FMO DATABASE

FMODB ID: YVR82

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

Total energy (hartree)

FMO2-HF: Electronic energy	-651242.096816
FMO2-HF: Nuclear repulsion	607387.878682
FMO2-HF: Total energy	-43854.218134
FMO2-MP2: Total energy	-43982.838551

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.
-3.064	-0.713	0.117	-0.893	-1.573	0.002

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 : -0.015 / 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	C	975	ILE	0	-0.011	-0.011	2.728	-2.317	-0.076	0.118	-0.888	-1.470	0.002
4	C	976	ASP	-1	-0.880	-0.932	5.085	-0.599	-0.489	-0.001	-0.005	-0.103	0.000
5	C	977	ASN	0	-0.077	-0.042	8.724	0.050	0.050	0.000	0.000	0.000	0.000
6	C	978	VAL	0	0.040	0.033	9.084	-0.032	-0.032	0.000	0.000	0.000	0.000
7	C	979	ALA	0	-0.014	-0.009	11.759	0.087	0.087	0.000	0.000	0.000	0.000
8	C	980	ASN	0	-0.006	-0.019	15.287	-0.051	-0.051	0.000	0.000	0.000	0.000
9	C	981	GLY	0	0.043	0.046	16.948	0.006	0.006	0.000	0.000	0.000	0.000
10	C	982	ASP	-1	-0.891	-0.958	18.002	-0.166	-0.166	0.000	0.000	0.000	0.000
11	C	983	ILE	0	-0.058	-0.006	20.088	-0.010	-0.010	0.000	0.000	0.000	0.000
12	C	984	SER	0	0.031	0.008	22.238	0.024	0.024	0.000	0.000	0.000	0.000
13	C	985	ALA	0	-0.038	-0.024	23.626	-0.007	-0.007	0.000	0.000	0.000	0.000
14	C	986	THR	0	-0.039	-0.038	24.814	0.003	0.003	0.000	0.000	0.000	0.000
15	C	987	SER	0	-0.027	-0.002	20.174	-0.014	-0.014	0.000	0.000	0.000	0.000
16	C	988	THR	0	-0.034	-0.013	18.122	0.019	0.019	0.000	0.000	0.000	0.000
17	C	989	ASP	-1	-0.868	-0.923	16.117	-0.361	-0.361	0.000	0.000	0.000	0.000
18	C	990	ALA	0	-0.022	-0.008	11.256	0.007	0.007	0.000	0.000	0.000	0.000
19	C	991	ILE	0	0.022	0.002	13.021	0.058	0.058	0.000	0.000	0.000	0.000
20	C	992	ASN	0	-0.016	-0.020	12.278	-0.020	-0.020	0.000	0.000	0.000	0.000
21	C	993	GLY	0	0.032	-0.006	13.132	0.070	0.070	0.000	0.000	0.000	0.000
22	C	994	SER	0	-0.005	0.001	14.670	0.067	0.067	0.000	0.000	0.000	0.000
23	C	995	GLN	0	0.048	0.019	16.698	-0.009	-0.009	0.000	0.000	0.000	0.000
24	C	996	LEU	0	0.045	0.032	14.621	0.029	0.029	0.000	0.000	0.000	0.000
25	C	997	TYR	0	-0.024	-0.014	18.101	0.037	0.037	0.000	0.000	0.000	0.000
26	C	998	ALA	0	-0.011	-0.003	19.763	0.020	0.020	0.000	0.000	0.000	0.000
27	C	999	VAL	0	0.026	0.011	21.084	0.015	0.015	0.000	0.000	0.000	0.000
28	C	1000	ALA	0	0.008	-0.004	19.842	0.016	0.016	0.000	0.000	0.000	0.000
29	C	1001	LYS	1	0.924	0.975	21.957	0.031	0.031	0.000	0.000	0.000	0.000
30	C	1002	GLY	0	0.031	0.015	24.758	0.007	0.007	0.000	0.000	0.000	0.000
31	C	1003	VAL	0	0.017	0.013	24.275	0.005	0.005	0.000	0.000	0.000	0.000
32	C	1004	THR	0	0.023	0.010	24.908	0.009	0.009	0.000	0.000	0.000	0.000
33	C	1005	ASN	0	-0.020	-0.011	27.101	0.010	0.010	0.000	0.000	0.000	0.000
34	C	1006	LEU	0	0.016	0.013	29.960	0.002	0.002	0.000	0.000	0.000	0.000
35	C	1007	ALA	0	0.016	0.015	29.074	0.002	0.002	0.000	0.000	0.000	0.000
36	C	1008	GLY	0	0.047	0.015	31.110	0.002	0.002	0.000	0.000	0.000	0.000
37	C	1009	GLN	0	-0.063	-0.038	33.339	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	1010	VAL	0	-0.084	-0.056	33.830	-0.001	-0.001	0.000	0.000	0.000	0.000
39	C	1011	ASN	0	0.062	0.047	34.585	0.003	0.003	0.000	0.000	0.000	0.000
40	C	1012	ASN	0	0.013	-0.003	36.522	0.003	0.003	0.000	0.000	0.000	0.000
41	C	1013	LEU	0	-0.098	-0.043	39.058	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	1014	GLU	-1	-0.853	-0.923	38.434	0.029	0.029	0.000	0.000	0.000	0.000
43	C	1015	GLY	0	0.024	0.023	40.717	0.001	0.001	0.000	0.000	0.000	0.000
44	C	1016	LYS	1	0.896	0.928	42.919	-0.010	-0.010	0.000	0.000	0.000	0.000
45	C	1017	VAL	0	0.042	0.023	43.784	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	1018	ASN	0	0.046	0.017	44.871	0.000	0.000	0.000	0.000	0.000	0.000
47	C	1019	LYS	1	0.918	0.957	47.352	-0.017	-0.017	0.000	0.000	0.000	0.000
48	C	1020	VAL	0	-0.029	-0.020	48.784	-0.001	-0.001	0.000	0.000	0.000	0.000
49	C	1021	GLY	0	0.058	0.033	50.272	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	1022	LYS	1	1.004	1.015	49.737	-0.026	-0.026	0.000	0.000	0.000	0.000
51	C	1023	ARG	1	0.880	0.928	52.450	-0.016	-0.016	0.000	0.000	0.000	0.000
52	C	1024	ALA	0	-0.021	0.006	54.703	-0.001	-0.001	0.000	0.000	0.000	0.000
53	C	1025	ASP	-1	-0.825	-0.912	55.617	0.017	0.017	0.000	0.000	0.000	0.000
54	C	1026	ALA	0	0.004	-0.015	57.785	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	1027	GLY	0	-0.037	0.001	59.191	-0.001	-0.001	0.000	0.000	0.000	0.000
56	C	1028	THR	0	0.028	0.011	60.790	-0.001	-0.001	0.000	0.000	0.000	0.000
57	C	1029	ALA	0	-0.008	-0.013	61.988	0.000	0.000	0.000	0.000	0.000	0.000
58	C	1030	SER	0	-0.024	-0.026	63.561	0.000	0.000	0.000	0.000	0.000	0.000
59	C	1031	ALA	0	0.019	0.006	65.323	0.000	0.000	0.000	0.000	0.000	0.000
60	C	1032	LEU	0	0.021	0.018	65.589	0.000	0.000	0.000	0.000	0.000	0.000
61	C	1033	ALA	0	-0.018	-0.004	68.298	0.000	0.000	0.000	0.000	0.000	0.000
62	C	1034	ALA	0	0.021	-0.001	70.013	0.000	0.000	0.000	0.000	0.000	0.000
63	C	1035	SER	0	-0.067	-0.028	71.168	0.000	0.000	0.000	0.000	0.000	0.000
64	C	1036	GLN	0	0.014	0.019	72.820	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	1037	LEU	0	-0.050	-0.017	74.492	0.000	0.000	0.000	0.000	0.000	0.000
66	C	1038	PRO	0	-0.024	-0.018	76.817	0.000	0.000	0.000	0.000	0.000	0.000
67	C	1039	GLN	0	0.014	0.001	80.567	0.000	0.000	0.000	0.000	0.000	0.000
68	C	1040	ALA	0	-0.036	-0.018	82.713	0.000	0.000	0.000	0.000	0.000	0.000
69	C	1041	THR	0	0.026	-0.011	86.358	0.000	0.000	0.000	0.000	0.000	0.000
70	C	1042	MET	0	0.002	0.008	89.200	0.000	0.000	0.000	0.000	0.000	0.000
71	C	1043	PRO	0	0.075	0.012	91.816	0.000	0.000	0.000	0.000	0.000	0.000
72	C	1044	GLY	0	0.031	0.041	92.734	0.000	0.000	0.000	0.000	0.000	0.000
73	C	1045	LYS	1	0.869	0.936	90.711	-0.006	-0.006	0.000	0.000	0.000	0.000
74	C	1046	SER	0	-0.024	-0.025	86.786	0.000	0.000	0.000	0.000	0.000	0.000
75	C	1047	MET	0	-0.038	0.017	83.149	0.000	0.000	0.000	0.000	0.000	0.000
76	C	1048	VAL	0	0.008	-0.009	81.486	0.000	0.000	0.000	0.000	0.000	0.000
77	C	1049	ALA	0	-0.003	0.006	78.726	0.000	0.000	0.000	0.000	0.000	0.000
78	C	1050	ILE	0	0.000	-0.011	73.444	0.000	0.000	0.000	0.000	0.000	0.000
79	C	1051	ALA	0	0.006	0.016	73.198	0.000	0.000	0.000	0.000	0.000	0.000
80	C	1052	GLY	0	0.016	-0.011	69.939	0.000	0.000	0.000	0.000	0.000	0.000
81	C	1053	SER	0	-0.062	-0.023	66.898	0.000	0.000	0.000	0.000	0.000	0.000
82	C	1054	SER	0	-0.008	-0.014	63.521	0.001	0.001	0.000	0.000	0.000	0.000
83	C	1055	TYR	0	0.025	0.008	59.154	0.000	0.000	0.000	0.000	0.000	0.000
84	C	1056	GLN	0	0.070	0.036	56.824	0.001	0.001	0.000	0.000	0.000	0.000
85	C	1057	GLY	0	-0.029	-0.006	57.268	0.001	0.001	0.000	0.000	0.000	0.000
86	C	1058	GLN	0	-0.058	-0.016	55.877	0.001	0.001	0.000	0.000	0.000	0.000
87	C	1059	ASN	0	0.053	0.016	59.919	-0.001	-0.001	0.000	0.000	0.000	0.000
88	C	1060	GLY	0	-0.028	-0.010	63.403	0.000	0.000	0.000	0.000	0.000	0.000
89	C	1061	LEU	0	-0.020	-0.011	65.600	0.000	0.000	0.000	0.000	0.000	0.000
90	C	1062	ALA	0	0.015	-0.003	68.700	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	1063	ILE	0	0.027	0.029	71.494	0.000	0.000	0.000	0.000	0.000	0.000
92	C	1064	GLY	0	0.056	0.019	74.793	0.000	0.000	0.000	0.000	0.000	0.000
93	C	1065	VAL	0	-0.032	0.010	77.303	0.000	0.000	0.000	0.000	0.000	0.000
94	C	1066	SER	0	0.014	0.004	80.687	0.000	0.000	0.000	0.000	0.000	0.000
95	C	1067	ARG	1	0.976	0.988	83.262	-0.004	-0.004	0.000	0.000	0.000	0.000
96	C	1068	ILE	0	-0.015	0.031	86.850	0.000	0.000	0.000	0.000	0.000	0.000
97	C	1069	SER	0	0.006	0.008	89.537	0.000	0.000	0.000	0.000	0.000	0.000
98	C	1070	ASP	-1	-0.808	-0.925	92.081	0.004	0.004	0.000	0.000	0.000	0.000
99	C	1071	ASN	0	-0.025	-0.021	94.414	0.000	0.000	0.000	0.000	0.000	0.000
100	C	1072	GLY	0	-0.027	-0.028	93.029	0.000	0.000	0.000	0.000	0.000	0.000
101	C	1073	LYS	1	0.935	0.978	92.037	-0.002	-0.002	0.000	0.000	0.000	0.000
102	C	1074	VAL	0	-0.005	0.004	87.396	0.000	0.000	0.000	0.000	0.000	0.000
103	C	1075	ILE	0	-0.011	0.006	84.701	0.000	0.000	0.000	0.000	0.000	0.000
104	C	1076	ILE	0	0.011	0.002	82.609	0.000	0.000	0.000	0.000	0.000	0.000
105	C	1077	ARG	1	0.925	0.956	77.929	-0.006	-0.006	0.000	0.000	0.000	0.000
106	C	1078	LEU	0	0.016	-0.003	77.077	0.000	0.000	0.000	0.000	0.000	0.000
107	C	1079	SER	0	-0.036	-0.029	73.829	0.000	0.000	0.000	0.000	0.000	0.000
108	C	1080	GLY	0	-0.015	0.011	71.395	0.000	0.000	0.000	0.000	0.000	0.000
109	C	1081	THR	0	-0.034	-0.022	67.083	0.000	0.000	0.000	0.000	0.000	0.000
110	C	1082	THR	0	0.011	0.018	64.655	0.000	0.000	0.000	0.000	0.000	0.000
111	C	1083	ASN	0	0.094	0.054	60.690	0.001	0.001	0.000	0.000	0.000	0.000
112	C	1084	SER	0	0.044	0.023	59.337	0.000	0.000	0.000	0.000	0.000	0.000
113	C	1085	GLN	0	-0.047	-0.036	54.371	0.001	0.001	0.000	0.000	0.000	0.000
114	C	1086	GLY	0	-0.029	-0.010	58.037	0.000	0.000	0.000	0.000	0.000	0.000
115	C	1087	LYS	1	0.800	0.902	56.234	-0.014	-0.014	0.000	0.000	0.000	0.000
116	C	1088	THR	0	0.028	0.000	61.182	0.000	0.000	0.000	0.000	0.000	0.000
117	C	1089	GLY	0	0.038	0.019	64.319	0.000	0.000	0.000	0.000	0.000	0.000
118	C	1090	VAL	0	-0.004	-0.011	66.826	0.000	0.000	0.000	0.000	0.000	0.000
119	C	1091	ALA	0	0.011	0.017	70.059	0.000	0.000	0.000	0.000	0.000	0.000
120	C	1092	ALA	0	-0.002	-0.010	72.495	0.000	0.000	0.000	0.000	0.000	0.000
121	C	1093	GLY	0	0.013	0.020	75.847	0.000	0.000	0.000	0.000	0.000	0.000
122	C	1094	VAL	0	-0.019	-0.009	78.389	0.000	0.000	0.000	0.000	0.000	0.000
123	C	1095	GLY	0	0.011	0.005	81.706	0.000	0.000	0.000	0.000	0.000	0.000
124	C	1096	TYR	0	0.007	-0.006	84.340	0.000	0.000	0.000	0.000	0.000	0.000
125	C	1097	GLN	0	0.032	0.022	87.768	0.000	0.000	0.000	0.000	0.000	0.000
126	C	1098	TRP	0	-0.002	-0.002	88.148	0.000	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)