FMO DATABASE

FMODB ID: 6613Z

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	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	-1090404.862925
FMO2-HF: Nuclear repulsion	1040218.196002
FMO2-HF: Total energy	-50186.666923
FMO2-MP2: Total energy	-50335.056372

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.
-25.128	-20.442	9.552	-6.983	-7.257	0.036

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 : 0.079 / q_NPA : 0.051

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	0.903	0.950	3.867	-0.923	2.135	-0.023	-1.768	-1.268	0.007
4	A	62	LEU	0	-0.007	0.002	7.014	-0.499	-0.499	0.000	0.000	0.000	0.000
5	A	63	ILE	0	-0.009	0.003	10.591	0.143	0.143	0.000	0.000	0.000	0.000
6	A	64	ALA	0	0.007	0.003	13.789	-0.084	-0.084	0.000	0.000	0.000	0.000
7	A	65	GLN	0	0.006	0.004	17.466	0.023	0.023	0.000	0.000	0.000	0.000
8	A	66	HIS	0	-0.022	-0.016	20.833	0.022	0.022	0.000	0.000	0.000	0.000
9	A	67	VAL	0	-0.017	-0.021	17.761	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	68	GLU	-1	-0.836	-0.868	20.884	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	69	TYR	0	-0.003	-0.021	18.932	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	70	TYR	0	-0.034	-0.032	21.410	0.010	0.010	0.000	0.000	0.000	0.000
13	A	71	SER	0	0.044	-0.005	22.910	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	72	ASP	-1	-0.912	-0.938	23.868	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	73	GLN	0	-0.067	-0.036	24.243	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	74	ALA	0	-0.026	-0.001	19.688	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	75	VAL	0	-0.041	-0.021	18.726	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	76	SER	0	0.002	0.002	16.838	0.022	0.022	0.000	0.000	0.000	0.000
19	A	77	TRP	0	-0.016	-0.001	18.776	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	78	PHE	0	0.014	-0.009	14.532	0.021	0.021	0.000	0.000	0.000	0.000
21	A	79	THR	0	0.030	0.010	19.094	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	80	GLN	0	-0.001	0.000	20.361	0.022	0.022	0.000	0.000	0.000	0.000
23	A	81	PRO	0	-0.046	-0.006	15.457	0.031	0.031	0.000	0.000	0.000	0.000
24	A	82	VAL	0	0.002	-0.016	13.441	-0.035	-0.035	0.000	0.000	0.000	0.000
25	A	83	LEU	0	0.019	0.014	8.401	0.107	0.107	0.000	0.000	0.000	0.000
26	A	84	THR	0	-0.057	-0.037	7.655	0.211	0.211	0.000	0.000	0.000	0.000
27	A	85	THR	0	0.033	0.009	4.840	0.404	0.404	0.000	0.000	0.000	0.000
28	A	86	PHE	0	-0.007	-0.014	2.174	2.511	3.711	1.182	-0.775	-1.607	0.000
29	A	87	ASP	-1	-0.863	-0.930	3.050	-6.722	-5.006	0.113	-1.042	-0.787	-0.010
30	A	88	LYS	1	0.922	0.949	3.852	0.744	1.127	0.003	-0.106	-0.281	-0.001
31	A	89	ASP	-1	-0.872	-0.923	6.134	0.377	0.377	0.000	0.000	0.000	0.000
32	A	90	LYS	1	0.799	0.905	1.853	-22.146	-24.172	8.261	-3.157	-3.078	0.040
33	A	91	ILE	0	0.062	0.036	5.444	0.354	0.354	0.000	0.000	0.000	0.000
34	A	92	PRO	0	-0.031	-0.031	6.259	-0.415	-0.415	0.000	0.000	0.000	0.000
35	A	93	THR	0	0.030	0.019	6.015	-0.102	-0.102	0.000	0.000	0.000	0.000
36	A	94	TRP	0	0.034	0.011	8.283	0.299	0.299	0.000	0.000	0.000	0.000
37	A	95	SER	0	-0.076	-0.030	9.372	0.036	0.036	0.000	0.000	0.000	0.000
38	A	96	VAL	0	0.015	-0.001	11.318	-0.050	-0.050	0.000	0.000	0.000	0.000
39	A	97	LYS	1	0.943	0.980	13.819	0.149	0.149	0.000	0.000	0.000	0.000
40	A	98	ALA	0	0.058	0.031	16.899	-0.038	-0.038	0.000	0.000	0.000	0.000
41	A	99	ASP	-1	-0.816	-0.884	19.856	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	100	LYS	1	0.880	0.945	21.062	0.137	0.137	0.000	0.000	0.000	0.000
43	A	101	ALA	0	-0.003	0.003	16.444	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	102	LYS	1	0.931	0.975	17.920	0.187	0.187	0.000	0.000	0.000	0.000
45	A	103	LEU	0	-0.026	0.004	11.865	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	104	THR	0	-0.013	-0.037	15.127	0.036	0.036	0.000	0.000	0.000	0.000
47	A	105	ASN	0	0.039	0.014	14.690	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.851	-0.897	14.441	-0.305	-0.305	0.000	0.000	0.000	0.000
49	A	107	ARG	1	0.887	0.945	8.792	0.263	0.263	0.000	0.000	0.000	0.000
50	A	108	MET	0	0.031	0.045	10.943	-0.162	-0.162	0.000	0.000	0.000	0.000
51	A	109	LEU	0	-0.020	-0.020	11.486	0.054	0.054	0.000	0.000	0.000	0.000
52	A	110	TYR	0	-0.032	-0.044	13.826	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	111	LEU	0	-0.007	-0.007	13.986	0.022	0.022	0.000	0.000	0.000	0.000
54	A	112	TYR	0	0.041	-0.006	18.321	0.002	0.002	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.051	0.035	22.057	0.016	0.016	0.000	0.000	0.000	0.000
56	A	114	HIS	1	0.835	0.882	22.669	0.108	0.108	0.000	0.000	0.000	0.000
57	A	115	VAL	0	-0.031	0.012	17.734	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	116	GLU	-1	-0.767	-0.850	18.712	-0.173	-0.173	0.000	0.000	0.000	0.000
59	A	117	VAL	0	-0.043	-0.017	13.284	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	118	ASN	0	-0.033	-0.046	14.462	0.062	0.062	0.000	0.000	0.000	0.000
61	A	119	ALA	0	0.023	0.017	13.017	-0.077	-0.077	0.000	0.000	0.000	0.000
62	A	120	LEU	0	-0.079	-0.044	9.848	0.111	0.111	0.000	0.000	0.000	0.000
63	A	121	VAL	0	0.035	0.033	10.804	0.092	0.092	0.000	0.000	0.000	0.000
64	A	122	PRO	0	0.021	0.012	13.514	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	123	ASP	-1	-0.865	-0.941	14.175	-0.396	-0.396	0.000	0.000	0.000	0.000
66	A	124	SER	0	0.002	-0.023	14.161	-0.118	-0.118	0.000	0.000	0.000	0.000
67	A	125	GLN	0	0.040	0.036	16.111	0.050	0.050	0.000	0.000	0.000	0.000
68	A	126	LEU	0	0.030	0.036	15.765	0.039	0.039	0.000	0.000	0.000	0.000
69	A	127	ARG	1	0.817	0.897	16.334	0.242	0.242	0.000	0.000	0.000	0.000
70	A	128	ARG	1	0.844	0.902	17.376	0.164	0.164	0.000	0.000	0.000	0.000
71	A	129	ILE	0	-0.001	0.001	16.321	0.000	0.000	0.000	0.000	0.000	0.000
72	A	130	THR	0	0.011	0.012	19.541	0.006	0.006	0.000	0.000	0.000	0.000
73	A	131	THR	0	-0.013	-0.025	20.588	0.003	0.003	0.000	0.000	0.000	0.000
74	A	132	ASP	-1	-0.828	-0.914	23.089	-0.140	-0.140	0.000	0.000	0.000	0.000
75	A	133	ASN	0	-0.045	-0.041	21.727	0.011	0.011	0.000	0.000	0.000	0.000
76	A	134	ALA	0	-0.015	0.019	17.459	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	135	GLN	0	-0.058	-0.040	16.248	0.030	0.030	0.000	0.000	0.000	0.000
78	A	136	ILE	0	0.009	0.011	9.872	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	137	ASN	0	0.051	0.039	9.652	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	138	LEU	0	-0.016	-0.019	6.830	-0.252	-0.252	0.000	0.000	0.000	0.000
81	A	139	VAL	0	-0.035	-0.008	5.131	-0.790	-0.785	-0.001	-0.001	-0.003	0.000
82	A	140	THR	0	-0.036	-0.052	5.962	-0.146	-0.146	0.000	0.000	0.000	0.000
83	A	141	GLN	0	0.006	-0.009	3.333	0.749	1.099	0.017	-0.134	-0.233	0.000
84	A	142	ASP	-1	-0.791	-0.841	7.932	-0.633	-0.633	0.000	0.000	0.000	0.000
85	A	143	VAL	0	-0.023	-0.027	11.745	-0.051	-0.051	0.000	0.000	0.000	0.000
86	A	144	THR	0	-0.014	-0.002	14.218	0.066	0.066	0.000	0.000	0.000	0.000
87	A	145	SER	0	0.042	-0.002	17.912	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	146	GLU	-1	-0.823	-0.916	20.930	-0.272	-0.272	0.000	0.000	0.000	0.000
89	A	147	ASP	-1	-0.814	-0.883	24.364	-0.158	-0.158	0.000	0.000	0.000	0.000
90	A	148	LEU	0	-0.020	-0.021	26.084	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	149	VAL	0	-0.019	0.001	21.443	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	150	THR	0	-0.023	-0.018	23.896	0.016	0.016	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.005	0.001	19.599	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	152	TYR	0	0.001	-0.025	21.220	0.040	0.040	0.000	0.000	0.000	0.000
95	A	153	GLY	0	0.035	0.010	20.879	-0.039	-0.039	0.000	0.000	0.000	0.000
96	A	154	THR	0	-0.042	-0.031	21.244	0.021	0.021	0.000	0.000	0.000	0.000
97	A	155	THR	0	-0.020	-0.009	23.738	0.013	0.013	0.000	0.000	0.000	0.000
98	A	156	PHE	0	-0.016	0.005	26.233	0.013	0.013	0.000	0.000	0.000	0.000
99	A	157	ASN	0	0.013	0.012	25.508	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	158	SER	0	0.030	0.006	25.490	0.016	0.016	0.000	0.000	0.000	0.000
101	A	159	SER	0	0.024	0.015	25.904	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	160	GLY	0	0.026	0.021	27.483	0.010	0.010	0.000	0.000	0.000	0.000
103	A	161	LEU	0	-0.081	-0.026	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	162	LYS	1	0.879	0.935	24.534	0.175	0.175	0.000	0.000	0.000	0.000
105	A	163	MET	0	-0.059	-0.013	17.483	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	164	ARG	1	0.873	0.939	18.258	0.284	0.284	0.000	0.000	0.000	0.000
107	A	165	GLY	0	0.066	0.014	16.112	0.031	0.031	0.000	0.000	0.000	0.000
108	A	166	ASN	0	-0.050	-0.025	10.004	-0.071	-0.071	0.000	0.000	0.000	0.000
109	A	167	LEU	0	0.034	0.022	8.573	0.041	0.041	0.000	0.000	0.000	0.000
110	A	168	ARG	1	0.846	0.922	6.530	1.085	1.085	0.000	0.000	0.000	0.000
111	A	169	SER	0	-0.077	-0.040	8.279	0.184	0.184	0.000	0.000	0.000	0.000
112	A	170	LYS	1	0.805	0.906	11.188	0.695	0.695	0.000	0.000	0.000	0.000
113	A	171	ASN	0	-0.006	0.012	13.205	0.136	0.136	0.000	0.000	0.000	0.000
114	A	172	ALA	0	0.015	-0.020	15.604	-0.065	-0.065	0.000	0.000	0.000	0.000
115	A	173	GLU	-1	-0.859	-0.906	18.297	-0.261	-0.261	0.000	0.000	0.000	0.000
116	A	174	LEU	0	-0.003	-0.011	21.938	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	175	ILE	0	-0.020	-0.006	22.926	0.011	0.011	0.000	0.000	0.000	0.000
118	A	176	GLU	-1	-0.759	-0.870	26.641	-0.136	-0.136	0.000	0.000	0.000	0.000
119	A	177	LYS	1	0.811	0.883	29.877	0.124	0.124	0.000	0.000	0.000	0.000
120	A	178	VAL	0	0.001	0.014	28.210	0.003	0.003	0.000	0.000	0.000	0.000
121	A	179	ARG	1	0.948	0.988	30.397	0.119	0.119	0.000	0.000	0.000	0.000
122	A	180	THR	0	-0.006	-0.032	29.256	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	181	SER	0	-0.027	-0.025	30.229	0.005	0.005	0.000	0.000	0.000	0.000
124	A	182	TYR	0	0.001	-0.001	30.253	0.004	0.004	0.000	0.000	0.000	0.000
125	A	183	GLU	-1	-0.830	-0.873	33.617	-0.116	-0.116	0.000	0.000	0.000	0.000
126	A	184	ILE	0	-0.057	-0.027	36.649	0.008	0.008	0.000	0.000	0.000	0.000

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