FMO DATABASE

FMODB ID: ZVNVN

Calculation Name: 1M4J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M4J

Chain ID: A

ChEMBL ID:

UniProt ID: Q91YR1

Base Structure: X-ray

Registration Date: 2023-09-22

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1258400.473896
FMO2-HF: Nuclear repulsion	1205106.518218
FMO2-HF: Total energy	-53293.955677
FMO2-MP2: Total energy	-53451.416801

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:7:ILE)

Summations of interaction energy for fragment #1(A:7:ILE)

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.
-2.526	3.049	1.096	-2.541	-4.125	-0.01

Interaction energy analysis for fragmet #1(A:7:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.003

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	9	ALA	0	-0.015	-0.014	3.806	1.028	2.854	-0.028	-0.907	-0.891	0.002
4	A	10	SER	0	0.019	-0.007	7.101	-0.313	-0.313	0.000	0.000	0.000	0.000
5	A	11	GLU	-1	-0.820	-0.944	9.170	0.279	0.279	0.000	0.000	0.000	0.000
6	A	12	ASP	-1	-0.867	-0.900	12.531	0.558	0.558	0.000	0.000	0.000	0.000
7	A	13	VAL	0	-0.030	-0.016	9.903	-0.094	-0.094	0.000	0.000	0.000	0.000
8	A	14	LYS	1	0.822	0.920	9.134	-0.584	-0.584	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.822	-0.858	13.797	0.171	0.171	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.050	0.013	15.202	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	17	PHE	0	-0.010	-0.016	10.068	-0.038	-0.038	0.000	0.000	0.000	0.000
12	A	18	ALA	0	-0.022	-0.005	16.087	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.781	0.856	19.197	-0.251	-0.251	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.005	0.000	18.405	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.946	0.974	15.462	-0.200	-0.200	0.000	0.000	0.000	0.000
16	A	22	ASN	0	-0.071	-0.017	21.199	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.044	0.011	23.616	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.865	0.930	23.696	-0.134	-0.134	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.011	-0.003	20.462	0.007	0.007	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.707	0.832	22.921	-0.089	-0.089	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.002	0.003	19.076	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	28	LEU	0	0.002	0.003	15.202	0.014	0.014	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.856	0.919	14.807	-0.222	-0.222	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.061	-0.039	8.843	0.043	0.043	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.044	0.007	10.156	-0.124	-0.124	0.000	0.000	0.000	0.000
26	A	32	ILE	0	-0.050	-0.027	4.844	0.221	0.221	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.948	-0.973	7.356	0.130	0.130	0.000	0.000	0.000	0.000
28	A	34	ASN	0	-0.050	-0.033	7.534	0.159	0.159	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.953	-0.975	3.212	-1.747	-1.194	0.015	-0.108	-0.459	0.000
30	A	36	GLN	0	0.019	0.013	2.727	0.803	2.385	0.923	-1.121	-1.383	-0.010
31	A	37	LEU	0	-0.043	-0.012	3.946	-1.948	-1.687	0.000	-0.032	-0.228	0.000
32	A	38	VAL	0	0.039	0.015	6.209	-0.169	-0.169	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.006	-0.008	9.976	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	40	GLY	0	0.000	0.012	13.205	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	41	SER	0	-0.010	-0.010	15.380	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	42	CYS	0	-0.015	-0.007	17.615	0.017	0.017	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.016	0.017	19.986	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	44	PRO	0	0.018	0.013	23.474	0.003	0.003	0.000	0.000	0.000	0.000
39	A	45	PRO	0	-0.031	-0.023	25.859	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.073	-0.032	27.939	0.001	0.001	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.909	-0.938	31.216	0.057	0.057	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.037	-0.041	31.430	0.003	0.003	0.000	0.000	0.000	0.000
43	A	49	TRP	0	0.038	-0.013	27.261	0.003	0.003	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.852	-0.920	28.485	0.041	0.041	0.000	0.000	0.000	0.000
45	A	51	GLN	0	0.005	0.023	30.793	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.697	-0.822	27.408	0.084	0.084	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.052	-0.055	23.398	0.006	0.006	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.786	-0.905	25.889	0.060	0.060	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.028	-0.017	27.218	0.001	0.001	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.034	-0.023	24.101	0.006	0.006	0.000	0.000	0.000	0.000
51	A	57	VAL	0	-0.005	-0.009	20.900	0.013	0.013	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.020	0.002	22.131	0.006	0.006	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.014	-0.005	23.818	0.000	0.000	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.002	0.012	19.495	0.008	0.008	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.034	0.000	18.438	0.018	0.018	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.844	-0.923	17.624	0.150	0.150	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.833	-0.925	19.986	0.048	0.048	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.834	0.910	19.684	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.009	-0.014	12.359	-0.031	-0.031	0.000	0.000	0.000	0.000
60	A	66	PRO	0	-0.028	-0.010	12.091	0.006	0.006	0.000	0.000	0.000	0.000
61	A	67	CYS	0	-0.084	-0.013	11.979	0.034	0.034	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.018	-0.024	7.156	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.014	0.007	12.791	0.040	0.040	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.022	0.007	12.810	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	71	PHE	0	0.040	0.003	16.661	0.010	0.010	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.854	0.946	20.465	-0.113	-0.113	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.040	0.031	22.670	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.783	-0.897	25.848	0.074	0.074	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.067	-0.041	27.920	0.000	0.000	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.016	-0.027	27.095	0.006	0.006	0.000	0.000	0.000	0.000
71	A	77	ASN	0	0.042	0.024	23.375	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	78	ALA	0	-0.008	-0.018	27.586	0.003	0.003	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.066	-0.033	20.450	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	80	GLY	0	0.036	0.032	24.128	0.009	0.009	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.037	-0.023	23.842	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.865	-0.892	22.950	0.044	0.044	0.000	0.000	0.000	0.000
77	A	83	TRP	0	-0.040	-0.035	18.810	0.015	0.015	0.000	0.000	0.000	0.000
78	A	84	ILE	0	0.006	0.019	20.141	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	85	PHE	0	-0.049	-0.038	10.536	0.015	0.015	0.000	0.000	0.000	0.000
80	A	86	ILE	0	0.016	0.008	16.504	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	87	ALA	0	-0.015	-0.015	13.685	0.028	0.028	0.000	0.000	0.000	0.000
82	A	88	TRP	0	0.011	0.008	14.616	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.017	-0.039	13.820	0.003	0.003	0.000	0.000	0.000	0.000
84	A	90	PRO	0	0.043	0.051	15.962	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	91	ASP	-1	-0.821	-0.907	18.188	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	92	HIS	0	-0.013	-0.002	20.573	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	93	SER	0	0.019	0.020	15.449	0.011	0.011	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.047	0.016	14.668	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.069	0.018	14.225	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	96	ARG	1	0.975	0.985	9.408	0.347	0.347	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.061	0.034	9.806	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	98	LYS	1	0.881	0.945	10.128	0.040	0.040	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.051	-0.026	9.856	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.023	0.021	3.961	-0.182	-0.024	0.000	-0.020	-0.137	0.000
95	A	101	TYR	0	0.075	0.048	5.888	0.003	0.003	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.001	0.018	8.258	0.009	0.009	0.000	0.000	0.000	0.000
97	A	103	ALA	0	-0.046	-0.023	6.006	0.002	0.002	0.000	0.000	0.000	0.000
98	A	104	THR	0	-0.015	-0.010	2.981	-1.096	-0.230	0.184	-0.289	-0.760	-0.002
99	A	105	ARG	1	0.845	0.917	5.441	0.069	0.069	0.000	0.000	0.000	0.000
100	A	106	ALA	0	0.010	-0.006	8.321	0.044	0.044	0.000	0.000	0.000	0.000
101	A	107	THR	0	0.021	0.007	3.574	-0.053	0.276	0.002	-0.064	-0.267	0.000
102	A	108	LEU	0	0.047	0.036	6.467	0.106	0.106	0.000	0.000	0.000	0.000
103	A	109	LYS	1	0.879	0.938	8.005	0.074	0.074	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.921	0.957	8.634	0.261	0.261	0.000	0.000	0.000	0.000
105	A	111	GLU	-1	-0.826	-0.918	6.951	0.386	0.386	0.000	0.000	0.000	0.000
106	A	112	PHE	0	-0.023	0.004	10.340	0.047	0.047	0.000	0.000	0.000	0.000
107	A	113	GLY	0	0.029	0.016	13.092	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.001	-0.021	15.079	0.002	0.002	0.000	0.000	0.000	0.000
109	A	115	GLY	0	0.008	0.014	16.258	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	116	HIS	0	-0.027	-0.012	17.377	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	117	ILE	0	-0.068	-0.033	15.549	0.008	0.008	0.000	0.000	0.000	0.000
112	A	118	LYS	1	0.871	0.945	19.030	-0.042	-0.042	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.775	-0.851	21.258	0.022	0.022	0.000	0.000	0.000	0.000
114	A	120	GLU	-1	-0.764	-0.857	15.355	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	121	VAL	0	0.005	0.017	18.368	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	122	PHE	0	-0.002	-0.004	14.975	0.007	0.007	0.000	0.000	0.000	0.000
117	A	123	GLY	0	0.030	0.011	18.259	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	124	THR	0	-0.094	-0.049	18.763	0.005	0.005	0.000	0.000	0.000	0.000
119	A	125	VAL	0	0.020	-0.005	20.692	0.004	0.004	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.888	0.930	23.202	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	127	GLU	-1	-0.957	-0.969	24.884	0.019	0.019	0.000	0.000	0.000	0.000
122	A	128	ASP	-1	-0.804	-0.901	22.965	0.011	0.011	0.000	0.000	0.000	0.000
123	A	129	VAL	0	-0.054	-0.037	19.979	0.000	0.000	0.000	0.000	0.000	0.000
124	A	130	SER	0	0.025	0.047	23.336	0.008	0.008	0.000	0.000	0.000	0.000
125	A	131	LEU	0	0.014	-0.001	26.323	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	132	HIS	0	-0.022	-0.014	28.131	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	133	GLY	0	0.037	0.012	26.981	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	134	TYR	0	-0.051	-0.057	24.352	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.856	0.905	26.272	-0.038	-0.038	0.000	0.000	0.000	0.000
130	A	136	LYS	1	0.942	0.974	28.306	-0.017	-0.017	0.000	0.000	0.000	0.000
131	A	137	TYR	0	-0.078	-0.051	21.397	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.051	-0.022	26.500	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	139	LEU	0	-0.099	-0.018	28.647	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ILE)