Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3JN1L

Calculation Name: 4IV1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IV1

Chain ID: B

ChEMBL ID:

UniProt ID: Q6PN23

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371138.837418
FMO2-HF: Nuclear repulsion 2289927.443584
FMO2-HF: Total energy -81211.393834
FMO2-MP2: Total energy -81450.760909


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:12:ASP)


Summations of interaction energy for fragment #1(B:12:ASP)
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.
-80.49-74.6776.423-5.921-6.3160.068
Interaction energy analysis for fragmet #1(B:12:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.824 / 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   
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].
3B14ILE0-0.0460.0002.044-36.016-30.8756.389-5.650-5.8810.068
4B15LEU00.0170.0183.7534.9535.6250.034-0.271-0.4350.000
5B16THR0-0.008-0.0136.515-5.111-5.1110.0000.0000.0000.000
6B17THR0-0.021-0.0029.4360.2840.2840.0000.0000.0000.000
7B18ARG10.9030.92912.337-18.271-18.2710.0000.0000.0000.000
8B19ASN0-0.0290.00315.196-0.380-0.3800.0000.0000.0000.000
9B20GLY00.0950.05818.699-0.466-0.4660.0000.0000.0000.000
10B21HIS0-0.013-0.00620.2311.1181.1180.0000.0000.0000.000
11B22THR0-0.034-0.02719.778-0.470-0.4700.0000.0000.0000.000
12B23THR00.0380.00414.575-0.041-0.0410.0000.0000.0000.000
13B24SER0-0.080-0.04914.184-1.287-1.2870.0000.0000.0000.000
14B25THR00.0280.0018.9100.4080.4080.0000.0000.0000.000
15B26THR0-0.036-0.0218.569-1.468-1.4680.0000.0000.0000.000
16B27GLN00.0510.0126.3705.0315.0310.0000.0000.0000.000
17B28SER0-0.0050.0077.2061.0701.0700.0000.0000.0000.000
18B29SER0-0.022-0.0116.037-4.755-4.7550.0000.0000.0000.000
19B30VAL00.026-0.0057.4661.9031.9030.0000.0000.0000.000
20B31GLY00.0540.0496.755-1.521-1.5210.0000.0000.0000.000
21B32VAL0-0.035-0.0207.596-1.098-1.0980.0000.0000.0000.000
22B33THR0-0.026-0.01210.7150.0200.0200.0000.0000.0000.000
23B34TYR00.012-0.00111.8340.2840.2840.0000.0000.0000.000
24B35GLY00.007-0.01616.600-0.352-0.3520.0000.0000.0000.000
25B36TYR0-0.004-0.01820.234-0.349-0.3490.0000.0000.0000.000
26B37SER00.0040.00521.660-0.182-0.1820.0000.0000.0000.000
27B38THR0-0.019-0.00616.6680.2220.2220.0000.0000.0000.000
28B39GLN0-0.027-0.01519.0310.3650.3650.0000.0000.0000.000
29B40GLU-1-0.766-0.86821.97611.91811.9180.0000.0000.0000.000
30B41ASP-1-0.788-0.87425.3949.7369.7360.0000.0000.0000.000
31B42HIS00.009-0.00128.9880.3590.3590.0000.0000.0000.000
32B43VAL00.0260.01428.620-0.183-0.1830.0000.0000.0000.000
33B44SER00.001-0.00631.558-0.079-0.0790.0000.0000.0000.000
34B45GLY0-0.003-0.01235.1530.0270.0270.0000.0000.0000.000
35B46PRO00.0280.01037.910-0.064-0.0640.0000.0000.0000.000
36B47ASN0-0.032-0.02337.337-0.088-0.0880.0000.0000.0000.000
37B48THR0-0.032-0.04137.5270.0060.0060.0000.0000.0000.000
38B49SER0-0.062-0.03040.441-0.119-0.1190.0000.0000.0000.000
39B50GLY00.0060.01839.339-0.143-0.1430.0000.0000.0000.000
40B51LEU0-0.022-0.00640.385-0.020-0.0200.0000.0000.0000.000
41B52GLU-1-0.813-0.85835.1868.4428.4420.0000.0000.0000.000
42B53THR0-0.0040.00235.0090.1030.1030.0000.0000.0000.000
43B54ARG10.8220.87723.551-12.095-12.0950.0000.0000.0000.000
44B55VAL00.0040.00130.332-0.119-0.1190.0000.0000.0000.000
45B56VAL00.0460.01425.8660.2350.2350.0000.0000.0000.000
46B57GLN00.0070.00026.1250.5550.5550.0000.0000.0000.000
47B58ALA0-0.015-0.01227.9410.0750.0750.0000.0000.0000.000
48B59GLU-1-0.804-0.84123.09712.89512.8950.0000.0000.0000.000
49B60ARG10.8580.91221.712-12.365-12.3650.0000.0000.0000.000
50B61PHE0-0.003-0.01715.482-0.434-0.4340.0000.0000.0000.000
51B62PHE0-0.045-0.02221.660-0.577-0.5770.0000.0000.0000.000
52B63LYS10.9060.93619.774-15.048-15.0480.0000.0000.0000.000
53B64LYS10.8910.94523.973-11.392-11.3920.0000.0000.0000.000
54B65HIS0-0.0100.00624.5560.3760.3760.0000.0000.0000.000
55B66LEU0-0.051-0.02223.410-0.189-0.1890.0000.0000.0000.000
56B67PHE00.0810.02725.185-0.373-0.3730.0000.0000.0000.000
57B68ASP-1-0.796-0.87026.67911.62111.6210.0000.0000.0000.000
58B69TRP00.0080.00321.173-0.192-0.1920.0000.0000.0000.000
59B70THR0-0.024-0.07227.0880.2540.2540.0000.0000.0000.000
60B71PRO00.0330.01229.555-0.028-0.0280.0000.0000.0000.000
61B72ASP-1-0.812-0.84931.0789.6139.6130.0000.0000.0000.000
62B73LYS10.8090.91730.091-10.228-10.2280.0000.0000.0000.000
63B74ALA00.0490.01330.0980.3720.3720.0000.0000.0000.000
64B75PHE00.005-0.00827.8890.1760.1760.0000.0000.0000.000
65B76GLY00.0030.00929.213-0.361-0.3610.0000.0000.0000.000
66B77HIS0-0.045-0.03129.526-0.419-0.4190.0000.0000.0000.000
67B78LEU0-0.048-0.03628.7020.3900.3900.0000.0000.0000.000
68B79GLU-1-0.831-0.88927.9179.9919.9910.0000.0000.0000.000
69B80LYS10.8250.89827.852-8.913-8.9130.0000.0000.0000.000
70B81LEU0-0.035-0.01725.556-0.217-0.2170.0000.0000.0000.000
71B82GLU-1-0.853-0.91827.7759.5529.5520.0000.0000.0000.000
72B83LEU0-0.082-0.02824.5860.0600.0600.0000.0000.0000.000
73B84PRO00.0200.01229.072-0.128-0.1280.0000.0000.0000.000
74B85THR00.0490.02928.411-0.376-0.3760.0000.0000.0000.000
75B86ASP-1-0.836-0.90631.0319.0839.0830.0000.0000.0000.000
76B87HIS00.000-0.01227.2800.0220.0220.0000.0000.0000.000
77B88LYS10.8740.91931.775-9.218-9.2180.0000.0000.0000.000
78B89GLY00.0410.02831.128-0.030-0.0300.0000.0000.0000.000
79B90VAL00.001-0.01030.357-0.150-0.1500.0000.0000.0000.000
80B91TYR00.011-0.02128.757-0.260-0.2600.0000.0000.0000.000
81B92GLY00.0210.01231.009-0.194-0.1940.0000.0000.0000.000
82B93HIS00.0250.01233.752-0.161-0.1610.0000.0000.0000.000
83B94LEU0-0.0160.00131.699-0.232-0.2320.0000.0000.0000.000
84B95VAL00.0290.00733.436-0.230-0.2300.0000.0000.0000.000
85B96ASP-1-0.847-0.90136.2097.4867.4860.0000.0000.0000.000
86B97SER0-0.0080.00738.742-0.258-0.2580.0000.0000.0000.000
87B98PHE00.0100.00537.372-0.069-0.0690.0000.0000.0000.000
88B99ALA0-0.0170.00539.4550.0580.0580.0000.0000.0000.000
89B100TYR0-0.020-0.01037.914-0.054-0.0540.0000.0000.0000.000
90B101MET0-0.017-0.00431.8510.0550.0550.0000.0000.0000.000
91B102ARG10.7860.87628.085-10.399-10.3990.0000.0000.0000.000
92B103ASN0-0.0070.01025.682-0.420-0.4200.0000.0000.0000.000
93B104GLY00.0890.06523.434-0.230-0.2300.0000.0000.0000.000
94B105TRP0-0.030-0.01821.835-0.187-0.1870.0000.0000.0000.000
95B106ASP-1-0.757-0.84715.53620.05820.0580.0000.0000.0000.000
96B107VAL00.010-0.01317.214-0.557-0.5570.0000.0000.0000.000
97B108GLU-1-0.765-0.83412.76424.58524.5850.0000.0000.0000.000
98B109VAL00.000-0.00516.139-1.281-1.2810.0000.0000.0000.000
99B110SER0-0.029-0.01316.2851.0621.0620.0000.0000.0000.000
100B111ALA00.0400.01417.411-1.133-1.1330.0000.0000.0000.000
101B112VAL0-0.014-0.00616.7260.5940.5940.0000.0000.0000.000
102B113GLY00.0590.01118.631-1.013-1.0130.0000.0000.0000.000
103B114ASN0-0.050-0.02618.3040.3920.3920.0000.0000.0000.000
104B115GLN00.0620.02016.537-0.311-0.3110.0000.0000.0000.000
105B116PHE0-0.019-0.00518.359-0.155-0.1550.0000.0000.0000.000
106B117ASN0-0.032-0.02221.431-0.415-0.4150.0000.0000.0000.000
107B118GLY00.0100.00121.1810.7060.7060.0000.0000.0000.000
108B119GLY00.0540.04522.799-0.365-0.3650.0000.0000.0000.000
109B120CYS0-0.137-0.07919.0910.8710.8710.0000.0000.0000.000
110B121LEU00.0380.03620.449-0.751-0.7510.0000.0000.0000.000
111B122LEU00.0280.01619.7890.8650.8650.0000.0000.0000.000
112B123VAL0-0.011-0.01318.323-0.438-0.4380.0000.0000.0000.000
113B124ALA00.0370.00119.5690.5530.5530.0000.0000.0000.000
114B125MET0-0.0200.00820.632-0.249-0.2490.0000.0000.0000.000
115B126VAL00.004-0.00323.084-0.027-0.0270.0000.0000.0000.000
116B127PRO00.0040.00026.475-0.029-0.0290.0000.0000.0000.000
117B128GLU-1-0.832-0.91628.8198.9368.9360.0000.0000.0000.000
118B129TRP0-0.048-0.03029.4960.0520.0520.0000.0000.0000.000
119B130LYS10.8440.89132.573-8.825-8.8250.0000.0000.0000.000
120B131GLU-1-0.787-0.88233.9869.1709.1700.0000.0000.0000.000
121B132PHE0-0.0180.01130.219-0.200-0.2000.0000.0000.0000.000
122B133THR00.007-0.03734.5380.0030.0030.0000.0000.0000.000
123B134PRO00.017-0.01834.7210.2340.2340.0000.0000.0000.000
124B135ARG10.9660.98134.066-7.683-7.6830.0000.0000.0000.000
125B136GLU-1-0.729-0.82233.0188.7438.7430.0000.0000.0000.000
126B137LYS10.8910.94730.224-9.195-9.1950.0000.0000.0000.000
127B138TYR0-0.025-0.01128.5740.3040.3040.0000.0000.0000.000
128B139GLN0-0.024-0.01127.7450.1790.1790.0000.0000.0000.000
129B140LEU00.0160.01126.0870.1130.1130.0000.0000.0000.000
130B141THR00.003-0.00221.5750.1570.1570.0000.0000.0000.000
131B142LEU0-0.0120.00222.6130.3500.3500.0000.0000.0000.000
132B143PHE0-0.0210.00424.119-0.144-0.1440.0000.0000.0000.000
133B144PRO00.0090.01519.8200.5470.5470.0000.0000.0000.000
134B145HIS0-0.031-0.01018.5240.1760.1760.0000.0000.0000.000
135B146GLN00.0120.01511.1501.1111.1110.0000.0000.0000.000
136B147PHE00.0520.01715.183-1.108-1.1080.0000.0000.0000.000
137B148ILE0-0.0190.00815.1181.3941.3940.0000.0000.0000.000
138B149SER00.007-0.00916.055-1.263-1.2630.0000.0000.0000.000
139B150PRO00.0700.03516.0391.1831.1830.0000.0000.0000.000
140B151ARG10.9280.98115.387-16.860-16.8600.0000.0000.0000.000
141B152THR0-0.066-0.03011.5730.1810.1810.0000.0000.0000.000
142B153ASN0-0.020-0.03211.3131.8851.8850.0000.0000.0000.000
143B154MET00.0520.04212.745-2.155-2.1550.0000.0000.0000.000
144B155THR0-0.021-0.01611.673-0.166-0.1660.0000.0000.0000.000
145B156ALA00.0280.03612.7800.9920.9920.0000.0000.0000.000
146B157HIS10.7910.85611.398-23.104-23.1040.0000.0000.0000.000
147B158ILE0-0.025-0.00413.4320.3930.3930.0000.0000.0000.000
148B159VAL0-0.019-0.00414.560-0.117-0.1170.0000.0000.0000.000
149B160VAL0-0.006-0.00217.300-0.148-0.1480.0000.0000.0000.000
150B161PRO00.0470.04520.8650.0750.0750.0000.0000.0000.000
151B162TYR0-0.035-0.03723.468-0.139-0.1390.0000.0000.0000.000
152B163LEU0-0.052-0.02627.0260.0070.0070.0000.0000.0000.000
153B164GLY00.0600.01929.436-0.044-0.0440.0000.0000.0000.000
154B165VAL0-0.023-0.01132.982-0.011-0.0110.0000.0000.0000.000
155B166ASN0-0.0050.01535.680-0.343-0.3430.0000.0000.0000.000
156B167ARG10.9070.96733.726-8.563-8.5630.0000.0000.0000.000
157B168TYR0-0.010-0.01833.4650.2890.2890.0000.0000.0000.000
158B169ASP-1-0.767-0.86534.1608.5898.5890.0000.0000.0000.000
159B170GLN0-0.005-0.01236.007-0.158-0.1580.0000.0000.0000.000
160B171TYR00.046-0.01129.826-0.209-0.2090.0000.0000.0000.000
161B172LYS10.7990.88135.729-7.865-7.8650.0000.0000.0000.000
162B173LYS10.8520.92338.821-7.468-7.4680.0000.0000.0000.000
163B174HIS10.7530.84634.012-8.993-8.9930.0000.0000.0000.000
164B175LYS10.8890.93732.242-9.158-9.1580.0000.0000.0000.000
165B176PRO00.0120.03429.713-0.012-0.0120.0000.0000.0000.000
166B177TRP00.016-0.00724.3590.2190.2190.0000.0000.0000.000
167B178THR0-0.032-0.01927.178-0.378-0.3780.0000.0000.0000.000
168B179LEU00.0110.02021.2600.2860.2860.0000.0000.0000.000
169B180VAL0-0.021-0.01124.020-0.505-0.5050.0000.0000.0000.000
170B181VAL0-0.014-0.00822.2670.7170.7170.0000.0000.0000.000
171B182MET0-0.0140.00624.235-0.726-0.7260.0000.0000.0000.000
172B183VAL0-0.0320.00124.4990.6230.6230.0000.0000.0000.000
173B184VAL0-0.012-0.00722.424-0.417-0.4170.0000.0000.0000.000
174B185SER0-0.015-0.02224.421-0.462-0.4620.0000.0000.0000.000
175B186PRO00.0690.02925.4520.4670.4670.0000.0000.0000.000
176B187LEU0-0.0340.00624.1800.2760.2760.0000.0000.0000.000
177B188THR00.0210.00225.710-0.331-0.3310.0000.0000.0000.000
178B189THR00.0340.00525.8770.4400.4400.0000.0000.0000.000
179B190ASN0-0.060-0.04126.307-0.126-0.1260.0000.0000.0000.000
180B191THR00.0170.00528.4480.1460.1460.0000.0000.0000.000
181B192VAL00.0290.02625.152-0.118-0.1180.0000.0000.0000.000
182B193SER0-0.0160.01324.0830.4790.4790.0000.0000.0000.000
183B194ALA00.0170.02223.439-0.356-0.3560.0000.0000.0000.000
184B195GLY00.0280.01125.318-0.118-0.1180.0000.0000.0000.000
185B196GLN0-0.034-0.02527.166-0.172-0.1720.0000.0000.0000.000
186B197ILE0-0.0220.00220.8390.3830.3830.0000.0000.0000.000
187B198LYS10.8320.90423.942-11.612-11.6120.0000.0000.0000.000
188B199VAL0-0.023-0.00721.7170.8150.8150.0000.0000.0000.000
189B200TYR0-0.002-0.00921.028-0.793-0.7930.0000.0000.0000.000
190B201ALA00.0340.01820.6420.7090.7090.0000.0000.0000.000
191B202ASN0-0.024-0.02116.401-1.508-1.5080.0000.0000.0000.000
192B203ILE00.0370.02218.7570.6830.6830.0000.0000.0000.000
193B204ALA00.0080.01119.754-0.352-0.3520.0000.0000.0000.000
194B205PRO0-0.0340.01221.4890.1850.1850.0000.0000.0000.000
195B206THR00.007-0.01919.5650.0400.0400.0000.0000.0000.000
196B207HIS0-0.042-0.04121.207-0.122-0.1220.0000.0000.0000.000
197B208VAL0-0.0070.01325.538-0.384-0.3840.0000.0000.0000.000
198B209HIS0-0.022-0.02627.866-0.112-0.1120.0000.0000.0000.000
199B210VAL0-0.041-0.01731.6060.0130.0130.0000.0000.0000.000
200B211ALA00.0740.02535.122-0.050-0.0500.0000.0000.0000.000
201B212GLY00.0250.01538.7930.0010.0010.0000.0000.0000.000
202B213GLU-1-0.899-0.95141.7907.6517.6510.0000.0000.0000.000
203B214LEU0-0.058-0.02242.122-0.204-0.2040.0000.0000.0000.000
204B215PRO0-0.009-0.00144.7220.0180.0180.0000.0000.0000.000
205B216SER0-0.021-0.01646.8070.0840.0840.0000.0000.0000.000
206B217LYS10.8360.88843.264-7.513-7.5130.0000.0000.0000.000
207B218GLU-1-0.961-0.95648.9036.4316.4310.0000.0000.0000.000