FMO DATABASE

FMODB ID: K23J3

Calculation Name: 3KML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KML

Chain ID: A

ChEMBL ID:

UniProt ID: P69687

Base Structure: X-ray

Registration Date: 2023-09-26

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1194714.253274
FMO2-HF: Nuclear repulsion	1140607.672036
FMO2-HF: Total energy	-54106.581237
FMO2-MP2: Total energy	-54266.757253

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:13:THR)

Summations of interaction energy for fragment #1(A:13:THR)

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.
0.912	2.957	-0.012	-1.021	-1.013	0.001

Interaction energy analysis for fragmet #1(A:13:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.005

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	15	ARG	1	0.949	0.971	3.824	-0.838	1.207	-0.012	-1.021	-1.013	0.001
4	A	16	VAL	0	-0.029	-0.013	5.552	0.198	0.198	0.000	0.000	0.000	0.000
5	A	17	ASP	-1	-0.779	-0.868	7.470	1.833	1.833	0.000	0.000	0.000	0.000
6	A	18	ASP	-1	-0.852	-0.930	6.990	-0.164	-0.164	0.000	0.000	0.000	0.000
7	A	19	ALA	0	0.009	0.009	9.556	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	20	THR	0	-0.018	-0.030	11.865	-0.055	-0.055	0.000	0.000	0.000	0.000
9	A	21	VAL	0	0.003	0.004	12.991	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	22	ALA	0	0.021	0.013	13.838	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	23	ILE	0	0.008	0.006	15.134	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.822	0.900	17.551	-0.250	-0.250	0.000	0.000	0.000	0.000
13	A	25	CYS	0	-0.049	-0.022	17.844	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	26	ALA	0	0.005	0.007	19.817	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	27	ILE	0	0.002	-0.004	21.279	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	28	ASN	0	0.003	-0.006	23.059	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	29	ASN	0	-0.013	-0.013	22.846	0.004	0.004	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.006	0.014	25.993	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	31	ILE	0	0.000	-0.004	26.963	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.008	0.000	28.908	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.759	-0.847	31.063	0.017	0.017	0.000	0.000	0.000	0.000
22	A	34	LEU	0	0.013	0.005	31.053	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.035	-0.013	32.578	0.000	0.000	0.000	0.000	0.000	0.000
24	A	36	ARG	1	0.773	0.871	34.732	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.023	0.025	37.053	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	38	THR	0	-0.036	-0.039	35.500	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	39	GLY	0	0.010	-0.008	36.528	0.000	0.000	0.000	0.000	0.000	0.000
28	A	40	SER	0	-0.029	-0.019	37.786	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	41	TYR	0	-0.046	-0.010	39.375	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	42	ASN	0	0.084	0.054	43.377	0.000	0.000	0.000	0.000	0.000	0.000
31	A	43	ARG	1	0.847	0.906	46.633	0.000	0.000	0.000	0.000	0.000	0.000
32	A	44	SER	0	-0.031	-0.005	49.413	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	45	SER	0	0.063	0.007	46.070	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.018	0.024	43.614	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	47	GLU	-1	-0.725	-0.794	46.564	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	48	SER	0	-0.048	-0.013	49.618	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	49	SER	0	-0.063	-0.053	44.957	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	50	SER	0	0.005	-0.009	45.376	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	51	GLY	0	0.016	0.012	46.674	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.048	-0.011	46.786	0.000	0.000	0.000	0.000	0.000	0.000
41	A	53	VAL	0	0.020	0.006	50.775	0.002	0.002	0.000	0.000	0.000	0.000
42	A	54	TRP	0	-0.007	0.000	52.178	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	55	THR	0	-0.030	-0.016	55.268	0.001	0.001	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.015	-0.017	58.633	0.000	0.000	0.000	0.000	0.000	0.000
45	A	57	GLY	0	0.015	0.015	60.251	0.000	0.000	0.000	0.000	0.000	0.000
46	A	58	PRO	0	-0.043	-0.008	62.116	0.001	0.001	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.028	-0.030	63.035	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	60	GLY	0	0.007	-0.017	60.946	0.001	0.001	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.883	-0.915	57.767	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	62	GLY	0	-0.023	-0.026	57.191	0.001	0.001	0.000	0.000	0.000	0.000
51	A	63	SER	0	-0.004	-0.008	53.993	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	64	TYR	0	-0.080	-0.050	48.970	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	SER	0	-0.035	-0.008	52.721	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	66	ILE	0	-0.020	-0.008	48.201	0.000	0.000	0.000	0.000	0.000	0.000
55	A	67	THR	0	-0.010	-0.014	50.675	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	68	THR	0	0.012	0.006	47.191	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	69	PRO	0	0.043	0.013	44.478	0.001	0.001	0.000	0.000	0.000	0.000
58	A	70	SER	0	-0.022	-0.018	42.344	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	71	GLN	0	0.063	0.022	42.311	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	72	PHE	0	0.018	-0.001	42.686	0.002	0.002	0.000	0.000	0.000	0.000
61	A	73	VAL	0	-0.004	0.009	37.188	0.000	0.000	0.000	0.000	0.000	0.000
62	A	74	PHE	0	0.032	0.024	39.557	0.001	0.001	0.000	0.000	0.000	0.000
63	A	75	LEU	0	-0.026	0.008	41.865	0.003	0.003	0.000	0.000	0.000	0.000
64	A	76	SER	0	-0.010	-0.002	37.977	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.014	-0.021	35.810	0.005	0.005	0.000	0.000	0.000	0.000
66	A	78	ALA	0	-0.018	-0.012	35.519	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	79	TRP	0	-0.009	-0.020	36.595	0.004	0.004	0.000	0.000	0.000	0.000
68	A	80	ALA	0	0.023	0.042	34.396	0.001	0.001	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.766	-0.887	36.536	0.019	0.019	0.000	0.000	0.000	0.000
70	A	82	PRO	0	0.025	0.002	36.658	0.002	0.002	0.000	0.000	0.000	0.000
71	A	83	ILE	0	0.011	0.013	36.293	0.005	0.005	0.000	0.000	0.000	0.000
72	A	84	GLU	-1	-0.810	-0.882	34.358	0.017	0.017	0.000	0.000	0.000	0.000
73	A	85	LEU	0	0.039	0.014	30.501	0.005	0.005	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.048	0.031	31.425	0.005	0.005	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.029	-0.013	31.812	0.015	0.015	0.000	0.000	0.000	0.000
76	A	88	LEU	0	0.007	0.021	28.806	0.010	0.010	0.000	0.000	0.000	0.000
77	A	89	CYS	0	-0.057	-0.028	27.290	0.007	0.007	0.000	0.000	0.000	0.000
78	A	90	THR	0	-0.025	-0.024	27.040	0.014	0.014	0.000	0.000	0.000	0.000
79	A	91	ASN	0	-0.036	-0.037	27.884	0.020	0.020	0.000	0.000	0.000	0.000
80	A	92	ALA	0	-0.006	0.015	23.712	0.015	0.015	0.000	0.000	0.000	0.000
81	A	93	LEU	0	0.015	0.007	22.910	0.024	0.024	0.000	0.000	0.000	0.000
82	A	94	GLY	0	0.027	0.026	23.551	0.027	0.027	0.000	0.000	0.000	0.000
83	A	95	ASN	0	-0.054	-0.026	21.116	0.011	0.011	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.035	0.017	17.817	0.052	0.052	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.019	0.011	15.928	0.008	0.008	0.000	0.000	0.000	0.000
86	A	98	GLN	0	0.048	0.033	10.044	-0.151	-0.151	0.000	0.000	0.000	0.000
87	A	99	THR	0	-0.054	-0.038	12.735	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.054	0.009	13.702	-0.036	-0.036	0.000	0.000	0.000	0.000
89	A	101	GLN	0	0.009	0.003	15.519	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	102	ALA	0	0.029	0.019	18.415	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.842	0.914	11.486	-0.048	-0.048	0.000	0.000	0.000	0.000
92	A	104	THR	0	0.038	0.016	18.193	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	105	VAL	0	-0.029	-0.009	20.047	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	106	VAL	0	0.035	0.013	21.363	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.051	-0.012	18.599	0.000	0.000	0.000	0.000	0.000	0.000
96	A	108	ARG	1	0.867	0.929	22.565	0.031	0.031	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.037	0.014	25.443	0.003	0.003	0.000	0.000	0.000	0.000
98	A	110	PHE	0	-0.001	-0.017	24.045	0.001	0.001	0.000	0.000	0.000	0.000
99	A	111	SER	0	-0.009	-0.005	26.335	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	112	GLU	-1	-0.869	-0.924	28.264	-0.025	-0.025	0.000	0.000	0.000	0.000
101	A	113	VAL	0	-0.014	-0.009	30.582	0.003	0.003	0.000	0.000	0.000	0.000
102	A	114	TRP	0	-0.072	-0.027	29.414	0.004	0.004	0.000	0.000	0.000	0.000
103	A	115	LYS	1	0.828	0.895	34.355	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	116	PRO	0	0.005	0.005	37.681	0.000	0.000	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.022	-0.012	40.786	0.002	0.002	0.000	0.000	0.000	0.000
106	A	118	PRO	0	-0.020	0.018	42.563	0.001	0.001	0.000	0.000	0.000	0.000
107	A	119	GLN	0	0.003	-0.028	44.415	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	120	VAL	0	0.025	0.007	46.795	0.001	0.001	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.026	0.014	49.543	0.000	0.000	0.000	0.000	0.000	0.000
110	A	122	VAL	0	-0.022	-0.007	48.443	0.001	0.001	0.000	0.000	0.000	0.000
111	A	123	ARG	1	0.845	0.898	49.056	0.006	0.006	0.000	0.000	0.000	0.000
112	A	124	PHE	0	0.015	0.006	43.524	0.001	0.001	0.000	0.000	0.000	0.000
113	A	125	PRO	0	0.016	0.012	46.005	0.001	0.001	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.847	-0.917	49.191	0.001	0.001	0.000	0.000	0.000	0.000
115	A	127	SER	0	-0.012	-0.010	49.571	0.000	0.000	0.000	0.000	0.000	0.000
116	A	128	ASP	-1	-0.886	-0.911	45.353	0.012	0.012	0.000	0.000	0.000	0.000
117	A	129	PHE	0	0.012	-0.009	42.774	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.776	0.857	40.403	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	131	VAL	0	0.000	0.006	34.787	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	132	TYR	0	0.028	0.011	36.889	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.831	0.876	27.624	0.054	0.054	0.000	0.000	0.000	0.000
122	A	134	TYR	0	-0.008	0.001	31.738	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	135	ASN	0	0.016	0.005	34.814	0.000	0.000	0.000	0.000	0.000	0.000
124	A	136	ALA	0	-0.004	-0.011	34.145	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	137	VAL	0	-0.008	0.005	32.810	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	138	LEU	0	0.011	0.005	31.206	0.001	0.001	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.822	-0.876	29.608	-0.062	-0.062	0.000	0.000	0.000	0.000
128	A	140	PRO	0	0.015	-0.005	27.305	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	141	LEU	0	-0.015	0.002	25.659	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	142	VAL	0	0.013	-0.003	25.173	0.001	0.001	0.000	0.000	0.000	0.000
131	A	143	THR	0	-0.001	0.002	24.138	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	144	ALA	0	-0.019	-0.002	21.620	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	145	LEU	0	-0.035	-0.015	20.434	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	146	LEU	0	-0.023	-0.018	20.581	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	147	GLY	0	0.023	0.017	19.021	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	148	ALA	0	-0.021	-0.009	16.269	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	149	PHE	0	-0.020	-0.025	15.215	0.012	0.012	0.000	0.000	0.000	0.000
138	A	150	ASP	-1	-0.932	-0.944	15.336	-0.279	-0.279	0.000	0.000	0.000	0.000
139	A	151	THR	0	-0.039	-0.040	8.951	-0.107	-0.107	0.000	0.000	0.000	0.000
140	A	152	ARG	1	0.938	0.984	8.491	0.970	0.970	0.000	0.000	0.000	0.000
141	A	153	ASN	0	0.053	0.042	5.387	-0.072	-0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:THR)