FMO DATABASE

FMODB ID: 94J12

Calculation Name: 2GMY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GMY

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D1C9

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1380613.284434
FMO2-HF: Nuclear repulsion	1322487.578383
FMO2-HF: Total energy	-58125.706051
FMO2-MP2: Total energy	-58295.576275

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
0.22999999999999	6.3	1.217	-3.139	-4.147	-0.018

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.002 / q_NPA : 1.007

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	4	ARG	1	0.835	0.920	2.566	16.703	21.119	0.976	-2.543	-2.849	-0.012
4	A	5	ILE	0	0.037	0.009	5.020	-1.727	-1.600	-0.001	-0.005	-0.121	0.000
5	A	6	ASN	0	0.003	0.008	7.553	3.076	3.076	0.000	0.000	0.000	0.000
6	A	7	TYR	0	0.060	0.014	9.499	1.710	1.710	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.026	0.021	12.466	1.246	1.246	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.911	0.951	12.222	21.625	21.625	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.001	0.002	11.710	0.756	0.756	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.001	-0.003	13.754	1.210	1.210	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.033	0.017	17.146	0.334	0.334	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.815	-0.893	19.253	-12.545	-12.545	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.020	0.014	18.743	0.454	0.454	0.000	0.000	0.000	0.000
14	A	15	PHE	0	0.006	-0.007	17.259	0.143	0.143	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.874	0.919	19.217	13.352	13.352	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.003	0.014	22.757	0.495	0.495	0.000	0.000	0.000	0.000
17	A	18	VAL	0	-0.002	-0.002	19.766	0.385	0.385	0.000	0.000	0.000	0.000
18	A	19	MET	0	-0.018	-0.010	20.711	0.138	0.138	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.005	0.006	23.185	0.441	0.441	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.009	0.012	24.601	0.410	0.410	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.805	-0.890	22.242	-11.935	-11.935	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.021	-0.015	24.925	0.309	0.309	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.005	0.011	27.746	0.335	0.335	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.026	0.007	26.539	0.286	0.286	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.011	0.014	26.043	0.167	0.167	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.052	-0.023	28.892	0.301	0.301	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.022	-0.014	31.548	0.360	0.360	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.004	-0.007	33.782	0.262	0.262	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.045	-0.007	31.301	0.168	0.168	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.777	-0.861	33.115	-8.007	-8.007	0.000	0.000	0.000	0.000
31	A	32	HIS	0	0.085	0.028	29.807	-0.286	-0.286	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.809	0.897	29.076	7.799	7.799	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.039	0.001	29.332	-0.251	-0.251	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.009	0.014	26.007	-0.308	-0.308	0.000	0.000	0.000	0.000
35	A	36	HIS	0	-0.036	-0.041	24.849	-0.657	-0.657	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.011	0.001	24.410	-0.399	-0.399	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.002	-0.002	25.100	-0.287	-0.287	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.818	0.893	21.218	11.280	11.280	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.009	0.017	19.692	-0.694	-0.694	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.828	0.896	20.622	10.090	10.090	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.039	0.015	21.721	-0.231	-0.231	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.006	-0.029	16.599	-0.725	-0.725	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.034	-0.014	16.860	-0.665	-0.665	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.062	-0.010	18.298	-0.307	-0.307	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.076	-0.056	16.806	-0.195	-0.195	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.015	0.027	14.670	-0.829	-0.829	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.127	-0.032	12.217	-1.715	-1.715	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.074	0.033	9.595	0.616	0.616	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.010	-0.016	9.362	0.412	0.412	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.005	-0.004	11.074	0.654	0.654	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.043	0.021	14.517	0.735	0.735	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.824	-0.897	13.154	-15.111	-15.111	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.017	-0.008	14.835	0.722	0.722	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.836	0.879	16.799	13.971	13.971	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.029	0.037	18.531	0.641	0.641	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.762	0.867	14.964	15.488	15.488	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.829	-0.897	20.858	-12.083	-12.083	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.018	-0.011	23.031	0.488	0.488	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.814	0.864	20.819	11.336	11.336	0.000	0.000	0.000	0.000
60	A	61	HIS	0	-0.073	-0.021	25.027	0.167	0.167	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.851	-0.914	26.751	-9.300	-9.300	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.037	-0.008	29.077	0.289	0.289	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.053	-0.012	27.706	0.243	0.243	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.039	0.013	28.760	-0.211	-0.211	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.728	-0.849	24.895	-10.470	-10.470	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.023	0.006	26.652	-0.165	-0.165	0.000	0.000	0.000	0.000
67	A	68	TRP	0	0.012	-0.007	25.870	-0.276	-0.276	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.017	0.019	22.705	-0.214	-0.214	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.073	-0.062	22.853	-0.567	-0.567	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.016	-0.002	24.459	-0.118	-0.118	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.041	0.057	23.618	0.128	0.128	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.025	-0.020	21.761	0.056	0.056	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.024	-0.024	23.561	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.025	0.014	27.036	0.407	0.407	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.849	0.926	29.372	9.065	9.065	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.869	-0.931	31.429	-7.720	-7.720	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.048	-0.011	31.017	0.214	0.214	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.011	-0.011	33.105	0.006	0.006	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.067	-0.024	30.880	0.091	0.091	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.061	-0.038	27.789	0.016	0.016	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.031	-0.011	34.182	0.197	0.197	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.877	-0.960	36.395	-7.337	-7.337	0.000	0.000	0.000	0.000
83	A	84	GLN	0	0.015	0.027	36.624	-0.087	-0.087	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.777	-0.880	32.541	-8.445	-8.445	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.856	0.925	32.731	7.531	7.531	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.007	0.021	33.951	-0.137	-0.137	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.008	0.001	30.560	-0.163	-0.163	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.007	-0.012	27.798	-0.301	-0.301	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.002	0.001	29.591	-0.245	-0.245	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.028	0.015	31.445	-0.133	-0.133	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.021	-0.001	25.485	-0.269	-0.269	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.772	-0.860	26.533	-10.296	-10.296	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.023	-0.009	27.384	-0.271	-0.271	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.040	0.018	27.827	-0.126	-0.126	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.061	-0.045	22.294	-0.418	-0.418	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.821	0.926	24.083	9.979	9.979	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.039	0.025	26.114	0.238	0.238	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.051	-0.028	26.463	0.264	0.264	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.933	-0.968	25.658	-10.534	-10.534	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.059	-0.041	29.385	0.389	0.389	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.007	0.009	31.597	0.264	0.264	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.078	-0.037	32.656	0.150	0.150	0.000	0.000	0.000	0.000
103	A	104	PRO	0	0.012	0.004	33.898	0.163	0.163	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.840	-0.924	37.046	-7.227	-7.227	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.891	-0.929	38.885	-7.127	-7.127	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.042	-0.029	34.605	0.005	0.005	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.014	0.001	36.741	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.962	-0.980	38.124	-6.528	-6.528	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.021	-0.027	38.078	0.112	0.112	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.030	-0.017	34.386	0.008	0.008	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.958	0.965	37.944	6.826	6.826	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.062	-0.005	41.164	0.126	0.126	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.045	-0.028	39.017	0.116	0.116	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.043	-0.011	35.353	-0.112	-0.112	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.005	-0.026	40.003	0.072	0.072	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.864	-0.954	39.872	-7.185	-7.185	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.918	-0.950	39.121	-7.623	-7.623	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.810	-0.884	37.000	-7.638	-7.638	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.039	0.024	35.331	-0.328	-0.328	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.002	0.014	34.416	-0.323	-0.323	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.827	0.916	33.167	7.618	7.618	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.023	0.010	30.896	-0.402	-0.402	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.010	-0.020	29.640	-0.382	-0.382	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.008	0.001	29.052	-0.384	-0.384	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.014	0.013	26.939	-0.482	-0.482	0.000	0.000	0.000	0.000
126	A	127	ILE	0	0.005	0.004	25.177	-0.562	-0.562	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.028	0.019	24.223	-0.512	-0.512	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.014	0.003	23.406	-0.617	-0.617	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.035	-0.005	18.640	-0.817	-0.817	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.040	0.027	19.214	-1.181	-1.181	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.021	0.003	19.211	-0.705	-0.705	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.013	-0.030	16.640	-1.636	-1.636	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.011	-0.042	14.919	-0.860	-0.860	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.894	0.938	13.994	12.819	12.819	0.000	0.000	0.000	0.000
135	A	136	ILE	0	0.004	0.016	13.512	-1.418	-1.418	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.019	-0.012	10.926	-1.969	-1.969	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.070	0.033	9.275	-2.681	-2.681	0.000	0.000	0.000	0.000
138	A	139	GLY	0	0.001	0.016	9.348	-2.236	-2.236	0.000	0.000	0.000	0.000
139	A	140	PHE	0	-0.017	-0.019	8.693	-2.246	-2.246	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.903	0.943	4.340	22.855	22.983	-0.001	-0.024	-0.102	0.000
141	A	142	SER	0	0.029	0.015	4.758	-4.961	-4.968	-0.001	-0.010	0.018	0.000
142	A	143	GLN	0	-0.042	-0.028	3.089	0.499	1.905	0.244	-0.557	-1.093	-0.006
143	A	144	HIS	0	-0.026	-0.006	6.075	0.167	0.167	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.004	0.005	8.897	-0.954	-0.954	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.016	0.002	9.546	0.517	0.517	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.863	-0.926	12.357	-14.691	-14.691	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.010	0.005	16.156	0.360	0.360	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)