FMO DATABASE

FMODB ID: 22VKR

Calculation Name: 3MY2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MY2

Chain ID: A

ChEMBL ID:

UniProt ID: P0ADV9

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	OptHSide
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	-1089546.709397
FMO2-HF: Nuclear repulsion	1039360.471797
FMO2-HF: Total energy	-50186.2376
FMO2-MP2: Total energy	-50334.654938

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:59:SER)

Summations of interaction energy for fragment #1(A:59: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.
-25.152	-19.66	8.215	-6.711	-6.998	0.033

Interaction energy analysis for fragmet #1(A:59:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.046

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	61	ARG	1	0.899	0.951	3.836	-1.587	1.502	-0.029	-1.799	-1.262	0.007
4	A	62	LEU	0	0.003	0.003	7.122	-0.485	-0.485	0.000	0.000	0.000	0.000
5	A	63	ILE	0	-0.012	0.001	10.266	0.128	0.128	0.000	0.000	0.000	0.000
6	A	64	ALA	0	0.006	0.005	13.634	-0.082	-0.082	0.000	0.000	0.000	0.000
7	A	65	GLN	0	0.005	0.008	16.986	0.026	0.026	0.000	0.000	0.000	0.000
8	A	66	HIS	0	-0.031	-0.029	20.190	0.018	0.018	0.000	0.000	0.000	0.000
9	A	67	VAL	0	-0.012	-0.024	17.476	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	68	GLU	-1	-0.848	-0.864	20.541	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	69	TYR	0	0.012	-0.003	18.648	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	70	TYR	0	-0.055	-0.047	21.160	0.011	0.011	0.000	0.000	0.000	0.000
13	A	71	SER	0	0.043	0.004	22.445	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	72	ASP	-1	-0.938	-0.960	23.523	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	73	GLN	0	-0.062	-0.039	23.695	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	74	ALA	0	0.000	0.010	19.408	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	75	VAL	0	-0.046	-0.021	18.689	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	76	SER	0	-0.005	0.000	16.255	0.029	0.029	0.000	0.000	0.000	0.000
19	A	77	TRP	0	-0.014	-0.003	18.370	-0.049	-0.049	0.000	0.000	0.000	0.000
20	A	78	PHE	0	0.028	0.000	14.108	0.023	0.023	0.000	0.000	0.000	0.000
21	A	79	THR	0	0.007	-0.009	18.888	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	80	GLN	0	-0.031	-0.014	19.998	0.020	0.020	0.000	0.000	0.000	0.000
23	A	81	PRO	0	-0.022	0.006	14.917	0.031	0.031	0.000	0.000	0.000	0.000
24	A	82	VAL	0	-0.001	-0.014	13.189	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	83	LEU	0	0.013	0.009	7.718	0.104	0.104	0.000	0.000	0.000	0.000
26	A	84	THR	0	-0.059	-0.027	7.669	0.160	0.160	0.000	0.000	0.000	0.000
27	A	85	THR	0	0.063	0.031	4.874	0.331	0.331	0.000	0.000	0.000	0.000
28	A	86	PHE	0	-0.042	-0.040	2.154	2.469	3.600	1.333	-0.818	-1.646	0.000
29	A	87	ASP	-1	-0.838	-0.919	3.012	-6.473	-4.628	0.168	-1.142	-0.871	-0.012
30	A	88	LYS	1	0.926	0.951	4.344	1.092	1.262	-0.001	-0.022	-0.147	0.000
31	A	89	ASP	-1	-0.863	-0.917	6.242	0.231	0.231	0.000	0.000	0.000	0.000
32	A	90	LYS	1	0.783	0.892	1.900	-21.202	-22.103	6.744	-2.891	-2.953	0.038
33	A	91	ILE	0	0.060	0.035	5.548	0.231	0.231	0.000	0.000	0.000	0.000
34	A	92	PRO	0	-0.046	-0.029	6.594	-0.392	-0.392	0.000	0.000	0.000	0.000
35	A	93	THR	0	0.018	-0.002	6.498	-0.240	-0.240	0.000	0.000	0.000	0.000
36	A	94	TRP	0	0.020	0.007	8.493	0.235	0.235	0.000	0.000	0.000	0.000
37	A	95	SER	0	-0.063	-0.020	9.574	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	96	VAL	0	0.025	-0.004	11.257	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	97	LYS	1	0.937	0.978	13.759	0.131	0.131	0.000	0.000	0.000	0.000
40	A	98	ALA	0	0.060	0.028	16.836	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	99	ASP	-1	-0.818	-0.888	19.348	-0.083	-0.083	0.000	0.000	0.000	0.000
42	A	100	LYS	1	0.937	0.978	20.782	0.138	0.138	0.000	0.000	0.000	0.000
43	A	101	ALA	0	0.004	0.001	16.109	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	102	LYS	1	0.935	0.988	17.833	0.194	0.194	0.000	0.000	0.000	0.000
45	A	103	LEU	0	-0.035	-0.005	11.536	-0.057	-0.057	0.000	0.000	0.000	0.000
46	A	104	THR	0	-0.012	-0.028	15.118	0.044	0.044	0.000	0.000	0.000	0.000
47	A	105	ASN	0	0.062	0.017	14.530	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.869	-0.914	13.889	-0.268	-0.268	0.000	0.000	0.000	0.000
49	A	107	ARG	1	0.902	0.964	8.251	0.201	0.201	0.000	0.000	0.000	0.000
50	A	108	MET	0	0.026	0.039	10.802	-0.161	-0.161	0.000	0.000	0.000	0.000
51	A	109	LEU	0	-0.026	-0.016	11.304	0.054	0.054	0.000	0.000	0.000	0.000
52	A	110	TYR	0	-0.035	-0.053	13.589	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	111	LEU	0	-0.007	0.002	13.883	0.032	0.032	0.000	0.000	0.000	0.000
54	A	112	TYR	0	0.025	-0.013	18.027	0.004	0.004	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.050	0.031	21.700	0.018	0.018	0.000	0.000	0.000	0.000
56	A	114	HIS	1	0.855	0.889	22.227	0.108	0.108	0.000	0.000	0.000	0.000
57	A	115	VAL	0	0.023	0.027	17.537	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	116	GLU	-1	-0.801	-0.863	18.482	-0.165	-0.165	0.000	0.000	0.000	0.000
59	A	117	VAL	0	-0.030	-0.005	13.374	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	118	ASN	0	-0.043	-0.049	14.847	0.049	0.049	0.000	0.000	0.000	0.000
61	A	119	ALA	0	0.022	0.018	13.686	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	120	LEU	0	-0.076	-0.036	10.041	0.097	0.097	0.000	0.000	0.000	0.000
63	A	121	VAL	0	0.026	0.015	11.246	0.077	0.077	0.000	0.000	0.000	0.000
64	A	122	PRO	0	0.024	0.011	14.035	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	123	ASP	-1	-0.875	-0.939	14.942	-0.360	-0.360	0.000	0.000	0.000	0.000
66	A	124	SER	0	-0.039	-0.034	14.769	-0.100	-0.100	0.000	0.000	0.000	0.000
67	A	125	GLN	0	0.029	0.026	16.768	0.046	0.046	0.000	0.000	0.000	0.000
68	A	126	LEU	0	0.037	0.033	16.022	0.035	0.035	0.000	0.000	0.000	0.000
69	A	127	ARG	1	0.838	0.900	16.855	0.222	0.222	0.000	0.000	0.000	0.000
70	A	128	ARG	1	0.846	0.895	17.962	0.169	0.169	0.000	0.000	0.000	0.000
71	A	129	ILE	0	0.004	0.021	16.224	0.011	0.011	0.000	0.000	0.000	0.000
72	A	130	THR	0	0.005	0.011	19.388	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	131	THR	0	-0.026	-0.033	20.438	0.002	0.002	0.000	0.000	0.000	0.000
74	A	132	ASP	-1	-0.871	-0.934	22.698	-0.151	-0.151	0.000	0.000	0.000	0.000
75	A	133	ASN	0	-0.042	-0.043	21.357	0.013	0.013	0.000	0.000	0.000	0.000
76	A	134	ALA	0	-0.017	0.017	17.340	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	135	GLN	0	-0.042	-0.027	16.113	0.024	0.024	0.000	0.000	0.000	0.000
78	A	136	ILE	0	-0.016	-0.011	9.766	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	137	ASN	0	0.051	0.046	9.829	-0.070	-0.070	0.000	0.000	0.000	0.000
80	A	138	LEU	0	-0.008	-0.017	6.582	-0.207	-0.207	0.000	0.000	0.000	0.000
81	A	139	VAL	0	-0.040	-0.012	5.168	-0.851	-0.845	-0.001	0.000	-0.005	0.000
82	A	140	THR	0	-0.055	-0.061	6.351	-0.109	-0.109	0.000	0.000	0.000	0.000
83	A	141	GLN	0	0.021	-0.002	3.800	0.761	0.913	0.001	-0.039	-0.114	0.000
84	A	142	ASP	-1	-0.809	-0.854	8.500	-0.588	-0.588	0.000	0.000	0.000	0.000
85	A	143	VAL	0	-0.010	-0.012	12.145	-0.062	-0.062	0.000	0.000	0.000	0.000
86	A	144	THR	0	-0.010	-0.005	14.419	0.062	0.062	0.000	0.000	0.000	0.000
87	A	145	SER	0	0.039	0.007	18.125	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	146	GLU	-1	-0.838	-0.925	21.028	-0.273	-0.273	0.000	0.000	0.000	0.000
89	A	147	ASP	-1	-0.824	-0.885	24.247	-0.163	-0.163	0.000	0.000	0.000	0.000
90	A	148	LEU	0	-0.034	-0.031	25.757	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	149	VAL	0	-0.009	0.007	21.658	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	150	THR	0	-0.041	-0.017	23.867	0.018	0.018	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.006	-0.001	19.966	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	152	TYR	0	0.013	-0.022	21.778	0.035	0.035	0.000	0.000	0.000	0.000
95	A	153	GLY	0	0.029	0.011	21.392	-0.036	-0.036	0.000	0.000	0.000	0.000
96	A	154	THR	0	-0.045	-0.033	22.035	0.017	0.017	0.000	0.000	0.000	0.000
97	A	155	THR	0	-0.010	-0.009	24.416	0.012	0.012	0.000	0.000	0.000	0.000
98	A	156	PHE	0	-0.019	0.003	26.789	0.013	0.013	0.000	0.000	0.000	0.000
99	A	157	ASN	0	0.012	0.008	26.129	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	158	SER	0	0.044	0.022	25.783	0.016	0.016	0.000	0.000	0.000	0.000
101	A	159	SER	0	0.021	0.003	26.489	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	160	GLY	0	0.037	0.034	27.588	0.010	0.010	0.000	0.000	0.000	0.000
103	A	161	LEU	0	-0.058	-0.026	27.744	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	162	LYS	1	0.897	0.944	24.599	0.173	0.173	0.000	0.000	0.000	0.000
105	A	163	MET	0	-0.059	-0.017	17.590	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	164	ARG	1	0.875	0.939	18.688	0.271	0.271	0.000	0.000	0.000	0.000
107	A	165	GLY	0	0.055	0.005	16.462	0.034	0.034	0.000	0.000	0.000	0.000
108	A	166	ASN	0	-0.060	-0.034	10.687	-0.122	-0.122	0.000	0.000	0.000	0.000
109	A	167	LEU	0	0.031	0.021	8.706	0.051	0.051	0.000	0.000	0.000	0.000
110	A	168	ARG	1	0.873	0.952	7.213	0.903	0.903	0.000	0.000	0.000	0.000
111	A	169	SER	0	-0.042	-0.029	8.968	0.123	0.123	0.000	0.000	0.000	0.000
112	A	170	LYS	1	0.854	0.946	11.310	0.683	0.683	0.000	0.000	0.000	0.000
113	A	171	ASN	0	-0.017	0.000	13.725	0.128	0.128	0.000	0.000	0.000	0.000
114	A	172	ALA	0	0.022	-0.019	16.090	-0.058	-0.058	0.000	0.000	0.000	0.000
115	A	173	GLU	-1	-0.862	-0.902	18.648	-0.250	-0.250	0.000	0.000	0.000	0.000
116	A	174	LEU	0	-0.018	-0.011	22.223	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	175	ILE	0	0.009	0.006	23.631	0.009	0.009	0.000	0.000	0.000	0.000
118	A	176	GLU	-1	-0.784	-0.876	27.064	-0.133	-0.133	0.000	0.000	0.000	0.000
119	A	177	LYS	1	0.810	0.886	30.202	0.122	0.122	0.000	0.000	0.000	0.000
120	A	178	VAL	0	0.021	0.016	28.684	0.001	0.001	0.000	0.000	0.000	0.000
121	A	179	ARG	1	0.926	0.970	30.886	0.117	0.117	0.000	0.000	0.000	0.000
122	A	180	THR	0	-0.011	-0.042	29.718	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	181	SER	0	-0.020	-0.023	30.765	0.004	0.004	0.000	0.000	0.000	0.000
124	A	182	TYR	0	-0.005	-0.001	30.891	0.006	0.006	0.000	0.000	0.000	0.000
125	A	183	GLU	-1	-0.848	-0.882	34.035	-0.113	-0.113	0.000	0.000	0.000	0.000
126	A	184	ILE	0	-0.046	-0.016	36.900	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:59:SER)