FMO DATABASE

FMODB ID: GN9M1

Calculation Name: 4MQD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219863.265608
FMO2-HF: Nuclear repulsion	1166752.858479
FMO2-HF: Total energy	-53110.40713
FMO2-MP2: Total energy	-53264.604868

3D Structure Molmil

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.
-0.826	2.153	0.237	-1.309	-1.908	0.001

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 : 0.051 / q_NPA : 0.024

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	0.019	0.024	3.222	-0.613	1.609	0.038	-1.014	-1.247	0.003
4	A	3	LYS	1	0.769	0.879	5.150	1.061	1.101	-0.001	-0.006	-0.033	0.000
5	A	4	SER	0	0.044	0.016	8.805	0.110	0.110	0.000	0.000	0.000	0.000
6	A	5	TRP	0	-0.012	-0.004	10.948	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	6	LYS	1	0.931	0.968	15.492	0.266	0.266	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.025	0.010	18.908	0.007	0.007	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.010	-0.001	20.664	0.027	0.027	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.805	-0.871	22.718	-0.115	-0.115	0.000	0.000	0.000	0.000
11	A	10	LEU	0	-0.014	-0.010	24.145	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.032	-0.023	26.966	0.003	0.003	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.010	0.010	26.015	0.000	0.000	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.020	-0.021	29.937	0.005	0.005	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.025	-0.027	31.621	0.001	0.001	0.000	0.000	0.000	0.000
16	A	15	HIS	0	0.046	0.024	31.324	0.002	0.002	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.036	0.043	27.743	0.004	0.004	0.000	0.000	0.000	0.000
18	A	17	PHE	0	-0.030	0.000	20.504	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	18	THR	0	-0.010	-0.013	23.641	0.008	0.008	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.002	-0.002	17.173	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.023	-0.010	20.616	0.018	0.018	0.000	0.000	0.000	0.000
22	A	21	GLN	0	0.060	0.028	18.744	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.857	0.941	20.336	0.160	0.160	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.881	-0.939	22.134	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.028	-0.021	24.204	0.014	0.014	0.000	0.000	0.000	0.000
26	A	25	THR	0	-0.013	-0.027	26.649	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	26	PRO	0	-0.004	0.020	26.056	0.008	0.008	0.000	0.000	0.000	0.000
28	A	27	PRO	0	-0.003	0.000	28.261	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.007	-0.013	29.675	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	29	MET	0	-0.043	-0.012	26.127	0.007	0.007	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.901	-0.957	30.947	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	31	TRP	0	-0.077	-0.035	26.249	0.004	0.004	0.000	0.000	0.000	0.000
33	A	32	THR	0	0.030	0.009	32.871	0.001	0.001	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.868	-0.948	33.174	0.001	0.001	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.866	-0.908	31.137	0.033	0.033	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.020	0.008	29.156	0.003	0.003	0.000	0.000	0.000	0.000
37	A	36	ILE	0	-0.029	-0.016	28.417	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.862	-0.923	28.942	0.012	0.012	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.785	0.887	25.612	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	39	GLY	0	0.030	0.022	24.479	0.001	0.001	0.000	0.000	0.000	0.000
41	A	40	TYR	0	-0.081	-0.063	22.690	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	41	ALA	0	0.044	0.032	24.700	0.009	0.009	0.000	0.000	0.000	0.000
43	A	42	ALA	0	-0.011	-0.012	23.080	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	43	ALA	0	-0.002	-0.004	24.990	0.007	0.007	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.885	-0.927	25.439	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	45	GLY	0	-0.015	-0.002	21.813	0.007	0.007	0.000	0.000	0.000	0.000
47	A	46	ALA	0	-0.038	-0.030	21.502	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	47	ILE	0	0.018	0.006	18.169	0.014	0.014	0.000	0.000	0.000	0.000
49	A	48	SER	0	0.011	0.012	22.075	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	49	PHE	0	-0.005	-0.014	18.106	0.009	0.009	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.872	-0.940	23.889	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.041	-0.031	25.365	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	52	GLN	0	0.010	-0.008	27.622	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.828	0.886	30.079	0.063	0.063	0.000	0.000	0.000	0.000
55	A	54	ASN	0	0.001	0.015	31.170	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	55	THR	0	0.023	0.006	30.250	0.001	0.001	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.836	0.909	30.197	0.102	0.102	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.041	0.042	25.860	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	58	PHE	0	-0.013	-0.017	22.859	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.021	0.015	18.815	0.002	0.002	0.000	0.000	0.000	0.000
61	A	60	LEU	0	-0.010	-0.018	16.801	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	61	PHE	0	0.030	0.022	12.331	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.819	0.889	10.152	0.397	0.397	0.000	0.000	0.000	0.000
64	A	63	LEU	0	0.012	0.018	6.234	0.150	0.150	0.000	0.000	0.000	0.000
65	A	64	ASN	0	-0.021	-0.015	2.858	-0.546	0.138	0.201	-0.284	-0.601	-0.002
66	A	65	SER	0	-0.054	-0.026	4.656	-0.326	-0.293	-0.001	-0.005	-0.027	0.000
67	A	66	SER	0	0.006	-0.007	6.105	0.114	0.114	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.877	-0.914	7.880	-0.456	-0.456	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.026	-0.034	11.512	0.028	0.028	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.025	0.014	14.373	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.010	0.004	16.829	0.041	0.041	0.000	0.000	0.000	0.000
72	A	71	SER	0	-0.015	-0.013	19.801	0.012	0.012	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.019	-0.010	19.411	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.852	-0.913	23.138	-0.029	-0.029	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.827	0.906	23.921	0.003	0.003	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.898	0.963	14.901	-0.078	-0.078	0.000	0.000	0.000	0.000
77	A	76	VAL	0	-0.001	0.018	19.114	0.014	0.014	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.032	-0.040	14.244	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.004	0.007	16.026	0.016	0.016	0.000	0.000	0.000	0.000
80	A	79	PRO	0	-0.018	-0.005	15.406	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.001	0.000	14.037	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	81	HIS	0	-0.020	-0.027	14.487	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.039	0.003	13.845	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	83	THR	0	0.014	-0.022	16.410	0.005	0.005	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.800	-0.889	19.185	-0.108	-0.108	0.000	0.000	0.000	0.000
86	A	85	ASN	0	-0.066	-0.038	15.214	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	86	GLY	0	-0.038	-0.012	16.221	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.014	-0.001	15.388	0.031	0.031	0.000	0.000	0.000	0.000
89	A	88	HIS	0	-0.009	0.002	18.505	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	89	ILE	0	-0.010	-0.010	17.390	0.006	0.006	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.815	-0.864	21.876	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	91	SER	0	0.051	-0.004	25.625	0.007	0.007	0.000	0.000	0.000	0.000
93	A	92	ILE	0	0.019	0.014	28.529	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	93	MET	0	-0.021	-0.013	32.218	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	SER	0	-0.014	0.003	28.227	0.000	0.000	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.821	0.892	27.818	0.142	0.142	0.000	0.000	0.000	0.000
97	A	96	ARG	1	0.860	0.918	25.108	0.107	0.107	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.047	-0.014	21.622	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	98	SER	0	0.011	-0.022	20.600	0.016	0.016	0.000	0.000	0.000	0.000
100	A	99	PHE	0	-0.031	-0.017	15.249	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	100	ASP	-1	-0.818	-0.897	14.595	-0.463	-0.463	0.000	0.000	0.000	0.000
102	A	101	LEU	0	0.035	0.019	10.352	-0.120	-0.120	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.054	0.020	9.711	0.064	0.064	0.000	0.000	0.000	0.000
104	A	103	LYS	1	0.826	0.916	12.636	0.124	0.124	0.000	0.000	0.000	0.000
105	A	104	GLY	0	-0.003	0.006	12.161	0.004	0.004	0.000	0.000	0.000	0.000
106	A	105	ASP	-1	-0.872	-0.909	12.136	0.115	0.115	0.000	0.000	0.000	0.000
107	A	106	TYR	0	-0.034	-0.043	8.327	0.024	0.024	0.000	0.000	0.000	0.000
108	A	107	GLN	0	-0.020	-0.018	10.342	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	108	LEU	0	0.005	0.012	11.689	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	109	THR	0	-0.029	-0.001	12.562	0.050	0.050	0.000	0.000	0.000	0.000
111	A	110	CYS	0	-0.038	-0.007	14.410	-0.055	-0.055	0.000	0.000	0.000	0.000
112	A	111	TRP	0	0.022	-0.001	12.162	0.027	0.027	0.000	0.000	0.000	0.000
113	A	112	THR	0	0.009	0.004	19.155	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	113	VAL	0	0.012	-0.005	20.516	0.012	0.012	0.000	0.000	0.000	0.000
115	A	114	PRO	0	0.037	0.017	23.662	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	115	ALA	0	-0.003	-0.005	26.993	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	116	GLU	-1	-0.983	-0.984	29.081	-0.053	-0.053	0.000	0.000	0.000	0.000
118	A	117	MET	0	-0.056	-0.023	25.496	0.003	0.003	0.000	0.000	0.000	0.000
119	A	118	SER	0	-0.032	-0.015	24.097	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.904	-0.951	22.231	-0.184	-0.184	0.000	0.000	0.000	0.000
121	A	120	LEU	0	-0.059	-0.038	21.819	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	121	HIS	0	-0.055	-0.023	25.903	0.011	0.011	0.000	0.000	0.000	0.000
123	A	122	ALA	0	0.021	0.007	27.623	0.009	0.009	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.788	-0.873	26.693	-0.082	-0.082	0.000	0.000	0.000	0.000
125	A	124	THR	0	-0.037	-0.016	20.996	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	125	TYR	0	0.050	0.022	20.921	0.013	0.013	0.000	0.000	0.000	0.000
127	A	126	ILE	0	0.006	0.009	14.854	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	127	ILE	0	-0.006	-0.020	14.263	0.035	0.035	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.809	-0.914	8.210	-0.591	-0.591	0.000	0.000	0.000	0.000
130	A	129	ALA	0	0.003	0.006	9.961	0.101	0.101	0.000	0.000	0.000	0.000
131	A	130	VAL	0	0.039	0.018	6.173	-0.099	-0.099	0.000	0.000	0.000	0.000
132	A	131	SER	0	0.008	-0.005	4.894	-0.083	-0.083	0.000	0.000	0.000	0.000
133	A	132	VAL	0	-0.060	-0.024	6.568	0.338	0.338	0.000	0.000	0.000	0.000

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