FMO DATABASE

FMODB ID: 2217R

Calculation Name: 4NJ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NJ6

Chain ID: A

ChEMBL ID:

UniProt ID: P93022

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-623416.206805
FMO2-HF: Nuclear repulsion	587851.516055
FMO2-HF: Total energy	-35564.69075
FMO2-MP2: Total energy	-35668.020039

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:1039:THR)

Summations of interaction energy for fragment #1(A:1039:THR)

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.
-4.751	-3.086	-0.017	-0.862	-0.786	0.003

Interaction energy analysis for fragmet #1(A:1039:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.023

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	1041	THR	0	0.034	0.026	3.742	-3.164	-1.499	-0.017	-0.862	-0.786	0.003
4	A	1042	ALA	0	-0.036	-0.014	6.486	0.623	0.623	0.000	0.000	0.000	0.000
5	A	1043	VAL	0	0.057	0.027	8.462	-0.087	-0.087	0.000	0.000	0.000	0.000
6	A	1044	GLN	0	-0.035	-0.032	11.544	0.064	0.064	0.000	0.000	0.000	0.000
7	A	1045	LYS	1	1.008	1.012	14.888	0.033	0.033	0.000	0.000	0.000	0.000
8	A	1046	ARG	1	0.968	0.991	18.606	0.131	0.131	0.000	0.000	0.000	0.000
9	A	1047	GLY	0	-0.027	-0.015	21.263	0.012	0.012	0.000	0.000	0.000	0.000
10	A	1048	SER	0	-0.040	-0.012	19.378	0.020	0.020	0.000	0.000	0.000	0.000
11	A	1049	VAL	0	-0.014	0.002	15.818	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	1050	GLY	0	0.009	0.011	13.457	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	1051	ARG	1	0.929	0.959	12.265	-0.193	-0.193	0.000	0.000	0.000	0.000
14	A	1052	SER	0	0.003	-0.010	6.677	-0.148	-0.148	0.000	0.000	0.000	0.000
15	A	1053	ILE	0	0.020	0.014	8.325	0.239	0.239	0.000	0.000	0.000	0.000
16	A	1054	ASP	-1	-0.826	-0.909	6.213	1.245	1.245	0.000	0.000	0.000	0.000
17	A	1055	VAL	0	0.049	-0.004	7.409	0.014	0.014	0.000	0.000	0.000	0.000
18	A	1056	ASN	0	0.016	0.005	6.763	-0.162	-0.162	0.000	0.000	0.000	0.000
19	A	1057	ARG	1	0.857	0.938	9.330	-1.213	-1.213	0.000	0.000	0.000	0.000
20	A	1058	TYR	0	-0.116	-0.109	11.968	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	1059	ARG	1	0.934	0.958	14.846	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	1060	GLY	0	0.038	0.012	17.600	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	1061	TYR	0	-0.025	-0.051	16.723	0.019	0.019	0.000	0.000	0.000	0.000
24	A	1062	ASP	-1	-0.889	-0.930	19.469	0.000	0.000	0.000	0.000	0.000	0.000
25	A	1063	GLU	-1	-0.904	-0.934	18.003	0.219	0.219	0.000	0.000	0.000	0.000
26	A	1064	LEU	0	0.024	0.015	13.977	0.014	0.014	0.000	0.000	0.000	0.000
27	A	1065	ARG	1	0.934	0.966	17.176	0.079	0.079	0.000	0.000	0.000	0.000
28	A	1066	HIS	0	0.014	-0.003	19.985	0.009	0.009	0.000	0.000	0.000	0.000
29	A	1067	ASP	-1	-0.817	-0.846	15.962	0.278	0.278	0.000	0.000	0.000	0.000
30	A	1068	LEU	0	-0.007	-0.012	14.227	0.006	0.006	0.000	0.000	0.000	0.000
31	A	1069	ALA	0	0.009	0.009	18.182	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	1070	ARG	1	0.906	0.957	19.478	-0.169	-0.169	0.000	0.000	0.000	0.000
33	A	1071	MET	0	-0.093	-0.043	13.544	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	1072	PHE	0	-0.086	-0.045	14.920	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	1073	GLY	0	-0.012	0.003	20.469	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	1074	ILE	0	-0.077	-0.032	22.546	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	1075	GLU	-1	-0.923	-0.981	24.707	0.085	0.085	0.000	0.000	0.000	0.000
38	A	1076	GLY	0	-0.020	-0.002	26.180	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	1077	GLN	0	-0.024	-0.013	26.233	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	1078	LEU	0	-0.015	-0.028	20.407	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	1079	GLU	-1	-0.837	-0.918	24.270	0.014	0.014	0.000	0.000	0.000	0.000
42	A	1080	ASP	-1	-0.834	-0.910	25.456	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	1081	PRO	0	-0.052	-0.029	24.846	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	1082	GLN	0	-0.077	-0.031	26.997	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	1083	THR	0	-0.011	-0.021	30.552	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	1084	SER	0	-0.073	-0.018	26.736	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	1085	ASP	-1	-0.904	-0.952	28.875	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	1086	TRP	0	-0.104	-0.055	23.500	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	1087	LYS	1	0.970	0.986	23.469	0.109	0.109	0.000	0.000	0.000	0.000
50	A	1088	LEU	0	0.003	0.009	17.150	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	1089	VAL	0	0.009	-0.001	17.553	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	1090	TYR	0	0.004	-0.016	13.083	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	1091	VAL	0	-0.032	-0.010	12.058	0.042	0.042	0.000	0.000	0.000	0.000
54	A	1092	ALA	0	0.083	0.047	12.133	-0.133	-0.133	0.000	0.000	0.000	0.000
55	A	1093	HIS	0	0.009	-0.002	10.588	0.039	0.039	0.000	0.000	0.000	0.000
56	A	1094	GLU	-1	-0.927	-0.966	14.695	-0.383	-0.383	0.000	0.000	0.000	0.000
57	A	1095	ASN	0	-0.097	-0.052	15.070	0.011	0.011	0.000	0.000	0.000	0.000
58	A	1096	ALA	0	0.013	0.020	16.407	0.055	0.055	0.000	0.000	0.000	0.000
59	A	1097	ILE	0	-0.018	-0.021	16.955	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	1098	LEU	0	0.003	0.013	17.195	0.043	0.043	0.000	0.000	0.000	0.000
61	A	1099	LEU	0	0.004	-0.003	18.660	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	1100	VAL	0	-0.008	-0.009	16.189	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	1101	GLY	0	-0.056	-0.049	18.816	0.034	0.034	0.000	0.000	0.000	0.000
64	A	1102	ASP	-1	-0.926	-0.942	20.717	-0.158	-0.158	0.000	0.000	0.000	0.000
65	A	1103	ASP	-1	-0.905	-0.937	18.018	-0.289	-0.289	0.000	0.000	0.000	0.000
66	A	1104	PRO	0	-0.007	0.022	20.085	0.024	0.024	0.000	0.000	0.000	0.000
67	A	1105	TRP	0	0.019	-0.003	13.586	-0.070	-0.070	0.000	0.000	0.000	0.000
68	A	1106	GLU	-1	-0.901	-0.957	14.860	-0.133	-0.133	0.000	0.000	0.000	0.000
69	A	1107	GLU	-1	-0.910	-0.965	13.944	-0.293	-0.293	0.000	0.000	0.000	0.000
70	A	1108	PHE	0	0.020	0.015	13.239	-0.108	-0.108	0.000	0.000	0.000	0.000
71	A	1109	VAL	0	-0.020	-0.018	9.496	-0.145	-0.145	0.000	0.000	0.000	0.000
72	A	1110	ASN	0	-0.047	-0.024	9.466	-0.239	-0.239	0.000	0.000	0.000	0.000
73	A	1111	CYS	0	-0.043	-0.005	10.499	-0.112	-0.112	0.000	0.000	0.000	0.000
74	A	1112	VAL	0	-0.036	0.018	8.796	-0.103	-0.103	0.000	0.000	0.000	0.000
75	A	1113	GLN	0	-0.064	-0.052	7.496	-0.541	-0.541	0.000	0.000	0.000	0.000
76	A	1114	SER	0	-0.103	-0.056	7.682	-0.181	-0.181	0.000	0.000	0.000	0.000
77	A	1115	ILE	0	0.073	0.039	9.980	0.109	0.109	0.000	0.000	0.000	0.000
78	A	1116	LYS	1	0.913	0.954	13.074	0.376	0.376	0.000	0.000	0.000	0.000
79	A	1117	ILE	0	0.023	0.023	16.167	0.009	0.009	0.000	0.000	0.000	0.000
80	A	1118	LEU	0	-0.034	-0.010	19.354	0.008	0.008	0.000	0.000	0.000	0.000
81	A	1119	SER	0	0.022	0.003	22.206	0.015	0.015	0.000	0.000	0.000	0.000
82	A	1120	SER	0	0.083	0.014	25.682	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	1121	ALA	0	0.007	0.007	28.657	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	1122	GLU	-1	-0.912	-0.967	21.901	-0.150	-0.150	0.000	0.000	0.000	0.000
85	A	1123	VAL	0	0.024	0.008	24.895	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	1124	GLN	0	-0.042	-0.028	26.465	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	1125	GLN	0	-0.033	-0.014	27.373	0.000	0.000	0.000	0.000	0.000	0.000
88	A	1126	MET	0	-0.049	0.008	22.653	-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:1039:THR)