FMO DATABASE

FMODB ID: QN1ZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1191190.485701
FMO2-HF: Nuclear repulsion	1137084.341027
FMO2-HF: Total energy	-54106.144674
FMO2-MP2: Total energy	-54266.333053

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.
-1.283	0.575	-0.027	-0.714	-1.116	0.002

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 : -0.005 / q_NPA : -0.021

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	1.023	1.018	3.793	-0.959	0.800	-0.026	-0.710	-1.023	0.002
4	A	16	VAL	0	-0.061	-0.038	5.319	0.153	0.252	-0.001	-0.004	-0.093	0.000
5	A	17	ASP	-1	-0.780	-0.879	7.561	0.833	0.833	0.000	0.000	0.000	0.000
6	A	18	ASP	-1	-0.896	-0.939	6.928	-0.240	-0.240	0.000	0.000	0.000	0.000
7	A	19	ALA	0	-0.004	-0.013	9.781	0.011	0.011	0.000	0.000	0.000	0.000
8	A	20	THR	0	-0.013	-0.016	11.675	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	21	VAL	0	0.019	0.003	12.964	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	22	ALA	0	0.008	0.011	14.014	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	23	ILE	0	0.011	0.003	14.913	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.828	0.912	17.516	-0.132	-0.132	0.000	0.000	0.000	0.000
13	A	25	CYS	0	-0.036	-0.021	17.881	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	26	ALA	0	-0.011	0.007	19.929	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	27	ILE	0	0.012	-0.001	21.441	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	28	ASN	0	-0.003	-0.008	23.096	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	29	ASN	0	-0.002	-0.006	23.169	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.007	0.018	26.033	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	31	ILE	0	0.010	0.003	27.111	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.024	-0.012	28.995	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.826	-0.899	31.161	0.018	0.018	0.000	0.000	0.000	0.000
22	A	34	LEU	0	0.017	0.003	30.912	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.041	-0.013	32.777	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	36	ARG	1	0.846	0.932	34.937	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.017	0.028	37.181	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	38	THR	0	-0.058	-0.057	35.609	0.000	0.000	0.000	0.000	0.000	0.000
27	A	39	GLY	0	0.041	0.014	36.238	0.001	0.001	0.000	0.000	0.000	0.000
28	A	40	SER	0	-0.025	-0.024	37.603	0.001	0.001	0.000	0.000	0.000	0.000
29	A	41	TYR	0	-0.052	-0.015	39.106	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	42	ASN	0	0.087	0.041	43.302	0.000	0.000	0.000	0.000	0.000	0.000
31	A	43	ARG	1	0.887	0.932	46.631	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	44	SER	0	-0.036	-0.009	49.324	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	45	SER	0	0.069	0.013	45.838	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.001	0.012	43.503	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	47	GLU	-1	-0.721	-0.788	46.237	0.012	0.012	0.000	0.000	0.000	0.000
36	A	48	SER	0	-0.055	-0.010	49.083	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	49	SER	0	-0.043	-0.033	44.800	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	50	SER	0	-0.003	-0.013	45.112	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	51	GLY	0	0.014	0.016	46.220	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.069	-0.020	46.534	0.000	0.000	0.000	0.000	0.000	0.000
41	A	53	VAL	0	0.032	0.007	50.487	0.000	0.000	0.000	0.000	0.000	0.000
42	A	54	TRP	0	-0.011	0.009	52.082	0.000	0.000	0.000	0.000	0.000	0.000
43	A	55	THR	0	-0.017	-0.005	55.253	0.000	0.000	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.023	-0.020	58.662	0.000	0.000	0.000	0.000	0.000	0.000
45	A	57	GLY	0	-0.015	-0.002	60.114	0.000	0.000	0.000	0.000	0.000	0.000
46	A	58	PRO	0	-0.024	0.022	61.472	0.000	0.000	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.028	-0.030	62.916	0.000	0.000	0.000	0.000	0.000	0.000
48	A	60	GLY	0	0.020	-0.015	60.772	0.000	0.000	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.909	-0.943	57.620	0.012	0.012	0.000	0.000	0.000	0.000
50	A	62	GLY	0	0.011	-0.011	56.677	0.000	0.000	0.000	0.000	0.000	0.000
51	A	63	SER	0	0.002	-0.020	53.832	0.000	0.000	0.000	0.000	0.000	0.000
52	A	64	TYR	0	-0.098	-0.059	49.057	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	SER	0	-0.031	-0.006	52.774	0.000	0.000	0.000	0.000	0.000	0.000
54	A	66	ILE	0	-0.018	-0.011	47.887	0.000	0.000	0.000	0.000	0.000	0.000
55	A	67	THR	0	0.003	0.007	50.722	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	68	THR	0	0.006	0.002	47.243	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	69	PRO	0	0.054	0.016	44.836	0.001	0.001	0.000	0.000	0.000	0.000
58	A	70	SER	0	-0.015	-0.012	42.437	0.001	0.001	0.000	0.000	0.000	0.000
59	A	71	GLN	0	0.047	0.001	42.210	0.001	0.001	0.000	0.000	0.000	0.000
60	A	72	PHE	0	0.011	-0.003	42.631	0.001	0.001	0.000	0.000	0.000	0.000
61	A	73	VAL	0	0.004	0.015	37.156	0.001	0.001	0.000	0.000	0.000	0.000
62	A	74	PHE	0	0.024	0.020	39.574	0.002	0.002	0.000	0.000	0.000	0.000
63	A	75	LEU	0	-0.032	0.000	41.652	0.001	0.001	0.000	0.000	0.000	0.000
64	A	76	SER	0	-0.031	-0.016	37.881	0.001	0.001	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.014	-0.021	35.616	0.000	0.000	0.000	0.000	0.000	0.000
66	A	78	ALA	0	-0.008	-0.008	35.286	0.002	0.002	0.000	0.000	0.000	0.000
67	A	79	TRP	0	0.005	-0.019	36.307	0.000	0.000	0.000	0.000	0.000	0.000
68	A	80	ALA	0	0.023	0.031	34.513	0.001	0.001	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.751	-0.891	36.600	0.029	0.029	0.000	0.000	0.000	0.000
70	A	82	PRO	0	0.036	0.007	36.782	0.002	0.002	0.000	0.000	0.000	0.000
71	A	83	ILE	0	0.018	0.017	36.431	0.002	0.002	0.000	0.000	0.000	0.000
72	A	84	GLU	-1	-0.832	-0.889	34.506	0.042	0.042	0.000	0.000	0.000	0.000
73	A	85	LEU	0	0.019	0.003	30.542	0.004	0.004	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.037	0.016	31.465	0.004	0.004	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.025	-0.027	32.049	0.005	0.005	0.000	0.000	0.000	0.000
76	A	88	LEU	0	0.001	0.021	28.486	0.005	0.005	0.000	0.000	0.000	0.000
77	A	89	CYS	0	-0.055	-0.024	27.270	0.005	0.005	0.000	0.000	0.000	0.000
78	A	90	THR	0	-0.031	-0.015	27.365	0.005	0.005	0.000	0.000	0.000	0.000
79	A	91	ASN	0	-0.029	-0.027	28.279	0.006	0.006	0.000	0.000	0.000	0.000
80	A	92	ALA	0	0.001	0.021	23.849	0.008	0.008	0.000	0.000	0.000	0.000
81	A	93	LEU	0	-0.002	-0.009	22.579	0.012	0.012	0.000	0.000	0.000	0.000
82	A	94	GLY	0	0.011	0.023	23.086	0.010	0.010	0.000	0.000	0.000	0.000
83	A	95	ASN	0	-0.017	-0.005	21.075	0.006	0.006	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.031	0.010	17.659	0.022	0.022	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.006	-0.005	16.053	0.008	0.008	0.000	0.000	0.000	0.000
86	A	98	GLN	0	0.047	0.022	10.168	-0.047	-0.047	0.000	0.000	0.000	0.000
87	A	99	THR	0	-0.065	-0.039	12.612	0.026	0.026	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.046	0.009	13.767	0.011	0.011	0.000	0.000	0.000	0.000
89	A	101	GLN	0	0.037	0.003	15.637	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	102	ALA	0	0.027	0.025	18.107	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.879	0.935	11.178	-0.238	-0.238	0.000	0.000	0.000	0.000
92	A	104	THR	0	-0.010	-0.005	17.901	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	105	VAL	0	-0.017	-0.001	19.897	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	106	VAL	0	0.039	0.010	21.057	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.038	-0.001	19.073	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	108	ARG	1	0.881	0.929	22.474	-0.074	-0.074	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.021	0.001	25.322	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	110	PHE	0	-0.004	-0.007	24.187	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	111	SER	0	-0.011	-0.006	25.948	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	112	GLU	-1	-0.869	-0.935	27.897	0.051	0.051	0.000	0.000	0.000	0.000
101	A	113	VAL	0	-0.040	-0.008	30.403	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	114	TRP	0	-0.066	-0.031	29.136	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	115	LYS	1	0.862	0.918	34.051	-0.038	-0.038	0.000	0.000	0.000	0.000
104	A	116	PRO	0	-0.011	0.007	37.254	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.018	-0.014	40.383	0.000	0.000	0.000	0.000	0.000	0.000
106	A	118	PRO	0	-0.046	-0.007	42.489	0.000	0.000	0.000	0.000	0.000	0.000
107	A	119	GLN	0	0.046	0.012	44.415	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	120	VAL	0	0.029	0.010	46.890	0.000	0.000	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.031	0.012	49.618	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	122	VAL	0	-0.022	-0.010	48.505	0.000	0.000	0.000	0.000	0.000	0.000
111	A	123	ARG	1	0.825	0.895	49.026	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	124	PHE	0	0.010	0.003	43.514	0.001	0.001	0.000	0.000	0.000	0.000
113	A	125	PRO	0	0.014	0.010	45.438	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.887	-0.948	48.718	0.015	0.015	0.000	0.000	0.000	0.000
115	A	127	SER	0	0.028	0.009	50.102	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	128	ASP	-1	-0.907	-0.925	45.089	0.024	0.024	0.000	0.000	0.000	0.000
117	A	129	PHE	0	-0.001	-0.018	42.610	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.759	0.864	40.307	-0.025	-0.025	0.000	0.000	0.000	0.000
119	A	131	VAL	0	0.016	0.024	34.561	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	132	TYR	0	0.012	0.006	36.799	0.001	0.001	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.860	0.903	27.395	-0.024	-0.024	0.000	0.000	0.000	0.000
122	A	134	TYR	0	-0.010	-0.008	31.521	0.001	0.001	0.000	0.000	0.000	0.000
123	A	135	ASN	0	0.001	-0.005	34.393	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	136	ALA	0	0.002	-0.006	33.945	0.000	0.000	0.000	0.000	0.000	0.000
125	A	137	VAL	0	-0.003	0.003	32.784	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	138	LEU	0	0.019	0.010	31.056	0.001	0.001	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.834	-0.881	29.564	0.016	0.016	0.000	0.000	0.000	0.000
128	A	140	PRO	0	0.026	0.003	27.228	0.001	0.001	0.000	0.000	0.000	0.000
129	A	141	LEU	0	-0.018	-0.006	25.457	0.000	0.000	0.000	0.000	0.000	0.000
130	A	142	VAL	0	0.005	-0.010	24.950	0.004	0.004	0.000	0.000	0.000	0.000
131	A	143	THR	0	-0.023	-0.005	23.584	0.004	0.004	0.000	0.000	0.000	0.000
132	A	144	ALA	0	0.001	-0.002	21.194	0.003	0.003	0.000	0.000	0.000	0.000
133	A	145	LEU	0	-0.014	0.000	19.978	0.003	0.003	0.000	0.000	0.000	0.000
134	A	146	LEU	0	-0.010	-0.008	20.133	0.007	0.007	0.000	0.000	0.000	0.000
135	A	147	GLY	0	0.007	0.008	19.051	0.007	0.007	0.000	0.000	0.000	0.000
136	A	148	ALA	0	-0.027	-0.007	15.918	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	149	PHE	0	-0.034	-0.035	15.071	0.009	0.009	0.000	0.000	0.000	0.000
138	A	150	ASP	-1	-0.941	-0.941	15.444	0.109	0.109	0.000	0.000	0.000	0.000
139	A	151	THR	0	-0.044	-0.032	9.157	-0.025	-0.025	0.000	0.000	0.000	0.000
140	A	152	ARG	1	0.951	0.984	8.420	-0.451	-0.451	0.000	0.000	0.000	0.000
141	A	153	ASN	0	0.072	0.040	5.564	-0.362	-0.362	0.000	0.000	0.000	0.000

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