0.025	0.020	8.450	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	1087	LYS	1	0.963	0.979	10.541	-0.213	-0.213	0.000	0.000	0.000	0.000
92	A	1088	PHE	0	-0.045	-0.052	10.789	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	1089	GLY	0	0.075	0.050	8.063	-0.061	-0.061	0.000	0.000	0.000	0.000
94	A	1090	ALA	0	-0.019	0.009	6.105	0.567	0.567	0.000	0.000	0.000	0.000
95	A	1091	HIS	1	0.879	0.935	2.935	-5.579	-6.233	6.984	-1.383	-4.947	-0.003
96	A	1092	LEU	0	0.012	0.026	4.885	-0.599	-0.556	-0.001	-0.007	-0.034	0.000
97	A	1093	GLY	0	-0.004	-0.013	5.575	-0.487	-0.487	0.000	0.000	0.000	0.000
98	A	1094	GLN	0	-0.063	-0.011	7.218	0.414	0.414	0.000	0.000	0.000	0.000
99	A	1095	PRO	0	0.025	0.019	10.240	-0.059	-0.059	0.000	0.000	0.000	0.000
100	A	1096	HIS	0	0.074	0.013	9.853	0.087	0.087	0.000	0.000	0.000	0.000
101	A	1097	SER	0	-0.041	-0.024	12.416	0.101	0.101	0.000	0.000	0.000	0.000
102	A	1098	THR	0	-0.002	-0.015	16.069	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	1099	THR	0	0.002	-0.003	18.995	0.027	0.027	0.000	0.000	0.000	0.000
104	A	1100	ILE	0	0.000	0.007	22.493	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	1101	ILE	0	-0.051	-0.038	25.471	0.016	0.016	0.000	0.000	0.000	0.000
106	A	1102	ILE	0	0.012	0.008	28.603	0.002	0.002	0.000	0.000	0.000	0.000
107	A	1103	ARG	1	0.912	0.936	29.954	0.157	0.157	0.000	0.000	0.000	0.000
108	A	1104	ASP	-1	-0.818	-0.916	34.556	-0.085	-0.085	0.000	0.000	0.000	0.000
109	A	1105	PRO	0	-0.010	0.005	37.850	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:988:MET)