FMO DATABASE

FMODB ID: 1N9KZ

Calculation Name: 3EMO-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMO

Chain ID: C

ChEMBL ID:

UniProt ID: Q48152

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-650133.373805
FMO2-HF: Nuclear repulsion	606277.695453
FMO2-HF: Total energy	-43855.678352
FMO2-MP2: Total energy	-43984.074207

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(C:973:VAL)

Summations of interaction energy for fragment #1(C:973:VAL)

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.
-3.084	-0.825	0.059	-1.016	-1.302	0

Interaction energy analysis for fragmet #1(C:973:VAL)

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 : -0.024

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	C	975	ILE	0	-0.001	0.006	3.214	-2.667	-0.408	0.059	-1.016	-1.302
4	C	976	ASP	-1	-0.861	-0.929	5.621	-0.391	-0.391	0.000	0.000	0.000
5	C	977	ASN	0	-0.077	-0.058	9.047	0.044	0.044	0.000	0.000	0.000
6	C	978	VAL	0	0.002	0.020	9.396	0.052	0.052	0.000	0.000	0.000
7	C	979	ALA	0	0.023	0.013	12.224	0.082	0.082	0.000	0.000	0.000
8	C	980	ASN	0	-0.057	-0.033	15.575	-0.035	-0.035	0.000	0.000	0.000
9	C	981	GLY	0	0.069	0.056	17.024	0.010	0.010	0.000	0.000	0.000
10	C	982	ASP	-1	-0.859	-0.958	18.239	-0.136	-0.136	0.000	0.000	0.000
11	C	983	ILE	0	-0.090	-0.026	20.219	-0.007	-0.007	0.000	0.000	0.000
12	C	984	SER	0	0.033	0.019	22.462	0.022	0.022	0.000	0.000	0.000
13	C	985	ALA	0	-0.036	-0.026	23.736	-0.007	-0.007	0.000	0.000	0.000
14	C	986	THR	0	-0.038	-0.028	24.777	0.007	0.007	0.000	0.000	0.000
15	C	987	SER	0	-0.030	-0.009	20.049	-0.014	-0.014	0.000	0.000	0.000
16	C	988	THR	0	-0.043	-0.027	17.807	0.016	0.016	0.000	0.000	0.000
17	C	989	ASP	-1	-0.854	-0.899	16.421	-0.314	-0.314	0.000	0.000	0.000
18	C	990	ALA	0	-0.026	-0.006	11.576	-0.002	-0.002	0.000	0.000	0.000
19	C	991	ILE	0	0.015	0.001	13.145	0.048	0.048	0.000	0.000	0.000
20	C	992	ASN	0	-0.006	-0.022	12.566	-0.019	-0.019	0.000	0.000	0.000
21	C	993	GLY	0	0.038	0.005	13.423	0.070	0.070	0.000	0.000	0.000
22	C	994	SER	0	0.001	-0.004	14.831	0.056	0.056	0.000	0.000	0.000
23	C	995	GLN	0	0.018	0.005	17.194	0.003	0.003	0.000	0.000	0.000
24	C	996	LEU	0	0.029	0.021	14.697	0.029	0.029	0.000	0.000	0.000
25	C	997	TYR	0	0.024	0.011	18.214	0.033	0.033	0.000	0.000	0.000
26	C	998	ALA	0	-0.004	0.000	20.031	0.019	0.019	0.000	0.000	0.000
27	C	999	VAL	0	0.031	0.020	21.210	0.014	0.014	0.000	0.000	0.000
28	C	1000	ALA	0	0.027	0.013	20.227	0.013	0.013	0.000	0.000	0.000
29	C	1001	LYS	1	0.921	0.972	22.366	0.025	0.025	0.000	0.000	0.000
30	C	1002	GLY	0	0.019	0.014	25.210	0.005	0.005	0.000	0.000	0.000
31	C	1003	VAL	0	0.007	-0.002	24.567	0.004	0.004	0.000	0.000	0.000
32	C	1004	THR	0	-0.025	-0.022	24.982	0.010	0.010	0.000	0.000	0.000
33	C	1005	ASN	0	-0.030	-0.024	27.535	0.006	0.006	0.000	0.000	0.000
34	C	1006	LEU	0	0.008	0.014	30.207	0.001	0.001	0.000	0.000	0.000
35	C	1007	ALA	0	0.033	0.017	29.374	0.001	0.001	0.000	0.000	0.000
36	C	1008	GLY	0	0.023	0.012	31.399	0.002	0.002	0.000	0.000	0.000
37	C	1009	GLN	0	-0.045	-0.028	33.652	-0.001	-0.001	0.000	0.000	0.000
38	C	1010	VAL	0	0.009	-0.007	34.359	-0.001	-0.001	0.000	0.000	0.000
39	C	1011	ASN	0	0.012	0.015	34.915	0.004	0.004	0.000	0.000	0.000
40	C	1012	ASN	0	0.002	-0.010	36.792	0.002	0.002	0.000	0.000	0.000
41	C	1013	LEU	0	-0.075	-0.030	39.178	-0.003	-0.003	0.000	0.000	0.000
42	C	1014	GLU	-1	-0.850	-0.918	39.258	0.033	0.033	0.000	0.000	0.000
43	C	1015	GLY	0	0.023	0.008	41.182	0.000	0.000	0.000	0.000	0.000
44	C	1016	LYS	1	0.868	0.932	43.139	-0.014	-0.014	0.000	0.000	0.000
45	C	1017	VAL	0	0.046	0.016	44.247	-0.002	-0.002	0.000	0.000	0.000
46	C	1018	ASN	0	0.052	0.028	44.915	-0.001	-0.001	0.000	0.000	0.000
47	C	1019	LYS	1	0.907	0.956	47.149	-0.021	-0.021	0.000	0.000	0.000
48	C	1020	VAL	0	-0.010	-0.012	49.122	-0.001	-0.001	0.000	0.000	0.000
49	C	1021	GLY	0	0.042	0.030	50.416	-0.001	-0.001	0.000	0.000	0.000
50	C	1022	LYS	1	0.961	0.978	49.268	-0.029	-0.029	0.000	0.000	0.000
51	C	1023	ARG	1	0.843	0.904	52.967	-0.018	-0.018	0.000	0.000	0.000
52	C	1024	ALA	0	0.024	0.027	55.182	-0.001	-0.001	0.000	0.000	0.000
53	C	1025	ASP	-1	-0.846	-0.924	55.317	0.020	0.020	0.000	0.000	0.000
54	C	1026	ALA	0	-0.022	-0.022	57.943	0.000	0.000	0.000	0.000	0.000
55	C	1027	GLY	0	-0.014	-0.001	59.607	-0.001	-0.001	0.000	0.000	0.000
56	C	1028	THR	0	0.004	-0.006	60.425	-0.001	-0.001	0.000	0.000	0.000
57	C	1029	ALA	0	0.026	0.019	62.320	0.000	0.000	0.000	0.000	0.000
58	C	1030	SER	0	0.013	0.001	64.024	0.000	0.000	0.000	0.000	0.000
59	C	1031	ALA	0	0.001	0.008	65.557	-0.001	-0.001	0.000	0.000	0.000
60	C	1032	LEU	0	0.019	0.013	65.186	0.000	0.000	0.000	0.000	0.000
61	C	1033	ALA	0	-0.012	0.003	68.385	0.000	0.000	0.000	0.000	0.000
62	C	1034	ALA	0	0.017	-0.012	70.062	0.000	0.000	0.000	0.000	0.000
63	C	1035	SER	0	-0.089	-0.049	71.367	0.000	0.000	0.000	0.000	0.000
64	C	1036	GLN	0	0.010	0.009	72.737	0.000	0.000	0.000	0.000	0.000
65	C	1037	LEU	0	-0.051	-0.006	74.416	0.000	0.000	0.000	0.000	0.000
66	C	1038	PRO	0	-0.002	-0.002	76.974	0.000	0.000	0.000	0.000	0.000
67	C	1039	GLN	0	0.019	0.014	80.761	0.000	0.000	0.000	0.000	0.000
68	C	1040	ALA	0	0.001	-0.004	83.158	0.000	0.000	0.000	0.000	0.000
69	C	1041	THR	0	0.019	-0.003	86.771	0.000	0.000	0.000	0.000	0.000
70	C	1042	MET	0	0.028	0.020	89.352	0.000	0.000	0.000	0.000	0.000
71	C	1043	PRO	0	0.062	0.020	92.059	0.000	0.000	0.000	0.000	0.000
72	C	1044	GLY	0	0.038	0.046	93.436	0.000	0.000	0.000	0.000	0.000
73	C	1045	LYS	1	0.841	0.913	91.268	-0.006	-0.006	0.000	0.000	0.000
74	C	1046	SER	0	-0.001	-0.007	87.352	0.000	0.000	0.000	0.000	0.000
75	C	1047	MET	0	-0.023	0.004	83.695	0.000	0.000	0.000	0.000	0.000
76	C	1048	VAL	0	0.004	-0.005	81.824	0.000	0.000	0.000	0.000	0.000
77	C	1049	ALA	0	0.001	0.004	79.315	0.000	0.000	0.000	0.000	0.000
78	C	1050	ILE	0	0.014	0.003	73.772	0.000	0.000	0.000	0.000	0.000
79	C	1051	ALA	0	0.010	0.013	73.956	0.000	0.000	0.000	0.000	0.000
80	C	1052	GLY	0	0.018	-0.007	70.114	0.000	0.000	0.000	0.000	0.000
81	C	1053	SER	0	-0.076	-0.039	66.740	0.000	0.000	0.000	0.000	0.000
82	C	1054	SER	0	0.001	-0.020	63.339	0.001	0.001	0.000	0.000	0.000
83	C	1055	TYR	0	0.025	0.012	59.122	0.000	0.000	0.000	0.000	0.000
84	C	1056	GLN	0	0.047	0.024	56.741	0.000	0.000	0.000	0.000	0.000
85	C	1057	GLY	0	-0.006	0.009	57.138	0.001	0.001	0.000	0.000	0.000
86	C	1058	GLN	0	-0.027	0.011	55.884	0.000	0.000	0.000	0.000	0.000
87	C	1059	ASN	0	0.048	0.030	59.799	-0.001	-0.001	0.000	0.000	0.000
88	C	1060	GLY	0	-0.010	-0.005	63.389	0.000	0.000	0.000	0.000	0.000
89	C	1061	LEU	0	-0.025	-0.010	65.804	0.000	0.000	0.000	0.000	0.000
90	C	1062	ALA	0	0.018	0.001	68.940	0.000	0.000	0.000	0.000	0.000
91	C	1063	ILE	0	0.025	0.011	71.640	0.000	0.000	0.000	0.000	0.000
92	C	1064	GLY	0	0.036	0.011	74.916	0.000	0.000	0.000	0.000	0.000
93	C	1065	VAL	0	-0.037	-0.003	77.497	0.000	0.000	0.000	0.000	0.000
94	C	1066	SER	0	0.024	0.011	80.929	0.000	0.000	0.000	0.000	0.000
95	C	1067	ARG	1	0.911	0.948	83.589	-0.005	-0.005	0.000	0.000	0.000
96	C	1068	ILE	0	0.011	0.026	87.022	0.000	0.000	0.000	0.000	0.000
97	C	1069	SER	0	-0.005	-0.015	89.808	0.000	0.000	0.000	0.000	0.000
98	C	1070	ASP	-1	-0.829	-0.932	92.483	0.004	0.004	0.000	0.000	0.000
99	C	1071	ASN	0	-0.010	0.011	94.986	0.000	0.000	0.000	0.000	0.000
100	C	1072	GLY	0	0.015	-0.003	93.657	0.000	0.000	0.000	0.000	0.000
101	C	1073	LYS	1	0.901	0.957	92.710	-0.003	-0.003	0.000	0.000	0.000
102	C	1074	VAL	0	-0.006	0.002	87.861	0.000	0.000	0.000	0.000	0.000
103	C	1075	ILE	0	0.005	0.015	84.681	0.000	0.000	0.000	0.000	0.000
104	C	1076	ILE	0	0.002	-0.001	83.200	0.000	0.000	0.000	0.000	0.000
105	C	1077	ARG	1	0.886	0.920	77.084	-0.007	-0.007	0.000	0.000	0.000
106	C	1078	LEU	0	-0.003	-0.002	77.422	0.000	0.000	0.000	0.000	0.000
107	C	1079	SER	0	-0.026	-0.018	73.867	0.000	0.000	0.000	0.000	0.000
108	C	1080	GLY	0	0.025	0.018	71.482	0.000	0.000	0.000	0.000	0.000
109	C	1081	THR	0	-0.029	-0.020	67.706	0.001	0.001	0.000	0.000	0.000
110	C	1082	THR	0	0.012	-0.009	65.000	0.000	0.000	0.000	0.000	0.000
111	C	1083	ASN	0	0.066	0.034	61.166	0.001	0.001	0.000	0.000	0.000
112	C	1084	SER	0	0.025	0.015	58.988	0.000	0.000	0.000	0.000	0.000
113	C	1085	GLN	0	0.012	0.020	54.827	0.001	0.001	0.000	0.000	0.000
114	C	1086	GLY	0	0.022	0.024	58.350	0.000	0.000	0.000	0.000	0.000
115	C	1087	LYS	1	0.739	0.855	56.754	-0.014	-0.014	0.000	0.000	0.000
116	C	1088	THR	0	0.053	0.022	61.294	0.000	0.000	0.000	0.000	0.000
117	C	1089	GLY	0	0.013	0.013	64.571	0.000	0.000	0.000	0.000	0.000
118	C	1090	VAL	0	-0.026	-0.016	66.888	0.000	0.000	0.000	0.000	0.000
119	C	1091	ALA	0	0.019	0.020	70.279	0.000	0.000	0.000	0.000	0.000
120	C	1092	ALA	0	-0.008	-0.009	72.654	0.000	0.000	0.000	0.000	0.000
121	C	1093	GLY	0	0.020	0.016	76.106	0.000	0.000	0.000	0.000	0.000
122	C	1094	VAL	0	-0.014	-0.011	78.814	0.000	0.000	0.000	0.000	0.000
123	C	1095	GLY	0	0.019	0.019	82.139	0.000	0.000	0.000	0.000	0.000
124	C	1096	TYR	0	0.022	0.012	84.710	0.000	0.000	0.000	0.000	0.000
125	C	1097	GLN	0	-0.013	-0.008	88.100	0.000	0.000	0.000	0.000	0.000
126	C	1098	TRP	0	-0.009	-0.003	88.241	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:973:VAL)