FMO DATABASE

FMODB ID: VR741

Calculation Name: 4MQD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MQD

Chain ID: A

ChEMBL ID:

UniProt ID: P12669

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1219156.694129
FMO2-HF: Nuclear repulsion	1166046.988441
FMO2-HF: Total energy	-53109.705688
FMO2-MP2: Total energy	-53263.815278

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-0.825	1.276	0.178	-0.79	-1.488	0

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / 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	2	ILE	0	0.052	0.038	3.317	-0.344	1.134	0.013	-0.547	-0.944	0.001
4	A	3	LYS	1	0.880	0.953	5.532	0.937	0.937	0.000	0.000	0.000	0.000
5	A	4	SER	0	0.029	0.014	9.009	0.066	0.066	0.000	0.000	0.000	0.000
6	A	5	TRP	0	-0.022	-0.006	10.783	0.044	0.044	0.000	0.000	0.000	0.000
7	A	6	LYS	1	0.928	0.966	15.433	0.221	0.221	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.032	0.013	18.890	0.010	0.010	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.033	-0.011	20.551	0.033	0.033	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.903	-0.942	22.760	-0.126	-0.126	0.000	0.000	0.000	0.000
11	A	10	LEU	0	-0.054	-0.037	24.352	0.006	0.006	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.052	-0.023	27.280	0.002	0.002	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.021	0.002	26.287	0.003	0.003	0.000	0.000	0.000	0.000
14	A	13	SER	0	0.003	-0.008	30.228	0.005	0.005	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.045	-0.038	31.887	0.000	0.000	0.000	0.000	0.000	0.000
16	A	15	HIS	0	0.037	0.011	31.130	0.003	0.003	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.061	0.046	27.828	0.001	0.001	0.000	0.000	0.000	0.000
18	A	17	PHE	0	-0.025	-0.004	20.784	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	18	THR	0	0.030	0.031	23.960	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.004	0.005	17.589	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.026	-0.013	21.036	0.013	0.013	0.000	0.000	0.000	0.000
22	A	21	GLN	0	0.051	0.009	19.170	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.885	0.954	20.614	0.035	0.035	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.898	-0.955	22.758	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.026	-0.016	25.007	0.008	0.008	0.000	0.000	0.000	0.000
26	A	25	THR	0	-0.015	-0.023	27.369	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	26	PRO	0	-0.019	0.014	26.433	0.006	0.006	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.009	0.002	28.783	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.019	-0.016	30.089	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	29	MET	0	-0.037	-0.012	26.566	0.008	0.008	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.923	-0.967	31.290	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	31	TRP	0	-0.050	-0.013	26.438	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	32	THR	0	0.034	0.017	33.104	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.836	-0.933	33.570	-0.043	-0.043	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.990	-0.985	31.391	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	35	ALA	0	-0.018	-0.012	29.487	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	36	ILE	0	-0.018	-0.011	28.772	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.953	-0.966	29.443	-0.069	-0.069	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.929	0.970	26.075	0.024	0.024	0.000	0.000	0.000	0.000
40	A	39	GLY	0	0.014	0.016	25.016	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	40	TYR	0	-0.095	-0.067	22.963	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	41	ALA	0	0.049	0.029	25.012	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	ALA	0	-0.018	-0.006	23.355	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.009	-0.010	25.157	0.006	0.006	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.957	-0.967	25.792	0.004	0.004	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.057	0.041	22.314	0.006	0.006	0.000	0.000	0.000	0.000
47	A	46	ALA	0	-0.052	-0.030	21.984	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	47	ILE	0	0.005	0.002	18.534	0.008	0.008	0.000	0.000	0.000	0.000
49	A	48	SER	0	-0.002	-0.014	22.506	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	49	PHE	0	-0.011	-0.025	18.293	0.001	0.001	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.870	-0.939	23.990	-0.079	-0.079	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.065	-0.034	25.739	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	52	GLN	0	0.008	-0.024	27.677	0.005	0.005	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.866	0.925	30.082	0.108	0.108	0.000	0.000	0.000	0.000
55	A	54	ASN	0	0.025	0.025	31.014	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	55	THR	0	0.005	-0.004	30.173	0.004	0.004	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.911	0.965	30.378	0.094	0.094	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.033	0.031	25.831	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	58	PHE	0	0.023	0.003	22.773	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.008	0.007	18.800	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	60	LEU	0	-0.011	-0.019	16.364	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	61	PHE	0	0.029	0.024	12.359	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.934	0.948	9.935	0.508	0.508	0.000	0.000	0.000	0.000
64	A	63	LEU	0	0.021	0.023	6.180	0.138	0.138	0.000	0.000	0.000	0.000
65	A	64	ASN	0	-0.017	-0.022	2.768	-0.505	0.082	0.166	-0.238	-0.515	-0.001
66	A	65	SER	0	-0.025	-0.001	4.638	-0.462	-0.426	-0.001	-0.005	-0.029	0.000
67	A	66	SER	0	0.010	-0.003	6.213	0.085	0.085	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.985	-0.984	7.963	-0.516	-0.516	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.024	-0.017	11.353	0.037	0.037	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.008	0.007	14.094	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.040	-0.034	16.967	0.039	0.039	0.000	0.000	0.000	0.000
72	A	71	SER	0	0.004	0.005	20.085	0.020	0.020	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.030	-0.020	19.722	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.834	-0.911	23.011	-0.106	-0.106	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.874	0.933	23.343	0.099	0.099	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.934	0.979	15.272	0.196	0.196	0.000	0.000	0.000	0.000
77	A	76	VAL	0	-0.002	0.016	19.342	0.016	0.016	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.021	-0.020	14.646	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.009	-0.004	16.545	0.022	0.022	0.000	0.000	0.000	0.000
80	A	79	PRO	0	-0.014	-0.004	15.768	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.012	-0.001	15.007	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	81	HIS	0	-0.022	-0.024	14.909	0.001	0.001	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.039	-0.001	14.156	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	83	THR	0	-0.019	-0.025	16.862	0.028	0.028	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.885	-0.963	19.439	0.082	0.082	0.000	0.000	0.000	0.000
86	A	85	ASN	0	-0.086	-0.047	15.192	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	86	GLY	0	0.000	0.006	16.777	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.023	0.001	15.677	0.018	0.018	0.000	0.000	0.000	0.000
89	A	88	HIS	0	-0.007	0.004	18.920	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	89	ILE	0	-0.004	-0.002	17.758	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.902	-0.948	22.139	-0.074	-0.074	0.000	0.000	0.000	0.000
92	A	91	SER	0	0.024	-0.002	25.820	0.004	0.004	0.000	0.000	0.000	0.000
93	A	92	ILE	0	0.012	0.005	28.568	0.003	0.003	0.000	0.000	0.000	0.000
94	A	93	MET	0	-0.021	-0.015	32.175	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	SER	0	0.003	0.024	28.484	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.938	0.959	28.083	0.123	0.123	0.000	0.000	0.000	0.000
97	A	96	ARG	1	0.961	0.993	25.373	0.059	0.059	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.037	-0.012	21.645	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	98	SER	0	0.014	-0.015	20.840	0.016	0.016	0.000	0.000	0.000	0.000
100	A	99	PHE	0	-0.014	-0.016	15.377	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	100	ASP	-1	-0.940	-0.971	15.339	-0.123	-0.123	0.000	0.000	0.000	0.000
102	A	101	LEU	0	-0.003	0.006	10.446	-0.070	-0.070	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.040	0.009	9.791	0.048	0.048	0.000	0.000	0.000	0.000
104	A	103	LYS	1	0.946	0.992	12.915	-0.152	-0.152	0.000	0.000	0.000	0.000
105	A	104	GLY	0	0.007	0.009	12.478	0.056	0.056	0.000	0.000	0.000	0.000
106	A	105	ASP	-1	-0.861	-0.901	12.847	0.118	0.118	0.000	0.000	0.000	0.000
107	A	106	TYR	0	-0.033	-0.049	8.661	0.015	0.015	0.000	0.000	0.000	0.000
108	A	107	GLN	0	-0.013	-0.013	10.602	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	108	LEU	0	-0.012	0.000	11.496	-0.066	-0.066	0.000	0.000	0.000	0.000
110	A	109	THR	0	0.002	0.009	12.905	0.042	0.042	0.000	0.000	0.000	0.000
111	A	110	CYS	0	-0.041	-0.010	14.865	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	111	TRP	0	0.009	-0.009	12.386	0.016	0.016	0.000	0.000	0.000	0.000
113	A	112	THR	0	0.004	-0.006	19.122	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	113	VAL	0	0.010	-0.004	20.643	0.003	0.003	0.000	0.000	0.000	0.000
115	A	114	PRO	0	0.040	0.028	23.623	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	115	ALA	0	-0.001	-0.007	27.097	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	116	GLU	-1	-0.980	-0.980	28.942	-0.111	-0.111	0.000	0.000	0.000	0.000
118	A	117	MET	0	-0.054	-0.020	25.685	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	118	SER	0	-0.055	-0.037	24.134	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.911	-0.956	22.334	-0.242	-0.242	0.000	0.000	0.000	0.000
121	A	120	LEU	0	-0.051	-0.034	21.816	0.003	0.003	0.000	0.000	0.000	0.000
122	A	121	HIS	0	-0.064	-0.022	26.021	0.016	0.016	0.000	0.000	0.000	0.000
123	A	122	ALA	0	0.025	-0.002	27.527	0.012	0.012	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.804	-0.892	26.551	-0.132	-0.132	0.000	0.000	0.000	0.000
125	A	124	THR	0	-0.033	-0.011	20.733	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	125	TYR	0	0.048	0.028	20.918	0.006	0.006	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.024	-0.002	14.673	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.009	-0.007	14.498	0.021	0.021	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.868	-0.938	8.781	-0.750	-0.750	0.000	0.000	0.000	0.000
130	A	129	ALA	0	-0.001	0.005	10.029	0.084	0.084	0.000	0.000	0.000	0.000
131	A	130	VAL	0	0.026	0.013	6.026	-0.154	-0.154	0.000	0.000	0.000	0.000
132	A	131	SER	0	0.002	-0.011	5.484	0.040	0.040	0.000	0.000	0.000	0.000
133	A	132	VAL	0	-0.042	-0.011	7.258	0.149	0.149	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)