Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52G6Z

Calculation Name: 3HKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q84T68

Base Structure: X-ray

Registration Date: 2023-06-26

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2313771.619436
FMO2-HF: Nuclear repulsion 2233426.077184
FMO2-HF: Total energy -80345.542253
FMO2-MP2: Total energy -80575.340801


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(A:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-237.788-231.23461.026-28.787-38.794-0.278
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.796 / q_NPA : 0.859
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].
3A7ASP-1-0.889-0.9432.955-66.351-62.4010.592-1.917-2.625-0.003
4A8GLY00.0140.0103.2284.3515.2460.017-0.358-0.5550.000
5A9ARG10.7820.9092.25273.25876.8024.249-2.192-5.6020.010
6A10ASN00.0190.0002.085-10.401-10.4817.914-3.203-4.631-0.044
7A11PRO00.0660.0162.331-16.122-12.7701.655-1.789-3.218-0.016
8A12ASN00.0410.0333.108-3.524-3.6450.0630.577-0.519-0.002
9A13GLN0-0.044-0.0173.1814.4725.0230.010-0.146-0.4150.000
10A14LEU00.0160.0092.754-13.408-12.2960.441-0.536-1.017-0.006
11A15ARG10.7450.8715.16142.89342.8930.0000.0000.0000.000
12A16PRO00.020-0.0056.6362.5382.5380.0000.0000.0000.000
13A17PHE00.0210.0049.7740.3100.3100.0000.0000.0000.000
14A18SER0-0.043-0.01912.3221.6331.6330.0000.0000.0000.000
15A19CYS00.017-0.01216.089-0.086-0.0860.0000.0000.0000.000
16A20THR0-0.0210.02219.0430.6110.6110.0000.0000.0000.000
17A21ARG10.8630.92022.55412.66512.6650.0000.0000.0000.000
18A22ASN00.001-0.01224.9820.0990.0990.0000.0000.0000.000
19A23PRO0-0.024-0.00424.1640.2510.2510.0000.0000.0000.000
20A24LEU0-0.037-0.01427.1170.3060.3060.0000.0000.0000.000
21A25ASP-1-0.841-0.91829.705-9.432-9.4320.0000.0000.0000.000
22A26ARG10.8810.93733.1298.4918.4910.0000.0000.0000.000
23A27ALA0-0.044-0.01929.5700.1240.1240.0000.0000.0000.000
24A28HIS00.0320.02231.612-0.077-0.0770.0000.0000.0000.000
25A29GLY00.0380.02028.2590.0110.0110.0000.0000.0000.000
26A30SER0-0.008-0.01225.365-0.115-0.1150.0000.0000.0000.000
27A31ALA00.0000.00320.6360.0590.0590.0000.0000.0000.000
28A32ARG10.9480.99419.35114.00214.0020.0000.0000.0000.000
29A33TRP00.005-0.01912.6070.8900.8900.0000.0000.0000.000
30A34ALA00.003-0.00813.907-0.064-0.0640.0000.0000.0000.000
31A35GLN00.0570.0308.0052.6752.6750.0000.0000.0000.000
32A36GLY0-0.0040.0119.017-1.692-1.6920.0000.0000.0000.000
33A37ASP-1-0.865-0.9369.934-21.511-21.5110.0000.0000.0000.000
34A38THR0-0.090-0.0509.4972.4102.4100.0000.0000.0000.000
35A39ILE0-0.025-0.00711.8810.1680.1680.0000.0000.0000.000
36A40VAL00.0230.00115.0910.8270.8270.0000.0000.0000.000
37A41LEU0-0.044-0.02217.5720.1200.1200.0000.0000.0000.000
38A42ALA00.0150.01120.6510.2510.2510.0000.0000.0000.000
39A43ALA0-0.019-0.01022.4960.2410.2410.0000.0000.0000.000
40A44VAL00.0230.00825.7160.0220.0220.0000.0000.0000.000
41A45TYR0-0.053-0.03528.3830.2260.2260.0000.0000.0000.000
42A46GLY00.0810.03732.0820.2320.2320.0000.0000.0000.000
43A47PRO0-0.0190.01733.685-0.082-0.0820.0000.0000.0000.000
44A48LYS10.9600.98535.5808.2958.2950.0000.0000.0000.000
45A49PRO00.0150.00938.130-0.022-0.0220.0000.0000.0000.000
46A50GLY0-0.0150.00241.3800.0450.0450.0000.0000.0000.000
47A51THR00.018-0.00538.341-0.256-0.2560.0000.0000.0000.000
48A52ARG10.8460.92334.6168.9678.9670.0000.0000.0000.000
49A53LYS10.9680.97239.8406.7246.7240.0000.0000.0000.000
50A54GLY0-0.017-0.00140.1770.1360.1360.0000.0000.0000.000
51A55GLU-1-0.896-0.93935.526-8.875-8.8750.0000.0000.0000.000
52A56ASN00.039-0.01038.7470.1080.1080.0000.0000.0000.000
53A57PRO00.0000.01740.6490.0700.0700.0000.0000.0000.000
54A58GLU-1-0.940-0.96641.538-6.995-6.9950.0000.0000.0000.000
55A59LYS10.8410.91936.4108.0678.0670.0000.0000.0000.000
56A60ALA0-0.030-0.00534.4670.0520.0520.0000.0000.0000.000
57A61SER00.0070.00133.953-0.164-0.1640.0000.0000.0000.000
58A62ILE0-0.009-0.01027.431-0.053-0.0530.0000.0000.0000.000
59A63GLU-1-0.815-0.90629.921-9.150-9.1500.0000.0000.0000.000
60A64VAL0-0.004-0.02523.647-0.194-0.1940.0000.0000.0000.000
61A65VAL0-0.0110.01126.7240.1540.1540.0000.0000.0000.000
62A66TRP00.021-0.01416.912-0.350-0.3500.0000.0000.0000.000
63A67LYS10.8880.93623.21611.91811.9180.0000.0000.0000.000
64A68PRO00.0530.02821.579-0.567-0.5670.0000.0000.0000.000
65A69MET0-0.038-0.00517.1780.2730.2730.0000.0000.0000.000
66A70THR0-0.001-0.01122.1370.5210.5210.0000.0000.0000.000
67A71GLY00.0170.02624.825-0.186-0.1860.0000.0000.0000.000
68A72GLN0-0.014-0.02327.2920.1180.1180.0000.0000.0000.000
69A73ILE0-0.0170.00323.739-0.202-0.2020.0000.0000.0000.000
70A74GLY00.0710.03323.7830.5480.5480.0000.0000.0000.000
71A75LYS10.8320.88521.81813.61813.6180.0000.0000.0000.000
72A76GLN00.0370.04116.022-0.613-0.6130.0000.0000.0000.000
73A77GLU-1-0.779-0.90019.419-14.299-14.2990.0000.0000.0000.000
74A78LYS10.8980.94220.58411.85711.8570.0000.0000.0000.000
75A79GLU-1-0.817-0.89619.784-14.167-14.1670.0000.0000.0000.000
76A80TYR0-0.032-0.02714.605-0.356-0.3560.0000.0000.0000.000
77A81GLU-1-0.843-0.92119.482-11.860-11.8600.0000.0000.0000.000
78A82MET0-0.0180.00522.6030.2780.2780.0000.0000.0000.000
79A83THR0-0.019-0.03117.9780.1970.1970.0000.0000.0000.000
80A84LEU00.0280.00818.8430.0630.0630.0000.0000.0000.000
81A85LYN00.0340.03520.9620.1380.1380.0000.0000.0000.000
82A86ARG10.9470.97420.91013.75713.7570.0000.0000.0000.000
83A87THR0-0.015-0.01118.9280.2010.2010.0000.0000.0000.000
84A88LEU00.002-0.00821.3830.1780.1780.0000.0000.0000.000
85A89GLN0-0.017-0.01424.0970.2320.2320.0000.0000.0000.000
86A90SER0-0.039-0.00124.1910.4220.4220.0000.0000.0000.000
87A91ILE00.0220.00521.8220.2200.2200.0000.0000.0000.000
88A92CYS0-0.0240.01425.4370.2170.2170.0000.0000.0000.000
89A93LEU0-0.038-0.02428.3530.1890.1890.0000.0000.0000.000
90A94LEU00.0360.00331.6320.2050.2050.0000.0000.0000.000
91A95THR00.008-0.01233.9850.2450.2450.0000.0000.0000.000
92A96VAL0-0.0320.00334.9140.1990.1990.0000.0000.0000.000
93A97HIS00.0130.00535.2290.3200.3200.0000.0000.0000.000
94A98PRO00.0480.01738.008-0.137-0.1370.0000.0000.0000.000
95A99ASN0-0.0020.00740.1030.0070.0070.0000.0000.0000.000
96A100THR00.0240.02336.0960.0550.0550.0000.0000.0000.000
97A101THR0-0.036-0.03134.361-0.167-0.1670.0000.0000.0000.000
98A102THR0-0.016-0.00829.6770.0820.0820.0000.0000.0000.000
99A103SER0-0.041-0.02030.504-0.103-0.1030.0000.0000.0000.000
100A104VAL00.014-0.00923.965-0.042-0.0420.0000.0000.0000.000
101A105ILE0-0.040-0.01925.8920.0550.0550.0000.0000.0000.000
102A106LEU00.0110.01718.413-0.259-0.2590.0000.0000.0000.000
103A107GLN0-0.049-0.02422.1270.7490.7490.0000.0000.0000.000
104A108VAL00.0390.01416.834-0.510-0.5100.0000.0000.0000.000
105A109VAL0-0.073-0.03418.0880.8940.8940.0000.0000.0000.000
106A110GLY00.0510.03115.9650.4890.4890.0000.0000.0000.000
107A111ASN0-0.032-0.03312.429-1.732-1.7320.0000.0000.0000.000
108A112ASP-1-0.798-0.9248.431-32.907-32.9070.0000.0000.0000.000
109A113GLY00.0840.0767.757-4.133-4.1330.0000.0000.0000.000
110A114SER0-0.015-0.0145.9341.3371.3370.0000.0000.0000.000
111A115LEU0-0.015-0.0048.5811.6841.6840.0000.0000.0000.000
112A116LEU0-0.0170.00312.2191.2511.2510.0000.0000.0000.000
113A117PRO00.0490.0109.5731.2011.2010.0000.0000.0000.000
114A118CYS0-0.0080.02310.8861.4641.4640.0000.0000.0000.000
115A119ALA00.011-0.00812.4611.3811.3810.0000.0000.0000.000
116A120ILE00.0210.00615.1211.2401.2400.0000.0000.0000.000
117A121ASN00.0080.01311.8312.1562.1560.0000.0000.0000.000
118A122ALA00.0150.00215.9110.9680.9680.0000.0000.0000.000
119A123CYS0-0.050-0.02317.8381.1581.1580.0000.0000.0000.000
120A124CYS0-0.0140.01619.1060.8660.8660.0000.0000.0000.000
121A125ALA00.0260.02019.5020.6350.6350.0000.0000.0000.000
122A126ALA0-0.025-0.01321.3960.6430.6430.0000.0000.0000.000
123A127LEU00.005-0.00423.5960.6040.6040.0000.0000.0000.000
124A128VAL00.0140.01323.6480.4720.4720.0000.0000.0000.000
125A129PHE0-0.006-0.01925.6920.3230.3230.0000.0000.0000.000
126A130ALA0-0.0120.00427.4500.3520.3520.0000.0000.0000.000
127A131GLY0-0.0250.00529.5400.3870.3870.0000.0000.0000.000
128A132ILE0-0.056-0.02728.6330.3460.3460.0000.0000.0000.000
129A133PRO00.002-0.00429.234-0.297-0.2970.0000.0000.0000.000
130A134LEU00.0060.01023.970-0.073-0.0730.0000.0000.0000.000
131A135LYS10.8460.92926.97710.62510.6250.0000.0000.0000.000
132A136HIS0-0.023-0.01422.7760.3630.3630.0000.0000.0000.000
133A137LEU00.0170.00019.676-0.029-0.0290.0000.0000.0000.000
134A138ALA00.000-0.01318.7020.0230.0230.0000.0000.0000.000
135A139VAL00.003-0.00113.059-0.180-0.1800.0000.0000.0000.000
136A140ALA0-0.016-0.01613.0880.0040.0040.0000.0000.0000.000
137A141ILE0-0.019-0.0227.057-1.191-1.1910.0000.0000.0000.000
138A142GLY00.0330.0267.4612.1922.1920.0000.0000.0000.000
139A143CYS0-0.068-0.0225.722-6.706-6.7060.0000.0000.0000.000
140A144GLY00.0620.0166.0573.7263.7260.0000.0000.0000.000
141A145VAL0-0.005-0.0227.321-1.655-1.6550.0000.0000.0000.000
142A146LEU0-0.036-0.0234.343-0.664-0.539-0.001-0.009-0.1140.000
143A147GLU-1-0.945-0.9698.614-24.384-24.3840.0000.0000.0000.000
144A148ASP-1-0.952-0.96711.311-16.158-16.1580.0000.0000.0000.000
145A149GLY00.0190.01111.9260.6780.6780.0000.0000.0000.000
146A150GLU-1-0.937-0.9757.613-25.560-25.5600.0000.0000.0000.000
147A151VAL00.0110.0147.402-2.759-2.7590.0000.0000.0000.000
148A152ILE0-0.032-0.0302.350-6.062-4.7133.127-0.887-3.5900.002
149A153LEU0-0.030-0.0112.9985.4856.5030.102-0.350-0.7710.001
150A154ASP-1-0.838-0.9281.845-77.403-77.9819.684-4.643-4.464-0.066
151A155THR00.0140.0112.353-16.953-15.0532.132-1.852-2.179-0.020
152A156ASN00.009-0.0013.3919.3169.4190.0080.170-0.2810.000
153A157LYS10.9620.9805.32123.48723.525-0.0010.000-0.0360.000
154A158ALA0-0.032-0.0207.1022.3172.3170.0000.0000.0000.000
155A159GLU-1-0.726-0.8401.694-129.445-140.04931.034-11.652-8.777-0.134
156A160GLU-1-0.802-0.8885.966-30.966-30.9660.0000.0000.0000.000
157A161GLN0-0.101-0.0368.3993.6993.6990.0000.0000.0000.000
158A162GLN0-0.055-0.0216.568-0.739-0.7390.0000.0000.0000.000
159A163LEU00.0000.0156.1851.7391.7390.0000.0000.0000.000
160A164LYS10.9690.98110.25919.50419.5040.0000.0000.0000.000
161A165SER0-0.023-0.01611.8981.6801.6800.0000.0000.0000.000
162A166PHE00.0310.0089.480-2.623-2.6230.0000.0000.0000.000
163A167ALA00.0070.00310.2912.8722.8720.0000.0000.0000.000
164A168HIS0-0.0130.00010.308-2.931-2.9310.0000.0000.0000.000
165A169LEU00.0160.01111.5182.3512.3510.0000.0000.0000.000
166A170VAL0-0.0130.00013.078-0.848-0.8480.0000.0000.0000.000
167A171PHE00.0560.02711.7491.2401.2400.0000.0000.0000.000
168A172PRO00.0030.01617.007-0.020-0.0200.0000.0000.0000.000
169A173ASN00.0460.02717.7281.0331.0330.0000.0000.0000.000
170A194LEU00.0170.00416.782-0.126-0.1260.0000.0000.0000.000
171A195ILE0-0.087-0.03719.3850.7510.7510.0000.0000.0000.000
172A196THR0-0.012-0.01918.4230.7150.7150.0000.0000.0000.000
173A197SER00.0190.00816.471-0.727-0.7270.0000.0000.0000.000
174A198ILE0-0.038-0.01215.7500.9740.9740.0000.0000.0000.000
175A199THR00.0480.02714.768-1.220-1.2200.0000.0000.0000.000
176A200HIS0-0.059-0.02714.0161.5561.5560.0000.0000.0000.000
177A201GLY00.0400.02814.599-1.118-1.1180.0000.0000.0000.000
178A202VAL0-0.042-0.02416.6270.4820.4820.0000.0000.0000.000
179A203MET0-0.0130.01012.907-1.604-1.6040.0000.0000.0000.000
180A204SER0-0.019-0.00517.6661.0141.0140.0000.0000.0000.000
181A205GLU-1-0.923-0.97718.596-13.693-13.6930.0000.0000.0000.000
182A206GLU-1-0.882-0.95518.547-14.927-14.9270.0000.0000.0000.000
183A207ASP-1-0.804-0.87914.710-20.182-20.1820.0000.0000.0000.000
184A208TYR0-0.021-0.03114.333-1.404-1.4040.0000.0000.0000.000
185A209PHE00.0130.00015.345-0.592-0.5920.0000.0000.0000.000
186A210SER00.0420.03012.527-0.989-0.9890.0000.0000.0000.000
187A211CYS0-0.064-0.02910.694-2.155-2.1550.0000.0000.0000.000
188A212ILE0-0.039-0.02711.332-1.148-1.1480.0000.0000.0000.000
189A213GLU-1-0.909-0.94812.696-22.560-22.5600.0000.0000.0000.000
190A214ARG10.8960.9416.86631.87631.8760.0000.0000.0000.000
191A215GLY00.005-0.0179.216-0.974-0.9740.0000.0000.0000.000
192A216LEU00.0020.00910.2110.2690.2690.0000.0000.0000.000
193A217ALA00.0130.01712.4280.5450.5450.0000.0000.0000.000
194A218ALA0-0.0050.0048.180-0.128-0.1280.0000.0000.0000.000
195A219SER0-0.056-0.04810.2500.6550.6550.0000.0000.0000.000
196A220SER00.0380.01612.2070.2330.2330.0000.0000.0000.000
197A221ARG10.9770.9919.80924.95524.9550.0000.0000.0000.000
198A222ILE00.0030.0049.5750.7360.7360.0000.0000.0000.000
199A223SER00.017-0.00413.5350.8990.8990.0000.0000.0000.000
200A224ASP-1-0.905-0.94716.535-15.240-15.2400.0000.0000.0000.000
201A225PHE0-0.036-0.01715.6170.8100.8100.0000.0000.0000.000
202A226MET0-0.068-0.04416.1741.0031.0030.0000.0000.0000.000
203A227ARG10.8820.93619.61914.17214.1720.0000.0000.0000.000
204A228THR00.0030.01621.1240.8670.8670.0000.0000.0000.000
205A229THR00.0170.00419.4860.4120.4120.0000.0000.0000.000
206A230LEU0-0.094-0.02318.5550.4560.4560.0000.0000.0000.000
207A231GLN0-0.0140.00122.5020.6280.6280.0000.0000.0000.000