FMO DATABASE

FMODB ID: K3KM3

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	OptAll
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	-1023526.53236
FMO2-HF: Nuclear repulsion	974235.036859
FMO2-HF: Total energy	-49291.495501
FMO2-MP2: Total energy	-49437.117756

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.
-302.39	-313.698	39.503	-13.885	-14.311	0.178

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 : -0.756 / q_NPA : -0.848

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

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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	0.903	0.943	3.161	-48.154	-44.771	0.420	-1.809	-1.994	0.008
4	A	6	ARG	1	0.866	0.917	1.758	-150.178	-163.331	39.080	-14.303	-11.624	0.163
5	A	7	SER	0	-0.034	-0.011	3.235	-6.242	-7.858	0.004	2.235	-0.624	0.007
6	A	8	SER	0	-0.004	-0.006	4.648	-4.103	-4.025	-0.001	-0.008	-0.069	0.000
7	A	9	THR	0	-0.005	-0.007	6.915	2.279	2.279	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.046	0.035	9.804	-1.416	-1.416	0.000	0.000	0.000	0.000
9	A	11	PHE	0	0.029	0.012	13.430	0.621	0.621	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.044	0.015	14.391	1.583	1.583	0.000	0.000	0.000	0.000
11	A	13	VAL	0	0.035	0.018	15.004	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.955	0.973	17.295	-16.428	-16.428	0.000	0.000	0.000	0.000
13	A	15	GLN	0	0.057	0.018	20.859	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.863	0.897	22.979	-12.618	-12.618	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.013	0.025	18.187	-0.080	-0.080	0.000	0.000	0.000	0.000
16	A	18	PHE	0	0.038	0.026	18.658	0.363	0.363	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.001	-0.011	20.415	-0.309	-0.309	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.825	0.907	21.495	-14.452	-14.452	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.005	0.016	16.617	-0.125	-0.125	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.052	0.024	20.416	-0.058	-0.058	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.042	-0.006	23.125	-0.408	-0.408	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.034	0.024	20.705	-0.401	-0.401	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.009	-0.009	21.161	-0.106	-0.106	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.048	-0.036	23.283	-0.492	-0.492	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.072	-0.037	26.189	-0.573	-0.573	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.784	-0.860	21.588	14.302	14.302	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.015	0.003	25.357	-0.322	-0.322	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.887	-0.931	28.487	9.170	9.170	0.000	0.000	0.000	0.000
29	A	31	ARG	1	0.805	0.875	27.313	-11.063	-11.063	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.023	0.002	28.244	-0.178	-0.178	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.007	-0.014	31.565	-0.255	-0.255	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.034	-0.012	34.775	0.126	0.126	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.002	0.003	36.079	0.158	0.158	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.970	0.987	35.802	-8.832	-8.832	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.029	0.032	29.775	0.146	0.146	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.020	-0.015	32.268	0.277	0.277	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.863	-0.945	33.486	8.772	8.772	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.006	-0.006	31.122	0.005	0.005	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.016	0.002	26.945	0.212	0.212	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.828	0.905	29.432	-9.051	-9.051	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.012	0.007	31.752	0.005	0.005	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.841	-0.881	26.316	10.795	10.795	0.000	0.000	0.000	0.000
43	A	45	PHE	0	-0.021	-0.020	23.694	0.359	0.359	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.830	0.888	28.258	-9.509	-9.509	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.826	-0.887	28.545	9.716	9.716	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.037	-0.017	24.325	0.087	0.087	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.031	0.029	27.720	0.110	0.110	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.051	-0.019	25.561	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.923	0.945	28.116	-10.060	-10.060	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.014	0.029	27.924	0.010	0.010	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.047	0.016	29.706	-0.685	-0.685	0.000	0.000	0.000	0.000
52	A	54	HIS	0	0.061	0.021	31.451	0.351	0.351	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.048	0.021	33.146	0.230	0.230	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.768	-0.876	26.190	12.589	12.589	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.018	0.028	28.520	0.379	0.379	0.000	0.000	0.000	0.000
56	A	58	TYR	0	0.005	0.002	30.117	0.113	0.113	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.882	0.928	28.329	-11.046	-11.046	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.013	-0.029	25.749	0.422	0.422	0.000	0.000	0.000	0.000
59	A	61	LEU	0	0.017	0.002	26.762	0.296	0.296	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.039	-0.018	29.266	-0.279	-0.279	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.721	-0.840	25.003	13.035	13.035	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.006	0.011	22.590	0.270	0.270	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.056	-0.014	26.030	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.895	-0.948	28.584	10.454	10.454	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.882	-0.941	23.118	14.010	14.010	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.036	-0.020	24.260	0.325	0.325	0.000	0.000	0.000	0.000
67	A	69	ILE	0	0.008	0.013	20.819	-0.166	-0.166	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.000	0.001	24.838	-0.212	-0.212	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.914	0.941	28.105	-10.179	-10.179	0.000	0.000	0.000	0.000
70	A	72	GLN	0	0.004	-0.013	31.902	-0.115	-0.115	0.000	0.000	0.000	0.000
71	A	73	ILE	0	0.023	0.020	34.943	-0.171	-0.171	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.838	0.899	37.541	-7.908	-7.908	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.033	0.023	40.824	-0.090	-0.090	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.851	0.919	44.227	-6.970	-6.970	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.945	0.969	46.147	-6.855	-6.855	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.867	-0.933	49.152	6.204	6.204	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.002	0.014	52.284	-0.126	-0.126	0.000	0.000	0.000	0.000
78	A	80	ALA	0	-0.062	-0.041	50.407	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	81	LYS	1	1.038	1.021	51.025	-5.657	-5.657	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.005	-0.009	49.415	0.047	0.047	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.023	0.021	45.118	0.269	0.269	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.815	-0.898	42.593	7.375	7.375	0.000	0.000	0.000	0.000
83	A	85	VAL	0	-0.009	0.002	40.497	0.109	0.109	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.020	-0.012	36.431	0.021	0.021	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.021	0.015	34.018	0.070	0.070	0.000	0.000	0.000	0.000
86	A	88	TYR	0	0.008	-0.006	30.706	-0.077	-0.077	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.002	-0.005	30.126	0.042	0.042	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.032	0.002	23.857	0.102	0.102	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.772	0.909	27.538	-11.436	-11.436	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.789	-0.897	22.715	14.033	14.033	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.029	-0.050	22.040	0.323	0.323	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.777	-0.872	19.415	16.004	16.004	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.027	0.014	18.086	1.277	1.277	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.010	-0.001	18.235	0.827	0.827	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.811	0.890	16.977	-14.784	-14.784	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.047	-0.022	13.054	1.757	1.757	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.012	0.002	13.535	1.784	1.784	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.851	0.888	14.771	-14.776	-14.776	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.939	0.987	9.920	-24.387	-24.387	0.000	0.000	0.000	0.000
100	A	102	GLN	0	0.001	-0.010	9.988	1.692	1.692	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.012	-0.006	10.859	1.484	1.484	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.874	0.943	7.418	-27.588	-27.588	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.016	0.014	5.687	0.182	0.182	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.819	-0.873	8.111	27.798	27.798	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.015	0.009	11.067	-0.924	-0.924	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.820	-0.898	6.495	28.092	28.092	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.708	0.836	8.614	-28.080	-28.080	0.000	0.000	0.000	0.000
108	A	110	CYS	0	-0.063	-0.031	9.358	-2.040	-2.040	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.839	0.903	11.206	-19.951	-19.951	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.934	0.949	5.773	-32.960	-32.960	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.019	0.004	11.409	-0.812	-0.812	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.001	-0.002	13.795	-1.102	-1.102	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.790	-0.885	13.392	17.546	17.546	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.807	0.890	14.195	-18.108	-18.108	0.000	0.000	0.000	0.000
115	A	117	ALA	0	0.018	0.013	16.154	-0.806	-0.806	0.000	0.000	0.000	0.000
116	A	118	LEU	0	-0.009	-0.008	19.100	-0.803	-0.803	0.000	0.000	0.000	0.000
117	A	119	SER	0	0.005	-0.005	18.695	-0.571	-0.571	0.000	0.000	0.000	0.000
118	A	120	ASP	-1	-0.865	-0.910	19.124	15.736	15.736	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.089	-0.047	21.620	-0.751	-0.751	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.037	0.005	24.052	-0.725	-0.725	0.000	0.000	0.000	0.000

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