FMO DATABASE

FMODB ID: R5QV8

Calculation Name: 1BM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BM9

Chain ID: A

ChEMBL ID:

UniProt ID: P0CI76

Base Structure: X-ray

Registration Date: 2023-03-13

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1018065.043329
FMO2-HF: Nuclear repulsion	968774.524999
FMO2-HF: Total energy	-49290.51833
FMO2-MP2: Total energy	-49436.062506

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-285.12	-284.222	21.501	-11.89	-10.508	0.13

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.817 / q_NPA : -0.921

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	5	LYS	1	0.952	0.972	3.816	-38.997	-36.751	-0.016	-1.107	-1.122	-0.001
4	A	6	ARG	1	0.916	0.952	1.801	-143.432	-145.104	21.517	-10.674	-9.171	0.130
5	A	7	SER	0	-0.013	-0.011	4.193	-5.573	-5.384	0.001	-0.087	-0.103	0.001
6	A	8	SER	0	-0.002	0.003	4.182	-3.749	-3.614	-0.001	-0.022	-0.112	0.000
7	A	9	THR	0	-0.039	-0.017	6.861	0.964	0.964	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.046	0.032	9.726	-1.576	-1.576	0.000	0.000	0.000	0.000
9	A	11	PHE	0	0.018	0.006	13.386	0.293	0.293	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.032	0.012	14.679	1.302	1.302	0.000	0.000	0.000	0.000
11	A	13	VAL	0	0.052	0.019	15.561	0.768	0.768	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.958	0.971	17.926	-15.826	-15.826	0.000	0.000	0.000	0.000
13	A	15	GLN	0	0.102	0.040	21.382	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.963	0.973	23.779	-12.299	-12.299	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.012	0.009	18.706	-0.113	-0.113	0.000	0.000	0.000	0.000
16	A	18	PHE	0	0.009	0.009	19.711	0.333	0.333	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.008	-0.021	21.152	-0.184	-0.184	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.876	0.935	21.888	-14.352	-14.352	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.036	0.032	17.508	-0.165	-0.165	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.045	0.015	20.998	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.023	-0.006	23.976	-0.451	-0.451	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.005	0.017	21.439	-0.402	-0.402	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.005	-0.011	22.077	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.043	-0.026	24.209	-0.453	-0.453	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.048	-0.030	27.248	-0.565	-0.565	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.842	-0.922	22.408	13.934	13.934	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.004	0.026	25.950	-0.456	-0.456	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.930	-0.950	29.466	9.039	9.039	0.000	0.000	0.000	0.000
29	A	31	ARG	1	0.862	0.919	28.615	-10.834	-10.834	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.024	-0.006	29.240	-0.069	-0.069	0.000	0.000	0.000	0.000
31	A	33	TYR	0	0.021	-0.007	32.594	-0.159	-0.159	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.010	-0.014	36.025	0.064	0.064	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.002	0.005	36.623	0.180	0.180	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.975	0.991	36.065	-8.874	-8.874	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.013	0.013	30.836	0.116	0.116	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.013	-0.006	33.524	0.280	0.280	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.866	-0.953	34.582	8.616	8.616	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.019	-0.005	32.142	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.003	-0.006	28.294	0.245	0.245	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.888	0.933	30.567	-8.846	-8.846	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.006	0.005	32.764	0.040	0.040	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.943	-0.960	27.583	10.727	10.727	0.000	0.000	0.000	0.000
43	A	45	PHE	0	0.000	0.008	24.716	0.284	0.284	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.833	0.896	29.385	-9.551	-9.551	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.866	-0.924	29.163	9.979	9.979	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.013	-0.005	25.416	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.047	0.040	28.794	0.054	0.054	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.067	-0.021	26.542	0.047	0.047	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.932	0.952	29.540	-9.827	-9.827	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.019	0.009	28.993	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.018	-0.016	30.374	-0.497	-0.497	0.000	0.000	0.000	0.000
52	A	54	HIS	0	0.026	0.008	32.123	0.329	0.329	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.088	0.030	33.469	0.094	0.094	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.869	-0.917	27.846	11.700	11.700	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.008	0.015	29.154	0.361	0.361	0.000	0.000	0.000	0.000
56	A	58	TYR	0	0.020	0.010	30.744	0.209	0.209	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.886	0.924	29.470	-10.556	-10.556	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.052	-0.044	26.174	0.413	0.413	0.000	0.000	0.000	0.000
59	A	61	LEU	0	0.020	0.010	27.576	0.283	0.283	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.023	-0.007	29.956	-0.263	-0.263	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.732	-0.854	25.712	12.838	12.838	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.011	0.001	23.723	0.280	0.280	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.076	-0.036	27.133	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.922	-0.972	29.784	10.271	10.271	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.950	-0.969	24.113	13.440	13.440	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.083	-0.036	26.291	0.229	0.229	0.000	0.000	0.000	0.000
67	A	69	ILE	0	0.020	0.011	22.500	0.031	0.031	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.015	-0.010	26.570	-0.172	-0.172	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.945	0.973	29.541	-9.746	-9.746	0.000	0.000	0.000	0.000
70	A	72	GLN	0	-0.005	-0.015	33.258	-0.108	-0.108	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.001	0.011	36.195	-0.156	-0.156	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.861	0.918	38.861	-7.665	-7.665	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.043	0.024	41.967	-0.091	-0.091	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.892	0.930	45.178	-6.893	-6.893	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.932	0.956	47.477	-6.707	-6.707	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.879	-0.946	49.473	6.073	6.073	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.018	0.012	52.837	-0.117	-0.117	0.000	0.000	0.000	0.000
78	A	80	ALA	0	-0.041	-0.030	51.129	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	81	LYS	1	1.021	1.022	52.040	-5.647	-5.647	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.033	-0.033	50.612	0.026	0.026	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.042	0.038	45.441	0.257	0.257	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.846	-0.908	43.538	7.270	7.270	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.022	0.014	41.523	0.111	0.111	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.011	-0.005	37.302	0.027	0.027	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.031	0.015	34.849	0.069	0.069	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.012	-0.002	31.644	-0.103	-0.103	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.049	0.013	31.410	0.024	0.024	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.026	0.001	25.071	0.093	0.093	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.868	0.942	29.072	-10.986	-10.986	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.810	-0.907	24.208	13.535	13.535	0.000	0.000	0.000	0.000
91	A	93	TYR	0	0.001	-0.005	22.899	0.536	0.536	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.797	-0.893	20.922	15.583	15.583	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.022	0.023	19.715	1.164	1.164	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.024	-0.019	19.821	0.857	0.857	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.838	0.907	18.508	-14.407	-14.407	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.040	-0.018	14.188	1.536	1.536	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.023	0.021	14.974	1.576	1.576	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.898	0.934	15.625	-14.495	-14.495	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.939	0.986	11.351	-22.913	-22.913	0.000	0.000	0.000	0.000
100	A	102	GLN	0	-0.002	-0.021	11.040	1.991	1.991	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.010	0.000	11.486	1.356	1.356	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.915	0.968	8.919	-26.198	-26.198	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.031	0.020	6.350	0.137	0.137	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.853	-0.910	8.679	28.503	28.503	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.017	0.015	11.440	-0.852	-0.852	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.797	-0.903	8.168	26.398	26.398	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.731	0.873	8.862	-27.258	-27.258	0.000	0.000	0.000	0.000
108	A	110	CYS	0	-0.043	-0.010	10.166	-1.917	-1.917	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.872	0.924	11.992	-19.270	-19.270	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.916	0.931	6.789	-34.549	-34.549	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.020	0.003	12.222	-0.938	-0.938	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.009	-0.009	14.615	-1.055	-1.055	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.814	-0.901	14.325	17.095	17.095	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.852	0.939	14.761	-18.141	-18.141	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.015	-0.010	16.678	-0.804	-0.804	0.000	0.000	0.000	0.000
116	A	118	LEU	0	0.002	0.006	19.819	-0.742	-0.742	0.000	0.000	0.000	0.000
117	A	119	SER	0	0.003	0.001	19.091	-0.586	-0.586	0.000	0.000	0.000	0.000
118	A	120	ASP	-1	-0.901	-0.950	19.252	15.177	15.177	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.112	-0.069	21.872	-0.706	-0.706	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.026	0.016	24.593	-0.610	-0.610	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)