FMO DATABASE

FMODB ID: 3955L

Calculation Name: 3WFN-D-Xray372

Preferred Name: Calmodulin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3WFN

Chain ID: D

ChEMBL ID: CHEMBL3562176

UniProt ID: P0DP26

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	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	154
LigandCharge	DLY=1,DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1344017.976241
FMO2-HF: Nuclear repulsion	1281460.463157
FMO2-HF: Total energy	-62557.513084
FMO2-MP2: Total energy	-62735.22476

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(D:-2:HIS)

Summations of interaction energy for fragment #1(D:-2:HIS)

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.
-8.15	-6.742	-0.014	-0.569	-0.823	0.002

Interaction energy analysis for fragmet #1(D:-2:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.035

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	D	0	HIS	0	0.021	0.017	3.832	1.216	2.563	-0.013	-0.557	-0.776	0.002
4	D	1	MET	0	-0.012	-0.010	6.748	-0.466	-0.466	0.000	0.000	0.000	0.000
5	D	2	ALA	0	0.034	-0.002	9.282	-0.050	-0.050	0.000	0.000	0.000	0.000
6	D	3	ASP	-1	-0.845	-0.917	4.643	-6.613	-6.552	-0.001	-0.012	-0.047	0.000
7	D	4	GLN	0	-0.098	-0.051	7.711	0.337	0.337	0.000	0.000	0.000	0.000
8	D	5	LEU	0	-0.027	0.002	11.011	0.302	0.302	0.000	0.000	0.000	0.000
9	D	6	THR	0	0.000	-0.007	11.829	-0.233	-0.233	0.000	0.000	0.000	0.000
10	D	7	GLU	-1	-0.951	-0.993	13.669	-1.127	-1.127	0.000	0.000	0.000	0.000
11	D	8	GLU	-1	-0.956	-0.973	14.420	-0.588	-0.588	0.000	0.000	0.000	0.000
12	D	9	GLN	0	0.101	0.047	16.058	-0.046	-0.046	0.000	0.000	0.000	0.000
13	D	10	ILE	0	-0.006	0.010	11.123	0.105	0.105	0.000	0.000	0.000	0.000
14	D	11	ALA	0	-0.020	-0.010	15.650	0.107	0.107	0.000	0.000	0.000	0.000
15	D	12	GLU	-1	-0.861	-0.925	18.474	-0.492	-0.492	0.000	0.000	0.000	0.000
16	D	13	PHE	0	0.024	-0.004	16.686	0.066	0.066	0.000	0.000	0.000	0.000
17	D	14	LYS	1	0.930	0.964	17.089	0.592	0.592	0.000	0.000	0.000	0.000
18	D	15	GLU	-1	-0.991	-0.987	19.773	-0.322	-0.322	0.000	0.000	0.000	0.000
19	D	16	ALA	0	-0.004	-0.013	23.063	0.046	0.046	0.000	0.000	0.000	0.000
20	D	17	PHE	0	-0.084	-0.037	21.011	0.031	0.031	0.000	0.000	0.000	0.000
21	D	18	SER	0	-0.012	-0.031	22.257	0.037	0.037	0.000	0.000	0.000	0.000
22	D	19	LEU	0	-0.040	0.005	24.524	0.034	0.034	0.000	0.000	0.000	0.000
23	D	20	PHE	0	-0.071	-0.039	27.994	0.013	0.013	0.000	0.000	0.000	0.000
24	D	21	ASP	-1	-0.801	-0.892	23.334	-0.123	-0.123	0.000	0.000	0.000	0.000
25	D	22	LYS	1	0.667	0.801	26.091	0.081	0.081	0.000	0.000	0.000	0.000
26	D	23	ASP	-1	-0.892	-0.937	23.772	-0.084	-0.084	0.000	0.000	0.000	0.000
27	D	24	GLY	0	-0.036	-0.020	23.119	0.006	0.006	0.000	0.000	0.000	0.000
28	D	25	ASP	-1	-0.913	-0.935	24.418	0.003	0.003	0.000	0.000	0.000	0.000
29	D	26	GLY	0	0.024	0.033	21.483	-0.016	-0.016	0.000	0.000	0.000	0.000
30	D	27	THR	0	-0.105	-0.077	20.805	-0.004	-0.004	0.000	0.000	0.000	0.000
31	D	28	ILE	0	0.088	0.070	22.958	-0.004	-0.004	0.000	0.000	0.000	0.000
32	D	29	THR	0	-0.029	-0.036	24.981	0.030	0.030	0.000	0.000	0.000	0.000
33	D	30	THR	0	0.043	0.016	25.845	-0.016	-0.016	0.000	0.000	0.000	0.000
34	D	31	LYS	1	0.854	0.916	27.876	0.041	0.041	0.000	0.000	0.000	0.000
35	D	32	GLU	-1	-0.907	-0.959	28.662	-0.092	-0.092	0.000	0.000	0.000	0.000
36	D	33	LEU	0	0.065	0.046	23.607	-0.015	-0.015	0.000	0.000	0.000	0.000
37	D	34	GLY	0	-0.068	-0.057	27.525	-0.010	-0.010	0.000	0.000	0.000	0.000
38	D	35	THR	0	-0.032	-0.004	28.430	0.004	0.004	0.000	0.000	0.000	0.000
39	D	36	VAL	0	0.044	0.048	24.801	-0.015	-0.015	0.000	0.000	0.000	0.000
40	D	37	MET	0	-0.028	-0.017	23.550	-0.020	-0.020	0.000	0.000	0.000	0.000
41	D	62	GLY	0	-0.020	-0.024	27.382	0.006	0.006	0.000	0.000	0.000	0.000
42	D	63	THR	0	-0.019	-0.019	23.415	-0.014	-0.014	0.000	0.000	0.000	0.000
43	D	64	ILE	0	-0.034	-0.008	20.033	0.025	0.025	0.000	0.000	0.000	0.000
44	D	65	ASP	-1	-0.783	-0.890	16.548	0.002	0.002	0.000	0.000	0.000	0.000
45	D	66	PHE	0	0.036	0.015	15.238	-0.038	-0.038	0.000	0.000	0.000	0.000
46	D	67	PRO	0	-0.009	-0.010	11.859	-0.083	-0.083	0.000	0.000	0.000	0.000
47	D	68	GLU	-1	-0.875	-0.932	13.868	0.081	0.081	0.000	0.000	0.000	0.000
48	D	69	PHE	0	0.010	-0.001	16.063	-0.013	-0.013	0.000	0.000	0.000	0.000
49	D	70	LEU	0	0.015	0.002	12.824	-0.044	-0.044	0.000	0.000	0.000	0.000
50	D	71	THR	0	-0.057	-0.031	12.766	-0.066	-0.066	0.000	0.000	0.000	0.000
51	D	72	MET	0	-0.066	-0.025	14.612	0.024	0.024	0.000	0.000	0.000	0.000
52	D	73	MET	0	-0.005	0.003	17.559	0.031	0.031	0.000	0.000	0.000	0.000
53	D	74	ALA	0	0.057	0.028	13.992	-0.001	-0.001	0.000	0.000	0.000	0.000
54	D	75	ARG	1	0.882	0.930	15.236	0.002	0.002	0.000	0.000	0.000	0.000
55	D	76	LYS	1	0.956	0.994	17.577	0.248	0.248	0.000	0.000	0.000	0.000
56	D	77	MET	0	-0.005	-0.007	17.260	0.015	0.015	0.000	0.000	0.000	0.000
57	D	78	LYS	1	0.953	0.991	14.143	0.370	0.370	0.000	0.000	0.000	0.000
58	D	79	ASP	-1	-0.953	-0.981	19.051	-0.125	-0.125	0.000	0.000	0.000	0.000
59	D	80	THR	0	-0.068	-0.039	22.402	0.039	0.039	0.000	0.000	0.000	0.000
60	D	81	ASP	-1	-0.833	-0.910	20.156	-0.514	-0.514	0.000	0.000	0.000	0.000
61	D	82	SER	0	-0.062	-0.031	22.080	0.035	0.035	0.000	0.000	0.000	0.000
62	D	83	GLU	-1	-0.874	-0.949	23.718	-0.130	-0.130	0.000	0.000	0.000	0.000
63	D	84	GLU	-1	-0.959	-0.976	26.326	-0.308	-0.308	0.000	0.000	0.000	0.000
64	D	85	GLU	-1	-0.929	-0.964	23.680	-0.308	-0.308	0.000	0.000	0.000	0.000
65	D	86	ILE	0	-0.039	-0.034	26.708	0.023	0.023	0.000	0.000	0.000	0.000
66	D	87	ARG	1	0.746	0.831	29.264	0.168	0.168	0.000	0.000	0.000	0.000
67	D	88	GLU	-1	-0.920	-0.948	29.768	-0.225	-0.225	0.000	0.000	0.000	0.000
68	D	89	ALA	0	-0.035	-0.021	29.921	0.010	0.010	0.000	0.000	0.000	0.000
69	D	90	PHE	0	0.002	-0.021	31.904	0.015	0.015	0.000	0.000	0.000	0.000
70	D	91	ARG	1	0.930	0.986	34.755	0.151	0.151	0.000	0.000	0.000	0.000
71	D	92	VAL	0	-0.027	-0.011	33.410	0.006	0.006	0.000	0.000	0.000	0.000
72	D	93	PHE	0	-0.039	-0.030	34.042	0.007	0.007	0.000	0.000	0.000	0.000
73	D	94	ASP	-1	-0.774	-0.840	38.704	-0.096	-0.096	0.000	0.000	0.000	0.000
74	D	95	LYS	1	0.878	0.927	41.059	0.080	0.080	0.000	0.000	0.000	0.000
75	D	96	ASP	-1	-0.947	-0.976	43.687	-0.090	-0.090	0.000	0.000	0.000	0.000
76	D	97	GLY	0	-0.058	-0.017	42.121	-0.003	-0.003	0.000	0.000	0.000	0.000
77	D	98	ASN	0	-0.036	-0.022	43.141	-0.005	-0.005	0.000	0.000	0.000	0.000
78	D	99	GLY	0	0.000	-0.002	41.211	0.003	0.003	0.000	0.000	0.000	0.000
79	D	100	TYR	0	-0.046	-0.030	41.970	0.006	0.006	0.000	0.000	0.000	0.000
80	D	101	ILE	0	0.005	0.012	38.985	-0.003	-0.003	0.000	0.000	0.000	0.000
81	D	102	SER	0	0.009	0.019	43.280	0.006	0.006	0.000	0.000	0.000	0.000
82	D	103	ALA	0	0.102	0.042	44.062	-0.002	-0.002	0.000	0.000	0.000	0.000
83	D	104	ALA	0	-0.053	-0.033	44.131	0.001	0.001	0.000	0.000	0.000	0.000
84	D	105	GLU	-1	-0.904	-0.958	42.301	-0.074	-0.074	0.000	0.000	0.000	0.000
85	D	106	LEU	0	0.033	0.013	37.441	-0.003	-0.003	0.000	0.000	0.000	0.000
86	D	107	ARG	1	0.911	0.939	39.794	0.013	0.013	0.000	0.000	0.000	0.000
87	D	108	HIS	0	-0.014	0.018	41.061	0.006	0.006	0.000	0.000	0.000	0.000
88	D	109	VAL	0	0.025	0.007	37.870	0.000	0.000	0.000	0.000	0.000	0.000
89	D	110	MET	0	-0.011	0.006	34.097	-0.002	-0.002	0.000	0.000	0.000	0.000
90	D	111	THR	0	-0.004	-0.005	36.434	0.004	0.004	0.000	0.000	0.000	0.000
91	D	112	ASN	0	-0.116	-0.077	38.951	0.006	0.006	0.000	0.000	0.000	0.000
92	D	113	LEU	0	-0.030	-0.004	35.171	-0.003	-0.003	0.000	0.000	0.000	0.000
93	D	114	GLY	0	0.049	0.034	31.814	0.007	0.007	0.000	0.000	0.000	0.000
94	D	115	GLU	-1	-0.916	-0.946	26.638	-0.069	-0.069	0.000	0.000	0.000	0.000
95	D	116	LYS	1	0.897	0.959	31.442	0.055	0.055	0.000	0.000	0.000	0.000
96	D	117	LEU	0	-0.011	-0.001	33.189	0.010	0.010	0.000	0.000	0.000	0.000
97	D	118	THR	0	-0.023	-0.018	35.807	0.000	0.000	0.000	0.000	0.000	0.000
98	D	119	ASP	-1	-0.868	-0.944	38.148	-0.001	-0.001	0.000	0.000	0.000	0.000
99	D	120	GLU	-1	-0.920	-0.968	38.900	0.032	0.032	0.000	0.000	0.000	0.000
100	D	121	GLU	-1	-0.812	-0.886	33.014	0.025	0.025	0.000	0.000	0.000	0.000
101	D	122	VAL	0	0.002	-0.001	37.240	-0.005	-0.005	0.000	0.000	0.000	0.000
102	D	123	ASP	-1	-0.837	-0.911	39.430	0.001	0.001	0.000	0.000	0.000	0.000
103	D	124	GLU	-1	-0.827	-0.880	37.187	0.031	0.031	0.000	0.000	0.000	0.000
104	D	125	MET	0	-0.016	-0.001	34.806	-0.004	-0.004	0.000	0.000	0.000	0.000
105	D	126	ILE	0	-0.028	-0.027	38.608	-0.006	-0.006	0.000	0.000	0.000	0.000
106	D	127	ARG	1	0.753	0.854	39.579	-0.024	-0.024	0.000	0.000	0.000	0.000
107	D	128	GLU	-1	-0.849	-0.908	36.306	0.016	0.016	0.000	0.000	0.000	0.000
108	D	129	ALA	0	-0.009	0.004	40.352	-0.005	-0.005	0.000	0.000	0.000	0.000
109	D	130	ASP	-1	-1.001	-0.993	41.627	-0.017	-0.017	0.000	0.000	0.000	0.000
110	D	131	ILE	0	-0.063	-0.019	44.961	0.000	0.000	0.000	0.000	0.000	0.000
111	D	132	ASP	-1	-0.858	-0.923	46.857	-0.043	-0.043	0.000	0.000	0.000	0.000
112	D	133	GLY	0	-0.044	-0.017	49.977	0.002	0.002	0.000	0.000	0.000	0.000
113	D	134	DAS	-1	-0.881	-0.928	51.434	-0.018	-0.018	0.000	0.000	0.000	0.000
114	D	135	GLY	0	-0.084	-0.087	49.904	-0.002	-0.002	0.000	0.000	0.000	0.000
115	D	136	GLN	0	-0.120	-0.054	46.774	-0.006	-0.006	0.000	0.000	0.000	0.000
116	D	137	VAL	0	0.050	0.023	40.588	0.005	0.005	0.000	0.000	0.000	0.000
117	D	138	ASN	0	0.065	0.042	41.302	-0.012	-0.012	0.000	0.000	0.000	0.000
118	D	139	TYR	0	-0.018	-0.057	36.770	0.000	0.000	0.000	0.000	0.000	0.000
119	D	140	GLU	-1	-0.775	-0.846	35.866	-0.130	-0.130	0.000	0.000	0.000	0.000
120	D	141	GLU	-1	-0.928	-0.975	36.714	-0.055	-0.055	0.000	0.000	0.000	0.000
121	D	142	PHE	0	0.001	-0.004	34.390	0.006	0.006	0.000	0.000	0.000	0.000
122	D	143	VAL	0	-0.011	-0.014	31.457	0.006	0.006	0.000	0.000	0.000	0.000
123	D	144	GLN	0	-0.041	-0.025	32.752	0.012	0.012	0.000	0.000	0.000	0.000
124	D	145	MET	0	-0.066	-0.001	33.779	0.012	0.012	0.000	0.000	0.000	0.000
125	D	146	MET	0	0.002	0.029	30.724	0.015	0.015	0.000	0.000	0.000	0.000
126	D	147	THR	0	0.460	0.617	28.411	0.017	0.017	0.000	0.000	0.000	0.000
127	D	148	ALA	0	0.345	0.318	25.306	-0.010	-0.010	0.000	0.000	0.000	0.000
128	D	149	DLY	2	0.619	0.662	22.140	0.126	0.126	0.000	0.000	0.000	0.000
129	D	150	GLY	-1	0.211	0.119	23.740	-0.178	-0.178	0.000	0.000	0.000	0.000
130	D	151	GLY	0	-0.158	-0.266	24.050	-0.013	-0.013	0.000	0.000	0.000	0.000
131	D	152	GLY	0	-0.101	-0.230	26.267	0.017	0.017	0.000	0.000	0.000	0.000
132	D	153	GLY	0	-0.462	-0.465	29.848	0.016	0.016	0.000	0.000	0.000	0.000
133	D	154	GLY	0	0.028	0.010	31.701	-0.009	-0.009	0.000	0.000	0.000	0.000
134	D	155	GLU	-1	-0.859	-0.944	32.143	-0.148	-0.148	0.000	0.000	0.000	0.000
135	D	156	GLU	-1	-0.939	-0.883	31.445	-0.106	-0.106	0.000	0.000	0.000	0.000
136	D	157	VAL	0	0.021	0.068	26.470	0.006	0.006	0.000	0.000	0.000	0.000
137	D	158	SER	0	-0.010	-0.022	28.595	-0.006	-0.006	0.000	0.000	0.000	0.000
138	D	159	ALA	0	0.018	0.003	30.834	0.008	0.008	0.000	0.000	0.000	0.000
139	D	160	VAL	0	-0.054	0.029	26.234	0.015	0.015	0.000	0.000	0.000	0.000
140	D	161	VAL	0	-0.056	0.012	25.797	0.013	0.013	0.000	0.000	0.000	0.000
141	D	162	LEU	0	-0.014	0.007	27.669	0.015	0.015	0.000	0.000	0.000	0.000
142	D	163	GLN	0	0.007	-0.018	30.220	0.009	0.009	0.000	0.000	0.000	0.000
143	D	164	ARG	1	0.768	0.878	22.114	0.172	0.172	0.000	0.000	0.000	0.000
144	D	165	ALA	0	0.037	0.014	26.997	0.026	0.026	0.000	0.000	0.000	0.000
145	D	166	TYR	0	-0.011	-0.034	27.895	0.020	0.020	0.000	0.000	0.000	0.000
146	D	167	ARG	1	0.782	0.862	28.399	0.020	0.020	0.000	0.000	0.000	0.000
147	D	168	GLY	0	-0.080	-0.037	26.137	0.026	0.026	0.000	0.000	0.000	0.000
148	D	169	HIS	0	-0.053	-0.044	26.778	0.024	0.024	0.000	0.000	0.000	0.000
149	D	170	LEU	0	0.009	0.002	29.707	0.018	0.018	0.000	0.000	0.000	0.000
150	D	171	ALA	0	-0.031	-0.013	26.603	0.016	0.016	0.000	0.000	0.000	0.000
151	D	172	ARG	1	0.875	0.931	25.040	-0.008	-0.008	0.000	0.000	0.000	0.000
152	D	173	ARG	1	0.949	0.979	28.440	-0.036	-0.036	0.000	0.000	0.000	0.000
153	D	174	GLY	0	-0.012	0.021	31.211	0.000	0.000	0.000	0.000	0.000	0.000
154	D	175	PHE	0	-0.097	-0.038	26.510	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:-2:HIS)