FMO DATABASE

FMODB ID: 7G1JK

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	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	-1088724.804959
FMO2-HF: Nuclear repulsion	1038539.446767
FMO2-HF: Total energy	-50185.358192
FMO2-MP2: Total energy	-50333.846487

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.
-14.677	-7.527	2.261	-4.31	-5.102	-0.004

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 : 0.003 / q_NPA : -0.007

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	0.913	0.961	3.836	-0.832	1.263	-0.029	-1.158	-0.908	0.002
4	A	62	LEU	0	0.012	0.005	7.103	-0.407	-0.407	0.000	0.000	0.000	0.000
5	A	63	ILE	0	-0.018	-0.003	10.257	0.046	0.046	0.000	0.000	0.000	0.000
6	A	64	ALA	0	0.014	0.007	13.618	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	65	GLN	0	0.002	0.010	16.975	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	66	HIS	0	-0.049	-0.054	20.179	0.031	0.031	0.000	0.000	0.000	0.000
9	A	67	VAL	0	-0.001	-0.011	17.567	0.027	0.027	0.000	0.000	0.000	0.000
10	A	68	GLU	-1	-0.815	-0.836	20.538	0.232	0.232	0.000	0.000	0.000	0.000
11	A	69	TYR	0	0.015	0.004	18.176	0.012	0.012	0.000	0.000	0.000	0.000
12	A	70	TYR	0	-0.081	-0.069	21.167	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	71	SER	0	0.052	-0.005	22.454	0.012	0.012	0.000	0.000	0.000	0.000
14	A	72	ASP	-1	-0.931	-0.944	23.536	0.232	0.232	0.000	0.000	0.000	0.000
15	A	73	GLN	0	-0.084	-0.053	23.855	0.005	0.005	0.000	0.000	0.000	0.000
16	A	74	ALA	0	0.005	0.017	19.379	0.016	0.016	0.000	0.000	0.000	0.000
17	A	75	VAL	0	-0.050	-0.018	18.834	0.039	0.039	0.000	0.000	0.000	0.000
18	A	76	SER	0	-0.003	0.000	16.123	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	77	TRP	0	-0.015	-0.008	18.415	0.009	0.009	0.000	0.000	0.000	0.000
20	A	78	PHE	0	0.025	-0.001	14.074	0.015	0.015	0.000	0.000	0.000	0.000
21	A	79	THR	0	-0.008	-0.016	18.891	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	80	GLN	0	-0.031	-0.011	19.991	0.024	0.024	0.000	0.000	0.000	0.000
23	A	81	PRO	0	-0.034	0.004	14.899	0.033	0.033	0.000	0.000	0.000	0.000
24	A	82	VAL	0	0.010	-0.020	13.200	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	83	LEU	0	0.006	0.009	7.672	0.148	0.148	0.000	0.000	0.000	0.000
26	A	84	THR	0	-0.070	-0.035	7.312	-0.120	-0.120	0.000	0.000	0.000	0.000
27	A	85	THR	0	0.054	0.028	4.837	0.442	0.442	0.000	0.000	0.000	0.000
28	A	86	PHE	0	-0.030	-0.028	2.096	1.030	2.247	1.721	-1.090	-1.848	-0.001
29	A	87	ASP	-1	-0.814	-0.903	2.954	-7.855	-5.971	0.239	-1.166	-0.957	-0.012
30	A	88	LYS	1	0.906	0.938	4.341	1.374	1.543	-0.001	-0.021	-0.147	0.000
31	A	89	ASP	-1	-0.864	-0.916	6.263	-1.698	-1.698	0.000	0.000	0.000	0.000
32	A	90	LYS	1	0.831	0.913	2.816	-8.250	-6.613	0.330	-0.838	-1.130	0.007
33	A	91	ILE	0	0.051	0.032	5.479	0.864	0.864	0.000	0.000	0.000	0.000
34	A	92	PRO	0	-0.035	-0.027	6.601	-0.402	-0.402	0.000	0.000	0.000	0.000
35	A	93	THR	0	-0.030	-0.018	6.701	0.013	0.013	0.000	0.000	0.000	0.000
36	A	94	TRP	0	0.022	-0.003	8.396	0.233	0.233	0.000	0.000	0.000	0.000
37	A	95	SER	0	-0.065	-0.019	9.559	0.047	0.047	0.000	0.000	0.000	0.000
38	A	96	VAL	0	0.038	-0.001	11.196	-0.038	-0.038	0.000	0.000	0.000	0.000
39	A	97	LYS	1	0.932	0.982	13.681	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	98	ALA	0	0.056	0.019	16.836	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	99	ASP	-1	-0.788	-0.863	19.493	0.162	0.162	0.000	0.000	0.000	0.000
42	A	100	LYS	1	0.949	0.977	20.802	-0.188	-0.188	0.000	0.000	0.000	0.000
43	A	101	ALA	0	0.003	0.004	16.481	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	102	LYS	1	0.943	0.988	18.395	-0.301	-0.301	0.000	0.000	0.000	0.000
45	A	103	LEU	0	-0.035	-0.003	11.795	0.030	0.030	0.000	0.000	0.000	0.000
46	A	104	THR	0	-0.006	-0.017	15.734	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	105	ASN	0	0.075	0.025	15.008	0.134	0.134	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.883	-0.930	14.666	0.534	0.534	0.000	0.000	0.000	0.000
49	A	107	ARG	1	0.890	0.959	8.561	-1.186	-1.186	0.000	0.000	0.000	0.000
50	A	108	MET	0	0.005	0.007	11.802	0.019	0.019	0.000	0.000	0.000	0.000
51	A	109	LEU	0	-0.010	-0.008	11.823	0.018	0.018	0.000	0.000	0.000	0.000
52	A	110	TYR	0	-0.018	-0.027	14.478	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	111	LEU	0	-0.011	-0.003	14.261	0.024	0.024	0.000	0.000	0.000	0.000
54	A	112	TYR	0	0.028	-0.002	18.587	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.029	0.019	22.209	0.010	0.010	0.000	0.000	0.000	0.000
56	A	114	HIS	1	0.840	0.879	22.446	-0.091	-0.091	0.000	0.000	0.000	0.000
57	A	115	VAL	0	0.026	0.031	17.617	0.006	0.006	0.000	0.000	0.000	0.000
58	A	116	GLU	-1	-0.849	-0.931	18.421	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	117	VAL	0	-0.027	-0.010	13.350	0.018	0.018	0.000	0.000	0.000	0.000
60	A	118	ASN	0	-0.052	-0.042	14.784	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	119	ALA	0	0.025	0.013	13.650	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	120	LEU	0	-0.076	-0.036	10.087	0.065	0.065	0.000	0.000	0.000	0.000
63	A	121	VAL	0	0.002	0.004	11.259	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	122	PRO	0	0.017	-0.004	14.018	0.033	0.033	0.000	0.000	0.000	0.000
65	A	123	ASP	-1	-0.916	-0.941	15.160	-0.552	-0.552	0.000	0.000	0.000	0.000
66	A	124	SER	0	-0.055	-0.055	14.724	-0.085	-0.085	0.000	0.000	0.000	0.000
67	A	125	GLN	0	0.030	0.020	16.761	0.069	0.069	0.000	0.000	0.000	0.000
68	A	126	LEU	0	0.037	0.033	15.605	0.036	0.036	0.000	0.000	0.000	0.000
69	A	127	ARG	1	0.861	0.925	17.111	0.248	0.248	0.000	0.000	0.000	0.000
70	A	128	ARG	1	0.914	0.961	17.919	0.034	0.034	0.000	0.000	0.000	0.000
71	A	129	ILE	0	0.003	0.022	16.186	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	130	THR	0	0.004	0.009	19.316	0.008	0.008	0.000	0.000	0.000	0.000
73	A	131	THR	0	-0.046	-0.037	20.403	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	132	ASP	-1	-0.872	-0.935	22.745	0.080	0.080	0.000	0.000	0.000	0.000
75	A	133	ASN	0	-0.044	-0.043	21.730	0.035	0.035	0.000	0.000	0.000	0.000
76	A	134	ALA	0	-0.010	0.014	17.576	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	135	GLN	0	-0.073	-0.059	16.755	0.043	0.043	0.000	0.000	0.000	0.000
78	A	136	ILE	0	-0.015	-0.004	10.150	-0.052	-0.052	0.000	0.000	0.000	0.000
79	A	137	ASN	0	0.049	0.043	10.753	0.252	0.252	0.000	0.000	0.000	0.000
80	A	138	LEU	0	-0.002	-0.017	7.477	-0.059	-0.059	0.000	0.000	0.000	0.000
81	A	139	VAL	0	-0.041	-0.014	6.153	0.966	0.966	0.000	0.000	0.000	0.000
82	A	140	THR	0	-0.059	-0.054	7.110	-0.074	-0.074	0.000	0.000	0.000	0.000
83	A	141	GLN	0	0.009	-0.009	3.687	-0.723	-0.575	0.001	-0.037	-0.112	0.000
84	A	142	ASP	-1	-0.810	-0.865	8.723	-0.090	-0.090	0.000	0.000	0.000	0.000
85	A	143	VAL	0	-0.016	-0.013	12.426	0.088	0.088	0.000	0.000	0.000	0.000
86	A	144	THR	0	-0.015	-0.006	14.612	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	145	SER	0	0.075	0.036	18.393	0.017	0.017	0.000	0.000	0.000	0.000
88	A	146	GLU	-1	-0.837	-0.920	21.275	0.095	0.095	0.000	0.000	0.000	0.000
89	A	147	ASP	-1	-0.812	-0.888	24.477	0.088	0.088	0.000	0.000	0.000	0.000
90	A	148	LEU	0	-0.016	-0.026	25.834	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	149	VAL	0	-0.010	0.012	21.773	0.007	0.007	0.000	0.000	0.000	0.000
92	A	150	THR	0	-0.044	-0.015	23.800	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.007	-0.003	20.018	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	152	TYR	0	0.016	-0.016	21.712	0.003	0.003	0.000	0.000	0.000	0.000
95	A	153	GLY	0	0.024	0.007	21.349	-0.026	-0.026	0.000	0.000	0.000	0.000
96	A	154	THR	0	-0.036	-0.022	21.987	0.004	0.004	0.000	0.000	0.000	0.000
97	A	155	THR	0	-0.018	-0.012	24.393	0.008	0.008	0.000	0.000	0.000	0.000
98	A	156	PHE	0	-0.011	0.004	26.757	0.012	0.012	0.000	0.000	0.000	0.000
99	A	157	ASN	0	0.014	0.008	26.159	-0.020	-0.020	0.000	0.000	0.000	0.000
100	A	158	SER	0	0.024	0.016	25.610	0.005	0.005	0.000	0.000	0.000	0.000
101	A	159	SER	0	0.028	0.004	26.427	0.001	0.001	0.000	0.000	0.000	0.000
102	A	160	GLY	0	0.021	0.022	27.509	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	161	LEU	0	-0.058	-0.024	27.668	0.007	0.007	0.000	0.000	0.000	0.000
104	A	162	LYS	1	0.911	0.969	24.718	-0.042	-0.042	0.000	0.000	0.000	0.000
105	A	163	MET	0	-0.062	-0.020	17.353	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	164	ARG	1	0.928	0.967	18.924	0.043	0.043	0.000	0.000	0.000	0.000
107	A	165	GLY	0	0.042	0.007	16.400	-0.027	-0.027	0.000	0.000	0.000	0.000
108	A	166	ASN	0	-0.067	-0.036	10.757	-0.096	-0.096	0.000	0.000	0.000	0.000
109	A	167	LEU	0	0.041	0.030	8.642	-0.057	-0.057	0.000	0.000	0.000	0.000
110	A	168	ARG	1	0.876	0.960	7.341	0.286	0.286	0.000	0.000	0.000	0.000
111	A	169	SER	0	-0.036	-0.033	8.945	-0.062	-0.062	0.000	0.000	0.000	0.000
112	A	170	LYS	1	0.919	0.973	10.783	0.928	0.928	0.000	0.000	0.000	0.000
113	A	171	ASN	0	0.016	0.023	13.696	0.049	0.049	0.000	0.000	0.000	0.000
114	A	172	ALA	0	0.009	-0.024	16.040	0.015	0.015	0.000	0.000	0.000	0.000
115	A	173	GLU	-1	-0.897	-0.934	18.594	-0.082	-0.082	0.000	0.000	0.000	0.000
116	A	174	LEU	0	-0.014	-0.013	22.167	0.016	0.016	0.000	0.000	0.000	0.000
117	A	175	ILE	0	-0.008	0.000	23.584	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	176	GLU	-1	-0.870	-0.940	26.997	0.016	0.016	0.000	0.000	0.000	0.000
119	A	177	LYS	1	0.886	0.932	30.132	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	178	VAL	0	0.022	0.017	28.619	0.002	0.002	0.000	0.000	0.000	0.000
121	A	179	ARG	1	0.955	0.986	30.817	0.012	0.012	0.000	0.000	0.000	0.000
122	A	180	THR	0	0.004	0.002	29.956	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	181	SER	0	-0.011	-0.019	30.715	0.002	0.002	0.000	0.000	0.000	0.000
124	A	182	TYR	0	-0.016	-0.011	30.761	0.003	0.003	0.000	0.000	0.000	0.000
125	A	183	GLU	-1	-0.905	-0.950	34.648	-0.043	-0.043	0.000	0.000	0.000	0.000
126	A	184	ILE	0	-0.024	0.001	36.853	0.003	0.003	0.000	0.000	0.000	0.000

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