FMO DATABASE

FMODB ID: 94L92

Calculation Name: 1GAK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GAK

Chain ID: A

ChEMBL ID:

UniProt ID: Q25063

Base Structure: X-ray

Registration Date: 2023-06-22

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1353984.124287
FMO2-HF: Nuclear repulsion	1295031.162966
FMO2-HF: Total energy	-58952.961321
FMO2-MP2: Total energy	-59119.726807

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:1:PHE)

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

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.
-3.026	3.356	1.64	-3.324	-4.697	-0.011

Interaction energy analysis for fragmet #1(A:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.004

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	3	ASP	-1	-0.770	-0.859	3.249	-2.397	1.103	-0.012	-1.787	-1.700	-0.004
4	A	4	VAL	0	-0.025	-0.005	5.103	-0.278	-0.161	-0.001	-0.005	-0.111	0.000
5	A	5	VAL	0	0.049	0.028	7.150	-0.221	-0.221	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.044	-0.023	10.642	0.047	0.047	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.044	0.002	13.047	-0.008	-0.008	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.919	0.945	16.467	0.149	0.149	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.054	0.018	18.641	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.800	-0.876	15.723	-0.098	-0.098	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.044	0.004	13.387	0.034	0.034	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.049	-0.024	16.394	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.019	-0.004	18.666	0.009	0.009	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.034	0.030	13.861	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.044	0.002	17.163	0.015	0.015	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.827	0.875	18.970	0.107	0.107	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.006	0.014	20.430	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.042	0.002	16.034	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.016	-0.004	19.736	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.028	-0.013	22.624	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.019	0.023	21.741	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.006	0.004	19.794	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.716	-0.837	24.023	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.801	-0.845	27.143	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.824	-0.904	25.087	-0.070	-0.070	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.032	0.003	27.698	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.051	-0.054	29.242	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.828	0.911	28.876	0.073	0.073	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.045	-0.021	28.329	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.008	-0.004	32.831	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.804	0.882	35.199	0.045	0.045	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.980	1.013	32.591	0.061	0.061	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.051	0.024	35.668	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.944	0.973	37.842	0.050	0.050	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.806	-0.895	40.786	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.021	0.002	40.152	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.866	0.933	44.177	0.035	0.035	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.031	0.024	43.030	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.032	-0.039	42.057	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.025	0.045	35.477	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.040	0.021	39.378	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.009	-0.016	37.631	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.048	0.014	36.179	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.026	0.013	33.083	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.020	-0.004	33.031	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.023	-0.021	31.509	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.037	0.012	30.331	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.010	0.022	28.435	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.870	0.926	26.904	0.074	0.074	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.857	0.942	25.995	0.101	0.101	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.059	0.051	23.337	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.002	0.003	22.280	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.772	0.852	21.132	0.096	0.096	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.834	-0.929	20.653	-0.156	-0.156	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.911	0.966	13.578	0.265	0.265	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.049	-0.030	16.449	-0.045	-0.045	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.029	-0.017	16.001	-0.032	-0.032	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.939	1.004	14.588	0.254	0.254	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.036	0.012	10.078	0.026	0.026	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.050	-0.018	11.330	-0.074	-0.074	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.006	0.001	9.136	0.075	0.075	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.788	-0.872	6.888	-1.575	-1.575	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.060	-0.034	8.402	0.074	0.074	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.018	-0.003	10.939	0.086	0.086	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.876	0.946	4.728	1.615	1.733	-0.001	-0.024	-0.092	0.000
66	A	66	TYR	0	0.021	-0.019	2.353	-1.458	0.844	1.643	-1.422	-2.523	-0.007
67	A	67	SER	0	-0.067	-0.035	7.376	0.195	0.195	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.809	0.870	10.609	0.161	0.161	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.865	0.929	3.198	-0.527	-0.182	0.011	-0.086	-0.271	0.000
70	A	70	ILE	0	-0.009	-0.004	8.378	0.107	0.107	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.036	-0.017	10.517	0.025	0.025	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.040	0.018	9.640	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.011	0.004	7.115	0.027	0.027	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.872	0.938	11.002	-0.087	-0.087	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.029	0.025	14.083	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.033	-0.011	15.622	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.022	0.010	16.483	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.044	0.045	13.982	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.045	0.011	17.225	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	80	LYS	1	1.048	1.023	19.644	0.045	0.045	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.966	1.001	21.541	0.008	0.008	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.015	-0.042	18.152	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.050	0.029	14.365	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.042	-0.035	17.498	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.952	0.970	20.059	0.032	0.032	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.015	0.026	12.909	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.043	0.025	16.023	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.765	0.839	17.328	0.075	0.075	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.005	0.004	13.225	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.029	0.011	12.742	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.018	0.011	15.404	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.007	-0.013	18.037	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.917	0.960	13.072	0.162	0.162	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.032	-0.014	13.761	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.064	0.041	17.160	0.007	0.007	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.021	0.009	19.610	0.008	0.008	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.033	0.009	16.144	0.004	0.004	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.009	-0.004	19.580	0.005	0.005	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.891	0.942	22.110	0.096	0.096	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.878	-0.934	22.362	-0.097	-0.097	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.003	-0.001	20.507	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.086	-0.090	24.776	0.010	0.010	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.001	0.007	27.403	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.768	-0.879	25.778	-0.102	-0.102	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.026	0.001	28.516	0.004	0.004	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.048	-0.034	30.953	0.005	0.005	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.880	0.926	28.579	0.090	0.090	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.889	-0.923	30.514	-0.082	-0.082	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.112	-0.052	33.856	0.003	0.003	0.000	0.000	0.000	0.000
110	A	110	GLN	0	-0.055	-0.031	36.700	0.007	0.007	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.034	0.018	37.823	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.011	0.001	37.589	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.930	0.968	39.141	0.049	0.049	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.036	0.014	37.104	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.022	-0.007	35.540	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	LYN	0	0.092	0.048	38.712	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.004	-0.003	35.405	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	THR	0	0.077	0.010	37.765	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.027	-0.001	38.432	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.034	0.017	35.378	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.003	0.029	33.870	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.981	0.989	33.877	0.046	0.046	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.979	1.000	33.502	0.063	0.063	0.000	0.000	0.000	0.000
124	A	124	TYR	0	0.027	0.006	25.593	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.014	-0.010	29.928	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.028	-0.023	31.111	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.822	0.938	25.940	0.115	0.115	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.689	-0.813	26.062	-0.104	-0.104	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.064	0.029	23.537	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.012	-0.004	21.812	-0.016	-0.016	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.016	-0.006	22.592	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.073	-0.036	21.990	0.005	0.005	0.000	0.000	0.000	0.000
133	A	133	PRO	0	0.028	0.021	19.682	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.904	0.932	13.615	0.219	0.219	0.000	0.000	0.000	0.000
135	A	136	ASN	0	-0.007	-0.019	8.195	0.161	0.161	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.868	-0.902	12.488	-0.203	-0.203	0.000	0.000	0.000	0.000

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